151
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Zhang M, Fu Q. Human evolutionary history in Eastern Eurasia using insights from ancient DNA. Curr Opin Genet Dev 2020; 62:78-84. [PMID: 32688244 DOI: 10.1016/j.gde.2020.06.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 05/22/2020] [Accepted: 06/17/2020] [Indexed: 12/12/2022]
Abstract
Advances in ancient genomics are providing unprecedented insight into modern human history. Here, we review recent progress uncovering prehistoric populations in Eastern Eurasia based on ancient DNA studies from the Upper Pleistocene to the Holocene. Many ancient populations existed during the Upper Pleistocene of Eastern Eurasia-some with no substantial ancestry related to present-day populations, some with an affinity to East Asians, and some who contributed to Native Americans. By the Holocene, the genetic composition across East Asia greatly shifted, with several substantial migrations. Three are southward: an increase in northern East Asian-related ancestry in southern East Asia; movement of East Asian-related ancestry into Southeast Asia, mixing with Basal Asian ancestry; and movement of southern East Asian ancestry to islands of Southeast Asia and the Southwest Pacific through the expansion of Austronesians. We anticipate that additional ancient DNA will magnify our understanding of the genetic history in Eastern Eurasia.
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Affiliation(s)
- Ming Zhang
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China; Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Qiaomei Fu
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China; Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China.
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152
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Robust genome-wide ancestry inference for heterogeneous datasets: illustrated using the 1,000 genome project with 3D facial images. Sci Rep 2020; 10:11850. [PMID: 32678112 PMCID: PMC7367291 DOI: 10.1038/s41598-020-68259-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Accepted: 06/19/2020] [Indexed: 11/17/2022] Open
Abstract
Estimates of individual-level genomic ancestry are routinely used in human genetics, and related fields. The analysis of population structure and genomic ancestry can yield insights in terms of modern and ancient populations, allowing us to address questions regarding admixture, and the numbers and identities of the parental source populations. Unrecognized population structure is also an important confounder to correct for in genome-wide association studies. However, it remains challenging to work with heterogeneous datasets from multiple studies collected by different laboratories with diverse genotyping and imputation protocols. This work presents a new approach and an accompanying open-source toolbox that facilitates a robust integrative analysis for population structure and genomic ancestry estimates for heterogeneous datasets. We show robustness against individual outliers and different protocols for the projection of new samples into a reference ancestry space, and the ability to reveal and adjust for population structure in a simulated case–control admixed population. Given that visually evident and easily recognizable patterns of human facial characteristics co-vary with genomic ancestry, and based on the integration of three different sources of genome data, we generate average 3D faces to illustrate genomic ancestry variations within the 1,000 Genome project and for eight ancient-DNA profiles, respectively.
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153
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Hallast P, Agdzhoyan A, Balanovsky O, Xue Y, Tyler-Smith C. A Southeast Asian origin for present-day non-African human Y chromosomes. Hum Genet 2020; 140:299-307. [PMID: 32666166 PMCID: PMC7864842 DOI: 10.1007/s00439-020-02204-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 07/02/2020] [Indexed: 12/17/2022]
Abstract
The genomes of present-day humans outside Africa originated almost entirely from a single out-migration ~ 50,000–70,000 years ago, followed by mixture with Neanderthals contributing ~ 2% to all non-Africans. However, the details of this initial migration remain poorly understood because no ancient DNA analyses are available from this key time period, and interpretation of present-day autosomal data is complicated due to subsequent population movements/reshaping. One locus, however, does retain male-specific information from this early period: the Y chromosome, where a detailed calibrated phylogeny has been constructed. Three present-day Y lineages were carried by the initial migration: the rare haplogroup D, the moderately rare C, and the very common FT lineage which now dominates most non-African populations. Here, we show that phylogenetic analyses of haplogroup C, D and FT sequences, including very rare deep-rooting lineages, together with phylogeographic analyses of ancient and present-day non-African Y chromosomes, all point to East/Southeast Asia as the origin 50,000–55,000 years ago of all known surviving non-African male lineages (apart from recent migrants). This observation contrasts with the expectation of a West Eurasian origin predicted by a simple model of expansion from a source near Africa, and can be interpreted as resulting from extensive genetic drift in the initial population or replacement of early western Y lineages from the east, thus informing and constraining models of the initial expansion.
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Affiliation(s)
- Pille Hallast
- Institute of Biomedicine and Translational Medicine, University of Tartu, 50411, Tartu, Estonia. .,Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
| | - Anastasia Agdzhoyan
- Vavilov Institute of General Genetics, Moscow, 119991, Russia.,Research Centre for Medical Genetics, Moscow, 115522, Russia
| | - Oleg Balanovsky
- Vavilov Institute of General Genetics, Moscow, 119991, Russia.,Research Centre for Medical Genetics, Moscow, 115522, Russia.,Biobank of North Eurasia, Moscow, 115201, Russia
| | - Yali Xue
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Chris Tyler-Smith
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
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154
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Pal G, Di L, Orunmuyi A, Olapade-Olaopa EO, Qiu W, Ogunwobi OO. Population Differentiation at the PVT1 Gene Locus: Implications for Prostate Cancer. G3 (BETHESDA, MD.) 2020; 10:2257-2264. [PMID: 32358016 PMCID: PMC7341130 DOI: 10.1534/g3.120.401291] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Accepted: 04/29/2020] [Indexed: 12/14/2022]
Abstract
Genetic variation in susceptibility to complex diseases, such as cancer, is well-established. Enrichment of disease associated alleles in specific populations could have implications for disease incidence and prevalence. Prostate cancer (PCa) is a disease with well-established higher incidence, prevalence, and worse outcomes among men of African ancestry in comparison to other populations. PCa is a multi-factorial, complex disease, but the exact mechanisms for its development and progression are unclear. The gene desert located on chromosome 8q24 is associated with aggressiveness of PCa. Interestingly, the non-protein coding gene locus Plasmacytoma Variant Translocation (PVT1) is present at chromosome 8q24 and is overexpressed in PCa. PVT1 gives rise to multiple transcripts with potentially different molecular and cellular functions. In an analysis of the PVT1 locus using data from the 1000 Genomes Project, we found the chromosomal region spanning PVT1 exons 4A and 4B to be highly differentiated between African and non-African populations. We further investigated levels of gene expression of PVT1 exons 4A and 4B and observed significant overexpression of these exons in PCa tissues relative to benign prostatic hyperplasia and to normal prostate tissues obtained from men of African ancestry. These results indicate that PVT1 exons 4A and 4B may have clinical implications in PCa a conclusion supported by the observation that transient and stable overexpression of PVT1 exons 4A and 4B significantly induce greater prostate epithelial cell migration and proliferation. We anticipate that further exploration of the role of PVT1 exons 4A and 4B may lead to the development of diagnostic, therapeutic, and other clinical applications in PCa.
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Affiliation(s)
- Gargi Pal
- Department of Biological Sciences, Hunter College of The City University of New York, NY
| | - Lia Di
- Department of Biological Sciences, Hunter College of The City University of New York, NY
| | | | | | - Weigang Qiu
- Department of Biological Sciences, Hunter College of The City University of New York, NY
| | - Olorunseun O Ogunwobi
- Department of Biological Sciences, Hunter College of The City University of New York, NY,
- Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY
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155
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Jiao X, Yang Z. Defining Species When There is Gene Flow. Syst Biol 2020; 70:108-119. [PMID: 32617579 DOI: 10.1093/sysbio/syaa052] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 06/23/2020] [Accepted: 06/23/2020] [Indexed: 12/20/2022] Open
Abstract
Whatever one's definition of species, it is generally expected that individuals of the same species should be genetically more similar to each other than they are to individuals of another species. Here, we show that in the presence of cross-species gene flow, this expectation may be incorrect. We use the multispecies coalescent model with continuous-time migration or episodic introgression to study the impact of gene flow on genetic differences within and between species and highlight a surprising but plausible scenario in which different population sizes and asymmetrical migration rates cause a genetic sequence to be on average more closely related to a sequence from another species than to a sequence from the same species. Our results highlight the extraordinary impact that even a small amount of gene flow may have on the genetic history of the species. We suggest that contrasting long-term migration rate and short-term hybridization rate, both of which can be estimated using genetic data, may be a powerful approach to detecting the presence of reproductive barriers and to define species boundaries.[Gene flow; introgression; migration; multispecies coalescent; species concept; species delimitation.].
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Affiliation(s)
- Xiyun Jiao
- Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Ziheng Yang
- Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
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156
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Kist NC, Lambert B, Campbell S, Katzourakis A, Lunn D, Lemey P, Iversen AKN. HIV-1 p24Gag adaptation to modern and archaic HLA-allele frequency differences in ethnic groups contributes to viral subtype diversification. Virus Evol 2020; 6:veaa085. [PMID: 33343925 PMCID: PMC7733611 DOI: 10.1093/ve/veaa085] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Pathogen-driven selection and past interbreeding with archaic human lineages have resulted in differences in human leukocyte antigen (HLA)-allele frequencies between modern human populations. Whether or not this variation affects pathogen subtype diversification is unknown. Here we show a strong positive correlation between ethnic diversity in African countries and both human immunodeficiency virus (HIV)-1 p24gag and subtype diversity. We demonstrate that ethnic HLA-allele differences between populations have influenced HIV-1 subtype diversification as the virus adapted to escape common antiviral immune responses. The evolution of HIV Subtype B (HIV-B), which does not appear to be indigenous to Africa, is strongly affected by immune responses associated with Eurasian HLA variants acquired through adaptive introgression from Neanderthals and Denisovans. Furthermore, we show that the increasing and disproportionate number of HIV-infections among African Americans in the USA drive HIV-B evolution towards an Africa-centric HIV-1 state. Similar adaptation of other pathogens to HLA variants common in affected populations is likely.
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Affiliation(s)
- Nicolaas C Kist
- Division of Clinical Neurology, Nuffield Department of Clinical Neurosciences, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
| | - Ben Lambert
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
- Department of Infectious Disease Epidemiology, School of Public Health, Faculty of Medicine, Imperial College London, Medical School Building St Mary’s Campus, Norfolk Place, London W2 1PG, UK
| | - Samuel Campbell
- Division of Clinical Neurology, Nuffield Department of Clinical Neurosciences, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
| | - Aris Katzourakis
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
| | - Daniel Lunn
- Department of Statistics, University of Oxford, St Giles’, Oxford OX1 3LB, UK
| | - Philippe Lemey
- Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven - University of Leuven, Leuven B-3000, Belgium
| | - Astrid K N Iversen
- Division of Clinical Neurology, Nuffield Department of Clinical Neurosciences, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
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157
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Shibata D. Visualizing Human Colorectal Cancer Intratumor Heterogeneity with Phylogeography. iScience 2020; 23:101304. [PMID: 32623333 PMCID: PMC7334596 DOI: 10.1016/j.isci.2020.101304] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 06/02/2020] [Accepted: 06/18/2020] [Indexed: 12/28/2022] Open
Abstract
Phylogeography combines ancestry with location and can be translated to intratumor heterogeneity (ITH) to visualize how tumors spread. ITH is common in human tumors, with many genetic and phenotypic differences between regions. The roles of ITH in progression are uncertain because many subclones lack discernable driver mutations. ITH can be visualized by mapping mutations onto microscopic sections, where subclones are directly associated with phenotypes, especially the deeper areas with the more invasive cells that confer worst clinical outcomes. Instead of a stepwise hierarchy where subclones segregate by phenotype with later branching subclones in more invasive areas, multiple subclones share superficial and invasive phenotype and are jigsaw arrayed in vertical columns. Phylogeography shows that both early and late subclones extend from the surface to the invasive front, suggesting that founder cells start with phenotypic plasticity and essentially all the drivers necessary to rapidly grow into large invasive tumors.
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Affiliation(s)
- Darryl Shibata
- Department of Pathology, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA.
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158
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Rausell A, Luo Y, Lopez M, Seeleuthner Y, Rapaport F, Favier A, Stenson PD, Cooper DN, Patin E, Casanova JL, Quintana-Murci L, Abel L. Common homozygosity for predicted loss-of-function variants reveals both redundant and advantageous effects of dispensable human genes. Proc Natl Acad Sci U S A 2020; 117:13626-13636. [PMID: 32487729 PMCID: PMC7306792 DOI: 10.1073/pnas.1917993117] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Humans homozygous or hemizygous for variants predicted to cause a loss of function (LoF) of the corresponding protein do not necessarily present with overt clinical phenotypes. We report here 190 autosomal genes with 207 predicted LoF variants, for which the frequency of homozygous individuals exceeds 1% in at least one human population from five major ancestry groups. No such genes were identified on the X and Y chromosomes. Manual curation revealed that 28 variants (15%) had been misannotated as LoF. Of the 179 remaining variants in 166 genes, only 11 alleles in 11 genes had previously been confirmed experimentally to be LoF. The set of 166 dispensable genes was enriched in olfactory receptor genes (41 genes). The 41 dispensable olfactory receptor genes displayed a relaxation of selective constraints similar to that observed for other olfactory receptor genes. The 125 dispensable nonolfactory receptor genes also displayed a relaxation of selective constraints consistent with greater redundancy. Sixty-two of these 125 genes were found to be dispensable in at least three human populations, suggesting possible evolution toward pseudogenes. Of the 179 LoF variants, 68 could be tested for two neutrality statistics, and 8 displayed robust signals of positive selection. These latter variants included a known FUT2 variant that confers resistance to intestinal viruses, and an APOL3 variant involved in resistance to parasitic infections. Overall, the identification of 166 genes for which a sizeable proportion of humans are homozygous for predicted LoF alleles reveals both redundancies and advantages of such deficiencies for human survival.
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Affiliation(s)
- Antonio Rausell
- Clinical Bioinformatics Laboratory, INSERM UMR1163, Necker Hospital for Sick Children, 75015 Paris, France;
- University of Paris, Imagine Institute, 75015 Paris, France
| | - Yufei Luo
- Clinical Bioinformatics Laboratory, INSERM UMR1163, Necker Hospital for Sick Children, 75015 Paris, France
- University of Paris, Imagine Institute, 75015 Paris, France
| | - Marie Lopez
- Human Evolutionary Genetics Unit, Institut Pasteur, UMR2000, CNRS, Paris 75015, France
| | - Yoann Seeleuthner
- University of Paris, Imagine Institute, 75015 Paris, France
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Necker Hospital for Sick Children, 75015 Paris, France
| | - Franck Rapaport
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065
| | - Antoine Favier
- Clinical Bioinformatics Laboratory, INSERM UMR1163, Necker Hospital for Sick Children, 75015 Paris, France
- University of Paris, Imagine Institute, 75015 Paris, France
| | - Peter D Stenson
- Institute of Medical Genetics, School of Medicine, Cardiff University, CF14 4XN Cardiff, United Kingdom
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, CF14 4XN Cardiff, United Kingdom
| | - Etienne Patin
- Human Evolutionary Genetics Unit, Institut Pasteur, UMR2000, CNRS, Paris 75015, France
| | - Jean-Laurent Casanova
- University of Paris, Imagine Institute, 75015 Paris, France;
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Necker Hospital for Sick Children, 75015 Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065
- Howard Hughes Medical Institute, New York, NY 10065
- Pediatric Hematology and Immunology Unit, Necker Hospital for Sick Children, 75015 Paris, France
| | - Lluis Quintana-Murci
- Human Evolutionary Genetics Unit, Institut Pasteur, UMR2000, CNRS, Paris 75015, France
- Human Genomics and Evolution, Collège de France, Paris 75005, France
| | - Laurent Abel
- University of Paris, Imagine Institute, 75015 Paris, France;
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Necker Hospital for Sick Children, 75015 Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065
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159
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Tay GK, Henschel A, Daw Elbait G, Al Safar HS. Genetic Diversity and Low Stratification of the Population of the United Arab Emirates. Front Genet 2020; 11:608. [PMID: 32595703 PMCID: PMC7304494 DOI: 10.3389/fgene.2020.00608] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Accepted: 05/19/2020] [Indexed: 01/09/2023] Open
Abstract
With high consanguinity rates on the Arabian Peninsula, it would not have been unexpected if the population of the United Arab Emirates (UAE) was shown to be relatively homogenous. However, this study of 1000 UAE nationals provided a contrasting perspective, one of a relatively heterogeneous population. Located at the apex of Europe, Asia, and Africa, the observed diversity could be explained by a plethora of migration patterns since the first Out-of-Africa movement. A strategy to explore the extent of genetic variation of the population of the UAE is presented. The first step involved a comprehensive population stratification study that was instructive for subsequent whole genome sequencing (WGS) of suitable representatives (which is described elsewhere). When these UAE data were compared to previous smaller studies from the region, the findings were consistent with a population that is a diverse and admixed group of people. However, rather than sharp and distinctive clusters, cluster analysis reveals low levels of stratification throughout the population. UAE emirates exhibit high within-Emirate-distance/among-Emirate distance ratios. Supervised admixture analysis showed a continuous gradient of ancestral populations, suggesting that admixture on the south eastern tip of the Arabian Peninsula occurred gradually. When visualized using a unique technique that combined admixture ratios and principal component analysis (PCA), unappreciated diversity was revealed while mitigating projection bias of conventional PCA. We observe low population stratification in the UAE in terms of homozygosity versus separation cluster coefficients. This holds for the UAE in a global context as well as for isolated cluster analysis of the Emirati birthplaces. However, the subtle clustering observed in the Emirates reflects geographic proximity and historic migration events. The analytical strategy used here highlights the complementary nature of data from genotype array and WGS for anthropological studies. Specifically, genotype array data were instructive to select representative subjects for WGS. Furthermore, from the 2.3 million allele frequencies obtained from genotype arrays, we identified 46,481 loci with allele frequencies that were significantly different with respect to other world populations. This comparison of allele frequencies facilitates variant prioritization in common diseases. In addition, these loci bear great potential as biomarkers in anthropological and forensic studies.
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Affiliation(s)
- Guan K Tay
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.,Department of Biomedical Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.,Faculty of Health and Medical Sciences, UWA Medical School, The University of Western Australia, Crawley, WA, Australia.,School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia
| | - Andreas Henschel
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.,Department of Computer Science, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Gihan Daw Elbait
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Habiba S Al Safar
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.,Department of Biomedical Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.,Department of Genetics and Molecular Biology, College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
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160
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Yan SM, McCoy RC. Archaic hominin genomics provides a window into gene expression evolution. Curr Opin Genet Dev 2020; 62:44-49. [PMID: 32615344 PMCID: PMC7483639 DOI: 10.1016/j.gde.2020.05.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 05/06/2020] [Accepted: 05/08/2020] [Indexed: 02/08/2023]
Abstract
Differences in gene expression are thought to account for most phenotypic differences within and between species. Consequently, gene expression is a powerful lens through which to study divergence between modern humans and our closest evolutionary relatives, the Neanderthals and Denisovans. Such insights complement biological knowledge gleaned from the fossil record, while also revealing general features of the mode and tempo of regulatory evolution. Because of the degradation of ancient RNA, gene expression profiles of archaic hominins must be studied by indirect means. As such, conclusions drawn from these studies are often laden with assumptions about the genetic architecture of gene expression, the complexity of which is increasingly apparent. Despite these challenges, rapid technical and conceptual advances in the fields of ancient genomics, functional genomics, statistical genomics, and genome engineering are revolutionizing understanding of hominin gene expression evolution.
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Affiliation(s)
- Stephanie M Yan
- Department of Biology, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Rajiv C McCoy
- Department of Biology, Johns Hopkins University, Baltimore, MD, 21218, USA.
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161
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Jermiin LS, Catullo RA, Holland BR. A new phylogenetic protocol: dealing with model misspecification and confirmation bias in molecular phylogenetics. NAR Genom Bioinform 2020; 2:lqaa041. [PMID: 33575594 PMCID: PMC7671319 DOI: 10.1093/nargab/lqaa041] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 05/18/2020] [Accepted: 06/04/2020] [Indexed: 12/15/2022] Open
Abstract
Molecular phylogenetics plays a key role in comparative genomics and has increasingly significant impacts on science, industry, government, public health and society. In this paper, we posit that the current phylogenetic protocol is missing two critical steps, and that their absence allows model misspecification and confirmation bias to unduly influence phylogenetic estimates. Based on the potential offered by well-established but under-used procedures, such as assessment of phylogenetic assumptions and tests of goodness of fit, we introduce a new phylogenetic protocol that will reduce confirmation bias and increase the accuracy of phylogenetic estimates.
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Affiliation(s)
- Lars S Jermiin
- CSIRO Land & Water, Canberra, ACT 2601, Australia
- Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
- School of Biology & Environment Science, University College Dublin, Belfield, Dublin 4, Ireland
- Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Renee A Catullo
- CSIRO Land & Water, Canberra, ACT 2601, Australia
- Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
- School of Science and Health & Hawkesbury Institute of the Environment, Western Sydney University, Penrith, NSW 2751, Australia
| | - Barbara R Holland
- School of Natural Sciences, University of Tasmania, Hobart, TAS 7001, Australia
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162
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McQuillan MA, Zhang C, Tishkoff SA, Platt A. The importance of including ethnically diverse populations in studies of quantitative trait evolution. Curr Opin Genet Dev 2020; 62:30-35. [PMID: 32604012 PMCID: PMC7942184 DOI: 10.1016/j.gde.2020.05.037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 05/26/2020] [Accepted: 05/28/2020] [Indexed: 10/24/2022]
Abstract
For many traits, human variation is less a matter of categorical differences than quantitative variation, such as height, where individuals fall along a continuum from short to tall. Most recent studies utilize large population-based samples with whole-genome sequences to study the evolution of these traits and have made significant progress implementing a broad spectrum of techniques. However, relatively few studies of quantitative trait evolution include ethnically diverse populations, which often harbor the highest levels of genetic and phenotypic diversity. Thus, our ability to draw inferences about quantitative trait adaptation has been limited. Here, we review recent studies examining human quantitative trait adaptation, and argue that including ethnically diverse populations, particularly from Africa, will be especially informative for our understanding of how humans adapt to the world around them.
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Affiliation(s)
- Michael A McQuillan
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Chao Zhang
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sarah A Tishkoff
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Alexander Platt
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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163
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Vicente M, Schlebusch CM. African population history: an ancient DNA perspective. Curr Opin Genet Dev 2020; 62:8-15. [DOI: 10.1016/j.gde.2020.05.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 05/04/2020] [Accepted: 05/06/2020] [Indexed: 11/30/2022]
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164
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Esteller-Cucala P, Maceda I, Børglum AD, Demontis D, Faraone SV, Cormand B, Lao O. Genomic analysis of the natural history of attention-deficit/hyperactivity disorder using Neanderthal and ancient Homo sapiens samples. Sci Rep 2020; 10:8622. [PMID: 32451437 PMCID: PMC7248073 DOI: 10.1038/s41598-020-65322-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 04/24/2020] [Indexed: 11/18/2022] Open
Abstract
Attention-deficit/hyperactivity disorder (ADHD) is an impairing neurodevelopmental condition highly prevalent in current populations. Several hypotheses have been proposed to explain this paradox, mainly in the context of the Paleolithic versus Neolithic cultural shift but especially within the framework of the mismatch theory. This theory elaborates on how a particular trait once favoured in an ancient environment might become maladaptive upon environmental changes. However, given the lack of genomic data available for ADHD, these theories have not been empirically tested. We took advantage of the largest GWAS meta-analysis available for this disorder consisting of over 20,000 individuals diagnosed with ADHD and 35,000 controls, to assess the evolution of ADHD-associated alleles in European populations using archaic, ancient and modern human samples. We also included Approximate Bayesian computation coupled with deep learning analyses and singleton density scores to detect human adaptation. Our analyses indicate that ADHD-associated alleles are enriched in loss of function intolerant genes, supporting the role of selective pressures in this early-onset phenotype. Furthermore, we observed that the frequency of variants associated with ADHD has steadily decreased since Paleolithic times, particularly in Paleolithic European populations compared to samples from the Neolithic Fertile Crescent. We demonstrate this trend cannot be explained by African admixture nor Neanderthal introgression, since introgressed Neanderthal alleles are enriched in ADHD risk variants. All analyses performed support the presence of long-standing selective pressures acting against ADHD-associated alleles until recent times. Overall, our results are compatible with the mismatch theory for ADHD but suggest a much older time frame for the evolution of ADHD-associated alleles compared to previous hypotheses.
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Affiliation(s)
- Paula Esteller-Cucala
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Institut de Biologia Evolutiva (UPF-CSIC), Barcelona, Spain
| | - Iago Maceda
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Anders D Børglum
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Centre for Integrative Sequencing, iSEQ, and Aarhus Genome Centre, Aarhus, Denmark
- Department of Biomedicine - Human Genetics, Aarhus University, Aarhus, Denmark
| | - Ditte Demontis
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Centre for Integrative Sequencing, iSEQ, and Aarhus Genome Centre, Aarhus, Denmark
- Department of Biomedicine - Human Genetics, Aarhus University, Aarhus, Denmark
| | - Stephen V Faraone
- Departments of Psychiatry and of Neuroscience and Physiology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Bru Cormand
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain.
- Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Spain.
- Institut de Recerca Sant Joan de Déu (IR-SJD), Esplugues de Llobregat, Spain.
| | - Oscar Lao
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.
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165
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Murga-Moreno J, Coronado-Zamora M, Bodelón A, Barbadilla A, Casillas S. PopHumanScan: the online catalog of human genome adaptation. Nucleic Acids Res 2020; 47:D1080-D1089. [PMID: 30335169 PMCID: PMC6323894 DOI: 10.1093/nar/gky959] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 10/04/2018] [Indexed: 12/20/2022] Open
Abstract
Since the migrations that led humans to colonize Earth, our species has faced frequent adaptive challenges that have left signatures in the landscape of genetic variation and that we can identify in our today’s genomes. Here, we (i) perform an outlier approach on eight different population genetic statistics for 22 non-admixed human populations of the Phase III of the 1000 Genomes Project to detect selective sweeps at different historical ages, as well as events of recurrent positive selection in the human lineage; and (ii) create PopHumanScan, an online catalog that compiles and annotates all candidate regions under selection to facilitate their validation and thoroughly analysis. Well-known examples of human genetic adaptation published elsewhere are included in the catalog, as well as hundreds of other attractive candidates that will require further investigation. Designed as a collaborative database, PopHumanScan aims to become a central repository to share information, guide future studies and help advance our understanding of how selection has modeled our genomes as a response to changes in the environment or lifestyle of human populations. PopHumanScan is open and freely available at https://pophumanscan.uab.cat.
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Affiliation(s)
- Jesús Murga-Moreno
- Institut de Biotecnologia i de Biomedicina and Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Marta Coronado-Zamora
- Institut de Biotecnologia i de Biomedicina and Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Alejandra Bodelón
- Institut de Biotecnologia i de Biomedicina and Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Antonio Barbadilla
- Institut de Biotecnologia i de Biomedicina and Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Sònia Casillas
- Institut de Biotecnologia i de Biomedicina and Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
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166
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Li M, DeRosa KL, Mann H, Spathis R, Roome A, Castellanos D, Gowen K, de Smet TS, Echard J, Casey K, Shamoon-Pour M, Garruto RM, Lum K. Recent kuru-induced female gene flow disrupted the coevolution of genes and languages in the Papua New Guinea highlands. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2020; 172:87-98. [PMID: 32150286 DOI: 10.1002/ajpa.24047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 01/06/2020] [Accepted: 02/28/2020] [Indexed: 11/07/2022]
Abstract
OBJECTIVES The island of New Guinea was settled by modern human over 50,000 years ago, and is currently characterized by a complex landscape and contains one-seventh of the world's languages. The Eastern Highlands of New Guinea were also the home to the devastating prion disease called kuru that primarily affected Fore-speaking populations, with some 68% of cases involving adult females. We characterized the mitochondrial DNA (mtDNA) diversity of highlanders from Papua New Guinea (PNG) to: (a) gain insight into the coevolution of genes and languages in situ over mountainous landscapes; and (b) evaluate the recent influence of kuru mortality on the pattern of female gene flow. MATERIALS AND METHODS We sequenced the mtDNA hypervariable segment 1 of 870 individuals from the Eastern and Southern Highlands of PNG using serums collected in the 1950s to 1960s. These highlanders were selected from villages representing 15 linguistic groups within the Trans-New Guinea phylum. Genetic, linguistic, and geographic distances were calculated separately and correlations among those distance matrices were assessed using the Mantel test. RESULTS Geographic, genetic, and linguistic patterns were independently correlated with each other (p < .05). Increased mtDNA diversity in kuru-affected populations and low Fst estimates between kuru-affected linguistic groups were observed. DISCUSSION In general, the genetic structure among the Highland populations was shaped by both geography and language, and language is a good predictor of mtDNA affinity in the PNG Highlands. High kuru female mortality increased female gene flow locally, disrupting coevolutionary pattern among genes, languages, and geography.
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Affiliation(s)
- Mian Li
- Department of Biological Sciences, Binghamton University, Binghamton, New York, USA
- Laboratory of Evolutionary Anthropology and Health, Binghamton University, Binghamton, New York, USA
| | - Kate L DeRosa
- Laboratory of Evolutionary Anthropology and Health, Binghamton University, Binghamton, New York, USA
- Department of Anthropology, Binghamton University, Binghamton, New York, USA
| | - Hayley Mann
- Laboratory of Evolutionary Anthropology and Health, Binghamton University, Binghamton, New York, USA
- Department of Anthropology, Binghamton University, Binghamton, New York, USA
| | - Rita Spathis
- Laboratory of Evolutionary Anthropology and Health, Binghamton University, Binghamton, New York, USA
- Department of Anthropology, Binghamton University, Binghamton, New York, USA
- Laboratory of Biomedical Anthropology and Neurosciences, Binghamton University, Binghamton, NY, United States
| | - Amanda Roome
- Department of Anthropology, Binghamton University, Binghamton, New York, USA
- Laboratory of Biomedical Anthropology and Neurosciences, Binghamton University, Binghamton, NY, United States
- Bassett Healthcare Research Institute, Cooperstown, New York, United States
| | - Daniel Castellanos
- Department of Anthropology, Binghamton University, Binghamton, New York, USA
| | - Kyle Gowen
- Laboratory of Evolutionary Anthropology and Health, Binghamton University, Binghamton, New York, USA
- Department of Anthropology, Binghamton University, Binghamton, New York, USA
| | - Timothy S de Smet
- Department of Anthropology, Binghamton University, Binghamton, New York, USA
- Department of Geological Sciences and Environmental Studies, Binghamton University, Binghamton, New York, USA
| | - Jessica Echard
- Department of Anthropology, Binghamton University, Binghamton, New York, USA
| | - Kalen Casey
- Department of Anthropology, Binghamton University, Binghamton, New York, USA
| | - Michel Shamoon-Pour
- Department of Anthropology, Binghamton University, Binghamton, New York, USA
| | - Ralph M Garruto
- Department of Biological Sciences, Binghamton University, Binghamton, New York, USA
- Department of Anthropology, Binghamton University, Binghamton, New York, USA
- Laboratory of Biomedical Anthropology and Neurosciences, Binghamton University, Binghamton, NY, United States
| | - Koji Lum
- Department of Biological Sciences, Binghamton University, Binghamton, New York, USA
- Laboratory of Evolutionary Anthropology and Health, Binghamton University, Binghamton, New York, USA
- Department of Anthropology, Binghamton University, Binghamton, New York, USA
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167
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Pierini F, Nutsua M, Böhme L, Özer O, Bonczarowska J, Susat J, Franke A, Nebel A, Krause-Kyora B, Lenz TL. Targeted analysis of polymorphic loci from low-coverage shotgun sequence data allows accurate genotyping of HLA genes in historical human populations. Sci Rep 2020; 10:7339. [PMID: 32355290 PMCID: PMC7193575 DOI: 10.1038/s41598-020-64312-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 04/14/2020] [Indexed: 01/15/2023] Open
Abstract
The highly polymorphic human leukocyte antigen (HLA) plays a crucial role in adaptive immunity and is associated with various complex diseases. Accurate analysis of HLA genes using ancient DNA (aDNA) data is crucial for understanding their role in human adaptation to pathogens. Here, we describe the TARGT pipeline for targeted analysis of polymorphic loci from low-coverage shotgun sequence data. The pipeline was successfully applied to medieval aDNA samples and validated using both simulated aDNA and modern empirical sequence data from the 1000 Genomes Project. Thus the TARGT pipeline enables accurate analysis of HLA polymorphisms in historical (and modern) human populations.
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Affiliation(s)
- Federica Pierini
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, 24306, Ploen, Germany.,Université Paris-Saclay, CNRS, Inria, Laboratoire de recherche en informatique, 91405, Orsay, France
| | - Marcel Nutsua
- Institute of Clinical Molecular Biology, Kiel University, 24105, Kiel, Germany
| | - Lisa Böhme
- Institute of Clinical Molecular Biology, Kiel University, 24105, Kiel, Germany
| | - Onur Özer
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, 24306, Ploen, Germany
| | - Joanna Bonczarowska
- Institute of Clinical Molecular Biology, Kiel University, 24105, Kiel, Germany
| | - Julian Susat
- Institute of Clinical Molecular Biology, Kiel University, 24105, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Kiel University, 24105, Kiel, Germany
| | - Almut Nebel
- Institute of Clinical Molecular Biology, Kiel University, 24105, Kiel, Germany
| | - Ben Krause-Kyora
- Institute of Clinical Molecular Biology, Kiel University, 24105, Kiel, Germany
| | - Tobias L Lenz
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, 24306, Ploen, Germany.
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168
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Langdon QK, Peris D, Eizaguirre JI, Opulente DA, Buh KV, Sylvester K, Jarzyna M, Rodríguez ME, Lopes CA, Libkind D, Hittinger CT. Postglacial migration shaped the genomic diversity and global distribution of the wild ancestor of lager-brewing hybrids. PLoS Genet 2020; 16:e1008680. [PMID: 32251477 PMCID: PMC7162524 DOI: 10.1371/journal.pgen.1008680] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 04/16/2020] [Accepted: 02/18/2020] [Indexed: 01/19/2023] Open
Abstract
The wild, cold-adapted parent of hybrid lager-brewing yeasts, Saccharomyces eubayanus, has a complex and understudied natural history. The exploration of this diversity can be used both to develop new brewing applications and to enlighten our understanding of the dynamics of yeast evolution in the wild. Here, we integrate whole genome sequence and phenotypic data of 200 S. eubayanus strains, the largest collection known to date. S. eubayanus has a multilayered population structure, consisting of two major populations that are further structured into six subpopulations. Four of these subpopulations are found exclusively in the Patagonian region of South America; one is found predominantly in Patagonia and sparsely in Oceania and North America; and one is specific to the Holarctic ecozone. Plant host associations differed between subpopulations and between S. eubayanus and its sister species, Saccharomyces uvarum. S. eubayanus is most abundant and genetically diverse in northern Patagonia, where some locations harbor more genetic diversity than is found outside of South America, suggesting that northern Patagonia east of the Andes was a glacial refugium for this species. All but one subpopulation shows isolation-by-distance, and gene flow between subpopulations is low. However, there are strong signals of ancient and recent outcrossing, including two admixed lineages, one that is sympatric with and one that is mostly isolated from its parental populations. Using our extensive biogeographical data, we build a robust model that predicts all known and a handful of additional regions of the globe that are climatically suitable for S. eubayanus, including Europe where host accessibility and competitive exclusion by other Saccharomyces species may explain its continued elusiveness. We conclude that this industrially relevant species has rich natural diversity with many factors contributing to its complex distribution and natural history. The mysterious wild parent of hybrid-lager brewing yeasts, Saccharomyces eubayanus, has been known for less than 10 years. In this time, it has become clear that lager hybrids arose from a subpopulation that has only been isolated in Tibet and North Carolina, USA; but the global diversity of this species has been less explored. Here, we use whole genome sequencing data for 200 strains (174 newly sequenced) to investigate the genetic diversity and geographical distribution of S. eubayanus. We find that its extensive wild diversity is largely centered in northern Patagonia, which likely was a glacial refugium for this species as three of six subpopulations are endemic to this region. In contrast, S. eubayanus is rarely isolated outside of Patagonia. In North America, isolates are dominated by an invasive, near-clonal admixed lineage; the result of an outcrossing and migration event. All subpopulations are well-differentiated, with low gene flow between them. This genetic isolation of subpopulations could be due to ecological factors, such as plant host associations. With modeling, we find that many areas of the world are climatically suitable to S. eubayanus, including Europe, where it has never been isolated. We propose complex ancestries and rich ecologies underlie the global distribution and diversity of this elusive and industrially important species.
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Affiliation(s)
- Quinn K. Langdon
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, United States of America
| | - David Peris
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, United States of America
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, United States of America
- Department of Food Biotechnology, Institute of Agrochemistry and Food Technology (IATA), CSIC, Valencia, Spain
| | - Juan I. Eizaguirre
- Centro de Referencia en Levaduras y Tecnología Cervecera (CRELTEC), Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales (IPATEC) – CONICET / Universidad Nacional del Comahue, Quintral 1250, Bariloche, Argentina
| | - Dana A. Opulente
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, United States of America
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, United States of America
| | - Kelly V. Buh
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, United States of America
| | - Kayla Sylvester
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, United States of America
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, United States of America
| | - Martin Jarzyna
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, United States of America
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, United States of America
| | - María E. Rodríguez
- Instituto de Investigación y Desarrollo en Ingeniería de Procesos, Biotecnología y Energías Alternativas (PROBIEN, CONICET-UNCo), Neuquén, Argentina
| | - Christian A. Lopes
- Instituto de Investigación y Desarrollo en Ingeniería de Procesos, Biotecnología y Energías Alternativas (PROBIEN, CONICET-UNCo), Neuquén, Argentina
| | - Diego Libkind
- Centro de Referencia en Levaduras y Tecnología Cervecera (CRELTEC), Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales (IPATEC) – CONICET / Universidad Nacional del Comahue, Quintral 1250, Bariloche, Argentina
- * E-mail: (CTH); (DL)
| | - Chris Todd Hittinger
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, United States of America
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, United States of America
- * E-mail: (CTH); (DL)
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169
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Bergström A, McCarthy SA, Hui R, Almarri MA, Ayub Q, Danecek P, Chen Y, Felkel S, Hallast P, Kamm J, Blanché H, Deleuze JF, Cann H, Mallick S, Reich D, Sandhu MS, Skoglund P, Scally A, Xue Y, Durbin R, Tyler-Smith C. Insights into human genetic variation and population history from 929 diverse genomes. Science 2020; 367:eaay5012. [PMID: 32193295 PMCID: PMC7115999 DOI: 10.1126/science.aay5012] [Citation(s) in RCA: 390] [Impact Index Per Article: 97.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 02/04/2020] [Indexed: 12/17/2022]
Abstract
Genome sequences from diverse human groups are needed to understand the structure of genetic variation in our species and the history of, and relationships between, different populations. We present 929 high-coverage genome sequences from 54 diverse human populations, 26 of which are physically phased using linked-read sequencing. Analyses of these genomes reveal an excess of previously undocumented common genetic variation private to southern Africa, central Africa, Oceania, and the Americas, but an absence of such variants fixed between major geographical regions. We also find deep and gradual population separations within Africa, contrasting population size histories between hunter-gatherer and agriculturalist groups in the past 10,000 years, and a contrast between single Neanderthal but multiple Denisovan source populations contributing to present-day human populations.
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Affiliation(s)
- Anders Bergström
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK.
- The Francis Crick Institute, London NW1 1AT, UK
| | - Shane A McCarthy
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - Ruoyun Hui
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge CB2 3ER, UK
| | | | - Qasim Ayub
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK
- Monash University Malaysia Genomics Facility, Tropical Medicine and Biology Multidisciplinary Platform, 47500 Bandar Sunway, Malaysia
- School of Science, Monash University Malaysia, 47500 Bandar Sunway, Malaysia
| | | | - Yuan Chen
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK
| | - Sabine Felkel
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna 1210, Austria
| | - Pille Hallast
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK
- Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu 50411, Estonia
| | - Jack Kamm
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Hélène Blanché
- Centre d'Etude du Polymorphisme Humain, Fondation Jean Dausset, 75010 Paris, France
- GENMED Labex, ANR-10-LABX-0013 Paris, France
| | - Jean-François Deleuze
- Centre d'Etude du Polymorphisme Humain, Fondation Jean Dausset, 75010 Paris, France
- GENMED Labex, ANR-10-LABX-0013 Paris, France
| | - Howard Cann
- Centre d'Etude du Polymorphisme Humain, Fondation Jean Dausset, 75010 Paris, France
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Manjinder S Sandhu
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK
- Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK
| | | | - Aylwyn Scally
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - Yali Xue
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK
| | - Richard Durbin
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
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170
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Abstract
Despite the efforts made to reconstruct the history of modern humans, there are still poorly explored regions that are key for understanding the phylogeography of our species. One of them is the Philippines, which is crucial to unravel the colonization of Southeast Asia and Oceania but where little is known about when and how the first humans arrived. In order to shed light into this settlement, we collected samples from 157 individuals of the Philippines with the four grandparents belonging to the same region and mitochondrial variants older than 20,000 years. Next, we analyzed the hypervariable I mtDNA region by approximate Bayesian computation based on extensive spatially explicit computer simulations to select among several migration routes towards the Philippines and to estimate population genetic parameters of this colonization. We found that the colonization of the Philippines occurred more than 60,000 years ago, with long-distance dispersal and from both north and south migration routes. Our results also suggest an environmental scenario especially optimal for humans, with large carrying capacity and population growth, in comparison to other regions of Asia. In all, our study suggests a rapid expansion of modern humans towards the Philippines that could be associated with the establisment of maritime technologies and favorable environmental conditions.
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171
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Der Sarkissian C, Möller P, Hofman CA, Ilsøe P, Rick TC, Schiøtte T, Sørensen MV, Dalén L, Orlando L. Unveiling the Ecological Applications of Ancient DNA From Mollusk Shells. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00037] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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172
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Human occupation of northern India spans the Toba super-eruption ~74,000 years ago. Nat Commun 2020; 11:961. [PMID: 32098950 PMCID: PMC7042215 DOI: 10.1038/s41467-020-14668-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 12/19/2019] [Indexed: 12/14/2022] Open
Abstract
India is located at a critical geographic crossroads for understanding the dispersal of Homo sapiens out of Africa and into Asia and Oceania. Here we report evidence for long-term human occupation, spanning the last ~80 thousand years, at the site of Dhaba in the Middle Son River Valley of Central India. An unchanging stone tool industry is found at Dhaba spanning the Toba eruption of ~74 ka (i.e., the Youngest Toba Tuff, YTT) bracketed between ages of 79.6 ± 3.2 and 65.2 ± 3.1 ka, with the introduction of microlithic technology ~48 ka. The lithic industry from Dhaba strongly resembles stone tool assemblages from the African Middle Stone Age (MSA) and Arabia, and the earliest artefacts from Australia, suggesting that it is likely the product of Homo sapiens as they dispersed eastward out of Africa. When modern humans colonized India is debated. Here, Clarkson and colleagues report an archaeological site in India that has been occupied for approximately 80,000 years and contains a stone tool assemblage attributed to Homo sapiens that matches artefacts from Africa, Arabia, and Australia.
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173
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Lucena-Perez M, Marmesat E, Kleinman-Ruiz D, Martínez-Cruz B, Węcek K, Saveljev AP, Seryodkin IV, Okhlopkov I, Dvornikov MG, Ozolins J, Galsandorj N, Paunovic M, Ratkiewicz M, Schmidt K, Godoy JA. Genomic patterns in the widespread Eurasian lynx shaped by Late Quaternary climatic fluctuations and anthropogenic impacts. Mol Ecol 2020; 29:812-828. [PMID: 31995648 PMCID: PMC7064982 DOI: 10.1111/mec.15366] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 12/27/2019] [Accepted: 01/16/2020] [Indexed: 12/28/2022]
Abstract
Disentangling the contribution of long-term evolutionary processes and recent anthropogenic impacts to current genetic patterns of wildlife species is key to assessing genetic risks and designing conservation strategies. Here, we used 80 whole nuclear genomes and 96 mitogenomes from populations of the Eurasian lynx covering a range of conservation statuses, climatic zones and subspecies across Eurasia to infer the demographic history, reconstruct genetic patterns, and discuss the influence of long-term isolation and/or more recent human-driven changes. Our results show that Eurasian lynx populations shared a common history until 100,000 years ago, when Asian and European populations started to diverge and both entered a period of continuous and widespread decline, with western populations, except Kirov, maintaining lower effective sizes than eastern populations. Population declines and increased isolation in more recent times probably drove the genetic differentiation between geographically and ecologically close westernmost European populations. By contrast, and despite the wide range of habitats covered, populations are quite homogeneous genetically across the Asian range, showing a pattern of isolation by distance and providing little genetic support for the several proposed subspecies. Mitogenomic and nuclear divergences and population declines starting during the Late Pleistocene can be mostly attributed to climatic fluctuations and early human influence, but the widespread and sustained decline since the Holocene is more probably the consequence of anthropogenic impacts which intensified in recent centuries, especially in western Europe. Genetic erosion in isolated European populations and lack of evidence for long-term isolation argue for the restoration of lost population connectivity.
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Affiliation(s)
- Maria Lucena-Perez
- Department of Integrative Ecology, Estación Biológica de Doñana (CSIC), Seville, Spain
| | - Elena Marmesat
- Department of Integrative Ecology, Estación Biológica de Doñana (CSIC), Seville, Spain
| | - Daniel Kleinman-Ruiz
- Department of Integrative Ecology, Estación Biológica de Doñana (CSIC), Seville, Spain
| | - Begoña Martínez-Cruz
- School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, UK
| | - Karolina Węcek
- Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland
| | - Alexander P Saveljev
- Department of Animal Ecology, Russian Research Institute of Game Management and Fur Farming, Kirov, Russia.,Biological Faculty of Moscow State University, Moscow, Russia
| | - Ivan V Seryodkin
- Laboratory of Ecology and Conservation of Animals, Pacific Institute of Geography of Far East Branch of Russian Academy of Sciences, Vladivostok, Russia.,Far Eastern Federal University, Vladivostok, Russia
| | - Innokentiy Okhlopkov
- Institute for Biological Problems of Cryolithozone, Siberian Division of the Russian Academy of Sciences, Yakutsk, Russia
| | - Mikhail G Dvornikov
- Department of Hunting Resources, Russian Research Institute of Game Management and Fur Farming, Kirov, Russia
| | - Janis Ozolins
- Department of Hunting and Wildlife Management, Latvijas Valsts mežzinātnes institūts "Silava", Salaspils, Latvia
| | - Naranbaatar Galsandorj
- Institute of General and Experimental Biology, Mongolian Academy of Science, Ulaanbaatar, Mongolia
| | | | | | - Krzysztof Schmidt
- Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland
| | - José A Godoy
- Department of Integrative Ecology, Estación Biológica de Doñana (CSIC), Seville, Spain
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174
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Aris-Brosou S. Direct Evidence of an Increasing Mutational Load in Humans. Mol Biol Evol 2020; 36:2823-2829. [PMID: 31424543 DOI: 10.1093/molbev/msz192] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The extent to which selection has shaped present-day human populations has attracted intense scrutiny, and examples of local adaptations abound. However, the evolutionary trajectory of alleles that, today, are deleterious has received much less attention. To address this question, the genomes of 2,062 individuals, including 1,179 ancient humans, were reanalyzed to assess how frequencies of risk alleles and their homozygosity changed through space and time in Europe over the past 45,000 years. Although the overall deleterious homozygosity has consistently decreased, risk alleles have steadily increased in frequency over that period of time. Those that increased most are associated with diseases such as asthma, Crohn disease, diabetes, and obesity, which are highly prevalent in present-day populations. These findings may not run against the existence of local adaptations but highlight the limitations imposed by drift and population dynamics on the strength of selection in purging deleterious mutations from human populations.
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Affiliation(s)
- Stéphane Aris-Brosou
- Department of Biology, University of Ottawa, Ottawa, ON, Canada.,Department of Mathematics and Statistics, University of Ottawa, Ottawa, ON, Canada
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175
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Identifying and Interpreting Apparent Neanderthal Ancestry in African Individuals. Cell 2020; 180:677-687.e16. [PMID: 32004458 DOI: 10.1016/j.cell.2020.01.012] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 11/13/2019] [Accepted: 01/07/2020] [Indexed: 01/27/2023]
Abstract
Admixture has played a prominent role in shaping patterns of human genomic variation, including gene flow with now-extinct hominins like Neanderthals and Denisovans. Here, we describe a novel probabilistic method called IBDmix to identify introgressed hominin sequences, which, unlike existing approaches, does not use a modern reference population. We applied IBDmix to 2,504 individuals from geographically diverse populations to identify and analyze Neanderthal sequences segregating in modern humans. Strikingly, we find that African individuals carry a stronger signal of Neanderthal ancestry than previously thought. We show that this can be explained by genuine Neanderthal ancestry due to migrations back to Africa, predominately from ancestral Europeans, and gene flow into Neanderthals from an early dispersing group of humans out of Africa. Our results refine our understanding of Neanderthal ancestry in African and non-African populations and demonstrate that remnants of Neanderthal genomes survive in every modern human population studied to date.
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176
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Jiao X, Flouri T, Rannala B, Yang Z. The Impact of Cross-Species Gene Flow on Species Tree Estimation. Syst Biol 2020; 69:830-847. [DOI: 10.1093/sysbio/syaa001] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 11/12/2019] [Accepted: 01/15/2020] [Indexed: 12/26/2022] Open
Abstract
Abstract
Recent analyses of genomic sequence data suggest cross-species gene flow is common in both plants and animals, posing challenges to species tree estimation. We examine the levels of gene flow needed to mislead species tree estimation with three species and either episodic introgressive hybridization or continuous migration between an outgroup and one ingroup species. Several species tree estimation methods are examined, including the majority-vote method based on the most common gene tree topology (with either the true or reconstructed gene trees used), the UPGMA method based on the average sequence distances (or average coalescent times) between species, and the full-likelihood method based on multilocus sequence data. Our results suggest that the majority-vote method based on gene tree topologies is more robust to gene flow than the UPGMA method based on coalescent times and both are more robust than likelihood assuming a multispecies coalescent (MSC) model with no cross-species gene flow. Comparison of the continuous migration model with the episodic introgression model suggests that a small amount of gene flow per generation can cause drastic changes to the genetic history of the species and mislead species tree methods, especially if the species diverged through radiative speciation events. Estimates of parameters under the MSC with gene flow suggest that African mosquito species in the Anopheles gambiae species complex constitute such an example of extreme impact of gene flow on species phylogeny. [IM; introgression; migration; MSci; multispecies coalescent; species tree.]
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Affiliation(s)
- Xiyun Jiao
- Department of Genetics, University College London, Gower Street, London WC1E 6BT, UK
| | - Tomáš Flouri
- Department of Genetics, University College London, Gower Street, London WC1E 6BT, UK
| | - Bruce Rannala
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
| | - Ziheng Yang
- Department of Genetics, University College London, Gower Street, London WC1E 6BT, UK
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177
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African climate response to orbital and glacial forcing in 140,000-y simulation with implications for early modern human environments. Proc Natl Acad Sci U S A 2020; 117:2255-2264. [PMID: 31964850 DOI: 10.1073/pnas.1917673117] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A climate/vegetation model simulates episodic wetter and drier periods at the 21,000-y precession period in eastern North Africa, the Arabian Peninsula, and the Levant over the past 140,000 y. Large orbitally forced wet/dry extremes occur during interglacial time, ∼130 to 80 ka, and conditions between these two extremes prevail during glacial time, ∼70 to 15 ka. Orbital precession causes high seasonality in Northern Hemisphere (NH) insolation at ∼125, 105, and 83 ka, with stronger and northward extended summer monsoon rains in North Africa and the Arabian Peninsula and increased winter rains in the Mediterranean Basin. The combined effects of these two seasonally distinct rainfall regimes increase vegetation and narrow the width of the Saharan-Arabian desert and semidesert zones. During the opposite phase of the precession cycle (∼115, 95, and 73 ka), NH seasonality is low, and decreased summer insolation and increased winter insolation cause monsoon and storm track rains to decrease and the width of the desert zone to increase. During glacial time (∼70 to 15 ka), forcing from large ice sheets and lowered greenhouse gas concentrations combine to increase winter Mediterranean storm track precipitation; the southward retreat of the northern limit of summer monsoon rains is relatively small, thereby limiting the expansion of deserts. The lowered greenhouse gas concentrations cause the near-equatorial zone to cool and reduce convection, causing drier climate with reduced forest cover. At most locations and times, the simulations agree with environmental observations. These changing regional patterns of climate/vegetation could have influenced the dispersal of early humans through expansions and contractions of well-watered corridors.
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178
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Jarrett P, Scragg R. Evolution, Prehistory and Vitamin D. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17020646. [PMID: 31963858 PMCID: PMC7027011 DOI: 10.3390/ijerph17020646] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Revised: 01/12/2020] [Accepted: 01/16/2020] [Indexed: 06/10/2023]
Abstract
Aspects of human evolutionary biology and prehistory are discussed in relation to vitamin D. The evolution of hairlessness, combined with the need for efficient eccrine sweat production for cooling, provided evolutionary pressure to protect the skin from ultraviolet damage by developing cutaneous pigmentation. There was a subsequent loss of pigmentation as humans journeyed to northern latitudes. Their increasing mastery of technology outstripped evolution's finite pace as further dispersal occurred around the globe. A timeline for the development of clothing to provide warmth, and the consequent shielding from ultraviolet light, which diminished vitamin D synthesis, can be inferred by an examination of mutations in the human louse.
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Affiliation(s)
- Paul Jarrett
- Department of Dermatology, Middlemore Hospital, Auckland 2025, New Zealand
- Department of Medicine, The University of Auckland, Auckland 1023, New Zealand
| | - Robert Scragg
- Department of Population Health, The University of Auckland, Auckland 1072, New Zealand;
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179
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Ming L, Yuan L, Yi L, Ding G, Hasi S, Chen G, Jambl T, Hedayat-Evright N, Batmunkh M, Badmaevna GK, Gan-Erdene T, Ts B, Zhang W, Zulipikaer A, Hosblig, Erdemt, Natyrov A, Mamay P, Narenbatu, Meng G, Narangerel C, Khongorzul O, He J, Hai L, Lin W, Sirendalai, Sarentuya, Aiyisi, Li Y, Wang Z, Jirimutu. Whole-genome sequencing of 128 camels across Asia reveals origin and migration of domestic Bactrian camels. Commun Biol 2020; 3:1. [PMID: 31925316 PMCID: PMC6946651 DOI: 10.1038/s42003-019-0734-6] [Citation(s) in RCA: 180] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 12/10/2019] [Indexed: 12/11/2022] Open
Abstract
The domestic Bactrian camels were treated as one of the principal means of locomotion between the eastern and western cultures in history. However, whether they originated from East Asia or Central Asia remains elusive. To address this question, we perform whole-genome sequencing of 128 camels across Asia. The extant wild and domestic Bactrian camels show remarkable genetic divergence, as they were split from dromedaries. The wild Bactrian camels also contribute little to the ancestry of domestic ones, although they share close habitat in East Asia. Interestingly, among the domestic Bactrian camels, those from Iran exhibit the largest genetic distance and the earliest split from all others in the phylogeny, despite evident admixture between domestic Bactrian camels and dromedaries living in Central Asia. Taken together, our study support the Central Asian origin of domestic Bactrian camels, which were then immigrated eastward to Mongolia where native wild Bactrian camels inhabit. Ming, Yuan et al. performed whole-genome sequencing on 128 wild and domesticated Bactrian camels across Asia. They show that wild and domestic Bactrian camels are genetically diverged from dromedaries, and that wild camels contributed little to domestic camel ancestry despite sharing a habitat in East Asia.
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Affiliation(s)
- Liang Ming
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, College of Food Science and Engineering, Inner Mongolia Agricultural University, Huhhot, China.,Inner Mongolia Institute of Camel Research, West Alax, Inner Mongolia, China
| | - Liyun Yuan
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,Bio-Med Big Data Center, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Li Yi
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, College of Food Science and Engineering, Inner Mongolia Agricultural University, Huhhot, China
| | - Guohui Ding
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,Gui'an Bio-Med Big Data Center, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Guiyang, China
| | - Surong Hasi
- Key Laboratory of Clinical Diagnosis and Treatment Technology in Animal Disease, Ministry of Agriculture, College of Veterinary Medicine, Inner Mongolia Agricultural University, Huhhot, China
| | - Gangliang Chen
- Bactrian Camel Academe of Altai, Xingjiang Wangyuan Camel Milk Limited Company, Fuhai County, Xijiang, China
| | - Tuyatsetseg Jambl
- College of Industrial Technology, Mongolian University of Science and Technology, Ulaanbaater, Mongolia
| | | | - Mijiddorj Batmunkh
- China-Mongolia Joint Laboratory for Biomacromolecule Research, Ulaanbaatar, Mongolia.,Mongolian Wild Camel Protection Area, Ministry of Nature and Environment, Ulaanbaatar, Mongolia
| | | | - Tudeviin Gan-Erdene
- Institute of Chemistry and Chemical Technology, Mongolian Academy of Sciences, Ulaanbaatar, Mongolia
| | - Batsukh Ts
- College of Industrial Technology, Mongolian University of Science and Technology, Ulaanbaater, Mongolia
| | - Wenbin Zhang
- Bactrian Camel Institute of Alxa, Inner Mongolia, China
| | - Azhati Zulipikaer
- Animal Science Institute, Xinjiang Academy of Animal Science, Urumqi, China
| | - Hosblig
- Animal Husbandry Bureau of North Urad, Bayannuur, Inner Mongolia, China
| | - Erdemt
- Animal Husbandry Workstation of West Sunid, Xiliingol, Inner Mongolia, China
| | - Arkady Natyrov
- Agrarian Faculty, Kalmyk State University, Republic of Kalmykia, Russia
| | | | - Narenbatu
- College of Animal Science, Inner Mongolia Agricultural University, Huhhot, China
| | - Gendalai Meng
- Department of Pharmacy, Affiliated Hospital of Inner Mongolia Medical University, Huhhot, China
| | | | - Orgodol Khongorzul
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, College of Food Science and Engineering, Inner Mongolia Agricultural University, Huhhot, China
| | - Jing He
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, College of Food Science and Engineering, Inner Mongolia Agricultural University, Huhhot, China
| | - Le Hai
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, College of Food Science and Engineering, Inner Mongolia Agricultural University, Huhhot, China
| | - Weili Lin
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Sirendalai
- Inner Mongolia Institute of Camel Research, West Alax, Inner Mongolia, China
| | - Sarentuya
- Inner Mongolia Institute of Camel Research, West Alax, Inner Mongolia, China
| | - Aiyisi
- College of Industrial Technology, Mongolian University of Science and Technology, Ulaanbaater, Mongolia
| | - Yixue Li
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China. .,Bio-Med Big Data Center, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China. .,Shanghai Center for Bioinformation Technology, Shanghai Industrial Technology Institute, Shanghai, China. .,Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, China.
| | - Zhen Wang
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.
| | - Jirimutu
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, College of Food Science and Engineering, Inner Mongolia Agricultural University, Huhhot, China. .,Inner Mongolia Institute of Camel Research, West Alax, Inner Mongolia, China. .,China-Mongolia Joint Laboratory for Biomacromolecule Research, Ulaanbaatar, Mongolia.
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180
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Oussalah A, Jeannesson-Thivisol E, Chéry C, Perrin P, Rouyer P, Josse T, Cano A, Barth M, Fouilhoux A, Mention K, Labarthe F, Arnoux JB, Maillot F, Lenaerts C, Dumesnil C, Wagner K, Terral D, Broué P, De Parscau L, Gay C, Kuster A, Bédu A, Besson G, Lamireau D, Odent S, Masurel A, Rodriguez-Guéant RM, Feillet F, Guéant JL, Namour F. Population and evolutionary genetics of the PAH locus to uncover overdominance and adaptive mechanisms in phenylketonuria: Results from a multiethnic study. EBioMedicine 2020; 51:102623. [PMID: 31923802 PMCID: PMC7000351 DOI: 10.1016/j.ebiom.2019.102623] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 12/20/2019] [Accepted: 12/22/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Phenylketonuria (PKU) is the most common inborn error of amino acid metabolism in Europe. The reasons underlying the high prevalence of heterozygous carriers are not clearly understood. We aimed to look for pathogenic PAH variant enrichment according to geographical areas and patients' ethnicity using a multiethnic nationwide cohort of patients with PKU in France. We subsequently appraised the population differentiation, balancing selection and the molecular evolutionary history of the PAH locus. METHODS The French nationwide PKU study included patients who have been referred at the national level to the University Hospital of Nancy, and for whom a molecular diagnosis of phenylketonuria was made by Sanger sequencing. We performed enrichment analyses by comparing alternative allele frequencies using Fisher's exact test with Bonferroni adjustment. We estimated the amount of genetic differentiation among populations using Wright's fixation index (Fst). To estimate the molecular evolutionary history of the PAH gene, we performed phylogenetic and evolutionary analyses using whole-genome and exome-sequencing data from healthy individuals and non-PKU patients, respectively. Finally, we used exome-wide association study to decipher potential genetic loci associated with population divergence on PAH. FINDINGS The study included 696 patients and revealed 132 pathogenic PAH variants. Three geographical areas showed significant enrichment for a pathogenic PAH variant: North of France (p.Arg243Leu), North-West of France (p.Leu348Val), and Mediterranean coast (p.Ala403Val). One PAH variant (p.Glu280Gln) was significantly enriched among North-Africans (OR = 23·23; 95% CI: 9·75-55·38). PAH variants exhibiting a strong genetic differentiation were significantly enriched in the 'Biopterin_H' domain (OR = 6·45; 95% CI: 1·99-20·84), suggesting a balancing selection pressure on the biopterin function of PAH. Phylogenetic and timetree analyses were consistent with population differentiation events on European-, African-, and Asian-ancestry populations. The five PAH variants most strongly associated with a high selection pressure were phylogenetically close and were located within the biopterin domain coding region of PAH or in its vicinity. Among the non-PAH loci potentially associated with population divergence, two reached exome-wide significance: SSPO (SCO-spondin) and DBH (dopamine beta-hydroxylase), involved in neuroprotection and metabolic adaptation, respectively. INTERPRETATION Our data provide evidence on the combination of evolutionary and adaptive events in populations with distinct ancestries, which may explain the overdominance of some genetic variants on PAH. FUNDING French National Institute of Health and Medical Research (INSERM) UMR_S 1256.
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Affiliation(s)
- Abderrahim Oussalah
- University of Lorraine, INSERM UMR_S 1256, Nutrition, Genetics, and Environmental Risk Exposure (NGERE), Faculty of Medicine of Nancy, Nancy, France; Department of Molecular Medicine, Division of Biochemistry, Molecular Biology, Nutrition, and Metabolism, University Hospital of Nancy, Nancy, France; Reference Centre for Inborn Errors of Metabolism (ORPHA67872), University Hospital of Nancy, Nancy F-54000, France.
| | - Elise Jeannesson-Thivisol
- Department of Molecular Medicine, Division of Biochemistry, Molecular Biology, Nutrition, and Metabolism, University Hospital of Nancy, Nancy, France; Reference Centre for Inborn Errors of Metabolism (ORPHA67872), University Hospital of Nancy, Nancy F-54000, France
| | - Céline Chéry
- University of Lorraine, INSERM UMR_S 1256, Nutrition, Genetics, and Environmental Risk Exposure (NGERE), Faculty of Medicine of Nancy, Nancy, France; Department of Molecular Medicine, Division of Biochemistry, Molecular Biology, Nutrition, and Metabolism, University Hospital of Nancy, Nancy, France; Reference Centre for Inborn Errors of Metabolism (ORPHA67872), University Hospital of Nancy, Nancy F-54000, France
| | - Pascal Perrin
- Department of Molecular Medicine, Division of Biochemistry, Molecular Biology, Nutrition, and Metabolism, University Hospital of Nancy, Nancy, France; Reference Centre for Inborn Errors of Metabolism (ORPHA67872), University Hospital of Nancy, Nancy F-54000, France
| | - Pierre Rouyer
- University of Lorraine, INSERM UMR_S 1256, Nutrition, Genetics, and Environmental Risk Exposure (NGERE), Faculty of Medicine of Nancy, Nancy, France
| | - Thomas Josse
- Department of Molecular Medicine, Division of Biochemistry, Molecular Biology, Nutrition, and Metabolism, University Hospital of Nancy, Nancy, France; Reference Centre for Inborn Errors of Metabolism (ORPHA67872), University Hospital of Nancy, Nancy F-54000, France
| | - Aline Cano
- Centre of Reference for Inborn Metabolic Diseases, University Hospital La Timone, Marseille, France
| | - Magalie Barth
- Department of Genetics, University Hospital of Angers, Angers, France
| | - Alain Fouilhoux
- Metabolic Diseases Unit, Woman-Mother-Child Hospital, University Hospital of Lyon, Lyon, France
| | | | | | - Jean-Baptiste Arnoux
- Reference Centre for Inherited Metabolic Diseases, Necker-Sick Children's Hospital, Imagine Institute, Paris Descartes University, Paris, France
| | - François Maillot
- Department of Internal Medicine, University Hospital of Tours, François Rabelais University, Tours, France
| | - Catherine Lenaerts
- Department of Paediatrics, University Hospital of Amiens, Amiens, France
| | - Cécile Dumesnil
- Paediatric Haematology and Oncology, University Hospital of Rouen, Rouen, France
| | - Kathy Wagner
- Department of Paediatrics, Lenval Hospital, Nice, France
| | - Daniel Terral
- Department of Paediatrics, University Hospital of Clermont-Ferrand, Clermont-Ferrand, France
| | - Pierre Broué
- Reference Centre for Inborn Errors of Metabolism, University Children Hospital, Toulouse, France
| | - Loic De Parscau
- Department of Paediatrics, University Hospital Morvan, Brest, France
| | - Claire Gay
- Department of Paediatrics, University Hospital of Saint-Etienne, Saint-Etienne, France
| | - Alice Kuster
- Paediatric Department, University Hospital of Nantes, Nantes, France
| | - Antoine Bédu
- Department of Neonatology, Mother and Child Hospital, Limoges, France
| | - Gérard Besson
- Department of Neurology, University Hospital of Grenoble, Grenoble, France
| | - Delphine Lamireau
- Department of Paediatrics, Pellegrin-Enfants Hospital, Bordeaux, France
| | - Sylvie Odent
- Department of Clinical Genetics, University Hospital of Rennes, Rennes, France
| | - Alice Masurel
- Department of Medical Genetics, Dijon Bourgogne University Hospital, Dijon, France
| | - Rosa-Maria Rodriguez-Guéant
- University of Lorraine, INSERM UMR_S 1256, Nutrition, Genetics, and Environmental Risk Exposure (NGERE), Faculty of Medicine of Nancy, Nancy, France; Department of Molecular Medicine, Division of Biochemistry, Molecular Biology, Nutrition, and Metabolism, University Hospital of Nancy, Nancy, France; Reference Centre for Inborn Errors of Metabolism (ORPHA67872), University Hospital of Nancy, Nancy F-54000, France
| | - François Feillet
- University of Lorraine, INSERM UMR_S 1256, Nutrition, Genetics, and Environmental Risk Exposure (NGERE), Faculty of Medicine of Nancy, Nancy, France; Reference Centre for Inborn Errors of Metabolism (ORPHA67872), University Hospital of Nancy, Nancy F-54000, France; Department of Paediatrics, University Hospital of Nancy, Nancy, France
| | - Jean-Louis Guéant
- University of Lorraine, INSERM UMR_S 1256, Nutrition, Genetics, and Environmental Risk Exposure (NGERE), Faculty of Medicine of Nancy, Nancy, France; Department of Molecular Medicine, Division of Biochemistry, Molecular Biology, Nutrition, and Metabolism, University Hospital of Nancy, Nancy, France; Reference Centre for Inborn Errors of Metabolism (ORPHA67872), University Hospital of Nancy, Nancy F-54000, France.
| | - Fares Namour
- University of Lorraine, INSERM UMR_S 1256, Nutrition, Genetics, and Environmental Risk Exposure (NGERE), Faculty of Medicine of Nancy, Nancy, France; Department of Molecular Medicine, Division of Biochemistry, Molecular Biology, Nutrition, and Metabolism, University Hospital of Nancy, Nancy, France; Reference Centre for Inborn Errors of Metabolism (ORPHA67872), University Hospital of Nancy, Nancy F-54000, France
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181
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de Leon J, Rajkumar AP, Kaithi AR, Schoretsanitis G, Kane JM, Wang CY, Tang YL, Lin SK, Hong KS, Farooq S, Ng CH, Ruan CJ, Andrade C. Do Asian Patients Require Only Half of the Clozapine Dose Prescribed for Caucasians? A Critical Overview. Indian J Psychol Med 2020; 42:4-10. [PMID: 31997860 PMCID: PMC6970303 DOI: 10.4103/ijpsym.ijpsym_379_19] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Revised: 09/24/2019] [Accepted: 10/07/2019] [Indexed: 12/12/2022] Open
Abstract
Since 1997, studies have found that Asians need lower clozapine doses than Caucasians. Caucasians with average clozapine metabolism may need from 300 to 600 mg/day to reach the therapeutic range (350 ng/ml). Thus, serum clozapine concentration-to-dose (C/D) ratios typically range between 0.60 (male smokers) and 1.20 (female non-smokers). A 2019 systematic review of clozapine levels demonstrated weighted mean C/D ratios of 1.57 in 876 East Asians and 1.07 in 1147 Caucasians (P < .001). In Asian countries, average clozapine doses are lower than 300 mg/day. After sex and smoking stratification in 5 Asian samples with clozapine concentrations, the clozapine dose required to reach 350 ng/ml in female non-smokers ranged from 145 to 189 mg/day and in male smokers, from 259 to 294 mg/day. Thus, in Asian patients with average metabolism (with no inducers other than smoking, with no inhibitors, and in the absence of extreme obesity), the dose needed for clinical response may range between 150 mg/day for female non-smokers to 300 mg/day for male smokers. Clozapine levels may help personalize dosing in clozapine poor metabolizers (PMs) and ultrarapid metabolizers (UMs). Asian PMs may need very low doses (50-150 mg/day) to obtain therapeutic concentrations. About 10% (range 2-13%) of Asians are genetic PM cases. Other PMs are patients taking CYP1A2 inhibitors such as fluvoxamine, oral contraceptives, and valproate. Temporary clozapine PM status may occur during severe systemic infections/inflammations with fever and C-reactive protein (CRP) elevations. Asian UMs include patients taking potent inducers such as phenytoin, and rarely, valproate.
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Affiliation(s)
- Jose de Leon
- Mental Health Research Center, Eastern State Hospital, Lexington, Kentucky, USA.,Psychiatry and Neurosciences Research Group (CTS-549), Institute of Neurosciences, University of Granada, Granada, Spain, and Biomedical Research Centre in Mental Health Net (CIBERSAM), Santiago Apóstol Hospital, University of the Basque Country, Vitoria, Spain
| | - Anto P Rajkumar
- Department of Psychiatry, Christian Medical College, Vellore, Tamil Nadu, India.,Institute of Mental Health, University of Nottingham, Nottingham, United Kingdom
| | | | - Georgios Schoretsanitis
- Department of Psychiatry, Zucker Hillside Hospital, Northwell Health, Glen Oaks, New York, USA
| | - John M Kane
- Department of Psychiatry, Zucker Hillside Hospital, Northwell Health, Glen Oaks, New York, USA.,Department of Psychiatry and Molecular Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, New York, USA
| | - Chuan-Yue Wang
- Department of Psychiatry, The National Clinical Research Centre for Mental Disorders and Beijing Key Lab of Mental Disorders and Beijing Institute for Brain Disorders Center of Schizophrenia, Beijing Anding Hospital, Capital Medical University, Beijing, China
| | - Yi-Lang Tang
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, Georgia, and Substance Abuse Treatment Program, Atlanta VA Medical Center, Decatur, Georgia, USA
| | - Shih-Ku Lin
- Department of General Psychiatry, Taipei City, Psychiatric Center, Taipei, Taiwan, and Department of Psychiatry, School of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Kyung Sue Hong
- Department of Psychiatry, Sungkyunkwan University School of Medicine, Samsung Medical Center, Seoul, Korea
| | - Saeed Farooq
- School of Primary, Community and Social Care, Faulty of Medicine and Health Sciences, Keele University, Staffordshire, and Midlands Partnership NHS Foundation Trust, Staffordshire, United Kingdom
| | - Chee H Ng
- Department of Psychiatry, The Melbourne Clinic and St Vincent's Hospital, The University of Melbourne, Melbourne, Victoria, Australia
| | - Can-Jun Ruan
- Laboratory of Clinical Psychopharmacology & The National Clinical Research Centre for Mental Disorders & Beijing Key Lab of Mental Disorders, Beijing Anding Hospital, Capital Medical University, Beijing, China
| | - Chittaranjan Andrade
- Department of Psychopharmacology, National Institute of Mental Health and Neurosciences, Bengaluru, Karnataka, India
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182
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Evolution and molecular epidemiology of polyomaviruses. INFECTION GENETICS AND EVOLUTION 2019; 79:104150. [PMID: 31870972 DOI: 10.1016/j.meegid.2019.104150] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 12/17/2019] [Accepted: 12/19/2019] [Indexed: 02/08/2023]
Abstract
Polyomaviruses (PyVs) are small DNA viruses that infect several species, including mammals, birds and fishes. Their study gained momentum after the report of previously unidentified viral species in the past decade, and especially, since the description of the first polyomavirus clearly oncogenic for humans. The aim of this work was to review the most relevant aspects of the evolution and molecular epidemiology of polyomaviruses, allowing to reveal general evolutionary patterns and to identify some unaddressed issues and future challenges. The main points analysed included: 1) the species and genera assignation criteria; 2) the hypotheses, mechanisms and timescale of the ancient and recent evolutionary history of polyomaviruses; and 3) the molecular epidemiology of human viruses, with special attention to JC, BK and Merkel cell polyomaviruses.
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183
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Ishikawa A, Kabeya N, Ikeya K, Kakioka R, Cech JN, Osada N, Leal MC, Inoue J, Kume M, Toyoda A, Tezuka A, Nagano AJ, Yamasaki YY, Suzuki Y, Kokita T, Takahashi H, Lucek K, Marques D, Takehana Y, Naruse K, Mori S, Monroig O, Ladd N, Schubert CJ, Matthews B, Peichel CL, Seehausen O, Yoshizaki G, Kitano J. A key metabolic gene for recurrent freshwater colonization and radiation in fishes. Science 2019; 364:886-889. [PMID: 31147520 DOI: 10.1126/science.aau5656] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Accepted: 04/17/2019] [Indexed: 01/10/2023]
Abstract
Colonization of new ecological niches has triggered large adaptive radiations. Although some lineages have made use of such opportunities, not all do so. The factors causing this variation among lineages are largely unknown. Here, we show that deficiency in docosahexaenoic acid (DHA), an essential ω-3 fatty acid, can constrain freshwater colonization by marine fishes. Our genomic analyses revealed multiple independent duplications of the fatty acid desaturase gene Fads2 in stickleback lineages that subsequently colonized and radiated in freshwater habitats, but not in close relatives that failed to colonize. Transgenic manipulation of Fads2 in marine stickleback increased their ability to synthesize DHA and survive on DHA-deficient diets. Multiple freshwater ray-finned fishes also show a convergent increase in Fads2 copies, indicating its key role in freshwater colonization.
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Affiliation(s)
- Asano Ishikawa
- Ecological Genetics Laboratory, National Institute of Genetics, Shizuoka, Japan.,Department of Genetics, Graduate University for Advanced Studies (SOKENDAI), Shizuoka, Japan
| | - Naoki Kabeya
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology, Tokyo, Japan.,Department of Aquatic Bioscience, The University of Tokyo, Tokyo, Japan
| | - Koki Ikeya
- Gifu World Freshwater Aquarium, Gifu, Japan
| | - Ryo Kakioka
- Ecological Genetics Laboratory, National Institute of Genetics, Shizuoka, Japan
| | - Jennifer N Cech
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Naoki Osada
- Graduate School of Bioengineering and Bioinformatics, Hokkaido University, Sapporo, Japan
| | - Miguel C Leal
- Department of Fish Ecology and Evolution, Eawag Swiss Federal Institute of Aquatic Science and Technology, Centre for Ecology, Evolution and Biogeochemistry, Kastanienbaum, Switzerland
| | - Jun Inoue
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Manabu Kume
- Ecological Genetics Laboratory, National Institute of Genetics, Shizuoka, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Shizuoka, Japan
| | - Ayumi Tezuka
- Faculty of Agriculture, Ryukoku University, Otsu, Shiga, Japan
| | | | - Yo Y Yamasaki
- Ecological Genetics Laboratory, National Institute of Genetics, Shizuoka, Japan
| | - Yuto Suzuki
- Department of Marine Bioscience, Fukui Prefectural University, Obama, Fukui, Japan
| | - Tomoyuki Kokita
- Department of Marine Bioscience, Fukui Prefectural University, Obama, Fukui, Japan
| | - Hiroshi Takahashi
- Department of Applied Aquabiology, National Fisheries University, Shimonoseki, Yamaguchi, Japan
| | - Kay Lucek
- Department of Fish Ecology and Evolution, Eawag Swiss Federal Institute of Aquatic Science and Technology, Centre for Ecology, Evolution and Biogeochemistry, Kastanienbaum, Switzerland.,Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - David Marques
- Department of Fish Ecology and Evolution, Eawag Swiss Federal Institute of Aquatic Science and Technology, Centre for Ecology, Evolution and Biogeochemistry, Kastanienbaum, Switzerland.,Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Yusuke Takehana
- Laboratory of Bioresources, National Institute for Basic Biology, Okazaki, Aichi, Japan
| | - Kiyoshi Naruse
- Laboratory of Bioresources, National Institute for Basic Biology, Okazaki, Aichi, Japan
| | - Seiichi Mori
- Biological Laboratory, Gifu Kyoritsu University, Ogaki, Gifu, Japan
| | - Oscar Monroig
- Instituto de Acuicultura Torre de la Sal (IATS-CSIC), Ribera de Cabanes, Castellón, Spain
| | - Nemiah Ladd
- Department of Surface Waters-Research and Management, Eawag Swiss Federal Institute of Aquatic Science and Technology, Centre for Ecology, Evolution and Biogeochemistry, Kastanienbaum, Switzerland.,Department of Earth Sciences, ETH-Zurich, Zurich Switzerland
| | - Carsten J Schubert
- Department of Surface Waters-Research and Management, Eawag Swiss Federal Institute of Aquatic Science and Technology, Centre for Ecology, Evolution and Biogeochemistry, Kastanienbaum, Switzerland
| | - Blake Matthews
- Department of Fish Ecology and Evolution, Eawag Swiss Federal Institute of Aquatic Science and Technology, Centre for Ecology, Evolution and Biogeochemistry, Kastanienbaum, Switzerland.,Department of Aquatic Ecology, Eawag Swiss Federal Institute of Aquatic Science and Technology, Centre for Ecology, Evolution and Biogeochemistry, Kastanienbaum, Switzerland
| | - Catherine L Peichel
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Ole Seehausen
- Department of Fish Ecology and Evolution, Eawag Swiss Federal Institute of Aquatic Science and Technology, Centre for Ecology, Evolution and Biogeochemistry, Kastanienbaum, Switzerland.,Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Goro Yoshizaki
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Jun Kitano
- Ecological Genetics Laboratory, National Institute of Genetics, Shizuoka, Japan. .,Department of Genetics, Graduate University for Advanced Studies (SOKENDAI), Shizuoka, Japan
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184
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Benn Torres J. Anthropological perspectives on genomic data, genetic ancestry, and race. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2019; 171 Suppl 70:74-86. [DOI: 10.1002/ajpa.23979] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 11/04/2019] [Accepted: 11/11/2019] [Indexed: 02/06/2023]
Affiliation(s)
- Jada Benn Torres
- Vanderbilt UniversityDepartment of Anthropology Nashville Tennessee
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185
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Crombie TA, Zdraljevic S, Cook DE, Tanny RE, Brady SC, Wang Y, Evans KS, Hahnel S, Lee D, Rodriguez BC, Zhang G, van der Zwagg J, Kiontke K, Andersen EC. Deep sampling of Hawaiian Caenorhabditis elegans reveals high genetic diversity and admixture with global populations. eLife 2019; 8:50465. [PMID: 31793880 PMCID: PMC6927746 DOI: 10.7554/elife.50465] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 12/02/2019] [Indexed: 01/04/2023] Open
Abstract
Hawaiian isolates of the nematode species Caenorhabditis elegans have long been known to harbor genetic diversity greater than the rest of the worldwide population, but this observation was supported by only a small number of wild strains. To better characterize the niche and genetic diversity of Hawaiian C. elegans and other Caenorhabditis species, we sampled different substrates and niches across the Hawaiian islands. We identified hundreds of new Caenorhabditis strains from known species and a new species, Caenorhabditis oiwi. Hawaiian C. elegans are found in cooler climates at high elevations but are not associated with any specific substrate, as compared to other Caenorhabditis species. Surprisingly, admixture analysis revealed evidence of shared ancestry between some Hawaiian and non-Hawaiian C. elegans strains. We suggest that the deep diversity we observed in Hawaii might represent patterns of ancestral genetic diversity in the C. elegans species before human influence.
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Affiliation(s)
- Tim A Crombie
- Department of Molecular Biosciences, Northwestern University, Evanston, United States
| | - Stefan Zdraljevic
- Department of Molecular Biosciences, Northwestern University, Evanston, United States.,Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, United States
| | - Daniel E Cook
- Department of Molecular Biosciences, Northwestern University, Evanston, United States.,Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, United States
| | - Robyn E Tanny
- Department of Molecular Biosciences, Northwestern University, Evanston, United States
| | - Shannon C Brady
- Department of Molecular Biosciences, Northwestern University, Evanston, United States.,Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, United States
| | - Ye Wang
- Department of Molecular Biosciences, Northwestern University, Evanston, United States
| | - Kathryn S Evans
- Department of Molecular Biosciences, Northwestern University, Evanston, United States.,Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, United States
| | - Steffen Hahnel
- Department of Molecular Biosciences, Northwestern University, Evanston, United States
| | - Daehan Lee
- Department of Molecular Biosciences, Northwestern University, Evanston, United States
| | - Briana C Rodriguez
- Department of Molecular Biosciences, Northwestern University, Evanston, United States
| | - Gaotian Zhang
- Department of Molecular Biosciences, Northwestern University, Evanston, United States
| | - Joost van der Zwagg
- Department of Molecular Biosciences, Northwestern University, Evanston, United States
| | - Karin Kiontke
- Department of Biology, New York University, New York, United States
| | - Erik C Andersen
- Department of Molecular Biosciences, Northwestern University, Evanston, United States
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186
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McHugo GP, Dover MJ, MacHugh DE. Unlocking the origins and biology of domestic animals using ancient DNA and paleogenomics. BMC Biol 2019; 17:98. [PMID: 31791340 PMCID: PMC6889691 DOI: 10.1186/s12915-019-0724-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 11/13/2019] [Indexed: 12/13/2022] Open
Abstract
Animal domestication has fascinated biologists since Charles Darwin first drew the parallel between evolution via natural selection and human-mediated breeding of livestock and companion animals. In this review we show how studies of ancient DNA from domestic animals and their wild progenitors and congeners have shed new light on the genetic origins of domesticates, and on the process of domestication itself. High-resolution paleogenomic data sets now provide unprecedented opportunities to explore the development of animal agriculture across the world. In addition, functional population genomics studies of domestic and wild animals can deliver comparative information useful for understanding recent human evolution.
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Affiliation(s)
- Gillian P McHugo
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, D04 V1W8, Ireland
| | - Michael J Dover
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, D04 V1W8, Ireland
| | - David E MacHugh
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, D04 V1W8, Ireland.
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, D04 V1W8, Ireland.
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187
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Chen P, Wu J, Luo L, Gao H, Wang M, Zou X, Li Y, Chen G, Luo H, Yu L, Han Y, Jia F, He G. Population Genetic Analysis of Modern and Ancient DNA Variations Yields New Insights Into the Formation, Genetic Structure, and Phylogenetic Relationship of Northern Han Chinese. Front Genet 2019; 10:1045. [PMID: 31737039 PMCID: PMC6832103 DOI: 10.3389/fgene.2019.01045] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 09/30/2019] [Indexed: 11/30/2022] Open
Abstract
Modern East Asians derived from the admixture of aborigines and incoming farmers expanding from Yellow and Yangtze River Basins. Distinct genetic differentiation and subsequent admixture between Northeast Asians and Southeast Asians subsequently evidenced by the mitochondrial DNA, Y-chromosomal variations, and autosomal SNPs. Recently, population geneticists have paid more attention to the genetic polymorphisms and background of southern-Han Chinese and southern native populations. The genetic legacy of northern-Han remains uncharacterized. Thus, we performed this comprehensive population genetic analyses of modern and ancient genetic variations aiming to yield new insight into the formation of modern Han, and the genetic ancestry and phylogenetic relationship of the northern-Han Chinese population. We first genotyped 25 forensic associated markers in 3,089 northern-Han Chinese individuals using the new-generation of the Huaxia Platinum System. And then we performed the first meta-analysis focused on the genetic affinity between Asian Neolithic∼Iron Age ancients and modern northern-Han Chinese by combining mitochondrial variations in 417 ancient individuals from 13 different archeological sites and 812 modern individuals, as well as Y-chromosomal variations in 114 ancient individuals from 12 Neolithic∼Iron Age sites and 2,810 modern subjects. We finally genotyped 643,897 genome-wide nucleotide polymorphisms (SNPs) in 20 Shanxi Han individuals and combined with 1,927 modern humans and 40 Eurasian ancient genomes to explore the genetic structure and admixture of northern-Han Chinese. We addressed genetic legacy, population structure and phylogenetic relationship of northern-Han Chinese via various analyses. Our population genetic results from five different reference datasets indicated that Shanxi Han shares a closer phylogenetic relationship with northern-neighbors and southern ethnically close groups than with Uyghur and Tibetan. Genome-wide variations revealed that modern northern-Han derived their ancestry from Yakut-related population (25.2%) and She-related population (74.8%). Summarily, the genetic mixing that led to the emergence of a Han Chinese ethnicity occurred at a very early period, probably in Neolithic times, and this mixing involved an ancient Tibeto-Burman population and a local pre-Sinitic population, which may have been linguistically Altaic.
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Affiliation(s)
- Pengyu Chen
- Center of Forensic Expertise, Affiliated Hospital of Zunyi Medical University, Zunyi, China.,Department of Forensic Medicine, Zunyi Medical University, Zunyi, China
| | - Jian Wu
- Center of Forensic Expertise, Affiliated Hospital of Zunyi Medical University, Zunyi, China.,Department of Forensic Medicine, Zunyi Medical University, Zunyi, China
| | - Li Luo
- Center of Forensic Expertise, Affiliated Hospital of Zunyi Medical University, Zunyi, China.,Department of Forensic Medicine, Zunyi Medical University, Zunyi, China
| | - Hongyan Gao
- Center of Forensic Expertise, Affiliated Hospital of Zunyi Medical University, Zunyi, China.,Department of Forensic Medicine, Zunyi Medical University, Zunyi, China
| | - Mengge Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Xing Zou
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Yingxiang Li
- Department of Bioinformatics, WeGene, Shenzhen, China
| | - Gang Chen
- Department of Bioinformatics, WeGene, Shenzhen, China
| | - Haibo Luo
- Department of Forensic Medicine, Zunyi Medical University, Zunyi, China
| | - Limei Yu
- Key Laboratory of Cell Engineering in Guizhou Province, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Yanyan Han
- Department of Nutrition and Food Hygiene, School of Public Health, Zunyi Medical University, Zunyi, China
| | - Fuquan Jia
- Department of Forensic Medicine, Inner Mongolia Medical University, Hohhot, China
| | - Guanglin He
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
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188
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Admixture in Mammals and How to Understand Its Functional Implications. Bioessays 2019; 41:e1900123. [DOI: 10.1002/bies.201900123] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 10/03/2019] [Indexed: 12/13/2022]
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189
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Abstract
For more than 50 years, biological anthropology has argued against the use of the biological race concept. Despite such efforts, aspects of the concept remain in circulation within society and within the discipline itself. As commonly articulated, anthropology's rejection of the biological race concept lacks an evolutionarily based explanatory grounding. Biological patterns of variation in living humans do not map onto commonly utilized categorizations of race, but this knowledge does not explain why human evolution has not produced such structures. This article attempts to offer one such explanation by constructing a biocultural framing of race around ancestry. By examining ancestry through two related lenses, genealogical and genetic, it is shown that the coherence of race as a biological concept has been disrupted by demographic changes in our recent evolutionary past. The biological construction of race is invalid not because it is impossible but because evolutionary forces have actively worked against such patterns in our evolutionary past.
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Affiliation(s)
- Adam P. Van Arsdale
- Department of Anthropology, Wellesley College, Wellesley, Massachusetts 02481, USA
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190
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Saber-Ayad M, Manzoor S, Radwan H, Hammoudeh S, Wardeh R, Ashraf A, Jabbar H, Hamoudi R. The FTO genetic variants are associated with dietary intake and body mass index amongst Emirati population. PLoS One 2019; 14:e0223808. [PMID: 31622411 PMCID: PMC6797190 DOI: 10.1371/journal.pone.0223808] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 09/27/2019] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND The risk of obesity is determined by complex interactions between genetic and environmental factors. Little research to date has investigated the interaction between gene and food intake. The aim of the current study is to explore the potential effect of fat mass and obesity-associated protein gene (FTO) rs9939609 and rs9930506 single nucleotide polymorphism (SNP) on the pattern of food intake in the Emirati population. METHODS Adult healthy Emirati subjects with Body mass index (BMI) of 16-40 kg/m2 were included in the study. Genotyping for FTO rs9939609(A>T) and rs9930506(A>G) was performed using DNA from saliva samples. Subjects were categorized according to the WHO classification by calculating the BMI to compare different classes. Dietary intake was assessed by a sixty-one-item FFQ that estimated food and beverage intakes over the past year. The daily energy, macronutrient, and micronutrient consumption were computed. RESULTS We included 169 subjects in the final analysis (mean age 30.49± 9.1years, 57.4% females). The mean BMI of the study population was 26.19 kg/m2. Both SNPs were in Hardy Weinberg Equilibrium. The rs9939609 AA genotype was significantly associated with higher BMI (p = 0.004); the effect was significant in females (p = 0.028), but not in males (p = 0.184). Carbohydrate intake was significantly higher in AA subjects with a trend of lower fat intake compared to other genotypes. The odds ratio for the AA was 3.78 in the fourth quartile and 2.67 for the A/T in the second quartile of total carbohydrate intake, considering the first quartile as a reference (95% CI = 1.017-14.1 and 1.03-6.88, respectively). Fat intake was significantly lower in the FTO rs9930506 GG subjects. The presence of FTO rs9930506 GG genotype decreased the fat intake in subjects with FTO rs9939609 AA (p = 0.037). CONCLUSIONS The results of this study highlight the interaction of the FTO risk alleles on the food intake in Emirati subjects. The FTO rs9939609 AA subjects had higher carbohydrate and lower fat intake. The latter was accentuated in presence of rs9930506 GG genotype.
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Affiliation(s)
- Maha Saber-Ayad
- College of Medicine, University of Sharjah, Sharjah, UAE
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, UAE
- College of Medicine, Cairo University, Cairo, Egypt
| | - Shaista Manzoor
- College of Medicine, University of Sharjah, Sharjah, UAE
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, UAE
| | - Hadia Radwan
- College of Medicine, University of Sharjah, Sharjah, UAE
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, UAE
- Clinical Nutrition and Dietetics Department, College of Health Sciences, University of Sharjah, Sharjah, UAE
| | - Sarah Hammoudeh
- College of Medicine, University of Sharjah, Sharjah, UAE
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, UAE
| | - Rahaf Wardeh
- College of Medicine, University of Sharjah, Sharjah, UAE
| | - Ahmed Ashraf
- College of Medicine, University of Sharjah, Sharjah, UAE
| | - Hussein Jabbar
- College of Medicine, University of Sharjah, Sharjah, UAE
| | - Rifat Hamoudi
- College of Medicine, University of Sharjah, Sharjah, UAE
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, UAE
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191
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Popejoy AB. Diversity In Precision Medicine And Pharmacogenetics: Methodological And Conceptual Considerations For Broadening Participation. PHARMACOGENOMICS & PERSONALIZED MEDICINE 2019; 12:257-271. [PMID: 31686892 PMCID: PMC6800456 DOI: 10.2147/pgpm.s179742] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 09/12/2019] [Indexed: 01/01/2023]
Abstract
Genome-wide association studies (GWAS) have revealed important links between genetic markers across the human genome and phenotypic traits, including risk factors for disease. Studies have shown that GWAS continue to be overwhelmingly conducted on people of primarily European descent, despite the fact that the vast majority of human genomic variation is present in non-European populations such as those in Africa. To enhance our understanding of diversity in the pharmacogenomics and precision medicine literature, this review provides a window into the representation of biogeographical populations that have been studied for pharmacogenetic traits, such as enzyme metabolism and adverse drug response. Using the Medical Subject Headings (MeSH) ontology search terms in PubMed, studies were identified that are either population-based, or include a description of the study population on the basis of biological or environmental diversity. The results of this scoping review indicate that the majority of relevant papers (>95% of studies tagged in PubMed with MeSH terms “precision medicine” or “pharmacogenetics”, N=23,701) are not annotated with the “population group” MeSH term, suggesting that the majority of studies in this literature are not population-based, or the authors chose not to describe the study population. Among those studies related to pharmacogenetics or precision medicine that are specific to human population groups (N=1006) and were included in the analysis after filtering and screening on eligibility criteria (N=192), the majority of single-population studies included individuals of African, Asian, and European origins, or genetic ancestry. Combining studies of single and multiple populations, 33% involve participants of Asian origin or ancestry; 30% European; 24% African; 10% Hispanic or Latino; and < 3% American Indian or Alaska Native. These data provide a baseline for future comparison, indicating which biogeographic groups have informed the pharmacogenomic knowledgebase specific to diverse human populations. Challenges and potential solutions to improve diversity in the field and in genetics research more broadly are discussed.
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Affiliation(s)
- Alice B Popejoy
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA.,Center for Computational, Evolutionary and Human Genomics (CEHG), Stanford University, Stanford, CA, USA.,Center for Integration of Research on Genetics and Ethics (CIRGE), Stanford University, Stanford, CA, USA
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192
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Abstract
PURPOSE OF REVIEW The goal of the review is to provide a comprehensive overview of the current understanding of the mechanisms underlying variation in human stature. RECENT FINDINGS Human height is an anthropometric trait that varies considerably within human populations as well as across the globe. Historically, much research focus was placed on understanding the biology of growth plate chondrocytes and how modifications to core chondrocyte proliferation and differentiation pathways potentially shaped height attainment in normal as well as pathological contexts. Recently, much progress has been made to improve our understanding regarding the mechanisms underlying the normal and pathological range of height variation within as well as between human populations, and today, it is understood to reflect complex interactions among a myriad of genetic, environmental, and evolutionary factors. Indeed, recent improvements in genetics (e.g., GWAS) and breakthroughs in functional genomics (e.g., whole exome sequencing, DNA methylation analysis, ATAC-sequencing, and CRISPR) have shed light on previously unknown pathways/mechanisms governing pathological and common height variation. Additionally, the use of an evolutionary perspective has also revealed important mechanisms that have shaped height variation across the planet. This review provides an overview of the current knowledge of the biological mechanisms underlying height variation by highlighting new research findings on skeletal growth control with an emphasis on previously unknown pathways/mechanisms influencing pathological and common height variation. In this context, this review also discusses how evolutionary forces likely shaped the genomic architecture of height across the globe.
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Affiliation(s)
| | - Terence D Capellini
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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193
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Large-Scale Whole-Genome Sequencing of Three Diverse Asian Populations in Singapore. Cell 2019; 179:736-749.e15. [DOI: 10.1016/j.cell.2019.09.019] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Revised: 06/24/2019] [Accepted: 09/19/2019] [Indexed: 12/19/2022]
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194
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Horwood PF, Tarantola A, Goarant C, Matsui M, Klement E, Umezaki M, Navarro S, Greenhill AR. Health Challenges of the Pacific Region: Insights From History, Geography, Social Determinants, Genetics, and the Microbiome. Front Immunol 2019; 10:2184. [PMID: 31572391 PMCID: PMC6753857 DOI: 10.3389/fimmu.2019.02184] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 08/29/2019] [Indexed: 02/06/2023] Open
Abstract
The Pacific region, also referred to as Oceania, is a geographically widespread region populated by people of diverse cultures and ethnicities. Indigenous people in the region (Melanesians, Polynesians, Micronesians, Papuans, and Indigenous Australians) are over-represented on national, regional, and global scales for the burden of infectious and non-communicable diseases. Although social and environmental factors such as poverty, education, and access to health-care are assumed to be major drivers of this disease burden, there is also developing evidence that genetic and microbiotic factors should also be considered. To date, studies investigating genetic and/or microbiotic links with vulnerabilities to infectious and non-communicable diseases have mostly focused on populations in Europe, Asia, and USA, with uncertain associations for other populations such as indigenous communities in Oceania. Recent developments in personalized medicine have shown that identifying ethnicity-linked genetic vulnerabilities can be important for medical management. Although our understanding of the impacts of the gut microbiome on health is still in the early stages, it is likely that equivalent vulnerabilities will also be identified through the interaction between gut microbiome composition and function with pathogens and the host immune system. As rapid economic, dietary, and cultural changes occur throughout Oceania it becomes increasingly important that further research is conducted within indigenous populations to address the double burden of high rates of infectious diseases and rapidly rising non-communicable diseases so that comprehensive development goals can be planned. In this article, we review the current knowledge on the impact of nutrition, genetics, and the gut microbiome on infectious diseases in indigenous people of the Pacific region.
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Affiliation(s)
- Paul F. Horwood
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD, Australia
| | | | - Cyrille Goarant
- Institut Pasteur de Nouvelle-Calédonie, Noumea, New Caledonia
| | - Mariko Matsui
- Institut Pasteur de Nouvelle-Calédonie, Noumea, New Caledonia
| | - Elise Klement
- Institut Pasteur de Nouvelle-Calédonie, Noumea, New Caledonia
- Internal Medicine and Infectious Diseases Department, Centre Hospitalier Territorial, Noumea, New Caledonia
| | - Masahiro Umezaki
- Department of Human Ecology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Severine Navarro
- Immunology Department, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Andrew R. Greenhill
- School of Health and Life Sciences, Federation University Australia, Churchill, VIC, Australia
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195
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Muriuki JM, Mentzer AJ, Band G, Gilchrist JJ, Carstensen T, Lule SA, Goheen MM, Joof F, Kimita W, Mogire R, Cutland CL, Diarra A, Rautanen A, Pomilla C, Gurdasani D, Rockett K, Mturi N, Ndungu FM, Scott JAG, Sirima SB, Morovat A, Prentice AM, Madhi SA, Webb EL, Elliott AM, Bejon P, Sandhu MS, Hill AVS, Kwiatkowski DP, Williams TN, Cerami C, Atkinson SH. The ferroportin Q248H mutation protects from anemia, but not malaria or bacteremia. SCIENCE ADVANCES 2019; 5:eaaw0109. [PMID: 31517041 PMCID: PMC6726445 DOI: 10.1126/sciadv.aaw0109] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 08/06/2019] [Indexed: 06/10/2023]
Abstract
Iron acquisition is critical for life. Ferroportin (FPN) exports iron from mature erythrocytes, and deletion of the Fpn gene results in hemolytic anemia and increased fatality in malaria-infected mice. The FPN Q248H mutation (glutamine to histidine at position 248) renders FPN partially resistant to hepcidin-induced degradation and was associated with protection from malaria in human studies of limited size. Using data from cohorts including over 18,000 African children, we show that the Q248H mutation is associated with modest protection against anemia, hemolysis, and iron deficiency, but we found little evidence of protection against severe malaria or bacteremia. We additionally observed no excess Plasmodium growth in Q248H erythrocytes ex vivo, nor evidence of selection driven by malaria exposure, suggesting that the Q248H mutation does not protect from malaria and is unlikely to deprive malaria parasites of iron essential for their growth.
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Affiliation(s)
- John Muthii Muriuki
- Kenya Medical Research Institute (KEMRI) Wellcome Trust Research Programme, Kilifi, Kenya
| | - Alexander J. Mentzer
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Gavin Band
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - James J. Gilchrist
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Department of Paediatrics, University of Oxford, Oxford, UK
| | | | - Swaib A. Lule
- Medical Research Council/Uganda Virus Research Institute and London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda
- London School of Hygiene and Tropical Medicine, London, UK
| | - Morgan M. Goheen
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Banjul, The Gambia
- University of North Carolina School of Medicine, CB 7435, Chapel Hill, North Carolina USA
| | - Fatou Joof
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Wandia Kimita
- Kenya Medical Research Institute (KEMRI) Wellcome Trust Research Programme, Kilifi, Kenya
| | - Reagan Mogire
- Kenya Medical Research Institute (KEMRI) Wellcome Trust Research Programme, Kilifi, Kenya
| | - Clare L. Cutland
- Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Amidou Diarra
- Centre de Recherche Action en Sante (GRAS), 06 BP 10248, Ouagadougou 06, Burkina Faso
| | - Anna Rautanen
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | | | - Kirk Rockett
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Neema Mturi
- Kenya Medical Research Institute (KEMRI) Wellcome Trust Research Programme, Kilifi, Kenya
| | - Francis M. Ndungu
- Kenya Medical Research Institute (KEMRI) Wellcome Trust Research Programme, Kilifi, Kenya
| | - J. Anthony G. Scott
- Kenya Medical Research Institute (KEMRI) Wellcome Trust Research Programme, Kilifi, Kenya
- London School of Hygiene and Tropical Medicine, London, UK
| | - Sodiomon B. Sirima
- Centre de Recherche Action en Sante (GRAS), 06 BP 10248, Ouagadougou 06, Burkina Faso
| | - Alireza Morovat
- Department of Clinical Biochemistry, Oxford University Hospitals, Oxford, UK
| | - Andrew M. Prentice
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Shabir A. Madhi
- Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Emily L. Webb
- London School of Hygiene and Tropical Medicine, London, UK
| | - Alison M. Elliott
- Medical Research Council/Uganda Virus Research Institute and London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda
- London School of Hygiene and Tropical Medicine, London, UK
| | - Philip Bejon
- Kenya Medical Research Institute (KEMRI) Wellcome Trust Research Programme, Kilifi, Kenya
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Adrian V. S. Hill
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Centre for Clinical Vaccinology and Tropical Medicine and the Jenner Institute Laboratories, University of Oxford, Oxford, UK
| | - Dominic P. Kwiatkowski
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Thomas N. Williams
- Kenya Medical Research Institute (KEMRI) Wellcome Trust Research Programme, Kilifi, Kenya
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Department of Medicine, Imperial College, London, UK
| | - Carla Cerami
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Sarah H. Atkinson
- Kenya Medical Research Institute (KEMRI) Wellcome Trust Research Programme, Kilifi, Kenya
- Department of Paediatrics, University of Oxford, Oxford, UK
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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196
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Oosting T, Star B, Barrett JH, Wellenreuther M, Ritchie PA, Rawlence NJ. Unlocking the potential of ancient fish DNA in the genomic era. Evol Appl 2019; 12:1513-1522. [PMID: 31462911 PMCID: PMC6708421 DOI: 10.1111/eva.12811] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 04/11/2019] [Accepted: 04/29/2019] [Indexed: 12/17/2022] Open
Abstract
Fish are the most diverse group of vertebrates, fulfil important ecological functions and are of significant economic interest for aquaculture and wild fisheries. Advances in DNA extraction methods, sequencing technologies and bioinformatic applications have advanced genomic research for nonmodel organisms, allowing the field of fish ancient DNA (aDNA) to move into the genomics era. This move is enabling researchers to investigate a multitude of new questions in evolutionary ecology that could not, until now, be addressed. In many cases, these new fields of research have relevance to evolutionary applications, such as the sustainable management of fisheries resources and the conservation of aquatic animals. Here, we focus on the application of fish aDNA to (a) highlight new research questions, (b) outline methodological advances and current challenges, (c) discuss how our understanding of fish ecology and evolution can benefit from aDNA applications and (d) provide a future perspective on how the field will help answer key questions in conservation and management. We conclude that the power of fish aDNA will be unlocked through the application of continually improving genomic resources and methods to well-chosen taxonomic groups represented by well-dated archaeological samples that can provide temporally and/or spatially extensive data sets.
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Affiliation(s)
- Tom Oosting
- School of Biological SciencesVictoria University of WellingtonWellingtonNew Zealand
| | - Bastiaan Star
- Department of Biosciences, Centre for Ecological and Evolutionary SynthesisUniversity of OsloOsloNorway
| | - James H. Barrett
- Department of ArchaeologyUniversity of CambridgeCambridgeUK
- Department of Archaeology and Cultural HistoryNTNU University MuseumTrondheimNorway
- Trinity Centre for Environmental HumanitiesTrinity College DublinDublinIreland
| | - Maren Wellenreuther
- Nelson Seafood Research UnitPlant and Food ResearchNelsonNew Zealand
- School of Biological SciencesUniversity of AucklandAucklandNew Zealand
| | - Peter A. Ritchie
- School of Biological SciencesVictoria University of WellingtonWellingtonNew Zealand
| | - Nicolas J. Rawlence
- Otago Palaeogenetics Laboratory, Department of ZoologyUniversity of OtagoDunedinNew Zealand
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197
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Small ST, Labbé F, Coulibaly YI, Nutman TB, King CL, Serre D, Zimmerman PA. Human Migration and the Spread of the Nematode Parasite Wuchereria bancrofti. Mol Biol Evol 2019; 36:1931-1941. [PMID: 31077328 PMCID: PMC6735882 DOI: 10.1093/molbev/msz116] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The human disease lymphatic filariasis causes the debilitating effects of elephantiasis and hydrocele. Lymphatic filariasis currently affects the lives of 90 million people in 52 countries. There are three nematodes that cause lymphatic filariasis, Brugia malayi, Brugia timori, and Wuchereria bancrofti, but 90% of all cases of lymphatic filariasis are caused solely by W. bancrofti (Wb). Here we use population genomics to reconstruct the probable route and timing of migration of Wb strains that currently infect Africa, Haiti, and Papua New Guinea (PNG). We used selective whole genome amplification to sequence 42 whole genomes of single Wb worms from populations in Haiti, Mali, Kenya, and PNG. Our results are consistent with a hypothesis of an Island Southeast Asia or East Asian origin of Wb. Our demographic models support divergence times that correlate with the migration of human populations. We hypothesize that PNG was infected at two separate times, first by the Melanesians and later by the migrating Austronesians. The migrating Austronesians also likely introduced Wb to Madagascar where later migrations spread it to continental Africa. From Africa, Wb spread to the New World during the transatlantic slave trade. Genome scans identified 17 genes that were highly differentiated among Wb populations. Among these are genes associated with human immune suppression, insecticide sensitivity, and proposed drug targets. Identifying the distribution of genetic diversity in Wb populations and selection forces acting on the genome will build a foundation to test future hypotheses and help predict response to current eradication efforts.
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Affiliation(s)
- Scott T Small
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN
| | - Frédéric Labbé
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN
| | - Yaya I Coulibaly
- Head Filariasis Unit, NIAID-Mali ICER, University of Bamako, Bamako, Mali
| | | | - Christopher L King
- Global Health and Disease, Case Western Reserve University, Cleveland, OH
| | - David Serre
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD
| | - Peter A Zimmerman
- Global Health and Disease, Case Western Reserve University, Cleveland, OH
- Department of Biology, Case Western Reserve University, Cleveland, OH
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198
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Abstract
Cryosphere services (CSs) refer to various benefits that humans directly or indirectly obtain from the cryosphere, which makes significant contributions to human well-being (HWB). To facilitate such research, we first present a classification system for conceptualizing, monitoring and assessing CSs based on the current process-based understanding of their nature and sustainability. Specifically, the CSs are grouped into five major categories (provisioning, regulating, cultural, bearing and supporting services) and 18 sub-categories. Then we provide a detailed overview on formation, current status and anticipated future changes of the identified types of the services, and their impact on HWB. Finally, the spatio-temporal scales, the links of the services with HWB and climate-dependence are further discussed. The research of CSs adopt interdisciplinary approach to address the formation mechanisms of CSs and their dynamic relationships with HWB, which is poised to provide a better understanding of the cryosphere’s role in human society and help enhance socio-ecological sustainability and HWB over cryosphere-affected areas. Notably, most CSs have been deteriorating under global warming and cryosphere shrinkage, further leading to negative impacts on associated HWB. Therefore, great attention should be paid to the changes in CSs and their cascading risks.
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199
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Signatures of Recent Positive Selection in Enhancers Across 41 Human Tissues. G3-GENES GENOMES GENETICS 2019; 9:2761-2774. [PMID: 31213516 PMCID: PMC6686946 DOI: 10.1534/g3.119.400186] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Evolutionary changes in enhancers are widely associated with variation in human traits and diseases. However, studies comprehensively quantifying levels of selection on enhancers at multiple evolutionary periods during recent human evolution and how enhancer evolution varies across human tissues are lacking. To address these questions, we integrated a dataset of 41,561 transcribed enhancers active in 41 different human tissues (FANTOM Consortium) with whole genome sequences of 1,668 individuals from the African, Asian, and European populations (1000 Genomes Project). Our analyses based on four different metrics (Tajima’s D, FST, H12, nSL) showed that ∼5.90% of enhancers showed evidence of recent positive selection and that genes associated with enhancers under very recent positive selection are enriched for diverse immune-related functions. The distributions of these metrics for brain and testis enhancers were often statistically significantly different and in the direction suggestive of less positive selection compared to those of other tissues; the same was true for brain and testis enhancers that are tissue-specific compared to those that are tissue-broad and for testis enhancers associated with tissue-enriched and non-tissue-enriched genes. These differences varied considerably across metrics and tissues and were generally in the form of changes in distributions’ shapes rather than shifts in their values. Collectively, these results suggest that many human enhancers experienced recent positive selection throughout multiple time periods in human evolutionary history, that this selection occurred in a tissue-dependent and immune-related functional context, and that much like the evolution of their protein-coding gene counterparts, the evolution of brain and testis enhancers has been markedly different from that of enhancers in other tissues.
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200
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Joseph TA, Pe'er I. Inference of Population Structure from Time-Series Genotype Data. Am J Hum Genet 2019; 105:317-333. [PMID: 31256878 PMCID: PMC6698887 DOI: 10.1016/j.ajhg.2019.06.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 06/04/2019] [Indexed: 10/26/2022] Open
Abstract
Sequencing ancient DNA can offer direct probing of population history. Yet, such data are commonly analyzed with standard tools that assume DNA samples are all contemporary. We present DyStruct, a model and inference algorithm for inferring shared ancestry from temporally sampled genotype data. DyStruct explicitly incorporates temporal dynamics by modeling individuals as mixtures of unobserved populations whose allele frequencies drift over time. We develop an efficient inference algorithm for our model using stochastic variational inference. On simulated data, we show that DyStruct outperforms the current state of the art when individuals are sampled over time. Using a dataset of 296 modern and 80 ancient samples, we demonstrate DyStruct is able to capture a well-supported admixture event of steppe ancestry into modern Europe. We further apply DyStruct to a genome-wide dataset of 2,067 modern and 262 ancient samples used to study the origin of farming in the Near East. We show that DyStruct provides new insight into population history when compared with alternate approaches, within feasible run time.
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Affiliation(s)
- Tyler A Joseph
- Department of Computer Science, Columbia University, New York, NY 10027, USA.
| | - Itsik Pe'er
- Department of Computer Science, Columbia University, New York, NY 10027, USA; Department of Systems Biology, Columbia University, New York, NY 10027, USA; Data Science Institute, Columbia University, New York, NY 10027, USA.
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