1
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Cotter DJ, Severson AL, Kang JTL, Godrej HN, Carmi S, Rosenberg NA. Modeling the effects of consanguinity on autosomal and X-chromosomal runs of homozygosity and identity-by-descent sharing. G3 (BETHESDA, MD.) 2024; 14:jkad264. [PMID: 37972246 PMCID: PMC10849319 DOI: 10.1093/g3journal/jkad264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 11/01/2023] [Accepted: 11/08/2023] [Indexed: 11/19/2023]
Abstract
Runs of homozygosity (ROH) and identity-by-descent (IBD) sharing can be studied in diploid coalescent models by noting that ROH and IBD-sharing at a genomic site are predicted to be inversely related to coalescence times-which in turn can be mathematically obtained in terms of parameters describing consanguinity rates. Comparing autosomal and X-chromosomal coalescent models, we consider ROH and IBD-sharing in relation to consanguinity that proceeds via multiple forms of first-cousin mating. We predict that across populations with different levels of consanguinity, (1) in a manner that is qualitatively parallel to the increase of autosomal IBD-sharing with autosomal ROH, X-chromosomal IBD-sharing increases with X-chromosomal ROH, owing to the dependence of both quantities on consanguinity levels; (2) even in the absence of consanguinity, X-chromosomal ROH and IBD-sharing levels exceed corresponding values for the autosomes, owing to the smaller population size and lower coalescence time for the X chromosome than for autosomes; (3) with matrilateral consanguinity, the relative increase in ROH and IBD-sharing on the X chromosome compared to the autosomes is greater than in the absence of consanguinity. Examining genome-wide SNPs in human populations for which consanguinity levels have been estimated, we find that autosomal and X-chromosomal ROH and IBD-sharing levels generally accord with the predictions. We find that each 1% increase in autosomal ROH is associated with an increase of 2.1% in X-chromosomal ROH, and each 1% increase in autosomal IBD-sharing is associated with an increase of 1.6% in X-chromosomal IBD-sharing. For each calculation, particularly for ROH, the estimate is reasonably close to the increase of 2% predicted by the population-size difference between autosomes and X chromosomes. The results support the utility of coalescent models for understanding patterns of genomic sharing and their dependence on sex-biased processes.
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Affiliation(s)
- Daniel J Cotter
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Alissa L Severson
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Jonathan T L Kang
- School of Math and Science, Singapore Polytechnic, 139651, Singapore
| | - Hormazd N Godrej
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Shai Carmi
- Braun School of Public Health and Community Medicine, Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Noah A Rosenberg
- Department of Biology, Stanford University, Stanford, CA 94305, USA
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2
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Izarraras-Gomez A, Ortega-Del Vecchyo D. Ancient DNA uncovers past migrations in California. Nature 2023; 624:43-44. [PMID: 37993617 DOI: 10.1038/d41586-023-03503-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2023]
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3
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Mooney JA, Agranat-Tamir L, Pritchard JK, Rosenberg NA. On the number of genealogical ancestors tracing to the source groups of an admixed population. Genetics 2023; 224:iyad079. [PMID: 37410594 PMCID: PMC10324943 DOI: 10.1093/genetics/iyad079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 04/05/2023] [Indexed: 07/08/2023] Open
Abstract
Members of genetically admixed populations possess ancestry from multiple source groups, and studies of human genetic admixture frequently estimate ancestry components corresponding to fractions of individual genomes that trace to specific ancestral populations. However, the same numerical ancestry fraction can represent a wide array of admixture scenarios within an individual's genealogy. Using a mechanistic model of admixture, we consider admixture genealogically: how many ancestors from the source populations does the admixture represent? We consider African-Americans, for whom continent-level estimates produce a 75-85% value for African ancestry on average and 15-25% for European ancestry. Genetic studies together with key features of African-American demographic history suggest ranges for parameters of a simple three-epoch model. Considering parameter sets compatible with estimates of current ancestry levels, we infer that if all genealogical lines of a random African-American born during 1960-1965 are traced back until they reach members of source populations, the mean over parameter sets of the expected number of genealogical lines terminating with African individuals is 314 (interquartile range 240-376), and the mean of the expected number terminating in Europeans is 51 (interquartile range 32-69). Across discrete generations, the peak number of African genealogical ancestors occurs in birth cohorts from the early 1700s, and the probability exceeds 50% that at least one European ancestor was born more recently than 1835. Our genealogical perspective can contribute to further understanding the admixture processes that underlie admixed populations. For African-Americans, the results provide insight both on how many of the ancestors of a typical African-American might have been forcibly displaced in the Transatlantic Slave Trade and on how many separate European admixture events might exist in a typical African-American genealogy.
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Affiliation(s)
- Jazlyn A Mooney
- Department of Biology, Stanford University, Stanford, CA 94305, USA
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | | | - Jonathan K Pritchard
- Department of Biology, Stanford University, Stanford, CA 94305, USA
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Noah A Rosenberg
- Department of Biology, Stanford University, Stanford, CA 94305, USA
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4
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Aqil A, Gill S, Gokcumen O, Malhi RS, Reese EA, Smith JL, Heaton TT, Lindqvist C. A paleogenome from a Holocene individual supports genetic continuity in Southeast Alaska. iScience 2023; 26:106581. [PMID: 37138779 PMCID: PMC10149335 DOI: 10.1016/j.isci.2023.106581] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 02/27/2023] [Accepted: 04/03/2023] [Indexed: 05/05/2023] Open
Abstract
Many specifics of the population histories of the Indigenous peoples of North America remain contentious owing to a dearth of physical evidence. Only few ancient human genomes have been recovered from the Pacific Northwest Coast, a region increasingly supported as a coastal migration route for the initial peopling of the Americas. Here, we report paleogenomic data from the remains of a ∼3,000-year-old female individual from Southeast Alaska, named Tatóok yík yées sháawat (TYYS). Our results demonstrate at least 3,000 years of matrilineal genetic continuity in Southeast Alaska, and that TYYS is most closely related to ancient and present-day northern Pacific Northwest Coast Indigenous Americans. We find no evidence of Paleo-Inuit (represented by Saqqaq) ancestry in present-day or ancient Pacific Northwest peoples. Instead, our analyses suggest the Saqqaq genome harbors Northern Native American ancestry. This study sheds further light on the human population history of the northern Pacific Northwest Coast.
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Affiliation(s)
- Alber Aqil
- Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260, USA
| | - Stephanie Gill
- Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260, USA
| | - Omer Gokcumen
- Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260, USA
| | - Ripan S. Malhi
- Department of Anthropology and Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | | | - Jane L. Smith
- USDA-Forest Service, Tongass National Forest, Petersburg, AK 99833, USA
| | - Timothy T. Heaton
- Department of Earth Sciences, University of South Dakota, Vermillion, SD 57069, USA
| | - Charlotte Lindqvist
- Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260, USA
- Corresponding author
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5
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Abstract
SignificanceCalifornia supports a high cultural and linguistic diversity of Indigenous peoples. In a partnership of researchers with the Muwekma Ohlone tribe, we studied genomes of eight present-day tribal members and 12 ancient individuals from two archaeological sites in the San Francisco Bay Area, spanning ∼2,000 y. We find that compared to genomes of Indigenous individuals from throughout the Americas, the 12 ancient individuals are most genetically similar to ancient individuals from Southern California, and that despite spanning a large time period, they share distinctive ancestry. This ancestry is also shared with present-day tribal members, providing evidence of genetic continuity between past and present Indigenous individuals in the region, in contrast to some popular reconstructions based on archaeological and linguistic information.
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Abstract
Throughout human history, large-scale migrations have facilitated the formation of populations with ancestry from multiple previously separated populations. This process leads to subsequent shuffling of genetic ancestry through recombination, producing variation in ancestry between populations, among individuals in a population, and along the genome within an individual. Recent methodological and empirical developments have elucidated the genomic signatures of this admixture process, bringing previously understudied admixed populations to the forefront of population and medical genetics. Under this theme, we present a collection of recent PLOS Genetics publications that exemplify recent progress in human genetic admixture studies, and we discuss potential areas for future work.
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Affiliation(s)
- Katharine L. Korunes
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina, United States of America
| | - Amy Goldberg
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina, United States of America
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7
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Marchi N, Excoffier L. Gene flow as a simple cause for an excess of high-frequency-derived alleles. Evol Appl 2020; 13:2254-2263. [PMID: 33005222 PMCID: PMC7513730 DOI: 10.1111/eva.12998] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 04/30/2020] [Accepted: 05/04/2020] [Indexed: 01/19/2023] Open
Abstract
Most human populations exhibit an excess of high-frequency variants, leading to a U-shaped site-frequency spectrum (uSFS). This pattern has been generally interpreted as a signature of ongoing episodes of positive selection, or as evidence for a mis-assignment of ancestral/derived allelic states, but uSFS has also been observed in populations receiving gene flow from a ghost population, in structured populations, or after range expansions. In order to better explain the prevalence of high-frequency variants in humans and other populations, we describe here which patterns of gene flow and population demography can lead to uSFS by using extensive coalescent simulations. We find that uSFS can often be observed in a population if gene flow brings a few ancestral alleles from a well-differentiated population. Gene flow can either consist in single pulses of admixture or continuous immigration, but different demographic conditions are necessary to observe uSFS in these two scenarios. Indeed, an extremely low and recent gene flow is required in the case of single admixture events, while with continuous immigration, uSFS occurs only if gene flow started recently at a high rate or if it lasted for a long time at a low rate. Overall, we find that a neutral uSFS occurs under more restrictive conditions in populations having received single pulses of gene flow than in populations exposed to continuous gene flow. We also show that the uSFS observed in human populations from the 1000 Genomes Project can easily be explained by gene flow from surrounding populations without requiring past episodes of positive selection. These results imply that uSFS should be common in non-isolated populations, such as most wild or domesticated plants and animals.
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Affiliation(s)
- Nina Marchi
- CMPGInstitute of Ecology and EvolutionUniversity of BerneBerneSwitzerland
- Swiss Institute of BioinformaticsLausanneSwitzerland
| | - Laurent Excoffier
- CMPGInstitute of Ecology and EvolutionUniversity of BerneBerneSwitzerland
- Swiss Institute of BioinformaticsLausanneSwitzerland
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8
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Kim HI, Ye B, Gosalia N, Köroğlu Ç, Hanson RL, Hsueh WC, Knowler WC, Baier LJ, Bogardus C, Shuldiner AR, Van Hout CV, Van Hout CV. Characterization of Exome Variants and Their Metabolic Impact in 6,716 American Indians from the Southwest US. Am J Hum Genet 2020; 107:251-264. [PMID: 32640185 DOI: 10.1016/j.ajhg.2020.06.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 06/10/2020] [Indexed: 12/21/2022] Open
Abstract
Applying exome sequencing to populations with unique genetic architecture has the potential to reveal novel genes and variants associated with traits and diseases. We sequenced and analyzed the exomes of 6,716 individuals from a Southwestern American Indian (SWAI) population with well-characterized metabolic traits. We found that the SWAI population has distinct allelic architecture compared to populations of European and East Asian ancestry, and there were many predicted loss-of-function (pLOF) and nonsynonymous variants that were highly enriched or private in the SWAI population. We used pLOF and nonsynonymous variants in the SWAI population to evaluate gene-burden associations of candidate genes from European genome-wide association studies (GWASs) for type 2 diabetes, body mass index, and four major plasma lipids. We found 19 significant gene-burden associations for 11 genes, providing additional evidence for prioritizing candidate effector genes of GWAS signals. Interestingly, these associations were mainly driven by pLOF and nonsynonymous variants that are unique or highly enriched in the SWAI population. Particularly, we found four pLOF or nonsynonymous variants in APOB, APOE, PCSK9, and TM6SF2 that are private or enriched in the SWAI population and associated with low-density lipoprotein (LDL) cholesterol levels. Their large estimated effects on LDL cholesterol levels suggest strong impacts on protein function and potential clinical implications of these variants in cardiovascular health. In summary, our study illustrates the utility and potential of exome sequencing in genetically unique populations, such as the SWAI population, to prioritize candidate effector genes within GWAS loci and to find additional variants in known disease genes with potential clinical impact.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Cristopher V Van Hout
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591, USA.
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9
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ADMIXPIPE: population analyses in ADMIXTURE for non-model organisms. BMC Bioinformatics 2020; 21:337. [PMID: 32727359 PMCID: PMC7391514 DOI: 10.1186/s12859-020-03701-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 07/23/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Research on the molecular ecology of non-model organisms, while previously constrained, has now been greatly facilitated by the advent of reduced-representation sequencing protocols. However, tools that allow these large datasets to be efficiently parsed are often lacking, or if indeed available, then limited by the necessity of a comparable reference genome as an adjunct. This, of course, can be difficult when working with non-model organisms. Fortunately, pipelines are currently available that avoid this prerequisite, thus allowing data to be a priori parsed. An oft-used molecular ecology program (i.e., STRUCTURE), for example, is facilitated by such pipelines, yet they are surprisingly absent for a second program that is similarly popular and computationally more efficient (i.e., ADMIXTURE). The two programs differ in that ADMIXTURE employs a maximum-likelihood framework whereas STRUCTURE uses a Bayesian approach, yet both produce similar results. Given these issues, there is an overriding (and recognized) need among researchers in molecular ecology for bioinformatic software that will not only condense output from replicated ADMIXTURE runs, but also infer from these data the optimal number of population clusters (K). RESULTS Here we provide such a program (i.e., ADMIXPIPE) that (a) filters SNPs to allow the delineation of population structure in ADMIXTURE, then (b) parses the output for summarization and graphical representation via CLUMPAK. Our benchmarks effectively demonstrate how efficient the pipeline is for processing large, non-model datasets generated via double digest restriction-site associated DNA sequencing (ddRAD). Outputs not only parallel those from STRUCTURE, but also visualize the variation among individual ADMIXTURE runs, so as to facilitate selection of the most appropriate K-value. CONCLUSIONS ADMIXPIPE successfully integrates ADMIXTURE analysis with popular variant call format (VCF) filtering software to yield file types readily analyzed by CLUMPAK. Large population genomic datasets derived from non-model organisms are efficiently analyzed via the parallel-processing capabilities of ADMIXTURE. ADMIXPIPE is distributed under the GNU Public License and freely available for Mac OSX and Linux platforms at: https://github.com/stevemussmann/admixturePipeline .
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10
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Goldberg A, Rastogi A, Rosenberg NA. Assortative mating by population of origin in a mechanistic model of admixture. Theor Popul Biol 2020; 134:129-146. [PMID: 32275920 DOI: 10.1016/j.tpb.2020.02.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 02/11/2020] [Accepted: 02/27/2020] [Indexed: 02/01/2023]
Abstract
Populations whose mating pairs have levels of similarity in phenotypes or genotypes that differ systematically from the level expected under random mating are described as experiencing assortative mating. Excess similarity in mating pairs is termed positive assortative mating, and excess dissimilarity is negative assortative mating. In humans, empirical studies suggest that mating pairs from various admixed populations - whose ancestry derives from two or more source populations - possess correlated ancestry components that indicate the occurrence of positive assortative mating on the basis of ancestry. Generalizing a two-sex mechanistic admixture model, we devise a model of one form of ancestry-assortative mating that occurs through preferential mating based on source population. Under the model, we study the moments of the admixture fraction distribution for different assumptions about mating preferences, including both positive and negative assortative mating by population. We demonstrate that whereas the mean admixture under assortative mating is equivalent to that of a corresponding randomly mating population, the variance of admixture depends on the level and direction of assortative mating. We consider two special cases of assortative mating by population: first, a single admixture event, and second, constant contributions to the admixed population over time. In contrast to standard settings in which positive assortment increases variation within a population, certain assortative mating scenarios allow the variance of admixture to decrease relative to a corresponding randomly mating population: with the three populations we consider, the variance-increasing effect of positive assortative mating within a population might be overwhelmed by a variance-decreasing effect emerging from mating preferences involving other pairs of populations. The effect of assortative mating is smaller on the X chromosome than on the autosomes because inheritance of the X in males depends only on the mother's ancestry, not on the mating pair. Because the variance of admixture is informative about the timing of admixture and possibly about sex-biased admixture contributions, the effects of assortative mating are important to consider in inferring features of population history from distributions of admixture values. Our model provides a framework to quantitatively study assortative mating under flexible scenarios of admixture over time.
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Affiliation(s)
- Amy Goldberg
- Department of Evolutionary Anthropology, Duke University, Durham, NC, USA; Department of Biology, Stanford University, Stanford, CA, USA.
| | - Ananya Rastogi
- Department of Systems Immunology & Braunschweig Integrated Centre of Systems Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
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11
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Simanovsky AL, Madbouly A, Halagan M, Maiers M, Louzoun Y. Single haplotype admixture models using large scale HLA genotype frequencies to reproduce human admixture. Immunogenetics 2019; 71:589-604. [PMID: 31741008 DOI: 10.1007/s00251-019-01144-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 10/19/2019] [Indexed: 12/20/2022]
Abstract
The human leukocyte antigen (HLA) is the most polymorphic region in humans. Anthropologists use HLA to trace populations' migration and evolution. However, recent admixture between populations can mask the ancestral haplotype frequency distribution. We present a statistical method based on high-resolution HLA haplotype frequencies to resolve population admixture using a non-negative matrix factorization formalism and validated using haplotype frequencies from 56 world populations. The result is a minimal set of source components (SCs) decoding roughly 90% of the total variance in the studied admixtures. These SCs agree with the geographical distribution, phylogenies, and recent admixture events of the studied groups. With the growing population of multi-ethnic individuals, or individuals that do not report race/ethnic information, the HLA matching process for stem-cell and solid organ transplants is becoming more challenging. The presented algorithm provides a framework that facilitates the breakdown of highly admixed populations into SCs, which can be used to better match the rapidly growing population of multi-ethnic individuals worldwide.
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Affiliation(s)
| | - Abeer Madbouly
- Bioinformatics Research, Center for International Blood and Marrow Transplant Research, Minneapolis, MN, USA
| | - Michael Halagan
- Bioinformatics Research, Center for International Blood and Marrow Transplant Research, Minneapolis, MN, USA
| | - Martin Maiers
- Bioinformatics Research, Center for International Blood and Marrow Transplant Research, Minneapolis, MN, USA
| | - Yoram Louzoun
- Department of Mathematics and Gonda brain research institute, Bar-Ilan University, 52900, Ramat-Gan, Israel.
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12
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Szpiech ZA, Mak ACY, White MJ, Hu D, Eng C, Burchard EG, Hernandez RD. Ancestry-Dependent Enrichment of Deleterious Homozygotes in Runs of Homozygosity. Am J Hum Genet 2019; 105:747-762. [PMID: 31543216 PMCID: PMC6817522 DOI: 10.1016/j.ajhg.2019.08.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 08/27/2019] [Indexed: 12/20/2022] Open
Abstract
Runs of homozygosity (ROH) are important genomic features that manifest when an individual inherits two haplotypes that are identical by descent. Their length distributions are informative about population history, and their genomic locations are useful for mapping recessive loci contributing to both Mendelian and complex disease risk. We have previously shown that ROH, and especially long ROH that are likely the result of recent parental relatedness, are enriched for homozygous deleterious coding variation in a worldwide sample of outbred individuals. However, the distribution of ROH in admixed populations and their relationship to deleterious homozygous genotypes is understudied. Here we analyze whole-genome sequencing data from 1,441 unrelated individuals from self-identified African American, Puerto Rican, and Mexican American populations. These populations are three-way admixed between European, African, and Native American ancestries and provide an opportunity to study the distribution of deleterious alleles partitioned by local ancestry and ROH. We re-capitulate previous findings that long ROH are enriched for deleterious variation genome-wide. We then partition by local ancestry and show that deleterious homozygotes arise at a higher rate when ROH overlap African ancestry segments than when they overlap European or Native American ancestry segments of the genome. These results suggest that, while ROH on any haplotype background are associated with an inflation of deleterious homozygous variation, African haplotype backgrounds may play a particularly important role in the genetic architecture of complex diseases for admixed individuals, highlighting the need for further study of these populations.
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Affiliation(s)
- Zachary A Szpiech
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA; Department of Biological Sciences, Auburn University, Auburn, AL 36842, USA.
| | - Angel C Y Mak
- Department of Medicine, University of California San Francisco, San Francisco, CA 94158, USA
| | - Marquitta J White
- Department of Medicine, University of California San Francisco, San Francisco, CA 94158, USA
| | - Donglei Hu
- Department of Medicine, University of California San Francisco, San Francisco, CA 94158, USA
| | - Celeste Eng
- Department of Medicine, University of California San Francisco, San Francisco, CA 94158, USA
| | - Esteban G Burchard
- Department of Medicine, University of California San Francisco, San Francisco, CA 94158, USA
| | - Ryan D Hernandez
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA; Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA 94158, USA; Department of Human Genetics, McGill University, Montreal, QC H3A 0G1, Canada; Genome Quebec Innovation Center, McGill University, Montreal, QC H3A 0G1, Canada.
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13
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Gnecchi-Ruscone GA, Sarno S, De Fanti S, Gianvincenzo L, Giuliani C, Boattini A, Bortolini E, Di Corcia T, Sanchez Mellado C, Dàvila Francia TJ, Gentilini D, Di Blasio AM, Di Cosimo P, Cilli E, Gonzalez-Martin A, Franceschi C, Franceschi ZA, Rickards O, Sazzini M, Luiselli D, Pettener D. Dissecting the Pre-Columbian Genomic Ancestry of Native Americans along the Andes-Amazonia Divide. Mol Biol Evol 2019; 36:1254-1269. [PMID: 30895292 PMCID: PMC6526910 DOI: 10.1093/molbev/msz066] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Extensive European and African admixture coupled with loss of Amerindian lineages makes the reconstruction of pre-Columbian history of Native Americans based on present-day genomes extremely challenging. Still open questions remain about the dispersals that occurred throughout the continent after the initial peopling from the Beringia, especially concerning the number and dynamics of diffusions into South America. Indeed, if environmental and historical factors contributed to shape distinct gene pools in the Andes and Amazonia, the origins of this East-West genetic structure and the extension of further interactions between populations residing along this divide are still not well understood. To this end, we generated new high-resolution genome-wide data for 229 individuals representative of one Central and ten South Amerindian ethnic groups from Mexico, Peru, Bolivia, and Argentina. Low levels of European and African admixture in the sampled individuals allowed the application of fine-scale haplotype-based methods and demographic modeling approaches. These analyses revealed highly specific Native American genetic ancestries and great intragroup homogeneity, along with limited traces of gene flow mainly from the Andes into Peruvian Amazonians. Substantial amount of genetic drift differentially experienced by the considered populations underlined distinct patterns of recent inbreeding or prolonged isolation. Overall, our results support the hypothesis that all non-Andean South Americans are compatible with descending from a common lineage, while we found low support for common Mesoamerican ancestors of both Andeans and other South American groups. These findings suggest extensive back-migrations into Central America from non-Andean sources or conceal distinct peopling events into the Southern Continent.
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Affiliation(s)
- Guido Alberto Gnecchi-Ruscone
- Laboratory of Molecular Anthropology and Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy.,Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Stefania Sarno
- Laboratory of Molecular Anthropology and Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Sara De Fanti
- Laboratory of Molecular Anthropology and Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Laura Gianvincenzo
- Laboratory of Molecular Anthropology and Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Cristina Giuliani
- Laboratory of Molecular Anthropology and Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Alessio Boattini
- Laboratory of Molecular Anthropology and Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Eugenio Bortolini
- Department of Cultural Heritage, University of Bologna, Ravenna, Italy
| | - Tullia Di Corcia
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Cesar Sanchez Mellado
- Faculty of Intercultural Education and Humanity, National Intercultural University of Amazon, Ucayali, Peru
| | | | - Davide Gentilini
- Center for Biomedical Research and Technologies, Italian Auxologic Institute IRCCS, Milan, Italy
| | - Anna Maria Di Blasio
- Center for Biomedical Research and Technologies, Italian Auxologic Institute IRCCS, Milan, Italy
| | | | - Elisabetta Cilli
- Department of Cultural Heritage, University of Bologna, Ravenna, Italy
| | - Antonio Gonzalez-Martin
- Department of Zoology and Physical Anthropology, Complutense University of Madrid, Madrid, Spain
| | - Claudio Franceschi
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
| | | | - Olga Rickards
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Marco Sazzini
- Laboratory of Molecular Anthropology and Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Donata Luiselli
- Department of Cultural Heritage, University of Bologna, Ravenna, Italy
| | - Davide Pettener
- Laboratory of Molecular Anthropology and Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
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14
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Flegontov P, Altınışık NE, Changmai P, Rohland N, Mallick S, Adamski N, Bolnick DA, Broomandkhoshbacht N, Candilio F, Culleton BJ, Flegontova O, Friesen TM, Jeong C, Harper TK, Keating D, Kennett DJ, Kim AM, Lamnidis TC, Lawson AM, Olalde I, Oppenheimer J, Potter BA, Raff J, Sattler RA, Skoglund P, Stewardson K, Vajda EJ, Vasilyev S, Veselovskaya E, Hayes MG, O'Rourke DH, Krause J, Pinhasi R, Reich D, Schiffels S. Palaeo-Eskimo genetic ancestry and the peopling of Chukotka and North America. Nature 2019; 570:236-240. [PMID: 31168094 PMCID: PMC6942545 DOI: 10.1038/s41586-019-1251-y] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 02/25/2019] [Indexed: 11/09/2022]
Abstract
Much of the American Arctic was first settled 5,000 years ago, by groups of people known as Palaeo-Eskimos. They were subsequently joined and largely displaced around 1,000 years ago by ancestors of the present-day Inuit and Yup'ik1-3. The genetic relationship between Palaeo-Eskimos and Native American, Inuit, Yup'ik and Aleut populations remains uncertain4-6. Here we present genomic data for 48 ancient individuals from Chukotka, East Siberia, the Aleutian Islands, Alaska, and the Canadian Arctic. We co-analyse these data with data from present-day Alaskan Iñupiat and West Siberian populations and published genomes. Using methods based on rare-allele and haplotype sharing, as well as established techniques4,7-9, we show that Palaeo-Eskimo-related ancestry is ubiquitous among people who speak Na-Dene and Eskimo-Aleut languages. We develop a comprehensive model for the Holocene peopling events of Chukotka and North America, and show that Na-Dene-speaking peoples, people of the Aleutian Islands, and Yup'ik and Inuit across the Arctic region all share ancestry from a single Palaeo-Eskimo-related Siberian source.
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Affiliation(s)
- Pavel Flegontov
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic.
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budĕjovice, Czech Republic.
- A. A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia.
| | - N Ezgi Altınışık
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Piya Changmai
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nicole Adamski
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Deborah A Bolnick
- Department of Anthropology, University of Connecticut, Storrs, CT, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
| | - Nasreen Broomandkhoshbacht
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Francesca Candilio
- School of Archaeology, University College Dublin, Dublin, Ireland
- Soprintendenza Archeologia, Belle Arti e Paesaggio per la città metropolitana di Cagliari e le province di Oristano e Sud Sardegna, Cagliari, Italy
| | - Brendan J Culleton
- Institutes of Energy and the Environment, Pennsylvania State University, University Park, PA, USA
| | - Olga Flegontova
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budĕjovice, Czech Republic
| | - T Max Friesen
- Department of Anthropology, University of Toronto, Toronto, ON, Canada
| | - Choongwon Jeong
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Thomas K Harper
- Department of Anthropology, Pennsylvania State University, University Park, PA, USA
| | - Denise Keating
- School of Archaeology, University College Dublin, Dublin, Ireland
| | - Douglas J Kennett
- Institutes of Energy and the Environment, Pennsylvania State University, University Park, PA, USA
- Department of Anthropology, Pennsylvania State University, University Park, PA, USA
- Department of Anthropology, University of California, Santa Barbara, CA, USA
| | - Alexander M Kim
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Anthropology, Harvard University, Cambridge, MA, USA
| | - Thiseas C Lamnidis
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Ann Marie Lawson
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Iñigo Olalde
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Jonas Oppenheimer
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Ben A Potter
- Department of Anthropology, University of Alaska Fairbanks, Fairbanks, AK, USA
| | - Jennifer Raff
- Department of Anthropology, University of Kansas, Lawrence, KS, USA
| | | | - Pontus Skoglund
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Francis Crick Institute, London, UK
| | - Kristin Stewardson
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Edward J Vajda
- Department of Modern and Classical Languages, Western Washington University, Bellingham, WA, USA
| | - Sergey Vasilyev
- Institute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow, Russia
| | | | - M Geoffrey Hayes
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Department of Anthropology, Northwestern University, Evanston, IL, USA
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | | | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Ron Pinhasi
- Department of Anthropology, University of Vienna, Vienna, Austria
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Stephan Schiffels
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany.
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15
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Arbisser IM, Rosenberg NA. F ST and the triangle inequality for biallelic markers. Theor Popul Biol 2019; 133:117-129. [PMID: 31132375 DOI: 10.1016/j.tpb.2019.05.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 05/10/2019] [Accepted: 05/21/2019] [Indexed: 12/01/2022]
Abstract
The population differentiation statistic FST, introduced by Sewall Wright, is often treated as a pairwise distance measure between populations. As was known to Wright, however, FST is not a true metric because allele frequencies exist for which it does not satisfy the triangle inequality. We prove that a stronger result holds: for biallelic markers whose allele frequencies differ across three populations, FSTnever satisfies the triangle inequality. We study the deviation from the triangle inequality as a function of the allele frequencies of three populations, identifying the frequency vector at which the deviation is maximal. We also examine the implications of the failure of the triangle inequality for four-point conditions for placement of groups of four populations on evolutionary trees. Next, we study the extent to which FST fails to satisfy the triangle inequality in human genomic data, finding that some loci produce deviations near the maximum. We provide results describing the consequences of the theory for various types of data analysis, including multidimensional scaling and inference of neighbor-joining trees from pairwise FST matrices.
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Affiliation(s)
- Ilana M Arbisser
- Department of Biology, Stanford University, Stanford, CA 94305, USA.
| | - Noah A Rosenberg
- Department of Biology, Stanford University, Stanford, CA 94305, USA
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16
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Vidal EA, Moyano TC, Bustos BI, Pérez-Palma E, Moraga C, Riveras E, Montecinos A, Azócar L, Soto DC, Vidal M, Di Genova A, Puschel K, Nürnberg P, Buch S, Hampe J, Allende ML, Cambiazo V, González M, Hodar C, Montecino M, Muñoz-Espinoza C, Orellana A, Reyes-Jara A, Travisany D, Vizoso P, Moraga M, Eyheramendy S, Maass A, De Ferrari GV, Miquel JF, Gutiérrez RA. Whole Genome Sequence, Variant Discovery and Annotation in Mapuche-Huilliche Native South Americans. Sci Rep 2019; 9:2132. [PMID: 30765821 PMCID: PMC6376018 DOI: 10.1038/s41598-019-39391-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 01/23/2019] [Indexed: 12/15/2022] Open
Abstract
Whole human genome sequencing initiatives help us understand population history and the basis of genetic diseases. Current data mostly focuses on Old World populations, and the information of the genomic structure of Native Americans, especially those from the Southern Cone is scant. Here we present annotation and variant discovery from high-quality complete genome sequences of a cohort of 11 Mapuche-Huilliche individuals (HUI) from Southern Chile. We found approximately 3.1 × 106 single nucleotide variants (SNVs) per individual and identified 403,383 (6.9%) of novel SNVs events. Analyses of large-scale genomic events detected 680 copy number variants (CNVs) and 4,514 structural variants (SVs), including 398 and 1,910 novel events, respectively. Global ancestry composition of HUI genomes revealed that the cohort represents a sample from a marginally admixed population from the Southern Cone, whose main genetic component derives from Native American ancestors. Additionally, we found that HUI genomes contain variants in genes associated with 5 of the 6 leading causes of noncommunicable diseases in Chile, which may have an impact on the risk of prevalent diseases in Chilean and Amerindian populations. Our data represents a useful resource that can contribute to population-based studies and for the design of early diagnostics or prevention tools for Native and admixed Latin American populations.
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Affiliation(s)
- Elena A Vidal
- FONDAP Center for Genome Regulation, Santiago, Chile
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
| | - Tomás C Moyano
- FONDAP Center for Genome Regulation, Santiago, Chile
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Bernabé I Bustos
- FONDAP Center for Genome Regulation, Santiago, Chile
- Centro de Investigaciones Biomédicas, Facultad de Ciencias Biológicas y Facultad de Medicina, Universidad Andres Bello, Santiago, Chile
| | - Eduardo Pérez-Palma
- FONDAP Center for Genome Regulation, Santiago, Chile
- Centro de Investigaciones Biomédicas, Facultad de Ciencias Biológicas y Facultad de Medicina, Universidad Andres Bello, Santiago, Chile
| | - Carol Moraga
- FONDAP Center for Genome Regulation, Santiago, Chile
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Eleodoro Riveras
- FONDAP Center for Genome Regulation, Santiago, Chile
- Departamento de Gastroenterología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Alejandro Montecinos
- FONDAP Center for Genome Regulation, Santiago, Chile
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Lorena Azócar
- FONDAP Center for Genome Regulation, Santiago, Chile
- Departamento de Gastroenterología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Daniela C Soto
- FONDAP Center for Genome Regulation, Santiago, Chile
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Mabel Vidal
- FONDAP Center for Genome Regulation, Santiago, Chile
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Alex Di Genova
- FONDAP Center for Genome Regulation, Santiago, Chile
- Laboratorio de Bioinformática y Matemática del Genoma (LBMG-Mathomics), Centro de Modelamiento Matemático, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Santiago, Chile
| | - Klaus Puschel
- Departamento de Medicina Familiar, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Peter Nürnberg
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
| | - Stephan Buch
- Medical Department I, University Hospital Dresden, TU Dresden, Germany
| | - Jochen Hampe
- Medical Department I, University Hospital Dresden, TU Dresden, Germany
| | - Miguel L Allende
- FONDAP Center for Genome Regulation, Santiago, Chile
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Verónica Cambiazo
- FONDAP Center for Genome Regulation, Santiago, Chile
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile
| | - Mauricio González
- FONDAP Center for Genome Regulation, Santiago, Chile
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile
| | - Christian Hodar
- FONDAP Center for Genome Regulation, Santiago, Chile
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile
| | - Martín Montecino
- FONDAP Center for Genome Regulation, Santiago, Chile
- Centro de Investigaciones Biomédicas, Facultad de Ciencias Biológicas y Facultad de Medicina, Universidad Andres Bello, Santiago, Chile
| | - Claudia Muñoz-Espinoza
- FONDAP Center for Genome Regulation, Santiago, Chile
- Centro de Biotecnología Vegetal, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Santiago, Chile
| | - Ariel Orellana
- FONDAP Center for Genome Regulation, Santiago, Chile
- Centro de Biotecnología Vegetal, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Santiago, Chile
| | - Angélica Reyes-Jara
- FONDAP Center for Genome Regulation, Santiago, Chile
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile
| | - Dante Travisany
- FONDAP Center for Genome Regulation, Santiago, Chile
- Laboratorio de Bioinformática y Matemática del Genoma (LBMG-Mathomics), Centro de Modelamiento Matemático, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Santiago, Chile
| | - Paula Vizoso
- FONDAP Center for Genome Regulation, Santiago, Chile
- Centro de Propagación y Conservación Vegetal (CEPROVEG), Facultad de Ciencias, Universidad Mayor, Santiago, Chile
| | - Mauricio Moraga
- Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
- Departamento de Antropología, Facultad de Ciencias Sociales, Universidad de Chile, Santiago, Chile
| | - Susana Eyheramendy
- Departmento de Estadística, Facultad de Matemáticas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Alejandro Maass
- FONDAP Center for Genome Regulation, Santiago, Chile
- Departamento de Medicina Familiar, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Giancarlo V De Ferrari
- FONDAP Center for Genome Regulation, Santiago, Chile.
- Centro de Investigaciones Biomédicas, Facultad de Ciencias Biológicas y Facultad de Medicina, Universidad Andres Bello, Santiago, Chile.
| | - Juan Francisco Miquel
- FONDAP Center for Genome Regulation, Santiago, Chile.
- Departamento de Gastroenterología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile.
| | - Rodrigo A Gutiérrez
- FONDAP Center for Genome Regulation, Santiago, Chile.
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile.
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17
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Moreno-Mayar JV, Vinner L, de Barros Damgaard P, de la Fuente C, Chan J, Spence JP, Allentoft ME, Vimala T, Racimo F, Pinotti T, Rasmussen S, Margaryan A, Iraeta Orbegozo M, Mylopotamitaki D, Wooller M, Bataille C, Becerra-Valdivia L, Chivall D, Comeskey D, Devièse T, Grayson DK, George L, Harry H, Alexandersen V, Primeau C, Erlandson J, Rodrigues-Carvalho C, Reis S, Bastos MQR, Cybulski J, Vullo C, Morello F, Vilar M, Wells S, Gregersen K, Hansen KL, Lynnerup N, Mirazón Lahr M, Kjær K, Strauss A, Alfonso-Durruty M, Salas A, Schroeder H, Higham T, Malhi RS, Rasic JT, Souza L, Santos FR, Malaspinas AS, Sikora M, Nielsen R, Song YS, Meltzer DJ, Willerslev E. Early human dispersals within the Americas. Science 2018; 362:science.aav2621. [DOI: 10.1126/science.aav2621] [Citation(s) in RCA: 102] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 10/30/2018] [Indexed: 12/16/2022]
Abstract
Studies of the peopling of the Americas have focused on the timing and number of initial migrations. Less attention has been paid to the subsequent spread of people within the Americas. We sequenced 15 ancient human genomes spanning from Alaska to Patagonia; six are ≥10,000 years old (up to ~18× coverage). All are most closely related to Native Americans, including those from an Ancient Beringian individual and two morphologically distinct “Paleoamericans.” We found evidence of rapid dispersal and early diversification that included previously unknown groups as people moved south. This resulted in multiple independent, geographically uneven migrations, including one that provides clues of a Late Pleistocene Australasian genetic signal, as well as a later Mesoamerican-related expansion. These led to complex and dynamic population histories from North to South America.
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18
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Scheib CL, Li H, Desai T, Link V, Kendall C, Dewar G, Griffith PW, Mörseburg A, Johnson JR, Potter A, Kerr SL, Endicott P, Lindo J, Haber M, Xue Y, Tyler-Smith C, Sandhu MS, Lorenz JG, Randall TD, Faltyskova Z, Pagani L, Danecek P, O'Connell TC, Martz P, Boraas AS, Byrd BF, Leventhal A, Cambra R, Williamson R, Lesage L, Holguin B, Ygnacio-De Soto E, Rosas J, Metspalu M, Stock JT, Manica A, Scally A, Wegmann D, Malhi RS, Kivisild T. Ancient human parallel lineages within North America contributed to a coastal expansion. Science 2018; 360:1024-1027. [PMID: 29853687 DOI: 10.1126/science.aar6851] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Accepted: 04/20/2018] [Indexed: 12/12/2022]
Abstract
Little is known regarding the first people to enter the Americas and their genetic legacy. Genomic analysis of the oldest human remains from the Americas showed a direct relationship between a Clovis-related ancestral population and all modern Central and South Americans as well as a deep split separating them from North Americans in Canada. We present 91 ancient human genomes from California and Southwestern Ontario and demonstrate the existence of two distinct ancestries in North America, which possibly split south of the ice sheets. A contribution from both of these ancestral populations is found in all modern Central and South Americans. The proportions of these two ancestries in ancient and modern populations are consistent with a coastal dispersal and multiple admixture events.
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Affiliation(s)
- C L Scheib
- Department of Archaeology, University of Cambridge, Cambridge CB2 3DZ, UK. .,Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Hongjie Li
- Department of Anthropology and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Tariq Desai
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - Vivian Link
- Department of Biology, Université de Fribourg, Fribourg, Switzerland
| | - Christopher Kendall
- Department of Anthropology, University of Toronto, Toronto, Ontario M5S 2S2, Canada
| | - Genevieve Dewar
- Department of Anthropology, University of Toronto, Toronto, Ontario M5S 2S2, Canada
| | | | | | - John R Johnson
- Santa Barbara Museum of Natural History, Santa Barbara, CA 93105, USA
| | - Amiee Potter
- Department of Anthropology, Portland State University, Portland, OR 97232, USA.,Knight Diagnostics Laboratory, Oregon Health & Science University, Portland, OR 97239, USA
| | - Susan L Kerr
- Department of Anthropology, Modesto Junior College, Modesto, CA 95350, USA
| | - Phillip Endicott
- Department Hommes Natures Societies, Musée de l'Homme, Paris 75016, France
| | - John Lindo
- Department of Anthropology, Emory University, Atlanta, GA 30322, USA
| | - Marc Haber
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Yali Xue
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Chris Tyler-Smith
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | | | - Joseph G Lorenz
- Department of Anthropology and Museum Studies, Central Washington University, Ellensburg, WA 98926, USA
| | - Tori D Randall
- Department of Anthropology, San Diego City College, San Diego, CA 92101, USA
| | - Zuzana Faltyskova
- Department of Archaeology, University of Cambridge, Cambridge CB2 3DZ, UK
| | - Luca Pagani
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia.,APE Lab, Department of Biology, University of Padova, Padova, Italy
| | - Petr Danecek
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Tamsin C O'Connell
- Department of Archaeology, University of Cambridge, Cambridge CB2 3DZ, UK
| | - Patricia Martz
- Department of Anthropology, California State University, Los Angeles, CA 90032, USA
| | | | - Brian F Byrd
- Far Western Anthropological Research Group Inc., Davis, CA 95618, USA
| | - Alan Leventhal
- Muwekma Ohlone Tribe of the San Francisco Bay Area, P.O. Box 360791, Milpitas, CA 95036, USA.,Department of Anthropology, San Jose State University, San Jose, CA 95192, USA
| | - Rosemary Cambra
- Muwekma Ohlone Tribe of the San Francisco Bay Area, P.O. Box 360791, Milpitas, CA 95036, USA
| | | | | | - Brian Holguin
- Department of Anthropology, University of California, Los Angeles, CA 90095, USA
| | - Ernestine Ygnacio-De Soto
- Barbareño Chumash, California Indian Advisory Committee, Santa Barbara Museum of Natural History, Santa Barbara, CA 93105, USA
| | | | - Mait Metspalu
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Jay T Stock
- Department of Archaeology, University of Cambridge, Cambridge CB2 3DZ, UK.,Department of Anthropology, University of Western Ontario, London, Ontario N6A 3K7, Canada
| | - Andrea Manica
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Aylwyn Scally
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - Daniel Wegmann
- Department of Biology, Université de Fribourg, Fribourg, Switzerland
| | - Ripan S Malhi
- Department of Anthropology and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Toomas Kivisild
- Department of Archaeology, University of Cambridge, Cambridge CB2 3DZ, UK. .,Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
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19
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Potter BA, Baichtal JF, Beaudoin AB, Fehren-Schmitz L, Haynes CV, Holliday VT, Holmes CE, Ives JW, Kelly RL, Llamas B, Malhi RS, Miller DS, Reich D, Reuther JD, Schiffels S, Surovell TA. Current evidence allows multiple models for the peopling of the Americas. SCIENCE ADVANCES 2018; 4:eaat5473. [PMID: 30101195 PMCID: PMC6082647 DOI: 10.1126/sciadv.aat5473] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 06/26/2018] [Indexed: 05/10/2023]
Abstract
Some recent academic and popular literature implies that the problem of the colonization of the Americas has been largely resolved in favor of one specific model: a Pacific coastal migration, dependent on high marine productivity, from the Bering Strait to South America, thousands of years before Clovis, the earliest widespread cultural manifestation south of the glacial ice. Speculations on maritime adaptations and typological links (stemmed points) across thousands of kilometers have also been advanced. A review of the current genetic, archeological, and paleoecological evidence indicates that ancestral Native American population expansion occurred after 16,000 years ago, consistent with the archeological record, particularly with the earliest securely dated sites after ~15,000 years ago. These data are largely consistent with either an inland (ice-free corridor) or Pacific coastal routes (or both), but neither can be rejected at present. Systematic archeological and paleoecological investigations, informed by geomorphology, are required to test each hypothesis.
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Affiliation(s)
- Ben A. Potter
- Department of Anthropology, University of Alaska Fairbanks, Fairbanks, AK 99775, USA
- Corresponding author.
| | - James F. Baichtal
- Tongass National Forest, U.S. Forest Service, Thorne Bay, AK 99919, USA
| | | | - Lars Fehren-Schmitz
- UCSC Paleogenomics Lab, Department of Anthropology, University of California at Santa Cruz, Santa Cruz, CA 95064, USA
| | - C. Vance Haynes
- School of Anthropology and Department of Geosciences, University of Arizona, Tucson, AZ 85721, USA
| | - Vance T. Holliday
- School of Anthropology and Department of Geosciences, University of Arizona, Tucson, AZ 85721, USA
| | - Charles E. Holmes
- Department of Anthropology, University of Alaska Fairbanks, Fairbanks, AK 99775, USA
| | - John W. Ives
- Institute of Prairie Archaeology, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| | - Robert L. Kelly
- Department of Anthropology, University of Wyoming, Laramie, WY 82071, USA
| | - Bastien Llamas
- Australian Centre for Ancient DNA, Environment Institute, School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Ripan S. Malhi
- Department of Anthropology and Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USA
| | - D. Shane Miller
- Department of Anthropology and Middle Eastern Cultures, Mississippi State University, Starkville, MS 39759, USA
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Joshua D. Reuther
- Department of Anthropology, University of Alaska Fairbanks, Fairbanks, AK 99775, USA
- Archaeology Department, University of Alaska Museum of the North, Fairbanks, AK 99775, USA
| | - Stephan Schiffels
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - Todd A. Surovell
- Department of Anthropology, University of Wyoming, Laramie, WY 82071, USA
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20
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Fortes-Lima C, Bybjerg-Grauholm J, Marin-Padrón LC, Gomez-Cabezas EJ, Bækvad-Hansen M, Hansen CS, Le P, Hougaard DM, Verdu P, Mors O, Parra EJ, Marcheco-Teruel B. Exploring Cuba's population structure and demographic history using genome-wide data. Sci Rep 2018; 8:11422. [PMID: 30061702 PMCID: PMC6065444 DOI: 10.1038/s41598-018-29851-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 07/10/2018] [Indexed: 12/31/2022] Open
Abstract
Cuba is the most populated country in the Caribbean and has a rich and heterogeneous genetic heritage. Here, we take advantage of dense genomic data from 860 Cuban individuals to reconstruct the genetic structure and ancestral origins of this population. We found distinct admixture patterns between and within the Cuban provinces. Eastern provinces have higher African and Native American ancestry contributions (average 26% and 10%, respectively) than the rest of the Cuban provinces (average 17% and 5%, respectively). Furthermore, in the Eastern Cuban region, we identified more intense sex-specific admixture patterns, strongly biased towards European male and African/Native American female ancestries. Our subcontinental ancestry analyses in Cuba highlight the Iberian population as the best proxy European source population, South American and Mesoamerican populations as the closest Native American ancestral component, and populations from West Central and Central Africa as the best proxy sources of the African ancestral component. Finally, we found complex admixture processes involving two migration pulses from both Native American and African sources. Most of the inferred Native American admixture events happened early during the Cuban colonial period, whereas the African admixture took place during the slave trade and more recently as a probable result of large-scale migrations from Haiti.
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Affiliation(s)
- Cesar Fortes-Lima
- UMR7206 Eco-Anthropology and Ethno-Biology, CNRS-MNHN-University Paris Diderot, Musée de l'Homme, Paris, 75016, France
| | - Jonas Bybjerg-Grauholm
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, 2300, Denmark.,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus University, Aarhus, 8000, Denmark
| | | | | | - Marie Bækvad-Hansen
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, 2300, Denmark.,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus University, Aarhus, 8000, Denmark
| | - Christine Søholm Hansen
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, 2300, Denmark.,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus University, Aarhus, 8000, Denmark
| | - Phuong Le
- Department of Anthropology, University of Toronto, Mississauga, ON L5L 1C6, Canada
| | - David Michael Hougaard
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, 2300, Denmark.,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus University, Aarhus, 8000, Denmark
| | - Paul Verdu
- UMR7206 Eco-Anthropology and Ethno-Biology, CNRS-MNHN-University Paris Diderot, Musée de l'Homme, Paris, 75016, France
| | - Ole Mors
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus University, Aarhus, 8000, Denmark.,Psychosis Research Unit, Aarhus University Hospital, Risskov, Aarhus, 8240, Denmark
| | - Esteban J Parra
- Department of Anthropology, University of Toronto, Mississauga, ON L5L 1C6, Canada.
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21
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Abstract
Signatures of recent historical admixture are ubiquitous in human populations. We present a mechanistic model of admixture with two source populations, encompassing recurrent admixture periods and study the distribution of admixture fractions for finite but arbitrary genome size. We provide simulation-based methods to estimate the introgression parameters and discuss the implications of reaching stationarity on estimability of parameters when there are recurrent admixture events with different rates.
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Affiliation(s)
- Erkan Ozge Buzbas
- Department of Statistical Science, University of Idaho, United States.
| | - Paul Verdu
- CNRS/MNHN/Université Paris Diderot/Sorbonne Paris Cité, France
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22
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Marchi N, Mennecier P, Georges M, Lafosse S, Hegay T, Dorzhu C, Chichlo B, Ségurel L, Heyer E. Close inbreeding and low genetic diversity in Inner Asian human populations despite geographical exogamy. Sci Rep 2018; 8:9397. [PMID: 29925873 PMCID: PMC6010435 DOI: 10.1038/s41598-018-27047-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 04/13/2018] [Indexed: 01/12/2023] Open
Abstract
When closely related individuals mate, they produce inbred offspring, which often have lower fitness than outbred ones. Geographical exogamy, by favouring matings between distant individuals, is thought to be an inbreeding avoidance mechanism; however, no data has clearly tested this prediction. Here, we took advantage of the diversity of matrimonial systems in humans to explore the impact of geographical exogamy on genetic diversity and inbreeding. We collected ethno-demographic data for 1,344 individuals in 16 populations from two Inner Asian cultural groups with contrasting dispersal behaviours (Turko-Mongols and Indo-Iranians) and genotyped genome-wide single nucleotide polymorphisms in 503 individuals. We estimated the population exogamy rate and confirmed the expected dispersal differences: Turko-Mongols are geographically more exogamous than Indo-Iranians. Unexpectedly, across populations, exogamy patterns correlated neither with the proportion of inbred individuals nor with their genetic diversity. Even more surprisingly, among Turko-Mongols, descendants from exogamous couples were significantly more inbred than descendants from endogamous couples, except for large distances (>40 km). Overall, 37% of the descendants from exogamous couples were closely inbred. This suggests that in Inner Asia, geographical exogamy is neither efficient in increasing genetic diversity nor in avoiding inbreeding, which might be due to kinship endogamy despite the occurrence of dispersal.
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Affiliation(s)
- Nina Marchi
- Eco-anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cité, Sorbonne Universités, 75016, Paris, France.
| | - Philippe Mennecier
- Eco-anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cité, Sorbonne Universités, 75016, Paris, France
| | - Myriam Georges
- Eco-anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cité, Sorbonne Universités, 75016, Paris, France.,LM2E-UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Institut Universitaire Européen de la Mer, Technopôle Brest-Iroise, Plouzane, 29280, France
| | - Sophie Lafosse
- Eco-anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cité, Sorbonne Universités, 75016, Paris, France
| | - Tatyana Hegay
- Republican Scientific Center of Immunology, Ministry of Public Health, Tashkent, 100060, Uzbekistan
| | - Choduraa Dorzhu
- Department of biology and ecology, Tuvan State University, Kyzyl, 667000, Russia
| | - Boris Chichlo
- Eco-anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cité, Sorbonne Universités, 75016, Paris, France
| | - Laure Ségurel
- Eco-anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cité, Sorbonne Universités, 75016, Paris, France
| | - Evelyne Heyer
- Eco-anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cité, Sorbonne Universités, 75016, Paris, France.
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23
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Lindo J, Rogers M, Mallott EK, Petzelt B, Mitchell J, Archer D, Cybulski JS, Malhi RS, DeGiorgio M. Patterns of Genetic Coding Variation in a Native American Population before and after European Contact. Am J Hum Genet 2018; 102:806-815. [PMID: 29706345 PMCID: PMC5986697 DOI: 10.1016/j.ajhg.2018.03.008] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 03/05/2018] [Indexed: 12/11/2022] Open
Abstract
The effects of European colonization on the genomes of Native Americans may have produced excesses of potentially deleterious features, mainly due to the severe reductions in population size and corresponding losses of genetic diversity. This assumption, however, neither considers actual genomic patterns that existed before colonization nor does it adequately capture the effects of admixture. In this study, we analyze the whole-exome sequences of modern and ancient individuals from a Northwest Coast First Nation, with a demographic history similar to other indigenous populations from the Americas. We show that in approximately ten generations from initial European contact, the modern individuals exhibit reduced levels of novel and low-frequency variants, a lower proportion of potentially deleterious alleles, and decreased heterozygosity when compared to their ancestors. This pattern can be explained by a dramatic population decline, resulting in the loss of potentially damaging low-frequency variants, and subsequent admixture. We also find evidence that the indigenous population was on a steady decline in effective population size for several thousand years before contact, which emphasizes regional demography over the common conception of a uniform expansion after entry into the Americas. This study examines the genomic consequences of colonialism on an indigenous group and describes the continuing role of gene flow among modern populations.
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Affiliation(s)
- John Lindo
- Department of Anthropology, Emory University, Atlanta, GA 30322, USA
| | - Mary Rogers
- Department of Anthropology, University of Illinois, Urbana, IL 61821, USA
| | - Elizabeth K Mallott
- Department of Anthropology, Northwestern University, Evanston, IL 60208, USA
| | | | | | - David Archer
- Department of Anthropology, Northwestern Community College, Prince Rupert, BC V8J 3P6, Canada
| | - Jerome S Cybulski
- Research, Canadian Museum of History, Gatineau, QC K1A 0M8, Canada; Department of Anthropology, University of Western Ontario, London, ON N6A 3K7, Canada; Department of Archaeology, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Ripan S Malhi
- Department of Anthropology, University of Illinois, Urbana, IL 61821, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61820, USA.
| | - Michael DeGiorgio
- Departments of Biology and Statistics, Pennsylvania State University, University Park, PA 16801, USA; Institute for CyberScience, Pennsylvania State University, University Park, PA 16801, USA.
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24
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Szathmáry EJE, Zegura SL, Hammer MF. Exceeding Hrdlička's aims: 100 Years of genetics in anthropology. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2018; 165:754-776. [PMID: 29574830 DOI: 10.1002/ajpa.23406] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 12/21/2017] [Accepted: 12/21/2017] [Indexed: 11/10/2022]
Affiliation(s)
- Emőke J E Szathmáry
- Department of Anthropology, St. Paul's College, University of Manitoba, 70 Dysart Road, Winnipeg, Manitoba, R3T 2M6, Canada
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25
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Moreno-Mayar JV, Potter BA, Vinner L, Steinrücken M, Rasmussen S, Terhorst J, Kamm JA, Albrechtsen A, Malaspinas AS, Sikora M, Reuther JD, Irish JD, Malhi RS, Orlando L, Song YS, Nielsen R, Meltzer DJ, Willerslev E. Terminal Pleistocene Alaskan genome reveals first founding population of Native Americans. Nature 2018; 553:203-207. [DOI: 10.1038/nature25173] [Citation(s) in RCA: 212] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 11/26/2017] [Indexed: 12/30/2022]
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26
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Dávila-Lara A, Affenzeller M, Tribsch A, Díaz V, Comes HP. AFLP diversity and spatial structure of Calycophyllum candidissimum (Rubiaceae), a dominant tree species of Nicaragua's critically endangered seasonally dry forest. Heredity (Edinb) 2017; 119:275-286. [PMID: 28767103 PMCID: PMC5597786 DOI: 10.1038/hdy.2017.45] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 05/30/2017] [Accepted: 06/16/2017] [Indexed: 11/08/2022] Open
Abstract
The Central American seasonally dry tropical (SDT) forest biome is one of the worlds' most endangered ecosystems, yet little is known about the genetic consequences of its recent fragmentation. A prominent constituent of this biome is Calycophyllum candidissimum, an insect-pollinated and wind-dispersed canopy tree of high socio-economic importance, particularly in Nicaragua. Here, we surveyed amplified fragment length polymorphisms across 13 populations of this species in Nicaragua to elucidate the relative roles of contemporary vs historical factors in shaping its genetic variation. Genetic diversity was low in all investigated populations (mean HE=0.125), and negatively correlated with latitude. Overall population differentiation was moderate (ΦST=0.109, P<0.001), and Bayesian analysis of population structure revealed two major latitudinal clusters (I: 'Pacific North'+'Central Highland'; II: 'Pacific South'), along with a genetic cline between I and II. Population-based cluster analyses indicated a strong pattern of 'isolation by distance' as confirmed by Mantel's test. Our results suggest that (1) the low genetic diversity of these populations reflects biogeographic/population history (colonisation from South America, Pleistocene range contractions) rather than recent human impact; whereas (2) the underlying process of their isolation by distance pattern, which is best explained by 'isolation by dispersal limitation', implies contemporary gene flow between neighbouring populations as likely facilitated by the species' efficient seed dispersal capacity. Overall, these results underscore that even tree species from highly decimated forest regions may be genetically resilient to habitat fragmentation due to species-typical dispersal characteristics, the necessity of broad-scale measures for their conservation notwithstanding.
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Affiliation(s)
- A Dávila-Lara
- Departamento de Biología, Universidad Nacional Autónoma de Nicaragua-León (UNAN), León, Nicaragua
- Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - M Affenzeller
- Department of Ecology and Evolution, University of Salzburg, Salzburg, Austria
| | - A Tribsch
- Department of Ecology and Evolution, University of Salzburg, Salzburg, Austria
| | - V Díaz
- Departamento de Biología, Universidad Nacional Autónoma de Nicaragua-León (UNAN), León, Nicaragua
| | - H P Comes
- Department of Ecology and Evolution, University of Salzburg, Salzburg, Austria
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27
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Kang JTL, Goldberg A, Edge MD, Behar DM, Rosenberg NA. Consanguinity Rates Predict Long Runs of Homozygosity in Jewish Populations. Hum Hered 2017; 82:87-102. [PMID: 28910803 DOI: 10.1159/000478897] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 06/14/2017] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVES Recent studies have highlighted the potential of analyses of genomic sharing to produce insight into the demographic processes affecting human populations. We study runs of homozygosity (ROH) in 18 Jewish populations, examining these groups in relation to 123 non-Jewish populations sampled worldwide. METHODS By sorting ROH into 3 length classes (short, intermediate, and long), we evaluate the impact of demographic processes on genomic patterns in Jewish populations. RESULTS We find that the portion of the genome appearing in long ROH - the length class most directly related to recent consanguinity - closely accords with data gathered from interviews during the 1950s on frequencies of consanguineous unions in various Jewish groups. CONCLUSION The high correlation between 1950s consanguinity levels and coverage by long ROH explains differences across populations in ROH patterns. The dissection of ROH into length classes and the comparison to consanguinity data assist in understanding a number of additional phenomena, including similarities of Jewish populations to Middle Eastern, European, and Central and South Asian non-Jewish populations in short ROH patterns, relative lengths of identity-by-descent tracts in different Jewish groups, and the "population isolate" status of the Ashkenazi Jews.
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28
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Ancient individuals from the North American Northwest Coast reveal 10,000 years of regional genetic continuity. Proc Natl Acad Sci U S A 2017; 114:4093-4098. [PMID: 28377518 DOI: 10.1073/pnas.1620410114] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Recent genomic studies of both ancient and modern indigenous people of the Americas have shed light on the demographic processes involved during the first peopling. The Pacific Northwest Coast proves an intriguing focus for these studies because of its association with coastal migration models and genetic ancestral patterns that are difficult to reconcile with modern DNA alone. Here, we report the low-coverage genome sequence of an ancient individual known as "Shuká Káa" ("Man Ahead of Us") recovered from the On Your Knees Cave (OYKC) in southeastern Alaska (archaeological site 49-PET-408). The human remains date to ∼10,300 calendar (cal) y B.P. We also analyze low-coverage genomes of three more recent individuals from the nearby coast of British Columbia dating from ∼6,075 to 1,750 cal y B.P. From the resulting time series of genetic data, we show that the Pacific Northwest Coast exhibits genetic continuity for at least the past 10,300 cal y B.P. We also infer that population structure existed in the late Pleistocene of North America with Shuká Káa on a different ancestral line compared with other North American individuals from the late Pleistocene or early Holocene (i.e., Anzick-1 and Kennewick Man). Despite regional shifts in mtDNA haplogroups, we conclude from individuals sampled through time that people of the northern Northwest Coast belong to an early genetic lineage that may stem from a late Pleistocene coastal migration into the Americas.
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29
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Prediction of biogeographical ancestry from genotype: a comparison of classifiers. Int J Legal Med 2016; 131:901-912. [DOI: 10.1007/s00414-016-1504-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 11/21/2016] [Indexed: 12/19/2022]
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Skoglund P, Reich D. A genomic view of the peopling of the Americas. Curr Opin Genet Dev 2016; 41:27-35. [PMID: 27507099 PMCID: PMC5161672 DOI: 10.1016/j.gde.2016.06.016] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 06/23/2016] [Accepted: 06/25/2016] [Indexed: 10/21/2022]
Abstract
Whole-genome studies have documented that most Native American ancestry stems from a single population that diversified within the continent more than twelve thousand years ago. However, this shared ancestry hides a more complex history whereby at least four distinct streams of Eurasian migration have contributed to present-day and prehistoric Native American populations. Whole genome studies enhanced by technological breakthroughs in ancient DNA now provide evidence of a sequence of events involving initial migrations from a structured Northeast Asian source population with differential relatedness to present-day Australasian populations, followed by a divergence into northern and southern Native American lineages. During the Holocene, new migrations from Asia introduced the Saqqaq/Dorset Paleoeskimo population to the North American Arctic ∼4500 years ago, ancestry that is potentially connected with ancestry found in Athabaskan-speakers today. This was then followed by a major new population turnover in the high Arctic involving Thule-related peoples who are the ancestors of present-day Inuit. We highlight several open questions that could be addressed through future genomic research.
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Affiliation(s)
- Pontus Skoglund
- Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Archaeology and Classical History, Stockholm, Sweden.
| | - David Reich
- Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Howard Hughes Medical Institute, Boston, MA, USA
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31
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A time transect of exomes from a Native American population before and after European contact. Nat Commun 2016; 7:13175. [PMID: 27845766 PMCID: PMC5116069 DOI: 10.1038/ncomms13175] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 09/07/2016] [Indexed: 12/20/2022] Open
Abstract
A major factor for the population decline of Native Americans after European contact has been attributed to infectious disease susceptibility. To investigate whether a pre-existing genetic component contributed to this phenomenon, here we analyse 50 exomes of a continuous population from the Northwest Coast of North America, dating from before and after European contact. We model the population collapse after European contact, inferring a 57% reduction in effective population size. We also identify signatures of positive selection on immune-related genes in the ancient but not the modern group, with the strongest signal deriving from the human leucocyte antigen (HLA) gene HLA-DQA1. The modern individuals show a marked frequency decrease in the same alleles, likely due to the environmental change associated with European colonization, whereby negative selection may have acted on the same gene after contact. The evident shift in selection pressures correlates to the regional European-borne epidemics of the 1800s. A First Nation population declined after European contact, likely as a result of infectious disease. Here, researchers partner with indigenous communities to analyse ancient and modern Native American exomes, and find a shift in selection pressure on immune genes, correlated to European-borne epidemics.
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32
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Bolnick DA, Raff JA, Springs LC, Reynolds AW, Miró-Herrans AT. Native American Genomics and Population Histories. ANNUAL REVIEW OF ANTHROPOLOGY 2016. [DOI: 10.1146/annurev-anthro-102215-100036] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Studies of Native American genetic diversity and population history have been transformed over the last decade by important developments in anthropological genetics. During this time, researchers have adopted new DNA technologies and computational approaches for analyzing genomic data, and they have become increasingly sensitive to the views of research participants and communities. As new methods are applied to long-standing questions, and as more research is conducted in collaboration with indigenous communities, we are gaining new insights into the history and diversity of indigenous populations. This review discusses the recent methodological advances and genetic studies that have improved our understanding of Native American genomics and population histories. We synthesize current knowledge about Native American genomic variation and build a model of population history in the Americas. We also discuss the broader implications of this research for anthropology and related disciplines, and we highlight challenges and other considerations for future research.
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Affiliation(s)
- Deborah A. Bolnick
- Department of Anthropology, University of Texas at Austin, Austin, Texas 78712;, , ,
- Population Research Center, University of Texas at Austin, Austin, Texas 78712
| | - Jennifer A. Raff
- Department of Anthropology, University of Kansas, Lawrence, Kansas 66045-7556
| | - Lauren C. Springs
- Department of Anthropology, University of Texas at Austin, Austin, Texas 78712;, , ,
| | - Austin W. Reynolds
- Department of Anthropology, University of Texas at Austin, Austin, Texas 78712;, , ,
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712
| | - Aida T. Miró-Herrans
- Department of Anthropology, University of Texas at Austin, Austin, Texas 78712;, , ,
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33
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Hunley K, Gwin K, Liberman B. A Reassessment of the Impact of European Contact on the Structure of Native American Genetic Diversity. PLoS One 2016; 11:e0161018. [PMID: 27579784 PMCID: PMC5007009 DOI: 10.1371/journal.pone.0161018] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 07/28/2016] [Indexed: 11/19/2022] Open
Abstract
Our current understanding of pre-Columbian history in the Americas rests in part on several trends identified in recent genetic studies. The goal of this study is to reexamine these trends in light of the impact of post-Columbian admixture and the methods used to study admixture. The previously-published data consist of 645 autosomal microsatellite genotypes from 1046 individuals in 63 populations. We used STRUCTURE to estimate ancestry proportions and tested the sensitivity of these estimates to the choice of the number of clusters, K. We used partial correlation analyses to examine the relationship between gene diversity and geographic distance from Beringia, controlling for non-Native American ancestry (from Africa, Europe and East Asia), and taking into account alternative paths of migration. Principal component analysis and multidimensional scaling were used to investigate the relationships between Andean and non-Andean populations and to explore gene-language correspondence. We found that 1) European and East Asian ancestry estimates decline as K increases, especially in Native Canadian populations, 2) a north-south decline in gene diversity is driven by low diversity in Amazonian and Paraguayan populations, not serial founder effects from Beringia, 3) controlling for non-Native American ancestry, populations in the Andes and Mesoamerica have higher gene diversity than populations in other regions, and 4) patterns of genetic and linguistic diversity are poorly correlated. We conclude that patterns of diversity previously attributed to pre-Columbian processes may in part reflect post-Columbian admixture and the choice of K in STRUCTURE analyses. Accounting for admixture, the pattern of diversity is inconsistent with a north-south founder effect process, though the genetic similarities between Mesoamerican and Andean populations are consistent with rapid dispersal along the western coast of the Americas. Further, even setting aside the disruptive effects of European contact, gene-language congruence is unlikely to have ever existed at the geographic scale analyzed here.
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Affiliation(s)
- Keith Hunley
- Department of Anthropology, University of New Mexico, Albuquerque, NM, 87131, United States of America
- * E-mail:
| | - Kiela Gwin
- Department of Anthropology, University of New Mexico, Albuquerque, NM, 87131, United States of America
| | - Brendan Liberman
- Department of Anthropology, University of New Mexico, Albuquerque, NM, 87131, United States of America
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34
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Behr AA, Liu KZ, Liu-Fang G, Nakka P, Ramachandran S. pong: fast analysis and visualization of latent clusters in population genetic data. Bioinformatics 2016; 32:2817-23. [PMID: 27283948 PMCID: PMC5018373 DOI: 10.1093/bioinformatics/btw327] [Citation(s) in RCA: 168] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2015] [Accepted: 05/18/2016] [Indexed: 01/06/2023] Open
Abstract
MOTIVATION A series of methods in population genetics use multilocus genotype data to assign individuals membership in latent clusters. These methods belong to a broad class of mixed-membership models, such as latent Dirichlet allocation used to analyze text corpora. Inference from mixed-membership models can produce different output matrices when repeatedly applied to the same inputs, and the number of latent clusters is a parameter that is often varied in the analysis pipeline. For these reasons, quantifying, visualizing, and annotating the output from mixed-membership models are bottlenecks for investigators across multiple disciplines from ecology to text data mining. RESULTS We introduce pong, a network-graphical approach for analyzing and visualizing membership in latent clusters with a native interactive D3.js visualization. pong leverages efficient algorithms for solving the Assignment Problem to dramatically reduce runtime while increasing accuracy compared with other methods that process output from mixed-membership models. We apply pong to 225 705 unlinked genome-wide single-nucleotide variants from 2426 unrelated individuals in the 1000 Genomes Project, and identify previously overlooked aspects of global human population structure. We show that pong outpaces current solutions by more than an order of magnitude in runtime while providing a customizable and interactive visualization of population structure that is more accurate than those produced by current tools. AVAILABILITY AND IMPLEMENTATION pong is freely available and can be installed using the Python package management system pip. pong's source code is available at https://github.com/abehr/pong CONTACT aaron_behr@alumni.brown.edu or sramachandran@brown.edu SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Aaron A Behr
- Department of Ecology and Evolutionary Biology Department of Computer Science, Brown University, Providence, RI, USA
| | - Katherine Z Liu
- Department of Computer Science, Brown University, Providence, RI, USA
| | - Gracie Liu-Fang
- Computer Science Department, Wellesley College, Wellesley, MA, USA
| | - Priyanka Nakka
- Department of Ecology and Evolutionary Biology Center for Computational Molecular Biology, Brown University, Providence, RI, USA
| | - Sohini Ramachandran
- Department of Ecology and Evolutionary Biology Center for Computational Molecular Biology, Brown University, Providence, RI, USA
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35
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Cox MP, Hudjashov G, Sim A, Savina O, Karafet TM, Sudoyo H, Lansing JS. Small Traditional Human Communities Sustain Genomic Diversity over Microgeographic Scales despite Linguistic Isolation. Mol Biol Evol 2016; 33:2273-84. [PMID: 27274003 PMCID: PMC4989104 DOI: 10.1093/molbev/msw099] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
At least since the Neolithic, humans have largely lived in networks of small, traditional communities. Often socially isolated, these groups evolved distinct languages and cultures over microgeographic scales of just tens of kilometers. Population genetic theory tells us that genetic drift should act quickly in such isolated groups, thus raising the question: do networks of small human communities maintain levels of genetic diversity over microgeographic scales? This question can no longer be asked in most parts of the world, which have been heavily impacted by historical events that make traditional society structures the exception. However, such studies remain possible in parts of Island Southeast Asia and Oceania, where traditional ways of life are still practiced. We captured genome-wide genetic data, together with linguistic records, for a case–study system—eight villages distributed across Sumba, a small, remote island in eastern Indonesia. More than 4,000 years after these communities were established during the Neolithic period, most speak different languages and can be distinguished genetically. Yet their nuclear diversity is not reduced, instead being comparable to other, even much larger, regional groups. Modeling reveals a separation of time scales: while languages and culture can evolve quickly, creating social barriers, sporadic migration averaged over many generations is sufficient to keep villages linked genetically. This loosely-connected network structure, once the global norm and still extant on Sumba today, provides a living proxy to explore fine-scale genome dynamics in the sort of small traditional communities within which the most recent episodes of human evolution occurred.
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Affiliation(s)
- Murray P Cox
- Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Georgi Hudjashov
- Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Andre Sim
- Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Olga Savina
- ARL Division of Biotechnology, University of Arizona
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36
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Flegontov P, Changmai P, Zidkova A, Logacheva MD, Altınışık NE, Flegontova O, Gelfand MS, Gerasimov ES, Khrameeva EE, Konovalova OP, Neretina T, Nikolsky YV, Starostin G, Stepanova VV, Travinsky IV, Tříska M, Tříska P, Tatarinova TV. Genomic study of the Ket: a Paleo-Eskimo-related ethnic group with significant ancient North Eurasian ancestry. Sci Rep 2016; 6:20768. [PMID: 26865217 PMCID: PMC4750364 DOI: 10.1038/srep20768] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 01/07/2016] [Indexed: 01/11/2023] Open
Abstract
The Kets, an ethnic group in the Yenisei River basin, Russia, are considered the last nomadic hunter-gatherers of Siberia, and Ket language has no transparent affiliation with any language family. We investigated connections between the Kets and Siberian and North American populations, with emphasis on the Mal'ta and Paleo-Eskimo ancient genomes, using original data from 46 unrelated samples of Kets and 42 samples of their neighboring ethnic groups (Uralic-speaking Nganasans, Enets, and Selkups). We genotyped over 130,000 autosomal SNPs, identified mitochondrial and Y-chromosomal haplogroups, and performed high-coverage genome sequencing of two Ket individuals. We established that Nganasans, Kets, Selkups, and Yukaghirs form a cluster of populations most closely related to Paleo-Eskimos in Siberia (not considering indigenous populations of Chukotka and Kamchatka). Kets are closely related to modern Selkups and to some Bronze and Iron Age populations of the Altai region, with all these groups sharing a high degree of Mal'ta ancestry. Implications of these findings for the linguistic hypothesis uniting Ket and Na-Dene languages into a language macrofamily are discussed.
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Affiliation(s)
- Pavel Flegontov
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budĕjovice, Czech Republic
| | - Piya Changmai
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Anastassiya Zidkova
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Maria D. Logacheva
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - N. Ezgi Altınışık
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Olga Flegontova
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budĕjovice, Czech Republic
| | - Mikhail S. Gelfand
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Evgeny S. Gerasimov
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Ekaterina E. Khrameeva
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, Russia
| | - Olga P. Konovalova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Tatiana Neretina
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Yuri V. Nikolsky
- Biomedical Cluster, Skolkovo Foundation, Skolkovo, Russia
- George Mason University, Fairfax, VA, USA
| | - George Starostin
- Russian State University for the Humanities, Moscow, Russia
- Russian Presidential Academy (RANEPA), Moscow, Russia
| | - Vita V. Stepanova
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, Russia
| | | | - Martin Tříska
- Children’s Hospital Los Angeles, Los Angeles, CA, USA
| | - Petr Tříska
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
- Instituto de Ciências Biomédicas da Universidade do Porto (ICBAS), Porto, Portugal
| | - Tatiana V. Tatarinova
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
- Children’s Hospital Los Angeles, Los Angeles, CA, USA
- Spatial Sciences Institute, University of Southern California, Los Angeles, CA, USA
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37
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Resolving the ancestry of Austronesian-speaking populations. Hum Genet 2016; 135:309-26. [PMID: 26781090 PMCID: PMC4757630 DOI: 10.1007/s00439-015-1620-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2015] [Accepted: 11/18/2015] [Indexed: 01/17/2023]
Abstract
There are two very different interpretations of the prehistory of Island Southeast Asia (ISEA), with genetic evidence invoked in support of both. The "out-of-Taiwan" model proposes a major Late Holocene expansion of Neolithic Austronesian speakers from Taiwan. An alternative, proposing that Late Glacial/postglacial sea-level rises triggered largely autochthonous dispersals, accounts for some otherwise enigmatic genetic patterns, but fails to explain the Austronesian language dispersal. Combining mitochondrial DNA (mtDNA), Y-chromosome and genome-wide data, we performed the most comprehensive analysis of the region to date, obtaining highly consistent results across all three systems and allowing us to reconcile the models. We infer a primarily common ancestry for Taiwan/ISEA populations established before the Neolithic, but also detected clear signals of two minor Late Holocene migrations, probably representing Neolithic input from both Mainland Southeast Asia and South China, via Taiwan. This latter may therefore have mediated the Austronesian language dispersal, implying small-scale migration and language shift rather than large-scale expansion.
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38
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Raff JA, Bolnick DA. Does Mitochondrial Haplogroup X Indicate Ancient Trans-Atlantic Migration to the Americas? A Critical Re-Evaluation. ACTA ACUST UNITED AC 2015. [DOI: 10.1179/2055556315z.00000000040] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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39
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Jacovas VC, Rovaris DL, Peréz O, de Azevedo S, Macedo GS, Sandoval JR, Salazar-Granara A, Villena M, Dugoujon JM, Bisso-Machado R, Petzl-Erler ML, Salzano FM, Ashton-Prolla P, Ramallo V, Bortolini MC. Genetic Variations in the TP53 Pathway in Native Americans Strongly Suggest Adaptation to the High Altitudes of the Andes. PLoS One 2015; 10:e0137823. [PMID: 26382048 PMCID: PMC4575214 DOI: 10.1371/journal.pone.0137823] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 08/24/2015] [Indexed: 02/05/2023] Open
Abstract
The diversity of the five single nucleotide polymorphisms located in genes of the TP53 pathway (TP53, rs1042522; MDM2, rs2279744; MDM4, rs1563828; USP7, rs1529916; and LIF, rs929271) were studied in a total of 282 individuals belonging to Quechua, Aymara, Chivay, Cabanaconde, Yanke, Taquile, Amantani, Anapia, Uros, Guarani Ñandeva, and Guarani Kaiowá populations, characterized as Native American or as having a high level (> 90%) of Native American ancestry. In addition, published data pertaining to 100 persons from five other Native American populations (Surui, Karitiana, Maya, Pima, and Piapoco) were analyzed. The populations were classified as living in high altitude (≥ 2,500 m) or in lowlands (< 2,500 m). Our analyses revealed that alleles USP7-G, LIF-T, and MDM2-T showed significant evidence that they were selected for in relation to harsh environmental variables related to high altitudes. Our results show for the first time that alleles of classical TP53 network genes have been evolutionary co-opted for the successful human colonization of the Andes.
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Affiliation(s)
- Vanessa Cristina Jacovas
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brasil
| | - Diego Luiz Rovaris
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brasil
| | - Orlando Peréz
- Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Puerto Madryn, Argentina
| | - Soledad de Azevedo
- Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Puerto Madryn, Argentina
| | - Gabriel Souza Macedo
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brasil
| | - José Raul Sandoval
- Facultad de Medicina Humana, Universidad de San Martin de Porres (USMP), Lima, Peru
| | | | - Mercedes Villena
- Instituto Boliviano de Biología de Altura (IBBA), Universidad Mayor de San Andres, La Paz, Bolivia
| | - Jean-Michel Dugoujon
- Anthropologie Moléculaire et Imagerie de Synthèse, CNRS UMR 5288, Université Paul Sabatier Toulouse III, Toulouse, 31000, France
| | - Rafael Bisso-Machado
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brasil
| | - Maria Luiza Petzl-Erler
- Laboratório de Genética Molecular, Departamento de Genética, Universidade Federal do Paraná, Curitiba, PR, Brasil
| | - Francisco Mauro Salzano
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brasil
| | - Patricia Ashton-Prolla
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brasil
- Serviço de Genética Medica, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
| | - Virginia Ramallo
- Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Puerto Madryn, Argentina
| | - Maria Cátira Bortolini
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brasil
- * E-mail:
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40
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The ancestry and affiliations of Kennewick Man. Nature 2015; 523:455-458. [PMID: 26087396 DOI: 10.1038/nature14625] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 06/10/2015] [Indexed: 12/20/2022]
Abstract
Kennewick Man, referred to as the Ancient One by Native Americans, is a male human skeleton discovered in Washington state (USA) in 1996 and initially radiocarbon dated to 8,340-9,200 calibrated years before present (BP). His population affinities have been the subject of scientific debate and legal controversy. Based on an initial study of cranial morphology it was asserted that Kennewick Man was neither Native American nor closely related to the claimant Plateau tribes of the Pacific Northwest, who claimed ancestral relationship and requested repatriation under the Native American Graves Protection and Repatriation Act (NAGPRA). The morphological analysis was important to judicial decisions that Kennewick Man was not Native American and that therefore NAGPRA did not apply. Instead of repatriation, additional studies of the remains were permitted. Subsequent craniometric analysis affirmed Kennewick Man to be more closely related to circumpacific groups such as the Ainu and Polynesians than he is to modern Native Americans. In order to resolve Kennewick Man's ancestry and affiliations, we have sequenced his genome to ∼1× coverage and compared it to worldwide genomic data including for the Ainu and Polynesians. We find that Kennewick Man is closer to modern Native Americans than to any other population worldwide. Among the Native American groups for whom genome-wide data are available for comparison, several seem to be descended from a population closely related to that of Kennewick Man, including the Confederated Tribes of the Colville Reservation (Colville), one of the five tribes claiming Kennewick Man. We revisit the cranial analyses and find that, as opposed to genome-wide comparisons, it is not possible on that basis to affiliate Kennewick Man to specific contemporary groups. We therefore conclude based on genetic comparisons that Kennewick Man shows continuity with Native North Americans over at least the last eight millennia.
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41
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Raghavan M, Steinrücken M, Harris K, Schiffels S, Rasmussen S, DeGiorgio M, Albrechtsen A, Valdiosera C, Ávila-Arcos MC, Malaspinas AS, Eriksson A, Moltke I, Metspalu M, Homburger JR, Wall J, Cornejo OE, Moreno-Mayar JV, Korneliussen TS, Pierre T, Rasmussen M, Campos PF, de Barros Damgaard P, Allentoft ME, Lindo J, Metspalu E, Rodríguez-Varela R, Mansilla J, Henrickson C, Seguin-Orlando A, Malmström H, Stafford T, Shringarpure SS, Moreno-Estrada A, Karmin M, Tambets K, Bergström A, Xue Y, Warmuth V, Friend AD, Singarayer J, Valdes P, Balloux F, Leboreiro I, Vera JL, Rangel-Villalobos H, Pettener D, Luiselli D, Davis LG, Heyer E, Zollikofer CPE, Ponce de León MS, Smith CI, Grimes V, Pike KA, Deal M, Fuller BT, Arriaza B, Standen V, Luz MF, Ricaut F, Guidon N, Osipova L, Voevoda MI, Posukh OL, Balanovsky O, Lavryashina M, Bogunov Y, Khusnutdinova E, Gubina M, Balanovska E, Fedorova S, Litvinov S, Malyarchuk B, Derenko M, Mosher MJ, Archer D, Cybulski J, Petzelt B, Mitchell J, Worl R, Norman PJ, Parham P, Kemp BM, Kivisild T, Tyler-Smith C, Sandhu MS, Crawford M, Villems R, Smith DG, Waters MR, Goebel T, Johnson JR, Malhi RS, Jakobsson M, Meltzer DJ, Manica A, Durbin R, Bustamante CD, Song YS, Nielsen R, Willerslev E. POPULATION GENETICS. Genomic evidence for the Pleistocene and recent population history of Native Americans. Science 2015. [PMID: 26198033 DOI: 10.1126/science.aab3884] [Citation(s) in RCA: 255] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
How and when the Americas were populated remains contentious. Using ancient and modern genome-wide data, we found that the ancestors of all present-day Native Americans, including Athabascans and Amerindians, entered the Americas as a single migration wave from Siberia no earlier than 23 thousand years ago (ka) and after no more than an 8000-year isolation period in Beringia. After their arrival to the Americas, ancestral Native Americans diversified into two basal genetic branches around 13 ka, one that is now dispersed across North and South America and the other restricted to North America. Subsequent gene flow resulted in some Native Americans sharing ancestry with present-day East Asians (including Siberians) and, more distantly, Australo-Melanesians. Putative "Paleoamerican" relict populations, including the historical Mexican Pericúes and South American Fuego-Patagonians, are not directly related to modern Australo-Melanesians as suggested by the Paleoamerican Model.
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Affiliation(s)
- Maanasa Raghavan
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Matthias Steinrücken
- Computer Science Division, University of California, Berkeley, CA 94720, USA.,Department of Statistics, University of California, Berkeley, CA 94720, USA.,Department of Biostatistics and Epidemiology, University of Massachusetts, Amherst, MA 01003, USA
| | - Kelley Harris
- Department of Mathematics, University of California, Berkeley, CA 94720, USA
| | - Stephan Schiffels
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Simon Rasmussen
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet, Building 208, 2800 Kongens Lyngby, Denmark
| | - Michael DeGiorgio
- Departments of Biology and Statistics, Pennsylvania State University, 502 Wartik Laboratory, University Park, PA 16802, USA
| | - Anders Albrechtsen
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
| | - Cristina Valdiosera
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.,Department of Archaeology and History, La Trobe University, Melbourne, Victoria 3086, Australia
| | - María C Ávila-Arcos
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.,Department of Genetics, School of Medicine, Stanford University, 300 Pasteur Dr. Lane Bldg Room L331, Stanford, California 94305, USA
| | - Anna-Sapfo Malaspinas
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Anders Eriksson
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK.,Integrative Systems Biology Laboratory, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Ida Moltke
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
| | - Mait Metspalu
- Estonian Biocentre, Evolutionary Biology Group, Tartu 51010, Estonia.,Department of Evolutionary Biology, University of Tartu, Tartu 51010, Estonia
| | - Julian R Homburger
- Department of Genetics, School of Medicine, Stanford University, 300 Pasteur Dr. Lane Bldg Room L331, Stanford, California 94305, USA
| | - Jeff Wall
- Institute for Human Genetics, University of California San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA
| | - Omar E Cornejo
- School of Biological Sciences, Washington State University, PO Box 644236, Heald 429, Pullman, Washington 99164, USA
| | - J Víctor Moreno-Mayar
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Thorfinn S Korneliussen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Tracey Pierre
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Morten Rasmussen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.,Department of Genetics, School of Medicine, Stanford University, 300 Pasteur Dr. Lane Bldg Room L331, Stanford, California 94305, USA
| | - Paula F Campos
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.,CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas 289, 4050-123 Porto, Portugal
| | - Peter de Barros Damgaard
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Morten E Allentoft
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - John Lindo
- Department of Anthropology, University of Illinois at Urbana-Champaign, 607 S. Mathews Ave, Urbana, IL 61801, USA
| | - Ene Metspalu
- Estonian Biocentre, Evolutionary Biology Group, Tartu 51010, Estonia.,Department of Evolutionary Biology, University of Tartu, Tartu 51010, Estonia
| | - Ricardo Rodríguez-Varela
- Centro Mixto, Universidad Complutense de Madrid-Instituto de Salud Carlos III de Evolución y Comportamiento Humano, Madrid, Spain
| | - Josefina Mansilla
- Instituto Nacional de Antropología e Historia, Moneda 13, Centro, Cuauhtémoc, 06060 Mexico Mexico City, Mexico
| | - Celeste Henrickson
- University of Utah, Department of Anthropology, 270 S 1400 E, Salt Lake City, Utah 84112, USA
| | - Andaine Seguin-Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Helena Malmström
- Department of Evolutionary Biology and Science for Life Laboratory, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - Thomas Stafford
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.,AMS 14C Dating Centre, Department of Physics and Astronomy, Aarhus University, Ny Munkegade 120, 8000 Aarhus, Denmark
| | - Suyash S Shringarpure
- Department of Genetics, School of Medicine, Stanford University, 300 Pasteur Dr. Lane Bldg Room L331, Stanford, California 94305, USA
| | - Andrés Moreno-Estrada
- Department of Genetics, School of Medicine, Stanford University, 300 Pasteur Dr. Lane Bldg Room L331, Stanford, California 94305, USA.,Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), CINVESTAV, Irapuato, Guanajuato 36821, Mexico
| | - Monika Karmin
- Estonian Biocentre, Evolutionary Biology Group, Tartu 51010, Estonia.,Department of Evolutionary Biology, University of Tartu, Tartu 51010, Estonia
| | - Kristiina Tambets
- Estonian Biocentre, Evolutionary Biology Group, Tartu 51010, Estonia
| | - Anders Bergström
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Yali Xue
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Vera Warmuth
- UCL Genetics Institute, Gower Street, London WC1E 6BT, UK.,Evolutionsbiologiskt Centrum, Norbyvägen 18D, 75236 Uppsala, Sweden
| | - Andrew D Friend
- Department of Geography, University of Cambridge, Downing Place, Cambridge CB2 3EN, UK
| | - Joy Singarayer
- Centre for Past Climate Change and Department of Meteorology, University of Reading, Earley Gate, PO Box 243, Reading, UK
| | - Paul Valdes
- School of Geographical Sciences, University Road, Clifton, Bristol BS8 1SS, UK
| | | | - Ilán Leboreiro
- Instituto Nacional de Antropología e Historia, Moneda 13, Centro, Cuauhtémoc, 06060 Mexico Mexico City, Mexico
| | - Jose Luis Vera
- Escuela Nacional de AntropologÍa e Historia, Periférico Sur y Zapote s/n. Colonia Isidro Fabela, Tlalpan, Isidro Fabela, 14030 Mexico City, Mexico
| | | | - Davide Pettener
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali (BiGeA), Università di Bologna, Via Selmi 3, 40126 Bologna, Italy
| | - Donata Luiselli
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali (BiGeA), Università di Bologna, Via Selmi 3, 40126 Bologna, Italy
| | - Loren G Davis
- Department of Anthropology, Oregon State University, 238 Waldo Hall, Corvallis, OR, 97331 USA
| | - Evelyne Heyer
- Museum National d'Histoire Naturelle, CNRS, Université Paris 7 Diderot, Sorbonne Paris Cité, Sorbonne Universités, Unité Eco-Anthropologie et Ethnobiologie (UMR7206), Paris, France
| | - Christoph P E Zollikofer
- Anthropological Institute and Museum, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Marcia S Ponce de León
- Anthropological Institute and Museum, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Colin I Smith
- Department of Archaeology and History, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Vaughan Grimes
- Department of Archaeology, Memorial University, Queen's College, 210 Prince Philip Drive, St. John's, Newfoundland, A1C 5S7, Canada.,Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig 04103, Germany
| | - Kelly-Anne Pike
- Department of Archaeology, Memorial University, Queen's College, 210 Prince Philip Drive, St. John's, Newfoundland, A1C 5S7, Canada
| | - Michael Deal
- Department of Archaeology, Memorial University, Queen's College, 210 Prince Philip Drive, St. John's, Newfoundland, A1C 5S7, Canada
| | - Benjamin T Fuller
- Department of Earth System Science, University of California, Irvine, Keck CCAMS Group, B321 Croul Hall, Irvine, California, 92697, USA
| | - Bernardo Arriaza
- Instituto de Alta Investigación, Universidad de Tarapacá, 18 de Septiembre 2222, Carsilla 6-D Arica, Chile
| | - Vivien Standen
- Departamento de Antropologia, Universidad de Tarapacá, 18 de Septiembre 2222. Casilla 6-D Arica, Chile
| | - Maria F Luz
- Fundação Museu do Homem Americano, Centro Cultural Sérgio Motta, Campestre, 64770-000 Sao Raimundo Nonato, Brazil
| | - Francois Ricaut
- Laboratoire d'Anthropologie Moléculaire et Imagérie de Synthèse UMR-5288, CNRS, Université de Toulouse, 31073 Toulouse, France
| | - Niede Guidon
- Fundação Museu do Homem Americano, Centro Cultural Sérgio Motta, Campestre, 64770-000 Sao Raimundo Nonato, Brazil
| | - Ludmila Osipova
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentyeva 10, 630090 Novosibirsk, Russia.,Novosibirsk State University, 2 Pirogova Str., 630090 Novosibirsk, Russia
| | - Mikhail I Voevoda
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentyeva 10, 630090 Novosibirsk, Russia.,Institute of Internal Medicine, Siberian Branch of RAS, 175/1 ul. B. Bogatkova, Novosibirsk 630089, Russia.,Novosibirsk State University, Laboratory of Molecular Epidemiology and Bioinformatics, 630090 Novosibirsk, Russia
| | - Olga L Posukh
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentyeva 10, 630090 Novosibirsk, Russia.,Novosibirsk State University, 2 Pirogova Str., 630090 Novosibirsk, Russia
| | - Oleg Balanovsky
- Vavilov Institute of General Genetics, Gubkina 3, 119333 Moscow, Russia.,Research Centre for Medical Genetics, Moskvorechie 1, 115478 Moscow, Russia
| | | | - Yuri Bogunov
- Vavilov Institute of General Genetics, Gubkina 3, 119333 Moscow, Russia
| | - Elza Khusnutdinova
- Institute of Biochemistry and Genetics, Ufa Scientific Center of RAS, Prospekt Oktyabrya 71, 450054 Ufa, Russia.,Department of Genetics and Fundamental Medicine, Bashkir State University, Zaki Validi 32, 450076 Ufa, Russia
| | - Marina Gubina
- Fundação Museu do Homem Americano, Centro Cultural Sérgio Motta, Campestre, 64770-000 Sao Raimundo Nonato, Brazil
| | - Elena Balanovska
- Research Centre for Medical Genetics, Moskvorechie 1, 115478 Moscow, Russia
| | - Sardana Fedorova
- Department of Molecular Genetics, Yakut Scientific Centre of Complex Medical Problems, Sergelyahskoe Shosse 4, 677010 Yakutsk, Russia.,Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, 677000 Yakutsk, Russia
| | - Sergey Litvinov
- Estonian Biocentre, Evolutionary Biology Group, Tartu 51010, Estonia.,Institute of Biochemistry and Genetics, Ufa Scientific Center of RAS, Prospekt Oktyabrya 71, 450054 Ufa, Russia
| | - Boris Malyarchuk
- Institute of Biological Problems of the North, Russian Academy of Sciences, Portovaya Street 18, Magadan 685000, Russia
| | - Miroslava Derenko
- Institute of Biological Problems of the North, Russian Academy of Sciences, Portovaya Street 18, Magadan 685000, Russia
| | - M J Mosher
- Department of Anthropology, Western Washington University, Bellingham Washington 98225, USA
| | - David Archer
- Department of Anthropology, Northwest Community College, 353 Fifth Street, Prince Rupert, British Columbia V8J 3L6, Canada
| | - Jerome Cybulski
- Canadian Museum of History, 100 Rue Laurier, Gatineau, Quebec K1A 0M8, Canada.,University of Western Ontario, London, Ontario N6A 3K7, Canada.,Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Barbara Petzelt
- Metlakatla Treaty Office, PO Box 224, Prince Rupert, BC, Canada V8J 3P6
| | | | - Rosita Worl
- Sealaska Heritage Institute, 105 S. Seward Street, Juneau, Alaska 99801, USA
| | - Paul J Norman
- Department of Structural Biology, Stanford University School of Medicine, D100 Fairchild Science Building, Stanford, California 94305-5126, USA
| | - Peter Parham
- Department of Structural Biology, Stanford University School of Medicine, D100 Fairchild Science Building, Stanford, California 94305-5126, USA
| | - Brian M Kemp
- School of Biological Sciences, Washington State University, PO Box 644236, Heald 429, Pullman, Washington 99164, USA.,Department of Anthropology, Washington State University, Pullman Washington 99163, USA
| | - Toomas Kivisild
- Estonian Biocentre, Evolutionary Biology Group, Tartu 51010, Estonia.,Division of Biological Anthropology, University of Cambridge, Henry Wellcome Building, Fitzwilliam Street, CB2 1QH, Cambridge, UK
| | - Chris Tyler-Smith
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Manjinder S Sandhu
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK.,Dept of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Michael Crawford
- Laboratory of Biological Anthropology, University of Kansas, 1415 Jayhawk Blvd., 622 Fraser Hall, Lawrence, Kansas 66045, USA
| | - Richard Villems
- Estonian Biocentre, Evolutionary Biology Group, Tartu 51010, Estonia.,Department of Evolutionary Biology, University of Tartu, Tartu 51010, Estonia
| | - David Glenn Smith
- Molecular Anthropology Laboratory, 209 Young Hall, Department of Anthropology, University of California, One Shields Avenue, Davis, California 95616, USA
| | - Michael R Waters
- Center for the Study of the First Americans, Texas A&M University, College Station, Texas 77843-4352, USA.,Department of Anthropology, Texas A&M University, College Station, Texas 77843-4352, USA.,Department of Geography, Texas A&M University, College Station, Texas 77843-4352, USA
| | - Ted Goebel
- Center for the Study of the First Americans, Texas A&M University, College Station, Texas 77843-4352, USA
| | - John R Johnson
- Santa Barbara Museum of Natural History, 2559 Puesta del Sol, Santa Barbara, CA 93105, USA
| | - Ripan S Malhi
- Department of Anthropology, University of Illinois at Urbana-Champaign, 607 S. Mathews Ave, Urbana, IL 61801, USA.,Carle R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, 61801, USA
| | - Mattias Jakobsson
- Department of Evolutionary Biology and Science for Life Laboratory, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - David J Meltzer
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.,Department of Anthropology, Southern Methodist University, Dallas, Texas 75275, USA
| | - Andrea Manica
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Richard Durbin
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Carlos D Bustamante
- Department of Genetics, School of Medicine, Stanford University, 300 Pasteur Dr. Lane Bldg Room L331, Stanford, California 94305, USA
| | - Yun S Song
- Computer Science Division, University of California, Berkeley, CA 94720, USA.,Department of Statistics, University of California, Berkeley, CA 94720, USA.,Department of Integrative Biology, University of California, 3060 Valley Life Sciences Bldg #3140, Berkeley, CA 94720, USA
| | - Rasmus Nielsen
- Department of Integrative Biology, University of California, 3060 Valley Life Sciences Bldg #3140, Berkeley, CA 94720, USA
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
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Yracheta JM, Lanaspa MA, Le MT, Abdelmalak MF, Alfonso J, Sánchez-Lozada LG, Johnson RJ. Diabetes and Kidney Disease in American Indians: Potential Role of Sugar-Sweetened Beverages. Mayo Clin Proc 2015; 90:813-23. [PMID: 26046414 DOI: 10.1016/j.mayocp.2015.03.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Revised: 03/19/2015] [Accepted: 03/24/2015] [Indexed: 10/23/2022]
Abstract
Since the early 20th century, a marked increase in obesity, diabetes, and chronic kidney disease has occurred in the American Indian population, especially the Pima Indians of the Southwest. Here, we review the current epidemic and attempt to identify remediable causes. A search was performed using PubMed and the search terms American Indian and obesity, American Indian and diabetes, American Indian and chronic kidney disease, and American Indian and sugar or fructose, Native American, Alaska Native, First Nations, Aboriginal, Amerind, and Amerindian for American Indian for articles linking American Indians with diabetes, obesity, chronic kidney disease, and sugar; additional references were identified in these publications traced to 1900 and articles were reviewed if they were directly discussing these topics. Multiple factors are involved in the increased risk for diabetes and kidney disease in the American Indian population, including poverty, overnutrition, poor health care, high intake of sugar, and genetic mechanisms. Genetic factors may be especially important in the Pima, as historical records suggest that this group was predisposed to obesity before exposure to Western culture and diet. Exposure to sugar-sweetened beverages may also be involved in the increased risk for chronic kidney disease. In these small populations in severe health crisis, we recommend further studies to investigate the role of excess added sugar, especially sugar-sweetened beverages, as a potentially remediable risk factor.
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Affiliation(s)
- Joseph M Yracheta
- Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, WA.
| | - Miguel A Lanaspa
- Division of Renal Diseases and Hypertension, University of Colorado, Aurora, CO; Colorado Research Partners LLC, Aurora, CO
| | - MyPhuong T Le
- Division of Renal Diseases and Hypertension, University of Colorado, Aurora, CO; Colorado Research Partners LLC, Aurora, CO
| | - Manal F Abdelmalak
- Division of Gastroenterology and Hepatology, Duke University, Durham, NC
| | - Javier Alfonso
- Division of Renal Diseases and Hypertension, University of Colorado, Aurora, CO
| | - Laura G Sánchez-Lozada
- Colorado Research Partners LLC, Aurora, CO; Laboratory of Renal Physiopathology and Department of Nephrology, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City, Mexico
| | - Richard J Johnson
- Division of Renal Diseases and Hypertension, University of Colorado, Aurora, CO; Colorado Research Partners LLC, Aurora, CO
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43
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Pugach I, Stoneking M. Genome-wide insights into the genetic history of human populations. INVESTIGATIVE GENETICS 2015; 6:6. [PMID: 25834724 PMCID: PMC4381409 DOI: 10.1186/s13323-015-0024-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 03/05/2015] [Indexed: 12/21/2022]
Abstract
Although mtDNA and the non-recombining Y chromosome (NRY) studies continue to provide valuable insights into the genetic history of human populations, recent technical, methodological and computational advances and the increasing availability of large-scale, genome-wide data from contemporary human populations around the world promise to reveal new aspects, resolve finer points, and provide a more detailed look at our past demographic history. Genome-wide data are particularly useful for inferring migrations, admixture, and fine structure, as well as for estimating population divergence and admixture times and fluctuations in effective population sizes. In this review, we highlight some of the stories that have emerged from the analyses of genome-wide SNP genotyping data concerning the human history of Southern Africa, India, Oceania, Island South East Asia, Europe and the Americas and comment on possible future study directions. We also discuss advantages and drawbacks of using SNP-arrays, with a particular focus on the ascertainment bias, and ways to circumvent it.
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Affiliation(s)
- Irina Pugach
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D04103 Leipzig, Germany
| | - Mark Stoneking
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D04103 Leipzig, Germany
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44
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Abstract
Sex-biased admixture has been observed in a wide variety of admixed populations. Genetic variation in sex chromosomes and functions of quantities computed from sex chromosomes and autosomes have often been examined to infer patterns of sex-biased admixture, typically using statistical approaches that do not mechanistically model the complexity of a sex-specific history of admixture. Here, expanding on a model of Verdu and Rosenberg (2011) that did not include sex specificity, we develop a model that mechanistically examines sex-specific admixture histories. Under the model, multiple source populations contribute to an admixed population, potentially with their male and female contributions varying over time. In an admixed population descended from two source groups, we derive the moments of the distribution of the autosomal admixture fraction from a specific source population as a function of sex-specific introgression parameters and time. Considering admixture processes that are constant in time, we demonstrate that surprisingly, although the mean autosomal admixture fraction from a specific source population does not reveal a sex bias in the admixture history, the variance of autosomal admixture is informative about sex bias. Specifically, the long-term variance decreases as the sex bias from a contributing source population increases. This result can be viewed as analogous to the reduction in effective population size for populations with an unequal number of breeding males and females. Our approach suggests that it may be possible to use the effect of sex-biased admixture on autosomal DNA to assist with methods for inference of the history of complex sex-biased admixture processes.
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