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Chotai M, Wei X, Messer PW. Signatures of selective sweeps in continuous-space populations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.26.605365. [PMID: 39091822 PMCID: PMC11291165 DOI: 10.1101/2024.07.26.605365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Selective sweeps describe the process by which an adaptive mutation arises and rapidly fixes in the population, thereby removing genetic variation in its genomic vicinity. The expected signatures of selective sweeps are relatively well understood in panmictic population models, yet natural populations often extend across larger geographic ranges where individuals are more likely to mate with those born nearby. To investigate how such spatial population structure can affect sweep dynamics and signatures, we simulated selective sweeps in populations inhabiting a two-dimensional continuous landscape. The maximum dispersal distance of offspring from their parents can be varied in our simulations from an essentially panmictic population to scenarios with increasingly limited dispersal. We find that in low-dispersal populations, adaptive mutations spread more slowly than in panmictic ones, while recombination becomes less effective at breaking up genetic linkage around the sweep locus. Together, these factors result in a trough of reduced genetic diversity around the sweep locus that looks very similar across dispersal rates. We also find that the site frequency spectrum around hard sweeps in low-dispersal populations becomes enriched for intermediate-frequency variants, making these sweeps appear softer than they are. Furthermore, haplotype heterozygosity at the sweep locus tends to be elevated in low-dispersal scenarios as compared to panmixia, contrary to what we observe in neutral scenarios without sweeps. The haplotype patterns generated by these hard sweeps in low-dispersal populations can resemble soft sweeps from standing genetic variation that arose from substantially older alleles. Our results highlight the need for better accounting for spatial population structure when making inferences about selective sweeps.
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Affiliation(s)
- Meera Chotai
- Department of Computational Biology, Cornell University
| | - Xinzhu Wei
- Department of Computational Biology, Cornell University
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2
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Sudbrack V, Mullon C. Fixation times of de novo and standing beneficial variants in subdivided populations. Genetics 2024; 227:iyae043. [PMID: 38527860 DOI: 10.1093/genetics/iyae043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 01/17/2024] [Accepted: 03/11/2024] [Indexed: 03/27/2024] Open
Abstract
The rate at which beneficial alleles fix in a population depends on the probability of and time to fixation of such alleles. Both of these quantities can be significantly impacted by population subdivision and limited gene flow. Here, we investigate how limited dispersal influences the rate of fixation of beneficial de novo mutations, as well as fixation time from standing genetic variation. We investigate this for a population structured according to the island model of dispersal allowing us to use the diffusion approximation, which we complement with simulations. We find that fixation may take on average fewer generations under limited dispersal than under panmixia when selection is moderate. This is especially the case if adaptation occurs from de novo recessive mutations, and dispersal is not too limited (such that approximately FST<0.2). The reason is that mildly limited dispersal leads to only a moderate increase in effective population size (which slows down fixation), but is sufficient to cause a relative excess of homozygosity due to inbreeding, thereby exposing rare recessive alleles to selection (which accelerates fixation). We also explore the effect of metapopulation dynamics through local extinction followed by recolonization, finding that such dynamics always accelerate fixation from standing genetic variation, while de novo mutations show faster fixation interspersed with longer waiting times. Finally, we discuss the implications of our results for the detection of sweeps, suggesting that limited dispersal mitigates the expected differences between the genetic signatures of sweeps involving recessive and dominant alleles.
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Affiliation(s)
- Vitor Sudbrack
- Department of Ecology and Evolution, University of Lausanne, Lausanne 1015, Vaud, Switzerland
| | - Charles Mullon
- Department of Ecology and Evolution, University of Lausanne, Lausanne 1015, Vaud, Switzerland
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3
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Adiba M, Rahman M, Akter H, Rahman MM, Uddin M, Ebihara A, Nabi A. Mutational landscape of mitochondrial cytochrome b and its flanking tRNA genes associated with increased mitochondrial DNA copy number and disease risk in children with autism. GENE REPORTS 2024; 35:101895. [DOI: 10.1016/j.genrep.2024.101895] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
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4
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Panigrahi M, Rajawat D, Nayak SS, Ghildiyal K, Sharma A, Jain K, Lei C, Bhushan B, Mishra BP, Dutt T. Landmarks in the history of selective sweeps. Anim Genet 2023; 54:667-688. [PMID: 37710403 DOI: 10.1111/age.13355] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 08/28/2023] [Indexed: 09/16/2023]
Abstract
Half a century ago, a seminal article on the hitchhiking effect by Smith and Haigh inaugurated the concept of the selection signature. Selective sweeps are characterised by the rapid spread of an advantageous genetic variant through a population and hence play an important role in shaping evolution and research on genetic diversity. The process by which a beneficial allele arises and becomes fixed in a population, leading to a increase in the frequency of other linked alleles, is known as genetic hitchhiking or genetic draft. Kimura's neutral theory and hitchhiking theory are complementary, with Kimura's neutral evolution as the 'null model' and positive selection as the 'signal'. Both are widely accepted in evolution, especially with genomics enabling precise measurements. Significant advances in genomic technologies, such as next-generation sequencing, high-density SNP arrays and powerful bioinformatics tools, have made it possible to systematically investigate selection signatures in a variety of species. Although the history of selection signatures is relatively recent, progress has been made in the last two decades, owing to the increasing availability of large-scale genomic data and the development of computational methods. In this review, we embark on a journey through the history of research on selective sweeps, ranging from early theoretical work to recent empirical studies that utilise genomic data.
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Affiliation(s)
- Manjit Panigrahi
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | - Divya Rajawat
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | | | - Kanika Ghildiyal
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | - Anurodh Sharma
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | - Karan Jain
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | - Chuzhao Lei
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Bharat Bhushan
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | - Bishnu Prasad Mishra
- Division of Animal Biotechnology, ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Triveni Dutt
- Livestock Production and Management Section, Indian Veterinary Research Institute, Bareilly, India
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5
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Pompei S, Bella E, Weitz JS, Grilli J, Lagomarsino MC. Metacommunity structure preserves genome diversity in the presence of gene-specific selective sweeps under moderate rates of horizontal gene transfer. PLoS Comput Biol 2023; 19:e1011532. [PMID: 37792894 PMCID: PMC10578598 DOI: 10.1371/journal.pcbi.1011532] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 10/16/2023] [Accepted: 09/19/2023] [Indexed: 10/06/2023] Open
Abstract
The horizontal transfer of genes is fundamental for the eco-evolutionary dynamics of microbial communities, such as oceanic plankton, soil, and the human microbiome. In the case of an acquired beneficial gene, classic population genetics would predict a genome-wide selective sweep, whereby the genome spreads clonally within the community and together with the beneficial gene, removing genome diversity. Instead, several sources of metagenomic data show the existence of "gene-specific sweeps", whereby a beneficial gene spreads across a bacterial community, maintaining genome diversity. Several hypotheses have been proposed to explain this process, including the decreasing gene flow between ecologically distant populations, frequency-dependent selection from linked deleterious allelles, and very high rates of horizontal gene transfer. Here, we propose an additional possible scenario grounded in eco-evolutionary principles. Specifically, we show by a mathematical model and simulations that a metacommunity where species can occupy multiple patches, acting together with a realistic (moderate) HGT rate, helps maintain genome diversity. Assuming a scenario of patches dominated by single species, our model predicts that diversity only decreases moderately upon the arrival of a new beneficial gene, and that losses in diversity can be quickly restored. We explore the generic behaviour of diversity as a function of three key parameters, frequency of insertion of new beneficial genes, migration rates and horizontal transfer rates.Our results provides a testable explanation for how diversity can be maintained by gene-specific sweeps even in the absence of high horizontal gene transfer rates.
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Affiliation(s)
- Simone Pompei
- IFOM ETS - The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Edoardo Bella
- Dipartimento di Fisica, Università degli Studi di Milano, via Celoria 16 Milano, Italy
| | - Joshua S. Weitz
- Department of Biology, University of Maryland, College Park, Maryland, United States of America
- Department of Physics, University of Maryland, College Park, Maryland, United States of America
- Institut de Biologie, École Normale Supérieure, Paris, France
| | - Jacopo Grilli
- Quantitative Life Sciences, The Abdus Salam International Centre for Theoretical Physics (ICTP), Trieste, Italy
| | - Marco Cosentino Lagomarsino
- IFOM ETS - The AIRC Institute of Molecular Oncology, Milan, Italy
- Dipartimento di Fisica, Università degli Studi di Milano, via Celoria 16 Milano, Italy
- I.N.F.N, via Celoria 16 Milano, Italy
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6
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Min J, Gupta M, Desai MM, Weissman DB. Spatial structure alters the site frequency spectrum produced by hitchhiking. Genetics 2022; 222:iyac139. [PMID: 36094352 PMCID: PMC9630975 DOI: 10.1093/genetics/iyac139] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 08/24/2022] [Indexed: 11/13/2022] Open
Abstract
The reduction of genetic diversity due to genetic hitchhiking is widely used to find past selective sweeps from sequencing data, but very little is known about how spatial structure affects hitchhiking. We use mathematical modeling and simulations to find the unfolded site frequency spectrum left by hitchhiking in the genomic region of a sweep in a population occupying a 1D range. For such populations, sweeps spread as Fisher waves, rather than logistically. We find that this leaves a characteristic 3-part site frequency spectrum at loci very close to the swept locus. Very low frequencies are dominated by recent mutations that occurred after the sweep and are unaffected by hitchhiking. At moderately low frequencies, there is a transition zone primarily composed of alleles that briefly "surfed" on the wave of the sweep before falling out of the wavefront, leaving a spectrum close to that expected in well-mixed populations. However, for moderate-to-high frequencies, there is a distinctive scaling regime of the site frequency spectrum produced by alleles that drifted to fixation in the wavefront and then were carried throughout the population. For loci slightly farther away from the swept locus on the genome, recombination is much more effective at restoring diversity in 1D populations than it is in well-mixed ones. We find that these signatures of space can be strong even in apparently well-mixed populations with negligible spatial genetic differentiation, suggesting that spatial structure may frequently distort the signatures of hitchhiking in natural populations.
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Affiliation(s)
- Jiseon Min
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
- NSF-Simons Center for Mathematical and Statistical Analysis of Biology, Harvard University, Cambridge, MA 02138, USA
- Quantitative Biology Initiative, Harvard University, Cambridge, MA 02138, USA
| | - Misha Gupta
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Michael M Desai
- NSF-Simons Center for Mathematical and Statistical Analysis of Biology, Harvard University, Cambridge, MA 02138, USA
- Quantitative Biology Initiative, Harvard University, Cambridge, MA 02138, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
- Department of Physics, Harvard University, Cambridge, MA 02138, USA
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7
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Gunn JC, Berkman LK, Koppelman J, Taylor AT, Brewer SK, Long JM, Eggert LS. Genomic divergence, local adaptation, and complex demographic history may inform management of a popular sportfish species complex. Ecol Evol 2022; 12:e9370. [PMID: 36225830 PMCID: PMC9534746 DOI: 10.1002/ece3.9370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 08/29/2022] [Accepted: 09/05/2022] [Indexed: 11/05/2022] Open
Abstract
The Neosho Bass (Micropterus velox), a former subspecies of the keystone top-predator and globally popular Smallmouth Bass (M. dolomieu), is endemic and narrowly restricted to small, clear streams of the Arkansas River Basin in the Central Interior Highlands (CIH) ecoregion, USA. Previous studies have detected some morphological, genetic, and genomic differentiation between the Neosho and Smallmouth Basses; however, the extent of neutral and adaptive divergence and patterns of intraspecific diversity are poorly understood. Furthermore, lineage diversification has likely been impacted by gene flow in some Neosho populations, which may be due to a combination of natural biogeographic processes and anthropogenic introductions. We assessed: (1) lineage divergence, (2) local directional selection (adaptive divergence), and (3) demographic history among Smallmouth Bass populations in the CIH using population genomic analyses of 50,828 single-nucleotide polymorphisms (SNPs) obtained through ddRAD-seq. Neosho and Smallmouth Bass formed monophyletic clades with 100% bootstrap support. We identified two major lineages within each species. We discovered six Neosho Bass populations (two nonadmixed and four admixed) and three nonadmixed Smallmouth Bass populations. We detected 29 SNPs putatively under directional selection in the Neosho range, suggesting populations may be locally adapted. Two populations were admixed via recent asymmetric secondary contact, perhaps after anthropogenic introduction. Two other populations were likely admixed via combinations of ancient and recent processes. These species comprise independently evolving lineages, some having experienced historical and natural admixture. These results may be critical for management of Neosho Bass as a distinct species and may aid in the conservation of other species with complex biogeographic histories.
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Affiliation(s)
- Joe C. Gunn
- Division of Biological SciencesUniversity of MissouriColumbiaMissouriUSA
| | | | | | - Andrew T. Taylor
- Department of BiologyUniversity of Central OklahomaEdmondOklahomaUSA
- Department of BiologyUniversity of North GeorgiaDahlonegaGeorgiaUSA
| | - Shannon K. Brewer
- U.S. Geological Survey, Alabama Cooperative Fish and Wildlife Research Unit, School of Fisheries, Aquaculture, and Aquatic SciencesAuburn UniversityAuburnAlabamaUSA
| | - James M. Long
- U.S. Geological Survey, Oklahoma Cooperative Fish and Wildlife Research Unit, Department of Natural Resource Ecology and ManagementOklahoma State UniversityStillwaterOklahomaUSA
| | - Lori S. Eggert
- Division of Biological SciencesUniversity of MissouriColumbiaMissouriUSA
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8
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Booker TR, Yeaman S, Whitlock MC. Global adaptation complicates the interpretation of genome scans for local adaptation. Evol Lett 2020; 5:4-15. [PMID: 33552532 PMCID: PMC7857299 DOI: 10.1002/evl3.208] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 10/27/2020] [Accepted: 11/12/2020] [Indexed: 12/14/2022] Open
Abstract
Spatially varying selection promotes variance in allele frequencies, increasing genetic differentiation between the demes of a metapopulation. For that reason, outliers in the genome‐wide distribution of summary statistics measuring genetic differentiation, such as FST, are often interpreted as evidence for alleles that contribute to local adaptation. However, theoretical studies have shown that in spatially structured populations the spread of beneficial mutations with spatially uniform fitness effects can also induce transient genetic differentiation. In recent years, numerous empirical studies have suggested that such species‐wide, or global, adaptation makes a substantial contribution to molecular evolution. In this perspective, we discuss how commonly such global adaptation may influence the genome‐wide distribution of FST and generate genetic differentiation patterns, which could be mistaken for local adaptation. To illustrate this, we use forward‐in‐time population genetic simulations assuming parameters for the rate and strength of beneficial mutations consistent with estimates from natural populations. We demonstrate that the spread of globally beneficial mutations in parapatric populations may frequently generate FST outliers, which could be misinterpreted as evidence for local adaptation. The spread of beneficial mutations causes selective sweeps at flanking sites, so in some cases, the effects of global versus local adaptation may be distinguished by examining patterns of nucleotide diversity within and between populations in addition to FST. However, when local adaptation has been only recently established, it may be much more difficult to distinguish from global adaptation, due to less accumulation of linkage disequilibrium at flanking sites. Through our discussion, we conclude that a large fraction of FST outliers that are presumed to arise from local adaptation may instead be due to global adaptation.
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Affiliation(s)
- Tom R Booker
- Department of Forest and Conservation Sciences University of British Columbia Vancouver Canada.,Biodiversity Research Centre University of British Columbia Vancouver Canada
| | - Sam Yeaman
- Department of Biological Sciences University of Calgary Calgary Canada
| | - Michael C Whitlock
- Biodiversity Research Centre University of British Columbia Vancouver Canada.,Department of Zoology University of British Columbia Vancouver Canada
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9
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Zhang XX, Cheng X, Li LL, Wang X, Zhou W, Chen XY, Hu XS. The wave of gene advance under diverse systems of mating. Heredity (Edinb) 2020; 125:253-268. [PMID: 32606419 PMCID: PMC7490428 DOI: 10.1038/s41437-020-0333-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 06/09/2020] [Accepted: 06/09/2020] [Indexed: 11/09/2022] Open
Abstract
Mating systems will influence gene spread across the natural distribution of a plant species. Existing theories have not fully explored the role of mating systems on the wave of advance of an advantageous gene. Here, we develop a theory to account for the rate of spread of both advantageous and neutral genes under different mating systems, based on migration-selection processes. We show that a complex relationship exists between selfing rate and the speed of gene spread. The interaction of selfing with gametophytic selection shapes the traveling wave of the advantageous gene. Selfing can impede (or enhance) the spread of an advantageous gene in the presence (or absence) of gametophytic selection. The interaction of selfing with recombination shapes the spread of a neutral gene. Linkage disequilibrium, mainly generated by selfing, enhances the traveling wave of the neutral gene that is tightly linked with the selective gene. Recombination gradually breaks down the genetic hitchhiking effects along the direction of advantageous gene spread, yielding decreasing waves of advance of neutral genes. The stochastic process does not alter the pattern of selfing effects except for increasing the uncertainty of the waves of advance of both advantageous and neutral genes. This theory helps us to explain how mating systems act as a barrier to spread of adaptive and neutral genes, and to interpret species cohesion maintained by a low level of adaptive gene flow.
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Affiliation(s)
- Xin-Xin Zhang
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangdong, 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangdong, 510642, China
| | - Xiang Cheng
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangdong, 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangdong, 510642, China
| | - Ling-Ling Li
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangdong, 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangdong, 510642, China
| | - Xi Wang
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangdong, 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangdong, 510642, China
| | - Wei Zhou
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangdong, 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangdong, 510642, China
| | - Xiao-Yang Chen
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangdong, 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangdong, 510642, China
| | - Xin-Sheng Hu
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangdong, 510642, China.
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangdong, 510642, China.
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10
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Adaptation in structured populations and fuzzy boundaries between hard and soft sweeps. PLoS Comput Biol 2019; 15:e1007426. [PMID: 31710623 PMCID: PMC6872172 DOI: 10.1371/journal.pcbi.1007426] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 11/21/2019] [Accepted: 09/20/2019] [Indexed: 11/19/2022] Open
Abstract
Selective sweeps, the genetic footprint of positive selection, have been extensively studied in the past decades, with dozens of methods developed to identify swept regions. However, these methods suffer from both false positive and false negative reports, and the candidates identified with different methods are often inconsistent with each other. We propose that a biological cause of this problem can be population subdivision, and a technical cause can be incomplete, or inaccurate, modeling of the dynamic process associated with sweeps. Here we used simulations to show how these effects interact and potentially cause bias. In particular, we show that sweeps maybe misclassified as either hard or soft, when the true time stage of a sweep and that implied, or pre-supposed, by the model do not match. We call this "temporal misclassification". Similarly, "spatial misclassification (softening)" can occur when hard sweeps, which are imported by migration into a new subpopulation, are falsely identified as soft. This can easily happen in case of local adaptation, i.e. when the sweeping allele is not under positive selection in the new subpopulation, and the underlying model assumes panmixis instead of substructure. The claim that most sweeps in the evolutionary history of humans were soft, may have to be reconsidered in the light of these findings.
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11
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Feder AF, Pennings PS, Hermisson J, Petrov DA. Evolutionary Dynamics in Structured Populations Under Strong Population Genetic Forces. G3 (BETHESDA, MD.) 2019; 9:3395-3407. [PMID: 31462443 PMCID: PMC6778802 DOI: 10.1534/g3.119.400605] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 08/16/2019] [Indexed: 12/16/2022]
Abstract
In the long-term neutral equilibrium, high rates of migration between subpopulations result in little population differentiation. However, in the short-term, even very abundant migration may not be enough for subpopulations to equilibrate immediately. In this study, we investigate dynamical patterns of short-term population differentiation in adapting populations via stochastic and analytical modeling through time. We characterize a regime in which selection and migration interact to create non-monotonic patterns of population differentiation over time when migration is weaker than selection, but stronger than drift. We demonstrate how these patterns can be leveraged to estimate high migration rates using approximate Bayesian computation. We apply this approach to estimate fast migration in a rapidly adapting intra-host Simian-HIV population sampled from different anatomical locations. We find differences in estimated migration rates between different compartments, even though all are above [Formula: see text] = 1. This work demonstrates how studying demographic processes on the timescale of selective sweeps illuminates processes too fast to leave signatures on neutral timescales.
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Affiliation(s)
- Alison F Feder
- Department of Biology, Stanford University,
- Department of Integrative Biology, University of California Berkeley
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12
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Sakamoto T, Innan H. The Evolutionary Dynamics of a Genetic Barrier to Gene Flow: From the Establishment to the Emergence of a Peak of Divergence. Genetics 2019; 212:1383-1398. [PMID: 31171654 PMCID: PMC6707448 DOI: 10.1534/genetics.119.302311] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 05/16/2019] [Indexed: 11/18/2022] Open
Abstract
Divergent selection works when an allele establishes in the subpopulations in which it is adaptive, but not in the ones in which it is deleterious. While such a locally adaptive allele is maintained, the target locus of selection works as a genetic barrier to gene flow or a barrier locus. The genetic divergence (or FST) around the barrier locus can be maintained, while in other regions of the genome, genetic variation can be mixed by gene flow or migration. In this work, we consider theoretically the evolutionary process of a barrier locus, from its birth to stable preservation. Under a simple two-population model, we use a diffusion approach to obtain analytical expressions for the probability of initial establishment of a locally adaptive allele, the reduction of genetic variation due to the spread of the adaptive allele, and the process to the development of a sharp peak of divergence (genomic island of divergence). Our results will be useful to understanding how genomes evolve through local adaptation and divergent selection.
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Affiliation(s)
- Takahiro Sakamoto
- SOKENDAI, The Graduate University for Advanced Studies, Hayama, Kanagawa 240-0193, Japan
| | - Hideki Innan
- SOKENDAI, The Graduate University for Advanced Studies, Hayama, Kanagawa 240-0193, Japan
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13
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Lee KM, Coop G. Population genomics perspectives on convergent adaptation. Philos Trans R Soc Lond B Biol Sci 2019; 374:20180236. [PMID: 31154979 PMCID: PMC6560269 DOI: 10.1098/rstb.2018.0236] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/21/2018] [Indexed: 01/12/2023] Open
Abstract
Convergent adaptation is the independent evolution of similar traits conferring a fitness advantage in two or more lineages. Cases of convergent adaptation inform our ideas about the ecological and molecular basis of adaptation. In judging the degree to which putative cases of convergent adaptation provide an independent replication of the process of adaptation, it is necessary to establish the degree to which the evolutionary change is unexpected under null models and to show that selection has repeatedly, independently driven these changes. Here, we discuss the issues that arise from these questions particularly for closely related populations, where gene flow and standing variation add additional layers of complexity. We outline a conceptual framework to guide intuition as to the extent to which evolutionary change represents the independent gain of information owing to selection and show that this is a measure of how surprised we should be by convergence. Additionally, we summarize the ways population and quantitative genetics and genomics may help us address questions related to convergent adaptation, as well as open new questions and avenues of research. This article is part of the theme issue 'Convergent evolution in the genomics era: new insights and directions'.
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Affiliation(s)
- Kristin M. Lee
- Center for Population Biology, University of California, Davis, CA 95616, USA
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
| | - Graham Coop
- Center for Population Biology, University of California, Davis, CA 95616, USA
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
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14
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Abstract
For almost 20 years, many inference methods have been developed to detect selective sweeps and localize the targets of directional selection in the genome. These methods are based on population genetic models that describe the effect of a beneficial allele (e.g., a new mutation) on linked neutral variation (driven by directional selection from a single copy to fixation). Here, I discuss these models, ranging from selective sweeps in a panmictic population of constant size to evolutionary traffic when simultaneous sweeps at multiple loci interfere, and emphasize the important role of demography and population structure in data analysis. In the past 10 years, soft sweeps that may arise after an environmental change from directional selection on standing variation have become a focus of population genetic research. In contrast to selective sweeps, they are caused by beneficial alleles that were neutrally segregating in a population before the environmental change or were present at a mutation-selection balance in appreciable frequency.
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15
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Vy HMT, Won YJ, Kim Y. Multiple Modes of Positive Selection Shaping the Patterns of Incomplete Selective Sweeps over African Populations of Drosophila melanogaster. Mol Biol Evol 2018; 34:2792-2807. [PMID: 28981697 DOI: 10.1093/molbev/msx207] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
It remains a challenge in evolutionary genetics to elucidate how beneficial mutations arise and propagate in a population and how selective pressures on mutant alleles are structured over space and time. By identifying "sweeping haplotypes (SHs)" that putatively carry beneficial alleles and are increasing (or have increased) rapidly in frequency, and surveying the geographic distribution of SH frequencies, we can indirectly infer how selective sweeps unfold in time and thus which modes of positive selection underlie those sweeps. Using population genomic data from African Drosophila melanogaster, we identified SHs from 37 candidate loci under selection. At more than half of loci, we identify single SHs. However, many other loci harbor multiple independent SHs, namely soft selective sweeps, either due to parallel evolution across space or a high beneficial mutation rate. At about a quarter of the loci, intermediate SH frequencies are found across multiple populations, which cannot be explained unless a certain form of frequency-dependent positive selection, such as heterozygote advantage, is invoked given the reasonable range of migration rates between African populations. At one locus, many independent SHs are observed over multiple populations but always together with ancestral haplotypes. This complex pattern is compatible with a large number of mutational targets in a gene and frequency-dependent selection on new variants. We conclude that very diverse modes of positive selection are operating at different sets of loci in D. melanogaster populations.
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Affiliation(s)
- Ha My T Vy
- Division of EcoScience, Ewha Womans University, Seoul, Korea
| | - Yong-Jin Won
- Division of EcoScience, Ewha Womans University, Seoul, Korea.,Department of Life Science, Ewha Womans University, Seoul, Korea
| | - Yuseob Kim
- Division of EcoScience, Ewha Womans University, Seoul, Korea.,Department of Life Science, Ewha Womans University, Seoul, Korea
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16
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Distinguishing Among Modes of Convergent Adaptation Using Population Genomic Data. Genetics 2017; 207:1591-1619. [PMID: 29046403 DOI: 10.1534/genetics.117.300417] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 09/30/2017] [Indexed: 11/18/2022] Open
Abstract
Geographically separated populations can convergently adapt to the same selection pressure. Convergent evolution at the level of a gene may arise via three distinct modes. The selected alleles can (1) have multiple independent mutational origins, (2) be shared due to shared ancestral standing variation, or (3) spread throughout subpopulations via gene flow. We present a model-based, statistical approach that utilizes genomic data to detect cases of convergent adaptation at the genetic level, identify the loci involved and distinguish among these modes. To understand the impact of convergent positive selection on neutral diversity at linked loci, we make use of the fact that hitchhiking can be modeled as an increase in the variance in neutral allele frequencies around a selected site within a population. We build on coalescent theory to show how shared hitchhiking events between subpopulations act to increase covariance in allele frequencies between subpopulations at loci near the selected site, and extend this theory under different models of migration and selection on the same standing variation. We incorporate this hitchhiking effect into a multivariate normal model of allele frequencies that also accounts for population structure. Based on this theory, we present a composite-likelihood-based approach that utilizes genomic data to identify loci involved in convergence, and distinguishes among alternate modes of convergent adaptation. We illustrate our method on genome-wide polymorphism data from two distinct cases of convergent adaptation. First, we investigate the adaptation for copper toxicity tolerance in two populations of the common yellow monkey flower, Mimulus guttatus We show that selection has occurred on an allele that has been standing in these populations prior to the onset of copper mining in this region. Lastly, we apply our method to data from four populations of the killifish, Fundulus heteroclitus, that show very rapid convergent adaptation for tolerance to industrial pollutants. Here, we identify a single locus at which both independent mutation events and selection on an allele shared via gene flow, either slightly before or during selection, play a role in adaptation across the species' range.
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17
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Kamdem C, Fouet C, White BJ. Chromosome arm-specific patterns of polymorphism associated with chromosomal inversions in the major African malaria vector, Anopheles funestus. Mol Ecol 2017; 26:5552-5566. [PMID: 28833796 PMCID: PMC5927613 DOI: 10.1111/mec.14335] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2016] [Revised: 08/08/2017] [Accepted: 08/14/2017] [Indexed: 02/02/2023]
Abstract
Chromosomal inversions facilitate local adaptation of beneficial mutations and modulate genetic polymorphism, but the extent of their effects within the genome is still insufficiently understood. The genome of Anopheles funestus, a malaria mosquito endemic to sub-Saharan Africa, contains an impressive number of paracentric polymorphic inversions, which are unevenly distributed among chromosomes and provide an excellent framework for investigating the genomic impacts of chromosomal rearrangements. Here, we present results of a fine-scale analysis of genetic variation within the genome of two weakly differentiated populations of Anopheles funestus inhabiting contrasting moisture conditions in Cameroon. Using population genomic analyses, we found that genetic divergence between the two populations is centred on regions of the genome corresponding to three inversions, which are characterized by high values of FST , absolute sequence divergence and fixed differences. Importantly, in contrast to the 2L chromosome arm, which is collinear, nucleotide diversity is significantly reduced along the entire length of three autosome arms bearing multiple overlapping chromosomal rearrangements. These findings support the idea that interactions between reduced recombination and natural selection within inversions contribute to sculpt nucleotide polymorphism across chromosomes in An. funestus.
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Affiliation(s)
- Colince Kamdem
- Department of Entomology, University of California, Riverside, CA 92521
| | - Caroline Fouet
- Department of Entomology, University of California, Riverside, CA 92521
| | - Bradley J. White
- Department of Entomology, University of California, Riverside, CA 92521
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18
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Rougemont Q, Gagnaire PA, Perrier C, Genthon C, Besnard AL, Launey S, Evanno G. Inferring the demographic history underlying parallel genomic divergence among pairs of parasitic and nonparasitic lamprey ecotypes. Mol Ecol 2016; 26:142-162. [PMID: 27105132 DOI: 10.1111/mec.13664] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 03/22/2016] [Accepted: 04/06/2016] [Indexed: 12/20/2022]
Abstract
Understanding the evolutionary mechanisms generating parallel genomic divergence patterns among replicate ecotype pairs remains an important challenge in speciation research. We investigated the genomic divergence between the anadromous parasitic river lamprey (Lampetra fluviatilis) and the freshwater-resident nonparasitic brook lamprey (Lampetra planeri) in nine population pairs displaying variable levels of geographic connectivity. We genotyped 338 individuals with RAD sequencing and inferred the demographic divergence history of each population pair using a diffusion approximation method. Divergence patterns in geographically connected population pairs were better explained by introgression after secondary contact, whereas disconnected population pairs have retained a signal of ancient migration. In all ecotype pairs, models accounting for differential introgression among loci outperformed homogeneous migration models. Generating neutral predictions from the inferred divergence scenarios to detect highly differentiated markers identified greater proportions of outliers in disconnected population pairs than in connected pairs. However, increased similarity in the most divergent genomic regions was found among connected ecotype pairs, indicating that gene flow was instrumental in generating parallelism at the molecular level. These results suggest that heterogeneous genomic differentiation and parallelism among replicate ecotype pairs have partly emerged through restricted introgression in genomic islands.
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Affiliation(s)
- Quentin Rougemont
- INRA, UMR 985 Ecologie et Santé des Ecosystèmes, 35042, Rennes, France.,Agrocampus Ouest, UMR ESE, 65 rue de Saint-Brieuc, 35042, Rennes, France
| | - Pierre-Alexandre Gagnaire
- Institut des Sciences de l'Evolution (UMR 5554), CNRS-UM2-IRD, Place Eugène Bataillon, F-34095, Montpellier, France.,Station Méditerranéenne de l'Environnement Littoral, Université de Montpellier, 2 Rue des Chantiers, F-34200, Sète, France
| | - Charles Perrier
- CEFE-CNRS, Centre D'Ecologie Fonctionnelle et Evolutive, Route de Mende, 34090, Montpellier, France
| | - Clémence Genthon
- Plateforme génomique INRA GenoToul Chemin de Borderouge - Auzeville, 31320, Castanet-Tolosan, France
| | - Anne-Laure Besnard
- INRA, UMR 985 Ecologie et Santé des Ecosystèmes, 35042, Rennes, France.,Agrocampus Ouest, UMR ESE, 65 rue de Saint-Brieuc, 35042, Rennes, France
| | - Sophie Launey
- INRA, UMR 985 Ecologie et Santé des Ecosystèmes, 35042, Rennes, France.,Agrocampus Ouest, UMR ESE, 65 rue de Saint-Brieuc, 35042, Rennes, France
| | - Guillaume Evanno
- INRA, UMR 985 Ecologie et Santé des Ecosystèmes, 35042, Rennes, France.,Agrocampus Ouest, UMR ESE, 65 rue de Saint-Brieuc, 35042, Rennes, France
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Nosenko T, Böndel KB, Kumpfmüller G, Stephan W. Adaptation to low temperatures in the wild tomato species Solanum chilense. Mol Ecol 2016; 25:2853-69. [PMID: 27037798 DOI: 10.1111/mec.13637] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 03/07/2016] [Accepted: 03/22/2016] [Indexed: 11/29/2022]
Abstract
Molecular adaptation to abiotic stresses in plants is a complex process based mainly on the modifications of gene transcriptional activity and the alteration of protein-protein interactions. We used a combination of population genetic, comparative transcriptomic and plant physiology approaches to investigate the mechanisms of adaptation to low temperatures in Solanum chilense populations distributed along Andean altitudinal gradients. We found that plants from all populations have high chilling tolerance, which does not correlate with temperatures in their native habitats. In contrast, tolerance to freezing shows a significant association with altitude and temperature variables. We also observed the differences in expression patterns of cold-response genes between plants from high- and low-altitude populations. These results suggest that genetic adaptations to low temperatures evolved in high-altitude populations of S. chilense. At the transcriptional level, these adaptations may include high levels of constitutive expression of the genes encoding ICE1, the key transcription factor of the cold signalling pathway, and chloroplast ω-3 fatty acid desaturase FAD7. At the sequence level, a signature of selection associated with the adaptation to high altitudes was detected at the C-terminal part of ICE1 encoding the ACT regulatory domain.
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Affiliation(s)
- Tetyana Nosenko
- Section of Evolutionary Biology, Department of Biology II, Ludwig-Maximilians University of Munich, Großhaderner Str. 2, Planegg-Martinsried, 82152, Germany
| | - Katharina B Böndel
- Section of Evolutionary Biology, Department of Biology II, Ludwig-Maximilians University of Munich, Großhaderner Str. 2, Planegg-Martinsried, 82152, Germany.,Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, King's Buildings, Charlotte Auerbach Road, Edinburgh, EH9, 3FL, UK
| | - Gabriele Kumpfmüller
- Section of Evolutionary Biology, Department of Biology II, Ludwig-Maximilians University of Munich, Großhaderner Str. 2, Planegg-Martinsried, 82152, Germany
| | - Wolfgang Stephan
- Section of Evolutionary Biology, Department of Biology II, Ludwig-Maximilians University of Munich, Großhaderner Str. 2, Planegg-Martinsried, 82152, Germany.,Museum für Naturkunde Berlin, Invalidenstr. 4, Berlin, 10115, Germany
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20
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Greven A, Pfaffelhuber P, Pokalyuk C, Wakolbinger A. The fixation time of a strongly beneficial allele in a structured population. ELECTRON J PROBAB 2016. [DOI: 10.1214/16-ejp3355] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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21
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Ralph PL, Coop G. Convergent Evolution During Local Adaptation to Patchy Landscapes. PLoS Genet 2015; 11:e1005630. [PMID: 26571125 PMCID: PMC4646681 DOI: 10.1371/journal.pgen.1005630] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Accepted: 10/07/2015] [Indexed: 11/18/2022] Open
Abstract
Species often encounter, and adapt to, many patches of similar environmental conditions across their range. Such adaptation can occur through convergent evolution if different alleles arise in different patches, or through the spread of shared alleles by migration acting to synchronize adaptation across the species. The tension between the two reflects the constraint imposed on evolution by the underlying genetic architecture versus how effectively selection and geographic isolation act to inhibit the geographic spread of locally adapted alleles. This paper studies the balance between these two routes to adaptation in a model of continuous environments with patchy selection pressures. We address the following questions: How long does it take for a novel allele to appear in a patch where it is locally adapted through mutation? Or, through migration from another, already adapted patch? Which is more likely to occur, as a function of distance between the patches? What population genetic signal is left by the spread of migrant alleles? To answer these questions we examine the family structure underlying migration-selection equilibrium surrounding an already adapted patch, treating those rare families that reach new patches as spatial branching processes. A main result is that patches further apart than a critical distance will likely evolve independent locally adapted alleles; this distance is proportional to the spatial scale of selection ([Formula: see text], where σ is the dispersal distance and sm is the selective disadvantage of these alleles between patches), and depends linearly on log(sm/μ), where μ is the mutation rate. This provides a way to understand the role of geographic separation between patches in promoting convergent adaptation and the genomic signals it leaves behind. We illustrate these ideas using the convergent evolution of cryptic coloration in the rock pocket mouse, Chaetodipus intermedius, as an empirical example.
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Affiliation(s)
- Peter L. Ralph
- Computational Biology and Bioinformatics, University of Southern California, Los Angeles, California, United States of America
- * E-mail:
| | - Graham Coop
- Evolution and Ecology, University of California, Davis, Davis, California, United States of America
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22
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Welch JJ, Jiggins CD. Standing and flowing: the complex origins of adaptive variation. Mol Ecol 2015; 23:3935-7. [PMID: 25088550 DOI: 10.1111/mec.12859] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Revised: 07/01/2014] [Accepted: 07/10/2014] [Indexed: 01/17/2023]
Abstract
A population faced with a new selection pressure can only adapt if appropriate genetic variation is available. This genetic variation might come from new mutations or from gene exchange with other populations or species, or it might already segregate in the population as standing genetic variation (which might itself have arisen from either mutation or gene flow). Understanding the relative importance of these sources of adaptive variation is a fundamental issue in evolutionary genetics (Orr & Betancourt ; Barrett & Schluter ; Gladyshev et al. ) and has practical implications for conservation, plant and animal breeding, biological control and infectious disease prevention (e.g. Robertson ; Soulé & Wilcox ; Prentis et al. ; Pennings ). In this issue of Molecular Ecology, Roesti et al. () make an important contribution to this longstanding debate.
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Affiliation(s)
- John J Welch
- Department of Genetics, University of Cambridge, Downing St., Cambridge, CB23EH, UK
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23
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Stephan W. Signatures of positive selection: from selective sweeps at individual loci to subtle allele frequency changes in polygenic adaptation. Mol Ecol 2015; 25:79-88. [PMID: 26108992 DOI: 10.1111/mec.13288] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 06/19/2015] [Accepted: 06/19/2015] [Indexed: 12/16/2022]
Abstract
In the past 15 years, numerous methods have been developed to detect selective sweeps underlying adaptations. These methods are based on relatively simple population genetic models, including one or two loci at which positive directional selection occurs, and one or two marker loci at which the impact of selection on linked neutral variation is quantified. Information about the phenotype under selection is not included in these models (except for fitness). In contrast, in the quantitative genetic models of adaptation, selection acts on one or more phenotypic traits, such that a genotype-phenotype map is required to bridge the gap to population genetics theory. Here I describe the range of population genetic models from selective sweeps in a panmictic population of constant size to evolutionary traffic when simultaneous sweeps at multiple loci interfere, and I also consider the case of polygenic selection characterized by subtle allele frequency shifts at many loci. Furthermore, I present an overview of the statistical tests that have been proposed based on these population genetics models to detect evidence for positive selection in the genome.
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Affiliation(s)
- Wolfgang Stephan
- Biocenter, Department of Biology, Ludwig-Maximilian University Munich, Grosshaderner Str. 2, 82152, Planegg-Martinsried, Germany.,Museum für Naturkunde, Berlin, Germany
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24
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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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25
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Gosset CC, Do Nascimento J, Augé MT, Bierne N. Evidence for adaptation from standing genetic variation on an antimicrobial peptide gene in the musselMytilus edulis. Mol Ecol 2014; 23:3000-12. [DOI: 10.1111/mec.12784] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Revised: 04/24/2014] [Accepted: 04/25/2014] [Indexed: 12/30/2022]
Affiliation(s)
- Célia C. Gosset
- Université Montpellier 2; Place Eugène Bataillon 34095 Montpellier France
- CNRS - Institut des Sciences de l'Evolution; UMR5554; Station Méditerranéenne de l'Environnement Littoral; Sète France
| | - Joana Do Nascimento
- Université Montpellier 2; Place Eugène Bataillon 34095 Montpellier France
- CNRS - Institut des Sciences de l'Evolution; UMR5554; Station Méditerranéenne de l'Environnement Littoral; Sète France
- Littoral Environnement et Sociétés; UMR7266; 2 rue Olympe de Gouges 17000 La Rochelle France
| | - Marie-Thérèse Augé
- Université Montpellier 2; Place Eugène Bataillon 34095 Montpellier France
- CNRS - Institut des Sciences de l'Evolution; UMR5554; Station Méditerranéenne de l'Environnement Littoral; Sète France
| | - Nicolas Bierne
- Université Montpellier 2; Place Eugène Bataillon 34095 Montpellier France
- CNRS - Institut des Sciences de l'Evolution; UMR5554; Station Méditerranéenne de l'Environnement Littoral; Sète France
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26
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Aeschbacher S, Bürger R. The effect of linkage on establishment and survival of locally beneficial mutations. Genetics 2014; 197:317-36. [PMID: 24610861 PMCID: PMC4012489 DOI: 10.1534/genetics.114.163477] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Accepted: 02/27/2014] [Indexed: 11/18/2022] Open
Abstract
We study invasion and survival of weakly beneficial mutations arising in linkage to an established migration-selection polymorphism. Our focus is on a continent-island model of migration, with selection at two biallelic loci for adaptation to the island environment. Combining branching and diffusion processes, we provide the theoretical basis for understanding the evolution of islands of divergence, the genetic architecture of locally adaptive traits, and the importance of so-called "divergence hitchhiking" relative to other mechanisms, such as "genomic hitchhiking", chromosomal inversions, or translocations. We derive approximations to the invasion probability and the extinction time of a de novo mutation. Interestingly, the invasion probability is maximized at a nonzero recombination rate if the focal mutation is sufficiently beneficial. If a proportion of migrants carries a beneficial background allele, the mutation is less likely to become established. Linked selection may increase the survival time by several orders of magnitude. By altering the timescale of stochastic loss, it can therefore affect the dynamics at the focal site to an extent that is of evolutionary importance, especially in small populations. We derive an effective migration rate experienced by the weakly beneficial mutation, which accounts for the reduction in gene flow imposed by linked selection. Using the concept of the effective migration rate, we also quantify the long-term effects on neutral variation embedded in a genome with arbitrarily many sites under selection. Patterns of neutral diversity change qualitatively and quantitatively as the position of the neutral locus is moved along the chromosome. This will be useful for population-genomic inference. Our results strengthen the emerging view that physically linked selection is biologically relevant if linkage is tight or if selection at the background locus is strong.
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Affiliation(s)
- Simon Aeschbacher
- Department of Mathematics, University of Vienna, 1090 Vienna, Austria
- Department of Evolution and Ecology, University of California, Davis, California 95616
| | - Reinhard Bürger
- Department of Mathematics, University of Vienna, 1090 Vienna, Austria
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27
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Hough J, Williamson RJ, Wright SI. Patterns of Selection in Plant Genomes. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2013. [DOI: 10.1146/annurev-ecolsys-110512-135851] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Plants show a wide range of variation in mating system, ploidy level, and demographic history, allowing for unique opportunities to investigate the evolutionary and genetic factors affecting genome-wide patterns of positive and negative selection. In this review, we highlight recent progress in our understanding of the extent and nature of selection on plant genomes. We discuss differences in selection as they relate to variation in demography, recombination, mating system, and ploidy. We focus on the population genetic consequences of these factors and argue that, although variation in the magnitude of purifying selection is well documented, quantifying rates of positive selection and disentangling the relative importance of recombination, demography, and ploidy are ongoing challenges. Large-scale comparative studies that examine the relative and joint importance of these processes, combined with explicit models of population history and selection, are key and feasible goals for future work.
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Affiliation(s)
- Josh Hough
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada, M5S 3B2;, ,
| | - Robert J. Williamson
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada, M5S 3B2;, ,
| | - Stephen I. Wright
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada, M5S 3B2;, ,
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28
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Chauhan K, Pande V, Das A. Analyses of genetic variations at microsatellite loci present in-and-around the Pfcrt gene in Indian Plasmodium falciparum. INFECTION GENETICS AND EVOLUTION 2013; 20:476-87. [PMID: 24157593 DOI: 10.1016/j.meegid.2013.10.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 10/10/2013] [Accepted: 10/10/2013] [Indexed: 10/26/2022]
Abstract
Evolution and spread of chloroquine resistant (CQR) malaria parasite Plasmodium falciparum have posed great threat in malaria intervention across the globe. The occurrence of K76T mutation in the P. falciparum chloroquine resistance transporter (pfcrt) gene has been widely attributed to CQR with four neighboring mutations providing compensatory fitness benefit to the parasite survival. Understanding evolutionary patterns of the pfcrt gene is of great relevance not only for devising new malaria control measures but also could serve as a model to understand evolution and spread of other human drug-resistant pathogens. Several studies, mainly based on differential patterns of diversities of the microsatellite loci placed in-and-around the pfcrt gene have indicated the role of positive natural selection under the 'hitchhiking' model of molecular evolution. However, the studies were restricted to limited number of microsatellite loci present inside the pfcrt gene. Moreover, comparatively higher level of diversities in microsatellite loci present inside the pfcrt gene than the loci flanking the pfcrt gene are hallmarks of Indian P. falciparum, presenting contrasting evolutionary models to global isolates. With a view to infer evolutionary patterns of the pfcrt gene in Indian P. falciparum, we have adopted a unique sampling scheme of two types of populations (cultured and field collected) and utilized 20 polymorphic microsatellite loci (16 located inside the pfcrt gene and four in the two flanking regions) to disentangle between genetic drift (inbred cultured isolates) and natural selection (field isolates). Data analyses employing different population genetic tests could not straightforwardly explain either the model invoking 'genetic hitchhiking' or 'genetic drift'. However, complex evolutionary models influenced by both demography and natural selection or an alternative model of natural selection (e.g. diversifying/balancing selection) might better explain the observed microsatellite variation in-and-around the pfcrt gene in Indian P. falciparum.
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Affiliation(s)
- Kshipra Chauhan
- Evolutionary Genomics and Bioinformatics Laboratory, Division of Genomics and Bioinformatics, National Institute of Malaria Research, Sector 8, Dwarka, New Delhi 110077, India
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29
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Bastide H, Gérard PR, Ogereau D, Cazemajor M, Montchamp-Moreau C. Local dynamics of a fast-evolving sex-ratio system in Drosophila simulans. Mol Ecol 2013; 22:5352-67. [PMID: 24118375 DOI: 10.1111/mec.12492] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Revised: 07/29/2013] [Accepted: 08/01/2013] [Indexed: 11/29/2022]
Abstract
By distorting Mendelian transmission to their own advantage, X-linked meiotic drive elements can rapidly spread in natural populations, generating a sex-ratio bias. One expected consequence is the triggering of a co-evolutionary arms race between the sex chromosome that carries the distorter and suppressors counteracting its effect. Such an arms race has been theoretically and experimentally established and can have many evolutionary consequences. However, its dynamics in contemporary populations is still poorly documented. Here, we investigate the fate of the young X-linked Paris driver in Drosophila simulans from sub-Saharan Africa to the Middle East. We provide the first example of the early dynamics of distorters and suppressors: we find consistent evidence that the driving chromosomes have been rising in the Middle East during the last decade. In addition, identical haplotypes are at high frequencies around the two co-evolving drive loci in remote populations, implying that the driving X chromosomes share a recent common ancestor and suggesting that East Africa could be the cradle of the Paris driver. The segmental duplication associated with drive presents an unusual structure in West Africa, which could reflect a secondary state of the driver. Together with our previous demonstration of driver decline in the Indian Ocean where suppression is complete, these data provide a unique picture of the complex dynamics of a co-evolutionary arms race currently taking place in natural populations of D. simulans.
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Affiliation(s)
- Héloïse Bastide
- Laboratoire Evolution Génomes Spéciation, CNRS, 91198, Gif-sur-Yvette Cedex, France; Université Paris-Sud, 91405, Orsay Cedex, France
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30
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Bierne N, Roze D, Welch JJ. Pervasive selection or is it…? Why are FST outliers sometimes so frequent? Mol Ecol 2013; 22:2061-4. [PMID: 23671920 DOI: 10.1111/mec.12241] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
It is now common for population geneticists to estimate FST for a large number of loci across the genome, before testing for selected loci as being outliers to the FST distribution. One surprising result of such FST scans is the often high proportion (>1% and sometimes >10%) of outliers detected, and this is often interpreted as evidence for pervasive local adaptation. In this issue of Molecular Ecolog, Fourcade et al. (2013) observe that a particularly high rate of FST outliers has often been found in river organisms, such as fishes or damselflies, despite there being no obvious reason why selection should affect a larger proportion of the genomes of these organisms. Using computer simulations, Fourcade et al. (2013) show that the strong correlation in co-ancestry produced in long onedimensional landscapes (such as rivers, valleys, peninsulas, oceanic ridges or coastlines) greatly increases the neutral variance in FST, especially when the landscape is further reticulated into fractal networks. As a consequence, outlier tests have a high rate of false positives, unless this correlation can be taken into account. Fourcade et al.'s study highlights an extreme case of the general problem, first noticed by Robertson (1975a,b) and Nei & Maruyama (1975), that correlated co-ancestry inflates the neutral variance in FST when compared to its expectation under an island model of population structure. Similar warnings about the validity of outlier tests have appeared regularly since then but have not been widely cited in the recent genomics literature. We further emphasize that FST outliers can arise in many different ways and that outlier tests are not designed for situations where the genetic architecture of local adaptation involves many loci.
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Microsatellite analysis of chloroquine resistance associated alleles and neutral loci reveal genetic structure of Indian Plasmodium falciparum. INFECTION GENETICS AND EVOLUTION 2013; 19:164-75. [PMID: 23871774 DOI: 10.1016/j.meegid.2013.07.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Revised: 07/03/2013] [Accepted: 07/06/2013] [Indexed: 11/20/2022]
Abstract
Efforts to control malignant malaria caused by Plasmodium falciparum are hampered by the parasite's acquisition of resistance to antimalarial drugs, e.g., chloroquine. This necessitates evaluating the spread of chloroquine resistance in any malaria-endemic area. India displays highly variable malaria epidemiology and also shares porous international borders with malaria-endemic Southeast Asian countries having multi-drug resistant malaria. Malaria epidemiology in India is believed to be affected by two major factors: high genetic diversity and evolving drug resistance in P. falciparum. How transmission intensity of malaria can influence the genetic structure of chloroquine-resistant P. falciparum population in India is unknown. Here, genetic diversity within and among P. falciparum populations is analyzed with respect to their prevalence and chloroquine resistance observed in 13 different locations in India. Microsatellites developed for P. falciparum, including three putatively neutral and seven microsatellites thought to be under a hitchhiking effect due to chloroquine selection were used. Genetic hitchhiking is observed in five of seven microsatellites flanking the gene responsible for chloroquine resistance. Genetic admixture analysis and F-statistics detected genetically distinct groups in accordance with transmission intensity of different locations and the probable use of chloroquine. A large genetic break between the chloroquine-resistant parasite of the Northeast-East-Island group and Southwest group (FST=0.253, P<0.001) suggests a long period of isolation or a possibility of different origin between them. A pattern of significant isolation by distance was observed in low transmission areas (r=0.49, P=0.003, N=83, Mantel test). An unanticipated pattern of spread of hitchhiking suggests genetic structure for Indian P. falciparum population. Overall, the study suggests that transmission intensity can be an efficient driver for genetic differentiation at both neutral and adaptive loci across India.
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Paape T, Bataillon T, Zhou P, J Y Kono T, Briskine R, Young ND, Tiffin P. Selection, genome-wide fitness effects and evolutionary rates in the model legume Medicago truncatula. Mol Ecol 2013; 22:3525-38. [PMID: 23773281 DOI: 10.1111/mec.12329] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Revised: 02/22/2013] [Accepted: 03/12/2013] [Indexed: 12/15/2022]
Abstract
Sequence data for >20 000 annotated genes from 56 accessions of Medicago truncatula were used to identify potential targets of positive selection, the determinants of evolutionary rate variation and the relative importance of positive and purifying selection in shaping nucleotide diversity. Based upon patterns of intraspecific diversity and interspecific divergence, c. 50-75% of nonsynonymous polymorphisms are subject to strong purifying selection and 1% of the sampled genes harbour a signature of positive selection. Combining polymorphism with expression data, we estimated the distribution of fitness effects and found that the proportion of deleterious mutations is significantly greater for expressed genes than for genes with undetected transcripts (nonexpressed) in a previous RNA-seq experiment and greater for broadly expressed genes than those expressed in only a single tissue. Expression level is the strongest correlate of evolutionary rates at nonsynonymous sites, and despite multiple genomic features being significantly correlated with evolutionary rates, they explain less than 20% of the variation in nonsynonymous rates (dN) and <15% of the variation in either synonymous rates (dS) or dN:dS. Among putative targets of selection were genes involved in defence against pathogens and herbivores, genes with roles in mediating the relationship with rhizobial symbionts and one-third of annotated histone-lysine methyltransferases. Adaptive evolution of the methyltransferases suggests that positive selection in gene expression may have occurred through evolution of enzymes involved in epigenetic modification.
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Affiliation(s)
- Timothy Paape
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, 8057, Switzerland
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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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Stochastic patterns of polymorphism after a selective sweep over a subdivided population. Genet Res (Camb) 2013; 95:57-67. [PMID: 23561486 DOI: 10.1017/s0016672313000062] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
The geographic structure of a population, which is modelled as a network of several small random-mating populations or demes exchanging migrants between them, limits the rapid spread of a beneficial allele under strong directional selection to the entire population. This weakens or modifies the hitchhiking effect of the beneficial allele on the pattern of genetic variation at linked neutral loci. Previous studies suggested that the characteristic patterns of polymorphism arise with selective sweeps in such a subdivided population. However, they did not fully address the stochastic pattern, as expected in an actual sample of DNA sequence, of such patterns. This study uses a novel method of individual-based forward-in-time simulation to generate multi-locus neutral polymorphism after a selective sweep in a moderately subdivided population. Population subdivision is shown to cause frequency spectrum to shift slightly such that Tajima's D becomes less negative than expected under a panmictic population. Similarly, the pattern of linkage disequilibrium showed very small change due to population subdivision. On the other hand, the value of Wright's F ST at closely linked neutral loci relative to that at unlinked loci greatly increased by population subdivision as predicted by previous studies. Finally, the distribution of the gradient of heterozygosity along the migration path of beneficial mutation, previously suggested to allow the inference of the direction of spread, was investigated. The variance of difference in heterozygosity was much larger than the mean, suggesting that such an inference may not be practical.
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Genomic signatures of selection at linked sites: unifying the disparity among species. Nat Rev Genet 2013; 14:262-74. [PMID: 23478346 DOI: 10.1038/nrg3425] [Citation(s) in RCA: 315] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Population genetics theory supplies powerful predictions about how natural selection interacts with genetic linkage to sculpt the genomic landscape of nucleotide polymorphism. Both the spread of beneficial mutations and the removal of deleterious mutations act to depress polymorphism levels, especially in low-recombination regions. However, empiricists have documented extreme disparities among species. Here we characterize the dominant features that could drive differences in linked selection among species--including roles for selective sweeps being 'hard' or 'soft'--and the concealing effects of demography and confounding genomic variables. We advocate targeted studies of closely related species to unify our understanding of how selection and linkage interact to shape genome evolution.
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Black coats in an admixed wolf × dog pack is melanism an indicator of hybridization in wolves? EUR J WILDLIFE RES 2013. [DOI: 10.1007/s10344-013-0703-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Barton NH, Etheridge AM, Kelleher J, Véber A. Genetic hitchhiking in spatially extended populations. Theor Popul Biol 2013; 87:75-89. [PMID: 23291619 DOI: 10.1016/j.tpb.2012.12.001] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Revised: 12/05/2012] [Accepted: 12/13/2012] [Indexed: 11/16/2022]
Abstract
When a mutation with selective advantage s spreads through a panmictic population, it may cause two lineages at a linked locus to coalesce; the probability of coalescence is exp(-2rT), where T∼log(2Ns)/s is the time to fixation, N is the number of haploid individuals, and r is the recombination rate. Population structure delays fixation, and so weakens the effect of a selective sweep. However, favourable alleles spread through a spatially continuous population behind a narrow wavefront; ancestral lineages are confined at the tip of this front, and so coalesce rapidly. In extremely dense populations, coalescence is dominated by rare fluctuations ahead of the front. However, we show that for moderate densities, a simple quasi-deterministic approximation applies: the rate of coalescence within the front is λ∼2g(η)/(ρℓ), where ρ is the population density and ℓ=σ2/s is the characteristic scale of the wavefront; g(η) depends only on the strength of random drift, η=ρσs/2. The net effect of a sweep on coalescence also depends crucially on whether two lineages are ever both within the wavefront at the same time: even in the extreme case when coalescence within the front is instantaneous, the net rate of coalescence may be lower than in a single panmictic population. Sweeps can also have a substantial impact on the rate of gene flow. A single lineage will jump to a new location when it is hit by a sweep, with mean square displacement σeff(2)/σ(2)=(8/3)(L/ℓ)(Λ/R); this can be substantial if the species' range, L, is large, even if the species-wide rate of sweeps per map length, Λ/R, is small. This effect is half as strong in two dimensions. In contrast, the rate of coalescence between lineages, at random locations in space and on the genetic map, is proportional to (c/L)(Λ/R), where c is the wavespeed: thus, on average, one-dimensional structure is likely to reduce coalescence due to sweeps, relative to panmixis. In two dimensions, genes must move along the front before they can coalesce; this process is rapid, being dominated by rare fluctuations. This leads to a dramatically higher rate of coalescence within the wavefront than if lineages simply diffused along the front. Nevertheless, the net rate of coalescence due to a sweep through a two-dimensional population is likely to be lower than it would be with panmixis.
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Affiliation(s)
- N H Barton
- Institute of Science and Technology, Am Campus I, A-3400 Klosterneuberg, Austria.
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Nolte V, Pandey RV, Kofler R, Schlötterer C. Genome-wide patterns of natural variation reveal strong selective sweeps and ongoing genomic conflict in Drosophila mauritiana. Genome Res 2013; 23:99-110. [PMID: 23051690 PMCID: PMC3530687 DOI: 10.1101/gr.139873.112] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Accepted: 09/24/2012] [Indexed: 12/25/2022]
Abstract
Although it is well understood that selection shapes the polymorphism pattern in Drosophila, signatures of classic selective sweeps are scarce. Here, we focus on Drosophila mauritiana, an island endemic, which is closely related to Drosophila melanogaster. Based on a new, annotated genome sequence, we characterized the genome-wide polymorphism by sequencing pooled individuals (Pool-seq). We show that the interplay between selection and recombination results in a genome-wide polymorphism pattern characteristic for D. mauritiana. Two large genomic regions (>500 kb) showed the signature of almost complete selective sweeps. We propose that the absence of population structure and limited geographic distribution could explain why such pronounced sweep patterns are restricted to D. mauritiana. Further evidence for strong adaptive evolution was detected for several nucleoporin genes, some of which were not previously identified as genes involved in genomic conflict. Since this adaptive evolution is continuing after the split of D. mauritiana and Drosophila simulans, we conclude that genomic conflict is not restricted to short episodes, but rather an ongoing process in Drosophila.
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Affiliation(s)
- Viola Nolte
- Institut für Populationsgenetik, Vetmeduni Vienna, 1210 Wien, Austria
| | - Ram Vinay Pandey
- Institut für Populationsgenetik, Vetmeduni Vienna, 1210 Wien, Austria
| | - Robert Kofler
- Institut für Populationsgenetik, Vetmeduni Vienna, 1210 Wien, Austria
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Flaxman SM, Feder JL, Nosil P. Spatially explicit models of divergence and genome hitchhiking. J Evol Biol 2012; 25:2633-50. [DOI: 10.1111/jeb.12013] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Revised: 08/24/2012] [Accepted: 09/09/2012] [Indexed: 12/11/2022]
Affiliation(s)
- S. M. Flaxman
- Department of Ecology and Evolutionary Biology; University of Colorado; Boulder CO USA
| | - J. L. Feder
- Department of Biological Sciences; University of Notre Dame; Notre Dame IN USA
| | - P. Nosil
- Department of Ecology and Evolutionary Biology; University of Colorado; Boulder CO USA
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Hartfield M. A framework for estimating the fixation time of an advantageous allele in stepping-stone models. J Evol Biol 2012; 25:1751-64. [PMID: 22805049 DOI: 10.1111/j.1420-9101.2012.02560.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Determining how population subdivision increases the fixation time of an advantageous allele is an important problem in evolutionary genetics as this influences many processes. Here, I lay out a framework for calculating the fixation time of a positively selected allele in a subdivided population, as a function of the number of demes present, the migration rate between them and the manner in which they are connected. Using this framework, it becomes clear that a beneficial allele's fixation time is significantly reduced through migration continuously introducing copies of the allele into a newly colonized subpopulation, increasing its frequency within these demes. The effect that migration has on allele frequency needs to be explicitly taken into account to produce a realistic estimate of fixation time. This behaviour is most prominent when demes are arranged on a two-dimensional torus, in comparison with populations where demes are arranged in a circle. This is because each subpopulation is connected to several neighbours over a torus, so that there are multiple paths that an allele can take in order to fix. As a consequence, some demes experience a greater influx and efflux of migrants than others. Analytical results are found to be very accurate when compared to stochastic simulations, and are generally robust if there are a large number of demes, or if the allele is weakly selected for.
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Affiliation(s)
- M Hartfield
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK.
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