A multi-dimensional coalescent process applied to multi-allelic selection models and migration models

Hey, Jody

doi:10.1016/0040-5809(91)90039-i

Cited by 77 publications

(82 citation statements)

References 12 publications

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“…To study these selective processes within a larger demographic framework we extend the now classic approach of assuming altered neutral model processes for loci linked to those under selection (e.g., Hudson and Kaplan 1988;Hey 1991;Charlesworth et al 1993Charlesworth et al , 1995Charlesworth et al , 1997Slatkin 1995;Gillespie 2001). Our method clusters loci into distinct groups characterized by different sets of parameters and is applicable to a wide range of biological questions.…”

Section: Discussionmentioning

confidence: 99%

Identifying Loci Under Selection Against Gene Flow in Isolation-with-Migration Models

et al. 2013

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When divergence occurs in the presence of gene flow, there can arise an interesting dynamic in which selection against gene flow, at sites associated with population-specific adaptations or genetic incompatibilities, can cause net gene flow to vary across the genome. Loci linked to sites under selection may experience reduced gene flow and may experience genetic bottlenecks by the action of nearby selective sweeps. Data from histories such as these may be poorly fitted by conventional neutral model approaches to demographic inference, which treat all loci as equally subject to forces of genetic drift and gene flow. To allow for demographic inference in the face of such histories, as well as the identification of loci affected by selection, we developed an isolation-withmigration model that explicitly provides for variation among genomic regions in migration rates and/or rates of genetic drift. The method allows for loci to fall into any of multiple groups, each characterized by a different set of parameters, thus relaxing the assumption that all loci share the same demography. By grouping loci, the method can be applied to data with multiple loci and still have tractable dimensionality and statistical power. We studied the performance of the method using simulated data, and we applied the method to study the divergence of two subspecies of European rabbits (Oryctolagus cuniculus).U NDERSTANDING speciation requires that we determine the role played by natural selection, as well as the roles of gene exchange and other demographic factors (Dobzhansky 1951;Maynard Smith 1966;Bush 1975;Endler 1977;Templeton 1981;Arnold 1997;Barton 2001). The genetic patterns of present-day populations potentially harbor much information about these processes, and in recent years investigators have developed sophisticated methods for quantifying different kinds of factors, including levels of gene flow between populations (Beerli and Felsenstein 1999;Nielsen and Wakeley 2001), admixture proportions (Chikhi et al. 2001), times of population separation (Nielsen and Wakeley 2001), and rates of population size change (Beaumont 1999;Hey 2005). This progress has been possible mainly through the development of full-likelihood model-based statistical methods that draw upon the coalescent theory of gene genealogies. However, quantifying the effects of selection in the divergence of populations has remained a challenging problem. Diffusion-theory-based methods can incorporate selection (Gutenkunst et al. 2009); however coalescent-based approaches to modeling selection do not readily admit to the kinds of flexibility required of divergence modeling (Hudson and Kaplan 1988;Neuhauser and Krone 1997;Wakeley 2008). As a result most of the model-based methods developed in recent years for studying divergence ignore the effects of selection and rely upon an assumption that neutral mutations and demography have been the sole determinants of patterns in the data (e.g., Kuhner et al. 1998;Beerli and Felsenstein 2001;Hey and Nielsen 2007 genome, ...

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Section: Discussionmentioning

confidence: 99%

Identifying Loci Under Selection Against Gene Flow in Isolation-with-Migration Models

et al. 2013

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“…The mean coalescence of two genes randomly chosen from the entire population is then given by T = Tw/S + (s -1) TJs. Slatkin (1991) (see also Hey 1991) worked out the formula for Tfor the case of n = 2. It is given by…”

Section: Effective Population Sizementioning

confidence: 99%

Effective population size, genetic diversity, and coalescence time in subdivided populations

1993

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A formula for the effective population size for the finite island model of subdivided populations is derived. The formula indicates that the effective size can be substantially greater than the actual number of individuals in the entire population when the migration rate among subpopulations is small. It is shown that the mean nucleotide diversity, coalescence time, and heterozygosity for genes sampled from the entire population can be predicted fairly well from the theory for randomly mating populations if the effective population size for the finite island model is used.

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“…Therefore, large, sudden changes in allele frequencies will force coalescence on the derived background only if X(t) is of order 1/N (and similarly for the ancestral background). For sites that are only partially linked to the selected locus, if recombination is moving the lineages across backgrounds at a sufficiently high rate compared to the neutral coalescent rate (Nr ) 1), then two lineages in this subdivided model coalesce at a rate close to 1/2N (see Hudson and Kaplan 1988;Hey 1991;Nordborg 1997; for a detailed discussion). As such, our approximation will therefore be worse close to the selected site, but is asymptotically correct for large r.…”

Section: Relation To Previous Modelsmentioning

confidence: 99%

Patterns of Neutral Diversity Under General Models of Selective Sweeps

2012

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Two major sources of stochasticity in the dynamics of neutral alleles result from resampling of finite populations (genetic drift) and the random genetic background of nearby selected alleles on which the neutral alleles are found (linked selection). There is now good evidence that linked selection plays an important role in shaping polymorphism levels in a number of species. One of the best-investigated models of linked selection is the recurrent full-sweep model, in which newly arisen selected alleles fix rapidly. However, the bulk of selected alleles that sweep into the population may not be destined for rapid fixation. Here we develop a general model of recurrent selective sweeps in a coalescent framework, one that generalizes the recurrent full-sweep model to the case where selected alleles do not sweep to fixation. We show that in a large population, only the initial rapid increase of a selected allele affects the genealogy at partially linked sites, which under fairly general assumptions are unaffected by the subsequent fate of the selected allele. We also apply the theory to a simple model to investigate the impact of recurrent partial sweeps on levels of neutral diversity and find that for a given reduction in diversity, the impact of recurrent partial sweeps on the frequency spectrum at neutral sites is determined primarily by the frequencies rapidly achieved by the selected alleles. Consequently, recurrent sweeps of selected alleles to low frequencies can have a profound effect on levels of diversity but can leave the frequency spectrum relatively unperturbed. In fact, the limiting coalescent model under a high rate of sweeps to low frequency is identical to the standard neutral model. The general model of selective sweeps we describe goes some way toward providing a more flexible framework to describe genomic patterns of diversity than is currently available.T HE high levels of genetic variation within natural populations have long fascinated population geneticists. One school of thought holds that a substantial proportion of this molecular polymorphism is neutral or very weakly deleterious (Kimura and Ohta 1971;Ohta 1973;Kimura 1983). For neutral polymorphism, the level of genetic diversity results from a balance between the introduction of alleles through mutation and their stochastic loss (Kimura and Crow 1964;Kimura 1969;Ewens 1972). Under the neutral theory of molecular evolution this stochasticity is thought to result mostly from genetic drift (Kimura 1983), the random resampling that occurs in finite populations, an effect that is exaggerated by fluctuating population size and large variation in reproductive success among individuals (see Charlesworth 2009, for a recent review). However, selection at linked sites may provide a major source of stochasticity as the dynamics of a neutral allele can be strongly influenced by the random genetic background on which selected alleles arise (Maynard Smith and Haigh 1974;Kaplan et al. 1989;Charlesworth et al. 1995;Hudson and Kaplan 1995b).In ma...

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A multi-dimensional coalescent process applied to multi-allelic selection models and migration models

Cited by 77 publications

References 12 publications

Identifying Loci Under Selection Against Gene Flow in Isolation-with-Migration Models

Identifying Loci Under Selection Against Gene Flow in Isolation-with-Migration Models

Effective population size, genetic diversity, and coalescence time in subdivided populations

Patterns of Neutral Diversity Under General Models of Selective Sweeps

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