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African mitochondrial haplogroup L7: a 100,000-year-old maternal human lineage discovered through reassessment and new sequencing. Sci Rep 2022; 12:10747. [PMID: 35750688 PMCID: PMC9232647 DOI: 10.1038/s41598-022-13856-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 05/30/2022] [Indexed: 11/17/2022] Open
Abstract
Archaeological and genomic evidence suggest that modern Homo sapiens have roamed the planet for some 300–500 thousand years. In contrast, global human mitochondrial (mtDNA) diversity coalesces to one African female ancestor (“Mitochondrial Eve”) some 145 thousand years ago, owing to the ¼ gene pool size of our matrilineally inherited haploid genome. Therefore, most of human prehistory was spent in Africa where early ancestors of Southern African Khoisan and Central African rainforest hunter-gatherers (RFHGs) segregated into smaller groups. Their subdivisions followed climatic oscillations, new modes of subsistence, local adaptations, and cultural-linguistic differences, all prior to their exodus out of Africa. Seven African mtDNA haplogroups (L0–L6) traditionally captured this ancient structure—these L haplogroups have formed the backbone of the mtDNA tree for nearly two decades. Here we describe L7, an eighth haplogroup that we estimate to be ~ 100 thousand years old and which has been previously misclassified in the literature. In addition, L7 has a phylogenetic sublineage L7a*, the oldest singleton branch in the human mtDNA tree (~ 80 thousand years). We found that L7 and its sister group L5 are both low-frequency relics centered around East Africa, but in different populations (L7: Sandawe; L5: Mbuti). Although three small subclades of African foragers hint at the population origins of L5'7, the majority of subclades are divided into Afro-Asiatic and eastern Bantu groups, indicative of more recent admixture. A regular re-estimation of the entire mtDNA haplotype tree is needed to ensure correct cladistic placement of new samples in the future.
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2
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Cumer T, Machado AP, Dumont G, Bontzorlos V, Ceccherelli R, Charter M, Dichmann K, Kassinis N, Lourenço R, Manzia F, Martens HD, Prévost L, Rakovic M, Roque I, Siverio F, Roulin A, Goudet J. Landscape and climatic variations shaped secondary contacts amid barn owls of the Western Palearctic. Mol Biol Evol 2021; 39:6454100. [PMID: 34893883 PMCID: PMC8789042 DOI: 10.1093/molbev/msab343] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The combined actions of climatic variations and landscape barriers shape the history of natural populations. When organisms follow their shifting niches, obstacles in the landscape can lead to the splitting of populations, on which evolution will then act independently. When two such populations are reunited, secondary contact occurs in a broad range of admixture patterns, from narrow hybrid zones to the complete dissolution of lineages. A previous study suggested that barn owls colonized the Western Palearctic after the last glaciation in a ring-like fashion around the Mediterranean Sea, and conjectured an admixture zone in the Balkans. Here, we take advantage of whole-genome sequences of 94 individuals across the Western Palearctic to reveal the complex history of the species in the region using observational and modeling approaches. Even though our results confirm that two distinct lineages colonized the region, one in Europe and one in the Levant, they suggest that it predates the last glaciation and identify a secondary contact zone between the two in Anatolia. We also show that barn owls recolonized Europe after the glaciation from two distinct glacial refugia: a previously identified western one in Iberia and a new eastern one in Italy. Both glacial lineages now communicate via eastern Europe, in a wide and permeable contact zone. This complex history of populations enlightens the taxonomy of Tyto alba in the region, highlights the key role played by mountain ranges and large water bodies as barriers and illustrates the power of population genomics in uncovering intricate demographic patterns.
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Affiliation(s)
- Tristan Cumer
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Ana Paula Machado
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Guillaume Dumont
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Vasileios Bontzorlos
- Green Fund, Kifisia, Athens, Greece.,"TYTO" - Organization for the Management and Conservation of Biodiversity in Agricultural Ecosystems, Larisa, Greece
| | | | - Motti Charter
- Shamir Research Institute, University of Haifa, Katzrin, Israel.,Department of Geography and Environmental Sciences, University of Haifa, Haifa, Israel
| | | | | | - Rui Lourenço
- MED Mediterranean Institute for Agriculture, Environment and Development, Laboratory of Ornithology, IIFA, University of Évora, Évora, Portugal
| | | | | | - Laure Prévost
- Association C.H.E.N.E, Centre d'Hébergement et d'Etude sur la Nature et l'Environnement, Allouville-Bellefosse, 76190, France
| | - Marko Rakovic
- Natural History Museum of Belgrade, Belgrade, Serbia
| | - Inês Roque
- MED Mediterranean Institute for Agriculture, Environment and Development, Laboratory of Ornithology, IIFA, University of Évora, Évora, Portugal
| | - Felipe Siverio
- Canary Islands' Ornithology and Natural History Group (GOHNIC), 38480 Buenavista del Norte, Tenerife, Canary Islands, Spain
| | - Alexandre Roulin
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Jérôme Goudet
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
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3
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Marchi N, Excoffier L. Gene flow as a simple cause for an excess of high-frequency-derived alleles. Evol Appl 2020; 13:2254-2263. [PMID: 33005222 PMCID: PMC7513730 DOI: 10.1111/eva.12998] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 04/30/2020] [Accepted: 05/04/2020] [Indexed: 01/19/2023] Open
Abstract
Most human populations exhibit an excess of high-frequency variants, leading to a U-shaped site-frequency spectrum (uSFS). This pattern has been generally interpreted as a signature of ongoing episodes of positive selection, or as evidence for a mis-assignment of ancestral/derived allelic states, but uSFS has also been observed in populations receiving gene flow from a ghost population, in structured populations, or after range expansions. In order to better explain the prevalence of high-frequency variants in humans and other populations, we describe here which patterns of gene flow and population demography can lead to uSFS by using extensive coalescent simulations. We find that uSFS can often be observed in a population if gene flow brings a few ancestral alleles from a well-differentiated population. Gene flow can either consist in single pulses of admixture or continuous immigration, but different demographic conditions are necessary to observe uSFS in these two scenarios. Indeed, an extremely low and recent gene flow is required in the case of single admixture events, while with continuous immigration, uSFS occurs only if gene flow started recently at a high rate or if it lasted for a long time at a low rate. Overall, we find that a neutral uSFS occurs under more restrictive conditions in populations having received single pulses of gene flow than in populations exposed to continuous gene flow. We also show that the uSFS observed in human populations from the 1000 Genomes Project can easily be explained by gene flow from surrounding populations without requiring past episodes of positive selection. These results imply that uSFS should be common in non-isolated populations, such as most wild or domesticated plants and animals.
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Affiliation(s)
- Nina Marchi
- CMPGInstitute of Ecology and EvolutionUniversity of BerneBerneSwitzerland
- Swiss Institute of BioinformaticsLausanneSwitzerland
| | - Laurent Excoffier
- CMPGInstitute of Ecology and EvolutionUniversity of BerneBerneSwitzerland
- Swiss Institute of BioinformaticsLausanneSwitzerland
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4
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Thorstensen MJ, Jeffrey JD, Treberg JR, Watkinson DA, Enders EC, Jeffries KM. Genomic signals found using RNA sequencing show signatures of selection and subtle population differentiation in walleye ( Sander vitreus) in a large freshwater ecosystem. Ecol Evol 2020; 10:7173-7188. [PMID: 32760520 PMCID: PMC7391302 DOI: 10.1002/ece3.6418] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 05/04/2020] [Accepted: 05/07/2020] [Indexed: 12/29/2022] Open
Abstract
RNA sequencing is an effective approach for studying aquatic species yielding both physiological and genomic data. However, its population genetic applications are not well-characterized. We investigate this possible role for RNA sequencing for population genomics in Lake Winnipeg, Manitoba, Canada, walleye (Sander vitreus). Lake Winnipeg walleye represent the largest component of the second-largest freshwater fishery in Canada. In the present study, large female walleye were sampled via nonlethal gill biopsy over two years at three spawning sites representing a latitudinal gradient in the lake. Genetic variation from sequenced mRNA was analyzed for neutral and adaptive markers to investigate population structure and possible adaptive variation. We find low population divergence (F ST = 0.0095), possible northward gene flow, and outlier loci that vary latitudinally in transcripts associated with cell membrane proteins and cytoskeletal function. These results indicate that Lake Winnipeg walleye may be effectively managed as a single demographically connected metapopulation with contributing subpopulations and suggest genomic differences possibly underlying observed phenotypic differences. Despite its high cost relative to other genotyping methods, RNA sequencing data can yield physiological in addition to genetic information discussed here. We therefore argue that it is useful for addressing diverse molecular questions in the conservation of freshwater species.
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Affiliation(s)
| | | | - Jason R. Treberg
- Department of Biological SciencesUniversity of ManitobaWinnipegMBCanada
| | | | - Eva C. Enders
- Freshwater Institute, Fisheries and Oceans CanadaWinnipegMBCanada
| | - Ken M. Jeffries
- Department of Biological SciencesUniversity of ManitobaWinnipegMBCanada
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5
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Lorente-Galdos B, Lao O, Serra-Vidal G, Santpere G, Kuderna LFK, Arauna LR, Fadhlaoui-Zid K, Pimenoff VN, Soodyall H, Zalloua P, Marques-Bonet T, Comas D. Whole-genome sequence analysis of a Pan African set of samples reveals archaic gene flow from an extinct basal population of modern humans into sub-Saharan populations. Genome Biol 2019; 20:77. [PMID: 31023378 PMCID: PMC6485163 DOI: 10.1186/s13059-019-1684-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 03/28/2019] [Indexed: 12/30/2022] Open
Abstract
Background Population demography and gene flow among African groups, as well as the putative archaic introgression of ancient hominins, have been poorly explored at the genome level. Results Here, we examine 15 African populations covering all major continental linguistic groups, ecosystems, and lifestyles within Africa through analysis of whole-genome sequence data of 21 individuals sequenced at deep coverage. We observe a remarkable correlation among genetic diversity and geographic distance, with the hunter-gatherer groups being more genetically differentiated and having larger effective population sizes throughout most modern-human history. Admixture signals are found between neighbor populations from both hunter-gatherer and agriculturalists groups, whereas North African individuals are closely related to Eurasian populations. Regarding archaic gene flow, we test six complex demographic models that consider recent admixture as well as archaic introgression. We identify the fingerprint of an archaic introgression event in the sub-Saharan populations included in the models (~ 4.0% in Khoisan, ~ 4.3% in Mbuti Pygmies, and ~ 5.8% in Mandenka) from an early divergent and currently extinct ghost modern human lineage. Conclusion The present study represents an in-depth genomic analysis of a Pan African set of individuals, which emphasizes their complex relationships and demographic history at population level. Electronic supplementary material The online version of this article (10.1186/s13059-019-1684-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Belen Lorente-Galdos
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (UPF/CSIC), Universitat Pompeu Fabra, 08003, Barcelona, Spain.,Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Oscar Lao
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, 08028, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Gerard Serra-Vidal
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (UPF/CSIC), Universitat Pompeu Fabra, 08003, Barcelona, Spain
| | - Gabriel Santpere
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (UPF/CSIC), Universitat Pompeu Fabra, 08003, Barcelona, Spain.,Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Lukas F K Kuderna
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (UPF/CSIC), Universitat Pompeu Fabra, 08003, Barcelona, Spain
| | - Lara R Arauna
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (UPF/CSIC), Universitat Pompeu Fabra, 08003, Barcelona, Spain
| | - Karima Fadhlaoui-Zid
- College of Science, Department of Biology, Taibah University, Al Madinah, Al Monawarah, Saudi Arabia.,Higher Institute of Biotechnology of Beja, University of Jendouba, Avenue Habib Bourguiba, BP, 382, 9000, Beja, Tunisia
| | - Ville N Pimenoff
- Oncology Data Analytics Program, Bellvitge Biomedical Research Institute (ICO-IDIBELL), Consortium for Biomedical Research in Epidemiology and Public Health, Hospitalet de Llobregat, Barcelona, Spain.,Department of Archaeology, University of Helsinki, Helsinki, Finland
| | - Himla Soodyall
- Division of Human Genetics, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and National Health Laboratory Service, Johannesburg, South Africa
| | - Pierre Zalloua
- School of Medicine, The Lebanese American University, Beirut, 1102-2801, Lebanon
| | - Tomas Marques-Bonet
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (UPF/CSIC), Universitat Pompeu Fabra, 08003, Barcelona, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, 08028, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats, ICREA, 08003, Barcelona, Spain
| | - David Comas
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (UPF/CSIC), Universitat Pompeu Fabra, 08003, Barcelona, Spain.
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6
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Cabrera VM, Marrero P, Abu-Amero KK, Larruga JM. Carriers of mitochondrial DNA macrohaplogroup L3 basal lineages migrated back to Africa from Asia around 70,000 years ago. BMC Evol Biol 2018; 18:98. [PMID: 29921229 PMCID: PMC6009813 DOI: 10.1186/s12862-018-1211-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 06/05/2018] [Indexed: 11/15/2022] Open
Abstract
Background The main unequivocal conclusion after three decades of phylogeographic mtDNA studies is the African origin of all extant modern humans. In addition, a southern coastal route has been argued for to explain the Eurasian colonization of these African pioneers. Based on the age of macrohaplogroup L3, from which all maternal Eurasian and the majority of African lineages originated, the out-of-Africa event has been dated around 60-70 kya. On the opposite side, we have proposed a northern route through Central Asia across the Levant for that expansion and, consistent with the fossil record, we have dated it around 125 kya. To help bridge differences between the molecular and fossil record ages, in this article we assess the possibility that mtDNA macrohaplogroup L3 matured in Eurasia and returned to Africa as basal L3 lineages around 70 kya. Results The coalescence ages of all Eurasian (M,N) and African (L3 ) lineages, both around 71 kya, are not significantly different. The oldest M and N Eurasian clades are found in southeastern Asia instead near of Africa as expected by the southern route hypothesis. The split of the Y-chromosome composite DE haplogroup is very similar to the age of mtDNA L3. An Eurasian origin and back migration to Africa has been proposed for the African Y-chromosome haplogroup E. Inside Africa, frequency distributions of maternal L3 and paternal E lineages are positively correlated. This correlation is not fully explained by geographic or ethnic affinities. This correlation rather seems to be the result of a joint and global replacement of the old autochthonous male and female African lineages by the new Eurasian incomers. Conclusions These results are congruent with a model proposing an out-of-Africa migration into Asia, following a northern route, of early anatomically modern humans carrying pre-L3 mtDNA lineages around 125 kya, subsequent diversification of pre-L3 into the basal lineages of L3, a return to Africa of Eurasian fully modern humans around 70 kya carrying the basal L3 lineages and the subsequent diversification of Eurasian-remaining L3 lineages into the M and N lineages in the outside-of-Africa context, and a second Eurasian global expansion by 60 kya, most probably, out of southeast Asia. Climatic conditions and the presence of Neanderthals and other hominins might have played significant roles in these human movements. Moreover, recent studies based on ancient DNA and whole-genome sequencing are also compatible with this hypothesis. Electronic supplementary material The online version of this article (10.1186/s12862-018-1211-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Vicente M Cabrera
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, E-38271 La Laguna, Tenerife, Spain.
| | - Patricia Marrero
- Research Support General Service, E-38271, La Laguna, Tenerife, Spain
| | - Khaled K Abu-Amero
- Glaucoma Research Chair, Department of Ophthalmology, College of Medicine, King Saud University, Riyadh, Saudi Arabia.,Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Jose M Larruga
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, E-38271 La Laguna, Tenerife, Spain
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7
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Havlickova L, He Z, Wang L, Langer S, Harper AL, Kaur H, Broadley MR, Gegas V, Bancroft I. Validation of an updated Associative Transcriptomics platform for the polyploid crop species Brassica napus by dissection of the genetic architecture of erucic acid and tocopherol isoform variation in seeds. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 93:181-192. [PMID: 29124814 PMCID: PMC5767744 DOI: 10.1111/tpj.13767] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 10/06/2017] [Accepted: 10/30/2017] [Indexed: 05/21/2023]
Abstract
An updated platform was developed to underpin association genetics studies in the polyploid crop species Brassica napus (oilseed rape). Based on 1.92 × 1012 bases of leaf mRNAseq data, functional genotypes, comprising 355 536 single-nucleotide polymorphism markers and transcript abundance were scored across a genetic diversity panel of 383 accessions using a transcriptome reference comprising 116 098 ordered coding DNA sequence (CDS) gene models. The use of the platform for Associative Transcriptomics was first tested by analysing the genetic architecture of variation in seed erucic acid content, as high-erucic rapeseed oil is highly valued for a variety of applications in industry. Known loci were identified, along with a previously undetected minor-effect locus. The platform was then used to analyse variation for the relative proportions of tocopherol (vitamin E) forms in seeds, and the validity of the most significant markers was assessed using a take-one-out approach. Furthermore, the analysis implicated expression variation of the gene Bo2g050970.1, an orthologue of VTE4 (which encodes a γ-tocopherol methyl transferase converting γ-tocopherol into α-tocopherol) associated with the observed trait variation. The establishment of the first full-scale Associative Transcriptomics platform for B. napus enables rapid progress to be made towards an understanding of the genetic architecture of trait variation in this important species, and provides an exemplar for other crops.
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Affiliation(s)
| | - Zhesi He
- Department of BiologyUniversity of YorkHeslingtonYorkYO10 5DDUK
| | - Lihong Wang
- Department of BiologyUniversity of YorkHeslingtonYorkYO10 5DDUK
| | - Swen Langer
- Department of BiologyUniversity of YorkHeslingtonYorkYO10 5DDUK
| | | | - Harjeevan Kaur
- Department of BiologyUniversity of YorkHeslingtonYorkYO10 5DDUK
| | - Martin R. Broadley
- Plant and Crop Sciences DivisionSchool of BiosciencesUniversity of NottinghamSutton Bonington CampusLoughboroughLE12 5RDUK
| | - Vasilis Gegas
- Limagrain UK Ltd.Joseph Nickerson Research CentreRothwellLN7 6DTUK
| | - Ian Bancroft
- Department of BiologyUniversity of YorkHeslingtonYorkYO10 5DDUK
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8
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Comparison of Single Genome and Allele Frequency Data Reveals Discordant Demographic Histories. G3-GENES GENOMES GENETICS 2017; 7:3605-3620. [PMID: 28893846 PMCID: PMC5677151 DOI: 10.1534/g3.117.300259] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Inference of demographic history from genetic data is a primary goal of population genetics of model and nonmodel organisms. Whole genome-based approaches such as the pairwise/multiple sequentially Markovian coalescent methods use genomic data from one to four individuals to infer the demographic history of an entire population, while site frequency spectrum (SFS)-based methods use the distribution of allele frequencies in a sample to reconstruct the same historical events. Although both methods are extensively used in empirical studies and perform well on data simulated under simple models, there have been only limited comparisons of them in more complex and realistic settings. Here we use published demographic models based on data from three human populations (Yoruba, descendants of northwest-Europeans, and Han Chinese) as an empirical test case to study the behavior of both inference procedures. We find that several of the demographic histories inferred by the whole genome-based methods do not predict the genome-wide distribution of heterozygosity, nor do they predict the empirical SFS. However, using simulated data, we also find that the whole genome methods can reconstruct the complex demographic models inferred by SFS-based methods, suggesting that the discordant patterns of genetic variation are not attributable to a lack of statistical power, but may reflect unmodeled complexities in the underlying demography. More generally, our findings indicate that demographic inference from a small number of genomes, routine in genomic studies of nonmodel organisms, should be interpreted cautiously, as these models cannot recapitulate other summaries of the data.
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9
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Accuracy of Demographic Inferences from the Site Frequency Spectrum: The Case of the Yoruba Population. Genetics 2017; 206:439-449. [PMID: 28341655 DOI: 10.1534/genetics.116.192708] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 03/23/2017] [Indexed: 01/23/2023] Open
Abstract
Some methods for demographic inference based on the observed genetic diversity of current populations rely on the use of summary statistics such as the Site Frequency Spectrum (SFS). Demographic models can be either model-constrained with numerous parameters, such as growth rates, timing of demographic events, and migration rates, or model-flexible, with an unbounded collection of piecewise constant sizes. It is still debated whether demographic histories can be accurately inferred based on the SFS. Here, we illustrate this theoretical issue on an example of demographic inference for an African population. The SFS of the Yoruba population (data from the 1000 Genomes Project) is fit to a simple model of population growth described with a single parameter (e.g., founding time). We infer a time to the most recent common ancestor of 1.7 million years (MY) for this population. However, we show that the Yoruba SFS is not informative enough to discriminate between several different models of growth. We also show that for such simple demographies, the fit of one-parameter models outperforms the stairway plot, a recently developed model-flexible method. The use of this method on simulated data suggests that it is biased by the noise intrinsically present in the data.
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10
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11
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Srivastava K, Polin H, Sheldon SL, Wagner FF, Grabmer C, Gabriel C, Denomme GA, Flegel WA. The DAU cluster: a comparative analysis of 18 RHD alleles, some forming partial D antigens. Transfusion 2016; 56:2520-2531. [PMID: 27480171 PMCID: PMC5499517 DOI: 10.1111/trf.13739] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 05/31/2016] [Accepted: 06/01/2016] [Indexed: 01/10/2023]
Abstract
BACKGROUND The Rh system is the most complex and polymorphic blood group system in humans with more than 460 alleles known for the RHD gene. The DAU cluster of RHD alleles is characterized by the single-nucleotide change producing the p.Thr379Met amino acid substitution. It is called the DAU-0 allele and has been postulated to be the primordial allele, from which all other alleles of the DAU cluster have eventually evolved. STUDY DESIGN AND METHODS For two novel DAU alleles, the nucleotide sequences of all 10 exons as well as adjacent intronic regions, including the 5' and 3' untranslated regions (UTR), were determined for the RHD and RHCE genes. A phylogenetic tree for all DAU alleles was established using the neighbor-joining method with Pan troglodytes as root. Standard hemagglutination and flow cytometry tests were performed. RESULTS We characterized two DAU alleles, DAU-11 and DAU-5.1, closely related to DAU-3 and DAU-5, respectively. A phylogenetic analysis of the 18 known DAU alleles indicated point mutations and interallelic recombination contributing to diversification of the DAU cluster. CONCLUSIONS The DAU alleles encode a group of RhD protein variants, some forming partial D antigens known to permit anti-D in carriers; all are expected to cause anti-D alloimmunization in recipients of red blood cell transfusions. The DAU alleles evolved through genomic point mutations and recombination. These results suggest that the cluster of DAU alleles represent a clade, which is concordant with our previous postulate that they derived from the primordial DAU-0 allele.
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Affiliation(s)
- Kshitij Srivastava
- Department of Transfusion Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland
| | - Helene Polin
- Red Cross Transfusion Service of Upper Austria, Linz, Austria
| | - Sherry Lynne Sheldon
- Department of Transfusion Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland
| | | | - Christoph Grabmer
- Department of Blood Group Serology and Transfusion Medicine, SALK-Paracelsus Medical University, Salzburg, Austria
| | - Christian Gabriel
- Red Cross Transfusion Service of Upper Austria, Linz, Austria
- Department of Blood Group Serology and Transfusion Medicine, Medical University of Graz, Graz, Austria
| | | | - Willy Albert Flegel
- Department of Transfusion Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland.
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12
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Siegismund CS, Schäfer I, Seibel P, Kühl U, Schultheiss HP, Lassner D. Mitochondrial haplogroups and expression studies of commonly used human cell lines. Mitochondrion 2016; 30:236-47. [PMID: 27562426 DOI: 10.1016/j.mito.2016.08.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 07/29/2016] [Accepted: 08/19/2016] [Indexed: 02/02/2023]
Abstract
We developed a multiplex fragment length analysis (MFLA) for clearly assigning mitochondrial haplogroups mostly endemic in Europe for future cardiac diagnostics. As a technical proof, 23 commonly used human cell lines were haplotyped as reference standards. The functional analysis on mtDNA copies per cell revealed no correlation to haplogroups but a relatively high rate of mitochondria per cell and at the same time a very low expression of all mitochondrial and some nuclear encoded mitochondrial related genes. Established MFLA is an easy to handle method for analysing European mitochondrial haplogroups to perform epidemic studies and elucidate correlations to distinct diseases.
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Affiliation(s)
| | - Ingo Schäfer
- University of Leipzig, Centre for Biotechnology and Biomedicine (BBZ), Molecular Cell Therapy, Deutscher Platz 5, D-04103 Leipzig, Germany
| | - Peter Seibel
- University of Leipzig, Centre for Biotechnology and Biomedicine (BBZ), Molecular Cell Therapy, Deutscher Platz 5, D-04103 Leipzig, Germany
| | - Uwe Kühl
- Institute for Cardiac Diagnostics and Therapy (IKDT), Moltkestr. 31, D-12203 Berlin, Germany; Department of Cardiology, Campus Virchow, Charité - University Hospital Berlin, Augustenburger Platz 1, D-13353, Germany
| | - Heinz-Peter Schultheiss
- Institute for Cardiac Diagnostics and Therapy (IKDT), Moltkestr. 31, D-12203 Berlin, Germany
| | - Dirk Lassner
- Institute for Cardiac Diagnostics and Therapy (IKDT), Moltkestr. 31, D-12203 Berlin, Germany
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13
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Climatic variability, plasticity, and dispersal: A case study from Lake Tana, Ethiopia. J Hum Evol 2016; 87:32-47. [PMID: 26472274 DOI: 10.1016/j.jhevol.2015.07.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Revised: 03/06/2015] [Accepted: 07/12/2015] [Indexed: 12/23/2022]
Abstract
The numerous dispersal events that have occurred during the prehistory of hominin lineages are the subject of longstanding and increasingly active debate in evolutionary anthropology. As well as research into the dating and geographic extent of such dispersals, there is an increasing focus on the factors that may have been responsible for dispersal. The growing body of detailed regional palaeoclimatic data is invaluable in demonstrating the often close relationship between changes in prehistoric environments and the movements of hominin populations. The scenarios constructed from such data are often overly simplistic, however, concentrating on the dynamics of cyclical contraction and expansion during severe and ameliorated conditions respectively. This contribution proposes a two-stage hypothesis of hominin dispersal in which populations (1) accumulate high levels of climatic tolerance during highly variable climatic phases, and (2) express such heightened tolerance via dispersal in subsequent low-variability phases. Likely dispersal phases are thus proposed to occur during stable climatic phases that immediately follow phases of high climatic variability. Employing high resolution palaeoclimatic data from Lake Tana, Ethiopia, the hypothesis is examined in relation to the early dispersal of Homo sapiens out of East Africa and into the Levant. A dispersal phase is identified in the Lake Tana record between c. 112,550 and c. 96,975 years ago, a date bracket that accords well with the dating evidence for H. sapiens occupation at the sites of Qafzeh and Skhul. Results are discussed in relation to the complex pattern of H. sapiens dispersal out of East Africa, with particular attention paid to the implications of recent genetic chronologies for the origin of non-African modern humans.
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14
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Crevecoeur I, Brooks A, Ribot I, Cornelissen E, Semal P. Late Stone Age human remains from Ishango (Democratic Republic of Congo): New insights on Late Pleistocene modern human diversity in Africa. J Hum Evol 2016; 96:35-57. [PMID: 27343771 DOI: 10.1016/j.jhevol.2016.04.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 04/08/2016] [Accepted: 04/19/2016] [Indexed: 12/11/2022]
Abstract
Although questions of modern human origins and dispersal are subject to intense research within and outside Africa, the processes of modern human diversification during the Late Pleistocene are most often discussed within the context of recent human genetic data. This situation is due largely to the dearth of human fossil remains dating to the final Pleistocene in Africa and their almost total absence from West and Central Africa, thus limiting our perception of modern human diversification within Africa before the Holocene. Here, we present a morphometric comparative analysis of the earliest Late Pleistocene modern human remains from the Central African site of Ishango in the Democratic Republic of Congo. The early Late Stone Age layer (eLSA) of this site, dated to the Last Glacial Maximum (25-20 Ky), contains more than one hundred fragmentary human remains. The exceptional associated archaeological context suggests these remains derived from a community of hunter-fisher-gatherers exhibiting complex social and cognitive behaviors including substantial reliance on aquatic resources, development of fishing technology, possible mathematical notations and repetitive use of space, likely on a seasonal basis. Comparisons with large samples of Late Pleistocene and early Holocene modern human fossils from Africa and Eurasia show that the Ishango human remains exhibit distinctive characteristics and a higher phenotypic diversity in contrast to recent African populations. In many aspects, as is true for the inner ear conformation, these eLSA human remains have more affinities with Middle to early Late Pleistocene fossils worldwide than with extant local African populations. In addition, cross-sectional geometric properties of the long bones are consistent with archaeological evidence suggesting reduced terrestrial mobility resulting from greater investment in and use of aquatic resources. Our results on the Ishango human remains provide insights into past African modern human diversity and adaptation that are consistent with genetic theories about the deep sub-structure of Late Pleistocene African populations and their complex evolutionary history of isolation and diversification.
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Affiliation(s)
- I Crevecoeur
- UMR 5199 PACEA, CNRS, Université de Bordeaux, Pessac, France.
| | - A Brooks
- Department of Anthropology, George Washington University, Washington DC, USA
| | - I Ribot
- Département d'Anthropologie, Université de Montréal, Montréal, Canada
| | - E Cornelissen
- Culturele Antropologie/Prehistorie en Archeologie, Koninklijk Museum voor Midden-Afrika (KMMA), Tervuren, Belgium
| | - P Semal
- Scientific Service of Heritage, Royal Belgian Institute of Natural Sciences (RBINS), Brussels, Belgium
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15
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Sazzini M, De Fanti S, Cherubini A, Quagliariello A, Profiti G, Martelli PL, Casadio R, Ricci C, Campieri M, Lanzini A, Volta U, Caio G, Franceschi C, Spisni E, Luiselli D. Ancient pathogen-driven adaptation triggers increased susceptibility to non-celiac wheat sensitivity in present-day European populations. GENES & NUTRITION 2016; 11:15. [PMID: 27551316 PMCID: PMC4968434 DOI: 10.1186/s12263-016-0532-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 05/11/2016] [Indexed: 02/08/2023]
Abstract
BACKGROUND Non-celiac wheat sensitivity is an emerging wheat-related syndrome showing peak prevalence in Western populations. Recent studies hypothesize that new gliadin alleles introduced in the human diet by replacement of ancient wheat with modern varieties can prompt immune responses mediated by the CXCR3-chemokine axis potentially underlying such pathogenic inflammation. This cultural shift may also explain disease epidemiology, having turned European-specific adaptive alleles previously targeted by natural selection into disadvantageous ones. METHODS To explore this evolutionary scenario, we performed ultra-deep sequencing of genes pivotal in the CXCR3-inflammatory pathway on individuals diagnosed for non-celiac wheat sensitivity and we applied anthropological evolutionary genetics methods to sequence data from worldwide populations to investigate the genetic legacy of natural selection on these loci. RESULTS Our results indicate that balancing selection has maintained two divergent CXCL10/CXCL11 haplotypes in Europeans, one responsible for boosting inflammatory reactions and another for encoding moderate chemokine expression. CONCLUSIONS This led to considerably higher occurrence of the former haplotype in Western people than in Africans and East Asians, suggesting that they might be more prone to side effects related to the consumption of modern wheat varieties. Accordingly, this study contributed to shed new light on some of the mechanisms potentially involved in the disease etiology and on the evolutionary bases of its present-day epidemiological patterns. Moreover, overrepresentation of disease homozygotes for the dis-adaptive haplotype plausibly accounts for their even more enhanced CXCR3-axis expression and for their further increase in disease risk, representing a promising finding to be validated by larger follow-up studies.
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Affiliation(s)
- Marco Sazzini
- Laboratory of Molecular Anthropology, Department of Biological, Geological and Environmental Sciences, 40126 Bologna, Italy
- Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, 40126 Bologna, Italy
| | - Sara De Fanti
- Laboratory of Molecular Anthropology, Department of Biological, Geological and Environmental Sciences, 40126 Bologna, Italy
- Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, 40126 Bologna, Italy
| | - Anna Cherubini
- Laboratory of Molecular Anthropology, Department of Biological, Geological and Environmental Sciences, 40126 Bologna, Italy
- Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, 40126 Bologna, Italy
| | - Andrea Quagliariello
- Laboratory of Molecular Anthropology, Department of Biological, Geological and Environmental Sciences, 40126 Bologna, Italy
- Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, 40126 Bologna, Italy
| | - Giuseppe Profiti
- Department of Biological, Biocomputing Group, Geological and Environmental Sciences, University of Bologna, 40126 Bologna, Italy
- CIRI Health Science and Technologies, University of Bologna, 40064 Ozzano dell’Emilia, Bologna, Italy
| | - Pier Luigi Martelli
- Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, 40126 Bologna, Italy
- Department of Biological, Biocomputing Group, Geological and Environmental Sciences, University of Bologna, 40126 Bologna, Italy
| | - Rita Casadio
- Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, 40126 Bologna, Italy
- Department of Biological, Biocomputing Group, Geological and Environmental Sciences, University of Bologna, 40126 Bologna, Italy
| | - Chiara Ricci
- Department of Clinical and Experimental Sciences, Gastroenterology Unit, Spedali Civili, University of Brescia, 25123 Brescia, Italy
| | - Massimo Campieri
- Department of Medical and Surgical Sciences, Digestive Diseases and Internal Medicine Unit, St. Orsola-Malpighi Hospital, University of Bologna, 40138 Bologna, Italy
| | - Alberto Lanzini
- Department of Clinical and Experimental Sciences, Gastroenterology Unit, Spedali Civili, University of Brescia, 25123 Brescia, Italy
| | - Umberto Volta
- Department of Medical and Surgical Sciences, Digestive Diseases and Internal Medicine Unit, St. Orsola-Malpighi Hospital, University of Bologna, 40138 Bologna, Italy
| | - Giacomo Caio
- Department of Medical and Surgical Sciences, Digestive Diseases and Internal Medicine Unit, St. Orsola-Malpighi Hospital, University of Bologna, 40138 Bologna, Italy
| | - Claudio Franceschi
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40126 Bologna, Italy
| | - Enzo Spisni
- Department of Biological, Unit of Gut Physiopathology and Nutrition, Geological and Environmental Sciences, University of Bologna, 40126 Bologna, Italy
| | - Donata Luiselli
- Laboratory of Molecular Anthropology, Department of Biological, Geological and Environmental Sciences, 40126 Bologna, Italy
- Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, 40126 Bologna, Italy
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16
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Hsieh P, Veeramah KR, Lachance J, Tishkoff SA, Wall JD, Hammer MF, Gutenkunst RN. Whole-genome sequence analyses of Western Central African Pygmy hunter-gatherers reveal a complex demographic history and identify candidate genes under positive natural selection. Genome Res 2016; 26:279-90. [PMID: 26888263 PMCID: PMC4772011 DOI: 10.1101/gr.192971.115] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 01/07/2016] [Indexed: 12/20/2022]
Abstract
African Pygmies practicing a mobile hunter-gatherer lifestyle are phenotypically and genetically diverged from other anatomically modern humans, and they likely experienced strong selective pressures due to their unique lifestyle in the Central African rainforest. To identify genomic targets of adaptation, we sequenced the genomes of four Biaka Pygmies from the Central African Republic and jointly analyzed these data with the genome sequences of three Baka Pygmies from Cameroon and nine Yoruba famers. To account for the complex demographic history of these populations that includes both isolation and gene flow, we fit models using the joint allele frequency spectrum and validated them using independent approaches. Our two best-fit models both suggest ancient divergence between the ancestors of the farmers and Pygmies, 90,000 or 150,000 yr ago. We also find that bidirectional asymmetric gene flow is statistically better supported than a single pulse of unidirectional gene flow from farmers to Pygmies, as previously suggested. We then applied complementary statistics to scan the genome for evidence of selective sweeps and polygenic selection. We found that conventional statistical outlier approaches were biased toward identifying candidates in regions of high mutation or low recombination rate. To avoid this bias, we assigned P-values for candidates using whole-genome simulations incorporating demography and variation in both recombination and mutation rates. We found that genes and gene sets involved in muscle development, bone synthesis, immunity, reproduction, cell signaling and development, and energy metabolism are likely to be targets of positive natural selection in Western African Pygmies or their recent ancestors.
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Affiliation(s)
- PingHsun Hsieh
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA
| | - Krishna R Veeramah
- Arizona Research Laboratories Division of Biotechnology, University of Arizona, Tucson, Arizona 85721, USA; Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York 11794, USA
| | - Joseph Lachance
- Department of Biology and Genetics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA; Department of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Sarah A Tishkoff
- Department of Biology and Genetics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Jeffrey D Wall
- Institute for Human Genetics, University of California, San Francisco, California 94143, USA
| | - Michael F Hammer
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA; Arizona Research Laboratories Division of Biotechnology, University of Arizona, Tucson, Arizona 85721, USA
| | - Ryan N Gutenkunst
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA; Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721, USA
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17
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Grine FE. The Late Quaternary Hominins of Africa: The Skeletal Evidence from MIS 6-2. AFRICA FROM MIS 6-2 2016. [DOI: 10.1007/978-94-017-7520-5_17] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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18
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Manjurano A, Sepúlveda N, Nadjm B, Mtove G, Wangai H, Maxwell C, Olomi R, Reyburn H, Drakeley CJ, Riley EM, Clark TG. USP38, FREM3, SDC1, DDC, and LOC727982 Gene Polymorphisms and Differential Susceptibility to Severe Malaria in Tanzania. J Infect Dis 2015; 212:1129-39. [PMID: 25805752 PMCID: PMC4559194 DOI: 10.1093/infdis/jiv192] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 03/16/2015] [Indexed: 12/20/2022] Open
Abstract
Populations exposed to Plasmodium falciparum infection develop genetic mechanisms of protection against severe malarial disease. Despite decades of genetic epidemiological research, the sickle cell trait (HbAS) sickle cell polymorphism, ABO blood group, and other hemoglobinopathies remain the few major determinants in severe malaria to be replicated across different African populations and study designs. Within a case-control study in a region of high transmission in Tanzania (n = 983), we investigated the role of 40 new loci identified in recent genome-wide studies. In 32 loci passing quality control procedures, we found polymorphisms in USP38, FREM3, SDC1, DDC, and LOC727982 genes to be putatively associated with differential susceptibility to severe malaria. Established candidates explained 7.4% of variation in severe malaria risk (HbAS polymorphism, 6.3%; α-thalassemia, 0.3%; ABO group, 0.3%; and glucose-6-phosphate dehydrogenase deficiency, 0.5%) and the new polymorphisms, another 4.3%. The regions encompassing the loci identified are promising targets for the design of future treatment and control interventions.
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Affiliation(s)
- Alphaxard Manjurano
- Joint Malaria Programme,Kilimanjaro Christian Medical College, Moshi
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Nuno Sepúlveda
- Departments ofImmunology and Infection
- Centre of Statistics and Applications, University of Lisbon, Portugal
| | | | - George Mtove
- Joint Malaria Programme,Kilimanjaro Christian Medical College, Moshi
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Hannah Wangai
- Joint Malaria Programme,Kilimanjaro Christian Medical College, Moshi
| | - Caroline Maxwell
- Joint Malaria Programme,Kilimanjaro Christian Medical College, Moshi
| | - Raimos Olomi
- Joint Malaria Programme,Kilimanjaro Christian Medical College, Moshi
| | - Hugh Reyburn
- Joint Malaria Programme,Kilimanjaro Christian Medical College, Moshi
- Departments ofImmunology and Infection
| | - Christopher J. Drakeley
- Joint Malaria Programme,Kilimanjaro Christian Medical College, Moshi
- Departments ofImmunology and Infection
| | - Eleanor M. Riley
- Joint Malaria Programme,Kilimanjaro Christian Medical College, Moshi
- Departments ofImmunology and Infection
| | - Taane G. Clark
- Pathogen Molecular Biology
- Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, United Kingdom
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19
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Positive Selection on Loci Associated with Drug and Alcohol Dependence. PLoS One 2015; 10:e0134393. [PMID: 26270548 PMCID: PMC4536217 DOI: 10.1371/journal.pone.0134393] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 07/08/2015] [Indexed: 01/20/2023] Open
Abstract
Much of the evolution of human behavior remains a mystery, including how certain disadvantageous behaviors are so prevalent. Nicotine addiction is one such phenotype. Several loci have been implicated in nicotine related phenotypes including the nicotinic receptor gene clusters (CHRNs) on chromosomes 8 and 15. Here we use 1000 Genomes sequence data from 3 populations (Africans, Asians and Europeans) to examine whether natural selection has occurred at these loci. We used Tajima’s D and the integrated haplotype score (iHS) to test for evidence of natural selection. Our results provide evidence for strong selection in the nicotinic receptor gene cluster on chromosome 8, previously found to be significantly associated with both nicotine and cocaine dependence, as well as evidence selection acting on the region containing the CHRNA5 nicotinic receptor gene on chromosome 15, that is genome wide significant for risk for nicotine dependence. To examine the possibility that this selection is related to memory and learning, we utilized genetic data from the Collaborative Studies on the Genetics of Alcoholism (COGA) to test variants within these regions with three tests of memory and learning, the Wechsler Adult Intelligence Scale (WAIS) Block Design, WAIS Digit Symbol and WAIS Information tests. Of the 17 SNPs genotyped in COGA in this region, we find one significantly associated with WAIS digit symbol test results. This test captures aspects of reaction time and memory, suggesting that a phenotype relating to memory and learning may have been the driving force behind selection at these loci. This study could begin to explain why these seemingly deleterious SNPs are present at their current frequencies.
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20
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Bancroft I, Fraser F, Morgan C, Trick M. Collinearity analysis of Brassica A and C genomes based on an updated inferred unigene order. Data Brief 2015. [PMID: 26217717 PMCID: PMC4510050 DOI: 10.1016/j.dib.2015.01.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
This data article includes SNP scoring across lines of the Brassica napus TNDH population based on Illumina sequencing of mRNA, expanded to 75 lines. The 21, 323 mapped markers defined 887 recombination bins, representing an updated genetic linkage map for the species. Based on this new map, 5 genome sequence scaffolds were split and the order and orientation of scaffolds updated to establish a new pseudomolecule specification. The order of unigenes and SNP array probes within these pseudomolecules was determined. Unigenes were assessed for sequence similarity to the A and C genomes. The 57, 246 that mapped to both enabled the collinearity of the A and C genomes to be illustrated graphically. Although the great majority was in collinear positions, some were not. Analyses of 60 such instances are presented, suggesting that the breakdown in collinearity was largely due to either the absence of the homoeologue on one genome (resulting in sequence match to a paralogue) or multiple similar sequences being present. The mRNAseq datasets for the TNDH lines are available from the SRA repository (ERA283648); the remaining datasets are supplied with this article.
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21
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Rishishwar L, Conley AB, Wigington CH, Wang L, Valderrama-Aguirre A, Jordan IK. Ancestry, admixture and fitness in Colombian genomes. Sci Rep 2015. [PMID: 26197429 PMCID: PMC4508918 DOI: 10.1038/srep12376] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The human dimension of the Columbian Exchange entailed substantial genetic admixture between ancestral source populations from Africa, the Americas and Europe, which had evolved separately for many thousands of years. We sought to address the implications of the creation of admixed American genomes, containing novel allelic combinations, for human health and fitness via analysis of an admixed Colombian population from Medellin. Colombian genomes from Medellin show a wide range of three-way admixture contributions from ancestral source populations. The primary ancestry component for the population is European (average = 74.6%, range = 45.0%–96.7%), followed by Native American (average = 18.1%, range = 2.1%–33.3%) and African (average = 7.3%, range = 0.2%–38.6%). Locus-specific patterns of ancestry were evaluated to search for genomic regions that are enriched across the population for particular ancestry contributions. Adaptive and innate immune system related genes and pathways are particularly over-represented among ancestry-enriched segments, including genes (HLA-B and MAPK10) that are involved in defense against endemic pathogens such as malaria. Genes that encode functions related to skin pigmentation (SCL4A5) and cutaneous glands (EDAR) are also found in regions with anomalous ancestry patterns. These results suggest the possibility that ancestry-specific loci were differentially retained in the modern admixed Colombian population based on their utility in the New World environment.
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Affiliation(s)
- Lavanya Rishishwar
- 1] School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA [2] PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia [3] BIOS Centro de Bioinformática y Biología Computacional, Manizales, Caldas, Colombia
| | - Andrew B Conley
- School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | | | - Lu Wang
- School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Augusto Valderrama-Aguirre
- 1] PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia [2] Biomedical Research Institute, Universidad Libre, Cali, Valle del Cauca, Colombia [3] Regenerar - Center of Excellence for Regenerative and Personalized Medicine, Cali, Valle del Cauca, Colombia
| | - I King Jordan
- 1] School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA [2] PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia [3] BIOS Centro de Bioinformática y Biología Computacional, Manizales, Caldas, Colombia
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22
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Exploring population size changes using SNP frequency spectra. Nat Genet 2015; 47:555-9. [PMID: 25848749 PMCID: PMC4414822 DOI: 10.1038/ng.3254] [Citation(s) in RCA: 237] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 02/26/2015] [Indexed: 02/05/2023]
Abstract
Inferring demographic history is an important task in population genetics. Many existing inference methods are based on pre-defined simplified population models, which are more suitable for hypothesis testing than for exploratory analysis. We developed a novel model-flexible method called stairway plot, which infers population size changes over time using SNP frequency spectra. This method is applicable for whole-genome sequences of hundreds of individuals. Using extensive simulation we demonstrated the usefulness of the method for inferring demographic history, especially recent population size changes. The method was applied to the whole genome sequence data of nine populations from the 1000 Genomes Project, and showed a pattern of human population fluctuations from 10 to 200 thousand years ago.
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23
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Cagliani R, Forni D, Biasin M, Comabella M, Guerini FR, Riva S, Pozzoli U, Agliardi C, Caputo D, Malhotra S, Montalban X, Bresolin N, Clerici M, Sironi M. Ancient and recent selective pressures shaped genetic diversity at AIM2-like nucleic acid sensors. Genome Biol Evol 2015; 6:830-45. [PMID: 24682156 PMCID: PMC4007548 DOI: 10.1093/gbe/evu066] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
AIM2-like receptors (ALRs) are a family of nucleic acid sensors essential for innate immune responses against viruses and bacteria. We performed an evolutionary analysis of ALR genes (MNDA, PYHIN1, IFI16, and AIM2) by analyzing inter- and intraspecies diversity. Maximum-likelihood analyses indicated that IFI16 and AIM2 evolved adaptively in primates, with branch-specific selection at the catarrhini lineage for IFI16. Application of a population genetics–phylogenetics approach also allowed identification of positive selection events in the human lineage. Positive selection in primates targeted sites located at the DNA-binding interface in both IFI16 and AIM2. In IFI16, several sites positively selected in primates and in the human lineage were located in the PYD domain, which is involved in protein–protein interaction and is bound by a human cytomegalovirus immune evasion protein. Finally, positive selection was found to target nuclear localization signals in IFI16 and the spacer region separating the two HIN domains. Population genetic analysis in humans revealed that an IFI16 genic region has been a target of long-standing balancing selection, possibly acting on two nonsynonymous polymorphisms located in the spacer region. Data herein indicate that ALRs have been repeatedly targeted by natural selection. The balancing selection region in IFI16 carries a variant with opposite risk effect for distinct autoimmune diseases, suggesting antagonistic pleiotropy. We propose that the underlying scenario is the result of an ancestral and still ongoing host–pathogen arms race and that the maintenance of susceptibility alleles for autoimmune diseases at IFI16 represents an evolutionary trade-off.
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Affiliation(s)
- Rachele Cagliani
- Bioinformatics Laboratory, Scientific Institute IRCCS E. Medea, Bosisio Parini (LC), Italy
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24
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Manjurano A, Sepulveda N, Nadjm B, Mtove G, Wangai H, Maxwell C, Olomi R, Reyburn H, Riley EM, Drakeley CJ, Clark TG. African glucose-6-phosphate dehydrogenase alleles associated with protection from severe malaria in heterozygous females in Tanzania. PLoS Genet 2015; 11:e1004960. [PMID: 25671784 PMCID: PMC4335500 DOI: 10.1371/journal.pgen.1004960] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Accepted: 12/17/2014] [Indexed: 11/24/2022] Open
Abstract
X-linked Glucose-6-phosphate dehydrogenase (G6PD) A- deficiency is prevalent in sub-Saharan Africa populations, and has been associated with protection from severe malaria. Whether females and/or males are protected by G6PD deficiency is uncertain, due in part to G6PD and malaria phenotypic complexity and misclassification. Almost all large association studies have genotyped a limited number of G6PD SNPs (e.g. G6PD202 / G6PD376), and this approach has been too blunt to capture the complete epidemiological picture. Here we have identified 68 G6PD polymorphisms and analysed 29 of these (i.e. those with a minor allele frequency greater than 1%) in 983 severe malaria cases and controls in Tanzania. We establish, across a number of SNPs including G6PD376, that only female heterozygotes are protected from severe malaria. Haplotype analysis reveals the G6PD locus to be under balancing selection, suggesting a mechanism of protection relying on alleles at modest frequency and avoiding fixation, where protection provided by G6PD deficiency against severe malaria is offset by increased risk of life-threatening complications. Our study also demonstrates that the much-needed large-scale studies of severe malaria and G6PD enzymatic function across African populations require the identification and analysis of the full repertoire of G6PD genetic markers. Glucose-6-phosphate dehydrogenase (G6PD) is an essential enzyme that protects red blood cells from oxidative damage. Numerous genetic variants of G6PD, residing in the X chromosome, are found among African populations: mutations causing A- deficiency can lead to serious clinical outcomes (including hemolytic anemia) but also confer protection against severe malaria. Epidemiological studies have used some of the genetic markers that cause A- deficiency to establish who is protected from severe malaria, with differing results. Whether females, with one or two copies of mutant genes, males with one copy, or both genders are protected is uncertain. This uncertainty is due to G6PD and malaria phenotypic complexity and misclassification, and to genetic differences between populations and the limited numbers of genetic markers (usually 2) considered. In this study we analysed more than 30 G6PD genetic markers in 506 Tanzanian children with severe malaria and 477 without malaria. We found that only females with one normal and one mutant copy of the gene (heterozygotes) were protected from severe malaria. Further, we established that the G6PD gene is under evolutionary pressure with the likely mechanism being selection by malaria. Our work demonstrates that studies of severe malaria and G6PD enzymatic function across African populations require, in addition to complete and accurate G6PD phenotypic classification, the identification and analysis of the full repertoire of G6PD genetic markers.
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Affiliation(s)
- Alphaxard Manjurano
- Joint Malaria Programme, Kilimanjaro Christian Medical College, Moshi, Tanzania
| | - Nuno Sepulveda
- Department of Infection and Immunology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Behzad Nadjm
- Joint Malaria Programme, Kilimanjaro Christian Medical College, Moshi, Tanzania
| | - George Mtove
- Joint Malaria Programme, Kilimanjaro Christian Medical College, Moshi, Tanzania
| | - Hannah Wangai
- Joint Malaria Programme, Kilimanjaro Christian Medical College, Moshi, Tanzania
| | - Caroline Maxwell
- Joint Malaria Programme, Kilimanjaro Christian Medical College, Moshi, Tanzania
| | - Raimos Olomi
- Joint Malaria Programme, Kilimanjaro Christian Medical College, Moshi, Tanzania
| | - Hugh Reyburn
- Joint Malaria Programme, Kilimanjaro Christian Medical College, Moshi, Tanzania
- Department of Infection and Immunology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Eleanor M. Riley
- Joint Malaria Programme, Kilimanjaro Christian Medical College, Moshi, Tanzania
- Department of Infection and Immunology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Christopher J. Drakeley
- Joint Malaria Programme, Kilimanjaro Christian Medical College, Moshi, Tanzania
- Department of Infection and Immunology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Taane G. Clark
- Pathogen Molecular Biology Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
- * E-mail:
| | - MalariaGEN Consortium
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
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Kang B, Cheng S, Peng J, Yan J, Zhang S. Interleukin-37 gene variants segregated anciently coexist during hominid evolution. Eur J Hum Genet 2015; 23:1392-8. [PMID: 25626704 DOI: 10.1038/ejhg.2014.302] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Revised: 12/11/2014] [Accepted: 12/19/2014] [Indexed: 11/09/2022] Open
Abstract
IL37 is a member of IL-1 cytokine family but conveys anti-inflammatory functions. The biological characteristic and genetic heterogeneity of IL37 are not fully understood yet. Here using the whole-genome sequencing data from 1000 Genomes Project, we performed population and evolutionary genetic analysis of human IL37 gene. First, 2184 IL37 gene sequences from different human populations were retrieved. The IL37 protein sequences were inferred from the coding DNA sequences and multiple species alignment was made. Then, the phylogenetic tree of IL37 was built and dN/dS ratios were calculated for each evolutionary branch, the classic McDonald and Kreitman test was also performed. Next, we conducted intraspecific evolutionary genetic analysis and built the genealogy network of 116 unique IL37 haplotypes through median-joining network analysis. Finally, we compared IL37 sequences between the modern and archaic humans. Our results for the first time provide solid evidence that common IL37 variants other than NCBI reference sequence are present worldwide. Our data also supports that IL37 variants are shaped and maintained by selection instead of neutral evolution. We further identified that human IL37 variants consist of two major haplogroups and their presence in archaic humans corroborates its ancient origin in hominid evolution. In conclusion, these data indicate that common IL37 variants are maintained among human populations by selective force, suggesting their potential involvements in immune regulation and human diseases. In addition, the ancient history of IL37 variants reveals interesting insight into the complicated human evolutionary history.
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Affiliation(s)
- Bin Kang
- Shanghai Public Health Clinical Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Shimeng Cheng
- Shanghai Public Health Clinical Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Jinbiao Peng
- Shanghai Public Health Clinical Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Jingjing Yan
- Shanghai Public Health Clinical Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Shuye Zhang
- Shanghai Public Health Clinical Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, China.,Key Laboratory of Medical Molecular Virology, Institute of Medical Microbiology, Shanghai Medical College of Fudan University, Shanghai, China
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26
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Lin YL, Pavlidis P, Karakoc E, Ajay J, Gokcumen O. The evolution and functional impact of human deletion variants shared with archaic hominin genomes. Mol Biol Evol 2015; 32:1008-19. [PMID: 25556237 PMCID: PMC4379406 DOI: 10.1093/molbev/msu405] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Allele sharing between modern and archaic hominin genomes has been variously interpreted to have originated from ancestral genetic structure or through non-African introgression from archaic hominins. However, evolution of polymorphic human deletions that are shared with archaic hominin genomes has yet to be studied. We identified 427 polymorphic human deletions that are shared with archaic hominin genomes, approximately 87% of which originated before the Human–Neandertal divergence (ancient) and only approximately 9% of which have been introgressed from Neandertals (introgressed). Recurrence, incomplete lineage sorting between human and chimp lineages, and hominid-specific insertions constitute the remaining approximately 4% of allele sharing between humans and archaic hominins. We observed that ancient deletions correspond to more than 13% of all common (>5% allele frequency) deletion variation among modern humans. Our analyses indicate that the genomic landscapes of both ancient and introgressed deletion variants were primarily shaped by purifying selection, eliminating large and exonic variants. We found 17 exonic deletions that are shared with archaic hominin genomes, including those leading to three fusion transcripts. The affected genes are involved in metabolism of external and internal compounds, growth and sperm formation, as well as susceptibility to psoriasis and Crohn’s disease. Our analyses suggest that these “exonic” deletion variants have evolved through different adaptive forces, including balancing and population-specific positive selection. Our findings reveal that genomic structural variants that are shared between humans and archaic hominin genomes are common among modern humans and can influence biomedically and evolutionarily important phenotypes.
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Affiliation(s)
- Yen-Lung Lin
- Department of Biological Sciences, State University of New York at Buffalo, NY, US
| | - Pavlos Pavlidis
- Institute of Molecular Biology and Biotechnology (IMBB), Foundation of Research and Technology-Hellas, Heraklion, Crete, Greece
| | - Emre Karakoc
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Jerry Ajay
- Department of Computer Science and Engineering, State University of New York at Buffalo, NY, US
| | - Omer Gokcumen
- Department of Biological Sciences, State University of New York at Buffalo, NY, US
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27
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Bentayebi K, Abada F, Ihzmad H, Amzazi S. Genetic ancestry of a Moroccan population as inferred from autosomal STRs. Meta Gene 2014; 2:427-38. [PMID: 25606427 PMCID: PMC4287812 DOI: 10.1016/j.mgene.2014.04.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Accepted: 04/19/2014] [Indexed: 10/25/2022] Open
Abstract
Detecting population substructure and ancestry is a critical issue for both association studies of health behaviors and forensic genetics. Determining aspects of a population's genetic history as potential sources of substructure can aid in design of future genetic studies. Within this context, fifteen autosomal short tandem repeat (STR), were used to examine population genetic structure and hypotheses of the origin of the modern Moroccan population from individuals belonging to three different ethnical groups from Morocco (Arab, Berber and Sahrawi), by comparing their autosomal STR variation with that of neighboring and non-neighboring populations in North Africa, Europe and Middle East as well as proposed ancestral populations in Morocco (Berber). We report on the results that the gradient of North African ancestry accounts for previous observations of low levels of sharing with Near East and a substantially increased gene flow especially from Morocco and Spain.
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Affiliation(s)
- K. Bentayebi
- Laboratoire de Biochimie Immunologie, Faculté des Sciences, Université Mohammed V, Morocco
| | - F. Abada
- Laboratoire de Biochimie Immunologie, Faculté des Sciences, Université Mohammed V, Morocco
| | - H. Ihzmad
- Laboratoire d'épidémiologie, Institut National d'Hygienne, Rabat, Morocco
| | - S. Amzazi
- Laboratoire de Biochimie Immunologie, Faculté des Sciences, Université Mohammed V, Morocco
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Kelso J, Prüfer K. Ancient humans and the origin of modern humans. Curr Opin Genet Dev 2014; 29:133-8. [DOI: 10.1016/j.gde.2014.09.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 09/03/2014] [Accepted: 09/05/2014] [Indexed: 01/06/2023]
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29
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An evolutionary analysis of antigen processing and presentation across different timescales reveals pervasive selection. PLoS Genet 2014; 10:e1004189. [PMID: 24675550 PMCID: PMC3967941 DOI: 10.1371/journal.pgen.1004189] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Accepted: 01/06/2014] [Indexed: 12/28/2022] Open
Abstract
The antigenic repertoire presented by MHC molecules is generated by the antigen processing and presentation (APP) pathway. We analyzed the evolutionary history of 45 genes involved in APP at the inter- and intra-species level. Results showed that 11 genes evolved adaptively in mammals. Several positively selected sites involve positions of fundamental importance to the protein function (e.g. the TAP1 peptide-binding domains, the sugar binding interface of langerin, and the CD1D trafficking signal region). In CYBB, all selected sites cluster in two loops protruding into the endosomal lumen; analysis of missense mutations responsible for chronic granulomatous disease (CGD) showed the action of different selective forces on the very same gene region, as most CGD substitutions involve aminoacid positions that are conserved in all mammals. As for ERAP2, different computational methods indicated that positive selection has driven the recurrent appearance of protein-destabilizing variants during mammalian evolution. Application of a population-genetics phylogenetics approach showed that purifying selection represented a major force acting on some APP components (e.g. immunoproteasome subunits and chaperones) and allowed identification of positive selection events in the human lineage. We also investigated the evolutionary history of APP genes in human populations by developing a new approach that uses several different tests to identify the selection target, and that integrates low-coverage whole-genome sequencing data with Sanger sequencing. This analysis revealed that 9 APP genes underwent local adaptation in human populations. Most positive selection targets are located within noncoding regions with regulatory function in myeloid cells or act as expression quantitative trait loci. Conversely, balancing selection targeted nonsynonymous variants in TAP1 and CD207 (langerin). Finally, we suggest that selected variants in PSMB10 and CD207 contribute to human phenotypes. Thus, we used evolutionary information to generate experimentally-testable hypotheses and to provide a list of sites to prioritize in follow-up analyses. Antigen-presenting cells digest intracellular and extracellular proteins and display the resulting antigenic repertoire on cell surface molecules for recognition by T cells. This process initiates cell-mediated immune responses and is essential to detect infections. The antigenic repertoire is generated by the antigen processing and presentation pathway. Because several pathogens evade immune recognition by hampering this process, genes involved in antigen processing and presentation may represent common natural selection targets. Thus, we analyzed the evolutionary history of these genes during mammalian evolution and in the more recent history of human populations. Evolutionary analyses in mammals indicated that positive selection targeted a very high proportion of genes (24%), and revealed that many selected sites affect positions of fundamental importance to the protein function. In humans, we found different signatures of natural selection acting both on regions that are expected to regulate gene expression levels or timing and on coding variants; two human selected polymorphisms may modulate the susceptibility to Crohn's disease and to HIV-1 infection. Therefore, we provide a comprehensive evolutionary analysis of antigen processing and we show that evolutionary studies can provide useful information concerning the location and nature of functional variants, ultimately helping to clarify phenotypic differences between and within species.
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Gazave E, Ma L, Chang D, Coventry A, Gao F, Muzny D, Boerwinkle E, Gibbs RA, Sing CF, Clark AG, Keinan A. Neutral genomic regions refine models of recent rapid human population growth. Proc Natl Acad Sci U S A 2014; 111:757-62. [PMID: 24379384 PMCID: PMC3896169 DOI: 10.1073/pnas.1310398110] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Human populations have experienced dramatic growth since the Neolithic revolution. Recent studies that sequenced a very large number of individuals observed an extreme excess of rare variants and provided clear evidence of recent rapid growth in effective population size, although estimates have varied greatly among studies. All these studies were based on protein-coding genes, in which variants are also impacted by natural selection. In this study, we introduce targeted sequencing data for studying recent human history with minimal confounding by natural selection. We sequenced loci far from genes that meet a wide array of additional criteria such that mutations in these loci are putatively neutral. As population structure also skews allele frequencies, we sequenced 500 individuals of relatively homogeneous ancestry by first analyzing the population structure of 9,716 European Americans. We used very high coverage sequencing to reliably call rare variants and fit an extensive array of models of recent European demographic history to the site frequency spectrum. The best-fit model estimates ∼ 3.4% growth per generation during the last ∼ 140 generations, resulting in a population size increase of two orders of magnitude. This model fits the data very well, largely due to our observation that assumptions of more ancient demography can impact estimates of recent growth. This observation and results also shed light on the discrepancy in demographic estimates among recent studies.
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Affiliation(s)
- Elodie Gazave
- Departments of Biological Statistics and Computational Biology and
| | - Li Ma
- Departments of Biological Statistics and Computational Biology and
| | - Diana Chang
- Departments of Biological Statistics and Computational Biology and
| | - Alex Coventry
- Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853
| | - Feng Gao
- Departments of Biological Statistics and Computational Biology and
| | - Donna Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030; and
| | - Eric Boerwinkle
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030; and
| | - Richard A. Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030; and
| | - Charles F. Sing
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48105
| | - Andrew G. Clark
- Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853
| | - Alon Keinan
- Departments of Biological Statistics and Computational Biology and
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31
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Rheindt FE, Fujita MK, Wilton PR, Edwards SV. Introgression and Phenotypic Assimilation in Zimmerius Flycatchers (Tyrannidae): Population Genetic and Phylogenetic Inferences from Genome-Wide SNPs. Syst Biol 2013; 63:134-52. [DOI: 10.1093/sysbio/syt070] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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32
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Hudjashov G, Villems R, Kivisild T. Global patterns of diversity and selection in human tyrosinase gene. PLoS One 2013; 8:e74307. [PMID: 24040225 PMCID: PMC3770694 DOI: 10.1371/journal.pone.0074307] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Accepted: 07/31/2013] [Indexed: 01/09/2023] Open
Abstract
Global variation in skin pigmentation is one of the most striking examples of environmental adaptation in humans. More than two hundred loci have been identified as candidate genes in model organisms and a few tens of these have been found to be significantly associated with human skin pigmentation in genome-wide association studies. However, the evolutionary history of different pigmentation genes is rather complex: some loci have been subjected to strong positive selection, while others evolved under the relaxation of functional constraints in low UV environment. Here we report the results of a global study of the human tyrosinase gene, which is one of the key enzymes in melanin production, to assess the role of its variation in the evolution of skin pigmentation differences among human populations. We observe a higher rate of non-synonymous polymorphisms in the European sample consistent with the relaxation of selective constraints. A similar pattern was previously observed in the MC1R gene and concurs with UV radiation-driven model of skin color evolution by which mutations leading to lower melanin levels and decreased photoprotection are subject to purifying selection at low latitudes while being tolerated or even favored at higher latitudes because they facilitate UV-dependent vitamin D production. Our coalescent date estimates suggest that the non-synonymous variants, which are frequent in Europe and North Africa, are recent and have emerged after the separation of East and West Eurasian populations.
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Affiliation(s)
- Georgi Hudjashov
- Evolutionary Biology Group, Estonian Biocentre, Tartu, Estonia
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
- * E-mail:
| | - Richard Villems
- Evolutionary Biology Group, Estonian Biocentre, Tartu, Estonia
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
- Estonian Academy of Sciences, Tallinn, Estonia
| | - Toomas Kivisild
- Evolutionary Biology Group, Estonian Biocentre, Tartu, Estonia
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
- Division of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom
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Harpur BA, Minaei S, Kent CF, Zayed A. Admixture increases diversity in managed honey bees: reply to De la Rúa et al. (2013). Mol Ecol 2013; 22:3211-5. [PMID: 24433573 DOI: 10.1111/mec.12332] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 03/26/2013] [Accepted: 03/29/2013] [Indexed: 11/30/2022]
Abstract
De la Rúa et al. (2013) express some concerns about the conclusions of our recent study showing that management increases genetic diversity of honey bees (Apis mellifera) by promoting admixture (Harpur et al. 2012). We provide a brief review of the literature on the population genetics of A. mellifera and show that we utilized appropriate sampling methods to estimate genetic diversity in the focal populations. Our finding of higher genetic diversity in two managed A. mellifera populations on two different continents is expected to be the norm given the large number of studies documenting admixture in honey bees. Our study focused on elucidating how management affects genetic diversity in honey bees, not on how to best manage bee colonies. We do not endorse the intentional admixture of honey bee populations, and we agree with De la Rúa et al. (2013) that native honey bee subspecies should be conserved.
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Affiliation(s)
- Brock A Harpur
- Department of Biology, York University, 4700 Keele Street, Toronto, M3J 1P3, Ontario, Canada
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34
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Gattepaille LM, Jakobsson M, Blum MGB. Inferring population size changes with sequence and SNP data: lessons from human bottlenecks. Heredity (Edinb) 2013; 110:409-19. [PMID: 23423148 PMCID: PMC3630807 DOI: 10.1038/hdy.2012.120] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Reconstructing historical variation of population size from sequence and single-nucleotide polymorphism (SNP) data is valuable for understanding the evolutionary history of species. Changes in the population size of humans have been thoroughly investigated, and we review different methodologies of demographic reconstruction, specifically focusing on human bottlenecks. In addition to the classical approaches based on the site-frequency spectrum (SFS) or based on linkage disequilibrium, we also review more recent approaches that utilize atypical shared genomic fragments, such as identical by descent or homozygous segments between or within individuals. Compared with methods based on the SFS, these methods are well suited for detecting recent bottlenecks. In general, all these various methods suffer from bias and dependencies on confounding factors such as population structure or poor specification of the mutational and recombination processes, which can affect the demographic reconstruction. With the exception of SFS-based methods, the effects of confounding factors on the inference methods remain poorly investigated. We conclude that an important step when investigating population size changes rests on validating the demographic model by investigating to what extent the fitted demographic model can reproduce the main features of the polymorphism data.
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Affiliation(s)
- L M Gattepaille
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
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35
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Cagliani R, Guerini FR, Rubio-Acero R, Baglio F, Forni D, Agliardi C, Griffanti L, Fumagalli M, Pozzoli U, Riva S, Calabrese E, Sikora M, Casals F, Comi GP, Bresolin N, Cáceres M, Clerici M, Sironi M. Long-standing balancing selection in the THBS4 gene: influence on sex-specific brain expression and gray matter volumes in Alzheimer disease. Hum Mutat 2013; 34:743-53. [PMID: 23420636 DOI: 10.1002/humu.22301] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Accepted: 02/01/2013] [Indexed: 01/08/2023]
Abstract
The THBS4 gene encodes a glycoprotein involved in inflammatory responses and synaptogenesis. THBS4 is expressed at higher levels in the brain of humans compared with nonhuman primates, and the protein accumulates in β-amyloid plaques. We analyzed THBS4 genetic variability in humans and show that two haplotypes (hap1 and hap2) are maintained by balancing selection and modulate THBS4 expression in lymphocytes. Indeed, the balancing selection region covers a predicted transcriptional enhancer. In humans, but not in macaques and chimpanzees, THBS4 brain expression increases with age, and variants in the balancing selection region interact with sex in influencing THBS4 expression (pinteraction = 0.038), with hap1 homozygous females showing lowest expression. In Alzheimer disease (AD) patients, significant interactions between sex and THBS4 genotype were detected for peripheral gray matter (pinteraction = 0.014) and total gray matter (pinteraction = 0.012) volumes. Similarly to the gene expression results, the interaction is mainly mediated by hap1 homozygous AD females, who show reduced volumes. Thus, the balancing selection target in THBS4 is likely represented by one or more variants that regulate tissue-specific and sex-specific gene expression. The selection signature associated with THBS4 might not be related to AD pathogenesis, but rather to inflammatory responses.
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36
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Evolutionary Analysis of the Contact System Indicates that Kininogen Evolved Adaptively in Mammals and in Human Populations. Mol Biol Evol 2013; 30:1397-408. [DOI: 10.1093/molbev/mst054] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
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37
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Associative transcriptomics of traits in the polyploid crop species Brassica napus. Nat Biotechnol 2013; 30:798-802. [PMID: 22820317 DOI: 10.1038/nbt.2302] [Citation(s) in RCA: 193] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Accepted: 06/13/2012] [Indexed: 02/01/2023]
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38
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Moleirinho A, Seixas S, Lopes AM, Bento C, Prata MJ, Amorim A. Evolutionary constraints in the β-globin cluster: the signature of purifying selection at the δ-globin (HBD) locus and its role in developmental gene regulation. Genome Biol Evol 2013; 5:559-71. [PMID: 23431002 PMCID: PMC3622298 DOI: 10.1093/gbe/evt029] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/16/2013] [Indexed: 12/15/2022] Open
Abstract
Human hemoglobins, the oxygen carriers in the blood, are composed by two α-like and two β-like globin monomers. The β-globin gene cluster located at 11p15.5 comprises one pseudogene and five genes whose expression undergoes two critical switches: the embryonic-to-fetal and fetal-to-adult transition. HBD encodes the δ-globin chain of the minor adult hemoglobin (HbA2), which is assumed to be physiologically irrelevant. Paradoxically, reduced diversity levels have been reported for this gene. In this study, we sought a detailed portrait of the genetic variation within the β-globin cluster in a large human population panel from different geographic backgrounds. We resequenced the coding and noncoding regions of the two adult β-globin genes (HBD and HBB) in European and African populations, and analyzed the data from the β-globin cluster (HBE, HBG2, HBG1, HBBP1, HBD, and HBB) in 1,092 individuals representing 14 populations sequenced as part of the 1000 Genomes Project. Additionally, we assessed the diversity levels in nonhuman primates using chimpanzee sequence data provided by the PanMap Project. Comprehensive analyses, based on classic neutrality tests, empirical and haplotype-based studies, revealed that HBD and its neighbor pseudogene HBBP1 have mainly evolved under purifying selection, suggesting that their roles are essential and nonredundant. Moreover, in the light of recent studies on the chromatin conformation of the β-globin cluster, we present evidence sustaining that the strong functional constraints underlying the decreased contemporary diversity at these two regions were not driven by protein function but instead are likely due to a regulatory role in ontogenic switches of gene expression.
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Affiliation(s)
- Ana Moleirinho
- Institute of Molecular Pathology and Immunology of University of Porto (IPATIMUP), Porto, Portugal.
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39
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[Screening and identification of 36 new STR loci in human Y chromosome]. YI CHUAN = HEREDITAS 2012. [PMID: 23208138 DOI: 10.3724/sp.j.1005.2012.01409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
133 candidate Y-STR loci were selected from NCBI STS database or by bioinformatics analysis in human Y-chromosome sequence, and were screened among 48 DNA samples around the world. Forty-one Y-STRs with high allelic frequency were validated, 36 of which were first reported. Two hundred haplotypes of the 41 STRs were identified among 200 randomly sampled male individuals in Shanghai, indicating 100% inter-individual discrimination. By network analysis of haplotypes of the 41 STRs among nine Jiang-surname male individuals with no consanguinity within 5 generations from a Jiang-surname individual gathering at Jiangshan, Zhejiang Province, and 7 Jiang-surname male individuals from the random shanghai population, 6 Jiang-surname individuals from Jiangshan were close with only 2-4 STR locus difference. These 41 Y-STR loci provide enough information by which individuals from each other with different early modern family origin can be effectively distinguished. This will promote studies on identification of non-lineal relationship in forensics, ancestry location of oversea Chinese, the surname origin and evolution, origin and migration of modern humans and many other studies of Contemporary Anthropology.
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Schlebusch CM, Soodyall H. Extensive Population Structure in San, Khoe, and Mixed Ancestry Populations from Southern Africa Revealed by 44 Short 5-SNP Haplotypes. Hum Biol 2012; 84:695-724. [DOI: 10.3378/027.084.0603] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/15/2013] [Indexed: 11/05/2022]
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41
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42
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Sankararaman S, Patterson N, Li H, Pääbo S, Reich D. The date of interbreeding between Neandertals and modern humans. PLoS Genet 2012; 8:e1002947. [PMID: 23055938 PMCID: PMC3464203 DOI: 10.1371/journal.pgen.1002947] [Citation(s) in RCA: 221] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Accepted: 07/27/2012] [Indexed: 12/26/2022] Open
Abstract
Comparisons of DNA sequences between Neandertals and present-day humans have shown that Neandertals share more genetic variants with non-Africans than with Africans. This could be due to interbreeding between Neandertals and modern humans when the two groups met subsequent to the emergence of modern humans outside Africa. However, it could also be due to population structure that antedates the origin of Neandertal ancestors in Africa. We measure the extent of linkage disequilibrium (LD) in the genomes of present-day Europeans and find that the last gene flow from Neandertals (or their relatives) into Europeans likely occurred 37,000–86,000 years before the present (BP), and most likely 47,000–65,000 years ago. This supports the recent interbreeding hypothesis and suggests that interbreeding may have occurred when modern humans carrying Upper Paleolithic technologies encountered Neandertals as they expanded out of Africa. One of the key discoveries from the analysis of the Neandertal genome is that Neandertals share more genetic variants with non-Africans than with Africans. This observation is consistent with two hypotheses: interbreeding between Neandertals and modern humans after modern humans emerged out of Africa or population structure in the ancestors of Neandertals and modern humans. These hypotheses make different predictions about the date of last gene exchange between the ancestors of Neandertals and modern non-Africans. We estimate this date by measuring the extent of linkage disequilibrium (LD) in the genomes of present-day Europeans and find that the last gene flow from Neandertals into Europeans likely occurred 37,000–86,000 years before the present (BP), and most likely 47,000–65,000 years ago. This supports the recent interbreeding hypothesis and suggests that interbreeding occurred when modern humans carrying Upper Paleolithic technologies encountered Neandertals as they expanded out of Africa.
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Affiliation(s)
- Sriram Sankararaman
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- * E-mail: (SS); (SP); (DR)
| | - Nick Patterson
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Heng Li
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Svante Pääbo
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- * E-mail: (SS); (SP); (DR)
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- * E-mail: (SS); (SP); (DR)
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Abstract
Because obesity is associated with diverse chronic diseases, little attention has been directed to the multiple beneficial functions of adipose tissue. Adipose tissue not only provides energy for growth, reproduction and immune function, but also secretes and receives diverse signaling molecules that coordinate energy allocation between these functions in response to ecological conditions. Importantly, many relevant ecological cues act on growth and physique, with adiposity responding as a counterbalancing risk management strategy. The large number of individual alleles associated with adipose tissue illustrates its integration with diverse metabolic pathways. However, phenotypic variation in age, sex, ethnicity and social status is further associated with different strategies for storing and using energy. Adiposity therefore represents a key means of phenotypic flexibility within and across generations, enabling a coherent life-history strategy in the face of ecological stochasticity. The sensitivity of numerous metabolic pathways to ecological cues makes our species vulnerable to manipulative globalized economic forces. The aim of this article is to understand how human adipose tissue biology interacts with modern environmental pressures to generate excess weight gain and obesity. The disease component of obesity might lie not in adipose tissue itself, but in its perturbation by our modern industrialized niche. Efforts to combat obesity could be more effective if they prioritized 'external' environmental change rather than attempting to manipulate 'internal' biology through pharmaceutical or behavioral means.
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Affiliation(s)
- Jonathan C K Wells
- Childhood Nutrition Research Centre, UCL Institute of Child Health, 30 Guilford Street, London, WC1N 1EH, UK.
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44
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Rosenberg NA. A population-genetic perspective on the similarities and differences among worldwide human populations. Hum Biol 2012; 83:659-84. [PMID: 22276967 DOI: 10.3378/027.083.0601] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Recent studies have produced a variety of advances in the investigation of genetic similarities and differences among human populations. Here, I pose a series of questions about human population-genetic similarities and differences, and I then answer these questions by numerical computation with a single shared population-genetic data set. The collection of answers obtained provides an introductory perspective for understanding key results on the features of worldwide human genetic variation.
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Affiliation(s)
- Noah A Rosenberg
- Department of Biology, Stanford University, Stanford, CA 94305, USA.
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45
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Harpur BA, Minaei S, Kent CF, Zayed A. Management increases genetic diversity of honey bees via admixture. Mol Ecol 2012; 21:4414-21. [PMID: 22564213 DOI: 10.1111/j.1365-294x.2012.05614.x] [Citation(s) in RCA: 112] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The process of domestication often brings about profound changes in levels of genetic variation in animals and plants. The honey bee, Apis mellifera, has been managed by humans for centuries for both honey and wax production and crop pollination. Human management and selective breeding are believed to have caused reductions in genetic diversity in honey bee populations, thereby contributing to the global declines threatening this ecologically and economically important insect. However, previous studies supporting this claim mostly relied on population genetic comparisons of European and African (or Africanized) honey bee races; such conclusions require reassessment given recent evidence demonstrating that the honey bee originated in Africa and colonized Europe via two independent expansions. We sampled honey bee workers from two managed populations in North America and Europe as well as several old-world progenitor populations in Africa, East and West Europe. Managed bees had highly introgressed genomes representing admixture between East and West European progenitor populations. We found that managed honey bees actually have higher levels of genetic diversity compared with their progenitors in East and West Europe, providing an unusual example whereby human management increases genetic diversity by promoting admixture. The relationship between genetic diversity and honey bee declines is tenuous given that managed bees have more genetic diversity than their progenitors and many viable domesticated animals.
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Affiliation(s)
- Brock A Harpur
- Department of Biology York University, Toronto, Ontario, Canada M3J 1P3
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46
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Blome MW, Cohen AS, Tryon CA, Brooks AS, Russell J. The environmental context for the origins of modern human diversity: A synthesis of regional variability in African climate 150,000–30,000 years ago. J Hum Evol 2012; 62:563-92. [DOI: 10.1016/j.jhevol.2012.01.011] [Citation(s) in RCA: 202] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2011] [Revised: 12/02/2011] [Accepted: 01/24/2012] [Indexed: 11/27/2022]
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47
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Weiss ML, Tackney J. An Introduction to Genetics. Hum Biol 2012. [DOI: 10.1002/9781118108062.ch3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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48
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Santovito A, Cervella P, Delpero M. Endothelial nitric oxide synthase intron 4 VNTR gene polymorphisms in European and African populations. Mol Biol Rep 2012; 39:6693-8. [DOI: 10.1007/s11033-012-1492-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2011] [Accepted: 01/24/2012] [Indexed: 01/05/2023]
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49
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Salm MPA, Horswell SD, Hutchison CE, Speedy HE, Yang X, Liang L, Schadt EE, Cookson WO, Wierzbicki AS, Naoumova RP, Shoulders CC. The origin, global distribution, and functional impact of the human 8p23 inversion polymorphism. Genome Res 2012; 22:1144-53. [PMID: 22399572 PMCID: PMC3371712 DOI: 10.1101/gr.126037.111] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Genomic inversions are an increasingly recognized source of genetic variation. However, a lack of reliable high-throughput genotyping assays for these structures has precluded a full understanding of an inversion's phylogenetic, phenotypic, and population genetic properties. We characterize these properties for one of the largest polymorphic inversions in man (the ∼4.5-Mb 8p23.1 inversion), a structure that encompasses numerous signals of natural selection and disease association. We developed and validated a flexible bioinformatics tool that utilizes SNP data to enable accurate, high-throughput genotyping of the 8p23.1 inversion. This tool was applied retrospectively to diverse genome-wide data sets, revealing significant population stratification that largely follows a clinal “serial founder effect” distribution model. Phylogenetic analyses establish the inversion's ancestral origin within the Homo lineage, indicating that 8p23.1 inversion has occurred independently in the Pan lineage. The human inversion breakpoint was localized to an inverted pair of human endogenous retrovirus elements within the large, flanking low-copy repeats; experimental validation of this breakpoint confirmed these elements as the likely intermediary substrates that sponsored inversion formation. In five data sets, mRNA levels of disease-associated genes were robustly associated with inversion genotype. Moreover, a haplotype associated with systemic lupus erythematosus was restricted to the derived inversion state. We conclude that the 8p23.1 inversion is an evolutionarily dynamic structure that can now be accommodated into the understanding of human genetic and phenotypic diversity.
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Affiliation(s)
- Maximilian P A Salm
- Centre for Endocrinology, Barts & the London School of Medicine & Dentistry, Queen Mary University of London, London, United Kingdom.
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50
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Seixas S, Ivanova N, Ferreira Z, Rocha J, Victor BL. Loss and gain of function in SERPINB11: an example of a gene under selection on standing variation, with implications for host-pathogen interactions. PLoS One 2012; 7:e32518. [PMID: 22393410 PMCID: PMC3290568 DOI: 10.1371/journal.pone.0032518] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2011] [Accepted: 02/01/2012] [Indexed: 12/26/2022] Open
Abstract
Serine protease inhibitors (SERPINs) are crucial in the regulation of diverse biological processes including inflammation and immune response. SERPINB11, located in the 18q21 gene cluster, is a polymorphic gene/pseudogene coding for a non-inhibitory SERPIN. In a genome-wide scan for recent selection, SERPINB11 was identified as a potential candidate gene for adaptive evolution in Yoruba. The present study sought a better understanding of the evolutionary history of SERPINB11, with special focus on evaluating its selective signature. Through the resequencing of coding and noncoding regions of SERPINB11 in 20 Yorubans and analyzing primate orthologous sequences, we identified a full-length SERPINB11 variant encoding a non-inhibitory SERPIN as the putative candidate of selection – probably driven to higher frequencies by an adaptive response using preexisting variation. In addition, we detected contrasting evolutionary features of SERPINB11 in primates: While primate phylogeny as a whole is under purifying selection, the human lineage shows evidence of positive selection in a few codons, all associated with the active SERPINB11. Comparative modeling studies suggest that positively selected codons reduce SERPINB11's ability to undergo the conformational changes typical of inhibitory SERPINs – suggesting that it is evolving towards a new non-inhibitory function in humans. Significant correlations between SERPINB11 variants and the environmental variables, pastoralism and pathogen richness, have led us to propose a selective advantage through host-pathogen interactions, possibly linked to an adaptive response combating the emergence of infectious diseases in recent human evolution. This work represents the first description of a resurrected gene in humans, and may well exemplify selection on standing variation triggered by drastic ecological shifts.
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Affiliation(s)
- Susana Seixas
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal.
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