1
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Çubukcu H, Kılınç GM. Evaluation of genotype imputation using Glimpse tools on low coverage ancient DNA. Mamm Genome 2024:10.1007/s00335-024-10053-4. [PMID: 39028337 DOI: 10.1007/s00335-024-10053-4] [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: 03/22/2024] [Accepted: 07/12/2024] [Indexed: 07/20/2024]
Abstract
Ancient DNA provides a unique frame for directly studying human population genetics in time and space. Still, since most of the ancient genomic data is low coverage, analysis is confronted with a low number of SNPs, genotype uncertainties, and reference-bias. Here, we for the first time benchmark the two distinct versions of Glimpse tools on 120 ancient human genomes from Eurasia including those largely from previously under-evaluated regions and compare the performance of genotype imputation with de facto analysis approaches for low coverage genomic data analysis. We further investigate the impact of two distinct reference panels on imputation accuracy for low coverage genomic data. We compute accuracy statistics and perform PCA and f4-statistics to explore the behaviour of genotype imputation on low coverage data regarding (i)two versions of Glimpse, (ii)two reference panels, (iii)four post-imputation filters and coverages, as well as (iv)data type and geographical origin of the samples on the analyses. Our results reveal that even for 0.1X coverage ancient human genomes, genotype imputation using Glimpse-v2 is suitable. Additionally, using the 1000 Genomes merged with Human Genome Diversity Panel improves the accuracy of imputation for the rare variants with low MAF, which might be important not only for ancient genomics but also for modern human genomic studies based on low coverage data and for haplotype-based analysis. Most importantly, we reveal that genotype imputation of low coverage ancient human genomes reduces the genetic affinity of the samples towards human reference genome. Through solving one of the most challenging biases in data analysis, so-called reference bias, genotype imputation using Glimpse v2 is promising for low coverage ancient human genomic data analysis and for rare-variant-based and haplotype-based analysis.
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Affiliation(s)
- Hande Çubukcu
- Department of Bioinformatics, Graduate School of Health Sciences, Hacettepe University, 06100, Ankara, Turkey
| | - Gülşah Merve Kılınç
- Department of Bioinformatics, Graduate School of Health Sciences, Hacettepe University, 06100, Ankara, Turkey.
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2
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Kendall C, Robinson J, Debortoli G, Nooranikhojasteh A, Christian D, Newman D, Sayers K, Cole S, Parra E, Schillaci M, Viola B. Global and local ancestry estimation in a captive baboon colony. PLoS One 2024; 19:e0305157. [PMID: 38959276 PMCID: PMC11221750 DOI: 10.1371/journal.pone.0305157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 05/24/2024] [Indexed: 07/05/2024] Open
Abstract
The last couple of decades have highlighted the importance of studying hybridization, particularly among primate species, as it allows us to better understand our own evolutionary trajectory. Here, we report on genetic ancestry estimates using dense, full genome data from 881 olive (Papio anubus), yellow (Papio cynocephalus), or olive-yellow crossed captive baboons from the Southwest National Primate Research Center. We calculated global and local ancestry information, imputed low coverage genomes (n = 830) to improve marker quality, and updated the genetic resources of baboons available to assist future studies. We found evidence of historical admixture in some putatively purebred animals and identified errors within the Southwest National Primate Research Center pedigree. We also compared the outputs between two different phasing and imputation pipelines along with two different global ancestry estimation software. There was good agreement between the global ancestry estimation software, with R2 > 0.88, while evidence of phase switch errors increased depending on what phasing and imputation pipeline was used. We also generated updated genetic maps and created a concise set of ancestry informative markers (n = 1,747) to accurately obtain global ancestry estimates.
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Affiliation(s)
| | - Jacqueline Robinson
- Institute for Human Genetics, University of California, San Francisco, San Francisco, California, United States of America
| | - Guilherme Debortoli
- Department of Anthropology, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - Amin Nooranikhojasteh
- Epigenomics Lab, Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - Debbie Christian
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, United States of America
| | - Deborah Newman
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, United States of America
| | - Kenneth Sayers
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, United States of America
| | - Shelley Cole
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, United States of America
| | - Esteban Parra
- Department of Anthropology, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - Michael Schillaci
- Department of Anthropology, University of Toronto Scarborough, Scarborough, Ontario, Canada
| | - Bence Viola
- Department of Anthropology, University of Toronto, Toronto, Ontario, Canada
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3
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Cooke NP, Murray M, Cassidy LM, Mattiangeli V, Okazaki K, Kasai K, Gakuhari T, Bradley DG, Nakagome S. Genomic imputation of ancient Asian populations contrasts local adaptation in pre- and post-agricultural Japan. iScience 2024; 27:110050. [PMID: 38883821 PMCID: PMC11176660 DOI: 10.1016/j.isci.2024.110050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 03/25/2024] [Accepted: 05/17/2024] [Indexed: 06/18/2024] Open
Abstract
Early modern humans lived as hunter-gatherers for millennia before agriculture, yet the genetic adaptations of these populations remain a mystery. Here, we investigate selection in the ancient hunter-gatherer-fisher Jomon and contrast pre- and post-agricultural adaptation in the Japanese archipelago. Building on the successful validation of imputation with ancient Asian genomes, we identify selection signatures in the Jomon, particularly robust signals from KITLG variants, which may have influenced dark pigmentation evolution. The Jomon lacks well-known adaptive variants (EDAR, ADH1B, and ALDH2), marking their emergence after the advent of farming in the archipelago. Notably, the EDAR and ADH1B variants were prevalent in the archipelago 1,300 years ago, whereas the ALDH2 variant could have emerged later due to its absence in other ancient genomes. Overall, our study underpins local adaptation unique to the Jomon population, which in turn sheds light on post-farming selection that continues to shape contemporary Asian populations.
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Affiliation(s)
- Niall P Cooke
- School of Medicine, Trinity College Dublin, Dublin, Ireland
| | | | - Lara M Cassidy
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | | | - Kenji Okazaki
- Department of Anatomy, Faculty of Medicine, Tottori University, Yonago, Japan
| | - Kenji Kasai
- Toyama Prefectural Center for Archaeological Operations, Toyama, Japan
| | - Takashi Gakuhari
- Institute for the Study of Ancient Civilizations and Cultural Resources, Kanazawa University, Kanazawa, Japan
| | - Daniel G Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Shigeki Nakagome
- School of Medicine, Trinity College Dublin, Dublin, Ireland
- Institute for the Study of Ancient Civilizations and Cultural Resources, Kanazawa University, Kanazawa, Japan
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4
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Erven JAM, Scheu A, Verdugo MP, Cassidy L, Chen N, Gehlen B, Street M, Madsen O, Mullin VE. A High-Coverage Mesolithic Aurochs Genome and Effective Leveraging of Ancient Cattle Genomes Using Whole Genome Imputation. Mol Biol Evol 2024; 41:msae076. [PMID: 38662789 PMCID: PMC11090068 DOI: 10.1093/molbev/msae076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 04/05/2024] [Accepted: 04/09/2024] [Indexed: 05/14/2024] Open
Abstract
Ancient genomic analyses are often restricted to utilizing pseudohaploid data due to low genome coverage. Leveraging low-coverage data by imputation to calculate phased diploid genotypes that enables haplotype-based interrogation and single nucleotide polymorphism (SNP) calling at unsequenced positions is highly desirable. This has not been investigated for ancient cattle genomes despite these being compelling subjects for archeological, evolutionary, and economic reasons. Here, we test this approach by sequencing a Mesolithic European aurochs (18.49×; 9,852 to 9,376 calBCE) and an Early Medieval European cow (18.69×; 427 to 580 calCE) and combine these with published individuals: two ancient and three modern. We downsample these genomes (0.25×, 0.5×, 1.0×, and 2.0×) and impute diploid genotypes, utilizing a reference panel of 171 published modern cattle genomes that we curated for 21.7 million (Mn) phased SNPs. We recover high densities of correct calls with an accuracy of >99.1% at variant sites for the lowest downsample depth of 0.25×, increasing to >99.5% for 2.0× (transversions only, minor allele frequency [MAF] ≥ 2.5%). The recovery of SNPs correlates with coverage; on average, 58% of sites are recovered for 0.25× increasing to 87% for 2.0×, utilizing an average of 3.5 million (Mn) transversions (MAF ≥2.5%), even in the aurochs, despite the highest temporal distance from the modern reference panel. Our imputed genomes behave similarly to directly called data in allele frequency-based analyses, for example consistently identifying runs of homozygosity >2 Mb, including a long homozygous region in the Mesolithic European aurochs.
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Affiliation(s)
- Jolijn A M Erven
- Groningen Institute of Archaeology, University of Groningen, Groningen, The Netherlands
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin D02 PN40, Ireland
| | - Amelie Scheu
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin D02 PN40, Ireland
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iOME), Johannes Gutenberg-University Mainz, 55099 Mainz, Germany
| | | | - Lara Cassidy
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin D02 PN40, Ireland
| | - Ningbo Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Birgit Gehlen
- Institute for Prehistory and Protohistory, University of Cologne, 50931 Cologne, Germany
| | - Martin Street
- LEIZA, Archaeological Research Centre and Museum for Human Behavioural Evolution, Schloss Monrepos, D - 56567 Neuwied, Germany
| | - Ole Madsen
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, The Netherlands
| | - Victoria E Mullin
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin D02 PN40, Ireland
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5
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Gnecchi-Ruscone GA, Rácz Z, Samu L, Szeniczey T, Faragó N, Knipper C, Friedrich R, Zlámalová D, Traverso L, Liccardo S, Wabnitz S, Popli D, Wang K, Radzeviciute R, Gulyás B, Koncz I, Balogh C, Lezsák GM, Mácsai V, Bunbury MME, Spekker O, le Roux P, Szécsényi-Nagy A, Mende BG, Colleran H, Hajdu T, Geary P, Pohl W, Vida T, Krause J, Hofmanová Z. Network of large pedigrees reveals social practices of Avar communities. Nature 2024; 629:376-383. [PMID: 38658749 PMCID: PMC11078744 DOI: 10.1038/s41586-024-07312-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 03/13/2024] [Indexed: 04/26/2024]
Abstract
From AD 567-568, at the onset of the Avar period, populations from the Eurasian Steppe settled in the Carpathian Basin for approximately 250 years1. Extensive sampling for archaeogenomics (424 individuals) and isotopes, combined with archaeological, anthropological and historical contextualization of four Avar-period cemeteries, allowed for a detailed description of the genomic structure of these communities and their kinship and social practices. We present a set of large pedigrees, reconstructed using ancient DNA, spanning nine generations and comprising around 300 individuals. We uncover a strict patrilineal kinship system, in which patrilocality and female exogamy were the norm and multiple reproductive partnering and levirate unions were common. The absence of consanguinity indicates that this society maintained a detailed memory of ancestry over generations. These kinship practices correspond with previous evidence from historical sources and anthropological research on Eurasian Steppe societies2. Network analyses of identity-by-descent DNA connections suggest that social cohesion between communities was maintained via female exogamy. Finally, despite the absence of major ancestry shifts, the level of resolution of our analyses allowed us to detect genetic discontinuity caused by the replacement of a community at one of the sites. This was paralleled with changes in the archaeological record and was probably a result of local political realignment.
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Affiliation(s)
| | - Zsófia Rácz
- Institute of Archaeological Sciences, ELTE - Eötvös Loránd University, Budapest, Hungary
| | - Levente Samu
- Institute of Archaeological Sciences, ELTE - Eötvös Loránd University, Budapest, Hungary
| | - Tamás Szeniczey
- Department of Biological Anthropology, ELTE - Eötvös Loránd University, Budapest, Hungary
| | - Norbert Faragó
- Institute of Archaeological Sciences, ELTE - Eötvös Loránd University, Budapest, Hungary
| | - Corina Knipper
- Curt Engelhorn Center for Archaeometry gGmbH, Mannheim, Germany
| | - Ronny Friedrich
- Curt Engelhorn Center for Archaeometry gGmbH, Mannheim, Germany
| | - Denisa Zlámalová
- Department of Archaeology and Museology, Faculty of Arts, Masaryk University, Brno, Czechia
| | - Luca Traverso
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Salvatore Liccardo
- Department of History, University of Vienna, Vienna, Austria
- Institute for Medieval Research, Austrian Academy of Sciences, Vienna, Austria
| | - Sandra Wabnitz
- Department of History, University of Vienna, Vienna, Austria
- Institute for Medieval Research, Austrian Academy of Sciences, Vienna, Austria
| | - Divyaratan Popli
- Department of Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Ke Wang
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- MOE Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Rita Radzeviciute
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - István Koncz
- Institute of Archaeological Sciences, ELTE - Eötvös Loránd University, Budapest, Hungary
| | - Csilla Balogh
- Department of Art History, Istanbul Medeniyet University, Istanbul, Turkey
| | - Gabriella M Lezsák
- Institute of History, HUN-REN Research Centre for the Humanities, Budapest, Hungary
| | - Viktor Mácsai
- Institute of Archaeological Sciences, ELTE - Eötvös Loránd University, Budapest, Hungary
| | - Magdalena M E Bunbury
- ARC Centre of Excellence for Australian Biodiversity and Heritage, College of Arts, Society and Education, James Cook University, Cairns, Queensland, Australia
| | - Olga Spekker
- Institute of Archaeological Sciences, ELTE - Eötvös Loránd University, Budapest, Hungary
- Department of Biological Anthropology, University of Szeged, Szeged, Hungary
| | - Petrus le Roux
- Department of Geological Sciences, University of Cape Town, Rondebosch, South Africa
| | - Anna Szécsényi-Nagy
- Institute of Archaeogenomics, HUN-REN Research Centre for the Humanities, Budapest, Hungary
| | - Balázs Gusztáv Mende
- Institute of Archaeogenomics, HUN-REN Research Centre for the Humanities, Budapest, Hungary
| | - Heidi Colleran
- BirthRites Lise Meitner Research Group, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Human Behavior, Ecology and Culture, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Tamás Hajdu
- Department of Biological Anthropology, ELTE - Eötvös Loránd University, Budapest, Hungary
| | | | - Walter Pohl
- Department of History, University of Vienna, Vienna, Austria
- Institute for Medieval Research, Austrian Academy of Sciences, Vienna, Austria
| | - Tivadar Vida
- Institute of Archaeological Sciences, ELTE - Eötvös Loránd University, Budapest, Hungary.
- Institute of Archaeology, HUN-REN Research Centre for the Humanities, Budapest, Hungary.
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
| | - Zuzana Hofmanová
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
- Department of Archaeology and Museology, Faculty of Arts, Masaryk University, Brno, Czechia.
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6
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Garrido Marques A, Rubinacci S, Malaspinas AS, Delaneau O, Sousa da Mota B. Assessing the impact of post-mortem damage and contamination on imputation performance in ancient DNA. Sci Rep 2024; 14:6227. [PMID: 38486065 PMCID: PMC10940295 DOI: 10.1038/s41598-024-56584-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 03/08/2024] [Indexed: 03/18/2024] Open
Abstract
Low-coverage imputation is becoming ever more present in ancient DNA (aDNA) studies. Imputation pipelines commonly used for present-day genomes have been shown to yield accurate results when applied to ancient genomes. However, post-mortem damage (PMD), in the form of C-to-T substitutions at the reads termini, and contamination with DNA from closely related species can potentially affect imputation performance in aDNA. In this study, we evaluated imputation performance (i) when using a genotype caller designed for aDNA, ATLAS, compared to bcftools, and (ii) when contamination is present. We evaluated imputation performance with principal component analyses and by calculating imputation error rates. With a particular focus on differently imputed sites, we found that using ATLAS prior to imputation substantially improved imputed genotypes for a very damaged ancient genome (42% PMD). Trimming the ends of the sequencing reads led to similar improvements in imputation accuracy. For the remaining genomes, ATLAS brought limited gains. Finally, to examine the effect of contamination on imputation, we added various amounts of reads from two present-day genomes to a previously downsampled high-coverage ancient genome. We observed that imputation accuracy drastically decreased for contamination rates above 5%. In conclusion, we recommend (i) accounting for PMD by either trimming sequencing reads or using a genotype caller such as ATLAS before imputing highly damaged genomes and (ii) only imputing genomes containing up to 5% of contamination.
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Affiliation(s)
| | - Simone Rubinacci
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Anna-Sapfo Malaspinas
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | | | - Bárbara Sousa da Mota
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland.
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7
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Martiniano R, Haber M, Almarri MA, Mattiangeli V, Kuijpers MCM, Chamel B, Breslin EM, Littleton J, Almahari S, Aloraifi F, Bradley DG, Lombard P, Durbin R. Ancient genomes illuminate Eastern Arabian population history and adaptation against malaria. CELL GENOMICS 2024; 4:100507. [PMID: 38417441 PMCID: PMC10943591 DOI: 10.1016/j.xgen.2024.100507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 11/01/2023] [Accepted: 01/31/2024] [Indexed: 03/01/2024]
Abstract
The harsh climate of Arabia has posed challenges in generating ancient DNA from the region, hindering the direct examination of ancient genomes for understanding the demographic processes that shaped Arabian populations. In this study, we report whole-genome sequence data obtained from four Tylos-period individuals from Bahrain. Their genetic ancestry can be modeled as a mixture of sources from ancient Anatolia, Levant, and Iran/Caucasus, with variation between individuals suggesting population heterogeneity in Bahrain before the onset of Islam. We identify the G6PD Mediterranean mutation associated with malaria resistance in three out of four ancient Bahraini samples and estimate that it rose in frequency in Eastern Arabia from 5 to 6 kya onward, around the time agriculture appeared in the region. Our study characterizes the genetic composition of ancient Arabians, shedding light on the population history of Bahrain and demonstrating the feasibility of studies of ancient DNA in the region.
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Affiliation(s)
- Rui Martiniano
- School of Biological and Environmental Sciences, Liverpool John Moores University, L3 3AF Liverpool, UK.
| | - Marc Haber
- Institute of Cancer and Genomic Sciences, University of Birmingham Dubai, Dubai, United Arab Emirates
| | - Mohamed A Almarri
- Department of Forensic Science and Criminology, Dubai Police GHQ, Dubai, United Arab Emirates; College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | | | - Mirte C M Kuijpers
- Department of Ecology, Behavior and Evolution, School of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Berenice Chamel
- Institut Français du Proche-Orient (MEAE/CNRS), Beirut, Lebanon
| | - Emily M Breslin
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Judith Littleton
- School of Social Sciences, University of Auckland, Auckland, New Zealand
| | - Salman Almahari
- Bahrain Authority for Culture and Antiquities, Manama, Kingdom of Bahrain
| | - Fatima Aloraifi
- Mersey and West Lancashire Teaching Hospitals NHS Trust, Whiston Hospital, Warrington Road, Prescot, L35 5DR Liverpool, UK
| | - Daniel G Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Pierre Lombard
- Bahrain Authority for Culture and Antiquities, Manama, Kingdom of Bahrain; Archéorient UMR 5133, CNRS, Université Lyon 2, Maison de l'Orient et de la Méditerranée - Jean Pouilloux, Lyon, France
| | - Richard Durbin
- Department of Genetics, University of Cambridge, CB2 3EH Cambridge, UK.
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8
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Woerner AE, Novroski NM, Mandape S, King JL, Crysup B, Coble MD. Identifying distant relatives using benchtop-scale sequencing. Forensic Sci Int Genet 2024; 69:103005. [PMID: 38171224 DOI: 10.1016/j.fsigen.2023.103005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 11/20/2023] [Accepted: 12/19/2023] [Indexed: 01/05/2024]
Abstract
The genetic component of forensic genetic genealogy (FGG) is an estimate of kinship, often conducted at genome scales between a great number of individuals. The promise of FGG is substantial: in concert with genealogical records and other nongenetic information, it can indirectly identify a person of interest. A downside of FGG is cost, as it is currently expensive and requires chemistries uncommon to forensic genetic laboratories (microarrays and high throughput sequencing). The more common benchtop sequencers can be coupled with a targeted PCR assay to conduct FGG, though such approaches have limited resolution for kinship. This study evaluates low-pass sequencing, an alternative strategy that is accessible to benchtop sequencers and can produce resolutions comparable to high-pass sequencing. Samples from a three-generation pedigree were augmented to include up to 7th degree relatives (using whole genome pedigree simulations) and the ability to recover the true kinship coefficient was assessed using algorithms qualitatively similar to those found in GEDmatch. We show that up to 7th degree relatives can be reliably inferred from 1 × whole genome sequencing obtainable from desktop sequencers.
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Affiliation(s)
- August E Woerner
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX, USA; Department of Microbiology, Immunology and Genetics, University of North Texas Health Science Center, Fort Worth, TX, USA.
| | - Nicole M Novroski
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX, USA; Department of Anthropology, University of Toronto, Mississauga, ON, Canada
| | - Sammed Mandape
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Jonathan L King
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Benjamin Crysup
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX, USA; Department of Microbiology, Immunology and Genetics, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Michael D Coble
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX, USA; Department of Microbiology, Immunology and Genetics, University of North Texas Health Science Center, Fort Worth, TX, USA
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9
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Poyraz L, Colbran LL, Mathieson I. Predicting Functional Consequences of Recent Natural Selection in Britain. Mol Biol Evol 2024; 41:msae053. [PMID: 38466119 PMCID: PMC10962637 DOI: 10.1093/molbev/msae053] [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: 10/16/2023] [Revised: 02/02/2024] [Accepted: 03/01/2024] [Indexed: 03/12/2024] Open
Abstract
Ancient DNA can directly reveal the contribution of natural selection to human genomic variation. However, while the analysis of ancient DNA has been successful at identifying genomic signals of selection, inferring the phenotypic consequences of that selection has been more difficult. Most trait-associated variants are noncoding, so we expect that a large proportion of the phenotypic effects of selection will also act through noncoding variation. Since we cannot measure gene expression directly in ancient individuals, we used an approach (Joint-Tissue Imputation [JTI]) developed to predict gene expression from genotype data. We tested for changes in the predicted expression of 17,384 protein coding genes over a time transect of 4,500 years using 91 present-day and 616 ancient individuals from Britain. We identified 28 genes at seven genomic loci with significant (false discovery rate [FDR] < 0.05) changes in predicted expression levels in this time period. We compared the results from our transcriptome-wide scan to a genome-wide scan based on estimating per-single nucleotide polymorphism (SNP) selection coefficients from time series data. At five previously identified loci, our approach allowed us to highlight small numbers of genes with evidence for significant shifts in expression from peaks that in some cases span tens of genes. At two novel loci (SLC44A5 and NUP85), we identify selection on gene expression not captured by scans based on genomic signatures of selection. Finally, we show how classical selection statistics (iHS and SDS) can be combined with JTI models to incorporate functional information into scans that use present-day data alone. These results demonstrate the potential of this type of information to explore both the causes and consequences of natural selection.
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Affiliation(s)
- Lin Poyraz
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Computational Biology, Cornell University, Ithaca, NY, USA
| | - Laura L Colbran
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Iain Mathieson
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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10
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Hui R, Scheib CL, D’Atanasio E, Inskip SA, Cessford C, Biagini SA, Wohns AW, Ali MQ, Griffith SJ, Solnik A, Niinemäe H, Ge XJ, Rose AK, Beneker O, O’Connell TC, Robb JE, Kivisild T. Genetic history of Cambridgeshire before and after the Black Death. SCIENCE ADVANCES 2024; 10:eadi5903. [PMID: 38232165 PMCID: PMC10793959 DOI: 10.1126/sciadv.adi5903] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 12/14/2023] [Indexed: 01/19/2024]
Abstract
The extent of the devastation of the Black Death pandemic (1346-1353) on European populations is known from documentary sources and its bacterial source illuminated by studies of ancient pathogen DNA. What has remained less understood is the effect of the pandemic on human mobility and genetic diversity at the local scale. Here, we report 275 ancient genomes, including 109 with coverage >0.1×, from later medieval and postmedieval Cambridgeshire of individuals buried before and after the Black Death. Consistent with the function of the institutions, we found a lack of close relatives among the friars and the inmates of the hospital in contrast to their abundance in general urban and rural parish communities. While we detect long-term shifts in local genetic ancestry in Cambridgeshire, we find no evidence of major changes in genetic ancestry nor higher differentiation of immune loci between cohorts living before and after the Black Death.
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Affiliation(s)
- Ruoyun Hui
- Alan Turing Institute, London, UK
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK
| | - Christiana L. Scheib
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
- St John’s College, University of Cambridge, Cambridge, UK
| | | | - Sarah A. Inskip
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK
- School of Archaeology and Ancient History, University of Leicester, Leicester, UK
| | - Craig Cessford
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK
- Cambridge Archaeological Unit, Department of Archaeology, University of Cambridge, Cambridge, UK
| | | | - Anthony W. Wohns
- School of Medicine, Stanford University, Stanford, CA, USA
- Department of Genetics and Biology, Stanford University, Stanford, CA, USA
| | | | - Samuel J. Griffith
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Anu Solnik
- Core Facility, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Helja Niinemäe
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Xiangyu Jack Ge
- Wellcome Genome Campus, Wellcome Sanger Institute, Hinxton, UK
| | - Alice K. Rose
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK
- Department of Archaeology, University of Durham, Durham, UK
| | - Owyn Beneker
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Tamsin C. O’Connell
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK
| | - John E. Robb
- Department of Archaeology, University of Cambridge, Cambridge, UK
| | - Toomas Kivisild
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
- Department of Human Genetics, KU Leuven, Leuven, Belgium
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11
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Mirchandani CD, Shultz AJ, Thomas GWC, Smith SJ, Baylis M, Arnold B, Corbett-Detig R, Enbody E, Sackton TB. A Fast, Reproducible, High-throughput Variant Calling Workflow for Population Genomics. Mol Biol Evol 2024; 41:msad270. [PMID: 38069903 PMCID: PMC10764099 DOI: 10.1093/molbev/msad270] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 10/27/2023] [Accepted: 11/22/2023] [Indexed: 01/05/2024] Open
Abstract
The increasing availability of genomic resequencing data sets and high-quality reference genomes across the tree of life present exciting opportunities for comparative population genomic studies. However, substantial challenges prevent the simple reuse of data across different studies and species, arising from variability in variant calling pipelines, data quality, and the need for computationally intensive reanalysis. Here, we present snpArcher, a flexible and highly efficient workflow designed for the analysis of genomic resequencing data in nonmodel organisms. snpArcher provides a standardized variant calling pipeline and includes modules for variant quality control, data visualization, variant filtering, and other downstream analyses. Implemented in Snakemake, snpArcher is user-friendly, reproducible, and designed to be compatible with high-performance computing clusters and cloud environments. To demonstrate the flexibility of this pipeline, we applied snpArcher to 26 public resequencing data sets from nonmammalian vertebrates. These variant data sets are hosted publicly to enable future comparative population genomic analyses. With its extensibility and the availability of public data sets, snpArcher will contribute to a broader understanding of genetic variation across species by facilitating the rapid use and reuse of large genomic data sets.
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Affiliation(s)
- Cade D Mirchandani
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Allison J Shultz
- Ornithology Department, Natural History Museum of Los Angeles County, Los Angeles, CA 90007, USA
| | | | - Sara J Smith
- Informatics Group, Harvard University, Cambridge, MA, USA
- Biology, Mount Royal University, Calgary, AB T3E 6K6, Canada
| | - Mara Baylis
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Brian Arnold
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
- Center for Statistics and Machine Learning, Princeton University, Princeton, NJ, USA
| | - Russ Corbett-Detig
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Erik Enbody
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
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12
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Ringbauer H, Huang Y, Akbari A, Mallick S, Olalde I, Patterson N, Reich D. Accurate detection of identity-by-descent segments in human ancient DNA. Nat Genet 2024; 56:143-151. [PMID: 38123640 PMCID: PMC10786714 DOI: 10.1038/s41588-023-01582-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 10/20/2023] [Indexed: 12/23/2023]
Abstract
Long DNA segments shared between two individuals, known as identity-by-descent (IBD), reveal recent genealogical connections. Here we introduce ancIBD, a method for identifying IBD segments in ancient human DNA (aDNA) using a hidden Markov model and imputed genotype probabilities. We demonstrate that ancIBD accurately identifies IBD segments >8 cM for aDNA data with an average depth of >0.25× for whole-genome sequencing or >1× for 1240k single nucleotide polymorphism capture data. Applying ancIBD to 4,248 ancient Eurasian individuals, we identify relatives up to the sixth degree and genealogical connections between archaeological groups. Notably, we reveal long IBD sharing between Corded Ware and Yamnaya groups, indicating that the Yamnaya herders of the Pontic-Caspian Steppe and the Steppe-related ancestry in various European Corded Ware groups share substantial co-ancestry within only a few hundred years. These results show that detecting IBD segments can generate powerful insights into the growing aDNA record, both on a small scale relevant to life stories and on a large scale relevant to major cultural-historical events.
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Affiliation(s)
- Harald Ringbauer
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA.
| | - Yilei Huang
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Bioinformatics Group, Institute of Computer Science, Universität Leipzig, Leipzig, Germany
| | - Ali Akbari
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Iñigo Olalde
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- BIOMICs Research Group, University of the Basque Country, Vitoria-Gasteiz, Spain
- Ikerbasque-Basque Foundation of Science, Bilbao, Spain
| | - Nick Patterson
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - David Reich
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA.
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA.
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13
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Childebayeva A, Zavala EI. Review: Computational analysis of human skeletal remains in ancient DNA and forensic genetics. iScience 2023; 26:108066. [PMID: 37927550 PMCID: PMC10622734 DOI: 10.1016/j.isci.2023.108066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2023] Open
Abstract
Degraded DNA is used to answer questions in the fields of ancient DNA (aDNA) and forensic genetics. While aDNA studies typically center around human evolution and past history, and forensic genetics is often more concerned with identifying a specific individual, scientists in both fields face similar challenges. The overlap in source material has prompted periodic discussions and studies on the advantages of collaboration between fields toward mutually beneficial methodological advancements. However, most have been centered around wet laboratory methods (sampling, DNA extraction, library preparation, etc.). In this review, we focus on the computational side of the analytical workflow. We discuss limitations and considerations to consider when working with degraded DNA. We hope this review provides a framework to researchers new to computational workflows for how to think about analyzing highly degraded DNA and prompts an increase of collaboration between the forensic genetics and aDNA fields.
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Affiliation(s)
- Ainash Childebayeva
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Anthropology, University of Kansas, Lawrence, KS, USA
| | - Elena I. Zavala
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Department of Biology, University of Oregon, Eugene, OR, USA
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14
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Poyraz L, Colbran LL, Mathieson I. Predicting functional consequences of recent natural selection in Britain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.16.562549. [PMID: 37904954 PMCID: PMC10614889 DOI: 10.1101/2023.10.16.562549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Ancient DNA can directly reveal the contribution of natural selection to human genomic variation. However, while the analysis of ancient DNA has been successful at identifying genomic signals of selection, inferring the phenotypic consequences of that selection has been more difficult. Most trait-associated variants are non-coding, so we expect that a large proportion of the phenotypic effects of selection will also act through non-coding variation. Since we cannot measure gene expression directly in ancient individuals, we used an approach (Joint-Tissue Imputation; JTI) developed to predict gene expression from genotype data. We tested for changes in the predicted expression of 17,384 protein coding genes over a time transect of 4500 years using 91 present-day and 616 ancient individuals from Britain. We identified 28 genes at seven genomic loci with significant (FDR < 0.05) changes in predicted expression levels in this time period. We compared the results from our transcriptome-wide scan to a genome-wide scan based on estimating per-SNP selection coefficients from time series data. At five previously identified loci, our approach allowed us to highlight small numbers of genes with evidence for significant shifts in expression from peaks that in some cases span tens of genes. At two novel loci (SLC44A5 and NUP85), we identify selection on gene expression not captured by scans based on genomic signatures of selection. Finally we show how classical selection statistics (iHS and SDS) can be combined with JTI models to incorporate functional information into scans that use present-day data alone. These results demonstrate the potential of this type of information to explore both the causes and consequences of natural selection.
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Affiliation(s)
- Lin Poyraz
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Computational Biology, Cornell University, Ithaca, NY, USA
| | - Laura L. Colbran
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Iain Mathieson
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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15
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Harney É, Micheletti S, Bruwelheide KS, Freyman WA, Bryc K, Akbari A, Jewett E, Comer E, Louis Gates H, Heywood L, Thornton J, Curry R, Ancona Esselmann S, Barca KG, Sedig J, Sirak K, Olalde I, Adamski N, Bernardos R, Broomandkhoshbacht N, Ferry M, Qiu L, Stewardson K, Workman JN, Zalzala F, Mallick S, Micco A, Mah M, Zhang Z, Rohland N, Mountain JL, Owsley DW, Reich D. The genetic legacy of African Americans from Catoctin Furnace. Science 2023; 381:eade4995. [PMID: 37535739 PMCID: PMC10958645 DOI: 10.1126/science.ade4995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 06/20/2023] [Indexed: 08/05/2023]
Abstract
Few African Americans have been able to trace family lineages back to ancestors who died before the 1870 United States Census, the first in which all Black people were listed by name. We analyzed 27 individuals from Maryland's Catoctin Furnace African American Cemetery (1774-1850), identifying 41,799 genetic relatives among consenting research participants in 23andMe, Inc.'s genetic database. One of the highest concentrations of close relatives is in Maryland, suggesting that descendants of the Catoctin individuals remain in the area. We find that many of the Catoctin individuals derived African ancestry from the Wolof or Kongo groups and European ancestry from Great Britain and Ireland. This study demonstrates the power of joint analysis of historical DNA and large datasets generated through direct-to-consumer ancestry testing.
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Affiliation(s)
- Éadaoin Harney
- 23andMe, Inc.; Sunnyvale, CA 94043, USA
- Department of Human Evolutionary Biology, Harvard University; Cambridge, MA, 02138, USA
| | | | - Karin S. Bruwelheide
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution; Washington DC 20560, USA
| | | | | | - Ali Akbari
- Department of Human Evolutionary Biology, Harvard University; Cambridge, MA, 02138, USA
- Department of Genetics, Harvard Medical School; Boston, MA, 02115, USA
| | | | - Elizabeth Comer
- Catoctin Furnace Historical Society; Thurmont, MD, 21788, USA
| | - Henry Louis Gates
- Hutchins Center for African and African American Research, Harvard University; Cambridge, MA 02138, USA
| | - Linda Heywood
- Department of History/African American Studies, Boston University; Brookline, MA 02446, USA
| | - John Thornton
- Department of History/African American Studies, Boston University; Brookline, MA 02446, USA
| | - Roslyn Curry
- 23andMe, Inc.; Sunnyvale, CA 94043, USA
- Department of Human Evolutionary Biology, Harvard University; Cambridge, MA, 02138, USA
| | | | - Kathryn G. Barca
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution; Washington DC 20560, USA
| | - Jakob Sedig
- Department of Human Evolutionary Biology, Harvard University; Cambridge, MA, 02138, USA
- Department of Genetics, Harvard Medical School; Boston, MA, 02115, USA
| | - Kendra Sirak
- Department of Human Evolutionary Biology, Harvard University; Cambridge, MA, 02138, USA
- Department of Genetics, Harvard Medical School; Boston, MA, 02115, USA
| | - Iñigo Olalde
- Department of Human Evolutionary Biology, Harvard University; Cambridge, MA, 02138, USA
- BIOMICs Research Group, Department of Zoology and Animal Cell Biology, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
- Ikerbasque—Basque Foundation of Science, Bilbao, Spain
| | - Nicole Adamski
- Department of Genetics, Harvard Medical School; Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School; Boston, MA, 02115, USA
| | - Rebecca Bernardos
- Department of Genetics, Harvard Medical School; Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School; Boston, MA, 02115, USA
| | - Nasreen Broomandkhoshbacht
- Department of Genetics, Harvard Medical School; Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School; Boston, MA, 02115, USA
| | - Matthew Ferry
- Department of Genetics, Harvard Medical School; Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School; Boston, MA, 02115, USA
| | - Lijun Qiu
- Department of Genetics, Harvard Medical School; Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School; Boston, MA, 02115, USA
| | - Kristin Stewardson
- Department of Genetics, Harvard Medical School; Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School; Boston, MA, 02115, USA
| | - J. Noah Workman
- Department of Genetics, Harvard Medical School; Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School; Boston, MA, 02115, USA
| | - Fatma Zalzala
- Department of Genetics, Harvard Medical School; Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School; Boston, MA, 02115, USA
| | - Shop Mallick
- Department of Genetics, Harvard Medical School; Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School; Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard; Cambridge, MA, 02142, USA
| | - Adam Micco
- Department of Genetics, Harvard Medical School; Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard; Cambridge, MA, 02142, USA
| | - Matthew Mah
- Department of Genetics, Harvard Medical School; Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School; Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard; Cambridge, MA, 02142, USA
| | - Zhao Zhang
- Department of Genetics, Harvard Medical School; Boston, MA, 02115, USA
| | | | - Nadin Rohland
- Department of Genetics, Harvard Medical School; Boston, MA, 02115, USA
| | | | - Douglas W. Owsley
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution; Washington DC 20560, USA
| | - David Reich
- Department of Human Evolutionary Biology, Harvard University; Cambridge, MA, 02138, USA
- Department of Genetics, Harvard Medical School; Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School; Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard; Cambridge, MA, 02142, USA
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16
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Todd ET, Fromentier A, Sutcliffe R, Running Horse Collin Y, Perdereau A, Aury JM, Èche C, Bouchez O, Donnadieu C, Wincker P, Kalbfleisch T, Petersen JL, Orlando L. Imputed genomes of historical horses provide insights into modern breeding. iScience 2023; 26:107104. [PMID: 37416458 PMCID: PMC10319840 DOI: 10.1016/j.isci.2023.107104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 04/25/2023] [Accepted: 06/08/2023] [Indexed: 07/08/2023] Open
Abstract
Historical genomes can provide important insights into recent genomic changes in horses, especially the development of modern breeds. In this study, we characterized 8.7 million genomic variants from a panel of 430 horses from 73 breeds, including newly sequenced genomes from 20 Clydesdales and 10 Shire horses. We used this modern genomic variation to impute the genomes of four historically important horses, consisting of publicly available genomes from 2 Przewalski's horses, 1 Thoroughbred, and a newly sequenced Clydesdale. Using these historical genomes, we identified modern horses with higher genetic similarity to those in the past and unveiled increased inbreeding in recent times. We genotyped variants associated with appearance and behavior to uncover previously unknown characteristics of these important historical horses. Overall, we provide insights into the history of Thoroughbred and Clydesdale breeds and highlight genomic changes in the endangered Przewalski's horse following a century of captive breeding.
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Affiliation(s)
- Evelyn T. Todd
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, 37 Allées Jules Guesde, Bâtiment A, 31000 Toulouse, France
| | - Aurore Fromentier
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, 37 Allées Jules Guesde, Bâtiment A, 31000 Toulouse, France
| | - Richard Sutcliffe
- Glasgow Museums Resource Centre, 200 Woodhead Road, Nitshill, G53 7NN Glasgow, UK
| | - Yvette Running Horse Collin
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, 37 Allées Jules Guesde, Bâtiment A, 31000 Toulouse, France
| | - Aude Perdereau
- Genoscope, Institut de biologie François Jacob, CEA, Université d’Evry, Université Paris-Saclay, 91042 Evry, France
| | - Jean-Marc Aury
- Genoscope, Institut de biologie François Jacob, CEA, Université d’Evry, Université Paris-Saclay, 91042 Evry, France
| | - Camille Èche
- GeT-PlaGe - Génome et Transcriptome - Plateforme Génomique, GET - Plateforme Génome & Transcriptome, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, 31326 Castanet-Tolosan Cedex, France
| | - Olivier Bouchez
- GeT-PlaGe - Génome et Transcriptome - Plateforme Génomique, GET - Plateforme Génome & Transcriptome, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, 31326 Castanet-Tolosan Cedex, France
| | - Cécile Donnadieu
- GeT-PlaGe - Génome et Transcriptome - Plateforme Génomique, GET - Plateforme Génome & Transcriptome, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, 31326 Castanet-Tolosan Cedex, France
| | - Patrick Wincker
- Genoscope, Institut de biologie François Jacob, CEA, Université d’Evry, Université Paris-Saclay, 91042 Evry, France
| | - Ted Kalbfleisch
- MH Gluck Equine Research Center, University of Kentucky, Lexington, KY 40546-0091, USA
| | - Jessica L. Petersen
- Department of Animal Science, University of Nebraska-Lincoln, 3940 Fair St, Lincoln, NE 68583-0908, USA
| | - Ludovic Orlando
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, 37 Allées Jules Guesde, Bâtiment A, 31000 Toulouse, France
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17
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Sousa da Mota B, Rubinacci S, Cruz Dávalos DI, G Amorim CE, Sikora M, Johannsen NN, Szmyt MH, Włodarczak P, Szczepanek A, Przybyła MM, Schroeder H, Allentoft ME, Willerslev E, Malaspinas AS, Delaneau O. Imputation of ancient human genomes. Nat Commun 2023; 14:3660. [PMID: 37339987 PMCID: PMC10282092 DOI: 10.1038/s41467-023-39202-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 06/02/2023] [Indexed: 06/22/2023] Open
Abstract
Due to postmortem DNA degradation and microbial colonization, most ancient genomes have low depth of coverage, hindering genotype calling. Genotype imputation can improve genotyping accuracy for low-coverage genomes. However, it is unknown how accurate ancient DNA imputation is and whether imputation introduces bias to downstream analyses. Here we re-sequence an ancient trio (mother, father, son) and downsample and impute a total of 43 ancient genomes, including 42 high-coverage (above 10x) genomes. We assess imputation accuracy across ancestries, time, depth of coverage, and sequencing technology. We find that ancient and modern DNA imputation accuracies are comparable. When downsampled at 1x, 36 of the 42 genomes are imputed with low error rates (below 5%) while African genomes have higher error rates. We validate imputation and phasing results using the ancient trio data and an orthogonal approach based on Mendel's rules of inheritance. We further compare the downstream analysis results between imputed and high-coverage genomes, notably principal component analysis, genetic clustering, and runs of homozygosity, observing similar results starting from 0.5x coverage, except for the African genomes. These results suggest that, for most populations and depths of coverage as low as 0.5x, imputation is a reliable method that can improve ancient DNA studies.
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Affiliation(s)
- Bárbara Sousa da Mota
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | - Simone Rubinacci
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | - Diana Ivette Cruz Dávalos
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | | | - Martin Sikora
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Niels N Johannsen
- Department of Archaeology and Heritage Studies, Aarhus University, Aarhus, Denmark
| | - Marzena H Szmyt
- Institute for Eastern Research, Adam Mickiewicz University in Poznań, Poznań, Poland
| | - Piotr Włodarczak
- Institute of Archaeology and Ethnology, Polish Academy of Sciences, Kraków, Poland
| | - Anita Szczepanek
- Institute of Archaeology and Ethnology, Polish Academy of Sciences, Kraków, Poland
- Department of Anatomy, Jagiellonian University, Medical College, Kraków, Poland
| | | | - Hannes Schroeder
- The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Morten E Allentoft
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Science, Curtin University, Bentley, WA, Australia
| | - Eske Willerslev
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- GeoGenetics Group, Department of Zoology, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- MARUM, University of Bremen, Bremen, Germany
| | - Anna-Sapfo Malaspinas
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland.
| | - Olivier Delaneau
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland.
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18
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Tomofuji Y, Sonehara K, Kishikawa T, Maeda Y, Ogawa K, Kawabata S, Nii T, Okuno T, Oguro-Igashira E, Kinoshita M, Takagaki M, Yamamoto K, Kurakawa T, Yagita-Sakamaki M, Hosokawa A, Motooka D, Matsumoto Y, Matsuoka H, Yoshimura M, Ohshima S, Nakamura S, Inohara H, Kishima H, Mochizuki H, Takeda K, Kumanogoh A, Okada Y. Reconstruction of the personal information from human genome reads in gut metagenome sequencing data. Nat Microbiol 2023:10.1038/s41564-023-01381-3. [PMID: 37188815 DOI: 10.1038/s41564-023-01381-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 04/12/2023] [Indexed: 05/17/2023]
Abstract
Human DNA present in faecal samples can result in a small number of human reads in gut shotgun metagenomic sequencing data. However, it is presently unclear how much personal information can be reconstructed from such reads, and this has not been quantitatively evaluated. Such a quantitative evaluation is necessary to clarify the ethical concerns related to data sharing and to enable efficient use of human genetic information in stool samples, such as for research and forensics. Here we used genomic approaches to reconstruct personal information from the faecal metagenomes of 343 Japanese individuals with associated human genotype data. Genetic sex could be accurately predicted based on the sequencing depth of sex chromosomes for 97.3% of the samples. Individuals could be re-identified from the matched genotype data based on human reads recovered from the faecal metagenomic data with 93.3% sensitivity using a likelihood score-based method. This method also enabled us to predict the ancestries of 98.3% of the samples. Finally, we performed ultra-deep shotgun metagenomic sequencing of five faecal samples as well as whole-genome sequencing of blood samples. Using genotype-calling approaches, we demonstrated that the genotypes of both common and rare variants could be reconstructed from faecal samples. This included clinically relevant variants. Our approach can be used to quantify personal information contained within gut metagenome data.
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Affiliation(s)
- Yoshihiko Tomofuji
- Department of Statistical Genetics, Graduate School of Medicine, Osaka University, Suita, Japan.
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan.
- Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
| | - Kyuto Sonehara
- Department of Statistical Genetics, Graduate School of Medicine, Osaka University, Suita, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan
- Department of Genome Informatics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Toshihiro Kishikawa
- Department of Statistical Genetics, Graduate School of Medicine, Osaka University, Suita, Japan
- Department of Otorhinolaryngology-Head and Neck Surgery, Graduate School of Medicine, Osaka University, Suita, Japan
- Department of Head and Neck Surgery, Aichi Cancer Center Hospital, Nagoya, Japan
| | - Yuichi Maeda
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Japan
- Laboratory of Immune Regulation, Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Kotaro Ogawa
- Department of Neurology, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Shuhei Kawabata
- Department of Neurosurgery, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Takuro Nii
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Japan
- Laboratory of Immune Regulation, Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Tatsusada Okuno
- Department of Neurology, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Eri Oguro-Igashira
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Japan
- Laboratory of Immune Regulation, Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Makoto Kinoshita
- Department of Neurology, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Masatoshi Takagaki
- Department of Neurosurgery, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Kenichi Yamamoto
- Department of Statistical Genetics, Graduate School of Medicine, Osaka University, Suita, Japan
- Department of Pediatrics, Graduate School of Medicine, Osaka University, Suita, Japan
- Laboratory of Statistical Immunology, WPI Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
| | - Takashi Kurakawa
- Laboratory of Immune Regulation, Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Mayu Yagita-Sakamaki
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Japan
- Laboratory of Immune Regulation, Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Akiko Hosokawa
- Department of Neurology, Graduate School of Medicine, Osaka University, Suita, Japan
- Department of Neurology, Suita Municipal Hospital, Suita, Japan
| | - Daisuke Motooka
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan
- Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Yuki Matsumoto
- Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Hidetoshi Matsuoka
- Department of Rheumatology and Allergology, NHO Osaka Minami Medical Center, Kawachinagano, Japan
| | - Maiko Yoshimura
- Department of Rheumatology and Allergology, NHO Osaka Minami Medical Center, Kawachinagano, Japan
| | - Shiro Ohshima
- Department of Rheumatology and Allergology, NHO Osaka Minami Medical Center, Kawachinagano, Japan
| | - Shota Nakamura
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan
- Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
- Center for Infectious Disease Education and Research, Osaka University, Suita, Japan
| | - Hidenori Inohara
- Department of Otorhinolaryngology-Head and Neck Surgery, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Haruhiko Kishima
- Department of Neurosurgery, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Hideki Mochizuki
- Department of Neurology, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Kiyoshi Takeda
- Laboratory of Immune Regulation, Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Suita, Japan
- Center for Infectious Disease Education and Research, Osaka University, Suita, Japan
- WPI Immunology Frontier Research Center, Osaka University, Suita, Japan
| | - Atsushi Kumanogoh
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Japan
- Department of Immunopathology, Immunology Frontier Research Center, Osaka University, Suita, Japan
| | - Yukinori Okada
- Department of Statistical Genetics, Graduate School of Medicine, Osaka University, Suita, Japan.
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan.
- Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
- Department of Genome Informatics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
- Laboratory of Statistical Immunology, WPI Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan.
- Center for Infectious Disease Education and Research, Osaka University, Suita, Japan.
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19
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Ringbauer H, Huang Y, Akbari A, Mallick S, Patterson N, Reich D. ancIBD - Screening for identity by descent segments in human ancient DNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.08.531671. [PMID: 36945531 PMCID: PMC10028887 DOI: 10.1101/2023.03.08.531671] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Long DNA sequences shared between two individuals, known as Identical by descent (IBD) segments, are a powerful signal for identifying close and distant biological relatives because they only arise when the pair shares a recent common ancestor. Existing methods to call IBD segments between present-day genomes cannot be straightforwardly applied to ancient DNA data (aDNA) due to typically low coverage and high genotyping error rates. We present ancIBD, a method to identify IBD segments for human aDNA data implemented as a Python package. Our approach is based on a Hidden Markov Model, using as input genotype probabilities imputed based on a modern reference panel of genomic variation. Through simulation and downsampling experiments, we demonstrate that ancIBD robustly identifies IBD segments longer than 8 centimorgan for aDNA data with at least either 0.25x average whole-genome sequencing (WGS) coverage depth or at least 1x average depth for in-solution enrichment experiments targeting a widely used aDNA SNP set ('1240k'). This application range allows us to screen a substantial fraction of the aDNA record for IBD segments and we showcase two downstream applications. First, leveraging the fact that biological relatives up to the sixth degree are expected to share multiple long IBD segments, we identify relatives between 10,156 ancient Eurasian individuals and document evidence of long-distance migration, for example by identifying a pair of two approximately fifth-degree relatives who were buried 1410km apart in Central Asia 5000 years ago. Second, by applying ancIBD, we reveal new details regarding the spread of ancestry related to Steppe pastoralists into Europe starting 5000 years ago. We find that the first individuals in Central and Northern Europe carrying high amounts of Steppe-ancestry, associated with the Corded Ware culture, share high rates of long IBD (12-25 cM) with Yamnaya herders of the Pontic-Caspian steppe, signaling a strong bottleneck and a recent biological connection on the order of only few hundred years, providing evidence that the Yamnaya themselves are a main source of Steppe ancestry in Corded Ware people. We also detect elevated sharing of long IBD segments between Corded Ware individuals and people associated with the Globular Amphora culture (GAC) from Poland and Ukraine, who were Copper Age farmers not yet carrying Steppe-like ancestry. These IBD links appear for all Corded Ware groups in our analysis, indicating that individuals related to GAC contexts must have had a major demographic impact early on in the genetic admixtures giving rise to various Corded Ware groups across Europe. These results show that detecting IBD segments in aDNA can generate new insights both on a small scale, relevant to understanding the life stories of people, and on the macroscale, relevant to large-scale cultural-historical events.
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Affiliation(s)
- Harald Ringbauer
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Yilei Huang
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Bioinformatics Group, Institute of Computer Science, Universität Leipzig, Leipzig, Germanÿ
| | - Ali Akbari
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Nick Patterson
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - David Reich
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
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20
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Ausmees K, Nettelblad C. Achieving improved accuracy for imputation of ancient DNA. Bioinformatics 2022; 39:6827812. [PMID: 36377787 PMCID: PMC9805568 DOI: 10.1093/bioinformatics/btac738] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 11/07/2022] [Accepted: 11/14/2022] [Indexed: 11/16/2022] Open
Abstract
MOTIVATION Genotype imputation has the potential to increase the amount of information that can be gained from the often limited biological material available in ancient samples. As many widely used tools have been developed with modern data in mind, their design is not necessarily reflective of the requirements in studies of ancient DNA. Here, we investigate if an imputation method based on the full probabilistic Li and Stephens model of haplotype frequencies might be beneficial for the particular challenges posed by ancient data. RESULTS We present an implementation called prophaser and compare imputation performance to two alternative pipelines that have been used in the ancient DNA community based on the Beagle software. Considering empirical ancient data downsampled to lower coverages as well as present-day samples with artificially thinned genotypes, we show that the proposed method is advantageous at lower coverages, where it yields improved accuracy and ability to capture rare variation. The software prophaser is optimized for running in a massively parallel manner and achieved reasonable runtimes on the experiments performed when executed on a GPU. AVAILABILITY AND IMPLEMENTATION The C++ code for prophaser is available in the GitHub repository https://github.com/scicompuu/prophaser. SUPPLEMENTARY INFORMATION Supplementary information is available at Bioinformatics online.
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21
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Greytak EM, Cady J, Vance N, Moore C, Armentrout SL. Investigative genetic genealogy for unidentified human remains cases in Oregon. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2022. [DOI: 10.1016/j.fsigss.2022.10.081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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22
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Todd ET, Tonasso-Calvière L, Chauvey L, Schiavinato S, Fages A, Seguin-Orlando A, Clavel P, Khan N, Pérez Pardal L, Patterson Rosa L, Librado P, Ringbauer H, Verdugo M, Southon J, Aury JM, Perdereau A, Vila E, Marzullo M, Prato O, Tecchiati U, Bagnasco Gianni G, Tagliacozzo A, Tinè V, Alhaique F, Cardoso JL, Valente MJ, Telles Antunes M, Frantz L, Shapiro B, Bradley DG, Boulbes N, Gardeisen A, Horwitz LK, Öztan A, Arbuckle BS, Onar V, Clavel B, Lepetz S, Vahdati AA, Davoudi H, Mohaseb A, Mashkour M, Bouchez O, Donnadieu C, Wincker P, Brooks SA, Beja-Pereira A, Wu DD, Orlando L. The genomic history and global expansion of domestic donkeys. Science 2022; 377:1172-1180. [PMID: 36074859 DOI: 10.1126/science.abo3503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Donkeys transformed human history as essential beasts of burden for long-distance movement, especially across semi-arid and upland environments. They remain insufficiently studied despite globally expanding and providing key support to low- to middle-income communities. To elucidate their domestication history, we constructed a comprehensive genome panel of 207 modern and 31 ancient donkeys, as well as 15 wild equids. We found a strong phylogeographic structure in modern donkeys that supports a single domestication in Africa ~5000 BCE, followed by further expansions in this continent and Eurasia and ultimately returning to Africa. We uncover a previously unknown genetic lineage in the Levant ~200 BCE, which contributed increasing ancestry toward Asia. Donkey management involved inbreeding and the production of giant bloodlines at a time when mules were essential to the Roman economy and military.
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Affiliation(s)
- Evelyn T Todd
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, Toulouse 31000, France
| | - Laure Tonasso-Calvière
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, Toulouse 31000, France
| | - Loreleï Chauvey
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, Toulouse 31000, France
| | - Stéphanie Schiavinato
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, Toulouse 31000, France
| | - Antoine Fages
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, Toulouse 31000, France
| | - Andaine Seguin-Orlando
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, Toulouse 31000, France
| | - Pierre Clavel
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, Toulouse 31000, France
| | - Naveed Khan
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, Toulouse 31000, France.,Department of Biotechnology, Abdul Wali Khan University, Mardan 23200, Pakistan
| | - Lucía Pérez Pardal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão 4485-661, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, Campus de Vairão, Universidade do Porto, Vairão 4485-661, Portugal
| | | | - Pablo Librado
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, Toulouse 31000, France
| | - Harald Ringbauer
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Marta Verdugo
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin D02 PN40, Ireland
| | - John Southon
- Earth System Science Department, University of California, Irvine, CA 92697, USA
| | - Jean-Marc Aury
- Genoscope, Institut de biologie François Jacob, CEA, Université d'Evry, Université Paris-Saclay, Evry 91042, France
| | - Aude Perdereau
- Genoscope, Institut de biologie François Jacob, CEA, Université d'Evry, Université Paris-Saclay, Evry 91042, France
| | - Emmanuelle Vila
- Laboratoire Archéorient, Université Lyon 2, Lyon 69007, France
| | - Matilde Marzullo
- Dipartimento di Beni Culturali e Ambientali, Università degli Studi di Milano, Milan 20122, Italy
| | - Ornella Prato
- Dipartimento di Beni Culturali e Ambientali, Università degli Studi di Milano, Milan 20122, Italy
| | - Umberto Tecchiati
- Dipartimento di Beni Culturali e Ambientali, Università degli Studi di Milano, Milan 20122, Italy
| | - Giovanna Bagnasco Gianni
- Dipartimento di Beni Culturali e Ambientali, Università degli Studi di Milano, Milan 20122, Italy
| | | | - Vincenzo Tinè
- Soprintendenza archeologia belle arti e paesaggio per le province di Verona, Rovigo e Vicenza, Verona 37121, Italy
| | | | - João Luís Cardoso
- ICArEHB, Campus de Gambelas, University of Algarve, Faro 8005-139, Portugal.,Universidade Aberta, Lisbon 1269-001, Portugal
| | - Maria João Valente
- Faculdade de Ciências Humanas e Sociais, Centro de Estudos de Arqueologia, Artes e Ciências do Património, Universidade do Algarve, Faro 8000-117, Portugal
| | - Miguel Telles Antunes
- Centre for Research on Science and Geological Engineering, Universidade NOVA de Lisboa, Lisbon 1099-085, Portugal
| | - Laurent Frantz
- Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, Munich 80539, Germany.,School of Biological and Behavioural Sciences, Queen Mary University of London, London E1 4DQ, United Kingdom
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064, USA.,Howard Hughes Medical Institute, University of California, Santa Cruz, CA 95064, USA
| | - Daniel G Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin D02 PN40, Ireland
| | - Nicolas Boulbes
- Institut de Paléontologie Humaine, Fondation Albert Ier, Paris / UMR 7194 HNHP, MNHN-CNRS-UPVD / EPCC Centre Européen de Recherche Préhistorique, Tautavel 66720, France
| | - Armelle Gardeisen
- Archéologie des Sociétés Méditéranéennes, Université Paul Valéry - Site Saint-Charles 2, Montpellier 34090, France
| | - Liora Kolska Horwitz
- National Natural History Collections, Edmond J. Safra Campus, Givat Ram, The Hebrew University, Jerusalem 9190401, Israel
| | - Aliye Öztan
- Archaeology Department, Ankara University, Ankara 06100, Turkey
| | - Benjamin S Arbuckle
- Department of Anthropology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Vedat Onar
- Osteoarchaeology Practice and Research Center and Department of Anatomy, Faculty of Veterinary Medicine, Istanbul University-Cerrahpaşa, Istanbul 34320, Turkey
| | - Benoît Clavel
- Archéozoologie, Archéobotanique, Sociétés, Pratiques et Environnements, Muséum National d'Histoire Naturelle, Paris 75005, France
| | - Sébastien Lepetz
- Archéozoologie, Archéobotanique, Sociétés, Pratiques et Environnements, Muséum National d'Histoire Naturelle, Paris 75005, France
| | - Ali Akbar Vahdati
- Provincial Office of the Iranian Center for Cultural Heritage, Handicrafts and Tourism Organisation, North Khorassan, Bojnord 9416745775, Iran
| | - Hossein Davoudi
- Archaezoology section, Bioarchaeology Laboratory of the Central Laboratory, University of Tehran, Tehran CP1417634934, Iran
| | - Azadeh Mohaseb
- Archéozoologie, Archéobotanique, Sociétés, Pratiques et Environnements, Muséum National d'Histoire Naturelle, Paris 75005, France.,Archaezoology section, Bioarchaeology Laboratory of the Central Laboratory, University of Tehran, Tehran CP1417634934, Iran
| | - Marjan Mashkour
- Archéozoologie, Archéobotanique, Sociétés, Pratiques et Environnements, Muséum National d'Histoire Naturelle, Paris 75005, France.,Archaezoology section, Bioarchaeology Laboratory of the Central Laboratory, University of Tehran, Tehran CP1417634934, Iran.,Department of Osteology, National Museum of Iran, Tehran 1136918111, Iran
| | - Olivier Bouchez
- GeT-PlaGe - Génome et Transcriptome - Plateforme Génomique, GET - Plateforme Génome & Transcriptome, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Castaneet-Tolosan Cedex 31326, France
| | - Cécile Donnadieu
- GeT-PlaGe - Génome et Transcriptome - Plateforme Génomique, GET - Plateforme Génome & Transcriptome, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Castaneet-Tolosan Cedex 31326, France
| | - Patrick Wincker
- Genoscope, Institut de biologie François Jacob, CEA, Université d'Evry, Université Paris-Saclay, Evry 91042, France
| | - Samantha A Brooks
- Department of Animal Science, UF Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Albano Beja-Pereira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão 4485-661, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, Campus de Vairão, Universidade do Porto, Vairão 4485-661, Portugal.,DGAOT, Faculty of Sciences, Universidade do Porto, Porto 4169-007, Portugal.,Sustainable Agrifood Production Research Centre (GreenUPorto), Universidade do Porto, Vairão 4485-646, Portugal
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.,Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Ludovic Orlando
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, Toulouse 31000, France
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23
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Cady J, Greytak EM. Whole-genome sequencing of degraded DNA for investigative genetic genealogy. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2022. [DOI: 10.1016/j.fsigss.2022.09.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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24
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Guellil M, van Dorp L, Inskip SA, Dittmar JM, Saag L, Tambets K, Hui R, Rose A, D’Atanasio E, Kriiska A, Varul L, Koekkelkoren AMHC, Goldina RD, Cessford C, Solnik A, Metspalu M, Krause J, Herbig A, Robb JE, Houldcroft CJ, Scheib CL. Ancient herpes simplex 1 genomes reveal recent viral structure in Eurasia. SCIENCE ADVANCES 2022; 8:eabo4435. [PMID: 35895820 PMCID: PMC9328674 DOI: 10.1126/sciadv.abo4435] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 06/10/2022] [Indexed: 05/05/2023]
Abstract
Human herpes simplex virus 1 (HSV-1), a life-long infection spread by oral contact, infects a majority of adults globally. Phylogeographic clustering of sampled diversity into European, pan-Eurasian, and African groups has suggested the virus codiverged with human migrations out of Africa, although a much younger origin has also been proposed. We present three full ancient European HSV-1 genomes and one partial genome, dating from the 3rd to 17th century CE, sequenced to up to 9.5× with paired human genomes up to 10.16×. Considering a dataset of modern and ancient genomes, we apply phylogenetic methods to estimate the age of sampled modern Eurasian HSV-1 diversity to 4.68 (3.87 to 5.65) ka. Extrapolation of estimated rates to a global dataset points to the age of extant sampled HSV-1 as 5.29 (4.60 to 6.12) ka, suggesting HSV-1 lineage replacement coinciding with the late Neolithic period and following Bronze Age migrations.
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Affiliation(s)
- Meriam Guellil
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, Tartu 51010, Estonia
| | - Lucy van Dorp
- UCL Genetics Institute, Department of Genetics, Evolution, and Environment, University College London, London WC1E 6BT, UK
| | - Sarah A. Inskip
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK
- Department of Archaeology and Ancient History, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - Jenna M. Dittmar
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK
- Department of Archaeology, University of Aberdeen, UK
| | - Lehti Saag
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, Tartu 51010, Estonia
- UCL Genetics Institute, Department of Genetics, Evolution, and Environment, University College London, London WC1E 6BT, UK
| | - Kristiina Tambets
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, Tartu 51010, Estonia
| | - Ruoyun Hui
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK
- Alan Turing Institute, 2QR, John Dodson House, 96 Euston Rd., London NW1 2DB, UK
| | - Alice Rose
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK
| | | | - Aivar Kriiska
- Department of Archaeology, Institute of History and Archaeology, University of Tartu, Tartu 51014, Estonia
| | - Liivi Varul
- Archaeological Research Collection, School of Humanities, Tallinn University, Tallinn 10130, Estonia
| | | | - Rimma D. Goldina
- Department History of Udmurtia, Archaeology and Ethnology, Udmurt State University, 1, Universitetskaya St. 1, 426034 Izhevsk, Russia
| | - Craig Cessford
- Cambridge Archaeological Unit, Department of Archaeology, University of Cambridge, Cambridge, UK
| | - Anu Solnik
- Core Facility, Institute of Genomics, University of Tartu, Riia 23B, Tartu 51010 Estonia
| | - Mait Metspalu
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, Tartu 51010, Estonia
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Alexander Herbig
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - John E. Robb
- Department of Archaeology, University of Cambridge, Cambridge, UK
| | | | - Christiana L. Scheib
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, Tartu 51010, Estonia
- St. John’s College, University of Cambridge, Cambridge, CB2 1TP, UK
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25
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Erven JAM, Çakirlar C, Bradley DG, Raemaekers DCM, Madsen O. Imputation of Ancient Whole Genome Sus scrofa DNA Introduces Biases Toward Main Population Components in the Reference Panel. Front Genet 2022; 13:872486. [PMID: 35903348 PMCID: PMC9315352 DOI: 10.3389/fgene.2022.872486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 05/20/2022] [Indexed: 11/13/2022] Open
Abstract
Sequencing ancient DNA to high coverage is often limited by sample quality and cost. Imputing missing genotypes can potentially increase information content and quality of ancient data, but requires different computational approaches than modern DNA imputation. Ancient imputation beyond humans has not been investigated. In this study we report results of a systematic evaluation of imputation of three whole genome ancient Sus scrofa samples from the Early and Late Neolithic (∼7,100–4,500 BP), to test the utility of imputation. We show how issues like genetic architecture and, reference panel divergence, composition and size affect imputation accuracy. We evaluate a variety of imputation methods, including Beagle5, GLIMPSE, and Impute5 with varying filters, pipelines, and variant calling methods. We achieved genotype concordance in most cases reaching above 90%; with the highest being 98% with ∼2,000,000 variants recovered using GLIMPSE. Despite this high concordance the sources of diversity present in the genotypes called in the original high coverage genomes were not equally imputed leading to biases in downstream analyses; a trend toward genotypes most common in the reference panel is observed. This demonstrates that the current reference panel does not possess the full diversity needed for accurate imputation of ancient Sus, due to missing variations from Near Eastern and Mesolithic wild boar. Imputation of ancient Sus scrofa holds potential but should be approached with caution due to these biases, and suggests that there is no universal approach for imputation of non-human ancient species.
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Affiliation(s)
- J. A. M. Erven
- Groningen Institute of Archaeology, University of Groningen, Groningen, Netherlands
- *Correspondence: J. A. M. Erven,
| | - C. Çakirlar
- Groningen Institute of Archaeology, University of Groningen, Groningen, Netherlands
| | - D. G. Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - D. C. M. Raemaekers
- Groningen Institute of Archaeology, University of Groningen, Groningen, Netherlands
| | - O. Madsen
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, Netherlands
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26
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Nagraj V, Scholz M, Jessa S, Ge J, Woerner AE, Huang M, Budowle B, Turner SD. vcferr: Development, validation, and application of a single nucleotide polymorphism genotyping error simulation framework. F1000Res 2022; 11:775. [PMID: 38779458 PMCID: PMC11109540 DOI: 10.12688/f1000research.122840.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/29/2022] [Indexed: 05/25/2024] Open
Abstract
Motivation: Genotyping error can impact downstream single nucleotide polymorphism (SNP)-based analyses. Simulating various modes and levels of error can help investigators better understand potential biases caused by miscalled genotypes. Methods: We have developed and validated vcferr, a tool to probabilistically simulate genotyping error and missingness in variant call format (VCF) files. We demonstrate how vcferr could be used to address a research question by introducing varying levels of error of different type into a sample in a simulated pedigree, and assessed how kinship analysis degrades as a function of the kind and type of error. Software availability: vcferr is available for installation via PyPi (https://pypi.org/project/vcferr/) or conda (https://anaconda.org/bioconda/vcferr). The software is released under the MIT license with source code available on GitHub (https://github.com/signaturescience/vcferr).
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Affiliation(s)
- V.P. Nagraj
- Signature Science LLC., Austin, TX, 78759, USA
| | | | | | - Jianye Ge
- Center for Human Identification, Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, Fort Worth, TX, 76107, USA
| | - August E. Woerner
- Center for Human Identification, Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, Fort Worth, TX, 76107, USA
| | - Meng Huang
- Center for Human Identification, Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, Fort Worth, TX, 76107, USA
| | - Bruce Budowle
- Center for Human Identification, Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, Fort Worth, TX, 76107, USA
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27
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Huang Y, Ringbauer H. hapCon: Estimating Contamination of Ancient Genomes by Copying from Reference Haplotypes. Bioinformatics 2022; 38:3768-3777. [PMID: 35695771 PMCID: PMC9344841 DOI: 10.1093/bioinformatics/btac390] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 06/03/2022] [Accepted: 06/09/2022] [Indexed: 11/14/2022] Open
Abstract
Motivation Human ancient DNA (aDNA) studies have surged in recent years, revolutionizing the study of the human past. Typically, aDNA is preserved poorly, making such data prone to contamination from other human DNA. Therefore, it is important to rule out substantial contamination before proceeding to downstream analysis. As most aDNA samples can only be sequenced to low coverages (<1× average depth), computational methods that can robustly estimate contamination in the low coverage regime are needed. However, the ultra low-coverage regime (0.1× and below) remains a challenging task for existing approaches. Results We present a new method to estimate contamination in aDNA for male modern humans. It utilizes a Li&Stephens haplotype copying model for haploid X chromosomes, with mismatches modeled as errors or contamination. We assessed this new approach, hapCon, on simulated and down-sampled empirical aDNA data. Our experiments demonstrate that hapCon outperforms a commonly used tool for estimating male X contamination (ANGSD), with substantially lower variance and narrower confidence intervals, especially in the low coverage regime. We found that hapCon provides useful contamination estimates for coverages as low as 0.1× for SNP capture data (1240k) and 0.02× for whole genome sequencing data, substantially extending the coverage limit of previous male X chromosome-based contamination estimation methods. Our experiments demonstrate that hapCon has little bias for contamination up to 25–30% as long as the contaminating source is specified within continental genetic variation, and that its application range extends to human aDNA as old as ∼45 000 and various global ancestries. Availability and implementation We make hapCon available as part of a python package (hapROH), which is available at the Python Package Index (https://pypi.org/project/hapROH) and can be installed via pip. The documentation provides example use cases as blueprints for custom applications (https://haproh.readthedocs.io/en/latest/hapCon.html). The program can analyze either BAM files or pileup files produced with samtools. An implementation of our software (hapCon) using Python and C is deposited at https://github.com/hyl317/hapROH. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yilei Huang
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany
| | - Harald Ringbauer
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany
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28
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Ausmees K, Sanchez-Quinto F, Jakobsson M, Nettelblad C. An empirical evaluation of genotype imputation of ancient DNA. G3 (BETHESDA, MD.) 2022; 12:6575448. [PMID: 35482488 PMCID: PMC9157144 DOI: 10.1093/g3journal/jkac089] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/05/2022] [Indexed: 12/12/2022]
Abstract
With capabilities of sequencing ancient DNA to high coverage often limited by sample quality or cost, imputation of missing genotypes presents a possibility to increase the power of inference as well as cost-effectiveness for the analysis of ancient data. However, the high degree of uncertainty often associated with ancient DNA poses several methodological challenges, and performance of imputation methods in this context has not been fully explored. To gain further insights, we performed a systematic evaluation of imputation of ancient data using Beagle v4.0 and reference data from phase 3 of the 1000 Genomes project, investigating the effects of coverage, phased reference, and study sample size. Making use of five ancient individuals with high-coverage data available, we evaluated imputed data for accuracy, reference bias, and genetic affinities as captured by principal component analysis. We obtained genotype concordance levels of over 99% for data with 1× coverage, and similar levels of accuracy and reference bias at levels as low as 0.75×. Our findings suggest that using imputed data can be a realistic option for various population genetic analyses even for data in coverage ranges below 1×. We also show that a large and varied phased reference panel as well as the inclusion of low- to moderate-coverage ancient individuals in the study sample can increase imputation performance, particularly for rare alleles. In-depth analysis of imputed data with respect to genetic variants and allele frequencies gave further insight into the nature of errors arising during imputation, and can provide practical guidelines for postprocessing and validation prior to downstream analysis.
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Affiliation(s)
- Kristiina Ausmees
- Department of Information Technology, Uppsala University, Uppsala 751 05, Sweden
| | - Federico Sanchez-Quinto
- Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City 14610, Mexico.,Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala 752 36, Sweden
| | - Mattias Jakobsson
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala 752 36, Sweden
| | - Carl Nettelblad
- Department of Information Technology, Uppsala University, Uppsala 751 05, Sweden
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29
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Marcos S, Parejo M, Estonba A, Alberdi A. Recovering High-Quality Host Genomes from Gut Metagenomic Data through Genotype Imputation. ADVANCED GENETICS (HOBOKEN, N.J.) 2022; 3:2100065. [PMID: 36620197 PMCID: PMC9744478 DOI: 10.1002/ggn2.202100065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 03/05/2022] [Indexed: 01/11/2023]
Abstract
Metagenomic datasets of host-associated microbial communities often contain host DNA that is usually discarded because the amount of data is too low for accurate host genetic analyses. However, genotype imputation can be employed to reconstruct host genotypes if a reference panel is available. Here, the performance of a two-step strategy is tested to impute genotypes from four types of reference panels built using different strategies to low-depth host genome data (≈2× coverage) recovered from intestinal samples of two chicken genetic lines. First, imputation accuracy is evaluated in 12 samples for which both low- and high-depth sequencing data are available, obtaining high imputation accuracies for all tested panels (>0.90). Second, the impact of reference panel choice in population genetics statistics on 100 chickens is assessed, all four panels yielding comparable results. In light of the observations, the feasibility and application of the applied imputation strategy are discussed for different species with regard to the host DNA proportion, genomic diversity, and availability of a reference panel. This method enables leveraging insofar discarded host DNA to get insights into the genetic structure of host populations, and in doing so, facilitates the implementation of hologenomic approaches that jointly analyze host and microbial genomic data.
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Affiliation(s)
- Sofia Marcos
- Applied Genomics and BioinformaticsUniversity of the Basque Country (UPV/EHU)LeioaBilbao48940Spain
| | - Melanie Parejo
- Applied Genomics and BioinformaticsUniversity of the Basque Country (UPV/EHU)LeioaBilbao48940Spain
| | - Andone Estonba
- Applied Genomics and BioinformaticsUniversity of the Basque Country (UPV/EHU)LeioaBilbao48940Spain
| | - Antton Alberdi
- Center for Evolutionary HologenomicsGLOBE InstituteUniversity of CopenhagenCopenhagen1353Denmark
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30
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Marciniak S, Bergey CM, Silva AM, Hałuszko A, Furmanek M, Veselka B, Velemínský P, Vercellotti G, Wahl J, Zariņa G, Longhi C, Kolář J, Garrido-Pena R, Flores-Fernández R, Herrero-Corral AM, Simalcsik A, Müller W, Sheridan A, Miliauskienė Ž, Jankauskas R, Moiseyev V, Köhler K, Király Á, Gamarra B, Cheronet O, Szeverényi V, Kiss V, Szeniczey T, Kiss K, Zoffmann ZK, Koós J, Hellebrandt M, Maier RM, Domboróczki L, Virag C, Novak M, Reich D, Hajdu T, von Cramon-Taubadel N, Pinhasi R, Perry GH. An integrative skeletal and paleogenomic analysis of stature variation suggests relatively reduced health for early European farmers. Proc Natl Acad Sci U S A 2022; 119:e2106743119. [PMID: 35389750 PMCID: PMC9169634 DOI: 10.1073/pnas.2106743119] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 02/24/2022] [Indexed: 12/02/2022] Open
Abstract
Human culture, biology, and health were shaped dramatically by the onset of agriculture ∼12,000 y B.P. This shift is hypothesized to have resulted in increased individual fitness and population growth as evidenced by archaeological and population genomic data alongside a decline in physiological health as inferred from skeletal remains. Here, we consider osteological and ancient DNA data from the same prehistoric individuals to study human stature variation as a proxy for health across a transition to agriculture. Specifically, we compared “predicted” genetic contributions to height from paleogenomic data and “achieved” adult osteological height estimated from long bone measurements for 167 individuals across Europe spanning the Upper Paleolithic to Iron Age (∼38,000 to 2,400 B.P.). We found that individuals from the Neolithic were shorter than expected (given their individual polygenic height scores) by an average of −3.82 cm relative to individuals from the Upper Paleolithic and Mesolithic (P = 0.040) and −2.21 cm shorter relative to post-Neolithic individuals (P = 0.068), with osteological vs. expected stature steadily increasing across the Copper (+1.95 cm relative to the Neolithic), Bronze (+2.70 cm), and Iron (+3.27 cm) Ages. These results were attenuated when we additionally accounted for genome-wide genetic ancestry variation: for example, with Neolithic individuals −2.82 cm shorter than expected on average relative to pre-Neolithic individuals (P = 0.120). We also incorporated observations of paleopathological indicators of nonspecific stress that can persist from childhood to adulthood in skeletal remains into our model. Overall, our work highlights the potential of integrating disparate datasets to explore proxies of health in prehistory.
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Affiliation(s)
- Stephanie Marciniak
- Department of Anthropology, Pennsylvania State University, University Park, PA 16802
| | - Christina M. Bergey
- Department of Anthropology, Pennsylvania State University, University Park, PA 16802
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08854
| | - Ana Maria Silva
- Research Centre for Anthropology and Health (Centro de Investigação em Antropologia e Saúde - CIAS), Department of Life Sciences, University of Coimbra, Coimbra 3000-456, Portugal
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Coimbra 3000-456, Portugal
- Archeology Center of the University of Lisbon (UNIARQ), University of Lisbon, Lisbon 1600-214, Portugal
| | - Agata Hałuszko
- Institute of Archaeology, University of Wrocław, Wrocław 50-139, Poland
- Archeolodzy.org Foundation, Wrocław 50-316, Poland
| | - Mirosław Furmanek
- Institute of Archaeology, University of Wrocław, Wrocław 50-139, Poland
| | - Barbara Veselka
- Department of Chemistry, Analytical Environmental and Geo-Chemistry Research Unit, Vrije Univeristeit Brussels, Brussels 1050, Belgium
- Department of Art Studies and Archaeology, Maritime Cultures Research Institute, Vrije Univeristeit Brussels, Brussels 1050, Belgium
| | - Petr Velemínský
- Department of Anthropology, National Museum, Prague 115-79, Czech Republic
| | - Giuseppe Vercellotti
- Department of Anthropology, Ohio State University, Columbus, OH 43210
- Institute for Research and Learning in Archaeology and Bioarchaeology, Columbus, OH 43215
| | - Joachim Wahl
- Institute for Scientific Archaeology, Working Group Palaeoanthropology, University of Tübingen, Tübingen 72074, Germany
| | - Gunita Zariņa
- Institute of Latvian History, University of Latvia, Riga 1050, Latvia
| | - Cristina Longhi
- Soprintendenza Archeologia, Belle Arti e Paesaggio, Rome 00186, Italy
| | - Jan Kolář
- Department of Vegetation Ecology, Institute of Botany of the Czech Academy of Sciences, Průhonice 252-43, Czech Republic
- Institute of Archaeology and Museology, Masaryk University, Brno 602-00, Czech Republic
| | - Rafael Garrido-Pena
- Department of Prehistory and Archaeology, Universidad Autónoma de Madrid, Madrid 28049, Spain
| | | | | | - Angela Simalcsik
- Olga Necrasov Center for Anthropological Research, Romanian Academy - Iasi Branch, Iasi 700481, Romania
- Orheiul Vechi Cultural-Natural Reserve, Orhei 3506, Republic of Moldova
| | - Werner Müller
- Laboratoire d'archéozoologie, Université de Neuchâtel, Neuchâtel 2000, Switzerland
| | - Alison Sheridan
- Department of Scottish History & Archaeology, National Museums Scotland, Edinburgh EH1 1JF, Scotland
| | - Žydrūnė Miliauskienė
- Department of Anatomy, Histology and Anthropology, Vilnius University, Vilnius 01513, Lithuania
| | - Rimantas Jankauskas
- Department of Anatomy, Histology and Anthropology, Vilnius University, Vilnius 01513, Lithuania
| | - Vyacheslav Moiseyev
- Department of Physical Anthropology, Peter the Great Museum of Anthropology and Ethnography (Kunstkamera), Russian Academy of Sciences, St. Petersburg 199034, Russia
| | - Kitti Köhler
- Institute of Archaeology, Research Centre for the Humanities, Eötvös Loránd Research Network, Budapest 1097, Hungary
| | - Ágnes Király
- Institute of Archaeology, Research Centre for the Humanities, Eötvös Loránd Research Network, Budapest 1097, Hungary
| | - Beatriz Gamarra
- Institut Català de Paleoecologia Humana i Evolució Social, Tarragona 43007, Spain
- Departament d’Història i Història de l’Art, Universitat Rovira i Virgili, Tarragona 43003, Spain
| | - Olivia Cheronet
- Department of Evolutionary Anthropology, University of Vienna, Vienna 1030, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna 1030, Austria
| | - Vajk Szeverényi
- Institute of Archaeology, Research Centre for the Humanities, Eötvös Loránd Research Network, Budapest 1097, Hungary
- Department of Archaeology, Déri Múzeum, Debrecen 4026, Hungary
| | - Viktória Kiss
- Institute of Archaeology, Research Centre for the Humanities, Eötvös Loránd Research Network, Budapest 1097, Hungary
| | - Tamás Szeniczey
- Department of Biological Anthropology, Eötvös Loránd University, Budapest 1053, Hungary
| | - Krisztián Kiss
- Department of Biological Anthropology, Eötvös Loránd University, Budapest 1053, Hungary
- Department of Anthropology, Hungarian Natural History Museum, Budapest 1083, Hungary
| | | | - Judit Koós
- Department of Archaeology, Herman Ottó Museum, Miskolc 3530, Hungary
| | | | - Robert M. Maier
- Department of Genetics, Harvard Medical School, Boston, MA 02115
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138
| | - László Domboróczki
- Department of Archaeology, István Dobó Castle Museum, Eger 3300, Hungary
| | - Cristian Virag
- Department of Archaeology, Satu Mare County Museum, Satu Mare 440031, Romania
| | - Mario Novak
- Centre for Applied Bioanthropology, Institute for Anthropological Research, Zagreb 10000, Croatia
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA 02115
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138
- The Max Planck–Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, Boston, MA 02115
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142
- HHMI, Harvard Medical School, Cambridge, MA 02138
| | - Tamás Hajdu
- Department of Biological Anthropology, Eötvös Loránd University, Budapest 1053, Hungary
| | - Noreen von Cramon-Taubadel
- Buffalo Human Evolutionary Morphology Lab, Department of Anthropology, University at Buffalo, Buffalo, NY 14261-0026
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, Vienna 1030, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna 1030, Austria
| | - George H. Perry
- Department of Anthropology, Pennsylvania State University, University Park, PA 16802
- Department of Biology, Pennsylvania State University, University Park, PA 16802
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802
- Deutsche Forschungsgemeinschaft (DFG) Center for Advanced Studies, University of Tübingen, Tübingen 72074, Germany
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Abstract
SignificanceCalifornia supports a high cultural and linguistic diversity of Indigenous peoples. In a partnership of researchers with the Muwekma Ohlone tribe, we studied genomes of eight present-day tribal members and 12 ancient individuals from two archaeological sites in the San Francisco Bay Area, spanning ∼2,000 y. We find that compared to genomes of Indigenous individuals from throughout the Americas, the 12 ancient individuals are most genetically similar to ancient individuals from Southern California, and that despite spanning a large time period, they share distinctive ancestry. This ancestry is also shared with present-day tribal members, providing evidence of genetic continuity between past and present Indigenous individuals in the region, in contrast to some popular reconstructions based on archaeological and linguistic information.
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Schneider M, Shrestha A, Ballvora A, Léon J. High-throughput estimation of allele frequencies using combined pooled-population sequencing and haplotype-based data processing. PLANT METHODS 2022; 18:34. [PMID: 35313910 PMCID: PMC8935755 DOI: 10.1186/s13007-022-00852-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 02/07/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND In addition to heterogeneity and artificial selection, natural selection is one of the forces used to combat climate change and improve agrobiodiversity in evolutionary plant breeding. Accurate identification of the specific genomic effects of natural selection will likely accelerate transfer between populations. Thus, insights into changes in allele frequency, adequate population size, gene flow and drift are essential. However, observing such effects often involves a trade-off between costs and resolution when a large sample of genotypes for many loci is analysed. Pool genotyping approaches achieve high resolution and precision in estimating allele frequency when sequence coverage is high. Nevertheless, high-coverage pool sequencing of large genomes is expensive. RESULTS Three pool samples (n = 300, 300, 288) from a barley backcross population were generated to assess the population's allele frequency. The tested population (BC2F21) has undergone 18 generations of natural adaption to conventional farming practice. The accuracies of estimated pool-based allele frequencies and genome coverage yields were compared using three next-generation sequencing genotyping methods. To achieve accurate allele frequency estimates with low sequence coverage, we employed a haplotyping approach. Low coverage allele frequencies of closely located single polymorphisms were aggregated into a single haplotype allele frequency, yielding 2-to-271-times higher depth and increased precision. When we combined different haplotyping tactics, we found that gene and chip marker-based haplotype analyses performed equivalently or better compared with simple contig haplotype windows. Comparing multiple pool samples and referencing against an individual sequencing approach revealed that whole-genome pool re-sequencing (WGS) achieved the highest correlation with individual genotyping (≥ 0.97). In contrast, transcriptome-based genotyping (MACE) and genotyping by sequencing (GBS) pool replicates were significantly associated with higher error rates and lower correlations, but are still valuable to detect large allele frequency variations. CONCLUSIONS The proposed strategy identified the allele frequency of populations with high accuracy at low cost. This is particularly relevant to evolutionary plant breeding of crops with very large genomes, such as barley. Whole-genome low coverage re-sequencing at 0.03 × coverage per genotype accurately estimated the allele frequency when a loci-based haplotyping approach was applied. The implementation of annotated haplotypes capitalises on the biological background and statistical robustness.
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Affiliation(s)
- Michael Schneider
- Institute of Crop Science and Resource Conservation, University of Bonn, Plant Breeding, Katzenburgweg 5, 53115, Bonn, Germany
- Institute for Quantitative Genetics and Genomics of Plants, University Duesseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Asis Shrestha
- Institute of Crop Science and Resource Conservation, University of Bonn, Plant Breeding, Katzenburgweg 5, 53115, Bonn, Germany
- Institute for Quantitative Genetics and Genomics of Plants, University Duesseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Agim Ballvora
- Institute of Crop Science and Resource Conservation, University of Bonn, Plant Breeding, Katzenburgweg 5, 53115, Bonn, Germany
| | - Jens Léon
- Institute of Crop Science and Resource Conservation, University of Bonn, Plant Breeding, Katzenburgweg 5, 53115, Bonn, Germany.
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33
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Wohns AW, Wong Y, Jeffery B, Akbari A, Mallick S, Pinhasi R, Patterson N, Reich D, Kelleher J, McVean G. A unified genealogy of modern and ancient genomes. Science 2022; 375:eabi8264. [PMID: 35201891 PMCID: PMC10027547 DOI: 10.1126/science.abi8264] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The sequencing of modern and ancient genomes from around the world has revolutionized our understanding of human history and evolution. However, the problem of how best to characterize ancestral relationships from the totality of human genomic variation remains unsolved. Here, we address this challenge with nonparametric methods that enable us to infer a unified genealogy of modern and ancient humans. This compact representation of multiple datasets explores the challenges of missing and erroneous data and uses ancient samples to constrain and date relationships. We demonstrate the power of the method to recover relationships between individuals and populations as well as to identify descendants of ancient samples. Finally, we introduce a simple nonparametric estimator of the geographical location of ancestors that recapitulates key events in human history.
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Affiliation(s)
- Anthony Wilder Wohns
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford; Oxford OX3 7LF, UK
| | - Yan Wong
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford; Oxford OX3 7LF, UK
| | - Ben Jeffery
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford; Oxford OX3 7LF, UK
| | - Ali Akbari
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- Department of Human Evolutionary Biology, Harvard University; Cambridge, MA 02138, USA
- Department of Genetics, Harvard Medical School; Boston, MA 02115, USA
| | - Swapan Mallick
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- Howard Hughes Medical Institute; Boston, MA 02115, USA
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna; 1090 Vienna, Austria
| | - Nick Patterson
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- Department of Human Evolutionary Biology, Harvard University; Cambridge, MA 02138, USA
- Howard Hughes Medical Institute; Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School; Boston, MA 02115, USA
| | - David Reich
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- Department of Human Evolutionary Biology, Harvard University; Cambridge, MA 02138, USA
- Howard Hughes Medical Institute; Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School; Boston, MA 02115, USA
| | - Jerome Kelleher
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford; Oxford OX3 7LF, UK
| | - Gil McVean
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford; Oxford OX3 7LF, UK
- Corresponding author.
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34
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Rogalla-Ładniak U. The overview of forensic genetic genealogy. ARCHIVES OF FORENSIC MEDICINE AND CRIMINOLOGY 2022; 72:211-222. [PMID: 37405841 DOI: 10.4467/16891716amsik.22.023.17623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/06/2023] Open
Abstract
Forensic genetic genealogy (FGG) benefits largely from popularity of genealogical research within (mostly) American society and the advent of new sequencing techniques that allow typing of challenging forensic samples. It is considered a true breakthrough for both active and especially cold cases where all other resources and methods have failed during investigation. Despite media coverage generally highlighting its powers, the method itself is considered very laborious and the investigation may easily got suspended at every stage due to many factors including no hits in the database or breaks in traceable lineages within the family tree. This review summarizes the scope of FGG use, mentions most concerns and misconceptions associated with the technique and points to the plausible solutions already suggested. It also brings together current guidelines and regulations intended to be followed by law enforcement authorities wishing to utilize genetic genealogy research.
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Affiliation(s)
- Urszula Rogalla-Ładniak
- Faculty of Medicine, Ludwik Rydygier Collegium Medicum in Bydgoszcz; Nicolaus Copernicus University in Toruń, Poland
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35
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Zhao C, Teng J, Zhang X, Wang D, Zhang X, Li S, Jiang X, Li H, Ning C, Zhang Q. Towards a Cost-Effective Implementation of Genomic Prediction Based on Low Coverage Whole Genome Sequencing in Dezhou Donkey. Front Genet 2021; 12:728764. [PMID: 34804115 PMCID: PMC8595392 DOI: 10.3389/fgene.2021.728764] [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: 06/22/2021] [Accepted: 09/20/2021] [Indexed: 11/25/2022] Open
Abstract
Low-coverage whole genome sequencing is a low-cost genotyping technology. Combined with genotype imputation approaches, it is likely to become a critical component of cost-effective genomic selection programs in agricultural livestock. Here, we used the low-coverage sequence data of 617 Dezhou donkeys to investigate the performance of genotype imputation for low-coverage whole genome sequence data and genomic prediction based on the imputed genotype data. The specific aims were as follows: 1) to measure the accuracy of genotype imputation under different sequencing depths, sample sizes, minor allele frequency (MAF), and imputation pipelines and 2) to assess the accuracy of genomic prediction under different marker densities derived from the imputed sequence data, different strategies for constructing the genomic relationship matrixes, and single-vs. multi-trait models. We found that a high imputation accuracy (>0.95) can be achieved for sequence data with a sequencing depth as low as 1x and the number of sequenced individuals ≥400. For genomic prediction, the best performance was obtained by using a marker density of 410K and a G matrix constructed using expected marker dosages. Multi-trait genomic best linear unbiased prediction (GBLUP) performed better than single-trait GBLUP. Our study demonstrates that low-coverage whole genome sequencing would be a cost-effective approach for genomic prediction in Dezhou donkey.
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Affiliation(s)
- Changheng Zhao
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an, China
| | - Jun Teng
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an, China
| | - Xinhao Zhang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an, China.,National Engineering Research Center for Gelatin-based TCM, Dong-E E-Jiao Co., Ltd., Dong'e County, China
| | - Dan Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an, China
| | - Xinyi Zhang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an, China
| | - Shiyin Li
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an, China
| | - Xin Jiang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an, China
| | - Haijing Li
- National Engineering Research Center for Gelatin-based TCM, Dong-E E-Jiao Co., Ltd., Dong'e County, China
| | - Chao Ning
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an, China
| | - Qin Zhang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an, China
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36
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Cox SL, Moots HM, Stock JT, Shbat A, Bitarello BD, Nicklisch N, Alt KW, Haak W, Rosenstock E, Ruff CB, Mathieson I. Predicting skeletal stature using ancient
DNA. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2021. [PMCID: PMC9298243 DOI: 10.1002/ajpa.24426] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Samantha L. Cox
- Department of Genetics, Perelman School of Medicine University of Pennsylvania Philadelphia Pennsylvania USA
- Physical Anthropology Section, Penn Museum University of Pennsylvania Philadelphia Pennsylvania USA
| | - Hannah M. Moots
- Department of Anthropology Stanford University Stanford California USA
| | - Jay T. Stock
- Department of Anthropology Western University London Ontario Canada
- Department of Archaeology Max Planck Institute for the Science of Human History Jena Germany
| | - Andrej Shbat
- Institute of Anatomy, First Faculty of Medicine Charles University Prague Czech Republic
| | - Bárbara D. Bitarello
- Department of Genetics, Perelman School of Medicine University of Pennsylvania Philadelphia Pennsylvania USA
| | - Nicole Nicklisch
- Center of Natural and Cultural Human History Danube Private University Krems Austria
| | - Kurt W. Alt
- Center of Natural and Cultural Human History Danube Private University Krems Austria
| | - Wolfgang Haak
- Department of Archaeogenetics Max Planck Institute for the Science of Human History Jena Germany
| | - Eva Rosenstock
- Bonn Center for ArchaeoSciences Institut für Archäologie und Kulturanthropologie, Universität Bonn Bonn Germany
| | - Christopher B. Ruff
- Center for Functional Anatomy and Evolution Johns Hopkins University School of Medicine Baltimore Maryland USA
| | - Iain Mathieson
- Department of Genetics, Perelman School of Medicine University of Pennsylvania Philadelphia Pennsylvania USA
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37
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Parental relatedness through time revealed by runs of homozygosity in ancient DNA. Nat Commun 2021; 12:5425. [PMID: 34521843 PMCID: PMC8440622 DOI: 10.1038/s41467-021-25289-w] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 07/21/2021] [Indexed: 02/08/2023] Open
Abstract
Parental relatedness of present-day humans varies substantially across the globe, but little is known about the past. Here we analyze ancient DNA, leveraging that parental relatedness leaves genomic traces in the form of runs of homozygosity. We present an approach to identify such runs in low-coverage ancient DNA data aided by haplotype information from a modern phased reference panel. Simulation and experiments show that this method robustly detects runs of homozygosity longer than 4 centimorgan for ancient individuals with at least 0.3 × coverage. Analyzing genomic data from 1,785 ancient humans who lived in the last 45,000 years, we detect low rates of first cousin or closer unions across most ancient populations. Moreover, we find a marked decay in background parental relatedness co-occurring with or shortly after the advent of sedentary agriculture. We observe this signal, likely linked to increasing local population sizes, across several geographic transects worldwide.
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38
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Kivisild T, Saag L, Hui R, Biagini SA, Pankratov V, D'Atanasio E, Pagani L, Saag L, Rootsi S, Mägi R, Metspalu E, Valk H, Malve M, Irdt K, Reisberg T, Solnik A, Scheib CL, Seidman DN, Williams AL, Tambets K, Metspalu M. Patterns of genetic connectedness between modern and medieval Estonian genomes reveal the origins of a major ancestry component of the Finnish population. Am J Hum Genet 2021; 108:1792-1806. [PMID: 34411538 DOI: 10.1016/j.ajhg.2021.07.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 07/23/2021] [Indexed: 11/20/2022] Open
Abstract
The Finnish population is a unique example of a genetic isolate affected by a recent founder event. Previous studies have suggested that the ancestors of Finnic-speaking Finns and Estonians reached the circum-Baltic region by the 1st millennium BC. However, high linguistic similarity points to a more recent split of their languages. To study genetic connectedness between Finns and Estonians directly, we first assessed the efficacy of imputation of low-coverage ancient genomes by sequencing a medieval Estonian genome to high depth (23×) and evaluated the performance of its down-sampled replicas. We find that ancient genomes imputed from >0.1× coverage can be reliably used in principal-component analyses without projection. By searching for long shared allele intervals (LSAIs; similar to identity-by-descent segments) in unphased data for >143,000 present-day Estonians, 99 Finns, and 14 imputed ancient genomes from Estonia, we find unexpectedly high levels of individual connectedness between Estonians and Finns for the last eight centuries in contrast to their clear differentiation by allele frequencies. High levels of sharing of these segments between Estonians and Finns predate the demographic expansion and late settlement process of Finland. One plausible source of this extensive sharing is the 8th-10th centuries AD migration event from North Estonia to Finland that has been proposed to explain uniquely shared linguistic features between the Finnish language and the northern dialect of Estonian and shared Christianity-related loanwords from Slavic. These results suggest that LSAI detection provides a computationally tractable way to detect fine-scale structure in large cohorts.
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Affiliation(s)
- Toomas Kivisild
- Department of Human Genetics, KU Leuven, Leuven 3000, Belgium; Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia; McDonald Institute for Archaeological Research, University of Cambridge, Cambridge CB2 3ER, UK.
| | - Lehti Saag
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia; Research Department of Genetics, Evolution, and Environment, University College London, London WC1E 6BT, UK
| | - Ruoyun Hui
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge CB2 3ER, UK; The Alan Turing Institute, British Library, 96 Euston Road, London NW1 2DB, UK
| | | | - Vasili Pankratov
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Eugenia D'Atanasio
- Instituto di Biologia e Patologia Molecolari, Consiglio Nazionale delle Ricerche, Rome, Italy
| | - Luca Pagani
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia; Department of Biology, University of Padova, 35131 Padova, Italy
| | - Lauri Saag
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Siiri Rootsi
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Reedik Mägi
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Ene Metspalu
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Heiki Valk
- Department of Archaeology, Institute of History and Archaeology, University of Tartu, Tartu 51014, Estonia
| | - Martin Malve
- Department of Archaeology, Institute of History and Archaeology, University of Tartu, Tartu 51014, Estonia
| | - Kadri Irdt
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Tuuli Reisberg
- Core Facility, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Anu Solnik
- Core Facility, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Christiana L Scheib
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia; McDonald Institute for Archaeological Research, University of Cambridge, Cambridge CB2 3ER, UK; St John's College, University of Cambridge, Cambridge CB2 1TP, UK
| | - Daniel N Seidman
- Department of Computational Biology, Cornell University, Ithaca, NY 14853, USA
| | - Amy L Williams
- Department of Computational Biology, Cornell University, Ithaca, NY 14853, USA
| | - Kristiina Tambets
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Mait Metspalu
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
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39
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Kim S, Shin JY, Kwon NJ, Kim CU, Kim C, Lee CS, Seo JS. Evaluation of low-pass genome sequencing in polygenic risk score calculation for Parkinson's disease. Hum Genomics 2021; 15:58. [PMID: 34454617 PMCID: PMC8403377 DOI: 10.1186/s40246-021-00357-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 08/22/2021] [Indexed: 12/02/2022] Open
Abstract
Background Low-pass sequencing (LPS) has been extensively investigated for applicability to various genetic studies due to its advantages over genotype array data including cost-effectiveness. Predicting the risk of complex diseases such as Parkinson’s disease (PD) using polygenic risk score (PRS) based on the genetic variations has shown decent prediction accuracy. Although ultra-LPS has been shown to be effective in PRS calculation, array data has been favored to the majority of PRS analysis, especially for PD.
Results Using eight high-coverage WGS, we assessed imputation approaches for downsampled LPS data ranging from 0.5 × to 7.0 × . We demonstrated that uncertain genotype calls of LPS diminished imputation accuracy, and an imputation approach using genotype likelihoods was plausible for LPS. Additionally, comparing imputation accuracies between LPS and simulated array illustrated that LPS had higher accuracies particularly at rare frequencies. To evaluate ultra-low coverage data in PRS calculation for PD, we prepared low-coverage WGS and genotype array of 87 PD cases and 101 controls. Genotype imputation of array and downsampled LPS were conducted using a population-specific reference panel, and we calculated risk scores based on the PD-associated SNPs from an East Asian meta-GWAS. The PRS models discriminated cases and controls as previously reported when both LPS and genotype array were used. Also strong correlations in PRS models for PD between LPS and genotype array were discovered. Conclusions Overall, this study highlights the potentials of LPS under 1.0 × followed by genotype imputation in PRS calculation and suggests LPS as attractive alternatives to genotype array in the area of precision medicine for PD. Supplementary Information The online version contains supplementary material available at 10.1186/s40246-021-00357-w.
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Affiliation(s)
- Sungjae Kim
- Precision Medicine Institute, Seoul, 08511, Republic of Korea.,Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, 03080, Republic of Korea
| | - Jong-Yeon Shin
- Precision Medicine Institute, Seoul, 08511, Republic of Korea
| | - Nak-Jung Kwon
- Precision Medicine Institute, Seoul, 08511, Republic of Korea
| | | | - Changhoon Kim
- Precision Medicine Institute, Seoul, 08511, Republic of Korea
| | - Chong Sik Lee
- Department of Neurology, Asan Medical Center, University of Ulsan College of Medicine, 88 Olympic-ro 43-gil, Pungnap 2(i)-dong, Songpa-gu, Seoul, 05505, Republic of Korea.
| | - Jeong-Sun Seo
- Precision Medicine Institute, Seoul, 08511, Republic of Korea. .,Asian Genome Institute, Seoul National University Bundang Hospital, 172 Dolma-ro, Seongnam, Bundang-gu, Gyeonggi-do, 13605, Republic of Korea.
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40
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Speidel L, Cassidy L, Davies RW, Hellenthal G, Skoglund P, Myers SR. Inferring Population Histories for Ancient Genomes Using Genome-Wide Genealogies. Mol Biol Evol 2021; 38:3497-3511. [PMID: 34129037 PMCID: PMC8383901 DOI: 10.1093/molbev/msab174] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Ancient genomes anchor genealogies in directly observed historical genetic variation and contextualize ancestral lineages with archaeological insights into their geography and cultural associations. However, the majority of ancient genomes are of lower coverage and cannot be directly built into genealogies. Here, we present a fast and scalable method, Colate, the first approach for inferring ancestral relationships through time between low-coverage genomes without requiring phasing or imputation. Our approach leverages sharing patterns of mutations dated using a genealogy to infer coalescence rates. For deeply sequenced ancient genomes, we additionally introduce an extension of the Relate algorithm for joint inference of genealogies incorporating such genomes. Application to 278 present-day and 430 ancient DNA samples of >0.5x mean coverage allows us to identify dynamic population structure and directional gene flow between early farmer and European hunter-gatherer groups. We further show that the previously reported, but still unexplained, increase in the TCC/TTC mutation rate, which is strongest in West Eurasia today, was already present at similar strength and widespread in the Late Glacial Period ~10k-15k years ago, but is not observed in samples >30k years old. It is strongest in Neolithic farmers, and highly correlated with recent coalescence rates between other genomes and a 10,000-year-old Anatolian hunter-gatherer. This suggests gene-flow among ancient peoples postdating the last glacial maximum as widespread and localizes the driver of this mutational signal in both time and geography in that region. Our approach should be widely applicable in future for addressing other evolutionary questions, and in other species.
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Affiliation(s)
- Leo Speidel
- Francis Crick Institute, London, United Kingdom
- Genetics Institute, University College London, London, United Kingdom
| | - Lara Cassidy
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Republic of Ireland
| | - Robert W Davies
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | | | | | - Simon R Myers
- Department of Statistics, University of Oxford, Oxford, United Kingdom
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
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41
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Irving-Pease EK, Muktupavela R, Dannemann M, Racimo F. Quantitative Human Paleogenetics: What can Ancient DNA Tell us About Complex Trait Evolution? Front Genet 2021; 12:703541. [PMID: 34422004 PMCID: PMC8371751 DOI: 10.3389/fgene.2021.703541] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/08/2021] [Indexed: 12/13/2022] Open
Abstract
Genetic association data from national biobanks and large-scale association studies have provided new prospects for understanding the genetic evolution of complex traits and diseases in humans. In turn, genomes from ancient human archaeological remains are now easier than ever to obtain, and provide a direct window into changes in frequencies of trait-associated alleles in the past. This has generated a new wave of studies aiming to analyse the genetic component of traits in historic and prehistoric times using ancient DNA, and to determine whether any such traits were subject to natural selection. In humans, however, issues about the portability and robustness of complex trait inference across different populations are particularly concerning when predictions are extended to individuals that died thousands of years ago, and for which little, if any, phenotypic validation is possible. In this review, we discuss the advantages of incorporating ancient genomes into studies of trait-associated variants, the need for models that can better accommodate ancient genomes into quantitative genetic frameworks, and the existing limits to inferences about complex trait evolution, particularly with respect to past populations.
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Affiliation(s)
- Evan K. Irving-Pease
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Rasa Muktupavela
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Michael Dannemann
- Center for Genomics, Evolution and Medicine, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Fernando Racimo
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
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42
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Yair S, Lee KM, Coop G. The timing of human adaptation from Neanderthal introgression. Genetics 2021; 218:iyab052. [PMID: 33787889 PMCID: PMC8128397 DOI: 10.1093/genetics/iyab052] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 02/26/2021] [Indexed: 12/26/2022] Open
Abstract
Admixture has the potential to facilitate adaptation by providing alleles that are immediately adaptive in a new environment or by simply increasing the long-term reservoir of genetic diversity for future adaptation. A growing number of cases of adaptive introgression are being identified in species across the tree of life, however the timing of selection, and therefore the importance of the different evolutionary roles of admixture, is typically unknown. Here, we investigate the spatio-temporal history of selection favoring Neanderthal-introgressed alleles in modern human populations. Using both ancient and present-day samples of modern humans, we integrate the known demographic history of populations, namely population divergence and migration, with tests for selection. We model how a sweep placed along different branches of an admixture graph acts to modify the variance and covariance in neutral allele frequencies among populations at linked loci. Using a method based on this model of allele frequencies, we study previously identified cases of adaptive Neanderthal introgression. From these, we identify cases in which Neanderthal-introgressed alleles were quickly beneficial and other cases in which they persisted at low frequency for some time. For some of the alleles that persisted at low frequency, we show that selection likely independently favored them later on in geographically separated populations. Our work highlights how admixture with ancient hominins has contributed to modern human adaptation and contextualizes observed levels of Neanderthal ancestry in present-day and ancient samples.
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Affiliation(s)
- Sivan Yair
- Center for Population Biology, University of California, Davis, Davis, CA 95616, USA
- Department of Evolution and Ecology, University of California, Davis, Davis, CA 95616, USA
| | - Kristin M Lee
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Graham Coop
- Center for Population Biology, University of California, Davis, Davis, CA 95616, USA
- Department of Evolution and Ecology, University of California, Davis, Davis, CA 95616, USA
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43
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Saupe T, Montinaro F, Scaggion C, Carrara N, Kivisild T, D'Atanasio E, Hui R, Solnik A, Lebrasseur O, Larson G, Alessandri L, Arienzo I, De Angelis F, Rolfo MF, Skeates R, Silvestri L, Beckett J, Talamo S, Dolfini A, Miari M, Metspalu M, Benazzi S, Capelli C, Pagani L, Scheib CL. Ancient genomes reveal structural shifts after the arrival of Steppe-related ancestry in the Italian Peninsula. Curr Biol 2021; 31:2576-2591.e12. [PMID: 33974848 DOI: 10.1016/j.cub.2021.04.022] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 11/28/2020] [Accepted: 04/09/2021] [Indexed: 12/30/2022]
Abstract
Across Europe, the genetics of the Chalcolithic/Bronze Age transition is increasingly characterized in terms of an influx of Steppe-related ancestry. The effect of this major shift on the genetic structure of populations in the Italian Peninsula remains underexplored. Here, genome-wide shotgun data for 22 individuals from commingled cave and single burials in Northeastern and Central Italy dated between 3200 and 1500 BCE provide the first genomic characterization of Bronze Age individuals (n = 8; 0.001-1.2× coverage) from the central Italian Peninsula, filling a gap in the literature between 1950 and 1500 BCE. Our study confirms a diversity of ancestry components during the Chalcolithic and the arrival of Steppe-related ancestry in the central Italian Peninsula as early as 1600 BCE, with this ancestry component increasing through time. We detect close patrilineal kinship in the burial patterns of Chalcolithic commingled cave burials and a shift away from this in the Bronze Age (2200-900 BCE) along with lowered runs of homozygosity, which may reflect larger changes in population structure. Finally, we find no evidence that the arrival of Steppe-related ancestry in Central Italy directly led to changes in frequency of 115 phenotypes present in the dataset, rather that the post-Roman Imperial period had a stronger influence, particularly on the frequency of variants associated with protection against Hansen's disease (leprosy). Our study provides a closer look at local dynamics of demography and phenotypic shifts as they occurred as part of a broader phenomenon of widespread admixture during the Chalcolithic/Bronze Age transition.
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Affiliation(s)
- Tina Saupe
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, Tartu 51010, Estonia.
| | - Francesco Montinaro
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, Tartu 51010, Estonia; Department of Biology-Genetics, University of Bari, Via E. Orabona, 4, Bari 70124, Italy
| | - Cinzia Scaggion
- Department of Geosciences, University of Padova, Via Gradenigo 6, Padova 35131, Italy
| | - Nicola Carrara
- Museum of Anthropology, University of Padova, Palazzo Cavalli, via Giotto 1, Padova 35121, Italy
| | - Toomas Kivisild
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, Tartu 51010, Estonia; Department of Human Genetics, KU Leuven, Leuven, Herestraat 49 3000, Belgium
| | - Eugenia D'Atanasio
- Institute of Molecular Biology and Pathology, CNR, Piazzale Aldo Moro 5, Rome 00185, Italy
| | - Ruoyun Hui
- McDonald Institute for Archaeological Research, University of Cambridge, Downing Street, Cambridge CB2 3ER, UK
| | - Anu Solnik
- Core Facility, Institute of Genomics, University of Tartu, Riia 23B, Tartu 51010, Estonia
| | - Ophélie Lebrasseur
- Department of Archaeology, Classics and Egyptology, University of Liverpool, 12-14 Abercromby Square, Liverpool L69 7WZ, UK; Palaeogenomics & Bio-Archaeology Research Network, School of Archaeology, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK
| | - Greger Larson
- Istituto Nazionale di Geofisica e Vulcanologia, Osservatorio Vesuviano, Via Diocleziano 328, Naples 80125, Italy
| | - Luca Alessandri
- Groningen Institute of Archaeology, University of Groningen, Poststraat 6, Groningen 9712, the Netherlands
| | - Ilenia Arienzo
- Istituto Nazionale di Geofisica e Vulcanologia, Osservatorio Vesuviano, Via Diocleziano 328, Naples 80125, Italy
| | - Flavio De Angelis
- Centre of Molecular Anthropology for Ancient DNA Studies, Department of Biology, University of Rome "Tor Vergata," Via della Ricerca Scientifica 1, Rome 00133, Italy
| | - Mario Federico Rolfo
- Department of History, Culture and Society, University of Rome "Tor Vergata," Via Columbia 1, Rome 00133, Italy
| | - Robin Skeates
- Department of Archaeology, Durham University, Lower Mountjoy, South Road, Durham DH1 3LE, UK
| | - Letizia Silvestri
- Department of History, Culture and Society, University of Rome "Tor Vergata," Via Columbia 1, Rome 00133, Italy
| | | | - Sahra Talamo
- Department of Chemistry "Giacomo Ciamician," University of Bologna, Via Selmi 2, Bologna 40126, Italy; Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig 04103, Germany
| | - Andrea Dolfini
- School of History, Classics and Archaeology, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Monica Miari
- Superintendency of Archeology, Fine Arts and Landscape for the metropolitan city of Bologna and the provinces of Modena, Reggio Emilia and Ferrara, Comune di Bologna, Sede Via Belle Arti n. 52, Bologna 40126, Italy
| | - Mait Metspalu
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, Tartu 51010, Estonia
| | - Stefano Benazzi
- Department of Cultural Heritage, University of Bologna, Via degli Ariani, 1, Ravenna 40126, Italy
| | - Cristian Capelli
- Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford OX1 3SZ, UK; Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, University of Parma, Parco Area delle Scienze 17/A, Parma 43124, Italy
| | - Luca Pagani
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, Tartu 51010, Estonia; Department of Biology, University of Padova, Via U. Bassi, 58/B, Padova 35122, Italy
| | - Christiana L Scheib
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, Tartu 51010, Estonia; St. John's College, University of Cambridge, St. John's Street, Cambridge CB2 1TP, UK.
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44
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Saag L, Vasilyev SV, Varul L, Kosorukova NV, Gerasimov DV, Oshibkina SV, Griffith SJ, Solnik A, Saag L, D'Atanasio E, Metspalu E, Reidla M, Rootsi S, Kivisild T, Scheib CL, Tambets K, Kriiska A, Metspalu M. Genetic ancestry changes in Stone to Bronze Age transition in the East European plain. SCIENCE ADVANCES 2021; 7:7/4/eabd6535. [PMID: 33523926 PMCID: PMC7817100 DOI: 10.1126/sciadv.abd6535] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 12/01/2020] [Indexed: 05/11/2023]
Abstract
The transition from Stone to Bronze Age in Central and Western Europe was a period of major population movements originating from the Ponto-Caspian Steppe. Here, we report new genome-wide sequence data from 30 individuals north of this area, from the understudied western part of present-day Russia, including 3 Stone Age hunter-gatherers (10,800 to 4250 cal BCE) and 26 Bronze Age farmers from the Corded Ware complex Fatyanovo Culture (2900 to 2050 cal BCE). We show that Eastern hunter-gatherer ancestry was present in northwestern Russia already from around 10,000 BCE. Furthermore, we see a change in ancestry with the arrival of farming-Fatyanovo Culture individuals were genetically similar to other Corded Ware cultures, carrying a mixture of Steppe and European early farmer ancestry. Thus, they likely originate from a fast migration toward the northeast from somewhere near modern-day Ukraine-the closest area where these ancestries coexisted from around 3000 BCE.
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Affiliation(s)
- Lehti Saag
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia.
| | - Sergey V Vasilyev
- Institute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Liivi Varul
- Archaeological Research Collection, School of Humanities, Tallinn University, Tallinn 10130, Estonia
| | - Natalia V Kosorukova
- Cherepovets State University and Cherepovets Museum Association, Cherepovets 162600, Russia
| | - Dmitri V Gerasimov
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera), Russian Academy of Sciences, St. Petersburg 199034, Russia
| | | | - Samuel J Griffith
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Anu Solnik
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Lauri Saag
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Eugenia D'Atanasio
- Institute of Molecular Biology and Pathology, National Research Council, Rome 00185, Italy
| | - Ene Metspalu
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Maere Reidla
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Siiri Rootsi
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Toomas Kivisild
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
- Department of Human Genetics, KU Leuven, Leuven 3000, Belgium
| | - Christiana Lyn Scheib
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
- St. John's College, University of Cambridge, Cambridge CB2 1TP, UK
| | - Kristiina Tambets
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Aivar Kriiska
- Department of Archaeology, Institute of History and Archaeology, University of Tartu, Tartu 51014, Estonia.
| | - Mait Metspalu
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia.
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