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Vilà-Valls L, Abdeli A, Lucas-Sánchez M, Bekada A, Calafell F, Benhassine T, Comas D. Understanding the genomic heterogeneity of North African Imazighen: from broad to microgeographical perspectives. Sci Rep 2024; 14:9979. [PMID: 38693301 PMCID: PMC11063056 DOI: 10.1038/s41598-024-60568-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 04/24/2024] [Indexed: 05/03/2024] Open
Abstract
The strategic location of North Africa has led to cultural and demographic shifts, shaping its genetic structure. Historical migrations brought different genetic components that are evident in present-day North African genomes, along with autochthonous components. The Imazighen (plural of Amazigh) are believed to be the descendants of autochthonous North Africans and speak various Amazigh languages, which belong to the Afro-Asiatic language family. However, the arrival of different human groups, especially during the Arab conquest, caused cultural and linguistic changes in local populations, increasing their heterogeneity. We aim to characterize the genetic structure of the region, using the largest Amazigh dataset to date and other reference samples. Our findings indicate microgeographical genetic heterogeneity among Amazigh populations, modeled by various admixture waves and different effective population sizes. A first admixture wave is detected group-wide around the twelfth century, whereas a second wave appears in some Amazigh groups around the nineteenth century. These events involved populations with higher genetic ancestry from south of the Sahara compared to the current North Africans. A plausible explanation would be the historical trans-Saharan slave trade, which lasted from the Roman times to the nineteenth century. Furthermore, our investigation shows that assortative mating in North Africa has been rare.
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Affiliation(s)
- Laura Vilà-Valls
- Departament de Medicina i Ciències de la Vida, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
| | - Amine Abdeli
- Laboratoire de Biologie Cellulaire et Moléculaire, Faculté Des Sciences Biologiques, Université des Sciences et de la Technologie Houari Boumediene, Alger, Algeria
| | - Marcel Lucas-Sánchez
- Departament de Medicina i Ciències de la Vida, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
| | - Asmahan Bekada
- Département de Biotechnologie, Faculté des Sciences de la Nature et de la Vie, Université Oran 1 (Ahmad Ben Bella), Oran, Algeria
| | - Francesc Calafell
- Departament de Medicina i Ciències de la Vida, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
| | - Traki Benhassine
- Laboratoire de Biologie Cellulaire et Moléculaire, Faculté Des Sciences Biologiques, Université des Sciences et de la Technologie Houari Boumediene, Alger, Algeria
| | - David Comas
- Departament de Medicina i Ciències de la Vida, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain.
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Lucas-Sánchez M, Abdeli A, Bekada A, Calafell F, Benhassine T, Comas D. The Impact of Recent Demography on Functional Genetic Variation in North African Human Groups. Mol Biol Evol 2024; 41:msad283. [PMID: 38152862 PMCID: PMC10783648 DOI: 10.1093/molbev/msad283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 11/22/2023] [Accepted: 12/19/2023] [Indexed: 12/29/2023] Open
Abstract
The strategic location of North Africa has made the region the core of a wide range of human demographic events, including migrations, bottlenecks, and admixture processes. This has led to a complex and heterogeneous genetic and cultural landscape, which remains poorly studied compared to other world regions. Whole-exome sequencing is particularly relevant to determine the effects of these demographic events on current-day North Africans' genomes, since it allows to focus on those parts of the genome that are more likely to have direct biomedical consequences. Whole-exome sequencing can also be used to assess the effect of recent demography in functional genetic variation and the efficacy of natural selection, a long-lasting debate. In the present work, we use newly generated whole-exome sequencing and genome-wide array genotypes to investigate the effect of demography in functional variation in 7 North African populations, considering both cultural and demographic differences and with a special focus on Amazigh (plur. Imazighen) groups. We detect genetic differences among populations related to their degree of isolation and the presence of bottlenecks in their recent history. We find differences in the functional part of the genome that suggest a relaxation of purifying selection in the more isolated groups, allowing for an increase of putatively damaging variation. Our results also show a shift in mutational load coinciding with major demographic events in the region and reveal differences within and between cultural and geographic groups.
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Affiliation(s)
- Marcel Lucas-Sánchez
- Departament de Medicina i Ciències de la Vida, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
| | - Amine Abdeli
- Faculté des Sciences Biologiques, Laboratoire de Biologie Cellulaire et Moléculaire, Université des Sciences et de la Technologie Houari Boumediene, Alger, Algeria
| | - Asmahan Bekada
- Département de Biotechnologie, Faculté des Sciences de la Nature et de la Vie, Université Oran 1 (Ahmad Ben Bella), Oran, Algeria
| | - Francesc Calafell
- Departament de Medicina i Ciències de la Vida, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
| | - Traki Benhassine
- Faculté des Sciences Biologiques, Laboratoire de Biologie Cellulaire et Moléculaire, Université des Sciences et de la Technologie Houari Boumediene, Alger, Algeria
| | - David Comas
- Departament de Medicina i Ciències de la Vida, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
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Antinucci M, Comas D, Calafell F. Population history modulates the fitness effects of Copy Number Variation in the Roma. Hum Genet 2023; 142:1327-1343. [PMID: 37311904 PMCID: PMC10449987 DOI: 10.1007/s00439-023-02579-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 06/02/2023] [Indexed: 06/15/2023]
Abstract
We provide the first whole genome Copy Number Variant (CNV) study addressing Roma, along with reference populations from South Asia, the Middle East and Europe. Using CNV calling software for short-read sequence data, we identified 3171 deletions and 489 duplications. Taking into account the known population history of the Roma, as inferred from whole genome nucleotide variation, we could discern how this history has shaped CNV variation. As expected, patterns of deletion variation, but not duplication, in the Roma followed those obtained from single nucleotide polymorphisms (SNPs). Reduced effective population size resulting in slightly relaxed natural selection may explain our observation of an increase in intronic (but not exonic) deletions within Loss of Function (LoF)-intolerant genes. Over-representation analysis for LoF-intolerant gene sets hosting intronic deletions highlights a substantial accumulation of shared biological processes in Roma, intriguingly related to signaling, nervous system and development features, which may be related to the known profile of private disease in the population. Finally, we show the link between deletions and known trait-related SNPs reported in the genome-wide association study (GWAS) catalog, which exhibited even frequency distributions among the studied populations. This suggests that, in general human populations, the strong association between deletions and SNPs associated to biomedical conditions and traits could be widespread across continental populations, reflecting a common background of potentially disease/trait-related CNVs.
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Affiliation(s)
- Marco Antinucci
- Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - David Comas
- Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Francesc Calafell
- Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain.
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Aizpurua-Iraola J, Abdeli A, Benhassine T, Calafell F, Comas D. Whole mitogenomes reveal that NW Africa has acted both as a source and a destination for multiple human movements. Sci Rep 2023; 13:10395. [PMID: 37369751 DOI: 10.1038/s41598-023-37549-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 06/23/2023] [Indexed: 06/29/2023] Open
Abstract
Despite being enclosed between the Mediterranean Sea and the Sahara Desert, North Africa has been the scenario of multiple human migrations that have shaped the genetic structure of its present-day populations. Despite its richness, North Africa remains underrepresented in genomic studies. To overcome this, we have sequenced and analyzed 264 mitogenomes from the Algerian Chaoui-speaking Imazighen (a.k.a. Berbers) living in the Aurès region. The maternal genetic composition of the Aurès is similar to Arab populations in the region, dominated by West Eurasian lineages with a moderate presence of M1/U6 North African and L sub-Saharan lineages. When focusing on the time and geographic origin of the North African specific clades within the non-autochthonous haplogroups, different geographical neighboring regions contributed to the North African maternal gene pool during time periods that could be attributed to previously suggested admixture events in the region, since Paleolithic times to recent historical movements such as the Arabization. We have also observed the role of North Africa as a source of geneflow mainly in Southern European regions since Neolithic times. Finally, the present work constitutes an effort to increase the representation of North African populations in genetic databases, which is key to understand their history.
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Affiliation(s)
- Julen Aizpurua-Iraola
- Departament de Medicina i Ciències de la Vida, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
| | - Amine Abdeli
- Laboratorie de Biologie Cellulaire et Moléculaire, Faculté des Sciences Biologiques, Université des Sciences et de la Technologie Houari Boumediene, Alger, Algeria
| | - Traki Benhassine
- Laboratorie de Biologie Cellulaire et Moléculaire, Faculté des Sciences Biologiques, Université des Sciences et de la Technologie Houari Boumediene, Alger, Algeria
| | - Francesc Calafell
- Departament de Medicina i Ciències de la Vida, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
| | - David Comas
- Departament de Medicina i Ciències de la Vida, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain.
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Aizpurua-Iraola J, Rasal R, Prieto L, Comas D, Bonet N, Casals F, Calafell F, Vásquez P. Population analysis of complete mitogenomes for 334 samples from El Salvador. Forensic Sci Int Genet 2023; 66:102906. [PMID: 37364481 DOI: 10.1016/j.fsigen.2023.102906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 06/09/2023] [Accepted: 06/10/2023] [Indexed: 06/28/2023]
Abstract
The use of mitochondrial DNA (mtDNA) in the field of forensic genetics is widely spread mainly due to its advantages when identifying highly degraded samples. In this sense, massive parallel sequencing has made the analysis of the whole mitogenome more accessible, noticeably increasing the informativeness of mtDNA haplotypes. The civil war (1980-1992) in El Salvador caused many deaths and disappearances (including children) all across the country and the economic and social instability after the war forced many people to emigration. For this reason, different organizations have collected DNA samples from relatives with the aim of identifying missing people. Thus, we present a dataset containing 334 complete mitogenomes from the Salvadoran general population. To the best of our knowledge, this is the first publication of a nationwide forensic-quality complete mitogenome database of any Latin American country. We found 293 different haplotypes, with a random match probability of 0.0041 and 26.6 mean pairwise differences, which is similar to other Latin American populations, and which represent a marked improvement from the values obtained with just control region sequences. These haplotypes belong to 54 different haplogroups, being 91% of them of Native American origin. Over a third (35.9%) of the individuals carried at least a heteroplasmic site (excluding length heteroplasmies). Ultimately, the present database aims to represent mtDNA haplotype diversity in the general Salvadoran populations as a basis for the identification of people that disappeared during or after the civil war.
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Affiliation(s)
- Julen Aizpurua-Iraola
- Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Departament de Medicina i Ciències de la Vida, Barcelona, Spain
| | - Raquel Rasal
- Genomics Core Facility, Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
| | - Lourdes Prieto
- Instituto de Ciencias Forenses, Universidad de Santiago de Compostela, Santiago de Compostela, Spain; Comisaría General de Policía Científica. DNA Laboratory, Madrid, Spain
| | - David Comas
- Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Departament de Medicina i Ciències de la Vida, Barcelona, Spain
| | - Núria Bonet
- Genomics Core Facility, Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
| | - Ferran Casals
- Genomics Core Facility, Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain; Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Spain; Institut de Biomedicina de la Universitat de Barcelona (IBUB), Universitat de Barcelona, Barcelona, Spain
| | - Francesc Calafell
- Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Departament de Medicina i Ciències de la Vida, Barcelona, Spain
| | - Patricia Vásquez
- Asociación Pro-Búsqueda de Niñas y Niños Desaparecidos de El Salvador, San Salvador, El Salvador
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Caro-Consuegra R, Lucas-Sánchez M, Comas D, Bosch E. Identifying signatures of positive selection in human populations from North Africa. Sci Rep 2023; 13:8166. [PMID: 37210386 DOI: 10.1038/s41598-023-35312-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 05/16/2023] [Indexed: 05/22/2023] Open
Abstract
Because of its location, North Africa (NA) has witnessed continuous demographic movements with an impact on the genomes of present-day human populations. Genomic data describe a complex scenario with varying proportions of at least four main ancestry components: Maghrebi, Middle Eastern-, European-, and West-and-East-African-like. However, the footprint of positive selection in NA has not been studied. Here, we compile genome-wide genotyping data from 190 North Africans and individuals from surrounding populations, investigate for signatures of positive selection using allele frequencies and linkage disequilibrium-based methods and infer ancestry proportions to discern adaptive admixture from post-admixture selection events. Our results show private candidate genes for selection in NA involved in insulin processing (KIF5A), immune function (KIF5A, IL1RN, TLR3), and haemoglobin phenotypes (BCL11A). We also detect signatures of positive selection related to skin pigmentation (SLC24A5, KITLG), and immunity function (IL1R1, CD44, JAK1) shared with European populations and candidate genes associated with haemoglobin phenotypes (HPSE2, HBE1, HBG2), other immune-related (DOCK2) traits, and insulin processing (GLIS3) traits shared with West and East African populations. Finally, the SLC8A1 gene, which codifies for a sodium-calcium exchanger, was the only candidate identified under post-admixture selection in Western NA.
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Affiliation(s)
- Rocio Caro-Consuegra
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, 08003, Barcelona, Spain
| | - Marcel Lucas-Sánchez
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, 08003, Barcelona, Spain
| | - David Comas
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, 08003, Barcelona, Spain
| | - Elena Bosch
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, 08003, Barcelona, Spain.
- Centro de Investigación Biomédica en Red de Salud Mental, Instituto de Salud Carlos III, 28029, Madrid, Spain.
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Couto-Silva CM, Nunes K, Venturini G, Araújo Castro e Silva M, Pereira LV, Comas D, Pereira A, Hünemeier T. Indigenous people from Amazon show genetic signatures of pathogen-driven selection. Sci Adv 2023; 9:eabo0234. [PMID: 36888716 PMCID: PMC9995071 DOI: 10.1126/sciadv.abo0234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 02/08/2023] [Indexed: 06/18/2023]
Abstract
Ecological conditions in the Amazon rainforests are historically favorable for the transmission of numerous tropical diseases, especially vector-borne diseases. The high diversity of pathogens likely contributes to the strong selective pressures for human survival and reproduction in this region. However, the genetic basis of human adaptation to this complex ecosystem remains unclear. This study investigates the possible footprints of genetic adaptation to the Amazon rainforest environment by analyzing the genomic data of 19 native populations. The results based on genomic and functional analysis showed an intense signal of natural selection in a set of genes related to Trypanosoma cruzi infection, which is the pathogen responsible for Chagas disease, a neglected tropical parasitic disease native to the Americas that is currently spreading worldwide.
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Affiliation(s)
- Cainã M. Couto-Silva
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, 05508090, Brazil
| | - Kelly Nunes
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, 05508090, Brazil
| | - Gabriela Venturini
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Laboratório de Genética e Cardiologia Molecular, Instituto do Coração, Hospital das Clínicas da Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, SP, Brazil
| | - Marcos Araújo Castro e Silva
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, 05508090, Brazil
- Institut de Biologia Evolutiva, Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - Lygia V. Pereira
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, 05508090, Brazil
| | - David Comas
- Institut de Biologia Evolutiva, Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - Alexandre Pereira
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Laboratório de Genética e Cardiologia Molecular, Instituto do Coração, Hospital das Clínicas da Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, SP, Brazil
| | - Tábita Hünemeier
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, 05508090, Brazil
- Institut de Biologia Evolutiva (CSIC/Universitat Pompeu Fabra), Barcelona 08003, Spain
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Vilà-Valls L, Aizpurua-Iraola J, Casinge S, Bojs K, Flores-Bello A, Font-Porterias N, Comas D. Genomic Insights into the Population History of the Resande or Swedish Travelers. Genome Biol Evol 2023; 15:6991919. [PMID: 36655389 PMCID: PMC9907538 DOI: 10.1093/gbe/evad006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 12/29/2022] [Accepted: 01/09/2023] [Indexed: 01/20/2023] Open
Abstract
The Resande are a minority ethnic group in Sweden, who were characterized by an itinerant way of life, and they have been suggested to originate from the mixture between Swedish and Romani populations. Because the population history of the Resande has been scarcely studied, we analyzed genome-wide genotype array data from unrelated Resande individuals in order to shed light on their origins and demographic history for the first time from a genetic perspective. Our results confirm the Romani-related ancestry of this population and suggest an admixture event between a Romani-like population and a general Swedish-like population that occurred approximately between the mid-18th and mid-19th centuries, two centuries after the arrival of the first historically reported Romani families in Sweden. This inferred date suggests that the Romani group involved in the admixture is related to the pre-18th-century arrivals of Romani in Scandinavia. In addition, a reduction in the population size is detected previous to the admixture event, suggesting a subtle signal of isolation. The present work constitutes a step forward toward a better representation of ethnic minorities and underrepresented groups in population genetic analyses. In order to know in more detail the complete history of human populations, it is time to focus on studying populations that have not been previously considered for a general scenario and that can provide valuable information to fill in the gaps that still remain uncovered.
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Affiliation(s)
- Laura Vilà-Valls
- Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Julen Aizpurua-Iraola
- Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
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Lucas-Sánchez M, Fadhlaoui-Zid K, Comas D. The genomic analysis of current-day North African populations reveals the existence of trans-Saharan migrations with different origins and dates. Hum Genet 2023; 142:305-320. [PMID: 36441222 PMCID: PMC9918576 DOI: 10.1007/s00439-022-02503-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 10/28/2022] [Indexed: 11/29/2022]
Abstract
The Sahara Desert has acted as a barrier to human gene-flow between the northern and central parts of Africa since its aridification. Nonetheless, some contacts between both sides of the desert have occurred throughout history, mainly driven by commercial activity. Part of this was the infamous trans-Saharan slave trade, which forcedly brought peoples from south of the Sahara to North Africa from Roman times until the nineteenth century. Although historical records exist, the genetic aspects of these trans-Saharan migrations have not been deeply studied. In the present study, we assess the genetic influence of trans-Saharan migrations in current-day North Africa and characterize its amount, geographical origin, and dates. We confirm the heterogeneous and generally low-frequency presence of genomic segments of sub-Saharan origin in present-day North Africans acquired in recent historical times, and we show evidence of at least two admixture events: one dated around the thirteenth-fourteenth centuries CE between North Africans and a Western-sub-Saharan-like source similar to current-day Senegambian populations, and another one dated around the seventeenth century CE involving Tunisians and an Eastern-sub-Saharan-like source related to current-day south-Sudan and Kenyan populations. Time and location coincide with the peak of trans-Saharan slave-trade activity between Western African empires and North African powers, and are also concordant with the possibility of continuous recent south-to-north gene-flow. These findings confirm the trans-Saharan human genetic contacts, providing new and precise evidence about its possible dates and geographical origins, which are pivotal to understanding the genomic composition of an underrepresented region such as North Africa.
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Affiliation(s)
- Marcel Lucas-Sánchez
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Barcelona, Spain
| | - Karima Fadhlaoui-Zid
- Laboratory of Genetics, Immunology, and Human Pathologies, Faculty of Science of Tunis, University of Tunis El Manar, Tunis, Tunisia ,College of Science, Department of Biology, Taibah University, Al Madinah Al Monawarah, Saudi Arabia
| | - David Comas
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Barcelona, Spain.
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Font-Porterias N, García-Fernández C, Aizpurua-Iraola J, Comas D, Torrents D, de Cid R, Calafell F. Sequence diversity of the uniparentally transmitted portions of the genome in the resident population of Catalonia. Forensic Sci Int Genet 2022; 61:102783. [DOI: 10.1016/j.fsigen.2022.102783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 09/23/2022] [Accepted: 09/26/2022] [Indexed: 11/30/2022]
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Font-Porterias N, McNelis MG, Comas D, Hlusko LJ. Evidence of selection in the ectodysplasin pathway among endangered aquatic mammals. Integr Org Biol 2022; 4:obac018. [PMID: 35874492 PMCID: PMC9299678 DOI: 10.1093/iob/obac018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 05/06/2022] [Accepted: 05/21/2022] [Indexed: 11/13/2022] Open
Abstract
Synopsis The ectodysplasin pathway has been a target of evolution repeatedly. Genetic variation in the key genes of this pathway (EDA, EDAR, and EDARADD) results in a rich source of pleiotropic effects across ectodermally-derived structures, including teeth, hair, sweat glands, and mammary glands. In addition, a non-canonical Wnt pathway has a very similar functional role, making variation in the WNT10A gene also of evolutionary significance. The adaptation of mammals to aquatic environments has occurred independently in at least 4 orders, whose species occupy a wide geographic range (from equatorial to polar regions) and exhibit great phenotypic variation in ectodermally-derived structures, including the presence or absence of fur and extreme lactational strategies. The role of the ectodysplasin pathway in the adaptation to aquatic environments has been never explored in mammalian species. In the present study, we analyze the genetic variation in orthologous coding sequences from EDA, EDAR, EDARADD, and WNT10A genes together with ectodermally-derived phenotypic variation from 34 aquatic and non-aquatic mammalian species to assess signals of positive selection, gene-trait coevolution, and genetic convergence. Our study reveals strong evidence of positive selection in a proportion of coding sites in EDA and EDAR genes in 3 endangered aquatic mammals (the Hawaiian monk seal, the Yangtze finless porpoise, and the sea otter). We hypothesize functional implications potentially related to the adaptation to the low-latitude aquatic environment in the Hawaiian monk seal and the freshwater in the Yangtze finless porpoise. The signal in the sea otter is likely the result of an increased genetic drift after an intense bottleneck and reduction of genetic diversity. Besides positive selection, we have not detected robust signals of gene-trait coevolution or convergent amino acid shifts in the ectodysplasin pathway associated with shared phenotypic traits among aquatic mammals. This study provides new evidence of the evolutionary role of the ectodysplasin pathway and encourages further investigation, including functional studies, to fully resolve its relationship with mammalian aquatic adaptation. Spanish La vía de la ectodisplasina ha sido objeto de la evolución repetidamente. La variación genética en los principales genes de esta vía (EDA, EDAR y EDARADD) da como resultado una gran diversidad de efectos pleiotrópicos en las estructuras derivadas del ectodermo, incluidos los dientes, el cabello, las glándulas sudoríparas y las glándulas mamarias. Además, una vía wnt no canónica tiene un papel funcional muy similar, por lo que la variación en el gen WNT10A también tiene importancia evolutiva. La adaptación de los mamíferos a los entornes acuáticos se ha producido de forma independiente en al menos cuatro órdenes, cuyas especies ocupan un amplio rango geográfico (desde regiones ecuatoriales a polares) y presentan una gran variación fenotípica en las estructuras derivadas del ectodermo, incluyendo la presencia o ausencia de pelaje y estrategias de lactancia muy diferentes. El papel de la vía de la ectodisplasina en la adaptación a entornos acuáticos no se ha explorado nunca en especies de mamíferos. En este estudio, analizamos la variación genética en las secuencias codificantes ortólogas de los genes EDA, EDAR, EDARADD y WNT10A junto con la variación fenotípica derivada del ectodermo de 34 especies de mamíferos acuáticos y no acuáticos para evaluar señales de selección positiva, coevolución gen-rasgo y convergencia genética. Nuestro estudio revela señales de selección positiva en regiones de las secuencias codificantes de los genes EDA y EDAR en tres mamíferos acuáticos en peligro de extinción (la foca monje de Hawái, la marsopa lisa y la nutria marina). Estas señales podrían tener implicaciones funcionales potencialmente relacionadas con la adaptación al entorno acuático de baja latitud en la foca monje de Hawái y el agua dulce en la marsopa lisa. La señal en la nutria marina es probablemente el resultado de una mayor deriva genética tras un intenso un cuello de botella y una reducción de la diversidad genética. A parte de selección positiva, no hemos detectado señales sólidas de coevolución gen-rasgo o cambios convergentes de aminoácidos en la vía de la ectodisplasina asociados a rasgos fenotípicos compartidos entre mamíferos acuáticos. Este estudio proporciona nuevas evidencias del papel evolutivo de la vía de la ectodisplasina y quiere promover futuras investigaciones con estudios funcionales para acabar de resolver la relación de esta vía con la adaptación acuática de los mamíferos.
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Affiliation(s)
- Neus Font-Porterias
- Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Institut de Biologia Evolutiva (UPF-CSIC) , Barcelona , Spain
| | - Madeline G McNelis
- Department of Integrative Biology, University of California Berkeley , California , USA
| | - David Comas
- Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Institut de Biologia Evolutiva (UPF-CSIC) , Barcelona , Spain
| | - Leslea J Hlusko
- Department of Integrative Biology, University of California Berkeley , California , USA
- National Research Center on Human Evolution (CENIEH) , Burgos , Spain
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12
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Clement-Lacroix P, Little CB, Smith MM, Cottereaux C, Merciris D, Meurisse S, Mollat P, Touitou R, Brebion F, Gosmini R, De Ceuninck F, Botez I, Lepescheux L, van der Aar E, Christophe T, Vandervoort N, Blanqué R, Comas D, Deprez P, Amantini D. Pharmacological characterization of GLPG1972/S201086, a potent and selective small-molecule inhibitor of ADAMTS5. Osteoarthritis Cartilage 2022; 30:291-301. [PMID: 34626798 DOI: 10.1016/j.joca.2021.08.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 07/29/2021] [Accepted: 08/09/2021] [Indexed: 02/02/2023]
Abstract
OBJECTIVE A disintegrin and metalloproteinase with thrombospondin motifs 5 (ADAMTS5) is a key enzyme in degradation of cartilage in osteoarthritis (OA). We report the pharmacological characterization of GLPG1972/S201086, a new, potent and selective small-molecule ADAMTS5 inhibitor. METHODS Potency and selectivity of GLPG1972/S201086 for ADAMTS5 were determined using fluorescently labeled peptide substrates. Inhibitory effects of GLPG1972/S201086 on interleukin-1α-stimulated glycosaminoglycan release in mouse femoral head cartilage explants and on interleukin-1β-stimulated release of an ADAMTS5-derived aggrecan neoepitope (quantified with ELISA) in human articular cartilage explants were determined. In the destabilization of the medial meniscus (DMM) mouse and menisectomized (MNX) rat models, effects of oral GLPG1972/S201086 on relevant OA histological and histomorphometric parameters were evaluated. RESULTS GLPG1972/S201086 inhibited human and rat ADAMTS5 (IC50 ± SD: 19 ± 2 nM and <23 ± 1 nM, respectively), with 8-fold selectivity over ADAMTS4, and 60->5,000-fold selectivity over other related proteases in humans. GLPG1972/S201086 dose-dependently inhibited cytokine-stimulated aggrenolysis in mouse and human cartilage explants (100% at 20 μM and 10 μM, respectively). In DMM mice, GLPG1972/S201086 (30-120 mg/kg b.i.d) vs vehicle reduced femorotibial cartilage proteoglycan loss (23-37%), cartilage structural damage (23-39%) and subchondral bone sclerosis (21-36%). In MNX rats, GLPG1972/S201086 (10-50 mg/kg b.i.d) vs vehicle reduced cartilage damage (OARSI score reduction, 6-23%), and decreased proteoglycan loss (∼27%) and subchondral bone sclerosis (77-110%). CONCLUSIONS GLPG1972/S201086 is a potent, selective and orally available ADAMTS5 inhibitor, demonstrating significant protective efficacy on both cartilage and subchondral bone in two relevant in vivo preclinical OA models.
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Affiliation(s)
| | - C B Little
- Raymond Purves Bone and Joint Research Laboratories, University of Sydney, Kolling Institute, Northern Sydney Local Health District, Royal North Shore Hospital, St Leonards, NSW, Australia.
| | - M M Smith
- Raymond Purves Bone and Joint Research Laboratories, University of Sydney, Kolling Institute, Northern Sydney Local Health District, Royal North Shore Hospital, St Leonards, NSW, Australia.
| | | | | | | | - P Mollat
- Galapagos SASU, Romainville, France.
| | - R Touitou
- Galapagos SASU, Romainville, France.
| | - F Brebion
- Galapagos SASU, Romainville, France.
| | - R Gosmini
- Galapagos SASU, Romainville, France.
| | | | - I Botez
- Institut de Recherches Servier, France.
| | | | | | | | | | - R Blanqué
- Galapagos SASU, Romainville, France.
| | - D Comas
- Galapagos SASU, Romainville, France.
| | - P Deprez
- Galapagos SASU, Romainville, France.
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Abstract
South America is home to one of the most culturally diverse present-day native populations. However, the dispersion pattern, genetic substructure, and demographic complexity within South America are still poorly understood. Based on genome-wide data of 58 native populations, we provide a comprehensive scenario of South American indigenous groups considering the genomic, environmental, and linguistic data. Clear patterns of genetic structure were inferred among the South American natives, presenting at least four primary genetic clusters in the Amazonian and savanna regions and three clusters in the Andes and Pacific coast. We detected a cline of genetic variation along a west-east axis, contradicting a hard Andes-Amazon divide. This longitudinal genetic variation seemed to have been shaped by both serial population bottlenecks and isolation by distance. Results indicated that present-day South American substructures recapitulate ancient macroregional ancestries and western Amazonia groups show genetic evidence of cultural exchanges that led to language replacement in precontact times. Finally, demographic inferences pointed to a higher resilience of the western South American groups regarding population collapses caused by the European invasion and indicated precontact population reductions and demic expansions in South America.
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Affiliation(s)
- Marcos Araújo Castro e Silva
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Tiago Ferraz
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Cainã M Couto-Silva
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Renan B Lemes
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Kelly Nunes
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - David Comas
- Departament de Ciències, Institut de Biologia Evolutiva, Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Tábita Hünemeier
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
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14
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Martínez-Cruz B, Mendizabal I, Harmant C, de Pablo R, Ioana M, Angelicheva D, Kouvatsi A, Makukh H, Netea MG, Pamjav H, Zalán A, Tournev I, Marushiakova E, Popov V, Bertranpetit J, Kalaydjieva L, Quintana-Murci L, Comas D. Correction to: Origins, admixture and founder lineages in European Roma. Eur J Hum Genet 2021; 30:490. [DOI: 10.1038/s41431-021-01020-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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15
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Flores-Bello A, Font-Porterias N, Aizpurua-Iraola J, Duarri-Redondo S, Comas D. The genetic scenario of Mercheros: an under-represented group within the Iberian Peninsula. BMC Genomics 2021; 22:897. [PMID: 34911433 PMCID: PMC8672588 DOI: 10.1186/s12864-021-08203-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 11/18/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The general picture of human genetic variation has been vastly depicted in the last years, yet many populations remain broadly understudied. In this work, we analyze for the first time the Merchero population, a Spanish minority ethnic group that has been scarcely studied and historically persecuted. Mercheros have been roughly characterised by an itinerant history, common traditional occupations, and the usage of their own language. RESULTS Here, we examine the demographic history and genetic scenario of Mercheros, by using genome-wide array data, whole mitochondrial sequences, and Y chromosome STR markers from 25 individuals. These samples have been complemented with a wide-range of present-day populations from Western Eurasia and North Africa. Our results show that the genetic diversity of Mercheros is explained within the context of the Iberian Peninsula, evidencing a modest signal of Roma admixture. In addition, Mercheros present low genetic isolation and intrapopulation heterogeneity. CONCLUSIONS This study represents the first genetic characterisation of the Merchero population, depicting their fine-scale ancestry components and genetic scenario within the Iberian Peninsula. Since ethnicity is not only influenced by genetic ancestry but also cultural factors, other studies from multiple disciplines are needed to further explore the Merchero population. As with Mercheros, there is a considerable gap of underrepresented populations and ethnic groups in publicly available genetic data. Thus, we encourage the consideration of more ethnically diverse population panels in human genetic studies, as an attempt to improve the representation of human populations and better reconstruct their fine-scale history.
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Affiliation(s)
- André Flores-Bello
- Departament de Ciències de la Salut i de la Vida, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, 08003, Barcelona, Spain
| | - Neus Font-Porterias
- Departament de Ciències de la Salut i de la Vida, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, 08003, Barcelona, Spain
| | - Julen Aizpurua-Iraola
- Departament de Ciències de la Salut i de la Vida, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, 08003, Barcelona, Spain
| | - Sara Duarri-Redondo
- Departament de Ciències de la Salut i de la Vida, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, 08003, Barcelona, Spain
| | - David Comas
- Departament de Ciències de la Salut i de la Vida, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, 08003, Barcelona, Spain.
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16
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Font-Porterias N, Giménez A, Carballo-Mesa A, Calafell F, Comas D. Admixture Has Shaped Romani Genetic Diversity in Clinically Relevant Variants. Front Genet 2021; 12:683880. [PMID: 34220960 PMCID: PMC8244592 DOI: 10.3389/fgene.2021.683880] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 05/13/2021] [Indexed: 01/04/2023] Open
Abstract
Genetic patterns of inter-population variation are a result of different demographic and adaptive histories, which gradually shape the frequency distribution of the variants. However, the study of clinically relevant mutations has a Eurocentric bias. The Romani, the largest transnational minority ethnic group in Europe, originated in South Asia and received extensive gene flow from West Eurasia. Most medical genetic studies have only explored founder mutations related to Mendelian disorders in this population. Here we analyze exome sequences and genome-wide array data of 89 healthy Spanish Roma individuals to study complex traits and disease. We apply a different framework and focus on variants with both increased and decreased allele frequencies, taking into account their local ancestry. We report several OMIM traits enriched for genes with deleterious variants showing increased frequencies in Roma or in non-Roma (e.g., obesity is enriched in Roma, with an associated variant linked to South Asian ancestry; while non-insulin dependent diabetes is enriched in non-Roma Europeans). In addition, previously reported pathogenic variants also show differences among populations, where some variants segregating at low frequency in non-Roma are virtually absent in the Roma. Lastly, we describe frequency changes in drug-response variation, where many of the variants increased in Roma are clinically associated with metabolic and cardiovascular-related drugs. These results suggest that clinically relevant variation in Roma cannot only be characterized in terms of founder mutations. Instead, we observe frequency differences compared to non-Roma: some variants are absent, while other have drifted to higher frequencies. As a result of the admixture events, these clinically damaging variants can be traced back to both European and South Asian-related ancestries. This can be attributed to a different prevalence of some genetic disorders or to the fact that genetic susceptibility variants are mostly studied in populations of European descent, and can differ in individuals with different ancestries.
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Affiliation(s)
- Neus Font-Porterias
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Barcelona, Spain
| | - Aaron Giménez
- Facultat de Sociologia, Universitat Autònoma de Barcelona, Barcelona, Spain
| | | | - Francesc Calafell
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Barcelona, Spain
| | - David Comas
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Barcelona, Spain
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17
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Flores-Bello A, Bauduer F, Salaberria J, Oyharçabal B, Calafell F, Bertranpetit J, Quintana-Murci L, Comas D. Genetic origins, singularity, and heterogeneity of Basques. Curr Biol 2021; 31:2167-2177.e4. [DOI: 10.1016/j.cub.2021.03.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 02/22/2021] [Accepted: 03/02/2021] [Indexed: 02/09/2023]
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18
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García A, Nores R, Motti JMB, Pauro M, Luisi P, Bravi CM, Fabra M, Gosling AL, Kardailsky O, Boocock J, Solé-Morata N, Matisoo-Smith EA, Comas D, Demarchi DA. Ancient and modern mitogenomes from Central Argentina: new insights into population continuity, temporal depth and migration in South America. Hum Mol Genet 2021; 30:1200-1217. [PMID: 33856032 DOI: 10.1093/hmg/ddab105] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 03/15/2021] [Accepted: 03/31/2021] [Indexed: 12/22/2022] Open
Abstract
The inverted triangle shape of South America places Argentina territory as a geographical crossroads between the two principal peopling streams that followed either the Pacific or the Atlantic coasts, which could have then merged in Central Argentina (CA). Although the genetic diversity from this region is therefore crucial to decipher past population movements in South America, its characterization has been overlooked so far. We report 92 modern and 22 ancient mitogenomes spanning a temporal range of 5000 years, which were compared with a large set of previously reported data. Leveraging this dataset representative of the mitochondrial diversity of the subcontinent, we investigate the maternal history of CA populations within a wider geographical context. We describe a large number of novel clades within the mitochondrial DNA tree, thus providing new phylogenetic interpretations for South America. We also identify several local clades of great temporal depth with continuity until the present time, which stem directly from the founder haplotypes, suggesting that they originated in the region and expanded from there. Moreover, the presence of lineages characteristic of other South American regions reveals the existence of gene flow to CA. Finally, we report some lineages with discontinuous distribution across the Americas, which suggest the persistence of relic lineages likely linked to the first population arrivals. The present study represents to date the most exhaustive attempt to elaborate a Native American genetic map from modern and ancient complete mitochondrial genomes in Argentina and provides relevant information about the general process of settlement in South America.
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Affiliation(s)
- Angelina García
- Departamento de Antropología, Facultad de Filosofía y Humanidades, Universidad Nacional de Córdoba, Córdoba 5000, Argentina.,Instituto de Antropología de Córdoba (IDACOR), CONICET, Universidad Nacional de Córdoba, Córdoba 5000, Argentina
| | - Rodrigo Nores
- Departamento de Antropología, Facultad de Filosofía y Humanidades, Universidad Nacional de Córdoba, Córdoba 5000, Argentina.,Instituto de Antropología de Córdoba (IDACOR), CONICET, Universidad Nacional de Córdoba, Córdoba 5000, Argentina
| | - Josefina M B Motti
- FACSO (NEIPHPA), Universidad Nacional del Centro de la Provincia de Buenos Aires, CONICET, Quequén 7631, Argentina
| | - Maia Pauro
- Departamento de Antropología, Facultad de Filosofía y Humanidades, Universidad Nacional de Córdoba, Córdoba 5000, Argentina.,Instituto de Antropología de Córdoba (IDACOR), CONICET, Universidad Nacional de Córdoba, Córdoba 5000, Argentina
| | - Pierre Luisi
- Departamento de Antropología, Facultad de Filosofía y Humanidades, Universidad Nacional de Córdoba, Córdoba 5000, Argentina
| | - Claudio M Bravi
- Instituto Multidisciplinario de Biología Celular (IMBICE), CCT La Plata CONICET, CICPBA, Universidad Nacional de La Plata, La Plata 1906, Argentina
| | - Mariana Fabra
- Departamento de Antropología, Facultad de Filosofía y Humanidades, Universidad Nacional de Córdoba, Córdoba 5000, Argentina.,Instituto de Antropología de Córdoba (IDACOR), CONICET, Universidad Nacional de Córdoba, Córdoba 5000, Argentina
| | - Anna L Gosling
- Department of Anatomy, University of Otago, Dunedin 9054, New Zealand
| | - Olga Kardailsky
- Department of Anatomy, University of Otago, Dunedin 9054, New Zealand
| | - James Boocock
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand.,Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Neus Solé-Morata
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona 08003, Spain
| | | | - David Comas
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - Darío A Demarchi
- Departamento de Antropología, Facultad de Filosofía y Humanidades, Universidad Nacional de Córdoba, Córdoba 5000, Argentina.,Instituto de Antropología de Córdoba (IDACOR), CONICET, Universidad Nacional de Córdoba, Córdoba 5000, Argentina
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Font-Porterias N, Caro-Consuegra R, Lucas-Sánchez M, Lopez M, Giménez A, Carballo-Mesa A, Bosch E, Calafell F, Quintana-Murci L, Comas D. The Counteracting Effects of Demography on Functional Genomic Variation: The Roma Paradigm. Mol Biol Evol 2021; 38:2804-2817. [PMID: 33713133 PMCID: PMC8233508 DOI: 10.1093/molbev/msab070] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Demographic history plays a major role in shaping the distribution of genomic variation. Yet the interaction between different demographic forces and their effects in the genomes is not fully resolved in human populations. Here, we focus on the Roma population, the largest transnational ethnic minority in Europe. They have a South Asian origin and their demographic history is characterized by recent dispersals, multiple founder events, and extensive gene flow from non-Roma groups. Through the analyses of new high-coverage whole exome sequences and genome-wide array data for 89 Iberian Roma individuals together with forward simulations, we show that founder effects have reduced their genetic diversity and proportion of rare variants, gene flow has counteracted the increase in mutational load, runs of homozygosity show ancestry-specific patterns of accumulation of deleterious homozygotes, and selection signals primarily derive from preadmixture adaptation in the Roma population sources. The present study shows how two demographic forces, bottlenecks and admixture, act in opposite directions and have long-term balancing effects on the Roma genomes. Understanding how demography and gene flow shape the genome of an admixed population provides an opportunity to elucidate how genomic variation is modeled in human populations.
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Affiliation(s)
- Neus Font-Porterias
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Barcelona, Spain
| | - Rocio Caro-Consuegra
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Barcelona, Spain
| | - Marcel Lucas-Sánchez
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Barcelona, Spain
| | - Marie Lopez
- Human Evolutionary Genetics Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
| | - Aaron Giménez
- Facultat de Sociologia, Universitat Autònoma de Barcelona, Barcelona, Spain
| | | | - Elena Bosch
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Reus, Spain
| | - Francesc Calafell
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Barcelona, Spain
| | - Lluís Quintana-Murci
- Human Evolutionary Genetics Unit, Institut Pasteur, UMR2000, CNRS, Paris, France.,Human Genomics and Evolution, Collège de France, Paris, France
| | - David Comas
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Barcelona, Spain
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20
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Lucas-Sánchez M, Serradell JM, Comas D. Population history of North Africa based on modern and ancient genomes. Hum Mol Genet 2020; 30:R17-R23. [PMID: 33284971 DOI: 10.1093/hmg/ddaa261] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 11/30/2020] [Accepted: 12/02/2020] [Indexed: 01/09/2023] Open
Abstract
Compared with the rest of the African continent, North Africa has provided limited genomic data. Nonetheless, the genetic data available show a complex demographic scenario characterized by extensive admixture and drift. Despite the continuous gene flow from the Middle East, Europe and sub-Saharan Africa, an autochthonous genetic component that dates back to pre-Holocene times is still present in North African groups. The comparison of ancient and modern genomes has evidenced a genetic continuity in the region since Epipaleolithic times. Later population movements, especially the gene flow from the Middle East associated with the Neolithic, have diluted the genetic autochthonous component, creating an east to west gradient. Recent historical movements, such as the Arabization, have also contributed to the genetic landscape observed currently in North Africa and have culturally transformed the region. Genome analyses have not shown evidence of a clear correlation between cultural and genetic diversity in North Africa, as there is no genetic pattern of differentiation between Tamazight (i.e. Berber) and Arab speakers as a whole. Besides the gene flow received from neighboring areas, the analysis of North African genomes has shown that the region has also acted as a source of gene flow since ancient times. As a result of the genetic uniqueness of North African groups and the lack of available data, there is an urgent need for the study of genetic variation in the region and its implications in health and disease.
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Affiliation(s)
- Marcel Lucas-Sánchez
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Jose M Serradell
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - David Comas
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, 08003 Barcelona, Spain
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21
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Bianco E, Laval G, Font-Porterias N, García-Fernández C, Dobon B, Sabido-Vera R, Sukarova Stefanovska E, Kučinskas V, Makukh H, Pamjav H, Quintana-Murci L, Netea MG, Bertranpetit J, Calafell F, Comas D. Recent Common Origin, Reduced Population Size, and Marked Admixture Have Shaped European Roma Genomes. Mol Biol Evol 2020; 37:3175-3187. [PMID: 32589725 DOI: 10.1093/molbev/msaa156] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The Roma Diaspora-traditionally known as Gypsies-remains among the least explored population migratory events in historical times. It involved the migration of Roma ancestors out-of-India through the plateaus of Western Asia ultimately reaching Europe. The demographic effects of the Diaspora-bottlenecks, endogamy, and gene flow-might have left marked molecular traces in the Roma genomes. Here, we analyze the whole-genome sequence of 46 Roma individuals pertaining to four migrant groups in six European countries. Our analyses revealed a strong, early founder effect followed by a drastic reduction of ∼44% in effective population size. The Roma common ancestors split from the Punjabi population, from Northwest India, some generations before the Diaspora started, <2,000 years ago. The initial bottleneck and subsequent endogamy are revealed by the occurrence of extensive runs of homozygosity and identity-by-descent segments in all Roma populations. Furthermore, we provide evidence of gene flow from Armenian and Anatolian groups in present-day Roma, although the primary contribution to Roma gene pool comes from non-Roma Europeans, which accounts for >50% of their genomes. The linguistic and historical differentiation of Roma in migrant groups is confirmed by the differential proportion, but not a differential source, of European admixture in the Roma groups, which shows a westward cline. In the present study, we found that despite the strong admixture Roma had in their diaspora, the signature of the initial bottleneck and the subsequent endogamy is still present in Roma genomes.
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Affiliation(s)
- Erica Bianco
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
| | - Guillaume Laval
- Human Evolutionary Genetics Unit, Department of Genomes and Genetics, UMR 2000, CNRS, Institut Pasteur, Paris, France
| | - Neus Font-Porterias
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
| | - Carla García-Fernández
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
| | - Begoña Dobon
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
| | - Rubén Sabido-Vera
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
| | - Emilija Sukarova Stefanovska
- Research Center for Genetic Engineering and Biotechnology "Georgi D. Efremov", Macedonian Academy of Science and Arts, Skopje, Macedonia
| | - Vaidutis Kučinskas
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Halyna Makukh
- Institute of Hereditary Pathology of the Ukrainian Academy of Medical Sciences, Lviv, Ukraine
| | - Horolma Pamjav
- Department of Reference Sample Analysis, Institute of Forensic Genetics, Hungarian Institute for Forensic Sciences, Budapest, Hungary
| | - Lluis Quintana-Murci
- Human Evolutionary Genetics Unit, Department of Genomes and Genetics, UMR 2000, CNRS, Institut Pasteur, Paris, France.,Chair Human Genomics and Evolution, Collège de France, Paris, France
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands.,Department for Genomics & Immunoregulation, Life and Medical Sciences 12 Institute (LIMES), University of Bonn, Bonn, Germany
| | - Jaume Bertranpetit
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
| | - Francesc Calafell
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
| | - David Comas
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
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22
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García-Fernández C, Font-Porterias N, Kučinskas V, Sukarova-Stefanovska E, Pamjav H, Makukh H, Dobon B, Bertranpetit J, Netea MG, Calafell F, Comas D. Author Correction: Sex-biased patterns shaped the genetic history of Roma. Sci Rep 2020; 10:18142. [PMID: 33077820 PMCID: PMC7573587 DOI: 10.1038/s41598-020-75277-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- C García-Fernández
- Institute of Evolutionary Biology (UPF‑CSIC), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - N Font-Porterias
- Institute of Evolutionary Biology (UPF‑CSIC), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - V Kučinskas
- Department of Human and Medical Genetics, Faculty of Medicine, Biomedical Science Institute, Vilnius University, Vilnius, Lithuania
| | - E Sukarova-Stefanovska
- Research Center for Genetic Engineering and Biotechnology "Georgi D. Efremov", Academy of Sciences and Arts of the Republic of North Macedonia - MASA, Skopje, Republic of North Macedonia
| | - H Pamjav
- Institute of Forensic Genetics, Hungarian Institute for Forensic Sciences, Budapest, Hungary
| | - H Makukh
- Institute of Hereditary Pathology, Ukrainian Academy of Medical Sciences, Lviv, Ukraine
| | - B Dobon
- Institute of Evolutionary Biology (UPF‑CSIC), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - J Bertranpetit
- Institute of Evolutionary Biology (UPF‑CSIC), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - M G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6525 GA, Nijmegen, the Netherlands.,Department of Human Genetics, University of Medicine and Pharmacy Craiova, Craiova, Romania.,Department for Genomics and Immunoregulation, Life and Medical Sciences Institute (LIMES), University of Bonn, 53115, Bonn, Germany
| | - F Calafell
- Institute of Evolutionary Biology (UPF‑CSIC), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain.
| | - D Comas
- Institute of Evolutionary Biology (UPF‑CSIC), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain.
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García-Fernández C, Font-Porterias N, Kučinskas V, Sukarova-Stefanovska E, Pamjav H, Makukh H, Dobon B, Bertranpetit J, Netea MG, Calafell F, Comas D. Sex-biased patterns shaped the genetic history of Roma. Sci Rep 2020; 10:14464. [PMID: 32879340 PMCID: PMC7468237 DOI: 10.1038/s41598-020-71066-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 08/07/2020] [Indexed: 12/30/2022] Open
Abstract
The Roma population is a European ethnic minority characterized by recent and multiple dispersals and founder effects. After their origin in South Asia around 1,500 years ago, they migrated West. In Europe, they diverged into ethnolinguistically distinct migrant groups that spread across the continent. Previous genetic studies based on genome-wide data and uniparental markers detected Roma founder events and West-Eurasian gene flow. However, to the best of our knowledge, it has not been assessed whether these demographic processes have equally affected both sexes in the population. The present study uses the largest and most comprehensive dataset of complete mitochondrial and Y chromosome Roma sequences to unravel the sex-biased patterns that have shaped their genetic history. The results show that the Roma maternal genetic pool carries a higher lineage diversity from South Asia, as opposed to a single paternal South Asian lineage. Nonetheless, the European gene flow events mainly occurred through the maternal lineages; however, a signal of this gene flow is also traceable in the paternal lineages. We also detect a higher female migration rate among European Roma groups. Altogether, these results suggest that sociocultural factors influenced the emergence of sex-biased genetic patterns at global and local scales in the Roma population through time.
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Affiliation(s)
- C García-Fernández
- Institute of Evolutionary Biology (UPF-CSIC), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - N Font-Porterias
- Institute of Evolutionary Biology (UPF-CSIC), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - V Kučinskas
- Department of Human and Medical Genetics, Faculty of Medicine, Biomedical Science Institute, Vilnius University, Vilnius, Lithuania
| | - E Sukarova-Stefanovska
- Research Center for Genetic Engineering and Biotechnology "Georgi D. Efremov", Academy of Sciences and Arts of the Republic of North Macedonia - MASA, Skopje, Republic of North Macedonia
| | - H Pamjav
- Institute of Forensic Genetics, Hungarian Institute for Forensic Sciences, Budapest, Hungary
| | - H Makukh
- Institute of Hereditary Pathology, Ukrainian Academy of Medical Sciences, Lviv, Ukraine
| | - B Dobon
- Institute of Evolutionary Biology (UPF-CSIC), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - J Bertranpetit
- Institute of Evolutionary Biology (UPF-CSIC), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - M G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6525 GA, Nijmegen, the Netherlands.,Department of Human Genetics, University of Medicine and Pharmacy Craiova, Craiova, Romania.,Department for Genomics and Immunoregulation, Life and Medical Sciences Institute (LIMES), University of Bonn, 53115, Bonn, Germany
| | - F Calafell
- Institute of Evolutionary Biology (UPF-CSIC), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain.
| | - D Comas
- Institute of Evolutionary Biology (UPF-CSIC), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain.
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24
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Biagini SA, Ramos-Luis E, Comas D, Calafell F. The place of metropolitan France in the European genomic landscape. Hum Genet 2020; 139:1091-1105. [DOI: 10.1007/s00439-020-02158-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 03/25/2020] [Indexed: 10/24/2022]
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Abstract
North African history and populations have exerted a pivotal influence on surrounding geographical regions, although scant genetic studies have addressed this issue. Our aim is to understand human historical migrations in the coastal surroundings of North Africa. We built a refined genome-wide dataset of North African populations to unearth the fine-scale genetic structure of the region, using haplotype information. The results suggest that the gene-flow from North Africa into the European Mediterranean coast (Tuscany and the Iberian Peninsula) arrived mainly from the Mediterranean coast of North Africa. In Tuscany, this North African admixture date estimate suggests the movement of peoples during the fall of the Roman Empire around the fourth century. In the Iberian Peninsula, the North African component probably reflects the impact of the Arab expansion since the seventh century and the subsequent expansion of the Christian Kingdoms. By contrast, the North African component in the Canary Islands has a source genetically related to present-day people from the Atlantic North African coast. We also find sub-Saharan gene-flow from the Senegambia region in the Canary Islands. Specifically, we detect a complex signal of admixture involving Atlantic, Senegambian and European sources intermixing around the fifteenth century, soon after the Castilian conquest. Our results highlight the differential genetic influence of North Africa into the surrounding coast and show that specific historical events have not only had a socio-cultural impact but additionally modified the gene pool of the populations.
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Affiliation(s)
- Lara R Arauna
- 1 Departament de Ciències Experimentals i de la Salut, Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra , Barcelona , Spain
| | - Garrett Hellenthal
- 2 UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London , London , UK
| | - David Comas
- 1 Departament de Ciències Experimentals i de la Salut, Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra , Barcelona , Spain
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26
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Mas-Sandoval A, Arauna LR, Gouveia MH, Barreto ML, Horta BL, Lima-Costa MF, Pereira AC, Salzano FM, Hünemeier T, Tarazona-Santos E, Bortolini MC, Comas D. Reconstructed Lost Native American Populations from Eastern Brazil Are Shaped by Differential Jê/Tupi Ancestry. Genome Biol Evol 2020; 11:2593-2604. [PMID: 31328768 PMCID: PMC6756188 DOI: 10.1093/gbe/evz161] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/17/2019] [Indexed: 01/19/2023] Open
Abstract
After the colonization of the Americas by Europeans and the consequent Trans-Atlantic Slave Trade, most Native American populations in eastern Brazil disappeared or went through an admixture process that configured a population composed of three main genetic components: the European, the sub-Saharan African, and the Native American. The study of the Native American genetic history is challenged by the lack of availability of genome-wide samples from Native American populations, the technical difficulties to develop ancient DNA studies, and the low proportions of the Native American component in the admixed Brazilian populations (on average 7%). We analyzed genome-wide data of 5,825 individuals from three locations of eastern Brazil: Salvador (North-East), Bambui (South-East), and Pelotas (South) and we reconstructed populations that emulate the Native American groups that were living in the 16th century around the sampling locations. This genetic reconstruction was performed after local ancestry analysis of the admixed Brazilian populations, through the rearrangement of the Native American haplotypes into reconstructed individuals with full Native American ancestry (51 reconstructed individuals in Salvador, 45 in Bambui, and 197 in Pelotas). We compared the reconstructed populations with nonadmixed Native American populations from other regions of Brazil through haplotype-based methods. Our results reveal a population structure shaped by the dichotomy of Tupi-/Jê-speaking ancestry related groups. We also show evidence of a decrease of the diversity of nonadmixed Native American groups after the European contact, in contrast with the reconstructed populations, suggesting a reservoir of the Native American genetic diversity within the admixed Brazilian population.
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Affiliation(s)
- Alex Mas-Sandoval
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil.,Departament de Ciències Experimentals i de la Salut, Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
| | - Lara R Arauna
- Departament de Ciències Experimentals i de la Salut, Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
| | - Mateus H Gouveia
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.,Center for Research on Genomics and Global Health, National Institutes of Health, Bethesda, Maryland
| | - Mauricio L Barreto
- Instituto de Saúde Coletiva, Universidade Federal da Bahia, Salvador, Bahia, Brazil.,Center for Data and Knowledge Integration for Health, Institute Gonçalo Muniz, Fundação Oswaldo Cruz, Salvador, Bahia, Brazil
| | - Bernardo L Horta
- Programa de Pós-Graduação em Epidemiologia, Universidade Federal de Pelotas, Rio Grande do Sul, Brazil
| | | | | | - Francisco M Salzano
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Tábita Hünemeier
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, Brazil
| | - Eduardo Tarazona-Santos
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Maria Cátira Bortolini
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - David Comas
- Departament de Ciències Experimentals i de la Salut, Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
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27
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Serra-Vidal G, Lucas-Sanchez M, Fadhlaoui-Zid K, Bekada A, Zalloua P, Comas D. Heterogeneity in Palaeolithic Population Continuity and Neolithic Expansion in North Africa. Curr Biol 2019; 29:3953-3959.e4. [DOI: 10.1016/j.cub.2019.09.050] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 08/02/2019] [Accepted: 09/19/2019] [Indexed: 01/16/2023]
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28
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Secolin R, Mas-Sandoval A, Arauna LR, Torres FR, de Araujo TK, Santos ML, Rocha CS, Carvalho BS, Cendes F, Lopes-Cendes I, Comas D. Distribution of local ancestry and evidence of adaptation in admixed populations. Sci Rep 2019; 9:13900. [PMID: 31554886 PMCID: PMC6761108 DOI: 10.1038/s41598-019-50362-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 09/11/2019] [Indexed: 12/14/2022] Open
Abstract
Admixed American populations have different global proportions of European, Sub-Saharan African, and Native-American ancestry. However, individuals who display the same global ancestry could exhibit remarkable differences in the distribution of local ancestry blocks. We studied for the first time the distribution of local ancestry across the genome of 264 Brazilian admixed individuals, ascertained within the scope of the Brazilian Initiative on Precision Medicine. We found a decreased proportion of European ancestry together with an excess of Native-American ancestry on chromosome 8p23.1 and showed that this is due to haplotypes created by chromosomal inversion events. Furthermore, Brazilian non-inverted haplotypes were more similar to Native-American haplotypes than to European haplotypes, in contrast to what was found in other American admixed populations. We also identified signals of recent positive selection on chromosome 8p23.1, and one gene within this locus, PPP1R3B, is related to glycogenesis and has been associated with an increased risk of type 2 diabetes and obesity. These findings point to a selection event after admixture, which is still not entirely understood in recent admixture events.
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Affiliation(s)
- Rodrigo Secolin
- Department of Medical Genetics and Genomic Medicine, University of Campinas-UNICAMP, and the Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, SP, Brazil.,Departament de Ciències Experimentals i de la Salut, Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
| | - Alex Mas-Sandoval
- Departament de Ciències Experimentals i de la Salut, Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain.,Department of Genetics, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Lara R Arauna
- Departament de Ciències Experimentals i de la Salut, Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
| | - Fábio R Torres
- Department of Medical Genetics and Genomic Medicine, University of Campinas-UNICAMP, and the Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, SP, Brazil
| | - Tânia K de Araujo
- Department of Medical Genetics and Genomic Medicine, University of Campinas-UNICAMP, and the Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, SP, Brazil
| | - Marilza L Santos
- Department of Medical Genetics and Genomic Medicine, University of Campinas-UNICAMP, and the Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, SP, Brazil
| | - Cristiane S Rocha
- Department of Medical Genetics and Genomic Medicine, University of Campinas-UNICAMP, and the Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, SP, Brazil
| | - Benilton S Carvalho
- Department of Statistics, Institute of Mathematics, Statistics and Scientific Computing, University of Campinas-UNICAMP, and the Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, SP, Brazil
| | - Fernando Cendes
- Department of Neurology, University of Campinas-UNICAMP, and the Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, SP, Brazil
| | - Iscia Lopes-Cendes
- Department of Medical Genetics and Genomic Medicine, University of Campinas-UNICAMP, and the Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, SP, Brazil.
| | - David Comas
- Departament de Ciències Experimentals i de la Salut, Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
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29
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Font-Porterias N, Arauna LR, Poveda A, Bianco E, Rebato E, Prata MJ, Calafell F, Comas D. European Roma groups show complex West Eurasian admixture footprints and a common South Asian genetic origin. PLoS Genet 2019; 15:e1008417. [PMID: 31545809 PMCID: PMC6779411 DOI: 10.1371/journal.pgen.1008417] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 10/07/2019] [Accepted: 09/12/2019] [Indexed: 02/07/2023] Open
Abstract
The Roma population is the largest transnational ethnic minority in Europe, characterized by a linguistic, cultural and historical heterogeneity. Comparative linguistics and genetic studies have placed the origin of European Roma in the Northwest of India. After their migration across Persia, they entered into the Balkan Peninsula, from where they spread into Europe, arriving in the Iberian Peninsula in the 15th century. Their particular demographic history has genetic implications linked to rare and common diseases. However, the South Asian source of the proto-Roma remains still untargeted and the West Eurasian Roma component has not been yet deeply characterized. Here, in order to describe both the South Asian and West Eurasian ancestries, we analyze previously published genome-wide data of 152 European Roma and 34 new Iberian Roma samples at a fine-scale and haplotype-based level, with special focus on the Iberian Roma genetic substructure. Our results suggest that the putative origin of the proto-Roma involves a Punjabi group with low levels of West Eurasian ancestry. In addition, we have identified a complex West Eurasian component (around 65%) in the Roma, as a result of the admixture events occurred with non-proto-Roma populations between 1270–1580. Particularly, we have detected the Balkan genetic footprint in all European Roma, and the Baltic and Iberian components in the Northern and Western Roma groups, respectively. Finally, our results show genetic substructure within the Iberian Roma, with different levels of West Eurasian admixture, as a result of the complex historical events occurred in the Peninsula. Human demographic processes and admixture events leave traceable footprints in the genomes of the populations and they can modulate the genetic architecture of complex diseases. Here, we aim to study the Roma people, an admixed population with a particular demographic history recognized as the largest ethnic minority in Europe. Previous studies suggest that they originated in South Asia 1,500 years ago and followed a diaspora towards Europe with extensive admixture with non-Roma West Eurasian groups. However, the genetic components of the Roma have not been deeply characterized. Our study reveals a common South Asian origin of all European Roma, closely related to a Punjabi group from Northwestern India. Through fine-scale haplotype-based methods, we describe a complex West Eurasian genetic component in the Roma groups, identifying a common Balkan ancestry and country-specific admixture footprints consistent with the dispersion through Europe. Our findings provide new insights into the demographic history and recent admixture events that have shaped the genetic composition of European Roma groups and could enable a better genetic characterization of complex disease in this population.
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Affiliation(s)
- Neus Font-Porterias
- Institute of Evolutionary Biology (UPF-CSIC), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Lara R. Arauna
- Institute of Evolutionary Biology (UPF-CSIC), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
- Unit of Human Evolutionary Genetics, Institut Pasteur, Paris, France
| | - Alaitz Poveda
- Department of Clinical Sciences, Genetic and Molecular Epidemiology Unit, Lund University Diabetes Centre, Lund University, Malmö, Sweden
| | - Erica Bianco
- Institute of Evolutionary Biology (UPF-CSIC), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Esther Rebato
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country UPV/EHU, Leioa, Spain
| | - Maria Joao Prata
- Instituto de Investigacão e Inovacão em Saude/Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal; Faculty of Sciences, University of Porto, Porto, Portugal
| | - Francesc Calafell
- Institute of Evolutionary Biology (UPF-CSIC), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - David Comas
- Institute of Evolutionary Biology (UPF-CSIC), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
- * E-mail:
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Urnikyte A, Flores-Bello A, Mondal M, Molyte A, Comas D, Calafell F, Bosch E, Kučinskas V. Patterns of genetic structure and adaptive positive selection in the Lithuanian population from high-density SNP data. Sci Rep 2019; 9:9163. [PMID: 31235771 PMCID: PMC6591479 DOI: 10.1038/s41598-019-45746-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 06/14/2019] [Indexed: 12/16/2022] Open
Abstract
The analysis of geographically specific regions and the characterization of fine-scale patterns of genetic diversity may facilitate a much better understanding of the microevolutionary processes affecting local human populations. Here we generated genome-wide high-density SNP genotype data in 425 individuals from six geographical regions in Lithuania and combined our dataset with available ancient and modern data to explore genetic population structure, ancestry components and signatures of natural positive selection in the Lithuanian population. Our results show that Lithuanians are a homogenous population, genetically differentiated from neighbouring populations but within the general expected European context. Moreover, we not only confirm that Lithuanians preserve one of the highest proportions of western, Scandinavian and eastern hunter-gather ancestry components found in European populations but also that of an steppe Early to Middle Bronze Age pastoralists, which together configure the genetic distinctiveness of the Lithuanian population. Finally, among the top signatures of positive selection detected in Lithuanians, we identified several candidate genes related with diet (PNLIP, PPARD), pigmentation (SLC24A5, TYRP1 and PPARD) and the immune response (BRD2, HLA-DOA, IL26 and IL22).
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Affiliation(s)
- A Urnikyte
- Department of Human and Medical Genetics, Biomedical Science Institute, Faculty of Medicine, Vilnius University, Santariskiu Street 2, LT-08661, Vilnius, Lithuania
| | - A Flores-Bello
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Doctor Aiguader 88, 08003, Barcelona, Catalonia, Spain
| | - M Mondal
- Institute of Genomics, University of Tartu, Riia 23b, Tartu, 51010 Tartu, Estonia
| | - A Molyte
- Department of Human and Medical Genetics, Biomedical Science Institute, Faculty of Medicine, Vilnius University, Santariskiu Street 2, LT-08661, Vilnius, Lithuania
| | - D Comas
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Doctor Aiguader 88, 08003, Barcelona, Catalonia, Spain
| | - F Calafell
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Doctor Aiguader 88, 08003, Barcelona, Catalonia, Spain
| | - E Bosch
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Doctor Aiguader 88, 08003, Barcelona, Catalonia, Spain.
| | - V Kučinskas
- Department of Human and Medical Genetics, Biomedical Science Institute, Faculty of Medicine, Vilnius University, Santariskiu Street 2, LT-08661, Vilnius, Lithuania.
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Pimenta J, Lopes AM, Carracedo A, Arenas M, Amorim A, Comas D. Spatially explicit analysis reveals complex human genetic gradients in the Iberian Peninsula. Sci Rep 2019; 9:7825. [PMID: 31127131 PMCID: PMC6534591 DOI: 10.1038/s41598-019-44121-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 05/09/2019] [Indexed: 12/17/2022] Open
Abstract
The Iberian Peninsula is a well-delimited geographic region with a rich and complex human history. However, the causes of its genetic structure and past migratory dynamics are not yet fully understood. In order to shed light on them, here we evaluated the gene flow and genetic structure throughout the Iberian Peninsula with spatially explicit modelling applied to a georeferenced genetic dataset composed of genome-wide SNPs from 746 individuals belonging to 17 different regions of the Peninsula. We found contrasting patterns of genetic structure throughout Iberia. In particular, we identified strong patterns of genetic differentiation caused by relevant barriers to gene flow in northern regions and, on the other hand, a large genetic similarity in central and southern regions. In addition, our results showed a preferential north to south migratory dynamics and suggest a sex-biased dispersal in Mediterranean and southern regions. The estimated genetic patterns did not fit with the geographical relief of the Iberian landscape and they rather seem to follow political and linguistic territorial boundaries.
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Affiliation(s)
- João Pimenta
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
- Institute of Evolutionary Biology (CSIC-UPF). Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
- Faculty of Sciences, University of Porto, Porto, Portugal
- Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
| | - Alexandra M Lopes
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
| | - Angel Carracedo
- Instituto de Ciencias Forenses, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Grupo de Medicina Xenómica, CIBERER, Santiago de Compostela, Spain
| | - Miguel Arenas
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain
- Biomedical Research Center (CINBIO), University of Vigo, 36310, Vigo, Spain
| | - António Amorim
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
- Faculty of Sciences, University of Porto, Porto, Portugal
| | - David Comas
- Institute of Evolutionary Biology (CSIC-UPF). Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain.
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Lorente-Galdos B, Lao O, Serra-Vidal G, Santpere G, Kuderna LFK, Arauna LR, Fadhlaoui-Zid K, Pimenoff VN, Soodyall H, Zalloua P, Marques-Bonet T, Comas D. Whole-genome sequence analysis of a Pan African set of samples reveals archaic gene flow from an extinct basal population of modern humans into sub-Saharan populations. Genome Biol 2019; 20:77. [PMID: 31023378 PMCID: PMC6485163 DOI: 10.1186/s13059-019-1684-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 03/28/2019] [Indexed: 12/30/2022] Open
Abstract
Background Population demography and gene flow among African groups, as well as the putative archaic introgression of ancient hominins, have been poorly explored at the genome level. Results Here, we examine 15 African populations covering all major continental linguistic groups, ecosystems, and lifestyles within Africa through analysis of whole-genome sequence data of 21 individuals sequenced at deep coverage. We observe a remarkable correlation among genetic diversity and geographic distance, with the hunter-gatherer groups being more genetically differentiated and having larger effective population sizes throughout most modern-human history. Admixture signals are found between neighbor populations from both hunter-gatherer and agriculturalists groups, whereas North African individuals are closely related to Eurasian populations. Regarding archaic gene flow, we test six complex demographic models that consider recent admixture as well as archaic introgression. We identify the fingerprint of an archaic introgression event in the sub-Saharan populations included in the models (~ 4.0% in Khoisan, ~ 4.3% in Mbuti Pygmies, and ~ 5.8% in Mandenka) from an early divergent and currently extinct ghost modern human lineage. Conclusion The present study represents an in-depth genomic analysis of a Pan African set of individuals, which emphasizes their complex relationships and demographic history at population level. Electronic supplementary material The online version of this article (10.1186/s13059-019-1684-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Belen Lorente-Galdos
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (UPF/CSIC), Universitat Pompeu Fabra, 08003, Barcelona, Spain.,Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Oscar Lao
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, 08028, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Gerard Serra-Vidal
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (UPF/CSIC), Universitat Pompeu Fabra, 08003, Barcelona, Spain
| | - Gabriel Santpere
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (UPF/CSIC), Universitat Pompeu Fabra, 08003, Barcelona, Spain.,Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Lukas F K Kuderna
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (UPF/CSIC), Universitat Pompeu Fabra, 08003, Barcelona, Spain
| | - Lara R Arauna
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (UPF/CSIC), Universitat Pompeu Fabra, 08003, Barcelona, Spain
| | - Karima Fadhlaoui-Zid
- College of Science, Department of Biology, Taibah University, Al Madinah, Al Monawarah, Saudi Arabia.,Higher Institute of Biotechnology of Beja, University of Jendouba, Avenue Habib Bourguiba, BP, 382, 9000, Beja, Tunisia
| | - Ville N Pimenoff
- Oncology Data Analytics Program, Bellvitge Biomedical Research Institute (ICO-IDIBELL), Consortium for Biomedical Research in Epidemiology and Public Health, Hospitalet de Llobregat, Barcelona, Spain.,Department of Archaeology, University of Helsinki, Helsinki, Finland
| | - Himla Soodyall
- Division of Human Genetics, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and National Health Laboratory Service, Johannesburg, South Africa
| | - Pierre Zalloua
- School of Medicine, The Lebanese American University, Beirut, 1102-2801, Lebanon
| | - Tomas Marques-Bonet
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (UPF/CSIC), Universitat Pompeu Fabra, 08003, Barcelona, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, 08028, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats, ICREA, 08003, Barcelona, Spain
| | - David Comas
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (UPF/CSIC), Universitat Pompeu Fabra, 08003, Barcelona, Spain.
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Biagini SA, Solé-Morata N, Matisoo-Smith E, Zalloua P, Comas D, Calafell F. People from Ibiza: an unexpected isolate in the Western Mediterranean. Eur J Hum Genet 2019; 27:941-951. [PMID: 30765884 DOI: 10.1038/s41431-019-0361-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 01/15/2019] [Accepted: 01/24/2019] [Indexed: 11/09/2022] Open
Abstract
In this study, we seek to understand and to correlate the genetic patterns observed in the population of the island of Ibiza in the Western Mediterranean basin with past events. Genome-wide genotypes of 189 samples representing 13 of 17 regions in Spain have been analyzed, in addition to 105 samples from the Levant, 157 samples from North Africa, and one ancient sample from the Phoenician Cas Molí site in Ibiza. Before the Catalans conquered the island in 1235 CE, Ibiza (Eivissa) had already been influenced by several cultures, starting with the Phoenicians, then the Carthaginians, followed by the Umayyads. The impact of these various cultures on the genetic structure of the islanders is still unexplored. Our results show a clear distinction between Ibiza and the rest of Spain. To investigate whether this was due to the Phoenician colonization or to more recent events, we compared the genomes of current Ibizans to that of an ancient Phoenician sample from Ibiza and to both modern Levantine and North African genomes. We did not identify any trace of Phoenician ancestry in the current Ibizans. Interestingly, the analysis of runs of homozygosity and changes in the effective population size through time support the idea that drift has shaped the genetic structure of current Ibizans. In addition to the small carrying capacity of the island, Ibiza experienced a series of dramatic demographic changes due to several instances of famine, war, malaria and plague that could have significantly contributed to its current genetic differentiation.
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Affiliation(s)
- Simone Andrea Biagini
- Departament de Ciències Experimentals i de la Salut, Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
| | - Neus Solé-Morata
- Departament de Ciències Experimentals i de la Salut, Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
| | | | - Pierre Zalloua
- School of Medicine, The Lebanese American University, Chouran, Beirut, Lebanon
| | - David Comas
- Departament de Ciències Experimentals i de la Salut, Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
| | - Francesc Calafell
- Departament de Ciències Experimentals i de la Salut, Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain.
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Flores-Bello A, Mas-Ponte D, Rosu ME, Bosch E, Calafell F, Comas D. Sequence diversity of the Rh blood group system in Basques. Eur J Hum Genet 2018; 26:1859-1866. [PMID: 30089826 PMCID: PMC6244411 DOI: 10.1038/s41431-018-0232-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 06/15/2018] [Accepted: 07/17/2018] [Indexed: 11/09/2022] Open
Abstract
Basques show specific cultural, demographic, and genetic characteristics that have placed them as an isolated and unique population within Europe, such as their non-Indo-European language, Euskara. They have historically lived along the Western Pyrenees, between Spain and France, in one of the most important European glacial refugia during the Last Glacial Maximum. The most striking genetic characteristic is their highest frequency of the RhD blood group negative allele, a variant related to the hemolytic disease of the newborn. Both demographic and adaptive processes have been suggested as possible causes of the high frequency of RhD negative in Basques, but neither hypothesis has been clearly demonstrated. While previous studies on the Rh system in Basques have been mostly focused on serological and genotyping diversity, in this work we analyze genotyping and next generation sequencing data in order to provide a general framework of the genetic scenario of the system in Basques. In particular, we genotyped the most relevant variants of the system (D/d, E/e, and C/c), and sequenced three ~6 kb flanking regions surrounding the Rh genes in Basques and also in other populations for comparison. Our results are in agreement with previous studies, with Basques presenting the highest frequency of the RHD deletion (47.2%). Haplotype analyses of D/d, E/e, and C/c variants confirmed an association between the RhC allele, previously suggested to be under positive selection, and the RhD positive variant in non-sub-Saharan populations, including Basques. We also found extreme differentiation for the C/c variant when comparing sub-Saharan to non-sub-Saharan populations.
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Affiliation(s)
- André Flores-Bello
- Institute of Evolutionary Biology (CSIC - UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - David Mas-Ponte
- Institute for Research in Biomedicine Barcelona, Barcelona, Spain
| | - Miruna E Rosu
- Department of Viroscience, Postgraduate School Molecular Medicine, Erasmus MC, Rotterdam, The Netherlands
| | - Elena Bosch
- Institute of Evolutionary Biology (CSIC - UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Francesc Calafell
- Institute of Evolutionary Biology (CSIC - UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - David Comas
- Institute of Evolutionary Biology (CSIC - UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain.
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Cabrera-Serrano M, Mavillard F, Biancalana V, Rivas E, Morar B, Hernández-Laín A, Olive M, Muelas N, Khan E, Carvajal A, Quiroga P, Diaz-Manera J, Davis M, Ávila R, Domínguez C, Romero NB, Vílchez JJ, Comas D, Laing NG, Laporte J, Kalaydjieva L, Paradas C. A Roma founder BIN1 mutation causes a novel phenotype of centronuclear myopathy with rigid spine. Neurology 2018; 91:e339-e348. [PMID: 29950440 DOI: 10.1212/wnl.0000000000005862] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Accepted: 04/16/2018] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVE To describe a large series of BIN1 patients, in which a novel founder mutation in the Roma population of southern Spain has been identified. METHODS Patients diagnosed with centronuclear myopathy (CNM) at 5 major reference centers for neuromuscular disease in Spain (n = 53) were screened for BIN1 mutations. Clinical, histologic, radiologic, and genetic features were analyzed. RESULTS Eighteen patients from 13 families carried the p.Arg234Cys variant; 16 of them were homozygous for it and 2 had compound heterozygous p.Arg234Cys/p.Arg145Cys mutations. Both BIN1 variants have only been identified in Roma, causing 100% of CNM in this ethnic group in our cohort. The haplotype analysis confirmed all families are related. In addition to clinical features typical of CNM, such as proximal limb weakness and ophthalmoplegia, most patients in our cohort presented with prominent axial weakness, often associated with rigid spine. Severe fat replacement of paravertebral muscles was demonstrated by muscle imaging. This phenotype seems to be specific to the p.Arg234Cys mutation, not reported in other BIN1 mutations. Extreme clinical variability was observed in the 2 compound heterozygous patients for the p.Arg234Cys/p.Arg145Cys mutations, from a congenital onset with catastrophic outcome to a late-onset disease. Screening of European Roma controls (n = 758) for the p.Arg234Cys variant identified a carrier frequency of 3.5% among the Spanish Roma. CONCLUSION We have identified a BIN1 founder Roma mutation associated with a highly specific phenotype, which is, from the present cohort, the main cause of CNM in Spain.
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Affiliation(s)
- Macarena Cabrera-Serrano
- From the Unidad de Enfermedades Neuromusculares, Department of Neurology (M.C.-S., C.P.), Instituto de Biomedicina de Sevilla (IBiS) (M.C.-S., F.M., C.P.), and Department of Pathology, Neuropathology Unit (E.R.), Hospital Universitario Virgen del Rocío, Sevilla, Spain; Laboratoire Diagnostic Génétique (V.B.), Faculté de Médecine-CHRU, Strasbourg; Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC) (V.B., R.Á., J.L.), Illkirch, France; Harry Perkins Institute of Medical Research and Centre for Medical Research (B.M., N.G.L., L.K.), University of Western Australia, Nedlands; Department of Pathology (Neuropathology) (A.H.-L.), Hospital Universitario 12 de Octubre, Madrid Research Institute; Neuropathology Unit (M.O.), Department of Pathology and Neuromuscular Unit, Department of Neurology, IDIBELL-Hospital de Bellvitge, Hospitalet de Llobregat, Barcelona; Department of Neurology and IIS La Fe (N.M., J.J.V.), Hospital Universitari i Politècnic La Fe, Valencia; Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER) (N.M., J.D.-M., J.J.V.); Department of Neurology (E.K.), Consulta de Enfermedades Neuromusculares y Unidad de ELA, Hospital General Universitario Santa Lucía, Cartagena, Murcia; Department of Neurology (A.C.), Hospital Virgen de las Nieves, Granada; Department of Neurology (P.Q.), Hospital Torrecárdenas, Almería; Unidad de Enfermedades Neuromusculares (J.D.-M.), Department of Neurology, Universidad Autónoma de Barcelona, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain; Department of Diagnostic Genomics (M.D.), PathWest Laboratory Medicine WA, Perth, Australia; Department of Neurology (C.D.), Hospital 12 de Octubre, Madrid, Spain; Unité de Morphologie Neuromusculaire (N.B.R.), Centre de Référence de Pathologie Neuromusculaire Paris-Est, Institut de Myologie, Groupe Hospitalier Universitaire La Pitié-Salpêtrière, Paris; Université Sorbonne (N.B.R.), UPMC Univ Paris 06, INSERM UMRS974, CNRS FRE3617, Center for Research in Myology, Groupe Hospitalier Universitaire La Pitié-Salpêtrière, Paris, France; Department of Medicine (J.J.V.), Universitat de Valencia; Department of Experimental and Health Sciences (D.C.), Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain; Centre National de la Recherche Scientifique (J.L.), UMR7104, Illkirch; and Institut National de la Santé et de la Recherche Médicale (J.L.), U964, Illkirch, France
| | - Fabiola Mavillard
- From the Unidad de Enfermedades Neuromusculares, Department of Neurology (M.C.-S., C.P.), Instituto de Biomedicina de Sevilla (IBiS) (M.C.-S., F.M., C.P.), and Department of Pathology, Neuropathology Unit (E.R.), Hospital Universitario Virgen del Rocío, Sevilla, Spain; Laboratoire Diagnostic Génétique (V.B.), Faculté de Médecine-CHRU, Strasbourg; Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC) (V.B., R.Á., J.L.), Illkirch, France; Harry Perkins Institute of Medical Research and Centre for Medical Research (B.M., N.G.L., L.K.), University of Western Australia, Nedlands; Department of Pathology (Neuropathology) (A.H.-L.), Hospital Universitario 12 de Octubre, Madrid Research Institute; Neuropathology Unit (M.O.), Department of Pathology and Neuromuscular Unit, Department of Neurology, IDIBELL-Hospital de Bellvitge, Hospitalet de Llobregat, Barcelona; Department of Neurology and IIS La Fe (N.M., J.J.V.), Hospital Universitari i Politècnic La Fe, Valencia; Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER) (N.M., J.D.-M., J.J.V.); Department of Neurology (E.K.), Consulta de Enfermedades Neuromusculares y Unidad de ELA, Hospital General Universitario Santa Lucía, Cartagena, Murcia; Department of Neurology (A.C.), Hospital Virgen de las Nieves, Granada; Department of Neurology (P.Q.), Hospital Torrecárdenas, Almería; Unidad de Enfermedades Neuromusculares (J.D.-M.), Department of Neurology, Universidad Autónoma de Barcelona, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain; Department of Diagnostic Genomics (M.D.), PathWest Laboratory Medicine WA, Perth, Australia; Department of Neurology (C.D.), Hospital 12 de Octubre, Madrid, Spain; Unité de Morphologie Neuromusculaire (N.B.R.), Centre de Référence de Pathologie Neuromusculaire Paris-Est, Institut de Myologie, Groupe Hospitalier Universitaire La Pitié-Salpêtrière, Paris; Université Sorbonne (N.B.R.), UPMC Univ Paris 06, INSERM UMRS974, CNRS FRE3617, Center for Research in Myology, Groupe Hospitalier Universitaire La Pitié-Salpêtrière, Paris, France; Department of Medicine (J.J.V.), Universitat de Valencia; Department of Experimental and Health Sciences (D.C.), Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain; Centre National de la Recherche Scientifique (J.L.), UMR7104, Illkirch; and Institut National de la Santé et de la Recherche Médicale (J.L.), U964, Illkirch, France
| | - Valerie Biancalana
- From the Unidad de Enfermedades Neuromusculares, Department of Neurology (M.C.-S., C.P.), Instituto de Biomedicina de Sevilla (IBiS) (M.C.-S., F.M., C.P.), and Department of Pathology, Neuropathology Unit (E.R.), Hospital Universitario Virgen del Rocío, Sevilla, Spain; Laboratoire Diagnostic Génétique (V.B.), Faculté de Médecine-CHRU, Strasbourg; Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC) (V.B., R.Á., J.L.), Illkirch, France; Harry Perkins Institute of Medical Research and Centre for Medical Research (B.M., N.G.L., L.K.), University of Western Australia, Nedlands; Department of Pathology (Neuropathology) (A.H.-L.), Hospital Universitario 12 de Octubre, Madrid Research Institute; Neuropathology Unit (M.O.), Department of Pathology and Neuromuscular Unit, Department of Neurology, IDIBELL-Hospital de Bellvitge, Hospitalet de Llobregat, Barcelona; Department of Neurology and IIS La Fe (N.M., J.J.V.), Hospital Universitari i Politècnic La Fe, Valencia; Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER) (N.M., J.D.-M., J.J.V.); Department of Neurology (E.K.), Consulta de Enfermedades Neuromusculares y Unidad de ELA, Hospital General Universitario Santa Lucía, Cartagena, Murcia; Department of Neurology (A.C.), Hospital Virgen de las Nieves, Granada; Department of Neurology (P.Q.), Hospital Torrecárdenas, Almería; Unidad de Enfermedades Neuromusculares (J.D.-M.), Department of Neurology, Universidad Autónoma de Barcelona, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain; Department of Diagnostic Genomics (M.D.), PathWest Laboratory Medicine WA, Perth, Australia; Department of Neurology (C.D.), Hospital 12 de Octubre, Madrid, Spain; Unité de Morphologie Neuromusculaire (N.B.R.), Centre de Référence de Pathologie Neuromusculaire Paris-Est, Institut de Myologie, Groupe Hospitalier Universitaire La Pitié-Salpêtrière, Paris; Université Sorbonne (N.B.R.), UPMC Univ Paris 06, INSERM UMRS974, CNRS FRE3617, Center for Research in Myology, Groupe Hospitalier Universitaire La Pitié-Salpêtrière, Paris, France; Department of Medicine (J.J.V.), Universitat de Valencia; Department of Experimental and Health Sciences (D.C.), Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain; Centre National de la Recherche Scientifique (J.L.), UMR7104, Illkirch; and Institut National de la Santé et de la Recherche Médicale (J.L.), U964, Illkirch, France
| | - Eloy Rivas
- From the Unidad de Enfermedades Neuromusculares, Department of Neurology (M.C.-S., C.P.), Instituto de Biomedicina de Sevilla (IBiS) (M.C.-S., F.M., C.P.), and Department of Pathology, Neuropathology Unit (E.R.), Hospital Universitario Virgen del Rocío, Sevilla, Spain; Laboratoire Diagnostic Génétique (V.B.), Faculté de Médecine-CHRU, Strasbourg; Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC) (V.B., R.Á., J.L.), Illkirch, France; Harry Perkins Institute of Medical Research and Centre for Medical Research (B.M., N.G.L., L.K.), University of Western Australia, Nedlands; Department of Pathology (Neuropathology) (A.H.-L.), Hospital Universitario 12 de Octubre, Madrid Research Institute; Neuropathology Unit (M.O.), Department of Pathology and Neuromuscular Unit, Department of Neurology, IDIBELL-Hospital de Bellvitge, Hospitalet de Llobregat, Barcelona; Department of Neurology and IIS La Fe (N.M., J.J.V.), Hospital Universitari i Politècnic La Fe, Valencia; Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER) (N.M., J.D.-M., J.J.V.); Department of Neurology (E.K.), Consulta de Enfermedades Neuromusculares y Unidad de ELA, Hospital General Universitario Santa Lucía, Cartagena, Murcia; Department of Neurology (A.C.), Hospital Virgen de las Nieves, Granada; Department of Neurology (P.Q.), Hospital Torrecárdenas, Almería; Unidad de Enfermedades Neuromusculares (J.D.-M.), Department of Neurology, Universidad Autónoma de Barcelona, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain; Department of Diagnostic Genomics (M.D.), PathWest Laboratory Medicine WA, Perth, Australia; Department of Neurology (C.D.), Hospital 12 de Octubre, Madrid, Spain; Unité de Morphologie Neuromusculaire (N.B.R.), Centre de Référence de Pathologie Neuromusculaire Paris-Est, Institut de Myologie, Groupe Hospitalier Universitaire La Pitié-Salpêtrière, Paris; Université Sorbonne (N.B.R.), UPMC Univ Paris 06, INSERM UMRS974, CNRS FRE3617, Center for Research in Myology, Groupe Hospitalier Universitaire La Pitié-Salpêtrière, Paris, France; Department of Medicine (J.J.V.), Universitat de Valencia; Department of Experimental and Health Sciences (D.C.), Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain; Centre National de la Recherche Scientifique (J.L.), UMR7104, Illkirch; and Institut National de la Santé et de la Recherche Médicale (J.L.), U964, Illkirch, France
| | - Bharti Morar
- From the Unidad de Enfermedades Neuromusculares, Department of Neurology (M.C.-S., C.P.), Instituto de Biomedicina de Sevilla (IBiS) (M.C.-S., F.M., C.P.), and Department of Pathology, Neuropathology Unit (E.R.), Hospital Universitario Virgen del Rocío, Sevilla, Spain; Laboratoire Diagnostic Génétique (V.B.), Faculté de Médecine-CHRU, Strasbourg; Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC) (V.B., R.Á., J.L.), Illkirch, France; Harry Perkins Institute of Medical Research and Centre for Medical Research (B.M., N.G.L., L.K.), University of Western Australia, Nedlands; Department of Pathology (Neuropathology) (A.H.-L.), Hospital Universitario 12 de Octubre, Madrid Research Institute; Neuropathology Unit (M.O.), Department of Pathology and Neuromuscular Unit, Department of Neurology, IDIBELL-Hospital de Bellvitge, Hospitalet de Llobregat, Barcelona; Department of Neurology and IIS La Fe (N.M., J.J.V.), Hospital Universitari i Politècnic La Fe, Valencia; Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER) (N.M., J.D.-M., J.J.V.); Department of Neurology (E.K.), Consulta de Enfermedades Neuromusculares y Unidad de ELA, Hospital General Universitario Santa Lucía, Cartagena, Murcia; Department of Neurology (A.C.), Hospital Virgen de las Nieves, Granada; Department of Neurology (P.Q.), Hospital Torrecárdenas, Almería; Unidad de Enfermedades Neuromusculares (J.D.-M.), Department of Neurology, Universidad Autónoma de Barcelona, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain; Department of Diagnostic Genomics (M.D.), PathWest Laboratory Medicine WA, Perth, Australia; Department of Neurology (C.D.), Hospital 12 de Octubre, Madrid, Spain; Unité de Morphologie Neuromusculaire (N.B.R.), Centre de Référence de Pathologie Neuromusculaire Paris-Est, Institut de Myologie, Groupe Hospitalier Universitaire La Pitié-Salpêtrière, Paris; Université Sorbonne (N.B.R.), UPMC Univ Paris 06, INSERM UMRS974, CNRS FRE3617, Center for Research in Myology, Groupe Hospitalier Universitaire La Pitié-Salpêtrière, Paris, France; Department of Medicine (J.J.V.), Universitat de Valencia; Department of Experimental and Health Sciences (D.C.), Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain; Centre National de la Recherche Scientifique (J.L.), UMR7104, Illkirch; and Institut National de la Santé et de la Recherche Médicale (J.L.), U964, Illkirch, France
| | - Aurelio Hernández-Laín
- From the Unidad de Enfermedades Neuromusculares, Department of Neurology (M.C.-S., C.P.), Instituto de Biomedicina de Sevilla (IBiS) (M.C.-S., F.M., C.P.), and Department of Pathology, Neuropathology Unit (E.R.), Hospital Universitario Virgen del Rocío, Sevilla, Spain; Laboratoire Diagnostic Génétique (V.B.), Faculté de Médecine-CHRU, Strasbourg; Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC) (V.B., R.Á., J.L.), Illkirch, France; Harry Perkins Institute of Medical Research and Centre for Medical Research (B.M., N.G.L., L.K.), University of Western Australia, Nedlands; Department of Pathology (Neuropathology) (A.H.-L.), Hospital Universitario 12 de Octubre, Madrid Research Institute; Neuropathology Unit (M.O.), Department of Pathology and Neuromuscular Unit, Department of Neurology, IDIBELL-Hospital de Bellvitge, Hospitalet de Llobregat, Barcelona; Department of Neurology and IIS La Fe (N.M., J.J.V.), Hospital Universitari i Politècnic La Fe, Valencia; Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER) (N.M., J.D.-M., J.J.V.); Department of Neurology (E.K.), Consulta de Enfermedades Neuromusculares y Unidad de ELA, Hospital General Universitario Santa Lucía, Cartagena, Murcia; Department of Neurology (A.C.), Hospital Virgen de las Nieves, Granada; Department of Neurology (P.Q.), Hospital Torrecárdenas, Almería; Unidad de Enfermedades Neuromusculares (J.D.-M.), Department of Neurology, Universidad Autónoma de Barcelona, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain; Department of Diagnostic Genomics (M.D.), PathWest Laboratory Medicine WA, Perth, Australia; Department of Neurology (C.D.), Hospital 12 de Octubre, Madrid, Spain; Unité de Morphologie Neuromusculaire (N.B.R.), Centre de Référence de Pathologie Neuromusculaire Paris-Est, Institut de Myologie, Groupe Hospitalier Universitaire La Pitié-Salpêtrière, Paris; Université Sorbonne (N.B.R.), UPMC Univ Paris 06, INSERM UMRS974, CNRS FRE3617, Center for Research in Myology, Groupe Hospitalier Universitaire La Pitié-Salpêtrière, Paris, France; Department of Medicine (J.J.V.), Universitat de Valencia; Department of Experimental and Health Sciences (D.C.), Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain; Centre National de la Recherche Scientifique (J.L.), UMR7104, Illkirch; and Institut National de la Santé et de la Recherche Médicale (J.L.), U964, Illkirch, France
| | - Montse Olive
- From the Unidad de Enfermedades Neuromusculares, Department of Neurology (M.C.-S., C.P.), Instituto de Biomedicina de Sevilla (IBiS) (M.C.-S., F.M., C.P.), and Department of Pathology, Neuropathology Unit (E.R.), Hospital Universitario Virgen del Rocío, Sevilla, Spain; Laboratoire Diagnostic Génétique (V.B.), Faculté de Médecine-CHRU, Strasbourg; Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC) (V.B., R.Á., J.L.), Illkirch, France; Harry Perkins Institute of Medical Research and Centre for Medical Research (B.M., N.G.L., L.K.), University of Western Australia, Nedlands; Department of Pathology (Neuropathology) (A.H.-L.), Hospital Universitario 12 de Octubre, Madrid Research Institute; Neuropathology Unit (M.O.), Department of Pathology and Neuromuscular Unit, Department of Neurology, IDIBELL-Hospital de Bellvitge, Hospitalet de Llobregat, Barcelona; Department of Neurology and IIS La Fe (N.M., J.J.V.), Hospital Universitari i Politècnic La Fe, Valencia; Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER) (N.M., J.D.-M., J.J.V.); Department of Neurology (E.K.), Consulta de Enfermedades Neuromusculares y Unidad de ELA, Hospital General Universitario Santa Lucía, Cartagena, Murcia; Department of Neurology (A.C.), Hospital Virgen de las Nieves, Granada; Department of Neurology (P.Q.), Hospital Torrecárdenas, Almería; Unidad de Enfermedades Neuromusculares (J.D.-M.), Department of Neurology, Universidad Autónoma de Barcelona, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain; Department of Diagnostic Genomics (M.D.), PathWest Laboratory Medicine WA, Perth, Australia; Department of Neurology (C.D.), Hospital 12 de Octubre, Madrid, Spain; Unité de Morphologie Neuromusculaire (N.B.R.), Centre de Référence de Pathologie Neuromusculaire Paris-Est, Institut de Myologie, Groupe Hospitalier Universitaire La Pitié-Salpêtrière, Paris; Université Sorbonne (N.B.R.), UPMC Univ Paris 06, INSERM UMRS974, CNRS FRE3617, Center for Research in Myology, Groupe Hospitalier Universitaire La Pitié-Salpêtrière, Paris, France; Department of Medicine (J.J.V.), Universitat de Valencia; Department of Experimental and Health Sciences (D.C.), Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain; Centre National de la Recherche Scientifique (J.L.), UMR7104, Illkirch; and Institut National de la Santé et de la Recherche Médicale (J.L.), U964, Illkirch, France
| | - Nuria Muelas
- From the Unidad de Enfermedades Neuromusculares, Department of Neurology (M.C.-S., C.P.), Instituto de Biomedicina de Sevilla (IBiS) (M.C.-S., F.M., C.P.), and Department of Pathology, Neuropathology Unit (E.R.), Hospital Universitario Virgen del Rocío, Sevilla, Spain; Laboratoire Diagnostic Génétique (V.B.), Faculté de Médecine-CHRU, Strasbourg; Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC) (V.B., R.Á., J.L.), Illkirch, France; Harry Perkins Institute of Medical Research and Centre for Medical Research (B.M., N.G.L., L.K.), University of Western Australia, Nedlands; Department of Pathology (Neuropathology) (A.H.-L.), Hospital Universitario 12 de Octubre, Madrid Research Institute; Neuropathology Unit (M.O.), Department of Pathology and Neuromuscular Unit, Department of Neurology, IDIBELL-Hospital de Bellvitge, Hospitalet de Llobregat, Barcelona; Department of Neurology and IIS La Fe (N.M., J.J.V.), Hospital Universitari i Politècnic La Fe, Valencia; Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER) (N.M., J.D.-M., J.J.V.); Department of Neurology (E.K.), Consulta de Enfermedades Neuromusculares y Unidad de ELA, Hospital General Universitario Santa Lucía, Cartagena, Murcia; Department of Neurology (A.C.), Hospital Virgen de las Nieves, Granada; Department of Neurology (P.Q.), Hospital Torrecárdenas, Almería; Unidad de Enfermedades Neuromusculares (J.D.-M.), Department of Neurology, Universidad Autónoma de Barcelona, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain; Department of Diagnostic Genomics (M.D.), PathWest Laboratory Medicine WA, Perth, Australia; Department of Neurology (C.D.), Hospital 12 de Octubre, Madrid, Spain; Unité de Morphologie Neuromusculaire (N.B.R.), Centre de Référence de Pathologie Neuromusculaire Paris-Est, Institut de Myologie, Groupe Hospitalier Universitaire La Pitié-Salpêtrière, Paris; Université Sorbonne (N.B.R.), UPMC Univ Paris 06, INSERM UMRS974, CNRS FRE3617, Center for Research in Myology, Groupe Hospitalier Universitaire La Pitié-Salpêtrière, Paris, France; Department of Medicine (J.J.V.), Universitat de Valencia; Department of Experimental and Health Sciences (D.C.), Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain; Centre National de la Recherche Scientifique (J.L.), UMR7104, Illkirch; and Institut National de la Santé et de la Recherche Médicale (J.L.), U964, Illkirch, France
| | - Eduardo Khan
- From the Unidad de Enfermedades Neuromusculares, Department of Neurology (M.C.-S., C.P.), Instituto de Biomedicina de Sevilla (IBiS) (M.C.-S., F.M., C.P.), and Department of Pathology, Neuropathology Unit (E.R.), Hospital Universitario Virgen del Rocío, Sevilla, Spain; Laboratoire Diagnostic Génétique (V.B.), Faculté de Médecine-CHRU, Strasbourg; Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC) (V.B., R.Á., J.L.), Illkirch, France; Harry Perkins Institute of Medical Research and Centre for Medical Research (B.M., N.G.L., L.K.), University of Western Australia, Nedlands; Department of Pathology (Neuropathology) (A.H.-L.), Hospital Universitario 12 de Octubre, Madrid Research Institute; Neuropathology Unit (M.O.), Department of Pathology and Neuromuscular Unit, Department of Neurology, IDIBELL-Hospital de Bellvitge, Hospitalet de Llobregat, Barcelona; Department of Neurology and IIS La Fe (N.M., J.J.V.), Hospital Universitari i Politècnic La Fe, Valencia; Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER) (N.M., J.D.-M., J.J.V.); Department of Neurology (E.K.), Consulta de Enfermedades Neuromusculares y Unidad de ELA, Hospital General Universitario Santa Lucía, Cartagena, Murcia; Department of Neurology (A.C.), Hospital Virgen de las Nieves, Granada; Department of Neurology (P.Q.), Hospital Torrecárdenas, Almería; Unidad de Enfermedades Neuromusculares (J.D.-M.), Department of Neurology, Universidad Autónoma de Barcelona, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain; Department of Diagnostic Genomics (M.D.), PathWest Laboratory Medicine WA, Perth, Australia; Department of Neurology (C.D.), Hospital 12 de Octubre, Madrid, Spain; Unité de Morphologie Neuromusculaire (N.B.R.), Centre de Référence de Pathologie Neuromusculaire Paris-Est, Institut de Myologie, Groupe Hospitalier Universitaire La Pitié-Salpêtrière, Paris; Université Sorbonne (N.B.R.), UPMC Univ Paris 06, INSERM UMRS974, CNRS FRE3617, Center for Research in Myology, Groupe Hospitalier Universitaire La Pitié-Salpêtrière, Paris, France; Department of Medicine (J.J.V.), Universitat de Valencia; Department of Experimental and Health Sciences (D.C.), Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain; Centre National de la Recherche Scientifique (J.L.), UMR7104, Illkirch; and Institut National de la Santé et de la Recherche Médicale (J.L.), U964, Illkirch, France
| | - Alejandra Carvajal
- From the Unidad de Enfermedades Neuromusculares, Department of Neurology (M.C.-S., C.P.), Instituto de Biomedicina de Sevilla (IBiS) (M.C.-S., F.M., C.P.), and Department of Pathology, Neuropathology Unit (E.R.), Hospital Universitario Virgen del Rocío, Sevilla, Spain; Laboratoire Diagnostic Génétique (V.B.), Faculté de Médecine-CHRU, Strasbourg; Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC) (V.B., R.Á., J.L.), Illkirch, France; Harry Perkins Institute of Medical Research and Centre for Medical Research (B.M., N.G.L., L.K.), University of Western Australia, Nedlands; Department of Pathology (Neuropathology) (A.H.-L.), Hospital Universitario 12 de Octubre, Madrid Research Institute; Neuropathology Unit (M.O.), Department of Pathology and Neuromuscular Unit, Department of Neurology, IDIBELL-Hospital de Bellvitge, Hospitalet de Llobregat, Barcelona; Department of Neurology and IIS La Fe (N.M., J.J.V.), Hospital Universitari i Politècnic La Fe, Valencia; Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER) (N.M., J.D.-M., J.J.V.); Department of Neurology (E.K.), Consulta de Enfermedades Neuromusculares y Unidad de ELA, Hospital General Universitario Santa Lucía, Cartagena, Murcia; Department of Neurology (A.C.), Hospital Virgen de las Nieves, Granada; Department of Neurology (P.Q.), Hospital Torrecárdenas, Almería; Unidad de Enfermedades Neuromusculares (J.D.-M.), Department of Neurology, Universidad Autónoma de Barcelona, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain; Department of Diagnostic Genomics (M.D.), PathWest Laboratory Medicine WA, Perth, Australia; Department of Neurology (C.D.), Hospital 12 de Octubre, Madrid, Spain; Unité de Morphologie Neuromusculaire (N.B.R.), Centre de Référence de Pathologie Neuromusculaire Paris-Est, Institut de Myologie, Groupe Hospitalier Universitaire La Pitié-Salpêtrière, Paris; Université Sorbonne (N.B.R.), UPMC Univ Paris 06, INSERM UMRS974, CNRS FRE3617, Center for Research in Myology, Groupe Hospitalier Universitaire La Pitié-Salpêtrière, Paris, France; Department of Medicine (J.J.V.), Universitat de Valencia; Department of Experimental and Health Sciences (D.C.), Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain; Centre National de la Recherche Scientifique (J.L.), UMR7104, Illkirch; and Institut National de la Santé et de la Recherche Médicale (J.L.), U964, Illkirch, France
| | - Pablo Quiroga
- From the Unidad de Enfermedades Neuromusculares, Department of Neurology (M.C.-S., C.P.), Instituto de Biomedicina de Sevilla (IBiS) (M.C.-S., F.M., C.P.), and Department of Pathology, Neuropathology Unit (E.R.), Hospital Universitario Virgen del Rocío, Sevilla, Spain; Laboratoire Diagnostic Génétique (V.B.), Faculté de Médecine-CHRU, Strasbourg; Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC) (V.B., R.Á., J.L.), Illkirch, France; Harry Perkins Institute of Medical Research and Centre for Medical Research (B.M., N.G.L., L.K.), University of Western Australia, Nedlands; Department of Pathology (Neuropathology) (A.H.-L.), Hospital Universitario 12 de Octubre, Madrid Research Institute; Neuropathology Unit (M.O.), Department of Pathology and Neuromuscular Unit, Department of Neurology, IDIBELL-Hospital de Bellvitge, Hospitalet de Llobregat, Barcelona; Department of Neurology and IIS La Fe (N.M., J.J.V.), Hospital Universitari i Politècnic La Fe, Valencia; Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER) (N.M., J.D.-M., J.J.V.); Department of Neurology (E.K.), Consulta de Enfermedades Neuromusculares y Unidad de ELA, Hospital General Universitario Santa Lucía, Cartagena, Murcia; Department of Neurology (A.C.), Hospital Virgen de las Nieves, Granada; Department of Neurology (P.Q.), Hospital Torrecárdenas, Almería; Unidad de Enfermedades Neuromusculares (J.D.-M.), Department of Neurology, Universidad Autónoma de Barcelona, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain; Department of Diagnostic Genomics (M.D.), PathWest Laboratory Medicine WA, Perth, Australia; Department of Neurology (C.D.), Hospital 12 de Octubre, Madrid, Spain; Unité de Morphologie Neuromusculaire (N.B.R.), Centre de Référence de Pathologie Neuromusculaire Paris-Est, Institut de Myologie, Groupe Hospitalier Universitaire La Pitié-Salpêtrière, Paris; Université Sorbonne (N.B.R.), UPMC Univ Paris 06, INSERM UMRS974, CNRS FRE3617, Center for Research in Myology, Groupe Hospitalier Universitaire La Pitié-Salpêtrière, Paris, France; Department of Medicine (J.J.V.), Universitat de Valencia; Department of Experimental and Health Sciences (D.C.), Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain; Centre National de la Recherche Scientifique (J.L.), UMR7104, Illkirch; and Institut National de la Santé et de la Recherche Médicale (J.L.), U964, Illkirch, France
| | - Jordi Diaz-Manera
- From the Unidad de Enfermedades Neuromusculares, Department of Neurology (M.C.-S., C.P.), Instituto de Biomedicina de Sevilla (IBiS) (M.C.-S., F.M., C.P.), and Department of Pathology, Neuropathology Unit (E.R.), Hospital Universitario Virgen del Rocío, Sevilla, Spain; Laboratoire Diagnostic Génétique (V.B.), Faculté de Médecine-CHRU, Strasbourg; Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC) (V.B., R.Á., J.L.), Illkirch, France; Harry Perkins Institute of Medical Research and Centre for Medical Research (B.M., N.G.L., L.K.), University of Western Australia, Nedlands; Department of Pathology (Neuropathology) (A.H.-L.), Hospital Universitario 12 de Octubre, Madrid Research Institute; Neuropathology Unit (M.O.), Department of Pathology and Neuromuscular Unit, Department of Neurology, IDIBELL-Hospital de Bellvitge, Hospitalet de Llobregat, Barcelona; Department of Neurology and IIS La Fe (N.M., J.J.V.), Hospital Universitari i Politècnic La Fe, Valencia; Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER) (N.M., J.D.-M., J.J.V.); Department of Neurology (E.K.), Consulta de Enfermedades Neuromusculares y Unidad de ELA, Hospital General Universitario Santa Lucía, Cartagena, Murcia; Department of Neurology (A.C.), Hospital Virgen de las Nieves, Granada; Department of Neurology (P.Q.), Hospital Torrecárdenas, Almería; Unidad de Enfermedades Neuromusculares (J.D.-M.), Department of Neurology, Universidad Autónoma de Barcelona, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain; Department of Diagnostic Genomics (M.D.), PathWest Laboratory Medicine WA, Perth, Australia; Department of Neurology (C.D.), Hospital 12 de Octubre, Madrid, Spain; Unité de Morphologie Neuromusculaire (N.B.R.), Centre de Référence de Pathologie Neuromusculaire Paris-Est, Institut de Myologie, Groupe Hospitalier Universitaire La Pitié-Salpêtrière, Paris; Université Sorbonne (N.B.R.), UPMC Univ Paris 06, INSERM UMRS974, CNRS FRE3617, Center for Research in Myology, Groupe Hospitalier Universitaire La Pitié-Salpêtrière, Paris, France; Department of Medicine (J.J.V.), Universitat de Valencia; Department of Experimental and Health Sciences (D.C.), Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain; Centre National de la Recherche Scientifique (J.L.), UMR7104, Illkirch; and Institut National de la Santé et de la Recherche Médicale (J.L.), U964, Illkirch, France
| | - Mark Davis
- From the Unidad de Enfermedades Neuromusculares, Department of Neurology (M.C.-S., C.P.), Instituto de Biomedicina de Sevilla (IBiS) (M.C.-S., F.M., C.P.), and Department of Pathology, Neuropathology Unit (E.R.), Hospital Universitario Virgen del Rocío, Sevilla, Spain; Laboratoire Diagnostic Génétique (V.B.), Faculté de Médecine-CHRU, Strasbourg; Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC) (V.B., R.Á., J.L.), Illkirch, France; Harry Perkins Institute of Medical Research and Centre for Medical Research (B.M., N.G.L., L.K.), University of Western Australia, Nedlands; Department of Pathology (Neuropathology) (A.H.-L.), Hospital Universitario 12 de Octubre, Madrid Research Institute; Neuropathology Unit (M.O.), Department of Pathology and Neuromuscular Unit, Department of Neurology, IDIBELL-Hospital de Bellvitge, Hospitalet de Llobregat, Barcelona; Department of Neurology and IIS La Fe (N.M., J.J.V.), Hospital Universitari i Politècnic La Fe, Valencia; Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER) (N.M., J.D.-M., J.J.V.); Department of Neurology (E.K.), Consulta de Enfermedades Neuromusculares y Unidad de ELA, Hospital General Universitario Santa Lucía, Cartagena, Murcia; Department of Neurology (A.C.), Hospital Virgen de las Nieves, Granada; Department of Neurology (P.Q.), Hospital Torrecárdenas, Almería; Unidad de Enfermedades Neuromusculares (J.D.-M.), Department of Neurology, Universidad Autónoma de Barcelona, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain; Department of Diagnostic Genomics (M.D.), PathWest Laboratory Medicine WA, Perth, Australia; Department of Neurology (C.D.), Hospital 12 de Octubre, Madrid, Spain; Unité de Morphologie Neuromusculaire (N.B.R.), Centre de Référence de Pathologie Neuromusculaire Paris-Est, Institut de Myologie, Groupe Hospitalier Universitaire La Pitié-Salpêtrière, Paris; Université Sorbonne (N.B.R.), UPMC Univ Paris 06, INSERM UMRS974, CNRS FRE3617, Center for Research in Myology, Groupe Hospitalier Universitaire La Pitié-Salpêtrière, Paris, France; Department of Medicine (J.J.V.), Universitat de Valencia; Department of Experimental and Health Sciences (D.C.), Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain; Centre National de la Recherche Scientifique (J.L.), UMR7104, Illkirch; and Institut National de la Santé et de la Recherche Médicale (J.L.), U964, Illkirch, France
| | - Rainiero Ávila
- From the Unidad de Enfermedades Neuromusculares, Department of Neurology (M.C.-S., C.P.), Instituto de Biomedicina de Sevilla (IBiS) (M.C.-S., F.M., C.P.), and Department of Pathology, Neuropathology Unit (E.R.), Hospital Universitario Virgen del Rocío, Sevilla, Spain; Laboratoire Diagnostic Génétique (V.B.), Faculté de Médecine-CHRU, Strasbourg; Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC) (V.B., R.Á., J.L.), Illkirch, France; Harry Perkins Institute of Medical Research and Centre for Medical Research (B.M., N.G.L., L.K.), University of Western Australia, Nedlands; Department of Pathology (Neuropathology) (A.H.-L.), Hospital Universitario 12 de Octubre, Madrid Research Institute; Neuropathology Unit (M.O.), Department of Pathology and Neuromuscular Unit, Department of Neurology, IDIBELL-Hospital de Bellvitge, Hospitalet de Llobregat, Barcelona; Department of Neurology and IIS La Fe (N.M., J.J.V.), Hospital Universitari i Politècnic La Fe, Valencia; Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER) (N.M., J.D.-M., J.J.V.); Department of Neurology (E.K.), Consulta de Enfermedades Neuromusculares y Unidad de ELA, Hospital General Universitario Santa Lucía, Cartagena, Murcia; Department of Neurology (A.C.), Hospital Virgen de las Nieves, Granada; Department of Neurology (P.Q.), Hospital Torrecárdenas, Almería; Unidad de Enfermedades Neuromusculares (J.D.-M.), Department of Neurology, Universidad Autónoma de Barcelona, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain; Department of Diagnostic Genomics (M.D.), PathWest Laboratory Medicine WA, Perth, Australia; Department of Neurology (C.D.), Hospital 12 de Octubre, Madrid, Spain; Unité de Morphologie Neuromusculaire (N.B.R.), Centre de Référence de Pathologie Neuromusculaire Paris-Est, Institut de Myologie, Groupe Hospitalier Universitaire La Pitié-Salpêtrière, Paris; Université Sorbonne (N.B.R.), UPMC Univ Paris 06, INSERM UMRS974, CNRS FRE3617, Center for Research in Myology, Groupe Hospitalier Universitaire La Pitié-Salpêtrière, Paris, France; Department of Medicine (J.J.V.), Universitat de Valencia; Department of Experimental and Health Sciences (D.C.), Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain; Centre National de la Recherche Scientifique (J.L.), UMR7104, Illkirch; and Institut National de la Santé et de la Recherche Médicale (J.L.), U964, Illkirch, France
| | - Cristina Domínguez
- From the Unidad de Enfermedades Neuromusculares, Department of Neurology (M.C.-S., C.P.), Instituto de Biomedicina de Sevilla (IBiS) (M.C.-S., F.M., C.P.), and Department of Pathology, Neuropathology Unit (E.R.), Hospital Universitario Virgen del Rocío, Sevilla, Spain; Laboratoire Diagnostic Génétique (V.B.), Faculté de Médecine-CHRU, Strasbourg; Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC) (V.B., R.Á., J.L.), Illkirch, France; Harry Perkins Institute of Medical Research and Centre for Medical Research (B.M., N.G.L., L.K.), University of Western Australia, Nedlands; Department of Pathology (Neuropathology) (A.H.-L.), Hospital Universitario 12 de Octubre, Madrid Research Institute; Neuropathology Unit (M.O.), Department of Pathology and Neuromuscular Unit, Department of Neurology, IDIBELL-Hospital de Bellvitge, Hospitalet de Llobregat, Barcelona; Department of Neurology and IIS La Fe (N.M., J.J.V.), Hospital Universitari i Politècnic La Fe, Valencia; Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER) (N.M., J.D.-M., J.J.V.); Department of Neurology (E.K.), Consulta de Enfermedades Neuromusculares y Unidad de ELA, Hospital General Universitario Santa Lucía, Cartagena, Murcia; Department of Neurology (A.C.), Hospital Virgen de las Nieves, Granada; Department of Neurology (P.Q.), Hospital Torrecárdenas, Almería; Unidad de Enfermedades Neuromusculares (J.D.-M.), Department of Neurology, Universidad Autónoma de Barcelona, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain; Department of Diagnostic Genomics (M.D.), PathWest Laboratory Medicine WA, Perth, Australia; Department of Neurology (C.D.), Hospital 12 de Octubre, Madrid, Spain; Unité de Morphologie Neuromusculaire (N.B.R.), Centre de Référence de Pathologie Neuromusculaire Paris-Est, Institut de Myologie, Groupe Hospitalier Universitaire La Pitié-Salpêtrière, Paris; Université Sorbonne (N.B.R.), UPMC Univ Paris 06, INSERM UMRS974, CNRS FRE3617, Center for Research in Myology, Groupe Hospitalier Universitaire La Pitié-Salpêtrière, Paris, France; Department of Medicine (J.J.V.), Universitat de Valencia; Department of Experimental and Health Sciences (D.C.), Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain; Centre National de la Recherche Scientifique (J.L.), UMR7104, Illkirch; and Institut National de la Santé et de la Recherche Médicale (J.L.), U964, Illkirch, France
| | - Norma Beatriz Romero
- From the Unidad de Enfermedades Neuromusculares, Department of Neurology (M.C.-S., C.P.), Instituto de Biomedicina de Sevilla (IBiS) (M.C.-S., F.M., C.P.), and Department of Pathology, Neuropathology Unit (E.R.), Hospital Universitario Virgen del Rocío, Sevilla, Spain; Laboratoire Diagnostic Génétique (V.B.), Faculté de Médecine-CHRU, Strasbourg; Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC) (V.B., R.Á., J.L.), Illkirch, France; Harry Perkins Institute of Medical Research and Centre for Medical Research (B.M., N.G.L., L.K.), University of Western Australia, Nedlands; Department of Pathology (Neuropathology) (A.H.-L.), Hospital Universitario 12 de Octubre, Madrid Research Institute; Neuropathology Unit (M.O.), Department of Pathology and Neuromuscular Unit, Department of Neurology, IDIBELL-Hospital de Bellvitge, Hospitalet de Llobregat, Barcelona; Department of Neurology and IIS La Fe (N.M., J.J.V.), Hospital Universitari i Politècnic La Fe, Valencia; Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER) (N.M., J.D.-M., J.J.V.); Department of Neurology (E.K.), Consulta de Enfermedades Neuromusculares y Unidad de ELA, Hospital General Universitario Santa Lucía, Cartagena, Murcia; Department of Neurology (A.C.), Hospital Virgen de las Nieves, Granada; Department of Neurology (P.Q.), Hospital Torrecárdenas, Almería; Unidad de Enfermedades Neuromusculares (J.D.-M.), Department of Neurology, Universidad Autónoma de Barcelona, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain; Department of Diagnostic Genomics (M.D.), PathWest Laboratory Medicine WA, Perth, Australia; Department of Neurology (C.D.), Hospital 12 de Octubre, Madrid, Spain; Unité de Morphologie Neuromusculaire (N.B.R.), Centre de Référence de Pathologie Neuromusculaire Paris-Est, Institut de Myologie, Groupe Hospitalier Universitaire La Pitié-Salpêtrière, Paris; Université Sorbonne (N.B.R.), UPMC Univ Paris 06, INSERM UMRS974, CNRS FRE3617, Center for Research in Myology, Groupe Hospitalier Universitaire La Pitié-Salpêtrière, Paris, France; Department of Medicine (J.J.V.), Universitat de Valencia; Department of Experimental and Health Sciences (D.C.), Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain; Centre National de la Recherche Scientifique (J.L.), UMR7104, Illkirch; and Institut National de la Santé et de la Recherche Médicale (J.L.), U964, Illkirch, France
| | - Juan J Vílchez
- From the Unidad de Enfermedades Neuromusculares, Department of Neurology (M.C.-S., C.P.), Instituto de Biomedicina de Sevilla (IBiS) (M.C.-S., F.M., C.P.), and Department of Pathology, Neuropathology Unit (E.R.), Hospital Universitario Virgen del Rocío, Sevilla, Spain; Laboratoire Diagnostic Génétique (V.B.), Faculté de Médecine-CHRU, Strasbourg; Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC) (V.B., R.Á., J.L.), Illkirch, France; Harry Perkins Institute of Medical Research and Centre for Medical Research (B.M., N.G.L., L.K.), University of Western Australia, Nedlands; Department of Pathology (Neuropathology) (A.H.-L.), Hospital Universitario 12 de Octubre, Madrid Research Institute; Neuropathology Unit (M.O.), Department of Pathology and Neuromuscular Unit, Department of Neurology, IDIBELL-Hospital de Bellvitge, Hospitalet de Llobregat, Barcelona; Department of Neurology and IIS La Fe (N.M., J.J.V.), Hospital Universitari i Politècnic La Fe, Valencia; Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER) (N.M., J.D.-M., J.J.V.); Department of Neurology (E.K.), Consulta de Enfermedades Neuromusculares y Unidad de ELA, Hospital General Universitario Santa Lucía, Cartagena, Murcia; Department of Neurology (A.C.), Hospital Virgen de las Nieves, Granada; Department of Neurology (P.Q.), Hospital Torrecárdenas, Almería; Unidad de Enfermedades Neuromusculares (J.D.-M.), Department of Neurology, Universidad Autónoma de Barcelona, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain; Department of Diagnostic Genomics (M.D.), PathWest Laboratory Medicine WA, Perth, Australia; Department of Neurology (C.D.), Hospital 12 de Octubre, Madrid, Spain; Unité de Morphologie Neuromusculaire (N.B.R.), Centre de Référence de Pathologie Neuromusculaire Paris-Est, Institut de Myologie, Groupe Hospitalier Universitaire La Pitié-Salpêtrière, Paris; Université Sorbonne (N.B.R.), UPMC Univ Paris 06, INSERM UMRS974, CNRS FRE3617, Center for Research in Myology, Groupe Hospitalier Universitaire La Pitié-Salpêtrière, Paris, France; Department of Medicine (J.J.V.), Universitat de Valencia; Department of Experimental and Health Sciences (D.C.), Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain; Centre National de la Recherche Scientifique (J.L.), UMR7104, Illkirch; and Institut National de la Santé et de la Recherche Médicale (J.L.), U964, Illkirch, France
| | - David Comas
- From the Unidad de Enfermedades Neuromusculares, Department of Neurology (M.C.-S., C.P.), Instituto de Biomedicina de Sevilla (IBiS) (M.C.-S., F.M., C.P.), and Department of Pathology, Neuropathology Unit (E.R.), Hospital Universitario Virgen del Rocío, Sevilla, Spain; Laboratoire Diagnostic Génétique (V.B.), Faculté de Médecine-CHRU, Strasbourg; Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC) (V.B., R.Á., J.L.), Illkirch, France; Harry Perkins Institute of Medical Research and Centre for Medical Research (B.M., N.G.L., L.K.), University of Western Australia, Nedlands; Department of Pathology (Neuropathology) (A.H.-L.), Hospital Universitario 12 de Octubre, Madrid Research Institute; Neuropathology Unit (M.O.), Department of Pathology and Neuromuscular Unit, Department of Neurology, IDIBELL-Hospital de Bellvitge, Hospitalet de Llobregat, Barcelona; Department of Neurology and IIS La Fe (N.M., J.J.V.), Hospital Universitari i Politècnic La Fe, Valencia; Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER) (N.M., J.D.-M., J.J.V.); Department of Neurology (E.K.), Consulta de Enfermedades Neuromusculares y Unidad de ELA, Hospital General Universitario Santa Lucía, Cartagena, Murcia; Department of Neurology (A.C.), Hospital Virgen de las Nieves, Granada; Department of Neurology (P.Q.), Hospital Torrecárdenas, Almería; Unidad de Enfermedades Neuromusculares (J.D.-M.), Department of Neurology, Universidad Autónoma de Barcelona, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain; Department of Diagnostic Genomics (M.D.), PathWest Laboratory Medicine WA, Perth, Australia; Department of Neurology (C.D.), Hospital 12 de Octubre, Madrid, Spain; Unité de Morphologie Neuromusculaire (N.B.R.), Centre de Référence de Pathologie Neuromusculaire Paris-Est, Institut de Myologie, Groupe Hospitalier Universitaire La Pitié-Salpêtrière, Paris; Université Sorbonne (N.B.R.), UPMC Univ Paris 06, INSERM UMRS974, CNRS FRE3617, Center for Research in Myology, Groupe Hospitalier Universitaire La Pitié-Salpêtrière, Paris, France; Department of Medicine (J.J.V.), Universitat de Valencia; Department of Experimental and Health Sciences (D.C.), Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain; Centre National de la Recherche Scientifique (J.L.), UMR7104, Illkirch; and Institut National de la Santé et de la Recherche Médicale (J.L.), U964, Illkirch, France
| | - Nigel G Laing
- From the Unidad de Enfermedades Neuromusculares, Department of Neurology (M.C.-S., C.P.), Instituto de Biomedicina de Sevilla (IBiS) (M.C.-S., F.M., C.P.), and Department of Pathology, Neuropathology Unit (E.R.), Hospital Universitario Virgen del Rocío, Sevilla, Spain; Laboratoire Diagnostic Génétique (V.B.), Faculté de Médecine-CHRU, Strasbourg; Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC) (V.B., R.Á., J.L.), Illkirch, France; Harry Perkins Institute of Medical Research and Centre for Medical Research (B.M., N.G.L., L.K.), University of Western Australia, Nedlands; Department of Pathology (Neuropathology) (A.H.-L.), Hospital Universitario 12 de Octubre, Madrid Research Institute; Neuropathology Unit (M.O.), Department of Pathology and Neuromuscular Unit, Department of Neurology, IDIBELL-Hospital de Bellvitge, Hospitalet de Llobregat, Barcelona; Department of Neurology and IIS La Fe (N.M., J.J.V.), Hospital Universitari i Politècnic La Fe, Valencia; Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER) (N.M., J.D.-M., J.J.V.); Department of Neurology (E.K.), Consulta de Enfermedades Neuromusculares y Unidad de ELA, Hospital General Universitario Santa Lucía, Cartagena, Murcia; Department of Neurology (A.C.), Hospital Virgen de las Nieves, Granada; Department of Neurology (P.Q.), Hospital Torrecárdenas, Almería; Unidad de Enfermedades Neuromusculares (J.D.-M.), Department of Neurology, Universidad Autónoma de Barcelona, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain; Department of Diagnostic Genomics (M.D.), PathWest Laboratory Medicine WA, Perth, Australia; Department of Neurology (C.D.), Hospital 12 de Octubre, Madrid, Spain; Unité de Morphologie Neuromusculaire (N.B.R.), Centre de Référence de Pathologie Neuromusculaire Paris-Est, Institut de Myologie, Groupe Hospitalier Universitaire La Pitié-Salpêtrière, Paris; Université Sorbonne (N.B.R.), UPMC Univ Paris 06, INSERM UMRS974, CNRS FRE3617, Center for Research in Myology, Groupe Hospitalier Universitaire La Pitié-Salpêtrière, Paris, France; Department of Medicine (J.J.V.), Universitat de Valencia; Department of Experimental and Health Sciences (D.C.), Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain; Centre National de la Recherche Scientifique (J.L.), UMR7104, Illkirch; and Institut National de la Santé et de la Recherche Médicale (J.L.), U964, Illkirch, France
| | - Jocelyn Laporte
- From the Unidad de Enfermedades Neuromusculares, Department of Neurology (M.C.-S., C.P.), Instituto de Biomedicina de Sevilla (IBiS) (M.C.-S., F.M., C.P.), and Department of Pathology, Neuropathology Unit (E.R.), Hospital Universitario Virgen del Rocío, Sevilla, Spain; Laboratoire Diagnostic Génétique (V.B.), Faculté de Médecine-CHRU, Strasbourg; Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC) (V.B., R.Á., J.L.), Illkirch, France; Harry Perkins Institute of Medical Research and Centre for Medical Research (B.M., N.G.L., L.K.), University of Western Australia, Nedlands; Department of Pathology (Neuropathology) (A.H.-L.), Hospital Universitario 12 de Octubre, Madrid Research Institute; Neuropathology Unit (M.O.), Department of Pathology and Neuromuscular Unit, Department of Neurology, IDIBELL-Hospital de Bellvitge, Hospitalet de Llobregat, Barcelona; Department of Neurology and IIS La Fe (N.M., J.J.V.), Hospital Universitari i Politècnic La Fe, Valencia; Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER) (N.M., J.D.-M., J.J.V.); Department of Neurology (E.K.), Consulta de Enfermedades Neuromusculares y Unidad de ELA, Hospital General Universitario Santa Lucía, Cartagena, Murcia; Department of Neurology (A.C.), Hospital Virgen de las Nieves, Granada; Department of Neurology (P.Q.), Hospital Torrecárdenas, Almería; Unidad de Enfermedades Neuromusculares (J.D.-M.), Department of Neurology, Universidad Autónoma de Barcelona, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain; Department of Diagnostic Genomics (M.D.), PathWest Laboratory Medicine WA, Perth, Australia; Department of Neurology (C.D.), Hospital 12 de Octubre, Madrid, Spain; Unité de Morphologie Neuromusculaire (N.B.R.), Centre de Référence de Pathologie Neuromusculaire Paris-Est, Institut de Myologie, Groupe Hospitalier Universitaire La Pitié-Salpêtrière, Paris; Université Sorbonne (N.B.R.), UPMC Univ Paris 06, INSERM UMRS974, CNRS FRE3617, Center for Research in Myology, Groupe Hospitalier Universitaire La Pitié-Salpêtrière, Paris, France; Department of Medicine (J.J.V.), Universitat de Valencia; Department of Experimental and Health Sciences (D.C.), Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain; Centre National de la Recherche Scientifique (J.L.), UMR7104, Illkirch; and Institut National de la Santé et de la Recherche Médicale (J.L.), U964, Illkirch, France
| | - Luba Kalaydjieva
- From the Unidad de Enfermedades Neuromusculares, Department of Neurology (M.C.-S., C.P.), Instituto de Biomedicina de Sevilla (IBiS) (M.C.-S., F.M., C.P.), and Department of Pathology, Neuropathology Unit (E.R.), Hospital Universitario Virgen del Rocío, Sevilla, Spain; Laboratoire Diagnostic Génétique (V.B.), Faculté de Médecine-CHRU, Strasbourg; Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC) (V.B., R.Á., J.L.), Illkirch, France; Harry Perkins Institute of Medical Research and Centre for Medical Research (B.M., N.G.L., L.K.), University of Western Australia, Nedlands; Department of Pathology (Neuropathology) (A.H.-L.), Hospital Universitario 12 de Octubre, Madrid Research Institute; Neuropathology Unit (M.O.), Department of Pathology and Neuromuscular Unit, Department of Neurology, IDIBELL-Hospital de Bellvitge, Hospitalet de Llobregat, Barcelona; Department of Neurology and IIS La Fe (N.M., J.J.V.), Hospital Universitari i Politècnic La Fe, Valencia; Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER) (N.M., J.D.-M., J.J.V.); Department of Neurology (E.K.), Consulta de Enfermedades Neuromusculares y Unidad de ELA, Hospital General Universitario Santa Lucía, Cartagena, Murcia; Department of Neurology (A.C.), Hospital Virgen de las Nieves, Granada; Department of Neurology (P.Q.), Hospital Torrecárdenas, Almería; Unidad de Enfermedades Neuromusculares (J.D.-M.), Department of Neurology, Universidad Autónoma de Barcelona, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain; Department of Diagnostic Genomics (M.D.), PathWest Laboratory Medicine WA, Perth, Australia; Department of Neurology (C.D.), Hospital 12 de Octubre, Madrid, Spain; Unité de Morphologie Neuromusculaire (N.B.R.), Centre de Référence de Pathologie Neuromusculaire Paris-Est, Institut de Myologie, Groupe Hospitalier Universitaire La Pitié-Salpêtrière, Paris; Université Sorbonne (N.B.R.), UPMC Univ Paris 06, INSERM UMRS974, CNRS FRE3617, Center for Research in Myology, Groupe Hospitalier Universitaire La Pitié-Salpêtrière, Paris, France; Department of Medicine (J.J.V.), Universitat de Valencia; Department of Experimental and Health Sciences (D.C.), Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain; Centre National de la Recherche Scientifique (J.L.), UMR7104, Illkirch; and Institut National de la Santé et de la Recherche Médicale (J.L.), U964, Illkirch, France
| | - Carmen Paradas
- From the Unidad de Enfermedades Neuromusculares, Department of Neurology (M.C.-S., C.P.), Instituto de Biomedicina de Sevilla (IBiS) (M.C.-S., F.M., C.P.), and Department of Pathology, Neuropathology Unit (E.R.), Hospital Universitario Virgen del Rocío, Sevilla, Spain; Laboratoire Diagnostic Génétique (V.B.), Faculté de Médecine-CHRU, Strasbourg; Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC) (V.B., R.Á., J.L.), Illkirch, France; Harry Perkins Institute of Medical Research and Centre for Medical Research (B.M., N.G.L., L.K.), University of Western Australia, Nedlands; Department of Pathology (Neuropathology) (A.H.-L.), Hospital Universitario 12 de Octubre, Madrid Research Institute; Neuropathology Unit (M.O.), Department of Pathology and Neuromuscular Unit, Department of Neurology, IDIBELL-Hospital de Bellvitge, Hospitalet de Llobregat, Barcelona; Department of Neurology and IIS La Fe (N.M., J.J.V.), Hospital Universitari i Politècnic La Fe, Valencia; Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER) (N.M., J.D.-M., J.J.V.); Department of Neurology (E.K.), Consulta de Enfermedades Neuromusculares y Unidad de ELA, Hospital General Universitario Santa Lucía, Cartagena, Murcia; Department of Neurology (A.C.), Hospital Virgen de las Nieves, Granada; Department of Neurology (P.Q.), Hospital Torrecárdenas, Almería; Unidad de Enfermedades Neuromusculares (J.D.-M.), Department of Neurology, Universidad Autónoma de Barcelona, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain; Department of Diagnostic Genomics (M.D.), PathWest Laboratory Medicine WA, Perth, Australia; Department of Neurology (C.D.), Hospital 12 de Octubre, Madrid, Spain; Unité de Morphologie Neuromusculaire (N.B.R.), Centre de Référence de Pathologie Neuromusculaire Paris-Est, Institut de Myologie, Groupe Hospitalier Universitaire La Pitié-Salpêtrière, Paris; Université Sorbonne (N.B.R.), UPMC Univ Paris 06, INSERM UMRS974, CNRS FRE3617, Center for Research in Myology, Groupe Hospitalier Universitaire La Pitié-Salpêtrière, Paris, France; Department of Medicine (J.J.V.), Universitat de Valencia; Department of Experimental and Health Sciences (D.C.), Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain; Centre National de la Recherche Scientifique (J.L.), UMR7104, Illkirch; and Institut National de la Santé et de la Recherche Médicale (J.L.), U964, Illkirch, France.
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Comas D, Luiselli D, Rickards O. Human population genetics of the Mediterranean. Ann Hum Biol 2018; 45:1-4. [PMID: 29382281 DOI: 10.1080/03014460.2017.1416909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- David Comas
- a Department of Experimental and Health Sciences , Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra , Barcelona , Spain
| | - Donata Luiselli
- b Lab. of Molecular Anthropology & Centre of Genome Biology, Department of Biological, Geological and Environmental , University of Bologna.,c Department of the Cultural Heritage, Campus of Ravenna , University of Bologna , Bologna , Italy
| | - Olga Rickards
- d Centre of Molecular Anthropology for Ancient DNA Studies, Department of Biology , University of Rome Tor Vergata , Rome , Italy
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Font-Porterias N, Solé-Morata N, Serra-Vidal G, Bekada A, Fadhlaoui-Zid K, Zalloua P, Calafell F, Comas D. The genetic landscape of Mediterranean North African populations through complete mtDNA sequences. Ann Hum Biol 2018; 45:98-104. [DOI: 10.1080/03014460.2017.1413133] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Neus Font-Porterias
- Departament de Ciències Experimentals i de la Salut, Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
| | - Neus Solé-Morata
- Departament de Ciències Experimentals i de la Salut, Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
| | - Gerard Serra-Vidal
- Departament de Ciències Experimentals i de la Salut, Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
| | - Asmahan Bekada
- Département de Biotechnologie, Faculté des Sciences de la Nature et de la Vie, Université Oran 1 (Ahmad Ben Bella), Oran, Algeria
| | - Karima Fadhlaoui-Zid
- Laboratoire de Génetique, Immunologie et Pathologies Humaines, Faculté des Sciences de Tunis, Campus Univesritaire El Manar II, Université El Manar, Tunis, Tunisia
| | - Pierre Zalloua
- School of Medicine, The Lebanese American University, Chouran, Beirut, Lebanon
| | - Francesc Calafell
- Departament de Ciències Experimentals i de la Salut, Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
| | - David Comas
- Departament de Ciències Experimentals i de la Salut, Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
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Viscardi LH, Paixão-Côrtes VR, Comas D, Salzano FM, Rovaris D, Bau CD, Amorim CEG, Bortolini MC. Searching for ancient balanced polymorphisms shared between Neanderthals and Modern Humans. Genet Mol Biol 2018; 41:67-81. [PMID: 29658973 PMCID: PMC5901502 DOI: 10.1590/1678-4685-gmb-2017-0308] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 11/26/2017] [Indexed: 01/06/2023] Open
Abstract
Hominin evolution is characterized by adaptive solutions often rooted in behavioral and cognitive changes. If balancing selection had an important and long-lasting impact on the evolution of these traits, it can be hypothesized that genes associated with them should carry an excess of shared polymorphisms (trans- SNPs) across recent Homo species. In this study, we investigate the role of balancing selection in human evolution using available exomes from modern (Homo sapiens) and archaic humans (H. neanderthalensis and Denisovan) for an excess of trans-SNP in two gene sets: one associated with the immune system (IMMS) and another one with behavioral system (BEHS). We identified a significant excess of trans-SNPs in IMMS (N=547), of which six of these located within genes previously associated with schizophrenia. No excess of trans-SNPs was found in BEHS, but five genes in this system harbor potential signals for balancing selection and are associated with psychiatric or neurodevelopmental disorders. Our approach evidenced recent Homo trans-SNPs that have been previously implicated in psychiatric diseases such as schizophrenia, suggesting that a genetic repertoire common to the immune and behavioral systems could have been maintained by balancing selection starting before the split between archaic and modern humans.
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Affiliation(s)
- Lucas Henriques Viscardi
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | | | - David Comas
- Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències Experimentals i de LaSalut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Francisco Mauro Salzano
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Diego Rovaris
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Claiton Dotto Bau
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Carlos Eduardo G. Amorim
- Department of Biological Sciences, Columbia University, New York, NY, U.S.A
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, U.S.A
| | - Maria Cátira Bortolini
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
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Emmerova B, Ehler E, Comas D, Votrubova J, Vanek D. Comparison of Y-chromosomal haplogroup predictors. Forensic Science International: Genetics Supplement Series 2017. [DOI: 10.1016/j.fsigss.2017.09.025] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Cabrera-Serrano M, Rivas-Infante E, Mavillard F, Morar B, Comas D, Carvajal A, Avila R, Muelas N, Olive M, Diaz J, Verges E, Romero N, Laporte J, Vilchez J, Laing N, Kalaydjieva L, Paradas C. BIN1 founder mutation in the Spanish gypsy population is the most frequent cause of adult onset centronuclear myopathies in the south of Spain. Neuromuscul Disord 2017. [DOI: 10.1016/j.nmd.2017.06.288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Pimenta J, Lopes AM, Comas D, Amorim A, Arenas M. Evaluating the Neolithic Expansion at Both Shores of the Mediterranean Sea. Mol Biol Evol 2017; 34:3232-3242. [DOI: 10.1093/molbev/msx256] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
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Franco-Jarava C, Comas D, Orren A, Hernández-González M, Colobran R. Complement factor 5 (C5) p.A252T mutation is prevalent in, but not restricted to, Sub-Saharan Africa: Implications for the susceptibility to meningococcal disease. Mol Immunol 2017. [DOI: 10.1016/j.molimm.2017.06.121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Arauna LR, Mendoza-Revilla J, Mas-Sandoval A, Izaabel H, Bekada A, Benhamamouch S, Fadhlaoui-Zid K, Zalloua P, Hellenthal G, Comas D. Recent Historical Migrations Have Shaped the Gene Pool of Arabs and Berbers in North Africa. Mol Biol Evol 2017; 34:318-329. [PMID: 27744413 PMCID: PMC5644363 DOI: 10.1093/molbev/msw218] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
North Africa is characterized by its diverse cultural and linguistic groups and its genetic heterogeneity. Genomic data has shown an amalgam of components mixed since pre-Holocean times. Though no differences have been found in uniparental and classical markers between Berbers and Arabs, the two main ethnic groups in the region, the scanty genomic data available have highlighted the singularity of Berbers. We characterize the genetic heterogeneity of North African groups, focusing on the putative differences of Berbers and Arabs, and estimate migration dates. We analyze genome-wide autosomal data in five Berber and six Arab groups, and compare them to Middle Easterns, sub-Saharans, and Europeans. Haplotype-based methods show a lack of correlation between geographical and genetic populations, and a high degree of genetic heterogeneity, without strong differences between Berbers and Arabs. Berbers enclose genetically diverse groups, from isolated endogamous groups with high autochthonous component frequencies, large homozygosity runs and low effective population sizes, to admixed groups with high frequencies of sub-Saharan and Middle Eastern components. Admixture time estimates show a complex pattern of recent historical migrations, with a peak around the 7th century C.E. coincident with the Arabization of the region; sub-Saharan migrations since the 1st century B.C. in agreement with Roman slave trade; and a strong migration in the 17th century C.E., coincident with a huge impact of the trans-Atlantic and trans-Saharan trade of sub-Saharan slaves in the Modern Era. The genetic complexity found should be taken into account when selecting reference groups in population genetics and biomedical studies.
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Affiliation(s)
- Lara R Arauna
- Departament de Ciències Experimentals i de la Salut, Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
| | - Javier Mendoza-Revilla
- Departament de Ciències Experimentals i de la Salut, Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain.,Genetics Institute, University College London, London, United Kingdom
| | - Alex Mas-Sandoval
- Departament de Ciències Experimentals i de la Salut, Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain.,Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Hassan Izaabel
- Laboratoire de Biologie Cellulaire et Génétique Moléculaire (LBCGM), Université IBNZOHR, Agadir, Morocco
| | - Asmahan Bekada
- Département de Biotechnologie, Faculté des Sciences de la Nature et de la Vie, Université Oran 1 (Ahmad Ben Bella), Oran, Algeria
| | - Soraya Benhamamouch
- Département de Biotechnologie, Faculté des Sciences de la Nature et de la Vie, Université Oran 1 (Ahmad Ben Bella), Oran, Algeria
| | - Karima Fadhlaoui-Zid
- Laboratoire de Génetique, Immunologie et Pathologies Humaines, Faculté des Sciences de Tunis, Campus Universitaire El Manar II, Université El Manar, Tunis, Tunisia
| | - Pierre Zalloua
- The Lebanese American University, Chouran, Beirut, Lebanon
| | | | - David Comas
- Departament de Ciències Experimentals i de la Salut, Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
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Reales G, Rovaris DL, Jacovas VC, Hünemeier T, Sandoval JR, Salazar-Granara A, Demarchi DA, Tarazona-Santos E, Felkl AB, Serafini MA, Salzano FM, Bisso-Machado R, Comas D, Paixão-Côrtes VR, Bortolini MC. A tale of agriculturalists and hunter-gatherers: Exploring the thrifty genotype hypothesis in native South Americans. Am J Phys Anthropol 2017; 163:591-601. [PMID: 28464262 DOI: 10.1002/ajpa.23233] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 04/06/2017] [Accepted: 04/06/2017] [Indexed: 01/30/2023]
Abstract
OBJECTIVES To determine genetic differences between agriculturalist and hunter-gatherer southern Native American populations for selected metabolism-related markers and to test whether Neel's thrifty genotype hypothesis (TGH) could explain the genetic patterns observed in these populations. MATERIALS AND METHODS 375 Native South American individuals from 17 populations were genotyped using six markers (APOE rs429358 and rs7412; APOA2 rs5082; CD36 rs3211883; TCF7L2 rs11196205; and IGF2BP2 rs11705701). Additionally, APOE genotypes from 39 individuals were obtained from the literature. AMOVA, main effects, and gene-gene interaction tests were performed. RESULTS We observed differences in allele distribution patterns between agriculturalists and hunter-gatherers for some markers. For instance, between-groups component of genetic variance (FCT ) for APOE rs429358 showed strong differences in allelic distributions between hunter-gatherers and agriculturalists (p = 0.00196). Gene-gene interaction analysis indicated that the APOE E4/CD36 TT and APOE E4/IGF2BP2 A carrier combinations occur at a higher frequency in hunter-gatherers, but this combination is not replicated in archaic (Neanderthal and Denisovan) and ancient (Anzick, Saqqaq, Ust-Ishim, Mal'ta) hunter-gatherer individuals. DISCUSSION A complex scenario explains the observed frequencies of the tested markers in hunter-gatherers. Different factors, such as pleotropic alleles, rainforest selective pressures, and population dynamics, may be collectively shaping the observed genetic patterns. We conclude that although TGH seems a plausible hypothesis to explain part of the data, other factors may be important in our tested populations.
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Affiliation(s)
- Guillermo Reales
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Diego L Rovaris
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Vanessa C Jacovas
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Tábita Hünemeier
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - José R Sandoval
- Facultad de Medicina Humana, Universidad de San Martin de Porres, Lima, Peru
| | | | - Darío A Demarchi
- Instituto de Antropología de Córdoba, CONICET, Universidad Nacional de Córdoba, Argentina
| | - Eduardo Tarazona-Santos
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Instituto de Ciências Biológicas, Belo Horizonte, Minas Gerais, Brazil
| | - Aline B Felkl
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Michele A Serafini
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Francisco M Salzano
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Rafael Bisso-Machado
- Polo de Desarrollo Universitario Diversidad Genética Humana, Centro Universitario de Tacuarembó, Universidad de la República, Tacuarembó, Uruguay
| | - David Comas
- Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències Experimentals i de La Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Vanessa R Paixão-Côrtes
- Departamento de Biologia Geral, Instituto de Biologia, Universidade Federal da Bahia, Salvador, Bahia, Brazil
| | - Maria Cátira Bortolini
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
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Franco-Jarava C, Comas D, Orren A, Hernández-González M, Colobran R. Complement factor 5 (C5) p.A252T mutation is prevalent in, but not restricted to, sub-Saharan Africa: implications for the susceptibility to meningococcal disease. Clin Exp Immunol 2017; 189:226-231. [PMID: 28369827 DOI: 10.1111/cei.12967] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/17/2017] [Indexed: 12/30/2022] Open
Abstract
Complement C5 deficiency (C5D) is a rare primary immunodeficiency associated with recurrent infections, particularly meningitis, by Neisseria species. To date, studies to elucidate the molecular basis of hereditary C5D have included fewer than 40 families, and most C5 mutations (13 of 17) have been found in single families. However, the recently described C5 p.A252T mutation is reported to be associated with approximately 7% of meningococcal disease cases in South Africa. This finding raises the question of whether the mutation may be prevalent in other parts of Africa or other continental regions. The aim of this study was to investigate the prevalence of C5 p.A252T in Africa and other regions and discuss the implications for prophylaxis against meningococcal disease. In total, 2710 samples from healthy donors within various populations worldwide were analysed by quantitative polymerase chain reaction (qPCR) assay to detect the C5 p.A252T mutation. Eleven samples were found to be heterozygous for p.A252T, and nine of these samples were from sub-Saharan African populations (allele frequency 0·94%). Interestingly, two other heterozygous samples were from individuals in populations outside Africa (Israel and Pakistan). These findings, together with data from genomic variation databases, indicate a 0·5-2% prevalence of the C5 p.A252T mutation in heterozygosity in sub-Saharan Africa. Therefore, this mutation may have a relevant role in meningococcal disease susceptibility in this geographical area.
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Affiliation(s)
- C Franco-Jarava
- Immunology Division, Department of Cell Biology, Physiology and Immunology, Hospital Universitari Vall d'Hebron (HUVH), Vall d'Hebron Research Institute (VHIR), Autonomous University of Barcelona (UAB), Barcelona, Spain
| | - D Comas
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
| | - A Orren
- Department of Clinical Sciences, University of Cape Town, Cape Town, South Africa.,Institute of Infection and Immunity, Cardiff University, Cardiff, UK.,Allergy Diagnostic and Clinical Research Unit, Department of Medicine, Lung Institute, University of Cape Town, Cape Town, South Africa
| | - M Hernández-González
- Immunology Division, Department of Cell Biology, Physiology and Immunology, Hospital Universitari Vall d'Hebron (HUVH), Vall d'Hebron Research Institute (VHIR), Autonomous University of Barcelona (UAB), Barcelona, Spain
| | - R Colobran
- Immunology Division, Department of Cell Biology, Physiology and Immunology, Hospital Universitari Vall d'Hebron (HUVH), Vall d'Hebron Research Institute (VHIR), Autonomous University of Barcelona (UAB), Barcelona, Spain
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Clement-Lacroix P, Little C, Meurisse S, Blanqué R, Mollat P, Brebion F, Gosmini R, De Ceuninck F, Botez I, Lepescheux L, van der Aar E, Christophe T, Vandervoort N, Cottereaux C, Comas D, Deprez P, Amantini D. GLPG1972: a potent, selective, orally available adamts-5 inhibitor for the treatment of OA. Osteoarthritis Cartilage 2017. [DOI: 10.1016/j.joca.2017.02.106] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
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Elhaik E, Tatarinova T, Chebotarev D, Piras IS, Calò CM, De Montis A, Atzori M, Marini M, Tofanelli S, Francalacci P, Pagani L, Tyler-Smith C, Xue Y, Cucca F, Schurr TG, Gaieski JB, Melendez C, Vilar MG, Owings AC, Gómez R, Fujita R, Santos FR, Comas D, Balanovsky O, Balanovska E, Zalloua P, Soodyall H, Pitchappan R, GaneshPrasad A, Hammer M, Matisoo-Smith L, Wells RS. Corrigendum: Geographic population structure analysis of worldwide human populations infers their biogeographical origins. Nat Commun 2016; 7:13468. [PMID: 27796289 PMCID: PMC5095557 DOI: 10.1038/ncomms13468] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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Mallick S, Li H, Lipson M, Mathieson I, Gymrek M, Racimo F, Zhao M, Chennagiri N, Nordenfelt S, Tandon A, Skoglund P, Lazaridis I, Sankararaman S, Fu Q, Rohland N, Renaud G, Erlich Y, Willems T, Gallo C, Spence JP, Song YS, Poletti G, Balloux F, van Driem G, de Knijff P, Romero IG, Jha AR, Behar DM, Bravi CM, Capelli C, Hervig T, Moreno-Estrada A, Posukh OL, Balanovska E, Balanovsky O, Karachanak-Yankova S, Sahakyan H, Toncheva D, Yepiskoposyan L, Tyler-Smith C, Xue Y, Abdullah MS, Ruiz-Linares A, Beall CM, Di Rienzo A, Jeong C, Starikovskaya EB, Metspalu E, Parik J, Villems R, Henn BM, Hodoglugil U, Mahley R, Sajantila A, Stamatoyannopoulos G, Wee JTS, Khusainova R, Khusnutdinova E, Litvinov S, Ayodo G, Comas D, Hammer MF, Kivisild T, Klitz W, Winkler CA, Labuda D, Bamshad M, Jorde LB, Tishkoff SA, Watkins WS, Metspalu M, Dryomov S, Sukernik R, Singh L, Thangaraj K, Pääbo S, Kelso J, Patterson N, Reich D. The Simons Genome Diversity Project: 300 genomes from 142 diverse populations. Nature 2016; 538:201-206. [PMID: 27654912 PMCID: PMC5161557 DOI: 10.1038/nature18964] [Citation(s) in RCA: 791] [Impact Index Per Article: 98.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 06/23/2016] [Indexed: 02/06/2023]
Abstract
Here we report the Simons Genome Diversity Project data set: high quality genomes from 300 individuals from 142 diverse populations. These genomes include at least 5.8 million base pairs that are not present in the human reference genome. Our analysis reveals key features of the landscape of human genome variation, including that the rate of accumulation of mutations has accelerated by about 5% in non-Africans compared to Africans since divergence. We show that the ancestors of some pairs of present-day human populations were substantially separated by 100,000 years ago, well before the archaeologically attested onset of behavioural modernity. We also demonstrate that indigenous Australians, New Guineans and Andamanese do not derive substantial ancestry from an early dispersal of modern humans; instead, their modern human ancestry is consistent with coming from the same source as that of other non-Africans.
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Affiliation(s)
- Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Heng Li
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Mark Lipson
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Iain Mathieson
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Melissa Gymrek
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
- Harvard-MIT Division of Health Sciences and Technology, MIT, Cambridge, Massachusetts 02139, USA
- New York Genome Center, New York, New York 10013, USA
| | - Fernando Racimo
- Department of Integrative Biology, University of California, Berkeley, California 94720-3140, USA
| | - Mengyao Zhao
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Niru Chennagiri
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Susanne Nordenfelt
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Arti Tandon
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Pontus Skoglund
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Iosif Lazaridis
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Sriram Sankararaman
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Qiaomei Fu
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, IVPP, CAS, Beijing 100044, China
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Gabriel Renaud
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Yaniv Erlich
- New York Genome Center, New York, New York 10013, USA
- Department of Computer Science, Columbia University, New York, New York 10027, USA
- Center for Computational Biology and Bioinformatics, Columbia University, New York, New York 10032, USA
| | - Thomas Willems
- New York Genome Center, New York, New York 10013, USA
- Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Carla Gallo
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 15102, Perú
| | - Jeffrey P Spence
- Computational Biology Graduate Group, University of California, Berkeley, California 94720, USA
| | - Yun S Song
- Computer Science Division, University of California, Berkeley, California 94720, USA
- Department of Statistics, University of California, Berkeley, California 94720, USA
- Department of Mathematics and Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Giovanni Poletti
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 15102, Perú
| | - Francois Balloux
- Genetics Institute, University College London, Gower Street, London WC1E 6BT, UK
| | - George van Driem
- Institute of Linguistics, University of Bern, Bern CH-3012, Switzerland
| | - Peter de Knijff
- Department of Human and Clinical Genetics, Postzone S5-P, Leiden University Medical Center, 2333 ZA Leiden, Netherlands
| | - Irene Gallego Romero
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, 636921 Singapore
| | - Aashish R Jha
- Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA
| | - Doron M Behar
- Estonian Biocentre, Evolutionary Biology group, Tartu 51010, Estonia
| | - Claudio M Bravi
- Laboratorio de Genética Molecular Poblacional, Instituto Multidisciplinario de Biología Celular (IMBICE), CCT-CONICET La Plata/CIC Buenos Aires/Universidad Nacional de La Plata, La Plata B1906APO, Argentina
| | | | - Tor Hervig
- Department of Clinical Science, University of Bergen, Bergen 5021, Norway
| | - Andres Moreno-Estrada
- National Laboratory of Genomics for Biodiversity (LANGEBIO), CINVESTAV, Irapuato, Guanajuato 36821, Mexico
| | - Olga L Posukh
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
- Novosibirsk State University, Novosibirsk 630090, Russia
| | | | - Oleg Balanovsky
- Research Centre for Medical Genetics, Moscow 115478, Russia
- Vavilov Institute for General Genetics, Moscow 119991, Russia
- Moscow Institute for Physics and Technology, Dolgoprudniy 141700, Russia
| | - Sena Karachanak-Yankova
- Department of Medical Genetics, National Human Genome Center, Medical University Sofia, Sofia 1431, Bulgaria
| | - Hovhannes Sahakyan
- Estonian Biocentre, Evolutionary Biology group, Tartu 51010, Estonia
- Laboratory of Ethnogenomics, Institute of Molecular Biology, National Academy of Sciences of Armenia, Yerevan 0014, Armenia
| | - Draga Toncheva
- Department of Medical Genetics, National Human Genome Center, Medical University Sofia, Sofia 1431, Bulgaria
| | - Levon Yepiskoposyan
- Laboratory of Ethnogenomics, Institute of Molecular Biology, National Academy of Sciences of Armenia, Yerevan 0014, Armenia
| | - Chris Tyler-Smith
- The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Yali Xue
- The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | | | - Andres Ruiz-Linares
- Department of Genetics, Evolution and Environment, University College London WC1E 6BT, UK
| | - Cynthia M Beall
- Department of Anthropology, Case Western Reserve University, Cleveland, Ohio 44106-7125, USA
| | - Anna Di Rienzo
- Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA
| | - Choongwon Jeong
- Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA
| | - Elena B Starikovskaya
- Laboratory of Human Molecular Genetics, Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Ene Metspalu
- Estonian Biocentre, Evolutionary Biology group, Tartu 51010, Estonia
- Department of Evolutionary Biology, University of Tartu, Tartu 51010, Estonia
| | - Jüri Parik
- Estonian Biocentre, Evolutionary Biology group, Tartu 51010, Estonia
| | - Richard Villems
- Estonian Biocentre, Evolutionary Biology group, Tartu 51010, Estonia
- Department of Evolutionary Biology, University of Tartu, Tartu 51010, Estonia
- Estonian Academy of Sciences, Tallinn 10130, Estonia
| | - Brenna M Henn
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York 11794, USA
| | | | - Robert Mahley
- Gladstone Institutes, San Francisco, California 94158, USA
| | - Antti Sajantila
- Department of Forensic Medicine, University of Helsinki, Helsinki 00014, Finland
| | - George Stamatoyannopoulos
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington 98195, USA
| | | | - Rita Khusainova
- Institute of Biochemistry and Genetics, Ufa Research Centre, Russian Academy of Sciences, Ufa 450054, Russia
- Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa 450074, Russia
| | - Elza Khusnutdinova
- Institute of Biochemistry and Genetics, Ufa Research Centre, Russian Academy of Sciences, Ufa 450054, Russia
- Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa 450074, Russia
| | - Sergey Litvinov
- Estonian Biocentre, Evolutionary Biology group, Tartu 51010, Estonia
- Institute of Biochemistry and Genetics, Ufa Research Centre, Russian Academy of Sciences, Ufa 450054, Russia
- Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa 450074, Russia
| | - George Ayodo
- Jaramogi Oginga Odinga University of Science and Technology, Bondo 40601, Kenya
| | - David Comas
- Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - Michael F Hammer
- ARL Division of Biotechnology, University of Arizona, Tucson, Arizona 85721, USA
| | - Toomas Kivisild
- Estonian Biocentre, Evolutionary Biology group, Tartu 51010, Estonia
- Division of Biological Anthropology, University of Cambridge, Fitzwilliam Street, Cambridge CB2 1QH, UK
| | - William Klitz
- New York Genome Center, New York, New York 10013, USA
| | - Cheryl A Winkler
- Basic Research Laboratory, Center for Cancer Research, NCI, Leidos Biomedical Research, Inc., Frederick National Laboratory, Frederick, Maryland 21702, USA
| | - Damian Labuda
- CHU Sainte-Justine, Pediatrics Departement, Université de Montréal, Québec H3T 1C5, Canada
| | - Michael Bamshad
- Department of Pediatrics, University of Washington, Seattle, Washington 98119, USA
| | - Lynn B Jorde
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Sarah A Tishkoff
- Departments of Genetics and Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - W Scott Watkins
- Department of Human Genetics, Eccles Institute of Human Genetics, University of Utah, Salt Lake City, Utah 84112, USA
| | - Mait Metspalu
- Estonian Biocentre, Evolutionary Biology group, Tartu 51010, Estonia
| | - Stanislav Dryomov
- Laboratory of Human Molecular Genetics, Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
- Department of Paleolithic Archaeology, Institute of Archaeology and Ethnography, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Rem Sukernik
- Laboratory of Human Molecular Genetics, Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
- Altai State University, Barnaul 656000, Russia
| | - Lalji Singh
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500 007, India
| | | | - Svante Pääbo
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Janet Kelso
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Nick Patterson
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
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Lazaridis I, Nadel D, Rollefson G, Merrett DC, Rohland N, Mallick S, Fernandes D, Novak M, Gamarra B, Sirak K, Connell S, Stewardson K, Harney E, Fu Q, Gonzalez-Fortes G, Jones ER, Roodenberg SA, Lengyel G, Bocquentin F, Gasparian B, Monge JM, Gregg M, Eshed V, Mizrahi AS, Meiklejohn C, Gerritsen F, Bejenaru L, Blüher M, Campbell A, Cavalleri G, Comas D, Froguel P, Gilbert E, Kerr SM, Kovacs P, Krause J, McGettigan D, Merrigan M, Merriwether DA, O'Reilly S, Richards MB, Semino O, Shamoon-Pour M, Stefanescu G, Stumvoll M, Tönjes A, Torroni A, Wilson JF, Yengo L, Hovhannisyan NA, Patterson N, Pinhasi R, Reich D. Genomic insights into the origin of farming in the ancient Near East. Nature 2016; 536:419-24. [PMID: 27459054 PMCID: PMC5003663 DOI: 10.1038/nature19310] [Citation(s) in RCA: 450] [Impact Index Per Article: 56.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 07/18/2016] [Indexed: 12/19/2022]
Abstract
We report genome-wide ancient DNA from 44 ancient Near Easterners ranging in time between ~12,000 and 1,400 bc, from Natufian hunter-gatherers to Bronze Age farmers. We show that the earliest populations of the Near East derived around half their ancestry from a 'Basal Eurasian' lineage that had little if any Neanderthal admixture and that separated from other non-African lineages before their separation from each other. The first farmers of the southern Levant (Israel and Jordan) and Zagros Mountains (Iran) were strongly genetically differentiated, and each descended from local hunter-gatherers. By the time of the Bronze Age, these two populations and Anatolian-related farmers had mixed with each other and with the hunter-gatherers of Europe to greatly reduce genetic differentiation. The impact of the Near Eastern farmers extended beyond the Near East: farmers related to those of Anatolia spread westward into Europe; farmers related to those of the Levant spread southward into East Africa; farmers related to those of Iran spread northward into the Eurasian steppe; and people related to both the early farmers of Iran and to the pastoralists of the Eurasian steppe spread eastward into South Asia.
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50
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Mondal M, Casals F, Xu T, Dall'Olio GM, Pybus M, Netea MG, Comas D, Laayouni H, Li Q, Majumder PP, Bertranpetit J. Genomic analysis of Andamanese provides insights into ancient human migration into Asia and adaptation. Nat Genet 2016; 48:1066-70. [DOI: 10.1038/ng.3621] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Accepted: 06/17/2016] [Indexed: 12/19/2022]
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