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Atağ G, Waldman S, Carmi S, Somel M. An explanation for the sister repulsion phenomenon in Patterson's f-statistics. Genetics 2024:iyae144. [PMID: 39292210 DOI: 10.1093/genetics/iyae144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2024] [Accepted: 08/19/2024] [Indexed: 09/19/2024] Open
Abstract
Patterson's f-statistics are among the most heavily utilized tools for analyzing genome-wide allele frequency data for demographic inference. Beyond studying admixture, f3- and f4-statistics are also used for clustering populations to identify groups with similar histories. However, previous studies have noted an unexpected behavior of f-statistics: multiple populations from a certain region systematically show higher genetic affinity to a more distant population than to their neighbors, a pattern that is mismatched with alternative measures of genetic similarity. We call this counter-intuitive pattern "sister repulsion". We first present a novel instance of sister repulsion, where genomes from Bronze Age East Anatolian sites show higher affinity toward Bronze Age Greece rather than each other. This is observed both using f3- and f4-statistics, contrasts with archaeological/historical expectation, and also contradicts genetic affinity patterns captured using principal components analysis or multidimensional scaling on genetic distances. We then propose a simple demographic model to explain this pattern, where sister populations receive gene flow from a genetically distant source. We calculate f3- and f4-statistics using simulated genetic data with varying population genetic parameters, confirming that low-level gene flow from an external source into populations from 1 region can create sister repulsion in f-statistics. Unidirectional gene flow between the studied regions (without an external source) can likewise create repulsion. Meanwhile, similar to our empirical observations, multidimensional scaling analyses of genetic distances still cluster sister populations together. Overall, our results highlight the impact of low-level admixture events when inferring demographic history using f-statistics.
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Affiliation(s)
- Gözde Atağ
- Department of Biological Sciences, Middle East Technical University, Ankara 06800, Turkey
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Shamam Waldman
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Shai Carmi
- Braun School of Public Health and Community Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Mehmet Somel
- Department of Biological Sciences, Middle East Technical University, Ankara 06800, Turkey
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2
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Tricou T, Tannier E, de Vienne DM. Ghost Lineages Highly Influence the Interpretation of Introgression Tests. Syst Biol 2022; 71:1147-1158. [PMID: 35169846 PMCID: PMC9366450 DOI: 10.1093/sysbio/syac011] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 02/01/2021] [Accepted: 02/08/2022] [Indexed: 11/29/2022] Open
Abstract
Most species are extinct, those that are not are often unknown. Sequenced and sampled species are often a minority of known ones. Past evolutionary events involving horizontal gene flow, such as horizontal gene transfer, hybridization, introgression, and admixture, are therefore likely to involve "ghosts," that is extinct, unknown, or unsampled lineages. The existence of these ghost lineages is widely acknowledged, but their possible impact on the detection of gene flow and on the identification of the species involved is largely overlooked. It is generally considered as a possible source of error that, with reasonable approximation, can be ignored. We explore the possible influence of absent species on an evolutionary study by quantifying the effect of ghost lineages on introgression as detected by the popular D-statistic method. We show from simulated data that under certain frequently encountered conditions, the donors and recipients of horizontal gene flow can be wrongly identified if ghost lineages are not taken into account. In particular, having a distant outgroup, which is usually recommended, leads to an increase in the error probability and to false interpretations in most cases. We conclude that introgression from ghost lineages should be systematically considered as an alternative possible, even probable, scenario. [ABBA-BABA; D-statistic; gene flow; ghost lineage; introgression; simulation.].
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Affiliation(s)
- Théo Tricou
- Laboratoire de Biométrie et Biologie Évolutive UMR5558, Univ Lyon, Université Lyon 1, CNRS, F-69622 Villeurbanne, France
| | - Eric Tannier
- Laboratoire de Biométrie et Biologie Évolutive UMR5558, Univ Lyon, Université Lyon 1, CNRS, F-69622 Villeurbanne, France
- Inria, Centre de Recherche de Lyon, F-69603 Villeurbanne, France
| | - Damien M de Vienne
- Laboratoire de Biométrie et Biologie Évolutive UMR5558, Univ Lyon, Université Lyon 1, CNRS, F-69622 Villeurbanne, France
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3
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Estimating bonobo ( Pan paniscus) and chimpanzee ( Pan troglodytes) evolutionary history from nucleotide site patterns. Proc Natl Acad Sci U S A 2022; 119:e2200858119. [PMID: 35452306 PMCID: PMC9170072 DOI: 10.1073/pnas.2200858119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
There is genomic evidence of widespread admixture in deep time between many closely related species, including humans. Our closest living relatives, bonobos and chimpanzees, may also exhibit such patterns. However, assessing the exact degree of interbreeding remains challenging because previous studies have resulted in multiple inconsistent demographic models. We use an approach that addresses these gaps by analyzing all lineages, simultaneously estimating parameters, and comparing previously models. We find evidence of considerable introgression from western into eastern chimpanzees. We also show more breeding females than males and evidence of male-biased dispersal in western chimpanzees. These findings highlight the extent of admixture in bonobo and chimpanzee evolutionary history and are consistent with substantial differences between past and present chimpanzee biogeography. Admixture appears increasingly ubiquitous in the evolutionary history of various taxa, including humans. Such gene flow likely also occurred among our closest living relatives: bonobos (Pan paniscus) and chimpanzees (Pan troglodytes). However, our understanding of their evolutionary history has been limited by studies that do not consider all Pan lineages or do not analyze all lineages simultaneously, resulting in conflicting demographic models. Here, we investigate this gap in knowledge using nucleotide site patterns calculated from whole-genome sequences from the autosomes of 71 bonobos and chimpanzees, representing all five extant Pan lineages. We estimated demographic parameters and compared all previously proposed demographic models for this clade. We further considered sex bias in Pan evolutionary history by analyzing the site patterns from the X chromosome. We show that 1) 21% of autosomal DNA in eastern chimpanzees derives from western chimpanzee introgression and that 2) all four chimpanzee lineages share a common ancestor about 987,000 y ago, much earlier than previous estimates. In addition, we suggest that 3) there was male reproductive skew throughout Pan evolutionary history and find evidence of 4) male-biased dispersal from western to eastern chimpanzees. Collectively, these results offer insight into bonobo and chimpanzee evolutionary history and suggest considerable differences between current and historic chimpanzee biogeography.
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4
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Refining models of archaic admixture in Eurasia with ArchaicSeeker 2.0. Nat Commun 2021; 12:6232. [PMID: 34716342 PMCID: PMC8556419 DOI: 10.1038/s41467-021-26503-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 10/06/2021] [Indexed: 12/30/2022] Open
Abstract
We developed a method, ArchaicSeeker 2.0, to identify introgressed hominin sequences and model multiple-wave admixture. The new method enabled us to discern two waves of introgression from both Denisovan-like and Neanderthal-like hominins in present-day Eurasian populations and an ancient Siberian individual. We estimated that an early Denisovan-like introgression occurred in Eurasia around 118.8-94.0 thousand years ago (kya). In contrast, we detected only one single episode of Denisovan-like admixture in indigenous peoples eastern to the Wallace-Line. Modeling ancient admixtures suggested an early dispersal of modern humans throughout Asia before the Toba volcanic super-eruption 74 kya, predating the initial peopling of Asia as proposed by the traditional Out-of-Africa model. Survived archaic sequences are involved in various phenotypes including immune and body mass (e.g., ZNF169), cardiovascular and lung function (e.g., HHAT), UV response and carbohydrate metabolism (e.g., HYAL1/HYAL2/HYAL3), while "archaic deserts" are enriched with genes associated with skin development and keratinization.
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5
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Larena M, McKenna J, Sanchez-Quinto F, Bernhardsson C, Ebeo C, Reyes R, Casel O, Huang JY, Hagada KP, Guilay D, Reyes J, Allian FP, Mori V, Azarcon LS, Manera A, Terando C, Jamero L, Sireg G, Manginsay-Tremedal R, Labos MS, Vilar RD, Latiph A, Saway RL, Marte E, Magbanua P, Morales A, Java I, Reveche R, Barrios B, Burton E, Salon JC, Kels MJT, Albano A, Cruz-Angeles RB, Molanida E, Granehäll L, Vicente M, Edlund H, Loo JH, Trejaut J, Ho SYW, Reid L, Lambeck K, Malmström H, Schlebusch C, Endicott P, Jakobsson M. Philippine Ayta possess the highest level of Denisovan ancestry in the world. Curr Biol 2021; 31:4219-4230.e10. [PMID: 34388371 PMCID: PMC8596304 DOI: 10.1016/j.cub.2021.07.022] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 05/04/2021] [Accepted: 07/12/2021] [Indexed: 12/30/2022]
Abstract
Multiple lines of evidence show that modern humans interbred with archaic Denisovans. Here, we report an account of shared demographic history between Australasians and Denisovans distinctively in Island Southeast Asia. Our analyses are based on ∼2.3 million genotypes from 118 ethnic groups of the Philippines, including 25 diverse self-identified Negrito populations, along with high-coverage genomes of Australopapuans and Ayta Magbukon Negritos. We show that Ayta Magbukon possess the highest level of Denisovan ancestry in the world-∼30%-40% greater than that of Australians and Papuans-consistent with an independent admixture event into Negritos from Denisovans. Together with the recently described Homo luzonensis, we suggest that there were multiple archaic species that inhabited the Philippines prior to the arrival of modern humans and that these archaic groups may have been genetically related. Altogether, our findings unveil a complex intertwined history of modern and archaic humans in the Asia-Pacific region, where distinct Islander Denisovan populations differentially admixed with incoming Australasians across multiple locations and at various points in time.
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Affiliation(s)
- Maximilian Larena
- Human Evolution, Department of Organismal Biology, Uppsala University, Norbyvägen 18C, 752 36 Uppsala, Sweden.
| | - James McKenna
- Human Evolution, Department of Organismal Biology, Uppsala University, Norbyvägen 18C, 752 36 Uppsala, Sweden
| | - Federico Sanchez-Quinto
- Human Evolution, Department of Organismal Biology, Uppsala University, Norbyvägen 18C, 752 36 Uppsala, Sweden; Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City 14610, Mexico
| | - Carolina Bernhardsson
- Human Evolution, Department of Organismal Biology, Uppsala University, Norbyvägen 18C, 752 36 Uppsala, Sweden
| | - Carlo Ebeo
- National Committee on Cultural Education, National Commission for Culture and the Arts, Intramuros, Manila, Philippines; National Museum of the Philippines, Padre Burgos Avenue, Rizal Park, Ermita, Manila, Philippines
| | - Rebecca Reyes
- Ayta Magbukon Cultural Bearer, Ayta Magbukon Indigenous Cultural Community, Abucay, Bataan, Philippines; National Commission on Indigenous Peoples, Philippines
| | - Ophelia Casel
- Mindanao Doctors Hospital and Cancer Center, Kabacan, Cotabato, Philippines
| | - Jin-Yuan Huang
- Molecular Anthropology and Transfusion Medicine Research Laboratory, Mackay Memorial Hospital, Taipei City 10449, Taiwan
| | - Kim Pullupul Hagada
- National Commission on Indigenous Peoples, Philippines; Young Indigenous Peoples Empowered to Act in Community Engagement, Diffun, Quirino
| | - Dennis Guilay
- Balangao Indigenous Cultural Community, Paracelis, Mountain Province, Cordillera Administrative Region, Philippines
| | - Jennelyn Reyes
- Department of Education - Bataan Division, Bataan, Philippines
| | - Fatima Pir Allian
- Nisa Ul Haqq fi Bangsamoro, Zamboanga City, Bangsamoro Autonomous Region in Muslim Mindanao, Philippines; Tarbilang Foundation, Inc., Bongao, Tawi-Tawi, Bangsamoro Autonomous Region in Muslim Mindanao, Philippines
| | - Virgilio Mori
- Tarbilang Foundation, Inc., Bongao, Tawi-Tawi, Bangsamoro Autonomous Region in Muslim Mindanao, Philippines
| | - Lahaina Sue Azarcon
- Center for Language and Culture, Quirino State University, Barangay Andres Bonifacio, Diffun, Quirino, Philippines
| | - Alma Manera
- Center for Language and Culture, Cagayan State University - Andrews Campus, Caritan Highway, Tuguegarao, Cagayan, Philippines
| | - Celito Terando
- Tagakaulo Indigenous Cultural Community, Malungon, Sarangani, Philippines; Sulong Tribu Program, Provincial Government of Sarangani, Glan, Sarangani, Philippines
| | - Lucio Jamero
- Ayta Magbukon Cultural Bearer, Ayta Magbukon Indigenous Cultural Community, Abucay, Bataan, Philippines
| | - Gauden Sireg
- Subanen Indigenous Cultural Community, Lakewood, Zamboanga del Sur, Philippines; Dumendingan Arts Guild Inc., Pagadian City, Zamboanga del Sur, Philippines
| | | | - Maria Shiela Labos
- Ateneo Institute of Anthropology, Ateneo de Davao University, Roxas Avenue, 8016 Davao City, Philippines; Museo Dabawenyo, Andres Bonifacio Rotunda, Poblacion District, Davao City, Philippines
| | - Richard Dian Vilar
- Cultural Outreach Program, Kaliwat Performing Artists Collective, Gumamela St., Lanang, Davao City, Philippines; Culture, Heritage, and Arts Office, Local Government Unit of Butuan, Butuan City, Philippines
| | - Acram Latiph
- Institute for Peace and Development in Mindanao, Mindanao State University - Marawi Campus, Marawi City, Lanao del Sur, Bangsamoro Autonomous Region in Muslim Mindanao, Philippines
| | | | - Erwin Marte
- Legal Affairs Office, Indigenous People's Mandatory Representative - Sangguniang Panlalawigan, Bukidnon, Northern Mindanao, Philippines
| | - Pablito Magbanua
- National Commission on Indigenous Peoples, Philippines; Cuyonon Indigenous Cultural Community, Cuyo Island, Palawan, Philippines
| | - Amor Morales
- Surigaonon Heritage Center, Surigao City, Surigao del Norte, Philippines
| | - Ismael Java
- Kabankalan City Cultural and Tourism Foundation, Inc., Kabankalan City, Negros Occidental, Philippines; Cultural Research and Documentation, Negros Museum, Gatuslao St., Bacolod, Negros Occidental, Philippines
| | - Rudy Reveche
- Cultural Research and Documentation, Negros Museum, Gatuslao St., Bacolod, Negros Occidental, Philippines; Culture and Arts Program, Colegio San Agustin, BS Aquino Drive, Bacolod, Negros Occidental, Philippines
| | - Becky Barrios
- Panaghiusa Alang Sa Kaugalingnan Ug Kalingkawasan, Inc., Bunawan, Agusan del Sur, Philippines; Agusan Manobo Indigenous Cultural Community, La Paz, Agusan del Sur, Philippines
| | - Erlinda Burton
- Museo de Oro, Xavier University - Ateneo de Cagayan, Corrales Avenue, Cagayan de Oro City, Philippines
| | - Jesus Christopher Salon
- Museo de Oro, Xavier University - Ateneo de Cagayan, Corrales Avenue, Cagayan de Oro City, Philippines; City Museum of Cagayan de Oro, Fernandez St., Cagayan de Oro City, Philippines
| | - Ma Junaliah Tuazon Kels
- Human Evolution, Department of Organismal Biology, Uppsala University, Norbyvägen 18C, 752 36 Uppsala, Sweden
| | - Adrian Albano
- Kalanguya Indigenous Cultural Community, Tinoc, Ifugao, Cordillera Administrative Region, Philippines; Office of Tinoc Campus Administrator, Ifugao State University, Tinoc, Ifugao, Cordillera Administrative Region, Philippines
| | | | - Edison Molanida
- Heritage Office, National Commission for Culture and the Arts, Intramuros, Manila, Philippines; Office of the Executive Director, National Commission for Culture and the Arts, Intramuros, Manila, Philippines
| | - Lena Granehäll
- Human Evolution, Department of Organismal Biology, Uppsala University, Norbyvägen 18C, 752 36 Uppsala, Sweden
| | - Mário Vicente
- Human Evolution, Department of Organismal Biology, Uppsala University, Norbyvägen 18C, 752 36 Uppsala, Sweden
| | - Hanna Edlund
- Human Evolution, Department of Organismal Biology, Uppsala University, Norbyvägen 18C, 752 36 Uppsala, Sweden
| | - Jun-Hun Loo
- Molecular Anthropology and Transfusion Medicine Research Laboratory, Mackay Memorial Hospital, Taipei City 10449, Taiwan
| | - Jean Trejaut
- Molecular Anthropology and Transfusion Medicine Research Laboratory, Mackay Memorial Hospital, Taipei City 10449, Taiwan
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Lawrence Reid
- Department of Linguistics, University of Hawai'i at Mānoa, Mānoa, HI, USA; National Museum of the Philippines, Padre Burgos Avenue, Rizal Park, Ermita, Manila, Philippines
| | - Kurt Lambeck
- Research School of Earth Sciences, The Australian National University, Canberra, ACT 0200, Australia
| | - Helena Malmström
- Human Evolution, Department of Organismal Biology, Uppsala University, Norbyvägen 18C, 752 36 Uppsala, Sweden; Palaeo-Research Institute, University of Johannesburg, PO Box 524, Auckland Park 2006, South Africa
| | - Carina Schlebusch
- Human Evolution, Department of Organismal Biology, Uppsala University, Norbyvägen 18C, 752 36 Uppsala, Sweden; Palaeo-Research Institute, University of Johannesburg, PO Box 524, Auckland Park 2006, South Africa; SciLifeLab, Stockholm and Uppsala, Sweden
| | - Phillip Endicott
- Department Hommes Natures Societies, Musée de l'Homme, 75016 Paris, Ile de France, France
| | - Mattias Jakobsson
- Human Evolution, Department of Organismal Biology, Uppsala University, Norbyvägen 18C, 752 36 Uppsala, Sweden; Palaeo-Research Institute, University of Johannesburg, PO Box 524, Auckland Park 2006, South Africa; SciLifeLab, Stockholm and Uppsala, Sweden.
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6
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Gopalan S, Atkinson EG, Buck LT, Weaver TD, Henn BM. Inferring archaic introgression from hominin genetic data. Evol Anthropol 2021; 30:199-220. [PMID: 33951239 PMCID: PMC8360192 DOI: 10.1002/evan.21895] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 08/03/2020] [Accepted: 03/29/2021] [Indexed: 01/05/2023]
Abstract
Questions surrounding the timing, extent, and evolutionary consequences of archaic admixture into human populations have a long history in evolutionary anthropology. More recently, advances in human genetics, particularly in the field of ancient DNA, have shed new light on the question of whether or not Homo sapiens interbred with other hominin groups. By the late 1990s, published genetic work had largely concluded that archaic groups made no lasting genetic contribution to modern humans; less than a decade later, this conclusion was reversed following the successful DNA sequencing of an ancient Neanderthal. This reversal of consensus is noteworthy, but the reasoning behind it is not widely understood across all academic communities. There remains a communication gap between population geneticists and paleoanthropologists. In this review, we endeavor to bridge this gap by outlining how technological advancements, new statistical methods, and notable controversies ultimately led to the current consensus.
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Affiliation(s)
- Shyamalika Gopalan
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, USA.,Department of Evolutionary Anthropology, Duke University, Durham, North Carolina, USA
| | - Elizabeth G Atkinson
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, USA.,Analytic and Translational Genetics Unit, Massachusetts General Hospital and Stanley Center for Psychiatric Research, Broad Institute, Boston, Massachusetts, USA
| | - Laura T Buck
- Research Centre in Evolutionary Anthropology and Palaeoecology, Liverpool John Moores University, Liverpool, UK
| | - Timothy D Weaver
- Department of Anthropology, University of California, Davis, California, USA
| | - Brenna M Henn
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, USA.,Department of Anthropology, University of California, Davis, California, USA.,UC Davis Genome Center, University of California, Davis, California, USA
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7
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Sjödin P, McKenna J, Jakobsson M. Estimating divergence times from DNA sequences. Genetics 2021; 217:iyab008. [PMID: 33769498 PMCID: PMC8049563 DOI: 10.1093/genetics/iyab008] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 12/11/2020] [Indexed: 11/23/2022] Open
Abstract
The patterns of genetic variation within and among individuals and populations can be used to make inferences about the evolutionary forces that generated those patterns. Numerous population genetic approaches have been developed in order to infer evolutionary history. Here, we present the "Two-Two (TT)" and the "Two-Two-outgroup (TTo)" methods; two closely related approaches for estimating divergence time based in coalescent theory. They rely on sequence data from two haploid genomes (or a single diploid individual) from each of two populations. Under a simple population-divergence model, we derive the probabilities of the possible sample configurations. These probabilities form a set of equations that can be solved to obtain estimates of the model parameters, including population split times, directly from the sequence data. This transparent and computationally efficient approach to infer population divergence time makes it possible to estimate time scaled in generations (assuming a mutation rate), and not as a compound parameter of genetic drift. Using simulations under a range of demographic scenarios, we show that the method is relatively robust to migration and that the TTo method can alleviate biases that can appear from drastic ancestral population size changes. We illustrate the utility of the approaches with some examples, including estimating split times for pairs of human populations as well as providing further evidence for the complex relationship among Neandertals and Denisovans and their ancestors.
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Affiliation(s)
- Per Sjödin
- Human Evolution, Department of Organismal Biology, Uppsala University, Norbyvägen 18 A, Uppsala 752 36, Sweden
| | - James McKenna
- Human Evolution, Department of Organismal Biology, Uppsala University, Norbyvägen 18 A, Uppsala 752 36, Sweden
| | - Mattias Jakobsson
- Human Evolution, Department of Organismal Biology, Uppsala University, Norbyvägen 18 A, Uppsala 752 36, Sweden
- Science for Life Laboratory, Uppsala University, Norbyvägen 18 A, Uppsala 752 36, Sweden
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8
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Rogers AR. Legofit: estimating population history from genetic data. BMC Bioinformatics 2019; 20:526. [PMID: 31660852 PMCID: PMC6819480 DOI: 10.1186/s12859-019-3154-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 10/14/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Our current understanding of archaic admixture in humans relies on statistical methods with large biases, whose magnitudes depend on the sizes and separation times of ancestral populations. To avoid these biases, it is necessary to estimate these parameters simultaneously with those describing admixture. Genetic estimates of population histories also confront problems of statistical identifiability: different models or different combinations of parameter values may fit the data equally well. To deal with this problem, we need methods of model selection and model averaging, which are lacking from most existing software. RESULTS The Legofit software package allows simultaneous estimation of parameters describing admixture, and the sizes and separation times of ancestral populations. It includes facilities for data manipulation, estimation, analysis of residuals, model selection, and model averaging. CONCLUSIONS Legofit uses genetic data to study the history of a subdivided population. It is unaffected by recent history and can therefore focus on the deep history of population size, subdivision, and admixture. It outperforms several statistical methods that have been widely used to study population history and should be useful in any species for which DNA sequence data is available from several populations.
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Affiliation(s)
- Alan R Rogers
- Department of Anthropology, University of Utah, Gardner Commons, Salt Lake City, USA.
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9
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Quattrini AM, Wu T, Soong K, Jeng MS, Benayahu Y, McFadden CS. A next generation approach to species delimitation reveals the role of hybridization in a cryptic species complex of corals. BMC Evol Biol 2019; 19:116. [PMID: 31170912 PMCID: PMC6555025 DOI: 10.1186/s12862-019-1427-y] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 04/23/2019] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Our ability to investigate processes shaping the evolutionary diversification of corals (Cnidaria: Anthozoa) is limited by a lack of understanding of species boundaries. Discerning species of corals has been challenging due to a multitude of factors, including homoplasious and plastic morphological characters and the use of molecular markers that are either not informative or have not completely sorted. Hybridization can also blur species boundaries by leading to incongruence between morphology and genetics. We used traditional DNA barcoding and restriction-site associated DNA sequencing combined with coalescence-based and allele-frequency methods to elucidate species boundaries and simultaneously examine the potential role of hybridization in a speciose genus of octocoral, Sinularia. RESULTS Species delimitations using two widely used DNA barcode markers, mtMutS and 28S rDNA, were incongruent with one another and with the morphospecies identifications. When mtMutS and 28S were concatenated, a 0.3% genetic distance threshold delimited the majority of morphospecies. In contrast, 12 of the 15 examined morphospecies formed well-supported monophyletic clades in both concatenated RAxML phylogenies and SNAPP species trees of > 6000 RADSeq loci. DAPC and Structure analyses also supported morphospecies assignments, but indicated the potential for two additional cryptic species. Three morphologically distinct species pairs could not, however, be distinguished genetically. ABBA-BABA tests demonstrated significant admixture between some of those species, suggesting that hybridization may confound species delimitation in Sinularia. CONCLUSIONS A genomic approach can help to guide species delimitation while simultaneously elucidating the processes generating coral diversity. Results support the hypothesis that hybridization is an important mechanism in the evolution of Anthozoa, including octocorals, and future research should examine the contribution of this mechanism in generating diversity across the coral tree of life.
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Affiliation(s)
- Andrea M. Quattrini
- Biology Department, Harvey Mudd College, 1250 N. Dartmouth Ave, Claremont, CA 91711 USA
| | - Tiana Wu
- Biology Department, Harvey Mudd College, 1250 N. Dartmouth Ave, Claremont, CA 91711 USA
| | - Keryea Soong
- Institute of Marine Biology, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Ming-Shiou Jeng
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Yehuda Benayahu
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 69978 Ramat Aviv, Israel
| | - Catherine S. McFadden
- Biology Department, Harvey Mudd College, 1250 N. Dartmouth Ave, Claremont, CA 91711 USA
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10
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Rodríguez-Varela R, Günther T, Krzewińska M, Storå J, Gillingwater TH, MacCallum M, Arsuaga JL, Dobney K, Valdiosera C, Jakobsson M, Götherström A, Girdland-Flink L. Genomic Analyses of Pre-European Conquest Human Remains from the Canary Islands Reveal Close Affinity to Modern North Africans. Curr Biol 2017; 27:3396-3402.e5. [PMID: 29107554 DOI: 10.1016/j.cub.2017.09.059] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 09/07/2017] [Accepted: 09/27/2017] [Indexed: 12/31/2022]
Abstract
The origins and genetic affinity of the aboriginal inhabitants of the Canary Islands, commonly known as Guanches, are poorly understood. Though radiocarbon dates on archaeological remains such as charcoal, seeds, and domestic animal bones suggest that people have inhabited the islands since the 5th century BCE [1-3], it remains unclear how many times, and by whom, the islands were first settled [4, 5]. Previously published ancient DNA analyses of uniparental genetic markers have shown that the Guanches carried common North African Y chromosome markers (E-M81, E-M78, and J-M267) and mitochondrial lineages such as U6b, in addition to common Eurasian haplogroups [6-8]. These results are in agreement with some linguistic, archaeological, and anthropological data indicating an origin from a North African Berber-like population [1, 4, 9]. However, to date there are no published Guanche autosomal genomes to help elucidate and directly test this hypothesis. To resolve this, we generated the first genome-wide sequence data and mitochondrial genomes from eleven archaeological Guanche individuals originating from Gran Canaria and Tenerife. Five of the individuals (directly radiocarbon dated to a time transect spanning the 7th-11th centuries CE) yielded sufficient autosomal genome coverage (0.21× to 3.93×) for population genomic analysis. Our results show that the Guanches were genetically similar over time and that they display the greatest genetic affinity to extant Northwest Africans, strongly supporting the hypothesis of a Berber-like origin. We also estimate that the Guanches have contributed 16%-31% autosomal ancestry to modern Canary Islanders, here represented by two individuals from Gran Canaria.
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Affiliation(s)
- Ricardo Rodríguez-Varela
- Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden; Centro Mixto, Universidad Complutense de Madrid-Instituto de Salud Carlos III de Evolución y Comportamiento Humano, 28029 Madrid, Spain.
| | - Torsten Günther
- Department of Organismal Biology, Uppsala University, 75236 Uppsala, Sweden
| | - Maja Krzewińska
- Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | - Jan Storå
- Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | - Thomas H Gillingwater
- Anatomy, Edinburgh Medical School: Biomedical Sciences, University of Edinburgh, Edinburgh EH8 9AG, UK
| | - Malcolm MacCallum
- Anatomy, Edinburgh Medical School: Biomedical Sciences, University of Edinburgh, Edinburgh EH8 9AG, UK
| | - Juan Luis Arsuaga
- Centro Mixto, Universidad Complutense de Madrid-Instituto de Salud Carlos III de Evolución y Comportamiento Humano, 28029 Madrid, Spain; Departamento de Paleontología, Facultad de Ciencias Geológicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Keith Dobney
- Department of Archaeology, School of Geosciences, University of Aberdeen, St. Mary's, Aberdeen AB24 3UF, UK; Department of Archaeology, Classics and Egyptology, University of Liverpool, Liverpool L69 7WZ, UK; Department of Archaeology, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Cristina Valdiosera
- Centro Mixto, Universidad Complutense de Madrid-Instituto de Salud Carlos III de Evolución y Comportamiento Humano, 28029 Madrid, Spain; Department of Archaeology and History, La Trobe University, Melbourne, VIC 3086, Australia
| | - Mattias Jakobsson
- Department of Organismal Biology, Uppsala University, 75236 Uppsala, Sweden
| | - Anders Götherström
- Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | - Linus Girdland-Flink
- Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden; Research Centre in Evolutionary Anthropology and Palaeoecology, School of Natural Sciences and Psychology, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, UK.
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11
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Abstract
Extensive DNA sequence data have made it possible to reconstruct human evolutionary history in unprecedented detail. We introduce a method to study the past several hundred thousand years. Our results show that (i) the Neanderthal-Denisovan lineage declined to a small size just after separating from the modern lineage, (ii) Neanderthals and Denisovans separated soon thereafter, and (iii) the subsequent Neanderthal population was large and deeply subdivided. They also (iv) support previous estimates of gene flow from Neanderthals into modern Eurasians. These results suggest an archaic human diaspora early in the Middle Pleistocene.
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12
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Hu H, Petousi N, Glusman G, Yu Y, Bohlender R, Tashi T, Downie JM, Roach JC, Cole AM, Lorenzo FR, Rogers AR, Brunkow ME, Cavalleri G, Hood L, Alpatty SM, Prchal JT, Jorde LB, Robbins PA, Simonson TS, Huff CD. Evolutionary history of Tibetans inferred from whole-genome sequencing. PLoS Genet 2017; 13:e1006675. [PMID: 28448578 PMCID: PMC5407610 DOI: 10.1371/journal.pgen.1006675] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 03/08/2017] [Indexed: 12/20/2022] Open
Abstract
The indigenous people of the Tibetan Plateau have been the subject of much recent interest because of their unique genetic adaptations to high altitude. Recent studies have demonstrated that the Tibetan EPAS1 haplotype is involved in high altitude-adaptation and originated in an archaic Denisovan-related population. We sequenced the whole-genomes of 27 Tibetans and conducted analyses to infer a detailed history of demography and natural selection of this population. We detected evidence of population structure between the ancestral Han and Tibetan subpopulations as early as 44 to 58 thousand years ago, but with high rates of gene flow until approximately 9 thousand years ago. The CMS test ranked EPAS1 and EGLN1 as the top two positive selection candidates, and in addition identified PTGIS, VDR, and KCTD12 as new candidate genes. The advantageous Tibetan EPAS1 haplotype shared many variants with the Denisovan genome, with an ancient gene tree divergence between the Tibetan and Denisovan haplotypes of about 1 million years ago. With the exception of EPAS1, we observed no evidence of positive selection on Denisovan-like haplotypes.
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Affiliation(s)
- Hao Hu
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Nayia Petousi
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Gustavo Glusman
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Yao Yu
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Ryan Bohlender
- Department of Anthropology, University of Utah, Salt Lake City, Utah, United States of America
| | - Tsewang Tashi
- Department of Medicine, University of Utah School of Medicine and George E. Wahlin Veterans Administration Medical Center, Salt Lake City, Utah, United States of America
| | - Jonathan M. Downie
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
| | - Jared C. Roach
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Amy M. Cole
- Department of Molecular and Cellular Therapeutics, The Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Felipe R. Lorenzo
- Department of Medicine, University of Utah School of Medicine and George E. Wahlin Veterans Administration Medical Center, Salt Lake City, Utah, United States of America
| | - Alan R. Rogers
- Department of Anthropology, University of Utah, Salt Lake City, Utah, United States of America
| | - Mary E. Brunkow
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Gianpiero Cavalleri
- Department of Molecular and Cellular Therapeutics, The Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Leroy Hood
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Sama M. Alpatty
- Skaggs School of Pharmacy and Pharmaceutical Science, UC San Diego, La Jolla, California, United States of America
| | - Josef T. Prchal
- Department of Medicine, University of Utah School of Medicine and George E. Wahlin Veterans Administration Medical Center, Salt Lake City, Utah, United States of America
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
| | - Lynn B. Jorde
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
| | - Peter A. Robbins
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Tatum S. Simonson
- Department of Medicine, Division of Physiology, University of California San Diego, La Jolla, California, United States of America
| | - Chad D. Huff
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
- * E-mail:
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13
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Mao X, Tsagkogeorga G, Bailey SE, Rossiter SJ. Genomics of introgression in the Chinese horseshoe bat (Rhinolophus sinicus) revealed by transcriptome sequencing. Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blx017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Xiuguang Mao
- Institute of Estuarine and Coastal Research, East China Normal University, Shanghai 200062, China
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
| | - Georgia Tsagkogeorga
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
| | - Sebastian E. Bailey
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
| | - Stephen J. Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
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Hunley KL, Cabana GS, Long JC. The apportionment of human diversity revisited. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2015; 160:561-9. [DOI: 10.1002/ajpa.22899] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 11/06/2015] [Accepted: 11/06/2015] [Indexed: 12/19/2022]
Affiliation(s)
- Keith L. Hunley
- Department of Anthropology; University of New Mexico; Albuquerque NM 87131
| | | | - Jeffrey C. Long
- Department of Anthropology; University of New Mexico; Albuquerque NM 87131
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15
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Eaton DAR, Hipp AL, González-Rodríguez A, Cavender-Bares J. Historical introgression among the American live oaks and the comparative nature of tests for introgression. Evolution 2015; 69:2587-601. [DOI: 10.1111/evo.12758] [Citation(s) in RCA: 153] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 07/09/2015] [Accepted: 08/03/2015] [Indexed: 12/29/2022]
Affiliation(s)
- Deren A. R. Eaton
- Department of Ecology and Evolutionary Biology; Yale University; New Haven Connecticut 06511
| | - Andrew L. Hipp
- The Morton Arboretum; Lisle Illinois 60532
- Department of Botany; The Field Museum; Chicago Illinois 60605
| | - Antonio González-Rodríguez
- Centro de Investigaciones en Ecosistemas; Universidad Nacional Autónoma de México; Morelia Michoacán 58190 Mexico
| | - Jeannine Cavender-Bares
- Department of Ecology, Evolution and Behavior; University of Minnesota; Saint Paul Minnesota 55108
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