scholarly journals Intermediate Migration Yields Optimal Adaptation in Structured, Asexual Populations

2014 ◽  
Author(s):  
Arthur Covert III ◽  
Claus O Wilke
Keyword(s):  
Genetic Variation ◽  
Gene Flow ◽  
Migration Rate ◽  
Appreciable Effect ◽  
Migration Rates ◽  
Optimal Migration ◽  
Digital Organisms ◽  
Asexual Populations ◽  
The Impact

Most evolving populations are subdivided into multiple subpopulations connected to each other by varying levels of gene flow. However, how population structure and gene flow (i.e., migration) affect adaptive evolution is not well understood. Here, we studied the impact of migration on asexually reproducing evolving computer programs (digital organisms). We found that digital organisms evolve the highest fitness values at intermediate migration rates, and we tested three hypotheses that could potentially explain this observation: (i) migration promotes passage through fitness valleys, (ii) migration increases genetic variation, and (iii) migration reduces clonal interference through a process called “leapfrogging”. We found that migration had no appreciable effect on the number of fitness valleys crossed and that genetic variation declined monotonously with increasing migration rates, instead of peaking at the optimal migration rate. However, the number of leapfrogging events, in which a superior beneficial mutation emerges on a genetic background that predates the previously best genotype in the population, did peak at the optimal migration rate. We thus conclude that in structured, asexual populations intermediate migration rates allow for optimal exploration of multiple, distinct fitness peaks, and thus yield the highest long-term adaptive success.

scholarly journals Long-Term Reciprocal Gene Flow in Wild and Domestic Geese Reveals Complex Domestication History

2020 ◽  
Vol 10 (9) ◽  
pp. 3061-3070 ◽  
Author(s):  
Marja E Heikkinen ◽  
Minna Ruokonen ◽  
Thomas A White ◽  
Michelle M Alexander ◽  
İslam Gündüz ◽  
...  
Keyword(s):  
Gene Flow ◽  
Wild Form ◽  
Nucleotide Polymorphisms ◽  
Anser Anser ◽  
Domestic Species ◽  
Genome Wide ◽  
Domestication Process ◽  
Historical Writings ◽  
The Impact

Abstract Hybridization has frequently been observed between wild and domestic species and can substantially impact genetic diversity of both counterparts. Geese show some of the highest levels of interspecific hybridization across all bird orders, and two of the goose species in the genus Anser have been domesticated providing an excellent opportunity for a joint study of domestication and hybridization. Until now, knowledge of the details of the goose domestication process has come from archaeological findings and historical writings supplemented with a few studies based on mitochondrial DNA. Here, we used genome-wide markers to make the first genome-based inference of the timing of European goose domestication. We also analyzed the impact of hybridization on the genome-wide genetic variation in current populations of the European domestic goose and its wild progenitor: the graylag goose (Anser anser). Our dataset consisted of 58 wild graylags sampled around Eurasia and 75 domestic geese representing 14 breeds genotyped for 33,527 single nucleotide polymorphisms. Demographic reconstruction and clustering analysis suggested that divergence between wild and domestic geese around 5,300 generations ago was followed by long-term genetic exchange, and that graylag populations have 3.2–58.0% admixture proportions with domestic geese, with distinct geographic patterns. Surprisingly, many modern European breeds share considerable (> 10%) ancestry with the Chinese domestic geese that is derived from the swan goose Anser cygnoid. We show that the domestication process can progress despite continued and pervasive gene flow from the wild form.

scholarly journals Long-term reciprocal gene flow in wild and domestic geese reveals complex domestication history

2019 ◽  
Author(s):  
Marja E. Heikkinen ◽  
Minna Ruokonen ◽  
Thomas A. White ◽  
Michelle M. Alexander ◽  
İslam Gündüz ◽  
...  
Keyword(s):  
Gene Flow ◽  
Gene Pools ◽  
Large Contribution ◽  
Wild Form ◽  
Wild Progenitor ◽  
Genome Wide ◽  
Domestication Process ◽  
Historical Writings ◽  
The Impact

AbstractHybridization has frequently been observed between wild and domestic species and can substantially impact genetic diversity of both counterparts. Geese show some of the highest levels of interspecific hybridization across all bird orders, and two of the goose species in genus Anser have been domesticated providing excellent opportunity for joint study of domestication and hybridization. Until now, knowledge on the details of the goose domestication process has come from archaeological findings and historical writings supplemented with few studies based on mitochondrial DNA. Here, we used genome-wide markers to make the first genome-based inference of the timing of European goose domestication. We also analyzed the impact of hybridization on the genome-wide genetic variation in current populations of the European domestic goose and its wild progenitor: the greylag goose (Anser anser). Our dataset consisted of 58 wild greylags sampled around Eurasia and 75 domestic geese representing 14 breeds genotyped for 33,527 single nucleotide polymorphisms. Demographic reconstruction and clustering analysis suggested that divergence between wild and domestic geese around 5,300 generations ago was followed by long-term genetic exchange, and that greylag populations have 3.2–58.0% admixture proportions with domestic geese, with distinct geographic patterns. Surprisingly, many modern European breeds share considerable (> 10%) ancestry with Chinese domestic geese that is derived from the swan goose Anser cygnoid. We show that domestication process can progress despite continued and pervasive gene flow from the wild form.Significance StatementReproductive isolation between conspecific wild and domestic populations is a cornerstone of the domestication process, yet gene flow between such wild and domestic populations has been frequently documented. European domestic geese and their wild progenitor (greylags) co-occur and can hybridize and we show that they represent a particularly persuasive case where wild and domestic populations are not isolated gene pools. Our study makes a first genome-based estimate of goose domestication, which up to now has mostly relied on archaeological findings and historical writings. We show ongoing gene flow between greylags and European domestic geese following domestication, but we also observe a surprisingly large contribution of Chinese domestic geese (a separate species) to the genetic make-up of European domestic geese.

scholarly journals Theory of the Effects of Population Structure and Sampling on Patterns of Linkage Disequilibrium Applied to Genomic Data From Humans

Genetics ◽  
2003 ◽  
Vol 164 (3) ◽  
pp. 1043-1053 ◽  
Author(s):  
John Wakeley ◽  
Sabin Lessard
Keyword(s):  
Population Structure ◽  
Linkage Disequilibrium ◽  
Migration Rate ◽  
Genomic Data ◽  
Genetic Associations ◽  
Migration Rates ◽  
Local Populations ◽  
Physical Linkage ◽  
Human Polymorphism

AbstractWe develop predictions for the correlation of heterozygosity and for linkage disequilibrium between two loci using a simple model of population structure that includes migration among local populations, or demes. We compare the results for a sample of size two from the same deme (a single-deme sample) to those for a sample of size two from two different demes (a scattered sample). The correlation in heterozygosity for a scattered sample is surprisingly insensitive to both the migration rate and the number of demes. In contrast, the correlation in heterozygosity for a single-deme sample is sensitive to both, and the effect of an increase in the number of demes is qualitatively similar to that of a decrease in the migration rate: both increase the correlation in heterozygosity. These same conclusions hold for a commonly used measure of linkage disequilibrium (r2). We compare the predictions of the theory to genomic data from humans and show that subdivision might account for a substantial portion of the genetic associations observed within the human genome, even though migration rates among local populations of humans are relatively large. Because correlations due to subdivision rather than to physical linkage can be large even in a single-deme sample, then if long-term migration has been important in shaping patterns of human polymorphism, the common practice of disease mapping using linkage disequilibrium in “isolated” local populations may be subject to error.

scholarly journals Influence of gene flow and breeding tactics on gene diversity within populations.

Genetics ◽  
1991 ◽  
Vol 129 (2) ◽  
pp. 573-583 ◽  
Author(s):  
R K Chesser
Keyword(s):  
Genetic Variation ◽  
Gene Flow ◽  
Population Size ◽  
Effective Population Size ◽  
Gene Diversity ◽  
Island Model ◽  
Effective Population ◽  
Migration Rates ◽  
Asymptotic Values ◽  
Fixation Indices

Abstract Expressions describing the accumulation of gene correlations within and among lineages and individuals of a population are derived. The model permits different migration rates by males and females and accounts for various breeding tactics within lineages. The resultant equations enable calculation of the probabilistic quantities for the fixation indices, rates of loss of genetic variation, accumulation of inbreeding, and coefficients of relationship for the population at any generation. All fixation indices were found to attain asymptotic values rapidly despite the consistent loss of genetic variation and accumulation of inbreeding within the population. The time required to attain asymptotic values, however, was prolonged when gene flow among lineages was relatively low (less than 20%). The degree of genetic differentiation among breeding groups, inbreeding coefficients, and gene correlations within lineages were found to be primarily functions of breeding tactics within groups rather than gene flow among groups. Thus, the asymptotic value of S. Wright's island model is not appropriate for describing genetic differences among groups within populations. An alternative solution is provided that under limited conditions will reduce to the original island model. The evolution of polygynous breeding tactics appears to be more favorable for promoting intragroup gene correlations than modification of migration rates. Inbreeding and variance effective sizes are derived for populations that are structured by different migration and breeding tactics. Processes that reduce the inbreeding effective population size result in a concomitant increase in variance effective population size.

scholarly journals Genetic structure and differentiation of the fire salamander Salamandra salamandra at the northern margin of its range in the Carpathians

2015 ◽  
Vol 36 (3) ◽  
pp. 301-311 ◽  
Author(s):  
Anna Najbar ◽  
Wiesław Babik ◽  
Bartłomiej Najbar ◽  
Maria Ogielska
Keyword(s):  
Mitochondrial Dna ◽  
Genetic Variation ◽  
Gene Flow ◽  
Genetic Drift ◽  
Nuclear Dna ◽  
Glacial Refugium ◽  
Northern Border ◽  
Fire Salamander ◽  
Salamandra Salamandra

Amphibian populations occurring at the margin of the species range exhibit lower genetic variation due to strong genetic drift and long-term isolation. Limited mobility and site fidelity together with habitat changes may accelerate genetic processes leading to local extinction. Here, we analyze genetic variation of the fire salamander subspecies Salamandra s. salamandra inhabiting the Outer Carpathian region in Poland, at the northern border of its distribution. Nuclear DNA polymorphism based on 10 microsatellite loci of 380 individuals sampled in 11 populations were analysed to measure gene flow between subpopulations and possible long-term isolation. Mitochondrial DNA control region analysis among 17 individuals representing 13 localities was used to detect the origin of populations which colonized Northern Europe after the last glaciation. Overall, pairwise FST’s and AMOVA test of ‘among group’ variation showed little differences in the allele frequencies and relatively high local gene flow. However, Bayesian clustering results revealed subtle structuring between eastern and western part of the studied region. Two extreme marginal populations from the Carpathian Piedmont revealed reduced genetic variation which may be attributed to strong influence of genetic drift. Only one mitochondrial DNA haplotype (type IIb) was found in all individuals and suggest that after the Last Glacial Maximum Salamandra salamandra migrated to the North-Western Europe from the single glacial refugium placed in the Balkan Peninsula.

scholarly journals The evolution of recombination rates in finite populations during ecological speciation

2016 ◽  
Vol 283 (1841) ◽  
pp. 20161243 ◽  
Author(s):  
James Reeve ◽  
Daniel Ortiz-Barrientos ◽  
Jan Engelstädter
Keyword(s):  
Gene Flow ◽  
Ecological Speciation ◽  
Joint Effect ◽  
Incipient Speciation ◽  
Finite Populations ◽  
Recombination Rates ◽  
Migration Rates ◽  
The Cost ◽  
The Hill

Recombination can impede ecological speciation with gene flow by mixing locally adapted genotypes with maladapted migrant genotypes from a divergent population. In such a scenario, suppression of recombination can be selectively favoured. However, in finite populations evolving under the influence of random genetic drift, recombination can also facilitate adaptation by reducing Hill–Robertson interference between loci under selection. In this case, increased recombination rates can be favoured. Although these two major effects on recombination have been studied individually, their joint effect on ecological speciation with gene flow remains unexplored. Using a mathematical model, we investigated the evolution of recombination rates in two finite populations that exchange migrants while adapting to contrasting environments. Our results indicate a two-step dynamic where increased recombination is first favoured (in response to the Hill–Robertson effect), and then disfavoured, as the cost of recombining locally with maladapted migrant genotypes increases over time (the maladaptive gene flow effect). In larger populations, a stronger initial benefit for recombination was observed, whereas high migration rates intensify the long-term cost of recombination. These dynamics may have important implications for our understanding of the conditions that facilitate incipient speciation with gene flow and the evolution of recombination in finite populations.

scholarly journals Defining Species When There is Gene Flow

2020 ◽  
Vol 70 (1) ◽  
pp. 108-119 ◽  
Author(s):  
Xiyun Jiao ◽  
Ziheng Yang
Keyword(s):  
Gene Flow ◽  
Migration Rates ◽  
Multispecies Coalescent ◽  
Hybridization Rate ◽  
Time Migration ◽  
Powerful Approach ◽  
Population Sizes ◽  
History Of ◽  
Definition Of ◽  
The Impact

Abstract Whatever one’s definition of species, it is generally expected that individuals of the same species should be genetically more similar to each other than they are to individuals of another species. Here, we show that in the presence of cross-species gene flow, this expectation may be incorrect. We use the multispecies coalescent model with continuous-time migration or episodic introgression to study the impact of gene flow on genetic differences within and between species and highlight a surprising but plausible scenario in which different population sizes and asymmetrical migration rates cause a genetic sequence to be on average more closely related to a sequence from another species than to a sequence from the same species. Our results highlight the extraordinary impact that even a small amount of gene flow may have on the genetic history of the species. We suggest that contrasting long-term migration rate and short-term hybridization rate, both of which can be estimated using genetic data, may be a powerful approach to detecting the presence of reproductive barriers and to define species boundaries.[Gene flow; introgression; migration; multispecies coalescent; species concept; species delimitation.]

scholarly journals The genetics of assisted gene flow: immediate costs and long-term benefits

2021 ◽  
Author(s):  
Jared A. Grummer ◽  
Tom R. Booker ◽  
Remi Matthey-Doret ◽  
Pirmin Nietlisbach ◽  
Andréa T. Thomaz ◽  
...  
Keyword(s):  
Climate Change ◽  
Genetic Variation ◽  
Gene Flow ◽  
Genetic Material ◽  
Population Level ◽  
Physiological Adaptation ◽  
Outbreeding Depression ◽  
Climate Change Scenarios ◽  
Animal Populations

ABSTRACTPlant and animal populations are facing several novel risks such as human-mediated habitat fragmentation and climate change that threaten their long-term productivity and persistence. With the genetic health of many populations deteriorating due to climate change outpacing physiological adaptation, human interventions in the form of assisted gene flow (AGF) may provide genetic variation to adapt populations to predicted climate change scenarios and result in more robust and productive populations. We ran genetic simulations to mimic a variety of AGF scenarios and measured their outcomes on population-level fitness to answer the question: in which circumstances is it worthwhile to perform AGF? Based on the parameters we explored, AGF may be harmful in certain situations over the short term (e.g., the first ∼10-20 generations), due to outbreeding depression and introducing deleterious genetic variation. Moreover, under many parameter sets, the benefits of AGF were relatively weak or took many generations to accrue. In general, when the adaptive trait is controlled by many loci of small effect, the benefits of assisted gene flow take much longer to realize–potentially too long for most climate-related management decisions. We also show that when translocation effort is divided across several generations and outbreeding depression is strong, the recipient population experiences a smaller decrease in fitness as compared to moving all individuals in a single effort. Importantly, in most cases, we show that the genomic integrity of the recipient population remains relatively intact following AGF; the amount of genetic material from the donor population typically ends up constituting no more of the recipient population’s genome than the fraction introduced. Our results will be useful for conservation practitioners and silviculturists, for instance, aiming to intervene and adaptively manage so that populations maintain a robust genetic health and maintain productivity into the future given anthropogenic climate change.

scholarly journals Investigating the Role of Hypoxia-Induced Migration in Glioblastoma Growth Rates

2019 ◽  
Author(s):  
Lee Curtin ◽  
Andrea Hawkins-Daarud ◽  
Kristoffer G. van der Zee ◽  
Kristin R. Swanson ◽  
Markus R. Owen
Keyword(s):  
Cell Migration ◽  
Migration Rate ◽  
Wave Speed ◽  
Primary Brain Tumor ◽  
Hypoxic Cell ◽  
Migration Rates ◽  
Eigenvector Analysis ◽  
Key Variables ◽  
The Impact ◽  
Eigenvalue And Eigenvector

AbstractWe analyze the wave-speed of the Proliferation Invasion Hypoxia Necrosis Angiogenesis (PIHNA) model that was previously created and applied to simulate the growth and spread of glioblastoma (GBM), a particularly aggressive primary brain tumor. We extend the PIHNA model by allowing for different hypoxic and normoxic cell migration rates and study the impact of these differences on the wave-speed dynamics. Through this analysis, we find key variables that drive the outward growth of the simulated GBM. We find a minimum tumor wave-speed for the model; this depends on the migration and proliferation rates of the normoxic cells and is achieved under certain conditions on the migration rates of the normoxic and hypoxic cells. If the hypoxic cell migration rate is greater than the normoxic cell migration rate above a threshold, the wave-speed increases above the predicted minimum. This increase in wave-speed is explored through an eigenvalue and eigenvector analysis of the linearized PIHNA model, which yields an expression for this threshold. The PIHNA model suggests that an inherently faster-diffusing hypoxic cell population can drive the outward growth of a GBM as a whole, and that this effect is more prominent for faster proliferating tumors that recover relatively slowly from a hypoxic phenotype.

scholarly journals OPTIMAL MIGRATION PROMOTES THE OUTBREAK OF COOPERATION IN HETEROGENEOUS POPULATIONS

2012 ◽  
Vol 15 (supp01) ◽  
pp. 1250059 ◽  
Author(s):  
FRANK SCHWEITZER ◽  
LAXMIDAR BEHERA
Keyword(s):  
Migration Rate ◽  
Spatial Location ◽  
Case Scenario ◽  
Worst Case ◽  
Heterogeneous Populations ◽  
Migration Rates ◽  
Optimal Migration ◽  
Threshold Frequency ◽  
Prisoners Dilemma ◽  
Small Bandwidth

We consider a population of agents that are heterogeneous with respect to (i) their strategy when interacting ngtimes with other agents in an iterated prisoners dilemma game, (ii) their spatial location on K different islands. After each generation, agents adopt strategies proportional to their average payoff received. Assuming a mix of two cooperating and two defecting strategies, we first investigate for isolated islands the conditions for an exclusive domination of each of these strategies and their possible coexistence. This allows to define a threshold frequency for cooperation that, dependent on ngand the initial mix of strategies, describes the outbreak of cooperation in the absence of migration. We then allow migration of a fixed fraction of the population after each generation. Assuming a worst case scenario where all islands are occupied by defecting strategies, whereas only one island is occupied by cooperators at the threshold frequency, we determine the optimal migration rate that allows the outbreak of cooperation on all islands. We further find that the threshold frequency divided by the number of islands, i.e., the relative effort for invading defecting islands with cooperators decreases with the number of islands. We also show that there is only a small bandwidth of migration rates, to allow the outbreak of cooperation. Larger migration rates destroy cooperation.

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