201
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Ancient X chromosomes reveal contrasting sex bias in Neolithic and Bronze Age Eurasian migrations. Proc Natl Acad Sci U S A 2017; 114:2657-2662. [PMID: 28223527 DOI: 10.1073/pnas.1616392114] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Dramatic events in human prehistory, such as the spread of agriculture to Europe from Anatolia and the late Neolithic/Bronze Age migration from the Pontic-Caspian Steppe, can be investigated using patterns of genetic variation among the people who lived in those times. In particular, studies of differing female and male demographic histories on the basis of ancient genomes can provide information about complexities of social structures and cultural interactions in prehistoric populations. We use a mechanistic admixture model to compare the sex-specifically-inherited X chromosome with the autosomes in 20 early Neolithic and 16 late Neolithic/Bronze Age human remains. Contrary to previous hypotheses suggested by the patrilocality of many agricultural populations, we find no evidence of sex-biased admixture during the migration that spread farming across Europe during the early Neolithic. For later migrations from the Pontic Steppe during the late Neolithic/Bronze Age, however, we estimate a dramatic male bias, with approximately five to 14 migrating males for every migrating female. We find evidence of ongoing, primarily male, migration from the steppe to central Europe over a period of multiple generations, with a level of sex bias that excludes a pulse migration during a single generation. The contrasting patterns of sex-specific migration during these two migrations suggest a view of differing cultural histories in which the Neolithic transition was driven by mass migration of both males and females in roughly equal numbers, perhaps whole families, whereas the later Bronze Age migration and cultural shift were instead driven by male migration, potentially connected to new technology and conquest.
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202
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Balanovsky O, Gurianov V, Zaporozhchenko V, Balaganskaya O, Urasin V, Zhabagin M, Grugni V, Canada R, Al-Zahery N, Raveane A, Wen SQ, Yan S, Wang X, Zalloua P, Marafi A, Koshel S, Semino O, Tyler-Smith C, Balanovska E. Phylogeography of human Y-chromosome haplogroup Q3-L275 from an academic/citizen science collaboration. BMC Evol Biol 2017; 17:18. [PMID: 28251872 PMCID: PMC5333174 DOI: 10.1186/s12862-016-0870-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Background The Y-chromosome haplogroup Q has three major branches: Q1, Q2, and Q3. Q1 is found in both Asia and the Americas where it accounts for about 90% of indigenous Native American Y-chromosomes; Q2 is found in North and Central Asia; but little is known about the third branch, Q3, also named Q1b-L275. Here, we combined the efforts of population geneticists and genetic genealogists to use the potential of full Y-chromosome sequencing for reconstructing haplogroup Q3 phylogeography and suggest possible linkages to events in population history. Results We analyzed 47 fully sequenced Y-chromosomes and reconstructed the haplogroup Q3 phylogenetic tree in detail. Haplogroup Q3-L275, derived from the oldest known split within Eurasian/American haplogroup Q, most likely occurred in West or Central Asia in the Upper Paleolithic period. During the Mesolithic and Neolithic epochs, Q3 remained a minor component of the West Asian Y-chromosome pool and gave rise to five branches (Q3a to Q3e), which spread across West, Central and parts of South Asia. Around 3–4 millennia ago (Bronze Age), the Q3a branch underwent a rapid expansion, splitting into seven branches, some of which entered Europe. One of these branches, Q3a1, was acquired by a population ancestral to Ashkenazi Jews and grew within this population during the 1st millennium AD, reaching up to 5% in present day Ashkenazi. Conclusions This study dataset was generated by a massive Y-chromosome genotyping effort in the genetic genealogy community, and phylogeographic patterns were revealed by a collaboration of population geneticists and genetic genealogists. This positive experience of collaboration between academic and citizen science provides a model for further joint projects. Merging data and skills of academic and citizen science promises to combine, respectively, quality and quantity, generalization and specialization, and achieve a well-balanced and careful interpretation of the paternal-side history of human populations. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0870-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Oleg Balanovsky
- Vavilov Institute of General Genetics, Moscow, Russia. .,Research Centre for Medical Genetics, Moscow, Russia.
| | | | - Valery Zaporozhchenko
- Vavilov Institute of General Genetics, Moscow, Russia.,Research Centre for Medical Genetics, Moscow, Russia
| | | | | | - Maxat Zhabagin
- National Laboratory Astana, Nazarbayev University, Astana, Republic of Kazakhstan
| | - Viola Grugni
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
| | | | - Nadia Al-Zahery
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Alessandro Raveane
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Shao-Qing Wen
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Shi Yan
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Xianpin Wang
- Department of Criminal Investigation, Xuanwei Public Security Bureau, Xuanwei, China
| | | | | | - Sergey Koshel
- Faculty of Geography, Lomonosov Moscow State University, Moscow, Russia
| | - Ornella Semino
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Chris Tyler-Smith
- The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Elena Balanovska
- Vavilov Institute of General Genetics, Moscow, Russia.,Research Centre for Medical Genetics, Moscow, Russia
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203
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Maisano Delser P, Neumann R, Ballereau S, Hallast P, Batini C, Zadik D, Jobling MA. Signatures of human European Palaeolithic expansion shown by resequencing of non-recombining X-chromosome segments. Eur J Hum Genet 2017; 25:485-492. [PMID: 28120839 PMCID: PMC5386427 DOI: 10.1038/ejhg.2016.207] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 11/07/2016] [Accepted: 12/14/2016] [Indexed: 11/09/2022] Open
Abstract
Human genetic diversity in Europe has been extensively studied using uniparentally inherited sequences (mitochondrial DNA (mtDNA) and the Y chromosome), which reveal very different patterns indicating sex-specific demographic histories. The X chromosome, haploid in males and inherited twice as often from mothers as from fathers, could provide insights into past female behaviours, but has not been extensively investigated. Here, we use HapMap single-nucleotide polymorphism data to identify genome-wide segments of the X chromosome in which recombination is historically absent and mutations are likely to be the only source of genetic variation, referring to these as phylogeographically informative haplotypes on autosomes and X chromosome (PHAXs). Three such sequences on the X chromosome spanning a total of ~49 kb were resequenced in 240 males from Europe, the Middle East and Africa at an average coverage of 181 ×. These PHAXs were confirmed to be essentially non-recombining across European samples. All three loci show highly homogeneous patterns across Europe and are highly differentiated from the African sample. Star-like structures of European-specific haplotypes in median-joining networks indicate past population expansions. Bayesian skyline plots and time-to-most-recent-common-ancestor estimates suggest expansions pre-dating the Neolithic transition, a finding that is more compatible with data on mtDNA than the Y chromosome, and with the female bias of X-chromosomal inheritance. This study demonstrates the potential of the use of X-chromosomal haplotype blocks, and the utility of the accurate ascertainment of rare variants for inferring human demographic history.
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Affiliation(s)
| | - Rita Neumann
- Department of Genetics, University of Leicester, Leicester, UK
| | | | - Pille Hallast
- Department of Genetics, University of Leicester, Leicester, UK
| | - Chiara Batini
- Department of Genetics, University of Leicester, Leicester, UK
| | - Daniel Zadik
- Department of Genetics, University of Leicester, Leicester, UK
| | - Mark A Jobling
- Department of Genetics, University of Leicester, Leicester, UK
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204
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Balanovska EV, Zhabagin MK, Agdzhoyan AT, Chukhryaeva MI, Markina NV, Balaganskaya OA, Skhalyakho RA, Yusupov YM, Utevska OM, Bogunov YV, Asilguzhin RR, Dolinina DO, Kagazezheva ZA, Damba LD, Zaporozhchenko VV, Romanov AG, Dibirova KD, Kuznetsova MA, Lavryashina MB, Pocheshkhova EA, Balanovsky OP. Population biobanks: Organizational models and prospects of application in gene geography and personalized medicine. RUSS J GENET+ 2016. [DOI: 10.1134/s1022795416120024] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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205
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Investigating mitochondrial DNA relationships in Neolithic Western Europe through serial coalescent simulations. Eur J Hum Genet 2016; 25:388-392. [PMID: 28029148 DOI: 10.1038/ejhg.2016.180] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 11/18/2016] [Accepted: 11/24/2016] [Indexed: 11/09/2022] Open
Abstract
Recent ancient DNA studies on European Neolithic human populations have provided persuasive evidence of a major migration of farmers originating from the Aegean, accompanied by sporadic hunter-gatherer admixture into early Neolithic populations, but increasing toward the Late Neolithic. In this context, ancient mitochondrial DNA data collected from the Neolithic necropolis of Gurgy (Paris Basin, France), the largest mitochondrial DNA sample obtained from a single archeological site for the Early/Middle Neolithic period, indicate little differentiation from farmers associated to both the Danubian and Mediterranean Neolithic migration routes, as well as from Western European hunter-gatherers. To test whether this pattern of differentiation could arise in a single unstructured population by genetic drift alone, we used serial coalescent simulations. We explore female effective population size parameter combinations at the time of the colonization of Europe 45000 years ago and the most recent of the Neolithic samples analyzed in this study 5900 years ago, and identify conditions under which population panmixia between hunter-gatherers/Early-Middle Neolithic farmers and Gurgy cannot be rejected. In relation to other studies on the current debate of the origins of Europeans, these results suggest increasing hunter-gatherer admixture into farmers' group migrating farther west in Europe.
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206
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Mendez FL. Differences in the effective population sizes of males and females do not require differences in their distribution of offspring number. Theor Popul Biol 2016; 114:19-28. [PMID: 27915040 DOI: 10.1016/j.tpb.2016.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 11/07/2016] [Accepted: 11/14/2016] [Indexed: 11/15/2022]
Abstract
Difference in male and female effective population sizes has, at times, been attributed to both sexes having unequal variance in their number of offspring. Such difference is paralleled by the relative effective sizes of autosomes, sex chromosomes, and mitochondrial DNA. I develop a simple framework to calculate the inbreeding effective population sizes for loci with different modes of inheritance. In this framework, I separate the effects due to mating strategy and those due to genetic transmission. I then show that, in addition to differences in the variance in offspring number, skew in the male/female effective sizes can also be caused by family composition. This approach can be used to illustrate the effect of induced behaviors on the relative male and female effective population sizes. In particular, I show the impact of the one-child policy formerly implemented in the People's Republic of China on the relative male and female effective population sizes. Furthermore, I argue that, under some strong constraints on family structure, the concepts of male and female effective population sizes are invalid.
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Affiliation(s)
- Fernando L Mendez
- Department of Genetics, Stanford University, Stanford, CA 94305, United States.
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207
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Gao F, Keinan A. Explosive genetic evidence for explosive human population growth. Curr Opin Genet Dev 2016; 41:130-139. [PMID: 27710906 PMCID: PMC5161661 DOI: 10.1016/j.gde.2016.09.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 08/26/2016] [Accepted: 09/11/2016] [Indexed: 11/19/2022]
Abstract
The advent of next-generation sequencing technology has allowed the collection of vast amounts of genetic variation data. A recurring discovery from studying larger and larger samples of individuals had been the extreme, previously unexpected, excess of very rare genetic variants, which has been shown to be mostly due to the recent explosive growth of human populations. Here, we review recent literature that inferred recent changes in population size in different human populations and with different methodologies, with many pointing to recent explosive growth, especially in European populations for which more data has been available. We also review the state-of-the-art methods and software for the inference of historical population size changes that lead to these discoveries. Finally, we discuss the implications of recent population growth on personalized genomics, on purifying selection in the non-equilibrium state it entails and, as a consequence, on the genetic architecture underlying complex disease and the performance of mapping methods in discovering rare variants that contribute to complex disease risk.
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Affiliation(s)
- Feng Gao
- Department of Biological Statistics and Computational Biology, Ithaca, NY 14850, United States
| | - Alon Keinan
- Department of Biological Statistics and Computational Biology, Ithaca, NY 14850, United States.
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208
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Safron A. What is orgasm? A model of sexual trance and climax via rhythmic entrainment. SOCIOAFFECTIVE NEUROSCIENCE & PSYCHOLOGY 2016; 6:31763. [PMID: 27799079 PMCID: PMC5087698 DOI: 10.3402/snp.v6.31763] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 08/04/2016] [Accepted: 08/05/2016] [Indexed: 01/07/2023]
Abstract
Orgasm is one of the most intense pleasures attainable to an organism, yet its underlying mechanisms remain poorly understood. On the basis of existing literatures, this article introduces a novel mechanistic model of sexual stimulation and orgasm. In doing so, it characterizes the neurophenomenology of sexual trance and climax, describes parallels in dynamics between orgasms and seizures, speculates on possible evolutionary origins of sex differences in orgasmic responding, and proposes avenues for future experimentation. Here, a model is introduced wherein sexual stimulation induces entrainment of coupling mechanical and neuronal oscillatory systems, thus creating synchronized functional networks within which multiple positive feedback processes intersect synergistically to contribute to sexual experience. These processes generate states of deepening sensory absorption and trance, potentially culminating in climax if critical thresholds are surpassed. The centrality of rhythmic stimulation (and its modulation by salience) for surpassing these thresholds suggests ways in which differential orgasmic responding between individuals-or with different partners-may serve as a mechanism for ensuring adaptive mate choice. Because the production of rhythmic stimulation combines honest indicators of fitness with cues relating to potential for investment, differential orgasmic response may serve to influence the probability of continued sexual encounters with specific mates.
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Affiliation(s)
- Adam Safron
- Department of Psychology, Northwestern University, Evanston, IL, USA;
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209
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Reconstructing Demography and Social Behavior During the Neolithic Expansion from Genomic Diversity Across Island Southeast Asia. Genetics 2016; 204:1495-1506. [PMID: 27683274 PMCID: PMC5161281 DOI: 10.1534/genetics.116.191379] [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] [Received: 06/17/2016] [Accepted: 09/16/2016] [Indexed: 11/18/2022] Open
Abstract
Archaeology, linguistics, and increasingly genetics are clarifying how populations moved from mainland Asia, through Island Southeast Asia, and out into the Pacific during the farming revolution. Yet key features of this process remain poorly understood, particularly how social behaviors intersected with demographic drivers to create the patterns of genomic diversity observed across Island Southeast Asia today. Such questions are ripe for computer modeling. Here, we construct an agent-based model to simulate human mobility across Island Southeast Asia from the Neolithic period to the present, with a special focus on interactions between individuals with Asian, Papuan, and mixed Asian-Papuan ancestry. Incorporating key features of the region, including its complex geography (islands and sea), demographic drivers (fecundity and migration), and social behaviors (marriage preferences), the model simultaneously tracks a full suite of genomic markers (autosomes, X chromosome, mitochondrial DNA, and Y chromosome). Using Bayesian inference, model parameters were determined that produce simulations that closely resemble the admixture profiles of 2299 individuals from 84 populations across Island Southeast Asia. The results highlight that greater propensity to migrate and elevated birth rates are related drivers behind the expansion of individuals with Asian ancestry relative to individuals with Papuan ancestry, that offspring preferentially resulted from marriages between Asian women and Papuan men, and that in contrast to current thinking, individuals with Asian ancestry were likely distributed across large parts of western Island Southeast Asia before the Neolithic expansion.
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210
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von Rueden CR, Jaeggi AV. Men's status and reproductive success in 33 nonindustrial societies: Effects of subsistence, marriage system, and reproductive strategy. Proc Natl Acad Sci U S A 2016; 113:10824-9. [PMID: 27601650 PMCID: PMC5047206 DOI: 10.1073/pnas.1606800113] [Citation(s) in RCA: 125] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Social status motivates much of human behavior. However, status may have been a relatively weak target of selection for much of human evolution if ancestral foragers tended to be more egalitarian. We test the "egalitarianism hypothesis" that status has a significantly smaller effect on reproductive success (RS) in foragers compared with nonforagers. We also test between alternative male reproductive strategies, in particular whether reproductive benefits of status are due to lower offspring mortality (parental investment) or increased fertility (mating effort). We performed a phylogenetic multilevel metaanalysis of 288 statistical associations between measures of male status (physical formidability, hunting ability, material wealth, political influence) and RS (mating success, wife quality, fertility, offspring mortality, and number of surviving offspring) from 46 studies in 33 nonindustrial societies. We found a significant overall effect of status on RS (r = 0.19), though this effect was significantly lower than for nonhuman primates (r = 0.80). There was substantial variation due to marriage system and measure of RS, in particular status associated with offspring mortality only in polygynous societies (r = -0.08), and with wife quality only in monogamous societies (r = 0.15). However, the effects of status on RS did not differ significantly by status measure or subsistence type: foraging, horticulture, pastoralism, and agriculture. These results suggest that traits that facilitate status acquisition were not subject to substantially greater selection with domestication of plants and animals, and are part of reproductive strategies that enhance fertility more than offspring well-being.
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Affiliation(s)
| | - Adrian V Jaeggi
- Department of Anthropology, Emory University, Atlanta, GA 30316
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211
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Webster TH, Wilson Sayres MA. Genomic signatures of sex-biased demography: progress and prospects. Curr Opin Genet Dev 2016; 41:62-71. [PMID: 27599147 DOI: 10.1016/j.gde.2016.08.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Revised: 07/06/2016] [Accepted: 08/02/2016] [Indexed: 01/09/2023]
Abstract
Sex-biased demographic events have played a crucial role in shaping human history. Many of these processes affect genetic variation and can therefore leave detectable signatures in the genome because autosomal, X-linked, Y-linked, and mitochondrial DNA inheritance differ between sexes. Here, we discuss how sex-biased processes shape patterns of genetic diversity across the genome, review recent genomic evidence for sex-biased demography in modern human populations, and suggest directions for future research.
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Affiliation(s)
- Timothy H Webster
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA.
| | - Melissa A Wilson Sayres
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA; Center for Evolution and Medicine, The Biodesign Institute at Arizona State University, Tempe, AZ 85287, USA.
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212
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Pankratov V, Litvinov S, Kassian A, Shulhin D, Tchebotarev L, Yunusbayev B, Möls M, Sahakyan H, Yepiskoposyan L, Rootsi S, Metspalu E, Golubenko M, Ekomasova N, Akhatova F, Khusnutdinova E, Heyer E, Endicott P, Derenko M, Malyarchuk B, Metspalu M, Davydenko O, Villems R, Kushniarevich A. East Eurasian ancestry in the middle of Europe: genetic footprints of Steppe nomads in the genomes of Belarusian Lipka Tatars. Sci Rep 2016; 6:30197. [PMID: 27453128 PMCID: PMC4958967 DOI: 10.1038/srep30197] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 06/29/2016] [Indexed: 12/04/2022] Open
Abstract
Medieval era encounters of nomadic groups of the Eurasian Steppe and largely sedentary East Europeans had a variety of demographic and cultural consequences. Amongst these outcomes was the emergence of the Lipka Tatars—a Slavic-speaking Sunni-Muslim minority residing in modern Belarus, Lithuania and Poland, whose ancestors arrived in these territories via several migration waves, mainly from the Golden Horde. Our results show that Belarusian Lipka Tatars share a substantial part of their gene pool with Europeans as indicated by their Y-chromosomal, mitochondrial and autosomal DNA variation. Nevertheless, Belarusian Lipkas still retain a strong genetic signal of their nomadic ancestry, witnessed by the presence of common Y-chromosomal and mitochondrial DNA variants as well as autosomal segments identical by descent between Lipkas and East Eurasians from temperate and northern regions. Hence, we document Lipka Tatars as a unique example of former Medieval migrants into Central Europe, who became sedentary, changed language to Slavic, yet preserved their faith and retained, both uni- and bi-parentally, a clear genetic echo of a complex population interplay throughout the Eurasian Steppe Belt, extending from Central Europe to northern China.
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Affiliation(s)
- Vasili Pankratov
- Institute of Genetics and Cytology, National Academy of Sciences of Belarus, Minsk, Belarus
| | - Sergei Litvinov
- Institute of Biochemistry and Genetics, Ufa Research Centre, RAS, Ufa, Bashkortostan, Russia.,Estonian Biocentre, Tartu, Estonia
| | - Alexei Kassian
- Institute of Linguistics, Russian Academy of Sciences, Moscow, Russia.,School for Advanced Studies in the Humanities, Russian Presidential Academy of National Economy and Public Administration, Moscow, Russia
| | - Dzmitry Shulhin
- Belarusian State University, Faculty of Applied Mathematics and Computer Science Department of Probability Theory and Mathematical Statistics, Minsk, Belarus
| | - Lieve Tchebotarev
- Center of analytical and genetic engineering studies, Institute of Microbiology, National Academy of Sciences of Belarus, Minsk, Belarus
| | | | - Märt Möls
- Institute of Mathematical Statistics, University of Tartu, Tartu, Estonia
| | - Hovhannes Sahakyan
- Estonian Biocentre, Tartu, Estonia.,Laboratory of Ethnogenomics, Institute of Molecular Biology, National Academy of Sciences of Armenia, Yerevan, 0014, Armenia
| | - Levon Yepiskoposyan
- Laboratory of Ethnogenomics, Institute of Molecular Biology, National Academy of Sciences of Armenia, Yerevan, 0014, Armenia
| | | | - Ene Metspalu
- Estonian Biocentre, Tartu, Estonia.,Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Maria Golubenko
- The Research Institute for Medical Genetics, 634050, Tomsk, Russia
| | - Natalia Ekomasova
- Department of Genetics and Fundamental Medicine of Bashkir State University, Ufa, Bashkortostan, Russia
| | - Farida Akhatova
- Department of Genetics and Fundamental Medicine of Bashkir State University, Ufa, Bashkortostan, Russia.,Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | - Elza Khusnutdinova
- Institute of Biochemistry and Genetics, Ufa Research Centre, RAS, Ufa, Bashkortostan, Russia.,Department of Genetics and Fundamental Medicine of Bashkir State University, Ufa, Bashkortostan, Russia
| | - Evelyne Heyer
- Eco-Anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Université Paris Diderot, Sorbonne Universités, Muséum national d'Histoire naturelle, Musée de l'Homme, Paris, France
| | - Phillip Endicott
- Eco-Anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Université Paris Diderot, Sorbonne Universités, Muséum national d'Histoire naturelle, Musée de l'Homme, Paris, France
| | - Miroslava Derenko
- Institute of Biological Problems of the North, Russian Academy of Sciences, Magadan, Russia
| | - Boris Malyarchuk
- Institute of Biological Problems of the North, Russian Academy of Sciences, Magadan, Russia
| | | | - Oleg Davydenko
- Institute of Genetics and Cytology, National Academy of Sciences of Belarus, Minsk, Belarus
| | - Richard Villems
- Estonian Biocentre, Tartu, Estonia.,Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Alena Kushniarevich
- Institute of Genetics and Cytology, National Academy of Sciences of Belarus, Minsk, Belarus.,Estonian Biocentre, Tartu, Estonia
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213
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Morozova I, Flegontov P, Mikheyev AS, Bruskin S, Asgharian H, Ponomarenko P, Klyuchnikov V, ArunKumar G, Prokhortchouk E, Gankin Y, Rogaev E, Nikolsky Y, Baranova A, Elhaik E, Tatarinova TV. Toward high-resolution population genomics using archaeological samples. DNA Res 2016; 23:295-310. [PMID: 27436340 PMCID: PMC4991838 DOI: 10.1093/dnares/dsw029] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Accepted: 05/22/2016] [Indexed: 12/30/2022] Open
Abstract
The term ‘ancient DNA’ (aDNA) is coming of age, with over 1,200 hits in the PubMed database, beginning in the early 1980s with the studies of ‘molecular paleontology’. Rooted in cloning and limited sequencing of DNA from ancient remains during the pre-PCR era, the field has made incredible progress since the introduction of PCR and next-generation sequencing. Over the last decade, aDNA analysis ushered in a new era in genomics and became the method of choice for reconstructing the history of organisms, their biogeography, and migration routes, with applications in evolutionary biology, population genetics, archaeogenetics, paleo-epidemiology, and many other areas. This change was brought by development of new strategies for coping with the challenges in studying aDNA due to damage and fragmentation, scarce samples, significant historical gaps, and limited applicability of population genetics methods. In this review, we describe the state-of-the-art achievements in aDNA studies, with particular focus on human evolution and demographic history. We present the current experimental and theoretical procedures for handling and analysing highly degraded aDNA. We also review the challenges in the rapidly growing field of ancient epigenomics. Advancement of aDNA tools and methods signifies a new era in population genetics and evolutionary medicine research.
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Affiliation(s)
- Irina Morozova
- Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland
| | - Pavel Flegontov
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic Bioinformatics Center, A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russian Federation
| | - Alexander S Mikheyev
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Sergey Bruskin
- Vavilov Institute of General Genetics RAS, Moscow, Russia
| | - Hosseinali Asgharian
- Department of Computational and Molecular Biology, University of Southern California, Los Angeles, CA, USA
| | - Petr Ponomarenko
- Center for Personalized Medicine, Children's Hospital Los Angeles, Los Angeles, CA, USA Spatial Sciences Institute, University of Southern California, Los Angeles, CA, USA
| | | | | | - Egor Prokhortchouk
- Research Center of Biotechnology RAS, Moscow, Russia Department of Biology, Lomonosov Moscow State University, Russia
| | | | - Evgeny Rogaev
- Vavilov Institute of General Genetics RAS, Moscow, Russia University of Massachusetts Medical School, Worcester, MA, USA
| | - Yuri Nikolsky
- Vavilov Institute of General Genetics RAS, Moscow, Russia F1 Genomics, San Diego, CA, USA School of Systems Biology, George Mason University, VA, USA
| | - Ancha Baranova
- School of Systems Biology, George Mason University, VA, USA Research Centre for Medical Genetics, Moscow, Russia Atlas Biomed Group, Moscow, Russia
| | - Eran Elhaik
- Department of Animal & Plant Sciences, University of Sheffield, Sheffield, South Yorkshire, UK
| | - Tatiana V Tatarinova
- Bioinformatics Center, A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russian Federation Center for Personalized Medicine, Children's Hospital Los Angeles, Los Angeles, CA, USA Spatial Sciences Institute, University of Southern California, Los Angeles, CA, USA
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Human Y Chromosome Haplogroup N: A Non-trivial Time-Resolved Phylogeography that Cuts across Language Families. Am J Hum Genet 2016; 99:163-73. [PMID: 27392075 DOI: 10.1016/j.ajhg.2016.05.025] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 05/22/2016] [Indexed: 11/21/2022] Open
Abstract
The paternal haplogroup (hg) N is distributed from southeast Asia to eastern Europe. The demographic processes that have shaped the vast extent of this major Y chromosome lineage across numerous linguistically and autosomally divergent populations have previously been unresolved. On the basis of 94 high-coverage re-sequenced Y chromosomes, we establish and date a detailed hg N phylogeny. We evaluate geographic structure by using 16 distinguishing binary markers in 1,631 hg N Y chromosomes from a collection of 6,521 samples from 56 populations. The more southerly distributed sub-clade N4 emerged before N2a1 and N3, found mostly in the north, but the latter two display more elaborate branching patterns, indicative of regional contrasts in recent expansions. In particular, a number of prominent and well-defined clades with common N3a3'6 ancestry occur in regionally dissimilar northern Eurasian populations, indicating almost simultaneous regional diversification and expansion within the last 5,000 years. This patrilineal genetic affinity is decoupled from the associated higher degree of language diversity.
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215
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Balanovsky OP, Zaporozhchenko VV. Chromosome as a chronicler: Genetic dating, historical events, and DNA-genealogic temptation. RUSS J GENET+ 2016. [DOI: 10.1134/s1022795416070048] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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216
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Trombetta B, Fantini G, D'Atanasio E, Sellitto D, Cruciani F. Evidence of extensive non-allelic gene conversion among LTR elements in the human genome. Sci Rep 2016; 6:28710. [PMID: 27346230 PMCID: PMC4921805 DOI: 10.1038/srep28710] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 06/06/2016] [Indexed: 12/16/2022] Open
Abstract
Long Terminal Repeats (LTRs) are nearly identical DNA sequences found at either end of Human Endogenous Retroviruses (HERVs). The high sequence similarity that exists among different LTRs suggests they could be substrate of ectopic gene conversion events. To understand the extent to which gene conversion occurs and to gain new insights into the evolutionary history of these elements in humans, we performed an intra-species phylogenetic study of 52 LTRs on different unrelated Y chromosomes. From this analysis, we obtained direct evidence that demonstrates the occurrence of ectopic gene conversion in several LTRs, with donor sequences located on both sex chromosomes and autosomes. We also found that some of these elements are characterized by an extremely high density of polymorphisms, showing one of the highest nucleotide diversities in the human genome, as well as a complex patchwork of sequences derived from different LTRs. Finally, we highlighted the limits of current short-read NGS studies in the analysis of genetic diversity of the LTRs in the human genome. In conclusion, our comparative re-sequencing analysis revealed that ectopic gene conversion is a common event in the evolution of LTR elements, suggesting complex genetic links among LTRs from different chromosomes.
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Affiliation(s)
- Beniamino Trombetta
- Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, Rome, Italy
| | - Gloria Fantini
- Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, Rome, Italy
| | - Eugenia D'Atanasio
- Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, Rome, Italy
| | | | - Fulvio Cruciani
- Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, Rome, Italy.,Istituto di Biologia e Patologia Molecolari, CNR, Rome, Italy.,Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza Università di Roma, Rome, Italy
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217
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Šarac J, Šarić T, Havaš Auguštin D, Novokmet N, Vekarić N, Mustać M, Grahovac B, Kapović M, Nevajda B, Glasnović A, Missoni S, Rootsi S, Rudan P. Genetic heritage of Croatians in the Southeastern European gene pool-Y chromosome analysis of the Croatian continental and Island population. Am J Hum Biol 2016; 28:837-845. [PMID: 27279290 DOI: 10.1002/ajhb.22876] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Revised: 03/22/2016] [Accepted: 05/10/2016] [Indexed: 12/20/2022] Open
Abstract
OBJECTIVES The research objective of this study is to enlarge and deepen the Y chromosome research on the Croatian population and enable additional insights into the population diversity and historic events that shaped the current genetic landscape of Croatia and Southeastern Europe (SEE). MATERIALS AND METHODS A high-resolution phylogenetic and phylogeographic analysis of 66 biallelic (SNPs) and 17 microsatellite (STRs) markers of the Y chromosome was performed using 720 Croatian samples. The obtained results were placed in a wider European context by comparison with ∼4450 samples from a number of other European populations. RESULTS A high diversity of haplogroups was observed in the overall Croatian sample, and all typical European Y chromosome haplogroups with corresponding clinal patterns were observed. Three distinct genetic signals were identifiable in the Croatian paternal gene pool - I2a1b-M423, R1a1a1b1a*-M558, and E1b1b1a1b1a-V13 haplogroups. DISCUSSION The analyses of the dominant and autochthonous I2a1b-M423 lineage (>30%) suggest that SEE had a significant role in the Upper Paleolithic, the R1a1a1b1a*-M558 lineage (19%) represents a signal from present day Slavic populations of Central Europe in the Croatian population, and the phylogeography of the E1b1b1a1b1a-V13 clade (around 9%) implies cultural diffusion of agriculture into Europe via the Balkan Peninsula. Am. J. Hum. Biol., 2016. © 2016 Wiley Periodicals, Inc. Am. J. Hum. Biol. 28:837-845, 2016. © 2016Wiley Periodicals, Inc.
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Affiliation(s)
- Jelena Šarac
- Institute for Anthropological Research, 10000, Zagreb, Croatia
| | - Tena Šarić
- Institute for Anthropological Research, 10000, Zagreb, Croatia
| | | | | | - Nenad Vekarić
- Institute for Historical Sciences, Croatian Academy of Sciences and Arts, 20000, Dubrovnik, Croatia
| | - Mate Mustać
- Occupational Health Clinic, 23000, Zadar, Croatia
| | - Blaženka Grahovac
- Department of Pathology and Pathological Anatomy, School of Medicine, University of Rijeka, 51000, Rijeka, Croatia
| | - Miljenko Kapović
- Department of Biology and Medical Genetics, School of Medicine, University of Rijeka, 51000, Rijeka, Croatia
| | | | | | - Saša Missoni
- Institute for Anthropological Research, 10000, Zagreb, Croatia.,"Josip Juraj Strossmayer" University of Osijek, School of Medicine, Osijek, Croatia
| | - Siiri Rootsi
- Estonian Biocentre and Institute for Molecular and Cell Biology, Department of Evolutionary Biology, , University of Tartu, 51010, Tartu, Estonia
| | - Pavao Rudan
- Institute for Anthropological Research, 10000, Zagreb, Croatia.,Anthropological Center of the Croatian Academy of Sciences and Arts, 10000, Zagreb, Croatia
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218
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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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219
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Poznik GD, Xue Y, Mendez FL, Willems TF, Massaia A, Wilson Sayres MA, Ayub Q, McCarthy SA, Narechania A, Kashin S, Chen Y, Banerjee R, Rodriguez-Flores JL, Cerezo M, Shao H, Gymrek M, Malhotra A, Louzada S, Desalle R, Ritchie GRS, Cerveira E, Fitzgerald TW, Garrison E, Marcketta A, Mittelman D, Romanovitch M, Zhang C, Zheng-Bradley X, Abecasis GR, McCarroll SA, Flicek P, Underhill PA, Coin L, Zerbino DR, Yang F, Lee C, Clarke L, Auton A, Erlich Y, Handsaker RE, Bustamante CD, Tyler-Smith C. Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences. Nat Genet 2016; 48:593-9. [PMID: 27111036 PMCID: PMC4884158 DOI: 10.1038/ng.3559] [Citation(s) in RCA: 194] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2015] [Accepted: 04/01/2016] [Indexed: 12/21/2022]
Abstract
We report the sequences of 1,244 human Y chromosomes randomly ascertained from 26 worldwide populations by the 1000 Genomes Project. We discovered more than 65,000 variants, including single-nucleotide variants, multiple-nucleotide variants, insertions and deletions, short tandem repeats, and copy number variants. Of these, copy number variants contribute the greatest predicted functional impact. We constructed a calibrated phylogenetic tree on the basis of binary single-nucleotide variants and projected the more complex variants onto it, estimating the number of mutations for each class. Our phylogeny shows bursts of extreme expansion in male numbers that have occurred independently among each of the five continental superpopulations examined, at times of known migrations and technological innovations.
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Affiliation(s)
- G David Poznik
- Program in Biomedical Informatics, Stanford University, Stanford, California, USA
- Department of Genetics, Stanford University, Stanford, California, USA
| | - Yali Xue
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Fernando L Mendez
- Department of Genetics, Stanford University, Stanford, California, USA
| | - Thomas F Willems
- Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- New York Genome Center, New York, New York, USA
| | - Andrea Massaia
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Melissa A Wilson Sayres
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
- Center for Evolution and Medicine, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Qasim Ayub
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Shane A McCarthy
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Apurva Narechania
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, USA
| | - Seva Kashin
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Yuan Chen
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Ruby Banerjee
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | | | - Maria Cerezo
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Haojing Shao
- Institute for Molecular Bioscience, University of Queensland, St Lucia, Queensland, Australia
| | - Melissa Gymrek
- New York Genome Center, New York, New York, USA
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Ankit Malhotra
- Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
| | - Sandra Louzada
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Rob Desalle
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, USA
| | - Graham R S Ritchie
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Eliza Cerveira
- Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
| | | | - Erik Garrison
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Anthony Marcketta
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, USA
| | - David Mittelman
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia, USA
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA
| | | | - Chengsheng Zhang
- Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
| | - Xiangqun Zheng-Bradley
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Gonçalo R Abecasis
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Steven A McCarroll
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Peter A Underhill
- Department of Genetics, Stanford University, Stanford, California, USA
| | - Lachlan Coin
- Institute for Molecular Bioscience, University of Queensland, St Lucia, Queensland, Australia
| | - Daniel R Zerbino
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Fengtang Yang
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Charles Lee
- Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
- Department of Life Sciences, Ewha Womans University, Seoul, Republic of Korea
| | - Laura Clarke
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Adam Auton
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Yaniv Erlich
- New York Genome Center, New York, New York, USA
- Department of Computer Science, Fu Foundation School of Engineering, Columbia University, New York, New York, USA
- Center for Computational Biology and Bioinformatics, Columbia University, New York, New York, USA
| | - Robert E Handsaker
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Carlos D Bustamante
- Department of Genetics, Stanford University, Stanford, California, USA
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | - Chris Tyler-Smith
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK
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220
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Barbieri C, Hübner A, Macholdt E, Ni S, Lippold S, Schröder R, Mpoloka SW, Purps J, Roewer L, Stoneking M, Pakendorf B. Refining the Y chromosome phylogeny with southern African sequences. Hum Genet 2016; 135:541-553. [PMID: 27043341 PMCID: PMC4835522 DOI: 10.1007/s00439-016-1651-0] [Citation(s) in RCA: 37] [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: 01/14/2016] [Accepted: 02/18/2016] [Indexed: 12/04/2022]
Abstract
The recent availability of large-scale sequence data for the human Y chromosome has revolutionized analyses of and insights gained from this non-recombining, paternally inherited chromosome. However, the studies to date focus on Eurasian variation, and hence the diversity of early-diverging branches found in Africa has not been adequately documented. Here, we analyze over 900 kb of Y chromosome sequence obtained from 547 individuals from southern African Khoisan- and Bantu-speaking populations, identifying 232 new sequences from basal haplogroups A and B. We identify new clades in the phylogeny, an older age for the root, and substantially older ages for some individual haplogroups. Furthermore, while haplogroup B2a is traditionally associated with the spread of Bantu speakers, we find that it probably also existed in Khoisan groups before the arrival of Bantu speakers. Finally, there is pronounced variation in branch length between major haplogroups; in particular, haplogroups associated with Bantu speakers have significantly longer branches. Technical artifacts cannot explain this branch length variation, which instead likely reflects aspects of the demographic history of Bantu speakers, such as recent population expansion and an older average paternal age. The influence of demographic factors on branch length variation has broader implications both for the human Y phylogeny and for similar analyses of other species.
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Affiliation(s)
- Chiara Barbieri
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany.
- Department of Linguistic and Cultural Evolution, Max Planck Institute for the Science of Human History, 07745, Jena, Germany.
| | - Alexander Hübner
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany
| | - Enrico Macholdt
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany
| | - Shengyu Ni
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany
| | - Sebastian Lippold
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany
| | - Roland Schröder
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany
| | | | - Josephine Purps
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin, 10559, Berlin, Germany
| | - Lutz Roewer
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin, 10559, Berlin, Germany
| | - Mark Stoneking
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany
| | - Brigitte Pakendorf
- Dynamique du Langage, UMR5596, CNRS & Université Lyon 2, 69363, Lyon Cedex 07, France.
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221
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Mendez FL, Poznik GD, Castellano S, Bustamante CD. The Divergence of Neandertal and Modern Human Y Chromosomes. Am J Hum Genet 2016; 98:728-34. [PMID: 27058445 PMCID: PMC4833433 DOI: 10.1016/j.ajhg.2016.02.023] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 02/26/2016] [Indexed: 01/22/2023] Open
Abstract
Sequencing the genomes of extinct hominids has reshaped our understanding of modern human origins. Here, we analyze ∼120 kb of exome-captured Y-chromosome DNA from a Neandertal individual from El Sidrón, Spain. We investigate its divergence from orthologous chimpanzee and modern human sequences and find strong support for a model that places the Neandertal lineage as an outgroup to modern human Y chromosomes—including A00, the highly divergent basal haplogroup. We estimate that the time to the most recent common ancestor (TMRCA) of Neandertal and modern human Y chromosomes is ∼588 thousand years ago (kya) (95% confidence interval [CI]: 447–806 kya). This is ∼2.1 (95% CI: 1.7–2.9) times longer than the TMRCA of A00 and other extant modern human Y-chromosome lineages. This estimate suggests that the Y-chromosome divergence mirrors the population divergence of Neandertals and modern human ancestors, and it refutes alternative scenarios of a relatively recent or super-archaic origin of Neandertal Y chromosomes. The fact that the Neandertal Y we describe has never been observed in modern humans suggests that the lineage is most likely extinct. We identify protein-coding differences between Neandertal and modern human Y chromosomes, including potentially damaging changes to PCDH11Y, TMSB4Y, USP9Y, and KDM5D. Three of these changes are missense mutations in genes that produce male-specific minor histocompatibility (H-Y) antigens. Antigens derived from KDM5D, for example, are thought to elicit a maternal immune response during gestation. It is possible that incompatibilities at one or more of these genes played a role in the reproductive isolation of the two groups.
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Affiliation(s)
- Fernando L Mendez
- Department of Genetics, Stanford University, Stanford, CA 94305, USA.
| | - G David Poznik
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Program in Biomedical Informatics, Stanford University, Stanford, CA 94305, USA
| | - Sergi Castellano
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Carlos D Bustamante
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA.
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222
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Tomaszkiewicz M, Rangavittal S, Cechova M, Campos Sanchez R, Fescemyer HW, Harris R, Ye D, O'Brien PCM, Chikhi R, Ryder OA, Ferguson-Smith MA, Medvedev P, Makova KD. A time- and cost-effective strategy to sequence mammalian Y Chromosomes: an application to the de novo assembly of gorilla Y. Genome Res 2016; 26:530-40. [PMID: 26934921 PMCID: PMC4817776 DOI: 10.1101/gr.199448.115] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 01/21/2016] [Indexed: 01/25/2023]
Abstract
The mammalian Y Chromosome sequence, critical for studying male fertility and dispersal, is enriched in repeats and palindromes, and thus, is the most difficult component of the genome to assemble. Previously, expensive and labor-intensive BAC-based techniques were used to sequence the Y for a handful of mammalian species. Here, we present a much faster and more affordable strategy for sequencing and assembling mammalian Y Chromosomes of sufficient quality for most comparative genomics analyses and for conservation genetics applications. The strategy combines flow sorting, short- and long-read genome and transcriptome sequencing, and droplet digital PCR with novel and existing computational methods. It can be used to reconstruct sex chromosomes in a heterogametic sex of any species. We applied our strategy to produce a draft of the gorilla Y sequence. The resulting assembly allowed us to refine gene content, evaluate copy number of ampliconic gene families, locate species-specific palindromes, examine the repetitive element content, and produce sequence alignments with human and chimpanzee Y Chromosomes. Our results inform the evolution of the hominine (human, chimpanzee, and gorilla) Y Chromosomes. Surprisingly, we found the gorilla Y Chromosome to be similar to the human Y Chromosome, but not to the chimpanzee Y Chromosome. Moreover, we have utilized the assembled gorilla Y Chromosome sequence to design genetic markers for studying the male-specific dispersal of this endangered species.
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Affiliation(s)
- Marta Tomaszkiewicz
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Samarth Rangavittal
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Monika Cechova
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Rebeca Campos Sanchez
- Genetics Program, The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Howard W Fescemyer
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Robert Harris
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Danling Ye
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Patricia C M O'Brien
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, United Kingdom
| | - Rayan Chikhi
- University of Lille 1/CNRS 59655 Villeneuve d'Ascq, France; Department of Computer Science and Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, USA; The Genome Sciences Institute of the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Oliver A Ryder
- San Diego Zoo Institute for Conservation Research, Escondido, California 92027, USA
| | | | - Paul Medvedev
- Department of Computer Science and Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, USA; The Genome Sciences Institute of the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA; Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Kateryna D Makova
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
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223
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Malyarchuk BA, Derenko M, Denisova G, Woźniak M, Rogalla U, Dambueva I, Grzybowski T. Y chromosome haplotype diversity in Mongolic-speaking populations and gene conversion at the duplicated STR DYS385a,b in haplogroup C3-M407. J Hum Genet 2016; 61:491-6. [DOI: 10.1038/jhg.2016.14] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 01/12/2016] [Accepted: 01/29/2016] [Indexed: 12/27/2022]
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224
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Hallast P, Maisano Delser P, Batini C, Zadik D, Rocchi M, Schempp W, Tyler-Smith C, Jobling MA. Great ape Y Chromosome and mitochondrial DNA phylogenies reflect subspecies structure and patterns of mating and dispersal. Genome Res 2016; 26:427-39. [PMID: 26883546 PMCID: PMC4817767 DOI: 10.1101/gr.198754.115] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 01/25/2016] [Indexed: 12/30/2022]
Abstract
The distribution of genetic diversity in great ape species is likely to have been affected by patterns of dispersal and mating. This has previously been investigated by sequencing autosomal and mitochondrial DNA (mtDNA), but large-scale sequence analysis of the male-specific region of the Y Chromosome (MSY) has not yet been undertaken. Here, we use the human MSY reference sequence as a basis for sequence capture and read mapping in 19 great ape males, combining the data with sequences extracted from the published whole genomes of 24 additional males to yield a total sample of 19 chimpanzees, four bonobos, 14 gorillas, and six orangutans, in which interpretable MSY sequence ranges from 2.61 to 3.80 Mb. This analysis reveals thousands of novel MSY variants and defines unbiased phylogenies. We compare these with mtDNA-based trees in the same individuals, estimating time-to-most-recent common ancestor (TMRCA) for key nodes in both cases. The two loci show high topological concordance and are consistent with accepted (sub)species definitions, but time depths differ enormously between loci and (sub)species, likely reflecting different dispersal and mating patterns. Gorillas and chimpanzees/bonobos present generally low and high MSY diversity, respectively, reflecting polygyny versus multimale–multifemale mating. However, particularly marked differences exist among chimpanzee subspecies: The western chimpanzee MSY phylogeny has a TMRCA of only 13.2 (10.8–15.8) thousand years, but that for central chimpanzees exceeds 1 million years. Cross-species comparison within a single MSY phylogeny emphasizes the low human diversity, and reveals species-specific branch length variation that may reflect differences in long-term generation times.
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Affiliation(s)
- Pille Hallast
- Department of Genetics, University of Leicester, Leicester LE1 7RH, United Kingdom; Institute of Molecular and Cell Biology, University of Tartu, Tartu 51010, Estonia
| | | | - Chiara Batini
- Department of Genetics, University of Leicester, Leicester LE1 7RH, United Kingdom
| | - Daniel Zadik
- Department of Genetics, University of Leicester, Leicester LE1 7RH, United Kingdom
| | - Mariano Rocchi
- Department of Biology, University of Bari, 70124 Bari, Italy
| | - Werner Schempp
- Institute of Human Genetics, University of Freiburg, 79106 Freiburg, Germany
| | - Chris Tyler-Smith
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Mark A Jobling
- Department of Genetics, University of Leicester, Leicester LE1 7RH, United Kingdom
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225
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Voskarides K, Mazières S, Hadjipanagi D, Di Cristofaro J, Ignatiou A, Stefanou C, King RJ, Underhill PA, Chiaroni J, Deltas C. Y-chromosome phylogeographic analysis of the Greek-Cypriot population reveals elements consistent with Neolithic and Bronze Age settlements. INVESTIGATIVE GENETICS 2016; 7:1. [PMID: 26870315 PMCID: PMC4750176 DOI: 10.1186/s13323-016-0032-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 02/02/2016] [Indexed: 12/15/2022]
Abstract
Background The archeological record indicates that the permanent settlement of Cyprus began with pioneering agriculturalists circa 11,000 years before present, (ca. 11,000 y BP). Subsequent colonization events followed, some recognized regionally. Here, we assess the Y-chromosome structure of Cyprus in context to regional populations and correlate it to phases of prehistoric colonization. Results Analysis of haplotypes from 574 samples showed that island-wide substructure was barely significant in a spatial analysis of molecular variance (SAMOVA). However, analyses of molecular variance (AMOVA) of haplogroups using 92 binary markers genotyped in 629 Cypriots revealed that the proportion of variance among the districts was irregularly distributed. Principal component analysis (PCA) revealed potential genetic associations of Greek-Cypriots with neighbor populations. Contrasting haplogroups in the PCA were used as surrogates of parental populations. Admixture analyses suggested that the majority of G2a-P15 and R1b-M269 components were contributed by Anatolia and Levant sources, respectively, while Greece Balkans supplied the majority of E-V13 and J2a-M67. Haplotype-based expansion times were at historical levels suggestive of recent demography. Conclusions Analyses of Cypriot haplogroup data are consistent with two stages of prehistoric settlement. E-V13 and E-M34 are widespread, and PCA suggests sourcing them to the Balkans and Levant/Anatolia, respectively. The persistent pre-Greek component is represented by elements of G2-U5(xL30) haplogroups: U5*, PF3147, and L293. J2b-M205 may contribute also to the pre-Greek strata. The majority of R1b-Z2105 lineages occur in both the westernmost and easternmost districts. Distinctively, sub-haplogroup R1b- M589 occurs only in the east. The absence of R1b- M589 lineages in Crete and the Balkans and the presence in Asia Minor are compatible with Late Bronze Age influences from Anatolia rather than from Mycenaean Greeks. Electronic supplementary material The online version of this article (doi:10.1186/s13323-016-0032-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Konstantinos Voskarides
- Molecular Medicine Research Center and Laboratory of Molecular and Medical Genetics, Department of Biological Sciences, University of Cyprus, Kallipoleos 75, 1678 Nicosia, Cyprus
| | - Stéphane Mazières
- Aix Marseille Université, ADES UMR7268, CNRS, EFS-AM, Marseille, France
| | - Despina Hadjipanagi
- Molecular Medicine Research Center and Laboratory of Molecular and Medical Genetics, Department of Biological Sciences, University of Cyprus, Kallipoleos 75, 1678 Nicosia, Cyprus
| | | | - Anastasia Ignatiou
- Molecular Medicine Research Center and Laboratory of Molecular and Medical Genetics, Department of Biological Sciences, University of Cyprus, Kallipoleos 75, 1678 Nicosia, Cyprus
| | - Charalambos Stefanou
- Molecular Medicine Research Center and Laboratory of Molecular and Medical Genetics, Department of Biological Sciences, University of Cyprus, Kallipoleos 75, 1678 Nicosia, Cyprus
| | - Roy J King
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA USA
| | - Peter A Underhill
- Department of Genetics, Stanford University, Stanford, California 94305 USA
| | - Jacques Chiaroni
- Aix Marseille Université, ADES UMR7268, CNRS, EFS-AM, Marseille, France
| | - Constantinos Deltas
- Molecular Medicine Research Center and Laboratory of Molecular and Medical Genetics, Department of Biological Sciences, University of Cyprus, Kallipoleos 75, 1678 Nicosia, Cyprus
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226
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Haber M, Mezzavilla M, Xue Y, Tyler-Smith C. Ancient DNA and the rewriting of human history: be sparing with Occam's razor. Genome Biol 2016; 17:1. [PMID: 26753840 PMCID: PMC4707776 DOI: 10.1186/s13059-015-0866-z] [Citation(s) in RCA: 289] [Impact Index Per Article: 36.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Ancient DNA research is revealing a human history far more complex than that inferred from parsimonious models based on modern DNA. Here, we review some of the key events in the peopling of the world in the light of the findings of work on ancient DNA.
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Affiliation(s)
- Marc Haber
- The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Massimo Mezzavilla
- The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK.,Institute for Maternal and Child Health, IRCCS BurloGarofolo, University of Trieste, 34137, Trieste, Italy
| | - Yali Xue
- The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Chris Tyler-Smith
- The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK.
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227
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Černý V, Čížková M, Poloni ES, Al‐Meeri A, Mulligan CJ. Comprehensive view of the population history of
A
rabia as inferred by mt
DNA
variation. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2015; 159:607-16. [DOI: 10.1002/ajpa.22920] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Revised: 11/06/2015] [Accepted: 11/23/2015] [Indexed: 01/25/2023]
Affiliation(s)
- Viktor Černý
- Archaeogenetics LaboratoryInstitute of Archaeology of the Academy of Sciences of the Czech Republic Czech Republic
| | - Martina Čížková
- Department of Anthropology and Human GeneticsFaculty of Science, Charles University in Prague Czech Republic
| | - Estella S. Poloni
- Department of Genetics and EvolutionAnthropology Unit, Laboratory of Anthropology, Genetics and Peopling History, University of GenevaGeneva Switzerland
| | - Ali Al‐Meeri
- Department of Clinical BiochemistryFaculty of Medicine and Health Sciences, University of Sana'aSana'a Yemen
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228
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Schregel J, Eiken HG, Grøndahl FA, Hailer F, Aspi J, Kojola I, Tirronen K, Danilov P, Rykov A, Poroshin E, Janke A, Swenson JE, Hagen SB. Y chromosome haplotype distribution of brown bears (Ursus arctos
) in Northern Europe provides insight into population history and recovery. Mol Ecol 2015; 24:6041-60. [DOI: 10.1111/mec.13448] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 10/17/2015] [Accepted: 10/26/2015] [Indexed: 11/28/2022]
Affiliation(s)
- Julia Schregel
- Norwegian Institute of Bioeconomy Research; NIBIO - Svanhovd; 9925 Svanvik Norway
- Department of Ecology and Natural Resource Management; Norwegian University of Life Sciences; 1432 Ås Norway
| | - Hans Geir Eiken
- Norwegian Institute of Bioeconomy Research; NIBIO - Svanhovd; 9925 Svanvik Norway
| | | | - Frank Hailer
- School of Biosciences; Cardiff University; Cardiff CF10 3AX Wales UK
- Biodiversity and Climate Research Centre (BiK-F); Senckenberg Gesellschaft für Naturforschung; Senckenberganlage 25 60325 Frankfurt am Main Germany
| | - Jouni Aspi
- Department of Genetics and Physiology; University of Oulu; P.O. Box 3000 90014 Oulu Finland
| | - Ilpo Kojola
- Natural Resources Institute; P.O. Box 16 96301 Rovaniemi Finland
| | - Konstantin Tirronen
- Institute of Biology; Karelian Research Centre of the Russian Academy of Science; 185910 Petrozavodsk Russian Federation
| | - Piotr Danilov
- Institute of Biology; Karelian Research Centre of the Russian Academy of Science; 185910 Petrozavodsk Russian Federation
| | - Alexander Rykov
- Pinezhsky Strict Nature Reserve; Pervomayskaja 123a 164610 Pinega Russian Federation
| | - Eugene Poroshin
- Institute of Biology; Komi Research Centre of the Russian Academy of Science; 016761 Syktvkar Russian Federation
| | - Axel Janke
- Biodiversity and Climate Research Centre (BiK-F); Senckenberg Gesellschaft für Naturforschung; Senckenberganlage 25 60325 Frankfurt am Main Germany
- Goethe University Frankfurt; Institute for Ecology; Evolution & Diversity; 60438 Frankfurt am Main Germany
| | - Jon E. Swenson
- Department of Ecology and Natural Resource Management; Norwegian University of Life Sciences; 1432 Ås Norway
- Norwegian Institute for Nature Research; 7485 Trondheim Norway
| | - Snorre B. Hagen
- Norwegian Institute of Bioeconomy Research; NIBIO - Svanhovd; 9925 Svanvik Norway
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229
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Carrier DR, Schilling N, Anders C. Muscle activation during maximal effort tasks: evidence of the selective forces that shaped the musculoskeletal system of humans. Biol Open 2015; 4:1635-42. [PMID: 26538637 PMCID: PMC4736035 DOI: 10.1242/bio.014381] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 10/08/2015] [Indexed: 11/20/2022] Open
Abstract
The selective forces that played a role in the evolution of the musculoskeletal system of the genus Homo have long been debated and remain poorly understood. In this investigation, we introduce a new approach for testing alternative hypotheses. Our analysis is based on the premise that natural selection can be expected to have resulted in muscles that are large enough to achieve necessary levels of maximum performance in essential behaviors, but not larger. We used surface electromyography in male subjects to identify maximum activation levels in 13 muscles of the back and leg during eight behaviors that have been suggested to have been important to foraging, hunting and fighting performance in early humans. We asked two questions: (1) what behaviors produce maximum activation in each of the investigated muscles and (2) are there specific behaviors that elicit maximum recruitment from all or most of the muscles? We found that in eight of the 13 muscles, the highest activity occurred during maximal effort vertical jumping (i.e. whole-body acceleration). Punching produced the highest median activity in the other five muscles. Together, jumping and punching accounted for 73% of the incidences of maximum activity among all of the muscles and from all of the subjects. Thus, the size of the muscles of the back and leg appear to be more related to the demands of explosive behaviors rather than those of high speed sprinting or sustained endurance running. These results are consistent with the hypothesis that selection on aggressive behavior played an important role in the evolution of the genus Homo.
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Affiliation(s)
- David R Carrier
- Department of Biology, University of Utah, 257S 1400E, Salt Lake City, UT 84112, USA
| | - Nadja Schilling
- Friedrich-Schiller-University, Institute of Systematic Zoology and Evolutionary Biology, Erbertstr. 1, Jena 07743, Germany
| | - Christoph Anders
- Clinic for Trauma, Hand and Reconstructive Surgery, Division of Motor Research, Pathophysiology and Biomechanics, Jena University Hospital, Bachstr. 18, Jena 07743, Germany
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230
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Negi N, Tamang R, Pande V, Sharma A, Shah A, Reddy AG, Vishnupriya S, Singh L, Chaubey G, Thangaraj K. The paternal ancestry of Uttarakhand does not imitate the classical caste system of India. J Hum Genet 2015; 61:167-72. [PMID: 26511066 DOI: 10.1038/jhg.2015.121] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 08/03/2015] [Accepted: 09/11/2015] [Indexed: 01/17/2023]
Abstract
Although, there have been rigorous research on the Indian caste system by several disciplines, it is still one of the most controversial socioscientific topic. Previous genetic studies on the subcontinent have supported a classical hierarchal sharing of genetic component by various castes of India. In the present study, we have used high-resolution mtDNA and Y chromosomal markers to characterize the genetic structuring of the Uttarakhand populations in the context of neighboring regions. Furthermore, we have tested whether the genetic structuring of caste populations at different social levels of this region, follow the classical chaturvarna system. Interestingly, we found that this region showed a high level of variation for East Eurasian ancestry in both maternal and paternal lines of descent. Moreover, the intrapopulation comparison showed a high level of heterogeneity, likely because of different caste hierarchy, interpolated on asymmetric admixture of populations inhabiting on both sides of the Himalayas.
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Affiliation(s)
- Neetu Negi
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India.,Department of Biotechnology, Kumaun University, Nainital, Uttarakhand, India
| | - Rakesh Tamang
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.,Estonian Biocentre, Tartu, Estonia.,Department of Zoology, University of Calcutta, Kolkata, India.,Department of Genetics, Osmania University, Hyderabad, India
| | - Veena Pande
- Department of Biotechnology, Kumaun University, Nainital, Uttarakhand, India
| | - Amrita Sharma
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Anish Shah
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Alla G Reddy
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | | | - Lalji Singh
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India.,Genome Foundation, Hyderabad, India
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231
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Genetic Heritage of the Balto-Slavic Speaking Populations: A Synthesis of Autosomal, Mitochondrial and Y-Chromosomal Data. PLoS One 2015; 10:e0135820. [PMID: 26332464 PMCID: PMC4558026 DOI: 10.1371/journal.pone.0135820] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 07/27/2015] [Indexed: 11/20/2022] Open
Abstract
The Slavic branch of the Balto-Slavic sub-family of Indo-European languages underwent rapid divergence as a result of the spatial expansion of its speakers from Central-East Europe, in early medieval times. This expansion–mainly to East Europe and the northern Balkans–resulted in the incorporation of genetic components from numerous autochthonous populations into the Slavic gene pools. Here, we characterize genetic variation in all extant ethnic groups speaking Balto-Slavic languages by analyzing mitochondrial DNA (n = 6,876), Y-chromosomes (n = 6,079) and genome-wide SNP profiles (n = 296), within the context of other European populations. We also reassess the phylogeny of Slavic languages within the Balto-Slavic branch of Indo-European. We find that genetic distances among Balto-Slavic populations, based on autosomal and Y-chromosomal loci, show a high correlation (0.9) both with each other and with geography, but a slightly lower correlation (0.7) with mitochondrial DNA and linguistic affiliation. The data suggest that genetic diversity of the present-day Slavs was predominantly shaped in situ, and we detect two different substrata: ‘central-east European’ for West and East Slavs, and ‘south-east European’ for South Slavs. A pattern of distribution of segments identical by descent between groups of East-West and South Slavs suggests shared ancestry or a modest gene flow between those two groups, which might derive from the historic spread of Slavic people.
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232
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Prokop JW, Deschepper CF. Chromosome Y genetic variants: impact in animal models and on human disease. Physiol Genomics 2015; 47:525-37. [PMID: 26286457 DOI: 10.1152/physiolgenomics.00074.2015] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Chromosome Y (chrY) variation has been associated with many complex diseases ranging from cancer to cardiovascular disorders. Functional roles of chrY genes outside of testes are suggested by the fact that they are broadly expressed in many other tissues and correspond to regulators of basic cellular functions (such as transcription, translation, and protein stability). However, the unique genetic properties of chrY (including the lack of meiotic crossover and the presence of numerous highly repetitive sequences) have made the identification of causal variants very difficult. Despite the prior lack of reliable sequences and/or data on genetic polymorphisms, earlier studies with animal chrY consomic strains have made it possible to narrow down the phenotypic contributions of chrY. Some of the evidence so far indicates that chrY gene variants associate with regulatory changes in the expression of other autosomal genes, in part via epigenetic effects. In humans, a limited number of studies have shown associations between chrY haplotypes and disease traits. However, recent sequencing efforts have made it possible to greatly increase the identification of genetic variants on chrY, which promises that future association of chrY with disease traits will be further refined. Continuing studies (both in humans and in animal models) will be critical to help explain the many sex-biased disease states in human that are contributed to not only by the classical sex steroid hormones, but also by chrY genetics.
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Affiliation(s)
- J W Prokop
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama; and
| | - C F Deschepper
- Institut de recherches cliniques de Montréal (IRCM) and Université de Montréal, Montreal, Quebec, Canada
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233
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Trombetta B, D'Atanasio E, Massaia A, Myres NM, Scozzari R, Cruciani F, Novelletto A. Regional Differences in the Accumulation of SNPs on the Male-Specific Portion of the Human Y Chromosome Replicate Autosomal Patterns: Implications for Genetic Dating. PLoS One 2015; 10:e0134646. [PMID: 26226630 PMCID: PMC4520482 DOI: 10.1371/journal.pone.0134646] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 07/10/2015] [Indexed: 12/21/2022] Open
Abstract
Factors affecting the rate and pattern of the mutational process are being identified for human autosomes, but the same relationships for the male specific portion of the Y chromosome (MSY) are not established. We considered 3,390 mutations occurring in 19 sequence bins identified by sequencing 1.5 Mb of the MSY from each of 104 present-day chromosomes. The occurrence of mutations was not proportional to the amount of sequenced bases in each bin, with a 2-fold variation. The regression of the number of mutations per unit sequence against a number of indicators of the genomic features of each bin, revealed the same fundamental patterns as in the autosomes. By considering the sequences of the same region from two precisely dated ancient specimens, we obtained a calibrated region-specific substitution rate of 0.716 × 10-9/site/year. Despite its lack of recombination and other peculiar features, the MSY then resembles the autosomes in displaying a marked regional heterogeneity of the mutation rate. An immediate implication is that a given figure for the substitution rate only makes sense if bound to a specific DNA region. By strictly applying this principle we obtained an unbiased estimate of the antiquity of lineages relevant to the genetic history of the human Y chromosome. In particular, the two deepest nodes of the tree highlight the survival, in Central-Western Africa, of lineages whose coalescence (291 ky, 95% C.I. 253-343) predates the emergence of anatomically modern features in the fossil record.
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Affiliation(s)
- Beniamino Trombetta
- Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza Università di Roma, Rome, Italy
| | - Eugenia D'Atanasio
- Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza Università di Roma, Rome, Italy
| | - Andrea Massaia
- Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza Università di Roma, Rome, Italy
| | | | - Rosaria Scozzari
- Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza Università di Roma, Rome, Italy
| | - Fulvio Cruciani
- Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza Università di Roma, Rome, Italy
- Istituto di Biologia e Patologia Molecolari, Consiglio Nazionale delle Ricerche, Rome, Italy
| | - Andrea Novelletto
- Dipartimento di Biologia, Università di Roma “Tor Vergata”, Rome, Italy
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234
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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: 252] [Impact Index Per Article: 28.0] [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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