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Osmond MM, Coop G. Genetic Signatures of Evolutionary Rescue by a Selective Sweep. Genetics 2020; 215:813-829. [PMID: 32398227 PMCID: PMC7337082 DOI: 10.1534/genetics.120.303173] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Accepted: 05/06/2020] [Indexed: 12/31/2022] Open
Abstract
One of the most useful models in population genetics is that of a selective sweep and the consequent hitch-hiking of linked neutral alleles. While variations on this model typically assume constant population size, many instances of strong selection and rapid adaptation in nature may co-occur with complex demography. Here, we extend the hitch-hiking model to evolutionary rescue, where adaptation and demography not only co-occur but are intimately entwined. Our results show how this feedback between demography and evolution determines-and restricts-the genetic signatures of evolutionary rescue, and how these differ from the signatures of sweeps in populations of constant size. In particular, we find rescue to harden sweeps from standing variance or new mutation (but not from migration), reduce genetic diversity both at the selected site and genome-wide, and increase the range of observed Tajima's D values. For a given initial rate of population decline, the feedback between demography and evolution makes all of these differences more dramatic under weaker selection, where bottlenecks are prolonged. Nevertheless, it is likely difficult to infer the co-incident timing of the sweep and bottleneck from these simple signatures, never mind a feedback between them. Temporal samples spanning contemporary rescue events may offer one way forward.
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Affiliation(s)
- Matthew M Osmond
- Center for Population Biology and Department of Evolution and Ecology, University of California, Davis, California 95616
| | - Graham Coop
- Center for Population Biology and Department of Evolution and Ecology, University of California, Davis, California 95616
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Barrett RDH, Laurent S, Mallarino R, Pfeifer SP, Xu CCY, Foll M, Wakamatsu K, Duke-Cohan JS, Jensen JD, Hoekstra HE. Linking a mutation to survival in wild mice. Science 2019; 363:499-504. [DOI: 10.1126/science.aav3824] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 12/06/2018] [Indexed: 12/19/2022]
Abstract
Adaptive evolution in new or changing environments can be difficult to predict because the functional connections between genotype, phenotype, and fitness are complex. Here, we make these explicit connections by combining field and laboratory experiments in wild mice. We first directly estimate natural selection on pigmentation traits and an underlying pigment locus, Agouti, by using experimental enclosures of mice on different soil colors. Next, we show how a mutation in Agouti associated with survival causes lighter coat color through changes in its protein binding properties. Together, our findings demonstrate how a sequence variant alters phenotype and then reveal the ensuing ecological consequences that drive changes in population allele frequency, thereby illuminating the process of evolution by natural selection.
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Hartfield M, Bataillon T, Glémin S. The Evolutionary Interplay between Adaptation and Self-Fertilization. Trends Genet 2017; 33:420-431. [PMID: 28495267 PMCID: PMC5450926 DOI: 10.1016/j.tig.2017.04.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 03/31/2017] [Accepted: 04/03/2017] [Indexed: 11/29/2022]
Abstract
Genome-wide surveys of nucleotide polymorphisms, obtained from next-generation sequencing, have uncovered numerous examples of adaptation in self-fertilizing organisms, especially regarding changes to climate, geography, and reproductive systems. Yet existing models for inferring attributes of adaptive mutations often assume idealized outcrossing populations, which risks mischaracterizing properties of these variants. Recent theoretical work is emphasizing how various aspects of self-fertilization affects adaptation, yet empirical data on these properties are lacking. We review theoretical and empirical studies demonstrating how self-fertilization alters the process of adaptation, illustrated using examples from current sequencing projects. We propose ideas for how future research can more accurately quantify aspects of adaptation in self-fertilizers, including incorporating the effects of standing variation, demographic history, and polygenic adaptation. Analysis of large-scale next-generation sequencing datasets are finding more examples of adaptive evolution at the genomic level. Advances in theoretical work has demonstrated how self-fertilisation affects different aspects of adaptation in these organisms, compared to outcrossers. Current software and statistical methods do not take different mating systems into account, which risks mischaracterising the presence or strength of adaptive mutations from genome scans. Development of new mathematical and statistical methods that explicitly consider self-fertilization and associated demographic effects will enable researchers to more accurately quantify adaptation in these organisms.
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Affiliation(s)
- Matthew Hartfield
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto ON, Canada M5S 3B2; Bioinformatics Research Centre, Aarhus University, 8000C, Aarhus, Denmark.
| | - Thomas Bataillon
- Bioinformatics Research Centre, Aarhus University, 8000C, Aarhus, Denmark
| | - Sylvain Glémin
- Institut des Sciences de l'Evolution (ISEM - UMR 5554 Universite de Montpellier-CNRS-IRD-EPHE), Place Eugene Bataillon, 34075 Montpellier, France; Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala, Sweden
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Moon S, Kim TH, Lee KT, Kwak W, Lee T, Lee SW, Kim MJ, Cho K, Kim N, Chung WH, Sung S, Park T, Cho S, Groenen MA, Nielsen R, Kim Y, Kim H. A genome-wide scan for signatures of directional selection in domesticated pigs. BMC Genomics 2015; 16:130. [PMID: 25765548 PMCID: PMC4349229 DOI: 10.1186/s12864-015-1330-x] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 02/06/2015] [Indexed: 11/10/2022] Open
Abstract
Background Animal domestication involved drastic phenotypic changes driven by strong artificial selection and also resulted in new populations of breeds, established by humans. This study aims to identify genes that show evidence of recent artificial selection during pig domestication. Results Whole-genome resequencing of 30 individual pigs from domesticated breeds, Landrace and Yorkshire, and 10 Asian wild boars at ~16-fold coverage was performed resulting in over 4.3 million SNPs for 19,990 genes. We constructed a comprehensive genome map of directional selection by detecting selective sweeps using an FST-based approach that detects directional selection in lineages leading to the domesticated breeds and using a haplotype-based test that detects ongoing selective sweeps within the breeds. We show that candidate genes under selection are significantly enriched for loci implicated in quantitative traits important to pig reproduction and production. The candidate gene with the strongest signals of directional selection belongs to group III of the metabolomics glutamate receptors, known to affect brain functions associated with eating behavior, suggesting that loci under strong selection include loci involved in behaviorial traits in domesticated pigs including tameness. Conclusions We show that a significant proportion of selection signatures coincide with loci that were previously inferred to affect phenotypic variation in pigs. We further identify functional enrichment related to behavior, such as signal transduction and neuronal activities, for those targets of selection during domestication in pigs. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1330-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sunjin Moon
- Department of Agricultural biotechnology, Seoul National University, Seoul, 151-921, Republic of Korea. .,Department of Life Science and Division of EcoScience, Ewha Womans University, Seoul, 120-750, Republic of Korea. .,Current address: Department of Genome Sciences, University of Washington, Seattle, WA, USA.
| | - Tae-Hun Kim
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Suwon, 441-706, Republic of Korea.
| | - Kyung-Tai Lee
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Suwon, 441-706, Republic of Korea.
| | - Woori Kwak
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 151-747, Republic of Korea. .,C&K Genomics, Seoul National University Research Park, Seoul, 151-919, Republic of Korea.
| | - Taeheon Lee
- Department of Agricultural biotechnology, Seoul National University, Seoul, 151-921, Republic of Korea.
| | - Si-Woo Lee
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Suwon, 441-706, Republic of Korea.
| | - Myung-Jick Kim
- Animal Genetic Resources Station, National Institute of Animal Science, Rural Development Administration, Suwon, 441-706, Republic of Korea.
| | - Kyuho Cho
- Swine Science Division, National Institute of Animal Science, Rural Development Administration, Suwon, 441-706, Republic of Korea.
| | - Namshin Kim
- Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-806, Republic of Korea.
| | - Won-Hyong Chung
- Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-806, Republic of Korea.
| | - Samsun Sung
- C&K Genomics, Seoul National University Research Park, Seoul, 151-919, Republic of Korea.
| | - Taesung Park
- Department of Statistics, Seoul National University, Seoul, Republic of Korea.
| | - Seoae Cho
- C&K Genomics, Seoul National University Research Park, Seoul, 151-919, Republic of Korea.
| | - Martien Am Groenen
- Animal Breeding and Genomics Centre, Wageningen University, De Elst 1, 6708 WD, Wageningen, The Netherlands.
| | - Rasmus Nielsen
- Department of Integrative Biology and Department of Statistics, University of California Berkeley, Berkeley, CA, 94820, USA.
| | - Yuseob Kim
- Department of Life Science and Division of EcoScience, Ewha Womans University, Seoul, 120-750, Republic of Korea.
| | - Heebal Kim
- Department of Agricultural biotechnology, Seoul National University, Seoul, 151-921, Republic of Korea. .,Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 151-747, Republic of Korea. .,C&K Genomics, Seoul National University Research Park, Seoul, 151-919, Republic of Korea.
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Posavi M, Gelembiuk GW, Larget B, Lee CE. Testing for beneficial reversal of dominance during salinity shifts in the invasive copepod Eurytemora affinis, and implications for the maintenance of genetic variation. Evolution 2014; 68:3166-83. [PMID: 25135455 DOI: 10.1111/evo.12502] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 07/08/2014] [Indexed: 01/21/2023]
Abstract
Maintenance of genetic variation at loci under selection has profound implications for adaptation under environmental change. In temporally and spatially varying habitats, non-neutral polymorphism could be maintained by heterozygote advantage across environments (marginal overdominance), which could be greatly increased by beneficial reversal of dominance across conditions. We tested for reversal of dominance and marginal overdominance in salinity tolerance in the saltwater-to-freshwater invading copepod Eurytemora affinis. We compared survival of F1 offspring generated by crossing saline and freshwater inbred lines (between-salinity F1 crosses) relative to within-salinity F1 crosses, across three salinities. We found evidence for both beneficial reversal of dominance and marginal overdominance in salinity tolerance. In support of reversal of dominance, survival of between-salinity F1 crosses was not different from that of freshwater F1 crosses under freshwater conditions and saltwater F1 crosses under saltwater conditions. In support of marginal overdominance, between-salinity F1 crosses exhibited significantly higher survival across salinities relative to both freshwater and saltwater F1 crosses. Our study provides a rare empirical example of complete beneficial reversal of dominance associated with environmental change. This mechanism might be crucial for maintaining genetic variation in salinity tolerance in E. affinis populations, allowing rapid adaptation to salinity changes during habitat invasions.
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Affiliation(s)
- Marijan Posavi
- Center of Rapid Evolution (CORE), University of Wisconsin, 430 Lincoln Drive, Madison, Wisconsin, 53706
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Schneider KA, Kim Y. Genetic hitchhiking under heterogeneous spatial selection pressures. PLoS One 2013; 8:e61742. [PMID: 23637897 PMCID: PMC3634857 DOI: 10.1371/journal.pone.0061742] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Accepted: 03/17/2013] [Indexed: 12/31/2022] Open
Abstract
During adaptive evolutionary processes substantial heterogeneity in selective pressure might act across local habitats in sympatry. Examples are selection for drug resistance in malaria or herbicide resistance in weeds. In such setups standard population-genetic assumptions (homogeneous constant selection pressures, random mating etc.) are likely to be violated. To avoid misinferences on the strength and pattern of natural selection it is therefore necessary to adjust population-genetic theory to meet the specifics driving adaptive processes in particular organisms. We introduce a deterministic model in which selection acts heterogeneously on a population of haploid individuals across different patches over which the population randomly disperses every generation. A fixed proportion of individuals mates exclusively within patches, whereas the rest mates randomly across all patches. We study how the allele frequencies at neutral markers are affected by the spread of a beneficial mutation at a closely linked locus (genetic hitchhiking). We provide an analytical solution for the frequency change and the expected heterozygosity at the neutral locus after a single copy of a beneficial mutation became fixed. We furthermore provide approximations of these solutions which allow for more obvious interpretations. In addition, we validate the results by stochastic simulations. Our results show that the application of standard population-genetic theory is accurate as long as differences across selective environments are moderate. However, if selective differences are substantial, as for drug resistance in malaria, herbicide resistance in weeds, or insecticide resistance in agriculture, it is necessary to adapt available theory to the specifics of particular organisms.
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Affiliation(s)
- Kristan A Schneider
- Department Fakultät Mathematik/Naturwissenschaften/Informatik, University of Applied Sciences Mittweida, Mittweida, Germany.
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Abstract
Genetic diversity is essential for population survival and adaptation to changing environments. Demographic processes (e.g., bottleneck and expansion) and spatial structure (e.g., migration, number, and size of populations) are known to shape the patterns of the genetic diversity of populations. However, the impact of temporal changes in migration on genetic diversity has seldom been considered, although such events might be the norm. Indeed, during the millions of years of a species' lifetime, repeated isolation and reconnection of populations occur. Geological and climatic events alternately isolate and reconnect habitats. We analytically document the dynamics of genetic diversity after an abrupt change in migration given the mutation rate and the number and sizes of the populations. We demonstrate that during transient dynamics, genetic diversity can reach unexpectedly high values that can be maintained over thousands of generations. We discuss the consequences of such processes for the evolution of species based on standing genetic variation and how they can affect the reconstruction of a population's demographic and evolutionary history from genetic data. Our results also provide guidelines for the use of genetic data for the conservation of natural populations.
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Guirao-Rico S, Aguadé M. Patterns of nucleotide diversity at the regions encompassing the Drosophila insulin-like peptide (dilp) genes: demography vs. positive selection in Drosophila melanogaster. PLoS One 2013; 8:e53593. [PMID: 23308258 PMCID: PMC3538593 DOI: 10.1371/journal.pone.0053593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Accepted: 12/03/2012] [Indexed: 11/18/2022] Open
Abstract
In Drosophila, the insulin-signaling pathway controls some life history traits, such as fertility and lifespan, and it is considered to be the main metabolic pathway involved in establishing adult body size. Several observations concerning variation in body size in the Drosophila genus are suggestive of its adaptive character. Genes encoding proteins in this pathway are, therefore, good candidates to have experienced adaptive changes and to reveal the footprint of positive selection. The Drosophila insulin-like peptides (DILPs) are the ligands that trigger the insulin-signaling cascade. In Drosophila melanogaster, there are several peptides that are structurally similar to the single mammalian insulin peptide. The footprint of recent adaptive changes on nucleotide variation can be unveiled through the analysis of polymorphism and divergence. With this aim, we have surveyed nucleotide sequence variation at the dilp1-7 genes in a natural population of D. melanogaster. The comparison of polymorphism in D. melanogaster and divergence from D. simulans at different functional classes of the dilp genes provided no evidence of adaptive protein evolution after the split of the D. melanogaster and D. simulans lineages. However, our survey of polymorphism at the dilp gene regions of D. melanogaster has provided some evidence for the action of positive selection at or near these genes. The regions encompassing the dilp1-4 genes and the dilp6 gene stand out as likely affected by recent adaptive events.
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Affiliation(s)
- Sara Guirao-Rico
- Departament de Genètica, i Institut de Recerca de la Biodiversitat, Universitat de Barcelona, Barcelona, Spain
| | - Montserrat Aguadé
- Departament de Genètica, i Institut de Recerca de la Biodiversitat, Universitat de Barcelona, Barcelona, Spain
- * E-mail:
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LI JUNRUI, LI HAIPENG, JAKOBSSON MATTIAS, LI SEN, SJÖDIN PER, LASCOUX MARTIN. Joint analysis of demography and selection in population genetics: where do we stand and where could we go? Mol Ecol 2011; 21:28-44. [DOI: 10.1111/j.1365-294x.2011.05308.x] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- JUNRUI LI
- Laboratory of Evolutionary Genomics, CAS Key Laboratory of Computational Biology, CAS‐MPG Partner Institute for Computational Biology, Chinese Academy of Sciences, Shanghai, China
- Graduate School of the Chinese Academy of Sciences, Beijing 100039, China
| | - HAIPENG LI
- Laboratory of Evolutionary Genomics, CAS Key Laboratory of Computational Biology, CAS‐MPG Partner Institute for Computational Biology, Chinese Academy of Sciences, Shanghai, China
| | - MATTIAS JAKOBSSON
- Department of Evolutionary Biology, Evolutionary Biology Centre, and Science for Life Laboratory, Uppsala University, 752 36 Uppsala, Sweden
| | - SEN LI
- Department of Evolutionary Biology, Evolutionary Biology Centre, and Science for Life Laboratory, Uppsala University, 752 36 Uppsala, Sweden
| | - PER SJÖDIN
- Department of Evolutionary Biology, Evolutionary Biology Centre, and Science for Life Laboratory, Uppsala University, 752 36 Uppsala, Sweden
| | - MARTIN LASCOUX
- Laboratory of Evolutionary Genomics, CAS Key Laboratory of Computational Biology, CAS‐MPG Partner Institute for Computational Biology, Chinese Academy of Sciences, Shanghai, China
- Program in Plant Ecology and Evolution, Department of Ecology and Genetics, Uppsala University, 752 36 Uppsala, Sweden
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Goldie X, Lanfear R, Bromham L. Diversification and the rate of molecular evolution: no evidence of a link in mammals. BMC Evol Biol 2011; 11:286. [PMID: 21967038 PMCID: PMC3205075 DOI: 10.1186/1471-2148-11-286] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2011] [Accepted: 10/04/2011] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Recent research has indicated a positive association between rates of molecular evolution and diversification in a number of taxa. However debate continues concerning the universality and cause of this relationship. Here, we present the first systematic investigation of this relationship within the mammals. We use phylogenetically independent sister-pair comparisons to test for a relationship between substitution rates and clade size at a number of taxonomic levels. Total, non-synonymous and synonymous substitution rates were estimated from mitochondrial and nuclear DNA sequences. RESULTS We found no evidence for an association between clade size and substitution rates in mammals, for either the nuclear or the mitochondrial sequences. We found significant associations between body size and substitution rates, as previously reported. CONCLUSIONS Our results present a contrast to previous research, which has reported significant positive associations between substitution rates and diversification for birds, angiosperms and reptiles. There are three possible reasons for the differences between the observed results in mammals versus other clades. First, there may be no link between substitution rates and diversification in mammals. Second, this link may exist, but may be much weaker in mammals than in other clades. Third, the link between substitution rates and diversification may exist in mammals, but may be confounded by other variables.
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Affiliation(s)
- Xavier Goldie
- Centre for Macroevolution and Macroecology, Division of Evolution, Ecology and Genetics, Research School of Biology, The Australian National University, Canberra, A.C.T. 0200, Australia
| | - Robert Lanfear
- Centre for Macroevolution and Macroecology, Division of Evolution, Ecology and Genetics, Research School of Biology, The Australian National University, Canberra, A.C.T. 0200, Australia
| | - Lindell Bromham
- Centre for Macroevolution and Macroecology, Division of Evolution, Ecology and Genetics, Research School of Biology, The Australian National University, Canberra, A.C.T. 0200, Australia
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Abstract
A central problem in population genetics is to detect and analyze positive natural selection by which beneficial mutations are driven to fixation. The hitchhiking effect of a rapidly spreading beneficial mutation, which results in local removal of standing genetic variation, allows such an analysis using DNA sequence polymorphism. However, the current mathematical theory that predicts the pattern of genetic hitchhiking relies on the assumption that a beneficial mutation increases to a high frequency in a single random-mating population, which is certainly violated in reality. Individuals in natural populations are distributed over a geographic space. The spread of a beneficial allele can be delayed by limited migration of individuals over the space and its hitchhiking effect can also be affected. To study this effect of geographic structure on genetic hitchhiking, we analyze a simple model of directional selection in a subdivided population. In contrast to previous studies on hitchhiking in subdivided populations, we mainly investigate the range of sufficiently high migration rates that would homogenize genetic variation at neutral loci. We provide a heuristic mathematical analysis that describes how the genealogical structure at a neutral locus linked to the locus under selection is expected to change in a population divided into two demes. Our results indicate that the overall strength of genetic hitchhiking--the degree to which expected heterozygosity decreases--is diminished by population subdivision, mainly because opportunity for the breakdown of hitchhiking by recombination increases as the spread of the beneficial mutation across demes is delayed when migration rate is much smaller than the strength of selection. Furthermore, the amount of genetic variation after a selective sweep is expected to be unequal over demes: a greater reduction in expected heterozygosity occurs in the subpopulation from which the beneficial mutation originates than in its neighboring subpopulations. This raises a possibility of detecting a "hidden" geographic structure of population by carefully analyzing the pattern of a selective sweep.
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