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Santos C, Phillips C, Oldoni F, Amigo J, Fondevila M, Pereira R, Carracedo Á, Lareu MV. Completion of a worldwide reference panel of samples for an ancestry informative Indel assay. Forensic Sci Int Genet 2015; 17:75-80. [DOI: 10.1016/j.fsigen.2015.03.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Revised: 03/17/2015] [Accepted: 03/21/2015] [Indexed: 12/20/2022]
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52
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Borinskaya SA, Yankovsky NK. Combination of genetic and humanitarian (cross-cultural) methods for the identification of human genes involved in the process of adaptation to evolutionary new environmental factors. RUSS J GENET+ 2015. [DOI: 10.1134/s1022795415040031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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Amorim CEG, Daub JT, Salzano FM, Foll M, Excoffier L. Detection of convergent genome-wide signals of adaptation to tropical forests in humans. PLoS One 2015; 10:e0121557. [PMID: 25849546 PMCID: PMC4388690 DOI: 10.1371/journal.pone.0121557] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 02/04/2015] [Indexed: 11/19/2022] Open
Abstract
Tropical forests are believed to be very harsh environments for human life. It is unclear whether human beings would have ever subsisted in those environments without external resources. It is therefore possible that humans have developed recent biological adaptations in response to specific selective pressures to cope with this challenge. To understand such biological adaptations we analyzed genome-wide SNP data under a Bayesian statistics framework, looking for outlier markers with an overly large extent of differentiation between populations living in a tropical forest, as compared to genetically related populations living outside the forest in Africa and the Americas. The most significant positive selection signals were found in genes related to lipid metabolism, the immune system, body development, and RNA Polymerase III transcription initiation. The results are discussed in the light of putative tropical forest selective pressures, namely food scarcity, high prevalence of pathogens, difficulty to move, and inefficient thermoregulation. Agreement between our results and previous studies on the pygmy phenotype, a putative prototype of forest adaptation, were found, suggesting that a few genetic regions previously described as associated with short stature may be evolving under similar positive selection in Africa and the Americas. In general, convergent evolution was less pervasive than local adaptation in one single continent, suggesting that Africans and Amerindians may have followed different routes to adapt to similar environmental selective pressures.
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Affiliation(s)
- Carlos Eduardo G. Amorim
- Computational and Molecular Population Genetics Laboratory, Institute of Ecology and Evolution, Berne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
- CAPES Foundation, Ministry of Education of Brazil, Brasília, Distrito Federal, Brazil
| | - Josephine T. Daub
- Computational and Molecular Population Genetics Laboratory, Institute of Ecology and Evolution, Berne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Francisco M. Salzano
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Matthieu Foll
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- School of Life Science, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Genetic Cancer Susceptibility Group, International Agency for Research on Cancer, Lyon, France
| | - Laurent Excoffier
- Computational and Molecular Population Genetics Laboratory, Institute of Ecology and Evolution, Berne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
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Genome-wide ancestry of 17th-century enslaved Africans from the Caribbean. Proc Natl Acad Sci U S A 2015; 112:3669-73. [PMID: 25755263 DOI: 10.1073/pnas.1421784112] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Between 1500 and 1850, more than 12 million enslaved Africans were transported to the New World. The vast majority were shipped from West and West-Central Africa, but their precise origins are largely unknown. We used genome-wide ancient DNA analyses to investigate the genetic origins of three enslaved Africans whose remains were recovered on the Caribbean island of Saint Martin. We trace their origins to distinct subcontinental source populations within Africa, including Bantu-speaking groups from northern Cameroon and non-Bantu speakers living in present-day Nigeria and Ghana. To our knowledge, these findings provide the first direct evidence for the ethnic origins of enslaved Africans, at a time for which historical records are scarce, and demonstrate that genomic data provide another type of record that can shed new light on long-standing historical questions.
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White L, Romagné F, Müller E, Erlebach E, Weihmann A, Parra G, Andrés AM, Castellano S. Genetic Adaptation to Levels of Dietary Selenium in Recent Human History. Mol Biol Evol 2015; 32:1507-18. [DOI: 10.1093/molbev/msv043] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
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Cagliani R, Forni D, Biasin M, Comabella M, Guerini FR, Riva S, Pozzoli U, Agliardi C, Caputo D, Malhotra S, Montalban X, Bresolin N, Clerici M, Sironi M. Ancient and recent selective pressures shaped genetic diversity at AIM2-like nucleic acid sensors. Genome Biol Evol 2015; 6:830-45. [PMID: 24682156 PMCID: PMC4007548 DOI: 10.1093/gbe/evu066] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
AIM2-like receptors (ALRs) are a family of nucleic acid sensors essential for innate immune responses against viruses and bacteria. We performed an evolutionary analysis of ALR genes (MNDA, PYHIN1, IFI16, and AIM2) by analyzing inter- and intraspecies diversity. Maximum-likelihood analyses indicated that IFI16 and AIM2 evolved adaptively in primates, with branch-specific selection at the catarrhini lineage for IFI16. Application of a population genetics–phylogenetics approach also allowed identification of positive selection events in the human lineage. Positive selection in primates targeted sites located at the DNA-binding interface in both IFI16 and AIM2. In IFI16, several sites positively selected in primates and in the human lineage were located in the PYD domain, which is involved in protein–protein interaction and is bound by a human cytomegalovirus immune evasion protein. Finally, positive selection was found to target nuclear localization signals in IFI16 and the spacer region separating the two HIN domains. Population genetic analysis in humans revealed that an IFI16 genic region has been a target of long-standing balancing selection, possibly acting on two nonsynonymous polymorphisms located in the spacer region. Data herein indicate that ALRs have been repeatedly targeted by natural selection. The balancing selection region in IFI16 carries a variant with opposite risk effect for distinct autoimmune diseases, suggesting antagonistic pleiotropy. We propose that the underlying scenario is the result of an ancestral and still ongoing host–pathogen arms race and that the maintenance of susceptibility alleles for autoimmune diseases at IFI16 represents an evolutionary trade-off.
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Affiliation(s)
- Rachele Cagliani
- Bioinformatics Laboratory, Scientific Institute IRCCS E. Medea, Bosisio Parini (LC), Italy
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Emery L, Magnaye K, Bigham A, Akey J, Bamshad M. Estimates of continental ancestry vary widely among individuals with the same mtDNA haplogroup. Am J Hum Genet 2015; 96:183-93. [PMID: 25620206 DOI: 10.1016/j.ajhg.2014.12.015] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 12/09/2014] [Indexed: 01/07/2023] Open
Abstract
The association between a geographical region and an mtDNA haplogroup(s) has provided the basis for using mtDNA haplogroups to infer an individual's place of origin and genetic ancestry. Although it is well known that ancestry inferences using mtDNA haplogroups and those using genome-wide markers are frequently discrepant, little empirical information exists on the magnitude and scope of such discrepancies between multiple mtDNA haplogroups and worldwide populations. We compared genetic-ancestry inferences made by mtDNA-haplogroup membership to those made by autosomal SNPs in ∼940 samples of the Human Genome Diversity Panel and recently admixed populations from the 1000 Genomes Project. Continental-ancestry proportions often varied widely among individuals sharing the same mtDNA haplogroup. For only half of mtDNA haplogroups did the highest average continental-ancestry proportion match the highest continental-ancestry proportion of a majority of individuals with that haplogroup. Prediction of an individual's mtDNA haplogroup from his or her continental-ancestry proportions was often incorrect. Collectively, these results indicate that for most individuals in the worldwide populations sampled, mtDNA-haplogroup membership provides limited information about either continental ancestry or continental region of origin.
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Mezzavilla M, Vozzi D, Pirastu N, Girotto G, d'Adamo P, Gasparini P, Colonna V. Genetic landscape of populations along the Silk Road: admixture and migration patterns. BMC Genet 2014; 15:131. [PMID: 25476266 PMCID: PMC4267745 DOI: 10.1186/s12863-014-0131-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Accepted: 11/19/2014] [Indexed: 01/29/2023] Open
Abstract
Background The ancient Silk Road has been a trading route between Europe and Central Asia from the 2nd century BCE to the 15th century CE. While most populations on this route have been characterized, the genetic background of others remains poorly understood, and little is known about past migration patterns. The scientific expedition “Marco Polo” has recently collected genetic and phenotypic data in six regions (Georgia, Armenia, Azerbaijan, Uzbekistan, Kazakhstan, Tajikistan) along the Silk Road to study the genetics of a number of phenotypes. Results We characterized the genetic structure of these populations within a worldwide context. We observed a West-East subdivision albeit the existence of a genetic component shared within Central Asia and nearby populations from Europe and Near East. We observed a contribution of up to 50% from Europe and Asia to most of the populations that have been analyzed. The contribution from Asia dates back to ~25 generations and is limited to the Eastern Silk Road. Time and direction of this contribution are consistent with the Mongolian expansion era. Conclusions We clarified the genetic structure of six populations from Central Asia and suggested a complex pattern of gene flow among them. We provided a map of migration events in time and space and we quantified exchanges among populations. Altogether these novel findings will support the future studies aimed at understanding the genetics of the phenotypes that have been collected during the Marco Polo campaign, they will provide insights into the history of these populations, and they will be useful to reconstruct the developments and events that have shaped modern Eurasians genomes. Electronic supplementary material The online version of this article (doi:10.1186/s12863-014-0131-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Massimo Mezzavilla
- Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Trieste, Italy. .,Department of Medical Sciences, University of Trieste, Trieste, Italy.
| | - Diego Vozzi
- Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Trieste, Italy.
| | - Nicola Pirastu
- Department of Medical Sciences, University of Trieste, Trieste, Italy.
| | - Giorgia Girotto
- Department of Medical Sciences, University of Trieste, Trieste, Italy.
| | - Pio d'Adamo
- Department of Medical Sciences, University of Trieste, Trieste, Italy.
| | - Paolo Gasparini
- Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Trieste, Italy. .,Department of Medical Sciences, University of Trieste, Trieste, Italy.
| | - Vincenza Colonna
- Institute of Genetics and Biophysics 'A. Buzzati-Traverso', National Research Council (CNR), via Pietro Castellino 111, 80131, Naples, Italy.
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Romanini C, Romero M, Salado Puerto M, Catelli L, Phillips C, Pereira R, Gusmão L, Vullo C. Ancestry informative markers: inference of ancestry in aged bone samples using an autosomal AIM-Indel multiplex. Forensic Sci Int Genet 2014; 16:58-63. [PMID: 25531060 DOI: 10.1016/j.fsigen.2014.11.025] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 10/25/2014] [Accepted: 11/28/2014] [Indexed: 01/22/2023]
Abstract
Ancestry informative markers (AIMs) can be useful to infer ancestry proportions of the donors of forensic evidence. The probability of success typing degraded samples, such as human skeletal remains, is strongly influenced by the DNA fragment lengths that can be amplified and the presence of PCR inhibitors. Several AIM panels are available amongst the many forensic marker sets developed for genotyping degraded DNA. Using a 46 AIM Insertion Deletion (Indel) multiplex, we analyzed human skeletal remains of post mortem time ranging from 35 to 60 years from four different continents (Sub-Saharan Africa, South and Central America, East Asia and Europe) to ascertain the genetic ancestry components. Samples belonging to non-admixed individuals could be assigned to their corresponding continental group. For the remaining samples with admixed ancestry, it was possible to estimate the proportion of co-ancestry components from the four reference population groups. The 46 AIM Indel set was informative enough to efficiently estimate the proportion of ancestry even in samples yielding partial profiles, a frequent occurrence when analyzing inhibited and/or degraded DNA extracts.
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Affiliation(s)
- Carola Romanini
- Forensic DNA Laboratory, Argentinean Forensic Anthropology Team (EAAF) Independencia 644,3A, 5000 Cordoba, Argentina
| | - Magdalena Romero
- Forensic DNA Laboratory, Argentinean Forensic Anthropology Team (EAAF) Independencia 644,3A, 5000 Cordoba, Argentina
| | - Mercedes Salado Puerto
- Forensic DNA Laboratory, Argentinean Forensic Anthropology Team (EAAF) Independencia 644,3A, 5000 Cordoba, Argentina
| | - Laura Catelli
- Forensic DNA Laboratory, Argentinean Forensic Anthropology Team (EAAF) Independencia 644,3A, 5000 Cordoba, Argentina
| | - Christopher Phillips
- Forensic Genetics Unit, Institute of Legal Medicine, Faculty of Medicine, University of Santiago de Compostela, ES-15705 Santiago de Compostela, Galicia, Spain
| | - Rui Pereira
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Leonor Gusmão
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal; DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - Carlos Vullo
- Forensic DNA Laboratory, Argentinean Forensic Anthropology Team (EAAF) Independencia 644,3A, 5000 Cordoba, Argentina.
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Jalkh N, Sahbatou M, Chouery E, Megarbane A, Leutenegger AL, Serre JL. Genome-wide inbreeding estimation within Lebanese communities using SNP arrays. Eur J Hum Genet 2014; 23:1364-9. [PMID: 25424710 DOI: 10.1038/ejhg.2014.246] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Revised: 08/29/2014] [Accepted: 09/19/2014] [Indexed: 12/14/2022] Open
Abstract
Consanguineous marriages have been widely practiced in several global communities with varying rates depending on religion, culture, and geography. In consanguineous marriages, parents pass to their children autozygous segments known as homozygous by descent segments. In this study, single-nucleotide polymorphisms were analyzed in 165 unrelated Lebanese people from Greek Orthodox, Maronite, Shiite and Sunni communities. Runs of homozygosity, total inbreeding levels, remote consanguinity, and population admixture and structure were estimated. The inbreeding coefficient value was estimated to be 1.61% in offspring of unrelated parents over three generations and 8.33% in offspring of first cousins. From these values, remote consanguinity values, resulting from genetic drift or recurrent consanguineous unions, were estimated in offspring of unrelated and first-cousin parents to be 0.61 and 1.2%, respectively. This remote consanguinity value suggests that for any unrelated marriages in Lebanon, the mates could be related as third cousins or as second cousins once removed. Under the assumption that 25% of marriages occur between first cousins, the mean inbreeding value of 2.3% may explain the increased incidence of recessive disease in offspring. Our analysis reveals a common ancestral population in the four Lebanese communities we studied.
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Affiliation(s)
- Nadine Jalkh
- Unité de Génétique Médicale et Laboratoire associé INSERM à l'Unité UMR_S910, Faculté de Médecine, Université Saint-Joseph, Beirut, Lebanon.,EA 2493 « pathologie cellulaire & génétique, de la conception à la naissance », Université de Versailles-Saint Quentin en Yvelines, Yvelines, France
| | | | - Eliane Chouery
- Unité de Génétique Médicale et Laboratoire associé INSERM à l'Unité UMR_S910, Faculté de Médecine, Université Saint-Joseph, Beirut, Lebanon
| | - André Megarbane
- Unité de Génétique Médicale et Laboratoire associé INSERM à l'Unité UMR_S910, Faculté de Médecine, Université Saint-Joseph, Beirut, Lebanon
| | | | - Jean-Louis Serre
- EA 2493 « pathologie cellulaire & génétique, de la conception à la naissance », Université de Versailles-Saint Quentin en Yvelines, Yvelines, France
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Mezzavilla M, Geppert M, Tyler-Smith C, Roewer L, Xue Y. Insights into the origin of rare haplogroup C3* Y chromosomes in South America from high-density autosomal SNP genotyping. Forensic Sci Int Genet 2014; 15:115-20. [PMID: 25435155 PMCID: PMC4312352 DOI: 10.1016/j.fsigen.2014.11.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Revised: 10/29/2014] [Accepted: 11/01/2014] [Indexed: 11/24/2022]
Abstract
Revisited the previous discovery of a rare Y haplogroup in two Ecuador populations. Hypotheses for the origin of the haplogroup tested with autosomal SNP genotype data. We favoured one of the three hypotheses, ‘founder plus drift’.
The colonization of Americas is thought to have occurred 15–20 thousand years ago (Kya), with little or no subsequent migration into South America until the European expansions beginning 0.5 Kya. Recently, however, haplogroup C3* Y chromosomes were discovered in two nearby Native American populations from Ecuador. Since this haplogroup is otherwise nearly absent from the Americas but is common in East Asia, and an archaeological link between Ecuador and Japan is known from 6 Kya, an additional migration 6 Kya was suggested. Here, we have generated high-density autosomal SNP genotypes from the Ecuadorian populations and compared them with genotypes from East Asia and elsewhere to evaluate three hypotheses: a recent migration from Japan, a single pulse of migration from Japan 6 Kya, and no migration after the First Americans. First, using forward-time simulations and an appropriate demographic model, we investigated our power to detect both ancient and recent gene flow at different levels. Second, we analyzed 207,321 single nucleotide polymorphisms from 16 Ecuadorian individuals, comparing them with populations from the HGDP panel using descriptive and formal tests for admixture. Our simulations revealed good power to detect recent admixture, and that ≥5% admixture 6 Kya ago could be detected. However, in the experimental data we saw no evidence of gene flow from Japan to Ecuador. In summary, we can exclude recent migration and probably admixture 6 Kya as the source of the C3* Y chromosomes in Ecuador, and thus suggest that they represent a rare founding lineage lost by drift elsewhere.
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Affiliation(s)
- Massimo Mezzavilla
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK; Medical Genetics, Department of Reproductive Sciences and Development, IRCCS-Burlo Garofolo, University of Trieste, Trieste, Italy
| | - Maria Geppert
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin, Berlin, Germany
| | - Chris Tyler-Smith
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Lutz Roewer
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin, Berlin, Germany
| | - Yali Xue
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK.
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Zidan J, Ben-Avraham D, Carmi S, Maray T, Friedman E, Atzmon G. Genotyping of geographically diverse Druze trios reveals substructure and a recent bottleneck. Eur J Hum Genet 2014; 23:1093-9. [PMID: 25370042 DOI: 10.1038/ejhg.2014.218] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 09/02/2014] [Accepted: 09/19/2014] [Indexed: 11/09/2022] Open
Abstract
Druze individuals rarely marry outside their faith (often practicing consanguinity) and are thus believed to form a genetic isolate. To comprehensively characterize the genetic structure of the Druze population, we recruited and genotyped 40 parent-offspring trios from the Upper Galilee in Israel and the Golan Heights, attempting to capture different extended families (clans) across various geographical locations. Principal component (PC) and ADMIXTURE analyses demonstrated that Druze are close to, yet distinct from, other Middle-Eastern groups (Bedouins and Palestinians), supporting the Druze's Middle-Eastern origin and their recent genetic isolation. Reconstruction of the Druze demographic history using identical-by-descent (IBD) segments suggested an ≈15-fold reduction in population size taking place ≈22-47 generations ago, close to the documented time of the foundation of the Druze faith at the 11th century. Combining the Galilee and Golan Druze genotypes with previously published data on Druze from the Carmel (Israel) and Lebanon demonstrated that all four Druze communities are genetically distinct. The Lebanese group shared less IBD segments (within the group and with other groups) compared with the Israeli Druze and showed higher heterozygosity (suggesting less consanguinity), but was less diverse in PC space. These findings suggest complex recent and ancient demographic history of the Druze population.
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Affiliation(s)
- Jamal Zidan
- The Oncology Department, Ziv Medical Center, The Faculty of Medicine in the Galilee, Bar-Ilan University, Zefat, Israel
| | - Dan Ben-Avraham
- Department of Medicine and Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Shai Carmi
- Department of Computer Science, Columbia University, New York, NY, USA
| | - Taiseer Maray
- Golan for Development, Madjal Shams, The Golan Heights, Israel
| | - Eitan Friedman
- 1] The Susanne Levy Gertner Oncogenetics Unit, The Danek Gertner Institute of Human Genetics, Chaim Sheba Medical Center, Tel-Hashomer, Israel [2] The Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Gil Atzmon
- Department of Medicine and Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
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Hassan MA, Saeij JP. Incorporating alternative splicing and mRNA editing into the genetic analysis of complex traits. Bioessays 2014; 36:1032-40. [PMID: 25171292 PMCID: PMC4280019 DOI: 10.1002/bies.201400079] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The nomination of candidate genes underlying complex traits is often focused on genetic variations that alter mRNA abundance or result in non-conservative changes in amino acids. Although inconspicuous in complex trait analysis, genetic variants that affect splicing or RNA editing can also generate proteomic diversity and impact genetic traits. Indeed, it is known that splicing and RNA editing modulate several traits in humans and model organisms. Using high-throughput RNA sequencing (RNA-seq) analysis, it is now possible to integrate the genetics of transcript abundance, alternative splicing (AS) and editing with the analysis of complex traits. We recently demonstrated that both AS and mRNA editing are modulated by genetic and environmental factors, and potentially engender phenotypic diversity in a genetically segregating mouse population. Therefore, the analysis of splicing and RNA editing can expand not only the regulatory landscape of transcriptome and proteome complexity, but also the repertoire of candidate genes for complex traits.
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Affiliation(s)
- Musa A. Hassan
- Massachusetts Institute of Technology, Department of Biology, Cambridge, MA, USA
| | - Jeroen P.J. Saeij
- Massachusetts Institute of Technology, Department of Biology, Cambridge, MA, USA
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Barthold JS, Wang Y, Kolon TF, Kollin C, Nordenskjöld A, Olivant Fisher A, Figueroa TE, BaniHani AH, Hagerty JA, Gonzalez R, Noh PH, Chiavacci RM, Harden KR, Abrams DJ, Kim CE, Mateson AB, Robbins AK, Li J, Akins RE, Hakonarson H, Devoto M. Phenotype specific association of the TGFBR3 locus with nonsyndromic cryptorchidism. J Urol 2014; 193:1637-45. [PMID: 25390077 DOI: 10.1016/j.juro.2014.10.097] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/21/2014] [Indexed: 11/19/2022]
Abstract
PURPOSE Based on a genome-wide association study of testicular dysgenesis syndrome showing a possible association with TGFBR3, we analyzed data from a larger, phenotypically restricted cryptorchidism population for potential replication of this signal. MATERIALS AND METHODS We excluded samples based on strict quality control criteria, leaving 844 cases and 2,718 controls of European ancestry that were analyzed in 2 separate groups based on genotyping platform (ie Illumina® HumanHap550, version 1 or 3, or Human610-Quad, version 1 BeadChip in group 1 and Human OmniExpress 12, version 1 BeadChip platform in group 2). Analyses included genotype imputation at the TGFBR3 locus, association analysis of imputed data with correction for population substructure, subsequent meta-analysis of data for groups 1 and 2, and selective genotyping of independent cases (330) and controls (324) for replication. We also measured Tgfbr3 mRNA levels and performed TGFBR3/betaglycan immunostaining in rat fetal gubernaculum. RESULTS We identified suggestive (p ≤ 1× 10(-4)) association of markers in/near TGFBR3, including rs9661103 (OR 1.40; 95% CI 1.20, 1.64; p = 2.71 × 10(-5)) and rs10782968 (OR 1.58; 95% CI 1.26, 1.98; p = 9.36 × 10(-5)) in groups 1 and 2, respectively. In subgroup analyses we observed strongest association of rs17576372 (OR 1.42; 95% CI 1.24, 1.60; p = 1.67 × 10(-4)) with proximal and rs11165059 (OR 1.32; 95% CI 1.15, 1.38; p = 9.42 × 10(-4)) with distal testis position, signals in strong linkage disequilibrium with rs9661103 and rs10782968, respectively. Association of the prior genome-wide association study signal (rs12082710) was marginal (OR 1.13; 95% CI 0.99, 1.28; p = 0.09 for group 1), and we were unable to replicate signals in our independent cohort. Tgfbr3/betaglycan was differentially expressed in wild-type and cryptorchid rat fetal gubernaculum. CONCLUSIONS These data suggest complex or phenotype specific association of cryptorchidism with TGFBR3 and the gubernaculum as a potential target of TGFβ signaling.
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Affiliation(s)
- Julia S Barthold
- Nemours Biomedical Research, Alfred I. duPont Hospital for Children, Wilmington, Delaware; Division of Urology, Alfred I. duPont Hospital for Children, Wilmington, Delaware.
| | - Yanping Wang
- Nemours Biomedical Research, Alfred I. duPont Hospital for Children, Wilmington, Delaware
| | - Thomas F Kolon
- Division of Urology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Claude Kollin
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Agneta Nordenskjöld
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Alicia Olivant Fisher
- Nemours Biomedical Research, Alfred I. duPont Hospital for Children, Wilmington, Delaware
| | - T Ernesto Figueroa
- Division of Urology, Alfred I. duPont Hospital for Children, Wilmington, Delaware
| | - Ahmad H BaniHani
- Division of Urology, Alfred I. duPont Hospital for Children, Wilmington, Delaware
| | - Jennifer A Hagerty
- Division of Urology, Alfred I. duPont Hospital for Children, Wilmington, Delaware
| | - Ricardo Gonzalez
- Division of Urology, Alfred I. duPont Hospital for Children, Wilmington, Delaware
| | - Paul H Noh
- Division of Urology, Alfred I. duPont Hospital for Children, Wilmington, Delaware
| | - Rosetta M Chiavacci
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Kisha R Harden
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Debra J Abrams
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Cecilia E Kim
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Abigail B Mateson
- Nemours Biomedical Research, Alfred I. duPont Hospital for Children, Wilmington, Delaware
| | - Alan K Robbins
- Nemours Biomedical Research, Alfred I. duPont Hospital for Children, Wilmington, Delaware
| | - Jin Li
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Robert E Akins
- Nemours Biomedical Research, Alfred I. duPont Hospital for Children, Wilmington, Delaware
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania; Division of Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Marcella Devoto
- Division of Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Biostatistics and Epidemiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Molecular Medicine, Sapienza University, Rome, Italy
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Ballester V, Guo X, Vendrell R, Haritunians T, Klomhaus AM, Li D, McGovern DPB, Rotter JI, Torres EA, Taylor KD. Association of NOD2 and IL23R with inflammatory bowel disease in Puerto Rico. PLoS One 2014; 9:e108204. [PMID: 25259511 PMCID: PMC4178120 DOI: 10.1371/journal.pone.0108204] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 08/18/2014] [Indexed: 12/19/2022] Open
Abstract
The Puerto Rico population may be modeled as an admixed population with contributions from three continents: Sub-Saharan Africa, Ancient America, and Europe. Extending the study of the genetics of inflammatory bowel disease (IBD) to an admixed population such as Puerto Rico has the potential to shed light on IBD genes identified in studies of European populations, find new genes contributing to IBD susceptibility, and provide basic information on IBD for the care of US patients of Puerto Rican and Latino descent. In order to study the association between immune-related genes and Crohn’s disease (CD) and ulcerative colitis (UC) in Puerto Rico, we genotyped 1159 Puerto Rican cases, controls, and family members with the ImmunoChip. We also genotyped 832 subjects from the Human Genome Diversity Panel to provide data for estimation of global and local continental ancestry. Association of SNPs was tested by logistic regression corrected for global continental descent and family structure. We observed the association between Crohn’s disease and NOD2 (rs17313265, 0.28 in CD, 0.19 in controls, OR 1.5, p = 9×10−6) and IL23R (rs11209026, 0.026 in CD, 0.0.071 in controls, OR 0.4, p = 3.8×10−4). The haplotype structure of both regions resembled that reported for European populations and “local” continental ancestry of the IL23R gene was almost entirely of European descent. We also observed suggestive evidence for the association of the BAZ1A promoter SNP with CD (rs1200332, 0.45 in CD, 0.35 in controls, OR 1.5, p = 2×10−6). Our estimate of continental ancestry surrounding this SNP suggested an origin in Ancient America for this putative susceptibility region. Our observations underscored the great difference between global continental ancestry and local continental ancestry at the level of the individual gene, particularly for immune-related loci.
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Affiliation(s)
- Veroushka Ballester
- Department of Medicine, Division of Gastroenterology, School of Medicine, University of Puerto Rico Medical Sciences Campus, San Juan, Puerto Rico
| | - Xiuqing Guo
- Institute of Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute at Harbor/UCLA Medical Center, Torrance, California, United States of America
| | - Roberto Vendrell
- Department of Medicine, Division of Gastroenterology, School of Medicine, University of Puerto Rico Medical Sciences Campus, San Juan, Puerto Rico
| | - Talin Haritunians
- Medical Genetics Institute & Inflammatory Bowel Disease Center, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - Alexandra M. Klomhaus
- Institute of Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute at Harbor/UCLA Medical Center, Torrance, California, United States of America
| | - Dalin Li
- Medical Genetics Institute & Inflammatory Bowel Disease Center, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - Dermot P. B. McGovern
- Medical Genetics Institute & Inflammatory Bowel Disease Center, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - Jerome I. Rotter
- Institute of Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute at Harbor/UCLA Medical Center, Torrance, California, United States of America
| | - Esther A. Torres
- Department of Medicine, Division of Gastroenterology, School of Medicine, University of Puerto Rico Medical Sciences Campus, San Juan, Puerto Rico
| | - Kent D. Taylor
- Institute of Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute at Harbor/UCLA Medical Center, Torrance, California, United States of America
- * E-mail:
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Lippold S, Xu H, Ko A, Li M, Renaud G, Butthof A, Schröder R, Stoneking M. Human paternal and maternal demographic histories: insights from high-resolution Y chromosome and mtDNA sequences. INVESTIGATIVE GENETICS 2014; 5:13. [PMID: 25254093 PMCID: PMC4174254 DOI: 10.1186/2041-2223-5-13] [Citation(s) in RCA: 132] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 08/22/2014] [Indexed: 02/07/2023]
Abstract
Background Comparisons of maternally-inherited mitochondrial DNA (mtDNA) and paternally-inherited non-recombining Y chromosome (NRY) variation have provided important insights into the impact of sex-biased processes (such as migration, residence pattern, and so on) on human genetic variation. However, such comparisons have been limited by the different molecular methods typically used to assay mtDNA and NRY variation (for example, sequencing hypervariable segments of the control region for mtDNA vs. genotyping SNPs and/or STR loci for the NRY). Here, we report a simple capture array method to enrich Illumina sequencing libraries for approximately 500 kb of NRY sequence, which we use to generate NRY sequences from 623 males from 51 populations in the CEPH Human Genome Diversity Panel (HGDP). We also obtained complete mtDNA genome sequences from the same individuals, allowing us to compare maternal and paternal histories free of any ascertainment bias. Results We identified 2,228 SNPs in the NRY sequences and 2,163 SNPs in the mtDNA sequences. Our results confirm the controversial assertion that genetic differences between human populations on a global scale are bigger for the NRY than for mtDNA, although the differences are not as large as previously suggested. More importantly, we find substantial regional variation in patterns of mtDNA versus NRY variation. Model-based simulations indicate very small ancestral effective population sizes (<100) for the out-of-Africa migration as well as for many human populations. We also find that the ratio of female effective population size to male effective population size (Nf/Nm) has been greater than one throughout the history of modern humans, and has recently increased due to faster growth in Nf than Nm. Conclusions The NRY and mtDNA sequences provide new insights into the paternal and maternal histories of human populations, and the methods we introduce here should be widely applicable for further such studies.
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Affiliation(s)
- Sebastian Lippold
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig D04103, Germany
| | - Hongyang Xu
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig D04103, Germany ; Department of Computational Genetics, CAS-MPG Partner Institute for Computational Biology, Shanghai 200031, China
| | - Albert Ko
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig D04103, Germany
| | - Mingkun Li
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig D04103, Germany ; Present address: Fondation Mérieux, 17 rue Bourgelat, Lyon 69002, France
| | - Gabriel Renaud
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig D04103, Germany
| | - Anne Butthof
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig D04103, Germany ; Present address: Institute of Biochemistry, Faculty of Medicine, University of Leipzig, Leipzig D04103, Germany
| | - Roland Schröder
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig D04103, Germany
| | - Mark Stoneking
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig D04103, Germany
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Raghavan M, DeGiorgio M, Albrechtsen A, Moltke I, Skoglund P, Korneliussen TS, Grønnow B, Appelt M, Gulløv HC, Friesen TM, Fitzhugh W, Malmström H, Rasmussen S, Olsen J, Melchior L, Fuller BT, Fahrni SM, Stafford T, Grimes V, Renouf MAP, Cybulski J, Lynnerup N, Lahr MM, Britton K, Knecht R, Arneborg J, Metspalu M, Cornejo OE, Malaspinas AS, Wang Y, Rasmussen M, Raghavan V, Hansen TVO, Khusnutdinova E, Pierre T, Dneprovsky K, Andreasen C, Lange H, Hayes MG, Coltrain J, Spitsyn VA, Götherström A, Orlando L, Kivisild T, Villems R, Crawford MH, Nielsen FC, Dissing J, Heinemeier J, Meldgaard M, Bustamante C, O'Rourke DH, Jakobsson M, Gilbert MTP, Nielsen R, Willerslev E. The genetic prehistory of the New World Arctic. Science 2014; 345:1255832. [PMID: 25170159 DOI: 10.1126/science.1255832] [Citation(s) in RCA: 147] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The New World Arctic, the last region of the Americas to be populated by humans, has a relatively well-researched archaeology, but an understanding of its genetic history is lacking. We present genome-wide sequence data from ancient and present-day humans from Greenland, Arctic Canada, Alaska, Aleutian Islands, and Siberia. We show that Paleo-Eskimos (~3000 BCE to 1300 CE) represent a migration pulse into the Americas independent of both Native American and Inuit expansions. Furthermore, the genetic continuity characterizing the Paleo-Eskimo period was interrupted by the arrival of a new population, representing the ancestors of present-day Inuit, with evidence of past gene flow between these lineages. Despite periodic abandonment of major Arctic regions, a single Paleo-Eskimo metapopulation likely survived in near-isolation for more than 4000 years, only to vanish around 700 years ago.
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Affiliation(s)
- Maanasa Raghavan
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Michael DeGiorgio
- Department of Biology, Pennsylvania State University, 502 Wartik Laboratory, University Park, PA 16802, USA
| | - Anders Albrechtsen
- Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen, Denmark
| | - Ida Moltke
- Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen, Denmark. Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Pontus Skoglund
- Department of Evolutionary Biology, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden. Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Thorfinn S Korneliussen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Bjarne Grønnow
- Arctic Centre at the Ethnographic Collections (SILA), National Museum of Denmark, Frederiksholms Kanal 12, 1220 Copenhagen, Denmark
| | - Martin Appelt
- Arctic Centre at the Ethnographic Collections (SILA), National Museum of Denmark, Frederiksholms Kanal 12, 1220 Copenhagen, Denmark
| | - Hans Christian Gulløv
- Arctic Centre at the Ethnographic Collections (SILA), National Museum of Denmark, Frederiksholms Kanal 12, 1220 Copenhagen, Denmark
| | - T Max Friesen
- Department of Anthropology, University of Toronto, Toronto, Ontario M5S 2S2, Canada
| | - William Fitzhugh
- Arctic Studies Center, Post Office Box 37012, Department of Anthropology, MRC 112, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013-7012, USA
| | - Helena Malmström
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark. Department of Evolutionary Biology, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
| | - Simon Rasmussen
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet, 2800 Kongens Lyngby, Denmark
| | - Jesper Olsen
- AMS 14C Dating Centre, Department of Physics and Astronomy, Aarhus University, Ny Munkegade 120, 8000 Aarhus C, Denmark
| | - Linea Melchior
- Anthropological Laboratory, Institute of Forensic Medicine, Faculty of Health Sciences, University of Copenhagen, Frederik V's Vej 11, 2100 Copenhagen, Denmark
| | - Benjamin T Fuller
- Department of Earth System Science, University of California, Irvine, CA 92697, USA
| | - Simon M Fahrni
- Department of Earth System Science, University of California, Irvine, CA 92697, USA
| | - Thomas Stafford
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark. AMS 14C Dating Centre, Department of Physics and Astronomy, Aarhus University, Ny Munkegade 120, 8000 Aarhus C, Denmark
| | - Vaughan Grimes
- Department of Archaeology, Memorial University, Queen's College, 210 Prince Philip Drive, St. John's, Newfoundland, A1C 5S7, Canada. Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - M A Priscilla Renouf
- Department of Archaeology, Memorial University, Queen's College, 210 Prince Philip Drive, St. John's, Newfoundland, A1C 5S7, Canada
| | - Jerome Cybulski
- Canadian Museum of History, 100 Rue Laurier, Gatineau, Quebec K1A 0M8, Canada. Department of Anthropology, University of Western Ontario, 1151 Richmond Street North, London N6A 5C2, Canada
| | - Niels Lynnerup
- Anthropological Laboratory, Institute of Forensic Medicine, Faculty of Health Sciences, University of Copenhagen, Frederik V's Vej 11, 2100 Copenhagen, Denmark
| | - Marta Mirazon Lahr
- Leverhulme Centre for Human Evolutionary Studies, Department of Archaeology and Anthropology, University of Cambridge, Cambridge CB2 1QH, UK
| | - Kate Britton
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany. Department of Archaeology, University of Aberdeen, St. Mary's Building, Elphinstone Road, Aberdeen AB24 3UF, Scotland, UK
| | - Rick Knecht
- Department of Archaeology, University of Aberdeen, St. Mary's Building, Elphinstone Road, Aberdeen AB24 3UF, Scotland, UK
| | - Jette Arneborg
- National Museum of Denmark, Frederiksholms kanal 12, 1220 Copenhagen, Denmark. School of Geosciences, University of Edinburgh, Edinburgh EH8 9XP, UK
| | - Mait Metspalu
- Estonian Biocentre, Evolutionary Biology Group, Tartu 51010, Estonia. Department of Evolutionary Biology, University of Tartu, Tartu 51010, Estonia
| | - Omar E Cornejo
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA 94305, USA. School of Biological Sciences, Washington State University, Post Office Box 644236, Pullman, WA 99164, USA
| | - Anna-Sapfo Malaspinas
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Yong Wang
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA. Ancestry.com DNA LLC, San Francisco, CA 94107, USA
| | - Morten Rasmussen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Vibha Raghavan
- Informatics and Bio-computing, Ontario Institute for Cancer Research, 661 University Avenue, Suite 510, Toronto, Ontario, M5G 0A3, Canada
| | - Thomas V O Hansen
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Blegdamsvej 9, 2100 Copenhagen, Denmark
| | - Elza Khusnutdinova
- Institute of Biochemistry and Genetics, Ufa Scientific Center of Russian Academy of Sciences, Ufa, Russia. Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, Bashkortostan 450074, Russia
| | - Tracey Pierre
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Kirill Dneprovsky
- State Museum for Oriental Art, 12a, Nikitsky Boulevard, Moscow 119019, Russia
| | - Claus Andreasen
- Greenland National Museum and Archives, Post Office Box 145, 3900 Nuuk, Greenland
| | - Hans Lange
- Greenland National Museum and Archives, Post Office Box 145, 3900 Nuuk, Greenland
| | - M Geoffrey Hayes
- Division of Endocrinology, Metabolism and Molecular Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA. Department of Anthropology, Weinberg College of Arts and Sciences, Northwestern University, Evanston, IL 60208, USA. Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Joan Coltrain
- Department of Anthropology, University of Utah, Salt Lake City, UT 84112, USA
| | - Victor A Spitsyn
- Research Centre for Medical Genetics of Russian Academy of Medical Sciences, 1 Moskvorechie, Moscow 115478, Russia
| | - Anders Götherström
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Toomas Kivisild
- Estonian Biocentre, Evolutionary Biology Group, Tartu 51010, Estonia. Department of Archaeology and Anthropology, University of Cambridge, Cambridge CB2 1QH, UK
| | - Richard Villems
- Estonian Biocentre, Evolutionary Biology Group, Tartu 51010, Estonia. Department of Evolutionary Biology, University of Tartu, Tartu 51010, Estonia
| | - Michael H Crawford
- Laboratory of Biological Anthropology, University of Kansas, Lawrence, KS 66045, USA
| | - Finn C Nielsen
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Blegdamsvej 9, 2100 Copenhagen, Denmark
| | - Jørgen Dissing
- Anthropological Laboratory, Institute of Forensic Medicine, Faculty of Health Sciences, University of Copenhagen, Frederik V's Vej 11, 2100 Copenhagen, Denmark
| | - Jan Heinemeier
- AMS 14C Dating Centre, Department of Physics and Astronomy, Aarhus University, Ny Munkegade 120, 8000 Aarhus C, Denmark
| | - Morten Meldgaard
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Carlos Bustamante
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Dennis H O'Rourke
- Department of Anthropology, University of Utah, Salt Lake City, UT 84112, USA
| | - Mattias Jakobsson
- Department of Evolutionary Biology, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
| | - M Thomas P Gilbert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Rasmus Nielsen
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.
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Verdu P, Pemberton TJ, Laurent R, Kemp BM, Gonzalez-Oliver A, Gorodezky C, Hughes CE, Shattuck MR, Petzelt B, Mitchell J, Harry H, William T, Worl R, Cybulski JS, Rosenberg NA, Malhi RS. Patterns of admixture and population structure in native populations of Northwest North America. PLoS Genet 2014; 10:e1004530. [PMID: 25122539 PMCID: PMC4133047 DOI: 10.1371/journal.pgen.1004530] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2014] [Accepted: 06/09/2014] [Indexed: 01/09/2023] Open
Abstract
The initial contact of European populations with indigenous populations of the Americas produced diverse admixture processes across North, Central, and South America. Recent studies have examined the genetic structure of indigenous populations of Latin America and the Caribbean and their admixed descendants, reporting on the genomic impact of the history of admixture with colonizing populations of European and African ancestry. However, relatively little genomic research has been conducted on admixture in indigenous North American populations. In this study, we analyze genomic data at 475,109 single-nucleotide polymorphisms sampled in indigenous peoples of the Pacific Northwest in British Columbia and Southeast Alaska, populations with a well-documented history of contact with European and Asian traders, fishermen, and contract laborers. We find that the indigenous populations of the Pacific Northwest have higher gene diversity than Latin American indigenous populations. Among the Pacific Northwest populations, interior groups provide more evidence for East Asian admixture, whereas coastal groups have higher levels of European admixture. In contrast with many Latin American indigenous populations, the variance of admixture is high in each of the Pacific Northwest indigenous populations, as expected for recent and ongoing admixture processes. The results reveal some similarities but notable differences between admixture patterns in the Pacific Northwest and those in Latin America, contributing to a more detailed understanding of the genomic consequences of European colonization events throughout the Americas. We collaborated with six indigenous communities in British Columbia and Southeast Alaska to generate and analyze genome-wide data for over 100 individuals. We then combined this dataset with existing data from populations worldwide, performing an investigation of the genetic structure of indigenous populations of the Pacific Northwest both locally and in relation to continental and worldwide geographic scales. On a regional scale, we identified differences between coastal and interior populations that are likely due to differences both in pre- and post-European contact histories. On a continental scale, we identified differences in genetic structure between populations in the Pacific Northwest and Central and South America, reflecting both differences prior to European contact as well as different post-contact histories of admixture. This study is among the first to analyze genome-wide diversity among indigenous North American populations, and it provides a comparative framework for understanding the effects of European colonization on indigenous communities throughout the Americas.
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Affiliation(s)
- Paul Verdu
- CNRS-MNHN-University Paris Diderot-Sorbonne Paris Cité, UMR7206 Eco-Anthropology and Ethno-Biology, Paris, France
| | - Trevor J. Pemberton
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Romain Laurent
- CNRS-MNHN-University Paris Diderot-Sorbonne Paris Cité, UMR7206 Eco-Anthropology and Ethno-Biology, Paris, France
| | - Brian M. Kemp
- Department of Anthropology and School of Biological Sciences, Washington State University, Pullman, Washington, United States of America
| | - Angelica Gonzalez-Oliver
- Departmento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autonóma de México, Mexico City, Mexico
| | - Clara Gorodezky
- Department of Immunology and Immunogenetics, Instituto de Diagnóstico y Referencia Epidemiológicos, Secretary of Health, Mexico City, Mexico
| | - Cris E. Hughes
- Department of Anthropology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Milena R. Shattuck
- Department of Anthropology, New York University, New York, New York, United States of America
| | - Barbara Petzelt
- Metlakatla Treaty Office, Metlakatla, British Columbia, Canada
| | | | - Harold Harry
- Stswecem'c/Xgat'tem Band, British Columbia, Canada
| | | | - Rosita Worl
- Seaalaska Heritage Institute, Juneau, Alaska, United States of America
| | | | - Noah A. Rosenberg
- Department of Biology, Stanford University, Stanford, California, United States of America
- * E-mail: (NAR); (RSM)
| | - Ripan S. Malhi
- Department of Anthropology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- * E-mail: (NAR); (RSM)
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Pemberton TJ, Rosenberg NA. Population-genetic influences on genomic estimates of the inbreeding coefficient: a global perspective. Hum Hered 2014; 77:37-48. [PMID: 25060268 DOI: 10.1159/000362878] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND/AIMS Culturally driven marital practices provide a key instance of an interaction between social and genetic processes in shaping patterns of human genetic variation, producing, for example, increased identity by descent through consanguineous marriage. A commonly used measure to quantify identity by descent in an individual is the inbreeding coefficient, a quantity that reflects not only consanguinity, but also other aspects of kinship in the population to which the individual belongs. Here, in populations worldwide, we examine the relationship between genomic estimates of the inbreeding coefficient and population patterns in genetic variation. METHODS Using genotypes at 645 microsatellites, we compare inbreeding coefficients from 5,043 individuals representing 237 populations worldwide to demographic consanguinity frequency estimates available for 26 populations as well as to other quantities that can illuminate population-genetic influences on inbreeding coefficients. RESULTS We observe higher inbreeding coefficient estimates in populations and geographic regions with known high levels of consanguinity or genetic isolation and in populations with an increased effect of genetic drift and decreased genetic diversity with increasing distance from Africa. For the small number of populations with specific consanguinity estimates, we find a correlation between inbreeding coefficients and consanguinity frequency (r = 0.349, p = 0.040). CONCLUSIONS The results emphasize the importance of both consanguinity and population-genetic factors in influencing variation in inbreeding coefficients, and they provide insight into factors useful for assessing the effect of consanguinity on genomic patterns in different populations.
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Affiliation(s)
- Trevor J Pemberton
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Man., Canada
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Huerta-Sánchez E, Jin X, Asan, Bianba Z, Peter BM, Vinckenbosch N, Liang Y, Yi X, He M, Somel M, Ni P, Wang B, Ou X, Huasang, Luosang J, Cuo ZXP, Li K, Gao G, Yin Y, Wang W, Zhang X, Xu X, Yang H, Li Y, Wang J, Wang J, Nielsen R. Altitude adaptation in Tibetans caused by introgression of Denisovan-like DNA. Nature 2014; 512:194-7. [PMID: 25043035 PMCID: PMC4134395 DOI: 10.1038/nature13408] [Citation(s) in RCA: 601] [Impact Index Per Article: 60.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Accepted: 04/28/2014] [Indexed: 01/01/2023]
Affiliation(s)
- Emilia Huerta-Sánchez
- 1] BGI-Shenzhen, Shenzhen 518083, China [2] Department of Integrative Biology, University of California, Berkeley, California 94720 USA [3] School of Natural Sciences, University of California, Merced, California 95343 USA [4]
| | - Xin Jin
- 1] BGI-Shenzhen, Shenzhen 518083, China [2] School of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510006, China [3]
| | - Asan
- 1] BGI-Shenzhen, Shenzhen 518083, China [2] Binhai Genomics Institute, BGI-Tianjin, Tianjin 300308, China [3] Tianjin Translational Genomics Center, BGI-Tianjin, Tianjin 300308, China [4]
| | - Zhuoma Bianba
- 1] The People's Hospital of Lhasa, Lhasa 850000, China [2]
| | - Benjamin M Peter
- Department of Integrative Biology, University of California, Berkeley, California 94720 USA
| | - Nicolas Vinckenbosch
- Department of Integrative Biology, University of California, Berkeley, California 94720 USA
| | - Yu Liang
- 1] BGI-Shenzhen, Shenzhen 518083, China [2] Binhai Genomics Institute, BGI-Tianjin, Tianjin 300308, China [3] Tianjin Translational Genomics Center, BGI-Tianjin, Tianjin 300308, China
| | - Xin Yi
- 1] BGI-Shenzhen, Shenzhen 518083, China [2] Binhai Genomics Institute, BGI-Tianjin, Tianjin 300308, China [3] Tianjin Translational Genomics Center, BGI-Tianjin, Tianjin 300308, China
| | - Mingze He
- 1] BGI-Shenzhen, Shenzhen 518083, China [2] Bioinformatics and Computational Biology Program, Iowa State University, Ames, Iowa 50011, USA
| | - Mehmet Somel
- Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey
| | | | - Bo Wang
- BGI-Shenzhen, Shenzhen 518083, China
| | | | - Huasang
- BGI-Shenzhen, Shenzhen 518083, China
| | | | - Zha Xi Ping Cuo
- The Second People's Hospital of Tibet Autonomous Region, Lhasa 850000, China
| | - Kui Li
- The People's Hospital of the Tibet Autonomous Region, Lhasa 850000, China
| | - Guoyi Gao
- The hospital of XiShuangBanNa Dai Nationalities, Autonomous Jinghong, 666100 Yunnan, China
| | - Ye Yin
- BGI-Shenzhen, Shenzhen 518083, China
| | - Wei Wang
- BGI-Shenzhen, Shenzhen 518083, China
| | - Xiuqing Zhang
- 1] BGI-Shenzhen, Shenzhen 518083, China [2] The Guangdong Enterprise Key Laboratory of Human Disease Genomics, BGI-Shenzhen, 518083 Shenzhen, China [3] Shenzhen Key Laboratory of Transomics Biotechnologies, BGI-Shenzhen, 518083 Shenzhen, China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen 518083, China
| | - Huanming Yang
- 1] BGI-Shenzhen, Shenzhen 518083, China [2] Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia [3] James D. Watson Institute of Genome Science, 310008 Hangzhou, China
| | | | - Jian Wang
- 1] BGI-Shenzhen, Shenzhen 518083, China [2] James D. Watson Institute of Genome Science, 310008 Hangzhou, China
| | - Jun Wang
- 1] BGI-Shenzhen, Shenzhen 518083, China [2] Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia [3] Department of Biology, University of Copenhagen, Ole MaaløesVej 5, 2200 Copenhagen, Denmark [4] Macau University of Science and Technology, AvenidaWai long, Taipa, Macau 999078, China [5] Department of Medicine, University of Hong Kong 999077, Hong Kong
| | - Rasmus Nielsen
- 1] BGI-Shenzhen, Shenzhen 518083, China [2] Department of Integrative Biology, University of California, Berkeley, California 94720 USA [3] Department of Statistics, University of California, Berkeley, California 94720, USA [4] Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
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Yorgov D, Edwards KL, Santorico SA. Use of admixture and association for detection of quantitative trait loci in the Type 2 Diabetes Genetic Exploration by Next-Generation Sequencing in Ethnic Samples (T2D-GENES) study. BMC Proc 2014; 8:S6. [PMID: 25519335 PMCID: PMC4143673 DOI: 10.1186/1753-6561-8-s1-s6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Admixture mapping and association testing have been successfully applied to the detection of genes for complex diseases. Methods have also been developed to combine these approaches. As an initial step to determine the feasibility of combining admixture and association mapping in the context of whole genome sequencing, we have applied several methods to data from the Genetic Analysis Workshop 18. Here, we describe the steps necessary to carry out such a study from selection of reference populations and preprocessing of data through to the testing itself. We detected one significant result with a Bonferroni corrected p-value of 0.032 at single nucleotide polymorphism rs12639065. Computing local ancestry for Hispanic populations was challenging because there are relatively few methods by which to handle 3-way admixture, and publicly available Native American reference panels are scarce. However, combining admixture and association is a promising approach for detection of quantitative trait loci because it might be able to elevate the power of detection by combining 2 different sources of genetic signal.
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Affiliation(s)
- Daniel Yorgov
- Department of Mathematical and Statistical Sciences, University of Colorado Denver, Denver, CO 80217-3364, USA
| | - Karen L Edwards
- Department of Epidemiology, School of Medicine, University of California Irvine, Irvine, CA 92697-7550, USA ; Department of Epidemiology, Institute for Public Health Genetics, University of Washington, Seattle, WA 98115, USA
| | - Stephanie A Santorico
- Department of Mathematical and Statistical Sciences, University of Colorado Denver, Denver, CO 80217-3364, USA
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Sironi M, Biasin M, Cagliani R, Gnudi F, Saulle I, Ibba S, Filippi G, Yahyaei S, Tresoldi C, Riva S, Trabattoni D, De Gioia L, Lo Caputo S, Mazzotta F, Forni D, Pontremoli C, Pineda JA, Pozzoli U, Rivero-Juarez A, Caruz A, Clerici M. Evolutionary analysis identifies an MX2 haplotype associated with natural resistance to HIV-1 infection. Mol Biol Evol 2014; 31:2402-14. [PMID: 24930137 DOI: 10.1093/molbev/msu193] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The protein product of the myxovirus resistance 2 (MX2) gene restricts HIV-1 and simian retroviruses. We demonstrate that MX2 evolved adaptively in mammals with distinct sites representing selection targets in distinct branches; selection mainly involved residues in loop 4, previously shown to carry antiviral determinants. Modeling data indicated that positively selected sites form a continuous surface on loop 4, which folds into two antiparallel α-helices protruding from the stalk domain. A population genetics-phylogenetics approach indicated that the coding region of MX2 mainly evolved under negative selection in the human lineage. Nonetheless, population genetic analyses demonstrated that natural selection operated on MX2 during the recent history of human populations: distinct selective events drove the frequency increase of two haplotypes in the populations of Asian and European ancestry. The Asian haplotype carries a susceptibility allele for melanoma; the European haplotype is tagged by rs2074560, an intronic variant. Analyses performed on three independent European cohorts of HIV-1-exposed seronegative individuals with different geographic origin and distinct exposure route showed that the ancestral (G) allele of rs2074560 protects from HIV-1 infection with a recessive effect (combined P = 1.55 × 10(-4)). The same allele is associated with lower in vitro HIV-1 replication and increases MX2 expression levels in response to IFN-α. Data herein exploit evolutionary information to identify a novel host determinant of HIV-1 infection susceptibility.
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Affiliation(s)
- Manuela Sironi
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Mara Biasin
- Department of Biomedical and Clinical Sciences, University of Milan, Milan, Italy
| | - Rachele Cagliani
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Federica Gnudi
- Department of Biomedical and Clinical Sciences, University of Milan, Milan, Italy
| | - Irma Saulle
- Department of Biomedical and Clinical Sciences, University of Milan, Milan, Italy
| | - Salomè Ibba
- Department of Biomedical and Clinical Sciences, University of Milan, Milan, Italy
| | - Giulia Filippi
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, Milan, Italy
| | - Sarah Yahyaei
- Department of Biomedical and Clinical Sciences, University of Milan, Milan, Italy
| | - Claudia Tresoldi
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Stefania Riva
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Daria Trabattoni
- Department of Biomedical and Clinical Sciences, University of Milan, Milan, Italy
| | - Luca De Gioia
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, Milan, Italy
| | | | | | - Diego Forni
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Chiara Pontremoli
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Juan Antonio Pineda
- Infectious Diseases and Microbiology Clinical Unit, Valme Hospital, Seville, Spain
| | - Uberto Pozzoli
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Antonio Rivero-Juarez
- Maimonides Institut for Biomedical Research (IMIBIC), Reina Sofia Universitary Hospital, University of Cordoba, Cordoba, Spain
| | - Antonio Caruz
- Immunogenetics Unit, Department of Experimental Biology, University of Jaen, Jaen, Spain
| | - Mario Clerici
- Department of Physiopathology and Transplantation, University of Milan, Milan, ItalyDon C. Gnocchi Foundation ONLUS, IRCCS, Milan, Italy
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73
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Hodgson JA, Mulligan CJ, Al-Meeri A, Raaum RL. Early back-to-Africa migration into the Horn of Africa. PLoS Genet 2014; 10:e1004393. [PMID: 24921250 PMCID: PMC4055572 DOI: 10.1371/journal.pgen.1004393] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Accepted: 04/07/2014] [Indexed: 11/19/2022] Open
Abstract
Genetic studies have identified substantial non-African admixture in the Horn of Africa (HOA). In the most recent genomic studies, this non-African ancestry has been attributed to admixture with Middle Eastern populations during the last few thousand years. However, mitochondrial and Y chromosome data are suggestive of earlier episodes of admixture. To investigate this further, we generated new genome-wide SNP data for a Yemeni population sample and merged these new data with published genome-wide genetic data from the HOA and a broad selection of surrounding populations. We used multidimensional scaling and ADMIXTURE methods in an exploratory data analysis to develop hypotheses on admixture and population structure in HOA populations. These analyses suggested that there might be distinct, differentiated African and non-African ancestries in the HOA. After partitioning the SNP data into African and non-African origin chromosome segments, we found support for a distinct African (Ethiopic) ancestry and a distinct non-African (Ethio-Somali) ancestry in HOA populations. The African Ethiopic ancestry is tightly restricted to HOA populations and likely represents an autochthonous HOA population. The non-African ancestry in the HOA, which is primarily attributed to a novel Ethio-Somali inferred ancestry component, is significantly differentiated from all neighboring non-African ancestries in North Africa, the Levant, and Arabia. The Ethio-Somali ancestry is found in all admixed HOA ethnic groups, shows little inter-individual variance within these ethnic groups, is estimated to have diverged from all other non-African ancestries by at least 23 ka, and does not carry the unique Arabian lactase persistence allele that arose about 4 ka. Taking into account published mitochondrial, Y chromosome, paleoclimate, and archaeological data, we find that the time of the Ethio-Somali back-to-Africa migration is most likely pre-agricultural.
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Affiliation(s)
- Jason A. Hodgson
- Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, Berkshire, United Kingdom
| | - Connie J. Mulligan
- Department of Anthropology and the Genetics Institute, University of Florida, Gainesville, Florida, United States of America
| | - Ali Al-Meeri
- Department of Biochemistry and Molecular Biology, Sana'a University, Sana'a, Yemen
| | - Ryan L. Raaum
- Department of Anthropology, Lehman College and The Graduate Center, The City University of New York, Bronx, New York, New York, United States of America
- The New York Consortium in Evolutionary Primatology (NYCEP), New York, New York, United States of America
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74
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Gautier M. Using genotyping data to assign markers to their chromosome type and to infer the sex of individuals: a Bayesian model-based classifier. Mol Ecol Resour 2014; 14:1141-59. [PMID: 24751186 DOI: 10.1111/1755-0998.12264] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 03/31/2014] [Accepted: 04/08/2014] [Indexed: 12/23/2022]
Abstract
The recent democratization of next-generation-sequencing-based approaches towards nonmodel species has made it cost-effective to produce large genotyping data sets for a wider range of species. However, when no detailed genome assembly is available, poor knowledge about the organization of the markers within the genome might hamper the optimal use of this abundant information. At the most basic level of genomic organization, the type of chromosome (autosomes, sex chromosomes, mitochondria or chloroplast in plants) may remain unknown for most markers which might be limiting or even misleading in some applications, particularly in population genetics. Conversely, the characterization of sex-linked markers allows molecular sexing of the individuals. In this study, we propose a Bayesian model-based classifier named detsex, to assign markers to their chromosome type and/or to perform sexing of individuals based on genotyping data. The performance of detsex is further evaluated by a comprehensive simulation study and by the analysis of real data sets from various origins (microsatellite and SNP data derived from genotyping assay designs and NGS experiments). Irrespective of the origin of the markers or the size of the data set, detsex was proved efficient (i) to identify the sex-linked markers, (ii) to perform molecular sexing of the individuals and (iii) to perform basic quality check of the genotyping data sets. The underlying structure of the model also allows to consider each of these potential applications either separately or jointly.
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Affiliation(s)
- Mathieu Gautier
- INRA, UMR CBGP (INRA - IRD - Cirad - Montpellier SupAgro), Campus International de Baillarguet, CS 30016, F-34988, Montferrier-sur-Lez, France; Institut de Biologie Computationnelle, 95 rue de la Galera, 34095, Montpellier, France
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75
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Engelken J, Carnero-Montoro E, Pybus M, Andrews GK, Lalueza-Fox C, Comas D, Sekler I, de la Rasilla M, Rosas A, Stoneking M, Valverde MA, Vicente R, Bosch E. Extreme population differences in the human zinc transporter ZIP4 (SLC39A4) are explained by positive selection in Sub-Saharan Africa. PLoS Genet 2014; 10:e1004128. [PMID: 24586184 PMCID: PMC3930504 DOI: 10.1371/journal.pgen.1004128] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Accepted: 12/05/2013] [Indexed: 12/17/2022] Open
Abstract
Extreme differences in allele frequency between West Africans and Eurasians were observed for a leucine-to-valine substitution (Leu372Val) in the human intestinal zinc uptake transporter, ZIP4, yet no further evidence was found for a selective sweep around the ZIP4 gene (SLC39A4). By interrogating allele frequencies in more than 100 diverse human populations and resequencing Neanderthal DNA, we confirmed the ancestral state of this locus and found a strong geographical gradient for the derived allele (Val372), with near fixation in West Africa. In extensive coalescent simulations, we show that the extreme differences in allele frequency, yet absence of a classical sweep signature, can be explained by the effect of a local recombination hotspot, together with directional selection favoring the Val372 allele in Sub-Saharan Africans. The possible functional effect of the Leu372Val substitution, together with two pathological mutations at the same codon (Leu372Pro and Leu372Arg) that cause acrodermatitis enteropathica (a disease phenotype characterized by extreme zinc deficiency), was investigated by transient overexpression of human ZIP4 protein in HeLa cells. Both acrodermatitis mutations cause absence of the ZIP4 transporter cell surface expression and nearly absent zinc uptake, while the Val372 variant displayed significantly reduced surface protein expression, reduced basal levels of intracellular zinc, and reduced zinc uptake in comparison with the Leu372 variant. We speculate that reduced zinc uptake by the ZIP4-derived Val372 isoform may act by starving certain pathogens of zinc, and hence may have been advantageous in Sub-Saharan Africa. Moreover, these functional results may indicate differences in zinc homeostasis among modern human populations with possible relevance for disease risk.
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Affiliation(s)
- Johannes Engelken
- Institute of Evolutionary Biology (CSIC-UPF), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain ; Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Elena Carnero-Montoro
- Institute of Evolutionary Biology (CSIC-UPF), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Marc Pybus
- Institute of Evolutionary Biology (CSIC-UPF), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Glen K Andrews
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas, United States of America
| | - Carles Lalueza-Fox
- Institute of Evolutionary Biology (CSIC-UPF), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - David Comas
- Institute of Evolutionary Biology (CSIC-UPF), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Israel Sekler
- Department of Physiology, Ben-Gurion University, Beer-Sheva, Israel
| | - Marco de la Rasilla
- Área de Prehistoria, Departamento de Historia, Universidad de Oviedo, Oviedo, Spain
| | - Antonio Rosas
- Group of Paleoanthropology MNCN-CSIC, Department of Paleobiology, National Museum of Natural Sciences, CSIC, Madrid, Spain
| | - Mark Stoneking
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Miguel A Valverde
- Laboratory of Molecular Physiology and Channelopathies, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Rubén Vicente
- Laboratory of Molecular Physiology and Channelopathies, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Elena Bosch
- Institute of Evolutionary Biology (CSIC-UPF), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
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Bendjilali N, Hsueh WC, He Q, Willcox DC, Nievergelt CM, Donlon TA, Kwok PY, Suzuki M, Willcox BJ. Who are the Okinawans? Ancestry, genome diversity, and implications for the genetic study of human longevity from a geographically isolated population. J Gerontol A Biol Sci Med Sci 2014; 69:1474-84. [PMID: 24444611 DOI: 10.1093/gerona/glt203] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Isolated populations have advantages for genetic studies of longevity from decreased haplotype diversity and long-range linkage disequilibrium. This permits smaller sample sizes without loss of power, among other utilities. Little is known about the genome of the Okinawans, a potential population isolate, recognized for longevity. Therefore, we assessed genetic diversity, structure, and admixture in Okinawans, and compared this with Caucasians, Chinese, Japanese, and Africans from HapMap II, genotyped on the same Affymetrix GeneChip Human Mapping 500K array. Principal component analysis, haplotype coverage, and linkage disequilibrium decay revealed a distinct Okinawan genome-more homogeneity, less haplotype diversity, and longer range linkage disequilibrium. Population structure and admixture analyses utilizing 52 global reference populations from the Human Genome Diversity Cell Line Panel demonstrated that Okinawans clustered almost exclusively with East Asians. Sibling relative risk (λs) analysis revealed that siblings of Okinawan centenarians have 3.11 times (females) and 3.77 times (males) more likelihood of centenarianism. These findings suggest that Okinawans are genetically distinct and share several characteristics of a population isolate, which are prone to develop extreme phenotypes (eg, longevity) from genetic drift, natural selection, and population bottlenecks. These data support further exploration of genetic influence on longevity in the Okinawans.
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Affiliation(s)
| | - Wen-Chi Hsueh
- Departments of Medicine and Epidemiology & Biostatistics, University of California, San Francisco
| | - Qimei He
- Pacific Health Research and Education Institute, Honolulu, Hawaii. Department of Research, Kuakini Medical Center, Honolulu, Hawaii
| | | | | | - Timothy A Donlon
- Pacific Health Research and Education Institute, Honolulu, Hawaii. Ohana Genetics, Honolulu, Hawaii
| | - Pui-Yan Kwok
- Department of Dermatology, Institute for Human Genetics, and Cardiovascular Research Institute, University of California, San Francisco
| | - Makoto Suzuki
- Okinawa Research Center for Longevity Science, Urasoe, Okinawa, Japan. Faculty of Medicine, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Bradley J Willcox
- Pacific Health Research and Education Institute, Honolulu, Hawaii. Department of Research, Kuakini Medical Center, Honolulu, Hawaii. Okinawa Research Center for Longevity Science, Urasoe, Okinawa, Japan. Department of Geriatric Medicine, John A Burns School of Medicine, University of Hawaii, Honolulu, Hawaii
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77
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Human and Helicobacter pylori coevolution shapes the risk of gastric disease. Proc Natl Acad Sci U S A 2014; 111:1455-60. [PMID: 24474772 DOI: 10.1073/pnas.1318093111] [Citation(s) in RCA: 163] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Helicobacter pylori is the principal cause of gastric cancer, the second leading cause of cancer mortality worldwide. However, H. pylori prevalence generally does not predict cancer incidence. To determine whether coevolution between host and pathogen influences disease risk, we examined the association between the severity of gastric lesions and patterns of genomic variation in matched human and H. pylori samples. Patients were recruited from two geographically distinct Colombian populations with significantly different incidences of gastric cancer, but virtually identical prevalence of H. pylori infection. All H. pylori isolates contained the genetic signatures of multiple ancestries, with an ancestral African cluster predominating in a low-risk, coastal population and a European cluster in a high-risk, mountain population. The human ancestry of the biopsied individuals also varied with geography, with mostly African ancestry in the coastal region (58%), and mostly Amerindian ancestry in the mountain region (67%). The interaction between the host and pathogen ancestries completely accounted for the difference in the severity of gastric lesions in the two regions of Colombia. In particular, African H. pylori ancestry was relatively benign in humans of African ancestry but was deleterious in individuals with substantial Amerindian ancestry. Thus, coevolution likely modulated disease risk, and the disruption of coevolved human and H. pylori genomes can explain the high incidence of gastric disease in the mountain population.
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78
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Haptoglobin (HP) and Haptoglobin-related protein (HPR) copy number variation, natural selection, and trypanosomiasis. Hum Genet 2013; 133:69-83. [PMID: 24005574 PMCID: PMC3898332 DOI: 10.1007/s00439-013-1352-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Accepted: 08/08/2013] [Indexed: 01/01/2023]
Abstract
Haptoglobin, coded by the HP gene, is a plasma protein that acts as a scavenger for free heme, and haptoglobin-related protein (coded by the HPR gene) forms part of the trypanolytic factor TLF-1, together with apolipoprotein L1 (ApoL1). We analyse the polymorphic small intragenic duplication of the HP gene, with alleles Hp1 and Hp2, in 52 populations, and find no evidence for natural selection either from extended haplotype analysis or from correlation with pathogen richness matrices. Using fiber-FISH, the paralog ratio test, and array-CGH data, we also confirm that the HPR gene is copy number variable, with duplication of the whole HPR gene at polymorphic frequencies in west and central Africa, up to an allele frequency of 15 %. The geographical distribution of the HPR duplication allele overlaps the region where the pathogen causing chronic human African trypanosomiasis, Trypanosoma brucei gambiense, is endemic. The HPR duplication has occurred on one SNP haplotype, but there is no strong evidence of extended homozygosity, a characteristic of recent natural selection. The HPR duplication shows a slight, non-significant undertransmission to human African trypanosomiasis-affected children of unaffected parents in the Democratic Republic of Congo. However, taken together with alleles of APOL1, there is an overall significant undertransmission of putative protective alleles to human African trypanosomiasis-affected children.
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79
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Aigner J, Villatoro S, Rabionet R, Roquer J, Jiménez-Conde J, Martí E, Estivill X. A common 56-kilobase deletion in a primate-specific segmental duplication creates a novel butyrophilin-like protein. BMC Genet 2013; 14:61. [PMID: 23829304 PMCID: PMC3729544 DOI: 10.1186/1471-2156-14-61] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Accepted: 05/21/2013] [Indexed: 12/22/2022] Open
Abstract
Background The Butyrophilin-like (BTNL) proteins are likely to play an important role in inflammation and immune response. Like the B7 protein family, many human and murine BTNL members have been shown to control T lymphocytes response, and polymorphisms in human BTNL2 have been linked to several inflammatory diseases, such as pulmonary sarcoidosis, inflammatory bowel disease and neonatal lupus. Results In this study we provide a comprehensive population, genomic and transcriptomic analysis of a 56-kb deletion copy number variant (CNV), located within two segmental duplications of two genes belonging to the BTNL family, namely BTNL8 and BTNL3. We confirm the presence of a novel BTNL8*3 fusion-protein product, and show an influence of the deletion variant on the expression level of several genes involved in immune function, including BTNL9, another member of the same family. Moreover, by genotyping HapMap and human diversity panel (HGDP) samples, we demonstrate a clear difference in the stratification of the BTNL8_BTNL3-del allele frequency between major continental human populations. Conclusion Despite tremendous progress in the field of structural variation, rather few CNVs have been functionally characterized so far. Here, we show clear functional consequences of a new deletion CNV (BTNL8_BTNL3-del) with potentially important implication in the human immune system and in inflammatory and proliferative disorders. In addition, the marked population differences found of BTNL8_BTNL3-del frequencies suggest that this deletion CNV might have evolved under positive selection due to environmental conditions in some populations, with potential phenotypic consequences.
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Affiliation(s)
- Johanna Aigner
- Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), Barcelona 08003, Spain
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80
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Nievergelt CM, Maihofer AX, Shekhtman T, Libiger O, Wang X, Kidd KK, Kidd JR. Inference of human continental origin and admixture proportions using a highly discriminative ancestry informative 41-SNP panel. INVESTIGATIVE GENETICS 2013; 4:13. [PMID: 23815888 PMCID: PMC3699392 DOI: 10.1186/2041-2223-4-13] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Accepted: 05/14/2013] [Indexed: 02/07/2023]
Abstract
Background Accurate determination of genetic ancestry is of high interest for many areas such as biomedical research, personal genomics and forensics. It remains an important topic in genetic association studies, as it has been shown that population stratification, if not appropriately considered, can lead to false-positive and -negative results. While large association studies typically extract ancestry information from available genome-wide SNP genotypes, many important clinical data sets on rare phenotypes and historical collections assembled before the GWAS area are in need of a feasible method (i.e., ease of genotyping, small number of markers) to infer the geographic origin and potential admixture of the study subjects. Here we report on the development, application and limitations of a small, multiplexable ancestry informative marker (AIM) panel of SNPs (or AISNP) developed specifically for this purpose. Results Based on worldwide populations from the HGDP, a 41-AIM AISNP panel for multiplex application with the ABI SNPlex and a subset with 31 AIMs for the Sequenome iPLEX system were selected and found to be highly informative for inferring ancestry among the seven continental regions Africa, the Middle East, Europe, Central/South Asia, East Asia, the Americas and Oceania. The panel was found to be least informative for Eurasian populations, and additional AIMs for a higher resolution are suggested. A large reference set including over 4,000 subjects collected from 120 global populations was assembled to facilitate accurate ancestry determination. We show practical applications of this AIM panel, discuss its limitations for admixed individuals and suggest ways to incorporate ancestry information into genetic association studies. Conclusion We demonstrated the utility of a small AISNP panel specifically developed to discern global ancestry. We believe that it will find wide application because of its feasibility and potential for a wide range of applications.
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Affiliation(s)
- Caroline M Nievergelt
- Department of Psychiatry, School of Medicine, University of San Diego California, La Jolla, CA, 92093, USA.
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81
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Porras-Hurtado L, Ruiz Y, Santos C, Phillips C, Carracedo A, Lareu MV. An overview of STRUCTURE: applications, parameter settings, and supporting software. Front Genet 2013; 4:98. [PMID: 23755071 PMCID: PMC3665925 DOI: 10.3389/fgene.2013.00098] [Citation(s) in RCA: 257] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Accepted: 05/14/2013] [Indexed: 12/22/2022] Open
Abstract
Objectives: We present an up-to-date review of STRUCTURE software: one of the most widely used population analysis tools that allows researchers to assess patterns of genetic structure in a set of samples. STRUCTURE can identify subsets of the whole sample by detecting allele frequency differences within the data and can assign individuals to those sub-populations based on analysis of likelihoods. The review covers STRUCTURE's most commonly used ancestry and frequency models, plus an overview of the main applications of the software in human genetics including case-control association studies (CCAS), population genetics, and forensic analysis. The review is accompanied by supplementary material providing a step-by-step guide to running STRUCTURE. Methods: With reference to a worked example, we explore the effects of changing the principal analysis parameters on STRUCTURE results when analyzing a uniform set of human genetic data. Use of the supporting software: CLUMPP and distruct is detailed and we provide an overview and worked example of STRAT software, applicable to CCAS. Conclusion: The guide offers a simplified view of how STRUCTURE, CLUMPP, distruct, and STRAT can be applied to provide researchers with an informed choice of parameter settings and supporting software when analyzing their own genetic data.
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Affiliation(s)
- Liliana Porras-Hurtado
- Universidad Tecnológica de Pereira Pereira, Colombia ; Forensic Genetics Unit, Institute of Legal Medicine, University of Santiago de Compostela Santiago de Compostela, Spain
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Population structure in a comprehensive genomic data set on human microsatellite variation. G3-GENES GENOMES GENETICS 2013; 3:891-907. [PMID: 23550135 PMCID: PMC3656735 DOI: 10.1534/g3.113.005728] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Over the past two decades, microsatellite genotypes have provided the data for landmark studies of human population-genetic variation. However, the various microsatellite data sets have been prepared with different procedures and sets of markers, so that it has been difficult to synthesize available data for a comprehensive analysis. Here, we combine eight human population-genetic data sets at the 645 microsatellite loci they share in common, accounting for procedural differences in the production of the different data sets, to assemble a single data set containing 5795 individuals from 267 worldwide populations. We perform a systematic analysis of genetic relatedness, detecting 240 intra-population and 92 inter-population pairs of previously unidentified close relatives and proposing standardized subsets of unrelated individuals for use in future studies. We then augment the human data with a data set of 84 chimpanzees at the 246 loci they share in common with the human samples. Multidimensional scaling and neighbor-joining analyses of these data sets offer new insights into the structure of human populations and enable a comparison of genetic variation patterns in chimpanzees with those in humans. Our combined data sets are the largest of their kind reported to date and provide a resource for use in human population-genetic studies.
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Huerta-Sánchez E, Degiorgio M, Pagani L, Tarekegn A, Ekong R, Antao T, Cardona A, Montgomery HE, Cavalleri GL, Robbins PA, Weale ME, Bradman N, Bekele E, Kivisild T, Tyler-Smith C, Nielsen R. Genetic signatures reveal high-altitude adaptation in a set of ethiopian populations. Mol Biol Evol 2013; 30:1877-88. [PMID: 23666210 PMCID: PMC3708501 DOI: 10.1093/molbev/mst089] [Citation(s) in RCA: 143] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The Tibetan and Andean Plateaus and Ethiopian highlands are the largest regions to have long-term high-altitude residents. Such populations are exposed to lower barometric pressures and hence atmospheric partial pressures of oxygen. Such “hypobaric hypoxia” may limit physical functional capacity, reproductive health, and even survival. As such, selection of genetic variants advantageous to hypoxic adaptation is likely to have occurred. Identifying signatures of such selection is likely to help understanding of hypoxic adaptive processes. Here, we seek evidence of such positive selection using five Ethiopian populations, three of which are from high-altitude areas in Ethiopia. As these populations may have been recipients of Eurasian gene flow, we correct for this admixture. Using single-nucleotide polymorphism genotype data from multiple populations, we find the strongest signal of selection in BHLHE41 (also known as DEC2 or SHARP1). Remarkably, a major role of this gene is regulation of the same hypoxia response pathway on which selection has most strikingly been observed in both Tibetan and Andean populations. Because it is also an important player in the circadian rhythm pathway, BHLHE41 might also provide insights into the mechanisms underlying the recognized impacts of hypoxia on the circadian clock. These results support the view that Ethiopian, Andean, and Tibetan populations living at high altitude have adapted to hypoxia differently, with convergent evolution affecting different genes from the same pathway.
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84
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Daub JT, Hofer T, Cutivet E, Dupanloup I, Quintana-Murci L, Robinson-Rechavi M, Excoffier L. Evidence for polygenic adaptation to pathogens in the human genome. Mol Biol Evol 2013; 30:1544-58. [PMID: 23625889 DOI: 10.1093/molbev/mst080] [Citation(s) in RCA: 149] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Most approaches aiming at finding genes involved in adaptive events have focused on the detection of outlier loci, which resulted in the discovery of individually "significant" genes with strong effects. However, a collection of small effect mutations could have a large effect on a given biological pathway that includes many genes, and such a polygenic mode of adaptation has not been systematically investigated in humans. We propose here to evidence polygenic selection by detecting signals of adaptation at the pathway or gene set level instead of analyzing single independent genes. Using a gene-set enrichment test to identify genome-wide signals of adaptation among human populations, we find that most pathways globally enriched for signals of positive selection are either directly or indirectly involved in immune response. We also find evidence for long-distance genotypic linkage disequilibrium, suggesting functional epistatic interactions between members of the same pathway. Our results show that past interactions with pathogens have elicited widespread and coordinated genomic responses, and suggest that adaptation to pathogens can be considered as a primary example of polygenic selection.
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Affiliation(s)
- Josephine T Daub
- Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Berne, Berne, Switzerland.
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85
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Bassaganyas L, Riveira-Muñoz E, García-Aragonés M, González JR, Cáceres M, Armengol L, Estivill X. Worldwide population distribution of the common LCE3C-LCE3B deletion associated with psoriasis and other autoimmune disorders. BMC Genomics 2013; 14:261. [PMID: 23594316 PMCID: PMC3639927 DOI: 10.1186/1471-2164-14-261] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Accepted: 01/02/2013] [Indexed: 01/29/2023] Open
Abstract
Background There is increasing evidence of the importance of copy number variants (CNV) in genetic diversity among individuals and populations, as well as in some common genetic diseases. We previously characterized a common 32-kb insertion/deletion variant of the PSORS4 locus at chromosome 1q21 that harbours the LCE3C and LCE3B genes. This variant allele (LCE3C_LCE3B-del) is common in patients with psoriasis and other autoimmune disorders from certain ethnic groups. Results Using array-CGH (Agilent 244 K) in samples from the HapMap and Human Genome Diversity Panel (HGDP) collections, we identified 54 regions showing population differences in comparison to Africans. We provided here a comprehensive population-genetic analysis of one of these regions, which involves the 32-kb deletion of the PSORS4 locus. By a PCR-based genotyping assay we characterised the profiles of the LCE3C_LCE3B-del and the linkage disequilibrium (LD) pattern between the variant allele and the tag SNP rs4112788. Our results show that most populations tend to have a higher frequency of the deleted allele than Sub-Saharan Africans. Furthermore, we found strong LD between rs4112788G and LCE3C_LCE3B-del in most non-African populations (r2 >0.8), in contrast to the low concordance between loci (r2 <0.3) in the African populations. Conclusions These results are another example of population variability in terms of biomedical interesting CNV. The frequency distribution of the LCE3C_LCE3B-del allele and the LD pattern across populations suggest that the differences between ethnic groups might not be due to natural selection, but the consequence of genetic drift caused by the strong bottleneck that occurred during “out of Africa” expansion.
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86
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Chang CL, Semyonov J, Cheng PJ, Huang SY, Park JI, Tsai HJ, Lin CY, Grützner F, Soong YK, Cai JJ, Hsu SYT. Widespread divergence of the CEACAM/PSG genes in vertebrates and humans suggests sensitivity to selection. PLoS One 2013; 8:e61701. [PMID: 23613906 PMCID: PMC3628338 DOI: 10.1371/journal.pone.0061701] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Accepted: 03/17/2013] [Indexed: 11/30/2022] Open
Abstract
In mammals, carcinoembryonic antigen cell adhesion molecules (CEACAMs) and pregnancy-specific glycoproteins (PSGs) play important roles in the regulation of pathogen transmission, tumorigenesis, insulin signaling turnover, and fetal–maternal interactions. However, how these genes evolved and to what extent they diverged in humans remain to be investigated specifically. Based on syntenic mapping of chordate genomes, we reveal that diverging homologs with a prototypic CEACAM architecture–including an extracellular domain with immunoglobulin variable and constant domain-like regions, and an intracellular domain containing ITAM motif–are present from cartilaginous fish to humans, but are absent in sea lamprey, cephalochordate or urochordate. Interestingly, the CEACAM/PSG gene inventory underwent radical divergence in various vertebrate lineages: from zero in avian species to dozens in therian mammals. In addition, analyses of genetic variations in human populations showed the presence of various types of copy number variations (CNVs) at the CEACAM/PSG locus. These copy number polymorphisms have 3–80% frequency in select populations, and encompass single to more than six PSG genes. Furthermore, we found that CEACAM/PSG genes contain a significantly higher density of nonsynonymous single nucleotide polymorphism (SNP) compared to the chromosome average, and many CEACAM/PSG SNPs exhibit high population differentiation. Taken together, our study suggested that CEACAM/PSG genes have had a more dynamic evolutionary history in vertebrates than previously thought. Given that CEACAM/PSGs play important roles in maternal–fetal interaction and pathogen recognition, these data have laid the groundwork for future analysis of adaptive CEACAM/PSG genotype-phenotypic relationships in normal and complicated pregnancies as well as other etiologies.
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Affiliation(s)
- Chia Lin Chang
- Department of Obstetrics and Gynecology, Chang Gung Memorial Hospital Linkou Medical Center, Chang Gung University, Kweishan, Taoyuan, Taiwan.
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87
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88
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Di Gaetano C, Matullo G, Piazza A, Ursino M, Gasparini M. A proximity-based method to identify genomic regions correlated with a continuously varying environmental variable. Evol Bioinform Online 2013; 9:29-42. [PMID: 23423242 PMCID: PMC3565544 DOI: 10.4137/ebo.s10211] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Knowledge of markers in the human genome which show spatial patterns and display extreme correlation with different environmental determinants play an important role in understanding the factors which affect the biological evolution of our species. We used the genotype data of more than half a million single nucleotide polymorphisms (SNPs) from the data set Human Genome Diversity Panel (HGDP-CEPH -CEPH) and we calculated Spearman's correlation between absolute latitude and one of the two allele frequencies of each SNP. We selected SNPs with a correlation coefficient within the upper 1% tail of the distribution. We then used a criterion of proximity between significant variants to focus on DNA regions showing a continuous signal over a portion of the genome. Based on external information and genome annotations, we demonstrated that most regions with the strongest signals also have biological relevance. We believe this proximity requirement adds an edge to our novel method compared to the existing literature, highlighting several genes (for example DTNB, DOT1L, TPCN2, RELN, MSRA, NRG3) related to body size or shape, human height, hair color, and schizophrenia. Our approach can be applied generally to any measure of association between polymorphic frequencies and continuously varying environmental variables.
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Affiliation(s)
- Cornelia Di Gaetano
- Department of Genetics, Biology and Biochemistry, University of Turin, Turin, Italy. ; HuGeF, Human Genetics Foundation, Turin, Italy
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89
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Maisano Delser P, Fuselli S. Human loci involved in drug biotransformation: worldwide genetic variation, population structure, and pharmacogenetic implications. Hum Genet 2013; 132:563-77. [PMID: 23354977 DOI: 10.1007/s00439-013-1268-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2012] [Accepted: 01/08/2013] [Indexed: 12/20/2022]
Abstract
Understanding the role of inheritance in individual variation in drug response is the focus of pharmacogenetics (PGx). A key part of this understanding is quantifying the role of genetic ancestry in this phenotypic outcome. To provide insight into the relationship between ethnicity and drug response, this study first infers the global distribution of PGx variation and defines its structure. Second, the study evaluates if geographic population structure stems from all PGx loci in general, or if structure is caused by specific genes. Lastly, we identify the genetic variants contributing the greatest proportion of such structure. Our study describes the global genetic structure of PGx loci across the 52 populations of the Human Genome Diversity Cell-Line Panel, the most inclusive set of human populations freely available for studies on human genetic variation. By analysing genetic variation at 1,001 single nucleotide polymorphisms (SNPs) involved in biotransformation of exogenous substances, we describe the between-populations PGx variation, as well geographical groupings of diversity. In addition, with discriminant analysis of principal component (DAPC), we infer how many and which groups of populations are supported by PGx variation, and identify which SNPs actually contribute to the PGx structure between such groups. Our results show that intergenic, synonymous and non-synonymous SNPs show similar levels of genetic variation across the globe. Conversely, loci coding for Cytochrome P450s (mainly metabolizing exogenous substances) show significantly higher levels of genetic diversity between populations than the other gene categories. Overall, genetic variation at PGx loci correlates with geographic distances between populations, and the apportionment of genetic variation is similar to that observed for the rest of the genome. In other words, the pattern of PGx variation has been mainly shaped by the demographic history of our species, as in the case of most of our genes. The population structure defined by PGx loci supports the presence of six genetic clusters reflecting geographic location of samples. In particular, the results of the DAPC analyses show that 27 SNPs substantially contribute to the first three discriminant functions. Among these SNPs, some, such as the intronic rs1403527 of NR1I2 and the non-synonymous rs699 of AGT, are known to be associated with specific drug responses. Their substantial variation between different groups of populations may have important implications for PGx practical applications.
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90
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Patillon B, Luisi P, Blanché H, Patin E, Cann HM, Génin E, Sabbagh A. Positive selection in the chromosome 16 VKORC1 genomic region has contributed to the variability of anticoagulant response in humans. PLoS One 2012; 7:e53049. [PMID: 23285254 PMCID: PMC3532425 DOI: 10.1371/journal.pone.0053049] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2012] [Accepted: 11/23/2012] [Indexed: 12/23/2022] Open
Abstract
VKORC1 (vitamin K epoxide reductase complex subunit 1, 16p11.2) is the main genetic determinant of human response to oral anticoagulants of antivitamin K type (AVK). This gene was recently suggested to be a putative target of positive selection in East Asian populations. In this study, we genotyped the HGDP-CEPH Panel for six VKORC1 SNPs and downloaded chromosome 16 genotypes from the HGDP-CEPH database in order to characterize the geographic distribution of footprints of positive selection within and around this locus. A unique VKORC1 haplotype carrying the promoter mutation associated with AVK sensitivity showed especially high frequencies in all the 17 HGDP-CEPH East Asian population samples. VKORC1 and 24 neighboring genes were found to lie in a 505 kb region of strong linkage disequilibrium in these populations. Patterns of allele frequency differentiation and haplotype structure suggest that this genomic region has been submitted to a near complete selective sweep in all East Asian populations and only in this geographic area. The most extreme scores of the different selection tests are found within a smaller 45 kb region that contains VKORC1 and three other genes (BCKDK, MYST1 (KAT8), and PRSS8) with different functions. Because of the strong linkage disequilibrium, it is not possible to determine if VKORC1 or one of the three other genes is the target of this strong positive selection that could explain present-day differences among human populations in AVK dose requirement. Our results show that the extended region surrounding a presumable single target of positive selection should be analyzed for genetic variation in a wide range of genetically diverse populations in order to account for other neighboring and confounding selective events and the hitchhiking effect.
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Affiliation(s)
- Blandine Patillon
- Inserm UMRS-946, Genetic Variability and Human Diseases, Institut Universitaire d'Hématologie, Université Paris Diderot, Paris, France.
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91
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Zhao K, Ishida Y, Oleksyk TK, Winkler CA, Roca AL. Evidence for selection at HIV host susceptibility genes in a West Central African human population. BMC Evol Biol 2012; 12:237. [PMID: 23217182 PMCID: PMC3537702 DOI: 10.1186/1471-2148-12-237] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Accepted: 11/27/2012] [Indexed: 01/14/2023] Open
Abstract
Background HIV-1 derives from multiple independent transfers of simian immunodeficiency virus (SIV) strains from chimpanzees to human populations. We hypothesized that human populations in west central Africa may have been exposed to SIV prior to the pandemic, and that previous outbreaks may have selected for genetic resistance to immunodeficiency viruses. To test this hypothesis, we examined the genomes of Biaka Western Pygmies, who historically resided in communities within the geographic range of the central African chimpanzee subspecies (Pan troglodytes troglodytes) that carries strains of SIV ancestral to HIV-1. Results SNP genotypes of the Biaka were compared to those of African human populations who historically resided outside the range of P. t. troglodytes, including the Mbuti Eastern Pygmies. Genomic regions showing signatures of selection were compared to the genomic locations of genes reported to be associated with HIV infection or pathogenesis. In the Biaka, a strong signal of selection was detected at CUL5, which codes for a component of the vif-mediated APOBEC3 degradation pathway. A CUL5 allele protective against AIDS progression was fixed in the Biaka. A signal of selection was detected at TRIM5, which codes for an HIV post-entry restriction factor. A protective mis-sense mutation in TRIM5 had the highest frequency in Biaka compared to other African populations, as did a protective allele for APOBEC3G, which codes for an anti-HIV-1 restriction factor. Alleles protective against HIV-1 for APOBEC3H, CXCR6 and HLA-C were at higher frequencies in the Biaka than in the Mbuti. Biaka genomes showed a strong signal of selection at TSG101, an inhibitor of HIV-1 viral budding. Conclusions We found protective alleles or evidence for selection in the Biaka at a number of genes associated with HIV-1 infection or progression. Pygmies have also been reported to carry genotypes protective against HIV-1 for the genes CCR5 and CCL3L1. Our hypothesis that HIV-1 may have shaped the genomes of some human populations in West Central Africa appears to merit further investigation.
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Affiliation(s)
- Kai Zhao
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Il 61801, USA
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92
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Patterson N, Moorjani P, Luo Y, Mallick S, Rohland N, Zhan Y, Genschoreck T, Webster T, Reich D. Ancient admixture in human history. Genetics 2012; 192:1065-93. [PMID: 22960212 PMCID: PMC3522152 DOI: 10.1534/genetics.112.145037] [Citation(s) in RCA: 1434] [Impact Index Per Article: 119.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2012] [Accepted: 08/28/2012] [Indexed: 12/11/2022] Open
Abstract
Population mixture is an important process in biology. We present a suite of methods for learning about population mixtures, implemented in a software package called ADMIXTOOLS, that support formal tests for whether mixture occurred and make it possible to infer proportions and dates of mixture. We also describe the development of a new single nucleotide polymorphism (SNP) array consisting of 629,433 sites with clearly documented ascertainment that was specifically designed for population genetic analyses and that we genotyped in 934 individuals from 53 diverse populations. To illustrate the methods, we give a number of examples that provide new insights about the history of human admixture. The most striking finding is a clear signal of admixture into northern Europe, with one ancestral population related to present-day Basques and Sardinians and the other related to present-day populations of northeast Asia and the Americas. This likely reflects a history of admixture between Neolithic migrants and the indigenous Mesolithic population of Europe, consistent with recent analyses of ancient bones from Sweden and the sequencing of the genome of the Tyrolean "Iceman."
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Affiliation(s)
- Nick Patterson
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA.
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93
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Late Pleistocene climate change and the global expansion of anatomically modern humans. Proc Natl Acad Sci U S A 2012; 109:16089-94. [PMID: 22988099 DOI: 10.1073/pnas.1209494109] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The extent to which past climate change has dictated the pattern and timing of the out-of-Africa expansion by anatomically modern humans is currently unclear [Stewart JR, Stringer CB (2012) Science 335:1317-1321]. In particular, the incompleteness of the fossil record makes it difficult to quantify the effect of climate. Here, we take a different approach to this problem; rather than relying on the appearance of fossils or archaeological evidence to determine arrival times in different parts of the world, we use patterns of genetic variation in modern human populations to determine the plausibility of past demographic parameters. We develop a spatially explicit model of the expansion of anatomically modern humans and use climate reconstructions over the past 120 ky based on the Hadley Centre global climate model HadCM3 to quantify the possible effects of climate on human demography. The combinations of demographic parameters compatible with the current genetic makeup of worldwide populations indicate a clear effect of climate on past population densities. Our estimates of this effect, based on population genetics, capture the observed relationship between current climate and population density in modern hunter-gatherers worldwide, providing supporting evidence for the realism of our approach. Furthermore, although we did not use any archaeological and anthropological data to inform the model, the arrival times in different continents predicted by our model are also broadly consistent with the fossil and archaeological records. Our framework provides the most accurate spatiotemporal reconstruction of human demographic history available at present and will allow for a greater integration of genetic and archaeological evidence.
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94
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Walsh S, Liu F, Wollstein A, Kovatsi L, Ralf A, Kosiniak-Kamysz A, Branicki W, Kayser M. The HIrisPlex system for simultaneous prediction of hair and eye colour from DNA. Forensic Sci Int Genet 2012; 7:98-115. [PMID: 22917817 DOI: 10.1016/j.fsigen.2012.07.005] [Citation(s) in RCA: 249] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Revised: 06/25/2012] [Accepted: 07/23/2012] [Indexed: 02/03/2023]
Abstract
Recently, the field of predicting phenotypes of externally visible characteristics (EVCs) from DNA genotypes with the final aim of concentrating police investigations to find persons completely unknown to investigating authorities, also referred to as Forensic DNA Phenotyping (FDP), has started to become established in forensic biology. We previously developed and forensically validated the IrisPlex system for accurate prediction of blue and brown eye colour from DNA, and recently showed that all major hair colour categories are predictable from carefully selected DNA markers. Here, we introduce the newly developed HIrisPlex system, which is capable of simultaneously predicting both hair and eye colour from DNA. HIrisPlex consists of a single multiplex assay targeting 24 eye and hair colour predictive DNA variants including all 6 IrisPlex SNPs, as well as two prediction models, a newly developed model for hair colour categories and shade, and the previously developed IrisPlex model for eye colour. The HIrisPlex assay was designed to cope with low amounts of template DNA, as well as degraded DNA, and preliminary sensitivity testing revealed full DNA profiles down to 63pg input DNA. The power of the HIrisPlex system to predict hair colour was assessed in 1551 individuals from three different parts of Europe showing different hair colour frequencies. Using a 20% subset of individuals, while 80% were used for model building, the individual-based prediction accuracies employing a prediction-guided approach were 69.5% for blond, 78.5% for brown, 80% for red and 87.5% for black hair colour on average. Results from HIrisPlex analysis on worldwide DNA samples imply that HIrisPlex hair colour prediction is reliable independent of bio-geographic ancestry (similar to previous IrisPlex findings for eye colour). We furthermore demonstrate that it is possible to infer with a prediction accuracy of >86% if a brown-eyed, black-haired individual is of non-European (excluding regions nearby Europe) versus European (including nearby regions) bio-geographic origin solely from the strength of HIrisPlex eye and hair colour probabilities, which can provide extra intelligence for future forensic applications. The HIrisPlex system introduced here, including a single multiplex test assay, an interactive tool and prediction guide, and recommendations for reporting final outcomes, represents the first tool for simultaneously establishing categorical eye and hair colour of a person from DNA. The practical forensic application of the HIrisPlex system is expected to benefit cases where other avenues of investigation, including STR profiling, provide no leads on who the unknown crime scene sample donor or the unknown missing person might be.
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Affiliation(s)
- Susan Walsh
- Department of Forensic Molecular Biology, Erasmus MC University Medical Centre Rotterdam, The Netherlands
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95
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Genomic patterns of homozygosity in worldwide human populations. Am J Hum Genet 2012; 91:275-92. [PMID: 22883143 DOI: 10.1016/j.ajhg.2012.06.014] [Citation(s) in RCA: 303] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Revised: 05/09/2012] [Accepted: 06/25/2012] [Indexed: 12/20/2022] Open
Abstract
Genome-wide patterns of homozygosity runs and their variation across individuals provide a valuable and often untapped resource for studying human genetic diversity and evolutionary history. Using genotype data at 577,489 autosomal SNPs, we employed a likelihood-based approach to identify runs of homozygosity (ROH) in 1,839 individuals representing 64 worldwide populations, classifying them by length into three classes-short, intermediate, and long-with a model-based clustering algorithm. For each class, the number and total length of ROH per individual show considerable variation across individuals and populations. The total lengths of short and intermediate ROH per individual increase with the distance of a population from East Africa, in agreement with similar patterns previously observed for locus-wise homozygosity and linkage disequilibrium. By contrast, total lengths of long ROH show large interindividual variations that probably reflect recent inbreeding patterns, with higher values occurring more often in populations with known high frequencies of consanguineous unions. Across the genome, distributions of ROH are not uniform, and they have distinctive continental patterns. ROH frequencies across the genome are correlated with local genomic variables such as recombination rate, as well as with signals of recent positive selection. In addition, long ROH are more frequent in genomic regions harboring genes associated with autosomal-dominant diseases than in regions not implicated in Mendelian diseases. These results provide insight into the way in which homozygosity patterns are produced, and they generate baseline homozygosity patterns that can be used to aid homozygosity mapping of genes associated with recessive diseases.
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96
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Using identity by descent estimation with dense genotype data to detect positive selection. Eur J Hum Genet 2012; 21:205-11. [PMID: 22781100 DOI: 10.1038/ejhg.2012.148] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Identification of genomic loci and segments that are identical by descent (IBD) allows inference on problems such as relatedness detection, IBD disease mapping, heritability estimation and detection of recent or ongoing positive selection. Here, employing a novel statistical method, we use IBD to find signals of selection in the Maasai from Kinyawa, Kenya (MKK). In doing so, we demonstrate the advantage of statistical tools that can probabilistically estimate IBD sharing without having to thin genotype data because of linkage disequilibrium (LD), and that allow for both inbreeding and more than one allele to be shared IBD. We use our novel method, GIBDLD, to estimate IBD sharing between all pairs of individuals at all genotyped SNPs in the MKK, and, by looking for genomic regions showing excess IBD sharing in unrelated pairs, find loci that are known to have undergone recent selection (eg, the LCT gene and the HLA region) as well as many novel loci. Intriguingly, those loci that show the highest amount of excess IBD, with the exception of HLA, also show a substantial number of unrelated pairs sharing all four of their alleles IBD. In contrast to other IBD detection methods, GIBDLD provides accurate probabilistic estimates at each locus for all nine possible IBD sharing states between a pair of individuals, thus allowing for consanguinity, while also modeling LD, thus removing the need to thin SNPs. These characteristics will prove valuable for those doing genetic studies, and estimating IBD, in the wide variety of human populations.
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Dall'Olio GM, Laayouni H, Luisi P, Sikora M, Montanucci L, Bertranpetit J. Distribution of events of positive selection and population differentiation in a metabolic pathway: the case of asparagine N-glycosylation. BMC Evol Biol 2012; 12:98. [PMID: 22731960 PMCID: PMC3426484 DOI: 10.1186/1471-2148-12-98] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2011] [Accepted: 06/25/2012] [Indexed: 01/11/2023] Open
Abstract
Background Asparagine N-Glycosylation is one of the most important forms of protein post-translational modification in eukaryotes. This metabolic pathway can be subdivided into two parts: an upstream sub-pathway required for achieving proper folding for most of the proteins synthesized in the secretory pathway, and a downstream sub-pathway required to give variability to trans-membrane proteins, and involved in adaptation to the environment and innate immunity. Here we analyze the nucleotide variability of the genes of this pathway in human populations, identifying which genes show greater population differentiation and which genes show signatures of recent positive selection. We also compare how these signals are distributed between the upstream and the downstream parts of the pathway, with the aim of exploring how forces of population differentiation and positive selection vary among genes involved in the same metabolic pathway but subject to different functional constraints. Results Our results show that genes in the downstream part of the pathway are more likely to show a signature of population differentiation, while events of positive selection are equally distributed among the two parts of the pathway. Moreover, events of positive selection are frequent on genes that are known to be at bifurcation points, and that are identified as being in key position by a network-level analysis such as MGAT3 and GCS1. Conclusions These findings indicate that the upstream part of the Asparagine N-Glycosylation pathway has lower diversity among populations, while the downstream part is freer to tolerate diversity among populations. Moreover, the distribution of signatures of population differentiation and positive selection can change between parts of a pathway, especially between parts that are exposed to different functional constraints. Our results support the hypothesis that genes involved in constitutive processes can be expected to show lower population differentiation, while genes involved in traits related to the environment should show higher variability. Taken together, this work broadens our knowledge on how events of population differentiation and of positive selection are distributed among different parts of a metabolic pathway.
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Affiliation(s)
- Giovanni Marco Dall'Olio
- IBE, Institut de Biologia Evolutiva (UPF-CSIC), Parc de Recerca Biomèdica de Barcelona (PRBB), Dr, Aiguader, 88, 08003, Barcelona, Catalonia, Spain
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Pemberton TJ, Li FY, Hanson EK, Mehta NU, Choi S, Ballantyne J, Belmont JW, Rosenberg NA, Tyler-Smith C, Patel PI. Impact of restricted marital practices on genetic variation in an endogamous Gujarati group. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2012; 149:92-103. [PMID: 22729696 DOI: 10.1002/ajpa.22101] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2011] [Accepted: 05/07/2012] [Indexed: 12/15/2022]
Abstract
Recent studies have examined the influence on patterns of human genetic variation of a variety of cultural practices. In India, centuries-old marriage customs have introduced extensive social structuring into the contemporary population, potentially with significant consequences for genetic variation. Social stratification in India is evident as social classes that are defined by endogamous groups known as castes. Within a caste, there exist endogamous groups known as gols (marriage circles), each of which comprises a small number of exogamous gotra (lineages). Thus, while consanguinity is strictly avoided and some randomness in mate selection occurs within the gol, gene flow is limited with groups outside the gol. Gujarati Patels practice this form of "exogamic endogamy." We have analyzed genetic variation in one such group of Gujarati Patels, the Chha Gaam Patels (CGP), who comprise individuals from six villages. Population structure analysis of 1,200 autosomal loci offers support for the existence of distinctive multilocus genotypes in the CGP with respect to both non-Gujaratis and other Gujaratis, and indicates that CGP individuals are genetically very similar. Analysis of Y-chromosomal and mitochondrial haplotypes provides support for both patrilocal and patrilineal practices within the gol, and a low-level of female gene flow into the gol. Our study illustrates how the practice of gol endogamy has introduced fine-scale genetic structure into the population of India, and contributes more generally to an understanding of the way in which marriage practices affect patterns of genetic variation.
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Affiliation(s)
- Trevor J Pemberton
- Institute for Genetic Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA.
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Machado LR, Hardwick RJ, Bowdrey J, Bogle H, Knowles TJ, Sironi M, Hollox EJ. Evolutionary history of copy-number-variable locus for the low-affinity Fcγ receptor: mutation rate, autoimmune disease, and the legacy of helminth infection. Am J Hum Genet 2012; 90:973-85. [PMID: 22608500 DOI: 10.1016/j.ajhg.2012.04.018] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Revised: 03/22/2012] [Accepted: 04/10/2012] [Indexed: 11/18/2022] Open
Abstract
Both sequence variation and copy-number variation (CNV) of the genes encoding receptors for immunoglobulin G (Fcγ receptors) have been genetically and functionally associated with a number of autoimmune diseases. However, the molecular nature and evolutionary context of this variation is unknown. Here, we describe the structure of the CNV, estimate its mutation rate and diversity, and place it in the context of the known functional alloantigen variation of these genes. Deletion of Fcγ receptor IIIB, associated with systemic lupus erythematosus, is a result of independent nonallelic homologous recombination events with a frequency of approximately 0.1%. We also show that pathogen diversity, in particular helminth diversity, has played a critical role in shaping the functional variation at these genes both between mammalian species and between human populations. Positively selected amino acids are involved in the interaction with IgG and include some amino acids that are known polymorphic alloantigens in humans. This supports a genetic contribution to the hygiene hypothesis, which states that past evolution in the context of helminth diversity has left humans with an array of susceptibility alleles for autoimmune disease in the context of a helminth-free environment. This approach shows the link between pathogens and autoimmune disease at the genetic level and provides a strategy for interrogating the genetic variation underlying autoimmune-disease risk and infectious-disease susceptibility.
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Rosenberg NA. A population-genetic perspective on the similarities and differences among worldwide human populations. Hum Biol 2012; 83:659-84. [PMID: 22276967 DOI: 10.3378/027.083.0601] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Recent studies have produced a variety of advances in the investigation of genetic similarities and differences among human populations. Here, I pose a series of questions about human population-genetic similarities and differences, and I then answer these questions by numerical computation with a single shared population-genetic data set. The collection of answers obtained provides an introductory perspective for understanding key results on the features of worldwide human genetic variation.
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Affiliation(s)
- Noah A Rosenberg
- Department of Biology, Stanford University, Stanford, CA 94305, USA.
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