201
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He G, Wang Z, Zou X, Chen X, Liu J, Wang M, Hou Y. Genetic diversity and phylogenetic characteristics of Chinese Tibetan and Yi minority ethnic groups revealed by non-CODIS STR markers. Sci Rep 2018; 8:5895. [PMID: 29651125 PMCID: PMC5897523 DOI: 10.1038/s41598-018-24291-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 03/13/2018] [Indexed: 12/16/2022] Open
Abstract
Non-CODIS STRs, with high polymorphism and allele frequency difference among ethnically and geographically different populations, play a crucial role in population genetics, molecular anthropology, and human forensics. In this work, 332 unrelated individuals from Sichuan Province (237 Tibetan individuals and 95 Yi individuals) are firstly genotyped with 21 non-CODIS autosomal STRs, and phylogenetic relationships with 26 previously investigated populations (9,444 individuals) are subsequently explored. In the Sichuan Tibetan and Yi, the combined power of discrimination (CPD) values are 0.9999999999999999999 and 0.9999999999999999993, and the combined power of exclusion (CPE) values are 0. 999997 and 0.999999, respectively. Analysis of molecular variance (AMOVA), principal component analysis (PCA), multidimensional scaling plots (MDS) and phylogenetic analysis demonstrated that Sichuan Tibetan has a close genetic relationship with Tibet Tibetan, and Sichuan Yi has a genetic affinity with Yunnan Bai group. Furthermore, significant genetic differences have widely existed between Chinese minorities (most prominently for Tibetan and Kazakh) and Han groups, but no population stratifications rather a homogenous group among Han populations distributed in Northern and Southern China are observed. Aforementioned results suggested that these 21 STRs are highly polymorphic and informative in the Sichuan Tibetan and Yi, which are suitable for population genetics and forensic applications.
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Affiliation(s)
- Guanglin He
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Zheng Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Xing Zou
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing, China
| | - Xu Chen
- Department of Clinical Laboratory, the First People's Hospital of Liangshan Yi Autonomous Prefecture, Xichang, Sichuan, China
| | - Jing Liu
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Mengge Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Yiping Hou
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, China.
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202
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Schumer M, Rosenthal GG, Andolfatto P. What do we mean when we talk about hybrid speciation? Heredity (Edinb) 2018; 120:379-382. [PMID: 29302049 PMCID: PMC5842215 DOI: 10.1038/s41437-017-0036-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 11/10/2017] [Accepted: 11/11/2017] [Indexed: 01/01/2023] Open
Affiliation(s)
- Molly Schumer
- Hanna Gray Fellow, Howard Hughes Medical Institute, Cambridge, MA, USA.
- Harvard Society of Fellows, Harvard University, Boston, MA, USA.
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA.
- Centro de Investigaciones Científicas de las Huastecas "Aguazarca", Calnali, Hidalgo, Mexico.
| | - Gil G Rosenthal
- Centro de Investigaciones Científicas de las Huastecas "Aguazarca", Calnali, Hidalgo, Mexico
- Department of Biology and Interdisciplinary Faculty of Ecology & Evolutionary Biology, Texas A&M University, College Station, TX, USA
| | - Peter Andolfatto
- Department of Ecology and Evolutionary Biology and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
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203
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Johnson KE, Voight BF. Patterns of shared signatures of recent positive selection across human populations. Nat Ecol Evol 2018; 2:713-720. [PMID: 29459708 PMCID: PMC5866773 DOI: 10.1038/s41559-018-0478-6] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 01/11/2018] [Indexed: 12/28/2022]
Abstract
Signatures of recent positive selection often overlap across human populations, but the question of how often these overlaps represent a single ancestral event remains unresolved. If a single selective event spread across many populations, the same sweeping haplotype should appear in each population and the selective pressure could be common across populations and environments. Identifying such shared selective events could identify genomic loci and human traits important in recent history across the globe. In addition, genomic annotations that recently became available could help attach these signatures to a potential gene and molecular phenotype selected across populations. Here, we present a catalogue of selective sweeps in humans, and identify those that overlap and share a sweeping haplotype. We connect these sweep overlaps with potential biological mechanisms at several loci, including potential new sites of adaptive introgression, the glycophorin locus associated with malarial resistance and the alcohol dehydrogenase cluster associated with alcohol dependency.
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Affiliation(s)
- Kelsey Elizabeth Johnson
- Genetics and Gene Regulation Program, Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Benjamin F Voight
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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204
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Browning SR, Browning BL, Zhou Y, Tucci S, Akey JM. Analysis of Human Sequence Data Reveals Two Pulses of Archaic Denisovan Admixture. Cell 2018; 173:53-61.e9. [PMID: 29551270 PMCID: PMC5866234 DOI: 10.1016/j.cell.2018.02.031] [Citation(s) in RCA: 205] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 11/21/2017] [Accepted: 02/12/2018] [Indexed: 01/27/2023]
Abstract
Anatomically modern humans interbred with Neanderthals and with a related archaic population known as Denisovans. Genomes of several Neanderthals and one Denisovan have been sequenced, and these reference genomes have been used to detect introgressed genetic material in present-day human genomes. Segments of introgression also can be detected without use of reference genomes, and doing so can be advantageous for finding introgressed segments that are less closely related to the sequenced archaic genomes. We apply a new reference-free method for detecting archaic introgression to 5,639 whole-genome sequences from Eurasia and Oceania. We find Denisovan ancestry in populations from East and South Asia and Papuans. Denisovan ancestry comprises two components with differing similarity to the sequenced Altai Denisovan individual. This indicates that at least two distinct instances of Denisovan admixture into modern humans occurred, involving Denisovan populations that had different levels of relatedness to the sequenced Altai Denisovan. VIDEO ABSTRACT.
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Affiliation(s)
- Sharon R Browning
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA.
| | - Brian L Browning
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Ying Zhou
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Serena Tucci
- Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - Joshua M Akey
- Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA; The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
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205
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Warren KA, Ritzman TB, Humphreys RA, Percival CJ, Hallgrímsson B, Ackermann RR. Craniomandibular form and body size variation of first generation mouse hybrids: A model for hominin hybridization. J Hum Evol 2018; 116:57-74. [PMID: 29477182 PMCID: PMC6699179 DOI: 10.1016/j.jhevol.2017.12.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 12/04/2017] [Accepted: 12/12/2017] [Indexed: 12/27/2022]
Abstract
Hybridization occurs in a number of mammalian lineages, including among primate taxa. Analyses of ancient genomes have shown that hybridization between our lineage and other archaic hominins in Eurasia occurred numerous times in the past. However, we still have limited empirical data on what a hybrid skeleton looks like, or how to spot patterns of hybridization among fossils for which there are no genetic data. Here we use experimental mouse models to supplement previous studies of primates. We characterize size and shape variation in the cranium and mandible of three wild-derived inbred mouse strains and their first generation (F1) hybrids. The three parent taxa in our analysis represent lineages that diverged over approximately the same period as the human/Neanderthal/Denisovan lineages and their hybrids are variably successful in the wild. Comparisons of body size, as quantified by long bone measurements, are also presented to determine whether the identified phenotypic effects of hybridization are localized to the cranium or represent overall body size changes. The results indicate that hybrid cranial and mandibular sizes, as well as limb length, exceed that of the parent taxa in all cases. All three F1 hybrid crosses display similar patterns of size and form variation. These results are generally consistent with earlier studies on primates and other mammals, suggesting that the effects of hybridization may be similar across very different scenarios of hybridization, including different levels of hybrid fitness. This paper serves to supplement previous studies aimed at identifying F1 hybrids in the fossil record and to introduce further research that will explore hybrid morphologies using mice as a proxy for better understanding hybridization in the hominin fossil record.
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Affiliation(s)
- Kerryn A Warren
- Department of Archaeology, University of Cape Town, South Africa; Human Evolution Research Institute, University of Cape Town, South Africa
| | - Terrence B Ritzman
- Department of Archaeology, University of Cape Town, South Africa; Human Evolution Research Institute, University of Cape Town, South Africa; Department of Neuroscience, Washington University School of Medicine, USA; School of Human Evolution and Social Change, Arizona State University, USA
| | - Robyn A Humphreys
- Department of Archaeology, University of Cape Town, South Africa; Human Evolution Research Institute, University of Cape Town, South Africa
| | - Christopher J Percival
- Department of Cell Biology and Anatomy, McCaig Institute for Bone and Joint Health, Alberta Children's Hospital Research Institute, University of Calgary, Canada; The Alberta Children's Hospital Research Institute, University of Calgary, Canada; The McCaig Institute for Bone and Joint Health, University of Calgary, Canada; Department of Anthropology, Stony Brook, USA
| | - Benedikt Hallgrímsson
- Department of Cell Biology and Anatomy, McCaig Institute for Bone and Joint Health, Alberta Children's Hospital Research Institute, University of Calgary, Canada; The Alberta Children's Hospital Research Institute, University of Calgary, Canada; The McCaig Institute for Bone and Joint Health, University of Calgary, Canada
| | - Rebecca Rogers Ackermann
- Department of Archaeology, University of Cape Town, South Africa; Human Evolution Research Institute, University of Cape Town, South Africa.
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206
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Yang MA, Fu Q. Insights into Modern Human Prehistory Using Ancient Genomes. Trends Genet 2018; 34:184-196. [DOI: 10.1016/j.tig.2017.11.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 11/26/2017] [Accepted: 11/29/2017] [Indexed: 01/05/2023]
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207
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Jagoda E, Lawson DJ, Wall JD, Lambert D, Muller C, Westaway M, Leavesley M, Capellini TD, Mirazón Lahr M, Gerbault P, Thomas MG, Migliano AB, Willerslev E, Metspalu M, Pagani L. Disentangling Immediate Adaptive Introgression from Selection on Standing Introgressed Variation in Humans. Mol Biol Evol 2018; 35:623-630. [PMID: 29220488 PMCID: PMC5850494 DOI: 10.1093/molbev/msx314] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Recent studies have reported evidence suggesting that portions of contemporary human genomes introgressed from archaic hominin populations went to high frequencies due to positive selection. However, no study to date has specifically addressed the postintrogression population dynamics of these putative cases of adaptive introgression. Here, for the first time, we specifically define cases of immediate adaptive introgression (iAI) in which archaic haplotypes rose to high frequencies in humans as a result of a selective sweep that occurred shortly after the introgression event. We define these cases as distinct from instances of selection on standing introgressed variation (SI), in which an introgressed haplotype initially segregated neutrally and subsequently underwent positive selection. Using a geographically diverse data set, we report novel cases of selection on introgressed variation in living humans and shortlist among these cases those whose selective sweeps are more consistent with having been the product of iAI rather than SI. Many of these novel inferred iAI haplotypes have potential biological relevance, including three that contain immune-related genes in West Siberians, South Asians, and West Eurasians. Overall, our results suggest that iAI may not represent the full picture of positive selection on archaically introgressed haplotypes in humans and that more work needs to be done to analyze the role of SI in the archaic introgression landscape of living humans.
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Affiliation(s)
- Evelyn Jagoda
- Human Evolutionary Biology, Harvard University, Cambridge, MA
| | - Daniel J Lawson
- Integrative Epidemiology Unit, Population Health Sciences, University of Bristol, Bristol, United Kingdom
| | - Jeffrey D Wall
- Institute for Human Genetics, University of California, San Francisco, CA
| | - David Lambert
- Australian Research Centre for Human Evolution, Environmental Futures Research Institute, Griffith University, Nathan, QLD, Australia
| | - Craig Muller
- Center for GeoGenetics, University of Copenhagen, Copenhagen, Denmark
| | - Michael Westaway
- Australian Research Centre for Human Evolution, Environmental Futures Research Institute, Griffith University, Nathan, QLD, Australia
| | - Matthew Leavesley
- Department of Anthropology and Sociology, University of Papua New Guinea, Port Moresby, Papua New Guinea
- Tropical Archaeology Research Laboratory, College for Education, Arts and Social Sciences, James Cook University, Cairns, Queensland, Australia
| | | | - Marta Mirazón Lahr
- Department of Archaeology, Leverhulme Centre for Human Evolutionary Studies, University of Cambridge, Cambridge, United Kingdom
| | - Pascale Gerbault
- Research Department of Genetics Evolution and Environment, University College London, London, United Kingdom
- UCL Genetics Institute, University College London, London, United Kingdom
| | - Mark G Thomas
- Research Department of Genetics Evolution and Environment, University College London, London, United Kingdom
- Department of Anthropology, University College London, London, United Kingdom
| | | | - Eske Willerslev
- Center for GeoGenetics, University of Copenhagen, Copenhagen, Denmark
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
- Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | | | - Luca Pagani
- Estonian Biocentre, Tartu, Estonia
- APE Lab, Department of Biology, University of Padova, Padova, Italy
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208
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Jégou B, Sankararaman S, Rolland AD, Reich D, Chalmel F. Meiotic Genes Are Enriched in Regions of Reduced Archaic Ancestry. Mol Biol Evol 2018; 34:1974-1980. [PMID: 28444387 DOI: 10.1093/molbev/msx141] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
About 1-6% of the genetic ancestry of modern humans today originates from admixture with archaic humans. It has recently been shown that autosomal genomic regions with a reduced proportion of Neanderthal and Denisovan ancestries (NA and DA) are significantly enriched in genes that are more expressed in testis than in other tissues. To determine whether a cellular segregation pattern would exist, we combined maps of archaic introgression with a cross-analysis of three transcriptomic datasets deciphering the transcriptional landscape of human gonadal cell types. We reveal that the regions deficient in both NA and DA contain a significant enrichment of genes transcribed in meiotic germ cells. The interbreeding of anatomically modern humans with archaic humans may have introduced archaic-derived alleles that contributed to genetic incompatibilities affecting meiosis that were subsequently purged by natural selection.
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Affiliation(s)
- B Jégou
- Inserm U1085-IRSET, Université de Rennes 1, Rennes, France.,Université Sorbonne Paris Cité (USPC), Paris, France.,EHESP - School of Public Health, Rennes, France
| | - S Sankararaman
- Department of Computer Science, UCLA, Los Angeles, CA.,Department of Human Genetics, UCLA, Los Angeles, CA
| | - A D Rolland
- Inserm U1085-IRSET, Université de Rennes 1, Rennes, France
| | - D Reich
- Department of Genetics, Harvard Medical School, Boston, MA.,Broad Institute of Harvard and MIT, Cambridge, MA.,Harvard Medical School, Howard Hughes Medical Institute, Boston, MA
| | - F Chalmel
- Inserm U1085-IRSET, Université de Rennes 1, Rennes, France
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209
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Yew CW, Lu D, Deng L, Wong LP, Ong RTH, Lu Y, Wang X, Yunus Y, Aghakhanian F, Mokhtar SS, Hoque MZ, Voo CLY, Abdul Rahman T, Bhak J, Phipps ME, Xu S, Teo YY, Kumar SV, Hoh BP. Genomic structure of the native inhabitants of Peninsular Malaysia and North Borneo suggests complex human population history in Southeast Asia. Hum Genet 2018; 137:161-173. [DOI: 10.1007/s00439-018-1869-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 01/22/2018] [Indexed: 11/28/2022]
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210
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Povysil G, Hochreiter S. IBD Sharing between Africans, Neandertals, and Denisovans. Genome Biol Evol 2018; 8:3406-3416. [PMID: 28158547 PMCID: PMC5381509 DOI: 10.1093/gbe/evw234] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/19/2016] [Indexed: 12/03/2022] Open
Abstract
Interbreeding between ancestors of humans and other hominins outside of Africa has been studied intensively, while their common history within Africa still lacks proper attention. However, shedding light on human evolution in this time period about which little is known, is essential for understanding subsequent events outside of Africa. We investigate the genetic relationships of humans, Neandertals, and Denisovans by identifying very short DNA segments in the 1000 Genomes Phase 3 data that these hominins share identical by descent (IBD). By focusing on low frequency and rare variants, we identify very short IBD segments with high confidence. These segments reveal events from a very distant past because shorter IBD segments are presumably older than longer ones. We extracted two types of very old IBD segments that are not only shared among humans, but also with Neandertals and/or Denisovans. The first type contains longer segments that are found primarily in Asians and Europeans where more segments are found in South Asians than in East Asians for both Neandertal and Denisovan. These longer segments indicate complex admixture events outside of Africa. The second type consists of shorter segments that are shared mainly by Africans and therefore may indicate events involving ancestors of humans and other ancient hominins within Africa. Our results from the autosomes are further supported by an analysis of chromosome X, on which segments that are shared by Africans and match the Neandertal and/or Denisovan genome were even more prominent. Our results indicate that interbreeding with other hominins was a common feature of human evolution starting already long before ancestors of modern humans left Africa.
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Affiliation(s)
- Gundula Povysil
- Institute of Bioinformatics, Johannes Kepler University Linz, Austria
| | - Sepp Hochreiter
- Institute of Bioinformatics, Johannes Kepler University Linz, Austria
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211
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Szpak M, Mezzavilla M, Ayub Q, Chen Y, Xue Y, Tyler-Smith C. FineMAV: prioritizing candidate genetic variants driving local adaptations in human populations. Genome Biol 2018; 19:5. [PMID: 29343290 PMCID: PMC5771147 DOI: 10.1186/s13059-017-1380-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 12/12/2017] [Indexed: 12/30/2022] Open
Abstract
We present a new method, Fine-Mapping of Adaptive Variation (FineMAV), which combines population differentiation, derived allele frequency, and molecular functionality to prioritize positively selected candidate variants for functional follow-up. We calibrate and test FineMAV using eight experimentally validated "gold standard" positively selected variants and simulations. FineMAV has good sensitivity and a low false discovery rate. Applying FineMAV to the 1000 Genomes Project Phase 3 SNP dataset, we report many novel selected variants, including ones in TGM3 and PRSS53 associated with hair phenotypes that we validate using available independent data. FineMAV is widely applicable to sequence data from both human and other species.
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Affiliation(s)
- Michał Szpak
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA UK
| | - Massimo Mezzavilla
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA UK
- Division of Experimental Genetics, Sidra Medical and Research Center, Doha, Qatar
| | - Qasim Ayub
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA UK
- Present Address: Genomics Facility, School of Science, Monash University Malaysia, Bandar Sunway, Selangor, Darul Ehsan Malaysia
| | - Yuan Chen
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA UK
| | - Yali Xue
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA UK
| | - Chris Tyler-Smith
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA UK
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212
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213
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Levchenko A, Kanapin A, Samsonova A, Gainetdinov RR. Human Accelerated Regions and Other Human-Specific Sequence Variations in the Context of Evolution and Their Relevance for Brain Development. Genome Biol Evol 2018; 10:166-188. [PMID: 29149249 PMCID: PMC5767953 DOI: 10.1093/gbe/evx240] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/14/2017] [Indexed: 12/24/2022] Open
Abstract
The review discusses, in a format of a timeline, the studies of different types of genetic variants, present in Homo sapiens, but absent in all other primate, mammalian, or vertebrate species, tested so far. The main characteristic of these variants is that they are found in regions of high evolutionary conservation. These sequence variations include single nucleotide substitutions (called human accelerated regions), deletions, and segmental duplications. The rationale for finding such variations in the human genome is that they could be responsible for traits, specific to our species, of which the human brain is the most remarkable. As became obvious, the vast majority of human-specific single nucleotide substitutions are found in noncoding, likely regulatory regions. A number of genes, associated with these human-specific alleles, often through novel enhancer activity, were in fact shown to be implicated in human-specific development of certain brain areas, including the prefrontal cortex. Human-specific deletions may remove regulatory sequences, such as enhancers. Segmental duplications, because of their large size, create new coding sequences, like new functional paralogs. Further functional study of these variants will shed light on evolution of our species, as well as on the etiology of neurodevelopmental disorders.
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Affiliation(s)
- Anastasia Levchenko
- Institute of Translational Biomedicine, Saint Petersburg State University, Russia
| | - Alexander Kanapin
- Institute of Translational Biomedicine, Saint Petersburg State University, Russia
- Department of Oncology, University of Oxford, United Kingdom
| | - Anastasia Samsonova
- Institute of Translational Biomedicine, Saint Petersburg State University, Russia
- Department of Oncology, University of Oxford, United Kingdom
| | - Raul R Gainetdinov
- Institute of Translational Biomedicine, Saint Petersburg State University, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow, Russia
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214
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215
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Rifkin RF, Potgieter M, Ramond J, Cowan DA. Ancient oncogenesis, infection and human evolution. Evol Appl 2017; 10:949-964. [PMID: 29151852 PMCID: PMC5680625 DOI: 10.1111/eva.12497] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 05/22/2017] [Indexed: 12/27/2022] Open
Abstract
The recent discovery that malignant neoplastic lesions date back nearly 2 million years ago not only highlights the antiquity of cancer in the human lineage, but also provides remarkable insight into ancestral hominin disease pathology. Using these Early Pleistocene examples as a point of departure, we emphasize the prominent role of viral and bacterial pathogens in oncogenesis and evaluate the impact of pathogens on human evolutionary processes in Africa. In the Shakespearean vernacular "what's past is prologue," we highlight the significance of novel information derived from ancient pathogenic DNA. In particular, and given the temporal depth of human occupation in sub-Saharan Africa, it is emphasized that the region is ideally positioned to play a strategic role in the discovery of ancient pathogenic drivers of not only human mortality, but also human evolution. Ancient African pathogen genome data can provide novel revelations concerning human-pathogen coevolutionary processes, and such knowledge is essential for forecasting the ways in which emerging zoonotic and increasingly transmissible diseases might influence human demography and longevity in the future.
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Affiliation(s)
- Riaan F. Rifkin
- Center for Microbial Ecology and Genomics (CMEG)Department of GeneticsUniversity of PretoriaHatfieldSouth Africa
| | - Marnie Potgieter
- Center for Microbial Ecology and Genomics (CMEG)Department of GeneticsUniversity of PretoriaHatfieldSouth Africa
| | - Jean‐Baptiste Ramond
- Center for Microbial Ecology and Genomics (CMEG)Department of GeneticsUniversity of PretoriaHatfieldSouth Africa
| | - Don A. Cowan
- Center for Microbial Ecology and Genomics (CMEG)Department of GeneticsUniversity of PretoriaHatfieldSouth Africa
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216
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Llamas B, Willerslev E, Orlando L. Human evolution: a tale from ancient genomes. Philos Trans R Soc Lond B Biol Sci 2017; 372:rstb.2015.0484. [PMID: 27994125 DOI: 10.1098/rstb.2015.0484] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/05/2016] [Indexed: 12/21/2022] Open
Abstract
The field of human ancient DNA (aDNA) has moved from mitochondrial sequencing that suffered from contamination and provided limited biological insights, to become a fully genomic discipline that is changing our conception of human history. Recent successes include the sequencing of extinct hominins, and true population genomic studies of Bronze Age populations. Among the emerging areas of aDNA research, the analysis of past epigenomes is set to provide more new insights into human adaptation and disease susceptibility through time. Starting as a mere curiosity, ancient human genetics has become a major player in the understanding of our evolutionary history.This article is part of the themed issue 'Evo-devo in the genomics era, and the origins of morphological diversity'.
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Affiliation(s)
- Bastien Llamas
- Australian Centre for ADNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350 K Copenhagen, Denmark.,Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK.,Wellcome Genome Campus Hinxton, Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350 K Copenhagen, Denmark .,Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, Université de Toulouse, University Paul Sabatier, CNRS UMR 5288, 31000 Toulouse, France
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217
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Xu D, Pavlidis P, Taskent RO, Alachiotis N, Flanagan C, DeGiorgio M, Blekhman R, Ruhl S, Gokcumen O. Archaic Hominin Introgression in Africa Contributes to Functional Salivary MUC7 Genetic Variation. Mol Biol Evol 2017; 34:2704-2715. [PMID: 28957509 PMCID: PMC5850612 DOI: 10.1093/molbev/msx206] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
One of the most abundant proteins in human saliva, mucin-7, is encoded by the MUC7 gene, which harbors copy number variable subexonic repeats (PTS-repeats) that affect the size and glycosylation potential of this protein. We recently documented the adaptive evolution of MUC7 subexonic copy number variation among primates. Yet, the evolution of MUC7 genetic variation in humans remained unexplored. Here, we found that PTS-repeat copy number variation has evolved recurrently in the human lineage, thereby generating multiple haplotypic backgrounds carrying five or six PTS-repeat copy number alleles. Contrary to previous studies, we found no associations between the copy number of PTS-repeats and protection against asthma. Instead, we revealed a significant association of MUC7 haplotypic variation with the composition of the oral microbiome. Furthermore, based on in-depth simulations, we conclude that a divergent MUC7 haplotype likely originated in an unknown African hominin population and introgressed into ancestors of modern Africans.
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Affiliation(s)
- Duo Xu
- Department of Biological Sciences, University at Buffalo, The State University of New York, Buffalo, NY
| | - Pavlos Pavlidis
- Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology - Hellas, Heraklion, Crete, Greece
| | - Recep Ozgur Taskent
- Department of Biological Sciences, University at Buffalo, The State University of New York, Buffalo, NY
| | - Nikolaos Alachiotis
- Institute of Computer Science (ICS), Foundation for Research and Technology - Hellas, Heraklion, Crete, Greece
| | - Colin Flanagan
- Department of Biological Sciences, University at Buffalo, The State University of New York, Buffalo, NY
| | - Michael DeGiorgio
- Department of Biology and the Institute for CyberScience, Pennsylvania State University, University Park, PA
| | - Ran Blekhman
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Twin Cities, MN
| | - Stefan Ruhl
- Department of Oral Biology, School of Dental Medicine, University at Buffalo, The State University of New York, Buffalo, NY
| | - Omer Gokcumen
- Department of Biological Sciences, University at Buffalo, The State University of New York, Buffalo, NY
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218
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Schmickl R, Marburger S, Bray S, Yant L. Hybrids and horizontal transfer: introgression allows adaptive allele discovery. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:5453-5470. [PMID: 29096001 DOI: 10.1093/jxb/erx297] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Evolution has devised countless remarkable solutions to diverse challenges. Understanding the mechanistic basis of these solutions provides insights into how biological systems can be subtly tweaked without maladaptive consequences. The knowledge gained from illuminating these mechanisms is equally important to our understanding of fundamental evolutionary mechanisms as it is to our hopes of developing truly rational plant breeding and synthetic biology. In particular, modern population genomic approaches are proving very powerful in the detection of candidate alleles for mediating consequential adaptations that can be tested functionally. Especially striking are signals gained from contexts involving genetic transfers between populations, closely related species, or indeed between kingdoms. Here we discuss two major classes of these scenarios, adaptive introgression and horizontal gene flow, illustrating discoveries made across kingdoms.
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Affiliation(s)
- Roswitha Schmickl
- Institute of Botany, The Czech Academy of Sciences, Zámek 1, 252 43 Průhonice, Czech Republic
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, 128 01 Prague, Czech Republic
| | - Sarah Marburger
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Sian Bray
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Levi Yant
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
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219
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Prüfer K, de Filippo C, Grote S, Mafessoni F, Korlević P, Hajdinjak M, Vernot B, Skov L, Hsieh P, Peyrégne S, Reher D, Hopfe C, Nagel S, Maricic T, Fu Q, Theunert C, Rogers R, Skoglund P, Chintalapati M, Dannemann M, Nelson BJ, Key FM, Rudan P, Kućan Ž, Gušić I, Golovanova LV, Doronichev VB, Patterson N, Reich D, Eichler EE, Slatkin M, Schierup MH, Andrés AM, Kelso J, Meyer M, Pääbo S. A high-coverage Neandertal genome from Vindija Cave in Croatia. Science 2017; 358:655-658. [PMID: 28982794 PMCID: PMC6185897 DOI: 10.1126/science.aao1887] [Citation(s) in RCA: 352] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 09/27/2017] [Indexed: 12/30/2022]
Abstract
To date, the only Neandertal genome that has been sequenced to high quality is from an individual found in Southern Siberia. We sequenced the genome of a female Neandertal from ~50,000 years ago from Vindija Cave, Croatia, to ~30-fold genomic coverage. She carried 1.6 differences per 10,000 base pairs between the two copies of her genome, fewer than present-day humans, suggesting that Neandertal populations were of small size. Our analyses indicate that she was more closely related to the Neandertals that mixed with the ancestors of present-day humans living outside of sub-Saharan Africa than the previously sequenced Neandertal from Siberia, allowing 10 to 20% more Neandertal DNA to be identified in present-day humans, including variants involved in low-density lipoprotein cholesterol concentrations, schizophrenia, and other diseases.
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Affiliation(s)
- Kay Prüfer
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.
| | - Cesare de Filippo
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Steffi Grote
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Fabrizio Mafessoni
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Petra Korlević
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Mateja Hajdinjak
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Benjamin Vernot
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Laurits Skov
- Bioinformatics Research Centre, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Pinghsun Hsieh
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Stéphane Peyrégne
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - David Reher
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Charlotte Hopfe
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Sarah Nagel
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Tomislav Maricic
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Qiaomei Fu
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
| | - Christoph Theunert
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
- Department of Integrative Biology, University of California, Berkeley, CA 94720-3140, USA
| | - Rebekah Rogers
- Department of Integrative Biology, University of California, Berkeley, CA 94720-3140, USA
| | - Pontus Skoglund
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Michael Dannemann
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Bradley J Nelson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Felix M Key
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Pavao Rudan
- Anthropology Center of the Croatian Academy of Sciences and Arts, 10000 Zagreb, Croatia
| | - Željko Kućan
- Anthropology Center of the Croatian Academy of Sciences and Arts, 10000 Zagreb, Croatia
| | - Ivan Gušić
- Anthropology Center of the Croatian Academy of Sciences and Arts, 10000 Zagreb, Croatia
| | | | | | - Nick Patterson
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - David Reich
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Montgomery Slatkin
- Department of Integrative Biology, University of California, Berkeley, CA 94720-3140, USA
| | - Mikkel H Schierup
- Bioinformatics Research Centre, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Aida M Andrés
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Janet Kelso
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Matthias Meyer
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Svante Pääbo
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.
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220
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Marciniak S, Perry GH. Harnessing ancient genomes to study the history of human adaptation. Nat Rev Genet 2017; 18:659-674. [PMID: 28890534 DOI: 10.1038/nrg.2017.65] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The past several years have witnessed an explosion of successful ancient human genome-sequencing projects, with genomic-scale ancient DNA data sets now available for more than 1,100 ancient human and archaic hominin (for example, Neandertal) individuals. Recent 'evolution in action' analyses have started using these data sets to identify and track the spatiotemporal trajectories of genetic variants associated with human adaptations to novel and changing environments, agricultural lifestyles, and introduced or co-evolving pathogens. Together with evidence of adaptive introgression of genetic variants from archaic hominins to humans and emerging ancient genome data sets for domesticated animals and plants, these studies provide novel insights into human evolution and the evolutionary consequences of human behaviour that go well beyond those that can be obtained from modern genomic data or the fossil and archaeological records alone.
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Affiliation(s)
- Stephanie Marciniak
- Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - George H Perry
- Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA
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221
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Sikora M, Seguin-Orlando A, Sousa VC, Albrechtsen A, Korneliussen T, Ko A, Rasmussen S, Dupanloup I, Nigst PR, Bosch MD, Renaud G, Allentoft ME, Margaryan A, Vasilyev SV, Veselovskaya EV, Borutskaya SB, Deviese T, Comeskey D, Higham T, Manica A, Foley R, Meltzer DJ, Nielsen R, Excoffier L, Mirazon Lahr M, Orlando L, Willerslev E. Ancient genomes show social and reproductive behavior of early Upper Paleolithic foragers. Science 2017; 358:659-662. [DOI: 10.1126/science.aao1807] [Citation(s) in RCA: 203] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 09/25/2017] [Indexed: 01/01/2023]
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222
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Dannemann M, Kelso J. The Contribution of Neanderthals to Phenotypic Variation in Modern Humans. Am J Hum Genet 2017; 101:578-589. [PMID: 28985494 PMCID: PMC5630192 DOI: 10.1016/j.ajhg.2017.09.010] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 09/05/2017] [Indexed: 11/03/2022] Open
Abstract
Assessing the genetic contribution of Neanderthals to non-disease phenotypes in modern humans has been difficult because of the absence of large cohorts for which common phenotype information is available. Using baseline phenotypes collected for 112,000 individuals by the UK Biobank, we can now elaborate on previous findings that identified associations between signatures of positive selection on Neanderthal DNA and various modern human traits but not any specific phenotypic consequences. Here, we show that Neanderthal DNA affects skin tone and hair color, height, sleeping patterns, mood, and smoking status in present-day Europeans. Interestingly, multiple Neanderthal alleles at different loci contribute to skin and hair color in present-day Europeans, and these Neanderthal alleles contribute to both lighter and darker skin tones and hair color, suggesting that Neanderthals themselves were most likely variable in these traits.
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223
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Tung J, Barreiro LB. The contribution of admixture to primate evolution. Curr Opin Genet Dev 2017; 47:61-68. [PMID: 28923540 DOI: 10.1016/j.gde.2017.08.010] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 08/08/2017] [Accepted: 08/31/2017] [Indexed: 12/16/2022]
Abstract
Genome-wide data on genetic variation are now available for multiple primate species and populations, facilitating analyses of evolutionary history within and across taxa. One emerging theme from these studies involves the central role of admixture. Genomic data sets indicate that both ancient gene flow following initial taxonomic divergence and ongoing gene flow at current species boundaries are common. These findings are of particular interest given evidence for a complex history of admixture in our own lineage, including examples of ecologically driven adaptive introgression. Like other aspects of human biology, studies of nonhuman primates thus provide both comparative context and a living model for understanding admixture dynamics in hominins. We highlight several open questions that could be addressed in future work.
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Affiliation(s)
- Jenny Tung
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA; Department of Biology, Duke University, Durham, NC 27708, USA; Duke University Population Research Institute, Duke University, Durham, NC 27708, USA; Institute of Primate Research, National Museums of Kenya, Karen, Nairobi, Kenya.
| | - Luis B Barreiro
- Department of Pediatrics, Sainte-Justine Hospital Research Centre, University of Montreal, Montreal, Canada
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224
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Neanderthal and Denisova tooth protein variants in present-day humans. PLoS One 2017; 12:e0183802. [PMID: 28902892 PMCID: PMC5597096 DOI: 10.1371/journal.pone.0183802] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 08/13/2017] [Indexed: 12/15/2022] Open
Abstract
Environment parameters, diet and genetic factors interact to shape tooth morphostructure. In the human lineage, archaic and modern hominins show differences in dental traits, including enamel thickness, but variability also exists among living populations. Several polymorphisms, in particular in the non-collagenous extracellular matrix proteins of the tooth hard tissues, like enamelin, are involved in dental structure variation and defects and may be associated with dental disorders or susceptibility to caries. To gain insights into the relationships between tooth protein polymorphisms and dental structural morphology and defects, we searched for non-synonymous polymorphisms in tooth proteins from Neanderthal and Denisova hominins. The objective was to identify archaic-specific missense variants that may explain the dental morphostructural variability between extinct and modern humans, and to explore their putative impact on present-day dental phenotypes. Thirteen non-collagenous extracellular matrix proteins specific to hard dental tissues have been selected, searched in the publicly available sequence databases of Neanderthal and Denisova individuals and compared with modern human genome data. A total of 16 non-synonymous polymorphisms were identified in 6 proteins (ameloblastin, amelotin, cementum protein 1, dentin matrix acidic phosphoprotein 1, enamelin and matrix Gla protein). Most of them are encoded by dentin and enamel genes located on chromosome 4, previously reported to show signs of archaic introgression within Africa. Among the variants shared with modern humans, two are ancestral (common with apes) and one is the derived enamelin major variant, T648I (rs7671281), associated with a thinner enamel and specific to the Homo lineage. All the others are specific to Neanderthals and Denisova, and are found at a very low frequency in modern Africans or East and South Asians, suggesting that they may be related to particular dental traits or disease susceptibility in these populations. This modern regional distribution of archaic dental polymorphisms may reflect persistence of archaic variants in some populations and may contribute in part to the geographic dental variations described in modern humans.
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225
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Huang M, Tu J, Lu Z. Recent Advances in Experimental Whole Genome Haplotyping Methods. Int J Mol Sci 2017; 18:E1944. [PMID: 28891974 PMCID: PMC5618593 DOI: 10.3390/ijms18091944] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 09/01/2017] [Accepted: 09/05/2017] [Indexed: 01/06/2023] Open
Abstract
Haplotype plays a vital role in diverse fields; however, the sequencing technologies cannot resolve haplotype directly. Pioneers demonstrated several approaches to resolve haplotype in the early years, which was extensively reviewed. Since then, numerous methods have been developed recently that have significantly improved phasing performance. Here, we review experimental methods that have emerged mainly over the past five years, and categorize them into five classes according to their maximum scale of contiguity: (i) encapsulation, (ii) 3D structure capture and construction, (iii) compartmentalization, (iv) fluorography, (v) long-read sequencing. Several subsections of certain methods are attached to each class as instances. We also discuss the relative advantages and disadvantages of different classes and make comparisons among representative methods of each class.
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Affiliation(s)
- Mengting Huang
- State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
| | - Jing Tu
- State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
| | - Zuhong Lu
- State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
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226
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Enciso-Romero J, Pardo-Díaz C, Martin SH, Arias CF, Linares M, McMillan WO, Jiggins CD, Salazar C. Evolution of novel mimicry rings facilitated by adaptive introgression in tropical butterflies. Mol Ecol 2017; 26:5160-5172. [PMID: 28777894 DOI: 10.1111/mec.14277] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 07/25/2017] [Accepted: 07/31/2017] [Indexed: 12/25/2022]
Abstract
Understanding the genetic basis of phenotypic variation and the mechanisms involved in the evolution of adaptive novelty, especially in adaptive radiations, is a major goal in evolutionary biology. Here, we used whole-genome sequence data to investigate the origin of the yellow hindwing bar in the Heliconius cydno radiation. We found modular variation associated with hindwing phenotype in two narrow noncoding regions upstream and downstream of the cortex gene, which was recently identified as a pigmentation pattern controller in multiple species of Heliconius. Genetic variation at each of these modules suggests an independent control of the dorsal and ventral hindwing patterning, with the upstream module associated with the ventral phenotype and the downstream module with the dorsal one. Furthermore, we detected introgression between H. cydno and its closely related species Heliconius melpomene in these modules, likely allowing both species to participate in novel mimicry rings. In sum, our findings support the role of regulatory modularity coupled with adaptive introgression as an elegant mechanism by which novel phenotypic combinations can evolve and fuel an adaptive radiation.
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Affiliation(s)
- Juan Enciso-Romero
- Biology Program, Faculty of Natural Sciences and Mathematics, Universidad del Rosario, Bogotá D.C, Colombia
| | - Carolina Pardo-Díaz
- Biology Program, Faculty of Natural Sciences and Mathematics, Universidad del Rosario, Bogotá D.C, Colombia
| | - Simon H Martin
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Carlos F Arias
- Biology Program, Faculty of Natural Sciences and Mathematics, Universidad del Rosario, Bogotá D.C, Colombia.,Smithsonian Tropical Research Institute, Balboa, Ancon, Panama
| | - Mauricio Linares
- Biology Program, Faculty of Natural Sciences and Mathematics, Universidad del Rosario, Bogotá D.C, Colombia
| | | | - Chris D Jiggins
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Camilo Salazar
- Biology Program, Faculty of Natural Sciences and Mathematics, Universidad del Rosario, Bogotá D.C, Colombia
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227
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Abstract
Genomic evidence has demonstrated that humans and Neanderthals interbred. Today, the genomes of most individuals outside Africa contain 2-3% Neanderthal DNA. However, it is still hotly debated why the Neanderthals went extinct and if humans contributed to the Neanderthal extinction. In this Q&A we explore what genomic data might have to say about this issue.
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Affiliation(s)
- Kelley Harris
- Department of Genetics, Stanford University, Stanford, CA, USA.
| | - Rasmus Nielsen
- Department of Integrative Biology, University of California, Berkeley, California, USA. .,Museum of Natural History, University of Copenhagen, Copenhagen, Denmark.
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228
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Peyrégne S, Boyle MJ, Dannemann M, Prüfer K. Detecting ancient positive selection in humans using extended lineage sorting. Genome Res 2017; 27:1563-1572. [PMID: 28720580 PMCID: PMC5580715 DOI: 10.1101/gr.219493.116] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 07/05/2017] [Indexed: 01/20/2023]
Abstract
Natural selection that affected modern humans early in their evolution has likely shaped some of the traits that set present-day humans apart from their closest extinct and living relatives. The ability to detect ancient natural selection in the human genome could provide insights into the molecular basis for these human-specific traits. Here, we introduce a method for detecting ancient selective sweeps by scanning for extended genomic regions where our closest extinct relatives, Neandertals and Denisovans, fall outside of the present-day human variation. Regions that are unusually long indicate the presence of lineages that reached fixation in the human population faster than expected under neutral evolution. Using simulations, we show that the method is able to detect ancient events of positive selection and that it can differentiate those from background selection. Applying our method to the 1000 Genomes data set, we find evidence for ancient selective sweeps favoring regulatory changes and present a list of genomic regions that are predicted to underlie positively selected human specific traits.
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Affiliation(s)
- Stéphane Peyrégne
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Michael James Boyle
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Michael Dannemann
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Kay Prüfer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
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229
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230
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Chintalapati M, Dannemann M, Prüfer K. Using the Neandertal genome to study the evolution of small insertions and deletions in modern humans. BMC Evol Biol 2017; 17:179. [PMID: 28778150 PMCID: PMC5543596 DOI: 10.1186/s12862-017-1018-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 07/19/2017] [Indexed: 12/24/2022] Open
Abstract
Background Small insertions and deletions occur in humans at a lower rate compared to nucleotide changes, but evolve under more constraint than nucleotide changes. While the evolution of insertions and deletions have been investigated using ape outgroups, the now available genome of a Neandertal can shed light on the evolution of indels in more recent times. Results We used the Neandertal genome together with several primate outgroup genomes to differentiate between human insertion/deletion changes that likely occurred before the split from Neandertals and those that likely arose later. Changes that pre-date the split from Neandertals show a smaller proportion of deletions than those that occurred later. The presence of a Neandertal-shared allele in Europeans or Asians but the absence in Africans was used to detect putatively introgressed indels in Europeans and Asians. A larger proportion of these variants reside in intergenic regions compared to other modern human variants, and some variants are linked to SNPs that have been associated with traits in modern humans. Conclusions Our results are in agreement with earlier results that suggested that deletions evolve under more constraint than insertions. When considering Neandertal introgressed variants, we find some evidence that negative selection affected these variants more than other variants segregating in modern humans. Among introgressed variants we also identify indels that may influence the phenotype of their carriers. In particular an introgressed deletion associated with a decrease in the time to menarche may constitute an example of a former Neandertal-specific trait contributing to modern human phenotypic diversity. Electronic supplementary material The online version of this article (doi:10.1186/s12862-017-1018-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Michael Dannemann
- Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany
| | - Kay Prüfer
- Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany.
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231
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232
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Neanderthal-Derived Genetic Variation Shapes Modern Human Cranium and Brain. Sci Rep 2017; 7:6308. [PMID: 28740249 PMCID: PMC5524936 DOI: 10.1038/s41598-017-06587-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 05/24/2017] [Indexed: 01/25/2023] Open
Abstract
Before their disappearance from the fossil record approximately 40,000 years ago, Neanderthals, the ancient hominin lineage most closely related to modern humans, interbred with ancestors of present-day humans. The legacy of this gene flow persists through Neanderthal-derived variants that survive in modern human DNA; however, the neural implications of this inheritance are uncertain. Here, using MRI in a large cohort of healthy individuals of European-descent, we show that the amount of Neanderthal-originating polymorphism carried in living humans is related to cranial and brain morphology. First, as a validation of our approach, we demonstrate that a greater load of Neanderthal-derived genetic variants (higher “NeanderScore”) is associated with skull shapes resembling those of known Neanderthal cranial remains, particularly in occipital and parietal bones. Next, we demonstrate convergent NeanderScore-related findings in the brain (measured by gray- and white-matter volume, sulcal depth, and gyrification index) that localize to the visual cortex and intraparietal sulcus. This work provides insights into ancestral human neurobiology and suggests that Neanderthal-derived genetic variation is neurologically functional in the contemporary population.
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233
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Deng L, Xu S. Adaptation of human skin color in various populations. Hereditas 2017; 155:1. [PMID: 28701907 PMCID: PMC5502412 DOI: 10.1186/s41065-017-0036-2] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 06/02/2017] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Skin color is a well-recognized adaptive trait and has been studied extensively in humans. Understanding the genetic basis of adaptation of skin color in various populations has many implications in human evolution and medicine. DISCUSSION Impressive progress has been made recently to identify genes associated with skin color variation in a wide range of geographical and temporal populations. In this review, we discuss what is currently known about the genetics of skin color variation. We enumerated several cases of skin color adaptation in global modern humans and archaic hominins, and illustrated why, when, and how skin color adaptation occurred in different populations. Finally, we provided a summary of the candidate loci associated with pigmentation, which could be a valuable reference for further evolutionary and medical studies. CONCLUSION Previous studies generally indicated a complex genetic mechanism underlying the skin color variation, expanding our understanding of the role of population demographic history and natural selection in shaping genetic and phenotypic diversity in humans. Future work is needed to dissect the genetic architecture of skin color adaptation in numerous ethnic minority groups around the world, which remains relatively obscure compared with that of major continental groups, and to unravel the exact genetic basis of skin color adaptation.
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Affiliation(s)
- Lian Deng
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological Sciences, CAS, Shanghai, 200031 China.,University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Shuhua Xu
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological Sciences, CAS, Shanghai, 200031 China.,University of Chinese Academy of Sciences, Beijing, 100049 China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210 China.,Collaborative Innovation Center of Genetics and Development, Shanghai, 200438 China
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234
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Hu H, Petousi N, Glusman G, Yu Y, Bohlender R, Tashi T, Downie JM, Roach JC, Cole AM, Lorenzo FR, Rogers AR, Brunkow ME, Cavalleri G, Hood L, Alpatty SM, Prchal JT, Jorde LB, Robbins PA, Simonson TS, Huff CD. Evolutionary history of Tibetans inferred from whole-genome sequencing. PLoS Genet 2017; 13:e1006675. [PMID: 28448578 PMCID: PMC5407610 DOI: 10.1371/journal.pgen.1006675] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 03/08/2017] [Indexed: 12/20/2022] Open
Abstract
The indigenous people of the Tibetan Plateau have been the subject of much recent interest because of their unique genetic adaptations to high altitude. Recent studies have demonstrated that the Tibetan EPAS1 haplotype is involved in high altitude-adaptation and originated in an archaic Denisovan-related population. We sequenced the whole-genomes of 27 Tibetans and conducted analyses to infer a detailed history of demography and natural selection of this population. We detected evidence of population structure between the ancestral Han and Tibetan subpopulations as early as 44 to 58 thousand years ago, but with high rates of gene flow until approximately 9 thousand years ago. The CMS test ranked EPAS1 and EGLN1 as the top two positive selection candidates, and in addition identified PTGIS, VDR, and KCTD12 as new candidate genes. The advantageous Tibetan EPAS1 haplotype shared many variants with the Denisovan genome, with an ancient gene tree divergence between the Tibetan and Denisovan haplotypes of about 1 million years ago. With the exception of EPAS1, we observed no evidence of positive selection on Denisovan-like haplotypes.
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Affiliation(s)
- Hao Hu
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Nayia Petousi
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Gustavo Glusman
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Yao Yu
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Ryan Bohlender
- Department of Anthropology, University of Utah, Salt Lake City, Utah, United States of America
| | - Tsewang Tashi
- Department of Medicine, University of Utah School of Medicine and George E. Wahlin Veterans Administration Medical Center, Salt Lake City, Utah, United States of America
| | - Jonathan M. Downie
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
| | - Jared C. Roach
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Amy M. Cole
- Department of Molecular and Cellular Therapeutics, The Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Felipe R. Lorenzo
- Department of Medicine, University of Utah School of Medicine and George E. Wahlin Veterans Administration Medical Center, Salt Lake City, Utah, United States of America
| | - Alan R. Rogers
- Department of Anthropology, University of Utah, Salt Lake City, Utah, United States of America
| | - Mary E. Brunkow
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Gianpiero Cavalleri
- Department of Molecular and Cellular Therapeutics, The Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Leroy Hood
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Sama M. Alpatty
- Skaggs School of Pharmacy and Pharmaceutical Science, UC San Diego, La Jolla, California, United States of America
| | - Josef T. Prchal
- Department of Medicine, University of Utah School of Medicine and George E. Wahlin Veterans Administration Medical Center, Salt Lake City, Utah, United States of America
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
| | - Lynn B. Jorde
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
| | - Peter A. Robbins
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Tatum S. Simonson
- Department of Medicine, Division of Physiology, University of California San Diego, La Jolla, California, United States of America
| | - Chad D. Huff
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
- * E-mail:
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235
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Onuki R, Yamaguchi R, Shibuya T, Kanehisa M, Goto S. Revealing phenotype-associated functional differences by genome-wide scan of ancient haplotype blocks. PLoS One 2017; 12:e0176530. [PMID: 28445522 PMCID: PMC5406033 DOI: 10.1371/journal.pone.0176530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 04/12/2017] [Indexed: 11/18/2022] Open
Abstract
Genome-wide scans for positive selection have become important for genomic medicine, and many studies aim to find genomic regions affected by positive selection that are associated with risk allele variations among populations. Most such studies are designed to detect recent positive selection. However, we hypothesize that ancient positive selection is also important for adaptation to pathogens, and has affected current immune-mediated common diseases. Based on this hypothesis, we developed a novel linkage disequilibrium-based pipeline, which aims to detect regions associated with ancient positive selection across populations from single nucleotide polymorphism (SNP) data. By applying this pipeline to the genotypes in the International HapMap project database, we show that genes in the detected regions are enriched in pathways related to the immune system and infectious diseases. The detected regions also contain SNPs reported to be associated with cancers and metabolic diseases, obesity-related traits, type 2 diabetes, and allergic sensitization. These SNPs were further mapped to biological pathways to determine the associations between phenotypes and molecular functions. Assessments of candidate regions to identify functions associated with variations in incidence rates of these diseases are needed in the future.
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Affiliation(s)
- Ritsuko Onuki
- Bioinformatics Team, Advanced Analysis Center, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba, Ibaraki, Japan
| | - Rui Yamaguchi
- Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, Japan
| | - Tetsuo Shibuya
- Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, Japan
| | - Minoru Kanehisa
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, Japan
| | - Susumu Goto
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, Japan
- * E-mail:
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236
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Nelson RM, Wallberg A, Simões ZLP, Lawson DJ, Webster MT. Genomewide analysis of admixture and adaptation in the Africanized honeybee. Mol Ecol 2017; 26:3603-3617. [PMID: 28378497 DOI: 10.1111/mec.14122] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 03/08/2016] [Accepted: 03/20/2017] [Indexed: 02/03/2023]
Abstract
Genetic exchange by hybridization or admixture can make an important contribution to evolution, and introgression of favourable alleles can facilitate adaptation to new environments. A small number of honeybees (Apis mellifera) with African ancestry were introduced to Brazil ~60 years ago, which dispersed and hybridized with existing managed populations of European origin, quickly spreading across much of the Americas in an example of a massive biological invasion. Here, we analyse whole-genome sequences of 32 Africanized honeybees sampled from throughout Brazil to study the effect of this process on genome diversity. By comparison with ancestral populations from Europe and Africa, we infer that these samples have 84% African ancestry, with the remainder from western European populations. However, this proportion varies across the genome and we identify signals of positive selection in regions with high European ancestry proportions. These observations are largely driven by one large gene-rich 1.4-Mbp segment on chromosome 11 where European haplotypes are present at a significantly elevated frequency and likely confer an adaptive advantage in the Africanized honeybee population. This region has previously been implicated in reproductive traits and foraging behaviour in worker bees. Finally, by analysing the distribution of ancestry tract lengths in the context of the known time of the admixture event, we are able to infer an average generation time of 2.0 years. Our analysis highlights the processes by which populations of mixed genetic ancestry form and adapt to new environments.
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Affiliation(s)
- Ronald M Nelson
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Andreas Wallberg
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Zilá Luz Paulino Simões
- Department of Biology, FFCLRP, University of São Paulo, Ribeirão Preto, Brazil.,Department of Genetics, FMRP, University of São Paulo, Ribeirão Preto, Brazil
| | - Daniel J Lawson
- Department of Mathematics, University of Bristol, Bristol, UK
| | - Matthew T Webster
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
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237
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Tracing the peopling of the world through genomics. Nature 2017; 541:302-310. [PMID: 28102248 DOI: 10.1038/nature21347] [Citation(s) in RCA: 329] [Impact Index Per Article: 41.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 12/13/2016] [Indexed: 12/13/2022]
Abstract
Advances in the sequencing and the analysis of the genomes of both modern and ancient peoples have facilitated a number of breakthroughs in our understanding of human evolutionary history. These include the discovery of interbreeding between anatomically modern humans and extinct hominins; the development of an increasingly detailed description of the complex dispersal of modern humans out of Africa and their population expansion worldwide; and the characterization of many of the genetic adaptions of humans to local environmental conditions. Our interpretation of the evolutionary history and adaptation of humans is being transformed by analyses of these new genomic data.
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238
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Schaefer NK, Shapiro B, Green RE. AD-LIBS: inferring ancestry across hybrid genomes using low-coverage sequence data. BMC Bioinformatics 2017; 18:203. [PMID: 28376731 PMCID: PMC5381037 DOI: 10.1186/s12859-017-1613-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 03/24/2017] [Indexed: 01/22/2023] Open
Abstract
Background Inferring the ancestry of each region of admixed individuals’ genomes is useful in studies ranging from disease gene mapping to speciation genetics. Current methods require high-coverage genotype data and phased reference panels, and are therefore inappropriate for many data sets. We present a software application, AD-LIBS, that uses a hidden Markov model to infer ancestry across hybrid genomes without requiring variant calling or phasing. This approach is useful for non-model organisms and in cases of low-coverage data, such as ancient DNA. Results We demonstrate the utility of AD-LIBS with synthetic data. We then use AD-LIBS to infer ancestry in two published data sets: European human genomes with Neanderthal ancestry and brown bear genomes with polar bear ancestry. AD-LIBS correctly infers 87–91% of ancestry in simulations and produces ancestry maps that agree with published results and global ancestry estimates in humans. In brown bears, we find more polar bear ancestry than has been published previously, using both AD-LIBS and an existing software application for local ancestry inference, HAPMIX. We validate AD-LIBS polar bear ancestry maps by recovering a geographic signal within bears that mirrors what is seen in SNP data. Finally, we demonstrate that AD-LIBS is more effective than HAPMIX at inferring ancestry when preexisting phased reference data are unavailable and genomes are sequenced to low coverage. Conclusions AD-LIBS is an effective tool for ancestry inference that can be used even when few individuals are available for comparison or when genomes are sequenced to low coverage. AD-LIBS is therefore likely to be useful in studies of non-model or ancient organisms that lack large amounts of genomic DNA. AD-LIBS can therefore expand the range of studies in which admixture mapping is a viable tool. Electronic supplementary material The online version of this article (doi:10.1186/s12859-017-1613-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nathan K Schaefer
- Department of Biomolecular Engineering, University of California, Santa Cruz, USA. .,UCSC Genomics Institute, University of California, Santa Cruz, USA.
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, USA.,UCSC Genomics Institute, University of California, Santa Cruz, USA
| | - Richard E Green
- Department of Biomolecular Engineering, University of California, Santa Cruz, USA.,UCSC Genomics Institute, University of California, Santa Cruz, USA
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239
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Lipson M, Reich D. A Working Model of the Deep Relationships of Diverse Modern Human Genetic Lineages Outside of Africa. Mol Biol Evol 2017; 34:889-902. [PMID: 28074030 PMCID: PMC5400393 DOI: 10.1093/molbev/msw293] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
A major topic of interest in human prehistory is how the large-scale genetic structure of modern populations outside of Africa was established. Demographic models have been developed that capture the relationships among small numbers of populations or within particular geographical regions, but constructing a phylogenetic tree with gene flow events for a wide diversity of non-Africans remains a difficult problem. Here, we report a model that provides a good statistical fit to allele-frequency correlation patterns among East Asians, Australasians, Native Americans, and ancient western and northern Eurasians, together with archaic human groups. The model features a primary eastern/western bifurcation dating to at least 45,000 years ago, with Australasians nested inside the eastern clade, and a parsimonious set of admixture events. While our results still represent a simplified picture, they provide a useful summary of deep Eurasian population history that can serve as a null model for future studies and a baseline for further discoveries.
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Affiliation(s)
- Mark Lipson
- Department of Genetics, Harvard Medical School, Boston, MA
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA
- Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, MA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA
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240
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Quach H, Quintana-Murci L. Living in an adaptive world: Genomic dissection of the genus Homo and its immune response. J Exp Med 2017; 214:877-894. [PMID: 28351985 PMCID: PMC5379985 DOI: 10.1084/jem.20161942] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2016] [Revised: 02/14/2017] [Accepted: 03/06/2017] [Indexed: 12/14/2022] Open
Abstract
More than a decade after the sequencing of the human genome, a deluge of genome-wide population data are generating a portrait of human genetic diversity at an unprecedented level of resolution. Genomic studies have provided new insight into the demographic and adaptive history of our species, Homo sapiens, including its interbreeding with other hominins, such as Neanderthals, and the ways in which natural selection, in its various guises, has shaped genome diversity. These studies, combined with functional genomic approaches, such as the mapping of expression quantitative trait loci, have helped to identify genes, functions, and mechanisms of prime importance for host survival and involved in phenotypic variation and differences in disease risk. This review summarizes new findings in this rapidly developing field, focusing on the human immune response. We discuss the importance of defining the genetic and evolutionary determinants driving immune response variation, and highlight the added value of population genomic approaches in settings relevant to immunity and infection.
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Affiliation(s)
- Hélène Quach
- Human Evolutionary Genetics Unit, Department of Genomes and Genetics, Institut Pasteur, 75015 Paris, France.,Center of Bioinformatics, Biostatistics and Integrative Biology, Institut Pasteur, 75015 Paris, France.,Centre National de la Recherche Scientifique, URA3012, 75015 Paris, France
| | - Lluis Quintana-Murci
- Human Evolutionary Genetics Unit, Department of Genomes and Genetics, Institut Pasteur, 75015 Paris, France .,Center of Bioinformatics, Biostatistics and Integrative Biology, Institut Pasteur, 75015 Paris, France.,Centre National de la Recherche Scientifique, URA3012, 75015 Paris, France
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241
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Chang D, Knapp M, Enk J, Lippold S, Kircher M, Lister A, MacPhee RDE, Widga C, Czechowski P, Sommer R, Hodges E, Stümpel N, Barnes I, Dalén L, Derevianko A, Germonpré M, Hillebrand-Voiculescu A, Constantin S, Kuznetsova T, Mol D, Rathgeber T, Rosendahl W, Tikhonov AN, Willerslev E, Hannon G, Lalueza-Fox C, Joger U, Poinar H, Hofreiter M, Shapiro B. The evolutionary and phylogeographic history of woolly mammoths: a comprehensive mitogenomic analysis. Sci Rep 2017; 7:44585. [PMID: 28327635 PMCID: PMC5361112 DOI: 10.1038/srep44585] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 02/10/2017] [Indexed: 11/09/2022] Open
Abstract
Near the end of the Pleistocene epoch, populations of the woolly mammoth (Mammuthus primigenius) were distributed across parts of three continents, from western Europe and northern Asia through Beringia to the Atlantic seaboard of North America. Nonetheless, questions about the connectivity and temporal continuity of mammoth populations and species remain unanswered. We use a combination of targeted enrichment and high-throughput sequencing to assemble and interpret a data set of 143 mammoth mitochondrial genomes, sampled from fossils recovered from across their Holarctic range. Our dataset includes 54 previously unpublished mitochondrial genomes and significantly increases the coverage of the Eurasian range of the species. The resulting global phylogeny confirms that the Late Pleistocene mammoth population comprised three distinct mitochondrial lineages that began to diverge ~1.0-2.0 million years ago (Ma). We also find that mammoth mitochondrial lineages were strongly geographically partitioned throughout the Pleistocene. In combination, our genetic results and the pattern of morphological variation in time and space suggest that male-mediated gene flow, rather than large-scale dispersals, was important in the Pleistocene evolutionary history of mammoths.
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Affiliation(s)
- Dan Chang
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Michael Knapp
- Department of Anatomy, University of Otago, 270 Great King Street, Dunedin 9016, New Zealand
| | - Jacob Enk
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L9, Canada
| | - Sebastian Lippold
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig D04103, Germany
| | - Martin Kircher
- Department of Genome Sciences, University of Washington, 3720 15 Ave NE, Seattle, WA 98195-5065, USA
| | - Adrian Lister
- Department of Earth Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Ross D. E. MacPhee
- Department of Mammalogy, American Museum of Natural History, 200 Central Park West, New York NY, 10024, USA
| | - Christopher Widga
- Center of Excellence in Paleontology, East Tennessee State University, 1212 Sunset Dr., Gray, TN 37615, USA
| | - Paul Czechowski
- Antarctic Biological Research Initiative, 31 Jobson Road, SA 5110, Australia
| | - Robert Sommer
- Department of Zoology, Institute of Biosciences, University of Rostock, Universitätsplatz 2, Rostock D-18055, Germany
| | - Emily Hodges
- Department of Biochemistry, Vanderbilt University School of Medicine, 2215 Garland Ave, Nashville, TN 37232, USA
| | - Nikolaus Stümpel
- Staatliches Naturhistorisches Museum Braunschweig, Pockelstrasse 10, Braunschweig 38106, Germany
| | - Ian Barnes
- Department of Earth Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Love Dalén
- Swedish Museum of Natural History, Department of Bioinformatics and Genetics, S-104 05 Stockholm, P.O. Box 50007, Sweden
| | - Anatoly Derevianko
- Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, 17, Novosibirsk, Akademia Lavrentieva, 630090, Russia
| | - Mietje Germonpré
- Operational Directorate “Earth and History of Life”, Royal Belgian Institute of Natural Sciences, Vautierstraat 29, Brussels 1000, Belgium
| | | | - Silviu Constantin
- “Emil Racoviţă” Institute of Speleology, Frumoasă 31, Bucharest, 01906, Romania
| | - Tatyana Kuznetsova
- Department of Palaeontology, Faculty of Geology, Moscow State University, ul. Leninskiye Gory, 1, Moscow, 119991, Russia
| | - Dick Mol
- Mammuthus Club International, Gudumholm 41, Hoofddorp, HG 2133, Netherlands
| | - Thomas Rathgeber
- Staatliches Museum für Naturkunde Stuttgart Rosenstein, Gewann 1, Stuttgart 70191, Germany
| | - Wilfried Rosendahl
- Department “World Cultures and Environment”, Reiss-Engelhorn-Museen, C 5, Zeughaus, Mannheim, 68159, Germany
| | - Alexey N. Tikhonov
- Zoological Institute Russian Academy of Sciences, Universitetskaya nab., 1 Saint-Petersburg 199034, Russia
- Institute of Applied Ecology of the North, North-Eastern Federal University, Lenina 1, Yakutsk, Russia
| | - Eske Willerslev
- Centre for GeoGenetics, Copenhagen University, Nørregade ‘10, Copenhagen, 1165, Denmark
- Department of Zoology, University of Cambridge, Downing St. Cambridge, CB2 3EJ, UK
- Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, UK
| | - Greg Hannon
- CRUK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Carles Lalueza-Fox
- Institute of Evolutionary Biology (CSIC-UPF), Doctor Aiguader, 88, Barcelona, 08003, Spain
| | - Ulrich Joger
- Staatliches Naturhistorisches Museum Braunschweig, Pockelstrasse 10, Braunschweig 38106, Germany
| | - Hendrik Poinar
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L9, Canada
| | - Michael Hofreiter
- Department of Mathematics and Natural Sciences, Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, Potsdam, 14476, Germany
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
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242
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Racimo F, Gokhman D, Fumagalli M, Ko A, Hansen T, Moltke I, Albrechtsen A, Carmel L, Huerta-Sánchez E, Nielsen R. Archaic Adaptive Introgression in TBX15/WARS2. Mol Biol Evol 2017; 34:509-524. [PMID: 28007980 PMCID: PMC5430617 DOI: 10.1093/molbev/msw283] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
A recent study conducted the first genome-wide scan for selection in Inuit from Greenland using single nucleotide polymorphism chip data. Here, we report that selection in the region with the second most extreme signal of positive selection in Greenlandic Inuit favored a deeply divergent haplotype that is closely related to the sequence in the Denisovan genome, and was likely introgressed from an archaic population. The region contains two genes, WARS2 and TBX15, and has previously been associated with adipose tissue differentiation and body-fat distribution in humans. We show that the adaptively introgressed allele has been under selection in a much larger geographic region than just Greenland. Furthermore, it is associated with changes in expression of WARS2 and TBX15 in multiple tissues including the adrenal gland and subcutaneous adipose tissue, and with regional DNA methylation changes in TBX15.
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Affiliation(s)
- Fernando Racimo
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA
| | - David Gokhman
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, Israel
| | - Matteo Fumagalli
- Department of Genetics, Evolution, and Environment, University College London, London, United Kingdom
| | - Amy Ko
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA
| | - Torben Hansen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ida Moltke
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Anders Albrechtsen
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Liran Carmel
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, Israel
| | | | - Rasmus Nielsen
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA
- Department of Statistics, University of California Berkeley, Berkeley, CA
- Museum of Natural History, University of Copenhagen, Copenhagen, Denmark
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243
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McCoy RC, Wakefield J, Akey JM. Impacts of Neanderthal-Introgressed Sequences on the Landscape of Human Gene Expression. Cell 2017; 168:916-927.e12. [PMID: 28235201 PMCID: PMC6219754 DOI: 10.1016/j.cell.2017.01.038] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 01/09/2017] [Accepted: 01/27/2017] [Indexed: 11/20/2022]
Abstract
Regulatory variation influencing gene expression is a key contributor to phenotypic diversity, both within and between species. Unfortunately, RNA degrades too rapidly to be recovered from fossil remains, limiting functional genomic insights about our extinct hominin relatives. Many Neanderthal sequences survive in modern humans due to ancient hybridization, providing an opportunity to assess their contributions to transcriptional variation and to test hypotheses about regulatory evolution. We developed a flexible Bayesian statistical approach to quantify allele-specific expression (ASE) in complex RNA-seq datasets. We identified widespread expression differences between Neanderthal and modern human alleles, indicating pervasive cis-regulatory impacts of introgression. Brain regions and testes exhibited significant downregulation of Neanderthal alleles relative to other tissues, consistent with natural selection influencing the tissue-specific regulatory landscape. Our study demonstrates that Neanderthal-inherited sequences are not silent remnants of ancient interbreeding but have measurable impacts on gene expression that contribute to variation in modern human phenotypes.
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Affiliation(s)
- Rajiv C McCoy
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Jon Wakefield
- Department of Statistics, University of Washington, Seattle, WA 98195, USA; Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Joshua M Akey
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
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244
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Massey SE. Strong Amerindian Mitonuclear Discordance in Puerto Rican Genomes Suggests Amerindian Mitochondrial Benefit. Ann Hum Genet 2017; 81:59-77. [DOI: 10.1111/ahg.12185] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 01/06/2017] [Indexed: 12/24/2022]
Affiliation(s)
- Steven E. Massey
- Biology Department; University of Puerto Rico - Rio Piedras; PO Box 23360 San Juan Puerto Rico 00931
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245
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Racimo F, Marnetto D, Huerta-Sánchez E. Signatures of Archaic Adaptive Introgression in Present-Day Human Populations. Mol Biol Evol 2017; 34:296-317. [PMID: 27756828 PMCID: PMC5400396 DOI: 10.1093/molbev/msw216] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Comparisons of DNA from archaic and modern humans show that these groups interbred, and in some cases received an evolutionary advantage from doing so. This process-adaptive introgression-may lead to a faster rate of adaptation than is predicted from models with mutation and selection alone. Within the last couple of years, a series of studies have identified regions of the genome that are likely examples of adaptive introgression. In many cases, once a region was ascertained as being introgressed, commonly used statistics based on both haplotype as well as allele frequency information were employed to test for positive selection. Introgression by itself, however, changes both the haplotype structure and the distribution of allele frequencies, thus confounding traditional tests for detecting positive selection. Therefore, patterns generated by introgression alone may lead to false inferences of positive selection. Here we explore models involving both introgression and positive selection to investigate the behavior of various statistics under adaptive introgression. In particular, we find that the number and allelic frequencies of sites that are uniquely shared between archaic humans and specific present-day populations are particularly useful for detecting adaptive introgression. We then examine the 1000 Genomes dataset to characterize the landscape of uniquely shared archaic alleles in human populations. Finally, we identify regions that were likely subject to adaptive introgression and discuss some of the most promising candidate genes located in these regions.
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Affiliation(s)
- Fernando Racimo
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA
| | - Davide Marnetto
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Turin, Italy
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246
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Terhorst J, Kamm JA, Song YS. Robust and scalable inference of population history from hundreds of unphased whole genomes. Nat Genet 2017; 49:303-309. [PMID: 28024154 PMCID: PMC5470542 DOI: 10.1038/ng.3748] [Citation(s) in RCA: 474] [Impact Index Per Article: 59.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 11/23/2016] [Indexed: 12/20/2022]
Abstract
It has recently been demonstrated that inference methods based on genealogical processes with recombination can uncover past population history in unprecedented detail. However, these methods scale poorly with sample size, limiting resolution in the recent past, and they require phased genomes, which contain switch errors that can catastrophically distort the inferred history. Here we present SMC++, a new statistical tool capable of analyzing orders of magnitude more samples than existing methods while requiring only unphased genomes (its results are independent of phasing). SMC++ can jointly infer population size histories and split times in diverged populations, and it employs a novel spline regularization scheme that greatly reduces estimation error. We apply SMC++ to analyze sequence data from over a thousand human genomes in Africa and Eurasia, hundreds of genomes from a Drosophila melanogaster population in Africa, and tens of genomes from zebra finch and long-tailed finch populations in Australia.
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Affiliation(s)
- Jonathan Terhorst
- Department of Statistics, University of California, Berkeley, Berkeley, California, USA
| | - John A Kamm
- Department of Statistics, University of California, Berkeley, Berkeley, California, USA
- Computer Science Division, University of California, Berkeley, Berkeley, California, USA
| | - Yun S Song
- Department of Statistics, University of California, Berkeley, Berkeley, California, USA
- Computer Science Division, University of California, Berkeley, Berkeley, California, USA
- Department of Integrative Biology, University of California, Berkeley, Berkeley, California, USA
- Departments of Biology and Mathematics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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247
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Medugorac I, Graf A, Grohs C, Rothammer S, Zagdsuren Y, Gladyr E, Zinovieva N, Barbieri J, Seichter D, Russ I, Eggen A, Hellenthal G, Brem G, Blum H, Krebs S, Capitan A. Whole-genome analysis of introgressive hybridization and characterization of the bovine legacy of Mongolian yaks. Nat Genet 2017; 49:470-475. [PMID: 28135247 DOI: 10.1038/ng.3775] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 12/23/2016] [Indexed: 12/16/2022]
Abstract
The yak is remarkable for its adaptation to high altitude and occupies a central place in the economies of the mountainous regions of Asia. At lower elevations, it is common to hybridize yaks with cattle to combine the yak's hardiness with the productivity of cattle. Hybrid males are sterile, however, preventing the establishment of stable hybrid populations, but not a limited introgression after backcrossing several generations of female hybrids to male yaks. Here we inferred bovine haplotypes in the genomes of 76 Mongolian yaks using high-density SNP genotyping and whole-genome sequencing. These yaks inherited ∼1.3% of their genome from bovine ancestors after nearly continuous admixture over at least the last 1,500 years. The introgressed regions are enriched in genes involved in nervous system development and function, and particularly in glutamate metabolism and neurotransmission. We also identified a novel mutation associated with a polled (hornless) phenotype originating from Mongolian Turano cattle. Our results suggest that introgressive hybridization contributed to the improvement of yak management and breeding.
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Affiliation(s)
- Ivica Medugorac
- Chair of Animal Genetics and Husbandry, Ludwig Maximilians University Munich, Munich, Germany
| | - Alexander Graf
- Laboratory for Functional Genome Analysis, Gene Center, Ludwig Maximilians University Munich, Munich, Germany
| | - Cécile Grohs
- GABI, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Sophie Rothammer
- Chair of Animal Genetics and Husbandry, Ludwig Maximilians University Munich, Munich, Germany
| | | | - Elena Gladyr
- Center of Biotechnology and Molecular Diagnostics of the L.K. Ernst Institute of Animal Husbandry, Moscow region, Russian Federation
| | - Natalia Zinovieva
- Center of Biotechnology and Molecular Diagnostics of the L.K. Ernst Institute of Animal Husbandry, Moscow region, Russian Federation
| | - Johanna Barbieri
- INRA, UMR 1388 Génétique, Physiologie et Systèmes d'Elevage GeT-PlaGe Genomic Facility, Castanet-Tolosan, France.,Université de Toulouse, INPT, ENSAT, UMR 1388 Génétique, Physiologie et Systèmes d'Elevage, Castanet-Tolosan, France
| | | | - Ingolf Russ
- Tierzuchtforschung e.V. München, Grub, Germany
| | - André Eggen
- AgriGenomics, Illumina, San Diego, California, USA
| | - Garrett Hellenthal
- Genetics Institute, Faculty of Life Sciences, University College London, London, UK
| | - Gottfried Brem
- Institute of Animal Breeding and Genetics, Department for Biomedical Sciences, University of Veterinary Medicine, Vienna, Austria
| | - Helmut Blum
- Laboratory for Functional Genome Analysis, Gene Center, Ludwig Maximilians University Munich, Munich, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis, Gene Center, Ludwig Maximilians University Munich, Munich, Germany
| | - Aurélien Capitan
- GABI, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France.,ALLICE, Paris, France
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248
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Deschamps M, Quintana-Murci L. Immunité innée et maladies chez l’homme. Med Sci (Paris) 2017; 32:1079-1086. [DOI: 10.1051/medsci/20163212011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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249
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Seoighe C, Scally A. Inference of Candidate Germline Mutator Loci in Humans from Genome-Wide Haplotype Data. PLoS Genet 2017; 13:e1006549. [PMID: 28095480 PMCID: PMC5283766 DOI: 10.1371/journal.pgen.1006549] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 01/31/2017] [Accepted: 12/20/2016] [Indexed: 12/27/2022] Open
Abstract
The rate of germline mutation varies widely between species but little is known about the extent of variation in the germline mutation rate between individuals of the same species. Here we demonstrate that an allele that increases the rate of germline mutation can result in a distinctive signature in the genomic region linked to the affected locus, characterized by a number of haplotypes with a locally high proportion of derived alleles, against a background of haplotypes carrying a typical proportion of derived alleles. We searched for this signature in human haplotype data from phase 3 of the 1000 Genomes Project and report a number of candidate mutator loci, several of which are located close to or within genes involved in DNA repair or the DNA damage response. To investigate whether mutator alleles remained active at any of these loci, we used de novo mutation counts from human parent-offspring trios in the 1000 Genomes and Genome of the Netherlands cohorts, looking for an elevated number of de novo mutations in the offspring of parents carrying a candidate mutator haplotype at each of these loci. We found some support for two of the candidate loci, including one locus just upstream of the BRSK2 gene, which is expressed in the testis and has been reported to be involved in the response to DNA damage.
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Affiliation(s)
- Cathal Seoighe
- School of Mathematics, Statistics and Applied Mathematics, NUI Galway, Galway, Ireland
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Aylwyn Scally
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
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250
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Brother or Other: The Place of Neanderthals in Human Evolution. VERTEBRATE PALEOBIOLOGY AND PALEOANTHROPOLOGY 2017. [DOI: 10.1007/978-3-319-46646-0_19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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