1
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Labuda D, Harding T, Milot E, Vézina H. The effective family size of immigrant founders predicts their long-term demographic outcome: From Québec settlers to their 20th-century descendants. PLoS One 2022; 17:e0266079. [PMID: 35507549 PMCID: PMC9067642 DOI: 10.1371/journal.pone.0266079] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 03/14/2022] [Indexed: 11/19/2022] Open
Abstract
Population history reconstruction, using extant genetic diversity data, routinely relies on simple demographic models to project the past through ascending genealogical-tree branches. Because genealogy and genetics are intimately related, we traced descending genealogies of the Québec founders to pursue their fate and to assess their contribution to the present-day population. Focusing on the female and male founder lines, we observed important sex-biased immigration in the early colony years and documented a remarkable impact of these early immigrants on the genetic make-up of 20th-century Québec. We estimated the immigrants’ survival ratio as a proportion of lineages found in the 1931–60 Québec to their number introduced within the immigration period. We assessed the effective family size, EFS, of all immigrant parents and their Québec-born descendants. The survival ratio of the earliest immigrants was the highest and declined over centuries in association with the immigrants’ EFS. Parents with high EFS left plentiful married descendants, putting EFS as the most important variable determining the parental demographic success throughout time for generations ahead. EFS of immigrant founders appears to predict their long-term demographic and, consequently, their genetic outcome. Genealogically inferred immigrants’ "autosomal" genetic contribution to 1931–60 Québec from consecutive immigration periods follow the same yearly pattern as the corresponding maternal and paternal lines. Québec genealogical data offer much broader information on the ancestral diversity distribution than genetic scrutiny of a limited population sample. Genealogically inferred population history could assist studies of evolutionary factors shaping population structure and provide tools to target specific health interventions.
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Affiliation(s)
- Damian Labuda
- Centre de Recherche, CHU Sainte-Justine, Université de Montréal, Montreal, Québec, Canada
- Département de Pédiatrie, Université de Montréal, Montreal, Québec, Canada
- * E-mail:
| | - Tommy Harding
- Centre de Recherche, CHU Sainte-Justine, Université de Montréal, Montreal, Québec, Canada
- Département de chimie, biochimie et physique, Université du Québec à Trois-Rivières, Trois-Rivières, Québec, Canada
| | - Emmanuel Milot
- Département de chimie, biochimie et physique, Université du Québec à Trois-Rivières, Trois-Rivières, Québec, Canada
| | - Hélène Vézina
- Projet BALSAC, Université du Québec à Chicoutimi, Chicoutimi, Québec, Canada
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2
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Foote AD, Martin MD, Louis M, Pacheco G, Robertson KM, Sinding MHS, Amaral AR, Baird RW, Baker CS, Ballance L, Barlow J, Brownlow A, Collins T, Constantine R, Dabin W, Dalla Rosa L, Davison NJ, Durban JW, Esteban R, Ferguson SH, Gerrodette T, Guinet C, Hanson MB, Hoggard W, Matthews CJD, Samarra FIP, de Stephanis R, Tavares SB, Tixier P, Totterdell JA, Wade P, Excoffier L, Gilbert MTP, Wolf JBW, Morin PA. Killer whale genomes reveal a complex history of recurrent admixture and vicariance. Mol Ecol 2019; 28:3427-3444. [PMID: 31131963 DOI: 10.1111/mec.15099] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 04/06/2019] [Accepted: 04/08/2019] [Indexed: 02/06/2023]
Abstract
Reconstruction of the demographic and evolutionary history of populations assuming a consensus tree-like relationship can mask more complex scenarios, which are prevalent in nature. An emerging genomic toolset, which has been most comprehensively harnessed in the reconstruction of human evolutionary history, enables molecular ecologists to elucidate complex population histories. Killer whales have limited extrinsic barriers to dispersal and have radiated globally, and are therefore a good candidate model for the application of such tools. Here, we analyse a global data set of killer whale genomes in a rare attempt to elucidate global population structure in a nonhuman species. We identify a pattern of genetic homogenisation at lower latitudes and the greatest differentiation at high latitudes, even between currently sympatric lineages. The processes underlying the major axis of structure include high drift at the edge of species' range, likely associated with founder effects and allelic surfing during postglacial range expansion. Divergence between Antarctic and non-Antarctic lineages is further driven by ancestry segments with up to four-fold older coalescence time than the genome-wide average; relicts of a previous vicariance during an earlier glacial cycle. Our study further underpins that episodic gene flow is ubiquitous in natural populations, and can occur across great distances and after substantial periods of isolation between populations. Thus, understanding the evolutionary history of a species requires comprehensive geographic sampling and genome-wide data to sample the variation in ancestry within individuals.
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Affiliation(s)
- Andrew D Foote
- CMPG, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | | | - Marie Louis
- Department of Biology, Section for Evolutionary Genomics, University of Copenhagen, Copenhagen, Denmark.,Scottish Oceans Institute, East Sands, University of St. Andrews, St. Andrews, UK
| | - George Pacheco
- Department of Biology, Section for Evolutionary Genomics, University of Copenhagen, Copenhagen, Denmark
| | - Kelly M Robertson
- Marine Mammal and Turtle Division, National Marine Fisheries Service, National Oceanographic and Atmospheric Administration, Southwest Fisheries Science Center, La Jolla, California
| | - Mikkel-Holger S Sinding
- Department of Biology, Section for Evolutionary Genomics, University of Copenhagen, Copenhagen, Denmark.,Greenland Institute of Natural Resources, Nuuk, Greenland
| | - Ana R Amaral
- American Museum of Natural History, New York City, New York.,Faculdade de Ciências Universidade de Lisboa, Centre for Ecology, Evolution and Environmental Changes, Lisboa, Portugal
| | | | - Charles Scott Baker
- Department of Fisheries and Wildlife, Marine Mammal Institute, Oregon State University, Newport, Oregon.,School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Lisa Ballance
- Marine Mammal and Turtle Division, National Marine Fisheries Service, National Oceanographic and Atmospheric Administration, Southwest Fisheries Science Center, La Jolla, California
| | - Jay Barlow
- Marine Mammal and Turtle Division, National Marine Fisheries Service, National Oceanographic and Atmospheric Administration, Southwest Fisheries Science Center, La Jolla, California
| | - Andrew Brownlow
- Scottish Marine Animal Stranding Scheme, SRUC Veterinary Services Drummondhill, Inverness, UK
| | - Tim Collins
- Ocean Giants Program, Wildlife Conservation Society, New York City, New York
| | | | - Willy Dabin
- Observatoire Pelagis, Université de La Rochelle-CNRS, La Rochelle, France
| | - Luciano Dalla Rosa
- Laboratório de Ecologia e Conservação da Megafauna Marinha, Instituto de Oceanografia, Universidade Federal do Rio Grande, Rio Grande, Brazil
| | - Nicholas J Davison
- Scottish Marine Animal Stranding Scheme, SRUC Veterinary Services Drummondhill, Inverness, UK
| | - John W Durban
- Marine Mammal and Turtle Division, National Marine Fisheries Service, National Oceanographic and Atmospheric Administration, Southwest Fisheries Science Center, La Jolla, California
| | - Ruth Esteban
- CIRCE, Conservation, Information and Research on Cetaceans, Algeciras, Spain
| | | | - Tim Gerrodette
- Marine Mammal and Turtle Division, National Marine Fisheries Service, National Oceanographic and Atmospheric Administration, Southwest Fisheries Science Center, La Jolla, California
| | - Christophe Guinet
- Centre d'Etudes Biologiques de Chizé (CEBC), CNRS-ULR, UMR, Chizé, France
| | - M Bradley Hanson
- National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Northwest Fisheries Science Center, Seattle, Washington
| | - Wayne Hoggard
- National Marine Fisheries Service, NOAA, Southeast Fisheries Science Center, Pascagoula, Mississippi
| | | | | | - Renaud de Stephanis
- CIRCE, Conservation, Information and Research on Cetaceans, Algeciras, Spain
| | - Sara B Tavares
- Scottish Oceans Institute, East Sands, University of St. Andrews, St. Andrews, UK
| | - Paul Tixier
- Centre d'Etudes Biologiques de Chizé (CEBC), CNRS-ULR, UMR, Chizé, France.,School of Life and Environmental Sciences (Burwood Campus), Deakin University, Geelong, Victoria, Australia
| | - John A Totterdell
- Marine Information and Research Group-Australia (MIRG), Quinns Rocks, Western Australia, Australia
| | - Paul Wade
- National Marine Mammal Laboratory, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Alaska Fisheries Science Center, Seattle, Washington
| | - Laurent Excoffier
- CMPG, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - M Thomas P Gilbert
- NTNU University Museum, Trondheim, Norway.,Department of Biology, Section for Evolutionary Genomics, University of Copenhagen, Copenhagen, Denmark
| | - Jochen B W Wolf
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany.,Department of Evolutionary Biology, Science of Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Phillip A Morin
- Marine Mammal and Turtle Division, National Marine Fisheries Service, National Oceanographic and Atmospheric Administration, Southwest Fisheries Science Center, La Jolla, California
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3
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Vyas DN, Mulligan CJ. Analyses of Neanderthal introgression suggest that Levantine and southern Arabian populations have a shared population history. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2019; 169:227-239. [PMID: 30889271 DOI: 10.1002/ajpa.23818] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 01/11/2019] [Accepted: 02/21/2019] [Indexed: 01/31/2023]
Abstract
OBJECTIVES Modern humans are thought to have interbred with Neanderthals in the Near East soon after modern humans dispersed out of Africa. This introgression event likely took place in either the Levant or southern Arabia depending on the dispersal route out of Africa that was followed. In this study, we compare Neanderthal introgression in contemporary Levantine and southern Arabian populations to investigate Neanderthal introgression and to study Near Eastern population history. MATERIALS AND METHODS We analyzed genotyping data on >400,000 autosomal SNPs from seven Levantine and five southern Arabian populations and compared these data to those from populations from around the world including Neanderthal and Denisovan genomes. We used f4 and D statistics to estimate and compare levels of Neanderthal introgression between Levantine, southern Arabian, and comparative global populations. We also identified 1,581 putative Neanderthal-introgressed SNPs within our dataset and analyzed their allele frequencies as a means to compare introgression patterns in Levantine and southern Arabian genomes. RESULTS We find that Levantine and southern Arabian populations have similar levels of Neanderthal introgression to each other but lower levels than other non-Africans. Furthermore, we find that introgressed SNPs have very similar allele frequencies in the Levant and southern Arabia, which indicates that Neanderthal introgression is similarly distributed in Levantine and southern Arabian genomes. DISCUSSION We infer that the ancestors of contemporary Levantine and southern Arabian populations received Neanderthal introgression prior to separating from each other and that there has been extensive gene flow between these populations.
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Affiliation(s)
- Deven N Vyas
- Department of Anthropology, University of Florida, Gainesville, Florida.,Genetics Institute, University of Florida, Gainesville, Florida
| | - Connie J Mulligan
- Department of Anthropology, University of Florida, Gainesville, Florida.,Genetics Institute, University of Florida, Gainesville, Florida
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4
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Torres R, Szpiech ZA, Hernandez RD. Human demographic history has amplified the effects of background selection across the genome. PLoS Genet 2018; 14:e1007387. [PMID: 29912945 PMCID: PMC6056204 DOI: 10.1371/journal.pgen.1007387] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 07/23/2018] [Accepted: 04/30/2018] [Indexed: 01/22/2023] Open
Abstract
Natural populations often grow, shrink, and migrate over time. Such demographic processes can affect genome-wide levels of genetic diversity. Additionally, genetic variation in functional regions of the genome can be altered by natural selection, which drives adaptive mutations to higher frequencies or purges deleterious ones. Such selective processes affect not only the sites directly under selection but also nearby neutral variation through genetic linkage via processes referred to as genetic hitchhiking in the context of positive selection and background selection (BGS) in the context of purifying selection. While there is extensive literature examining the consequences of selection at linked sites at demographic equilibrium, less is known about how non-equilibrium demographic processes influence the effects of hitchhiking and BGS. Utilizing a global sample of human whole-genome sequences from the Thousand Genomes Project and extensive simulations, we investigate how non-equilibrium demographic processes magnify and dampen the consequences of selection at linked sites across the human genome. When binning the genome by inferred strength of BGS, we observe that, compared to Africans, non-African populations have experienced larger proportional decreases in neutral genetic diversity in strong BGS regions. We replicate these findings in admixed populations by showing that non-African ancestral components of the genome have also been affected more severely in these regions. We attribute these differences to the strong, sustained/recurrent population bottlenecks that non-Africans experienced as they migrated out of Africa and throughout the globe. Furthermore, we observe a strong correlation between FST and the inferred strength of BGS, suggesting a stronger rate of genetic drift. Forward simulations of human demographic history with a model of BGS support these observations. Our results show that non-equilibrium demography significantly alters the consequences of selection at linked sites and support the need for more work investigating the dynamic process of multiple evolutionary forces operating in concert.
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Affiliation(s)
- Raul Torres
- Biomedical Sciences Graduate Program, University of California San Francisco, San Francisco, CA, United States of America
| | - Zachary A. Szpiech
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, United States of America
| | - Ryan D. Hernandez
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, United States of America
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, United States of America
- Institute for Computational Health Sciences, University of California San Francisco, San Francisco, CA, United States of America
- Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA, United States of America
- * E-mail:
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5
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Vahia MN, Yadav N, Ladiwala U, Mathur D. A diffusion based study of population dynamics: Prehistoric migrations into South Asia. PLoS One 2017; 12:e0176985. [PMID: 28493906 PMCID: PMC5426639 DOI: 10.1371/journal.pone.0176985] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2016] [Accepted: 04/20/2017] [Indexed: 01/04/2023] Open
Abstract
A diffusion equation has been used to study migration of early humans into the South Asian subcontinent. The diffusion equation is tempered by a set of parameters that account for geographical features like proximity to water resources, altitude, and flatness of land. The ensuing diffusion of populations is followed in time-dependent computer simulations carried out over a period of 10,000 YBP. The geographical parameters are determined from readily-available satellite data. The results of our computer simulations are compared to recent genetic data so as to better correlate the migratory patterns of various populations; they suggest that the initial populations started to coalesce around 4,000 YBP before the commencement of a period of relative geographical isolation of each population group. The period during which coalescence of populations occurred appears consistent with the established timeline associated with the Harappan civilization and also, with genetic admixing that recent genetic mapping data reveal. Our results may contribute to providing a timeline for the movement of prehistoric people. Most significantly, our results appear to suggest that the Ancestral Austro-Asiatic population entered the subcontinent through an easterly direction, potentially resolving a hitherto-contentious issue.
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Affiliation(s)
- Mayank N. Vahia
- Tata Institute of Fundamental Research, Mumbai, India
- * E-mail:
| | - Nisha Yadav
- Tata Institute of Fundamental Research, Mumbai, India
| | - Uma Ladiwala
- Tata Institute of Fundamental Research, Mumbai, India
| | - Deepak Mathur
- Tata Institute of Fundamental Research, Mumbai, India
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6
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Bailey SF, Bataillon T. Can the experimental evolution programme help us elucidate the genetic basis of adaptation in nature? Mol Ecol 2016; 25:203-18. [PMID: 26346808 PMCID: PMC5019151 DOI: 10.1111/mec.13378] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 08/26/2015] [Accepted: 09/04/2015] [Indexed: 02/04/2023]
Abstract
There have been a variety of approaches taken to try to characterize and identify the genetic basis of adaptation in nature, spanning theoretical models, experimental evolution studies and direct tests of natural populations. Theoretical models can provide formalized and detailed hypotheses regarding evolutionary processes and patterns, from which experimental evolution studies can then provide important proofs of concepts and characterize what is biologically reasonable. Genetic and genomic data from natural populations then allow for the identification of the particular factors that have and continue to play an important role in shaping adaptive evolution in the natural world. Further to this, experimental evolution studies allow for tests of theories that may be difficult or impossible to test in natural populations for logistical and methodological reasons and can even generate new insights, suggesting further refinement of existing theories. However, as experimental evolution studies often take place in a very particular set of controlled conditions--that is simple environments, a small range of usually asexual species, relatively short timescales--the question remains as to how applicable these experimental results are to natural populations. In this review, we discuss important insights coming from experimental evolution, focusing on four key topics tied to the evolutionary genetics of adaptation, and within those topics, we discuss the extent to which the experimental work compliments and informs natural population studies. We finish by making suggestions for future work in particular a need for natural population genomic time series data, as well as the necessity for studies that combine both experimental evolution and natural population approaches.
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Affiliation(s)
- Susan F. Bailey
- Bioinformatics Research CentreAarhus UniversityC.F. Møllers Allé 8DK‐8000Aarhus CDenmark
| | - Thomas Bataillon
- Bioinformatics Research CentreAarhus UniversityC.F. Møllers Allé 8DK‐8000Aarhus CDenmark
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7
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Tassi F, Ghirotto S, Mezzavilla M, Vilaça ST, De Santi L, Barbujani G. Early modern human dispersal from Africa: genomic evidence for multiple waves of migration. INVESTIGATIVE GENETICS 2015; 6:13. [PMID: 26550467 PMCID: PMC4636834 DOI: 10.1186/s13323-015-0030-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 10/27/2015] [Indexed: 12/22/2022]
Abstract
Background Anthropological and genetic data agree in indicating the African continent as the main place of origin for anatomically modern humans. However, it is unclear whether early modern humans left Africa through a single, major process, dispersing simultaneously over Asia and Europe, or in two main waves, first through the Arab Peninsula into southern Asia and Oceania, and later through a northern route crossing the Levant. Results Here, we show that accurate genomic estimates of the divergence times between European and African populations are more recent than those between Australo-Melanesia and Africa and incompatible with the effects of a single dispersal. This difference cannot possibly be accounted for by the effects of either hybridization with archaic human forms in Australo-Melanesia or back migration from Europe into Africa. Furthermore, in several populations of Asia we found evidence for relatively recent genetic admixture events, which could have obscured the signatures of the earliest processes. Conclusions We conclude that the hypothesis of a single major human dispersal from Africa appears hardly compatible with the observed historical and geographical patterns of genome diversity and that Australo-Melanesian populations seem still to retain a genomic signature of a more ancient divergence from Africa Electronic supplementary material The online version of this article (doi:10.1186/s13323-015-0030-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Francesca Tassi
- Department of Life Sciences and Biotechnologies, University of Ferrara, Ferrara, Italy
| | - Silvia Ghirotto
- Department of Life Sciences and Biotechnologies, University of Ferrara, Ferrara, Italy
| | - Massimo Mezzavilla
- Institute for Maternal and Child Health-IRCCS "BurloGarofolo", University of Trieste, Trieste, Italy
| | - Sibelle Torres Vilaça
- Department of Life Sciences and Biotechnologies, University of Ferrara, Ferrara, Italy.,Present Address: Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Lisa De Santi
- Department of Life Sciences and Biotechnologies, University of Ferrara, Ferrara, Italy
| | - Guido Barbujani
- Department of Life Sciences and Biotechnologies, University of Ferrara, Ferrara, Italy
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8
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Campbell MC, Hirbo JB, Townsend JP, Tishkoff SA. The peopling of the African continent and the diaspora into the new world. Curr Opin Genet Dev 2015; 29:120-32. [PMID: 25461616 DOI: 10.1016/j.gde.2014.09.003] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Revised: 09/03/2014] [Accepted: 09/05/2014] [Indexed: 12/22/2022]
Abstract
Africa is the birthplace of anatomically modern humans, and is the geographic origin of human migration across the globe within the last 100,000 years. The history of African populations has consisted of a number of demographic events that have influenced patterns of genetic and phenotypic variation across the continent. With the increasing amount of genomic data and corresponding developments in computational methods, researchers are able to explore long-standing evolutionary questions, expanding our understanding of human history within and outside of Africa. This review will summarize some of the recent findings regarding African demographic history, including the African Diaspora, and will briefly explore their implications for disease susceptibility in populations of African descent.
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9
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Evolutionary genetic bases of longevity and senescence. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 847:1-44. [PMID: 25916584 DOI: 10.1007/978-1-4939-2404-2_1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Senescence, as a time-dependent developmental process, affects all organisms at every stage in their development and growth. During this process, genetic, epigenetic and environmental factors are known to introduce a wide range of variation for longevity among individuals. As an important life-history trait, longevity shows ontogenetic relationships with other complex traits, and hence may be viewed as a composite trait. Factors that influence the origin and maintenance of diversity of life are ultimately governed by Darwinian processes. Here we review evolutionary genetic mechanisms underlying longevity and senescence in humans from a life-history and genotype-epigenetic-phenotype (G-E-P) map prospective. We suggest that synergistic and cascading effects of cis-ruptive mechanisms in the genome, and epigenetic disruptive processes in relation to environmental factors may lead to sequential slippage in the G-E-P space. These mechanisms accompany age, stage and individual specific senescent processes, influenced by positive pleiotropy of certain genes, superior genome integrity, negative-frequency dependent selection and other factors that universally regulate rarity in nature. Finally we interpret life span as an inherent property of self-organizing systems that, accordingly, maintain species-specific limits for the entire complex of fitness traits. We conclude that Darwinian approaches provide unique opportunities to discover the biological bases of longevity as well as devise individual specific medical or other interventions toward improving health span.
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10
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On the unfounded enthusiasm for soft selective sweeps. Nat Commun 2014; 5:5281. [DOI: 10.1038/ncomms6281] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 09/17/2014] [Indexed: 11/09/2022] Open
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11
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Pickrell JK, Reich D. Toward a new history and geography of human genes informed by ancient DNA. Trends Genet 2014; 30:377-89. [PMID: 25168683 PMCID: PMC4163019 DOI: 10.1016/j.tig.2014.07.007] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Revised: 07/21/2014] [Accepted: 07/28/2014] [Indexed: 12/12/2022]
Abstract
Genetic information contains a record of the history of our species, and technological advances have transformed our ability to access this record. Many studies have used genome-wide data from populations today to learn about the peopling of the globe and subsequent adaptation to local conditions. Implicit in this research is the assumption that the geographic locations of people today are informative about the geographic locations of their ancestors in the distant past. However, it is now clear that long-range migration, admixture, and population replacement subsequent to the initial out-of-Africa expansion have altered the genetic structure of most of the world's human populations. In light of this we argue that it is time to critically reevaluate current models of the peopling of the globe, as well as the importance of natural selection in determining the geographic distribution of phenotypes. We specifically highlight the transformative potential of ancient DNA. By accessing the genetic make-up of populations living at archaeologically known times and places, ancient DNA makes it possible to directly track migrations and responses to natural selection.
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Affiliation(s)
- Joseph K Pickrell
- New York Genome Center, New York, NY, USA; Department of Biological Sciences, Columbia University, New York, NY, USA.
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA.
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12
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Impact of range expansions on current human genomic diversity. Curr Opin Genet Dev 2014; 29:22-30. [PMID: 25156518 DOI: 10.1016/j.gde.2014.07.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2014] [Revised: 07/09/2014] [Accepted: 07/25/2014] [Indexed: 12/19/2022]
Abstract
The patterns of population genetic diversity depend to a large extent on past demographic history. Most human populations are known to have gone recently through a series of range expansions within and out of Africa, but these spatial expansions are rarely taken into account when interpreting observed genomic diversity, possibly because they are difficult to model. Here we review available evidence in favour of range expansions out of Africa, and we discuss several of their consequences on neutral and selected diversity, including some recent observations on an excess of rare neutral and selected variants in large samples. We further show that in spatially subdivided populations, the sampling strategy can severely impact the resulting genetic diversity and be confounded by past demography. We conclude that ignoring the spatial structure of human population can lead to some misinterpretations of extant genetic diversity.
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13
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Benguigui M, Arenas M. Spatial and temporal simulation of human evolution. Methods, frameworks and applications. Curr Genomics 2014; 15:245-55. [PMID: 25132795 PMCID: PMC4133948 DOI: 10.2174/1389202915666140506223639] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Revised: 04/05/2014] [Accepted: 05/04/2014] [Indexed: 01/29/2023] Open
Abstract
Analyses of human evolution are fundamental to understand the current gradients of human diversity. In this concern, genetic samples collected from current populations together with archaeological data are the most important resources to study human evolution. However, they are often insufficient to properly evaluate a variety of evolutionary scenarios, leading to continuous debates and discussions. A commonly applied strategy consists of the use of computer simulations based on, as realistic as possible, evolutionary models, to evaluate alternative evolutionary scenarios through statistical correlations with the real data. Computer simulations can also be applied to estimate evolutionary parameters or to study the role of each parameter on the evolutionary process. Here we review the mainly used methods and evolutionary frameworks to perform realistic spatially explicit computer simulations of human evolution. Although we focus on human evolution, most of the methods and software we describe can also be used to study other species. We also describe the importance of considering spatially explicit models to better mimic human evolutionary scenarios based on a variety of phenomena such as range expansions, range shifts, range contractions, sex-biased dispersal, long-distance dispersal or admixtures of populations. We finally discuss future implementations to improve current spatially explicit simulations and their derived applications in human evolution.
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Affiliation(s)
- Macarena Benguigui
- Centre for Molecular Biology "Severo Ochoa", Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Miguel Arenas
- Centre for Molecular Biology "Severo Ochoa", Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
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14
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Dall'Olio GM, Bertranpetit J, Wagner A, Laayouni H. Human genome variation and the concept of genotype networks. PLoS One 2014; 9:e99424. [PMID: 24911413 PMCID: PMC4049842 DOI: 10.1371/journal.pone.0099424] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Accepted: 05/14/2014] [Indexed: 12/29/2022] Open
Abstract
Genotype networks are a concept used in systems biology to study sets of genotypes having the same phenotype, and the ability of these to bring forth novel phenotypes. In the past they have been applied to determine the genetic heterogeneity, and stability to mutations, of systems such as metabolic networks and RNA folds. Recently, they have been the base for reconciling the neutralist and selectionist views on evolution. Here, we adapted this concept to the study of population genetics data. Specifically, we applied genotype networks to the human 1000 genomes dataset, and analyzed networks composed of short haplotypes of Single Nucleotide Variants (SNV). The result is a scan of how properties related to genetic heterogeneity and stability to mutations are distributed along the human genome. We found that genes involved in acquired immunity, such as some HLA and MHC genes, tend to have the most heterogeneous and connected networks, and that coding regions tend to be more heterogeneous and stable to mutations than non-coding regions. We also found, using coalescent simulations, that regions under selection have more extended and connected networks. The application of the concept of genotype networks can provide a new opportunity to understand the evolutionary processes that shaped our genome. Learning how the genotype space of each region of our genome has been explored during the evolutionary history of the human species can lead to a better understanding on how selective pressures and neutral factors have shaped genetic diversity within populations and among individuals. Combined with the availability of larger datasets of sequencing data, genotype networks represent a new approach to the study of human genetic diversity that looks to the whole genome, and goes beyond the classical division between selection and neutrality methods.
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Affiliation(s)
| | - Jaume Bertranpetit
- Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
| | - Andreas Wagner
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
- The Swiss Institute of Bioinformatics, Lausanne, Switzerland
- The Santa Fe Institute, Santa Fe, New Mexico, United States of America
| | - Hafid Laayouni
- Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
- Universitat Autonòma de Barcelona, Barcelona, Spain
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Choudhury A, Hazelhurst S, Meintjes A, Achinike-Oduaran O, Aron S, Gamieldien J, Jalali Sefid Dashti M, Mulder N, Tiffin N, Ramsay M. Population-specific common SNPs reflect demographic histories and highlight regions of genomic plasticity with functional relevance. BMC Genomics 2014; 15:437. [PMID: 24906912 PMCID: PMC4092225 DOI: 10.1186/1471-2164-15-437] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Accepted: 05/19/2014] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Population differentiation is the result of demographic and evolutionary forces. Whole genome datasets from the 1000 Genomes Project (October 2012) provide an unbiased view of genetic variation across populations from Europe, Asia, Africa and the Americas. Common population-specific SNPs (MAF > 0.05) reflect a deep history and may have important consequences for health and wellbeing. Their interpretation is contextualised by currently available genome data. RESULTS The identification of common population-specific (CPS) variants (SNPs and SSV) is influenced by admixture and the sample size under investigation. Nine of the populations in the 1000 Genomes Project (2 African, 2 Asian (including a merged Chinese group) and 5 European) revealed that the African populations (LWK and YRI), followed by the Japanese (JPT) have the highest number of CPS SNPs, in concordance with their histories and given the populations studied. Using two methods, sliding 50-SNP and 5-kb windows, the CPS SNPs showed distinct clustering across large genome segments and little overlap of clusters between populations. iHS enrichment score and the population branch statistic (PBS) analyses suggest that selective sweeps are unlikely to account for the clustering and population specificity. Of interest is the association of clusters close to recombination hotspots. Functional analysis of genes associated with the CPS SNPs revealed over-representation of genes in pathways associated with neuronal development, including axonal guidance signalling and CREB signalling in neurones. CONCLUSIONS Common population-specific SNPs are non-randomly distributed throughout the genome and are significantly associated with recombination hotspots. Since the variant alleles of most CPS SNPs are the derived allele, they likely arose in the specific population after a split from a common ancestor. Their proximity to genes involved in specific pathways, including neuronal development, suggests evolutionary plasticity of selected genomic regions. Contrary to expectation, selective sweeps did not play a large role in the persistence of population-specific variation. This suggests a stochastic process towards population-specific variation which reflects demographic histories and may have some interesting implications for health and susceptibility to disease.
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Affiliation(s)
- Ananyo Choudhury
- />Sydney Brenner Institute of Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
- />Division of Human Genetics, National Health Laboratory Service, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Scott Hazelhurst
- />Sydney Brenner Institute of Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
- />School of Electrical & Information Engineering, University of the Witwatersrand, Johannesburg, South Africa
| | - Ayton Meintjes
- />Department Clinical Laboratory Sciences, Computational Biology Group, IDM, University of Cape Town, Cape Town, South Africa
| | - Ovokeraye Achinike-Oduaran
- />Sydney Brenner Institute of Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
- />Division of Human Genetics, National Health Laboratory Service, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Shaun Aron
- />Sydney Brenner Institute of Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Junaid Gamieldien
- />South African National Bioinformatics Institute/Medical Research Council of South Africa Bioinformatics Unit, University of the Western Cape, Bellville, South Africa
| | - Mahjoubeh Jalali Sefid Dashti
- />South African National Bioinformatics Institute/Medical Research Council of South Africa Bioinformatics Unit, University of the Western Cape, Bellville, South Africa
| | - Nicola Mulder
- />Department Clinical Laboratory Sciences, Computational Biology Group, IDM, University of Cape Town, Cape Town, South Africa
| | - Nicki Tiffin
- />South African National Bioinformatics Institute/Medical Research Council of South Africa Bioinformatics Unit, University of the Western Cape, Bellville, South Africa
| | - Michèle Ramsay
- />Sydney Brenner Institute of Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
- />Division of Human Genetics, National Health Laboratory Service, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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Veeramah KR, Hammer MF. The impact of whole-genome sequencing on the reconstruction of human population history. Nat Rev Genet 2014; 15:149-62. [PMID: 24492235 DOI: 10.1038/nrg3625] [Citation(s) in RCA: 127] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Examining patterns of molecular genetic variation in both modern-day and ancient humans has proved to be a powerful approach to learn about our origins. Rapid advances in DNA sequencing technology have allowed us to characterize increasing amounts of genomic information. Although this clearly provides unprecedented power for inference, it also introduces more complexity into the way we use and interpret such data. Here, we review ongoing debates that have been influenced by improvements in our ability to sequence DNA and discuss some of the analytical challenges that need to be overcome in order to fully exploit the rich historical information that is contained in the entirety of the human genome.
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Affiliation(s)
- Krishna R Veeramah
- 1] Arizona Research Laboratories Division of Biotechnology, Room 231, Life Sciences South, 1007 East Lowell Street, University of Arizona, Tucson, Arizona 85721, USA. [2] Stony Brook University, Stony Brook, New York 11794-5245, USA
| | - Michael F Hammer
- Arizona Research Laboratories Division of Biotechnology, Room 231, Life Sciences South, 1007 East Lowell Street, University of Arizona, Tucson, Arizona 85721, USA
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17
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Stäubert C, Le Duc D, Schöneberg T. Examining the Dynamic Evolution of G Protein-Coupled Receptors. METHODS IN PHARMACOLOGY AND TOXICOLOGY 2014. [DOI: 10.1007/978-1-62703-779-2_2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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Labuda D, Yotova V, Lefebvre JF, Moreau C, Utermann G, Williams SM. X-linked MTMR8 diversity and evolutionary history of sub-Saharan populations. PLoS One 2013; 8:e80710. [PMID: 24282552 PMCID: PMC3839994 DOI: 10.1371/journal.pone.0080710] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Accepted: 10/07/2013] [Indexed: 01/04/2023] Open
Abstract
The genetic diversity within an 11 kb segment of the MTMR8 gene in a sample of 111 sub-Saharan and 49 non-African X chromosomes was investigated to assess the early evolutionary history of sub-Saharan Africans and the out-of-Africa expansion. The analyses revealed a complex genetic structure of the Africans that contributed to the emergence of modern humans. We observed partitioning of two thirds of old lineages among southern, west/central and east African populations indicating ancient population stratification predating the out of Africa migration. Age estimates of these lineages, older than coalescence times of uniparentally inherited markers, raise the question whether contemporary humans originated from a single population or as an amalgamation of different populations separated by years of independent evolution, thus suggesting a greater antiquity of our species than generally assumed. While the oldest sub-Saharan lineages, ∼500 thousand years, are found among Khoe-San from southern-Africa, a distinct haplotype found among Biaka is likely due to admixture from an even older population. An East African population that gave rise to non-Africans underwent a selective sweep affecting the subcentromeric region where MTMR8 is located. This and similar sweeps in four other regions of the X chromosome, documented in the literature, effectively reduced genetic diversity of non-African chromosomes and therefore may have exacerbated the effect of the demographic bottleneck usually ascribed to the out of Africa migration. Our data is suggestive, however, that a bottleneck, occurred in Africa before range expansion.
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Affiliation(s)
- Damian Labuda
- Centre de Recherche, CHU Sainte-Justine, Université de Montréal, Montréal, Québec, Canada
- Département de Pédiatrie, Université de Montréal, Montréal, Québec, Canada
- * E-mail:
| | - Vania Yotova
- Centre de Recherche, CHU Sainte-Justine, Université de Montréal, Montréal, Québec, Canada
| | - Jean-François Lefebvre
- Centre de Recherche, CHU Sainte-Justine, Université de Montréal, Montréal, Québec, Canada
| | - Claudia Moreau
- Centre de Recherche, CHU Sainte-Justine, Université de Montréal, Montréal, Québec, Canada
| | - Gerd Utermann
- Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Scott M. Williams
- Department of Genetics, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, United States of America
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Hicks C, Miele L, Koganti T, Young-Gaylor L, Rogers D, Vijayakumar V, Megason G. Analysis of Patterns of Gene Expression Variation within and between Ethnic Populations in Pediatric B-ALL. Cancer Inform 2013; 12:155-73. [PMID: 24023509 PMCID: PMC3762614 DOI: 10.4137/cin.s11831] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
B-Precursor acute lymphoblastic leukemia (B-ALL) is the most common childhood cancer. Although 80% of B-ALL patients are able to be cured, significant challenges persist. Significant disparities in clinical outcomes and mortality rates exist between racial/ethnic populations. The objective of this study was to determine whether gene expression levels significantly differ between ethnic populations. We compared gene expression levels between four ethnic populations (Whites, Blacks, Hispanics, and Asians) in the United States. Additionally, we performed network and pathway analysis to identify gene networks and pathways. Gene expression data involved 198 samples distributed as follows: 126 Whites, 51 Hispanics, 13 Blacks, and 8 Asians. We identified 300 highly significantly (P < 0.001) differentially expressed genes between the four ethnic populations. Among the identified genes included the genes PHF6, BRD3, CRLF2, and RNF135 which have been implicated in pediatric B-ALL. We identified key pathways implicated in B-ALL including the PDGF, PI3/AKT, ERBB2-ERBB3, and IL-15 signaling pathways.
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Affiliation(s)
- Chindo Hicks
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS. ; Cancer Institute, University of Mississippi Medical Center, Jackson, MS. ; Chindren's Cancer Center University of Mississippi Medical Center, Jackson, MS
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20
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Daub JT, Hofer T, Cutivet E, Dupanloup I, Quintana-Murci L, Robinson-Rechavi M, Excoffier L. Evidence for polygenic adaptation to pathogens in the human genome. Mol Biol Evol 2013; 30:1544-58. [PMID: 23625889 DOI: 10.1093/molbev/mst080] [Citation(s) in RCA: 149] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Most approaches aiming at finding genes involved in adaptive events have focused on the detection of outlier loci, which resulted in the discovery of individually "significant" genes with strong effects. However, a collection of small effect mutations could have a large effect on a given biological pathway that includes many genes, and such a polygenic mode of adaptation has not been systematically investigated in humans. We propose here to evidence polygenic selection by detecting signals of adaptation at the pathway or gene set level instead of analyzing single independent genes. Using a gene-set enrichment test to identify genome-wide signals of adaptation among human populations, we find that most pathways globally enriched for signals of positive selection are either directly or indirectly involved in immune response. We also find evidence for long-distance genotypic linkage disequilibrium, suggesting functional epistatic interactions between members of the same pathway. Our results show that past interactions with pathogens have elicited widespread and coordinated genomic responses, and suggest that adaptation to pathogens can be considered as a primary example of polygenic selection.
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Affiliation(s)
- Josephine T Daub
- Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Berne, Berne, Switzerland.
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Ascunce MS, Toups MA, Kassu G, Fane J, Scholl K, Reed DL. Nuclear genetic diversity in human lice (Pediculus humanus) reveals continental differences and high inbreeding among worldwide populations. PLoS One 2013; 8:e57619. [PMID: 23460886 PMCID: PMC3583987 DOI: 10.1371/journal.pone.0057619] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Accepted: 01/24/2013] [Indexed: 11/19/2022] Open
Abstract
Understanding the evolution of parasites is important to both basic and applied evolutionary biology. Knowledge of the genetic structure of parasite populations is critical for our ability to predict how an infection can spread through a host population and for the design of effective control methods. However, very little is known about the genetic structure of most human parasites, including the human louse (Pediculus humanus). This species is composed of two ecotypes: the head louse (Pediculus humanus capitis De Geer), and the clothing (body) louse (Pediculus humanus humanus Linnaeus). Hundreds of millions of head louse infestations affect children every year, and this number is on the rise, in part because of increased resistance to insecticides. Clothing lice affect mostly homeless and refugee-camp populations and although they are less prevalent than head lice, the medical consequences are more severe because they vector deadly bacterial pathogens. In this study we present the first assessment of the genetic structure of human louse populations by analyzing the nuclear genetic variation at 15 newly developed microsatellite loci in 93 human lice from 11 sites in four world regions. Both ecotypes showed heterozygote deficits relative to Hardy-Weinberg equilibrium and high inbreeding values, an expected pattern given their parasitic life history. Bayesian clustering analyses assigned lice to four distinct genetic clusters that were geographically structured. The low levels of gene flow among louse populations suggested that the evolution of insecticide resistance in lice would most likely be affected by local selection pressures, underscoring the importance of tailoring control strategies to population-specific genetic makeup and evolutionary history. Our panel of microsatellite markers provides powerful data to investigate not only ecological and evolutionary processes in lice, but also those in their human hosts because of the long-term coevolutionary association between lice and humans.
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Affiliation(s)
- Marina S Ascunce
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, United States of America.
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