The distribution of the coalescence time and the number of pairwise nucleotide differences in the “isolation with migration” model

Wilkinson‐Herbots, Hilde

doi:10.1016/j.tpb.2007.11.001

Cited by 61 publications

(43 citation statements)

References 24 publications

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Section: Discussionmentioning

confidence: 99%

“…Wilkinson-Herbots (2008) recently obtained expressions for the expected mean and variance of pairwise sequence divergence (samples of size 2 drawn either from the same subpopulation or from different subpopulations in a finite island model) in a generalized IM model (see also Excoffier 2004). As our simulations were motivated mainly by patterns in empirical data, we have focused on larger sample sizes and aspects other than pairwise sequence diversity, but the underlying model of population subdivision with variable timing and magnitude of population expansion is identical to that studied by Wilkinson-Herbots (2008). For the most part, our simulations implemented 100 demes and a sample size of 20, and thus should approach the many-demes limit utilized in Wakeley's studies of the island model (e.g., Wakeley 1999Wakeley , 2001Wakeley , 2004Wakeley and Aliacar 2001) and more recently shown by De and Durrett (2007) for the stepping-stone model.…”

Section: Discussionmentioning

confidence: 99%

“…This scheme ought to be plausible under range expansions, e.g., as exemplified by migration out of Africa by both humans and Drosophila melanogaster and subsequent colonization of expansive areas, or temperate-zone populations expanding from glacial refugia, or following a speciation event such as that inferred for the two wild tomato species Solanum peruvianum and S. chilense (Städler et al , 2008. Moreover, this is essentially a generalized ''isolation with migration'' (IM) model of divergence with a large number of extant demes (Nielsen and Wakeley 2001;Hey and Nielsen 2004;Wilkinson-Herbots 2008). Looking forward in time, at time t the ancestral population splits into I demes of equal size and in equal proportions.…”

Section: Models and Methodsmentioning

confidence: 99%

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The Impact of Sampling Schemes on the Site Frequency Spectrum in Nonequilibrium Subdivided Populations

Städler

Haubold

Merino³

et al. 2009

Genetics

195

296

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Using coalescent simulations, we study the impact of three different sampling schemes on patterns of neutral diversity in structured populations. Specifically, we are interested in two summary statistics based on the site frequency spectrum as a function of migration rate, demographic history of the entire substructured population (including timing and magnitude of specieswide expansions), and the sampling scheme. Using simulations implementing both finite-island and two-dimensional stepping-stone spatial structure, we demonstrate strong effects of the sampling scheme on Tajima's D (D T ) and Fu and Li's D (D FL ) statistics, particularly under specieswide (range) expansions. Pooled samples yield average D T and D FL values that are generally intermediate between those of local and scattered samples. Local samples (and to a lesser extent, pooled samples) are influenced by local, rapid coalescence events in the underlying coalescent process. These processes result in lower proportions of external branch lengths and hence lower proportions of singletons, explaining our finding that the sampling scheme affects D FL more than it does D T . Under specieswide expansion scenarios, these effects of spatial sampling may persist up to very high levels of gene flow (Nm . 25), implying that local samples cannot be regarded as being drawn from a panmictic population. Importantly, many data sets on humans, Drosophila, and plants contain signatures of specieswide expansions and effects of sampling scheme that are predicted by our simulation results. This suggests that validating the assumption of panmixia is crucial if robust demographic inferences are to be made from local or pooled samples. However, future studies should consider adopting a framework that explicitly accounts for the genealogical effects of population subdivision and empirical sampling schemes.A LTHOUGH most (if not all) species are characterized by various degrees of population subdivision, population geneticists continue to employ models of panmictic populations of constant size (the neutral equilibrium, NE, model) when testing for selection and/ or demographic changes through time. Motivated by empirical data sets that were found to be incompatible with expectations under the NE model, recent largescale studies have employed coalescent simulations of demographic changes such as bottlenecks and/or population expansions in attempts to estimate parameters of such (arguably) biologically more realistic scenarios (e.g., Marth et al. 2004;Nordborg et al. 2005;Ometto et al. 2005;Schmid et al. 2005;Heuertz et al. 2006;Li and Stephan 2006;Pyhäjärvi et al. 2007;Ross-Ibarra et al. 2008). However, such simulations still assume unstructured populations, while the empirical data may derive from subdivided species and a variety of sampling schemes. The data typically collected in such projects consist of multilocus DNA sequences from which genealogical information is extracted, e.g., on the number of segregating sites (S ), the average pairwise sequence diversity...

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Models and Methodsmentioning

confidence: 99%

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The Impact of Sampling Schemes on the Site Frequency Spectrum in Nonequilibrium Subdivided Populations

Städler

Haubold

Merino³

et al. 2009

Genetics

195

296

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“…Moreover, "isolation-with-migration" methods simultaneously model the differentiation of the species / populations and the hybridization/gene flow rates between them (Becquet & Przeworski, 2007, 2009Hey & Nielsen, 2004, 2007Wilkinson-Herbots, 2008). This area is currently at the fore of phylogenetics and holds considerable promise for the methodological development of the analysis and interpretation of genealogical relationships of alleles.…”

Section: Reconstruction Of Genealogical Relationships Using Dna Sequementioning

confidence: 99%

Biogeography of Flowering Plants: A Case Study in Mignonettes (Resedaceae) and Sedges (Carex, Cyperaceae)

Martín‐Bravo¹

2012

Global Advances in Biogeography

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“…This speciation model predicts that the distribution of interspecific divergence is largely determined by a single, shared species split (Wilkinson-Herbots, 2008). But speciation is often more complex: in some cases, speciation may advance by divergent ecological or sexual selection in the face of ongoing gene flow (Nosil, 2012), while, in other cases, allopatrically diverging populations may come into secondary contact and hybridize before reproductive isolation is complete (Seehausen et al, 2014).…”

Section: General Patterns Of Introgressionmentioning

confidence: 99%

Crossing species boundaries : the hybrid histories of the true geese

Ottenburghs¹

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. Crossing Species Boundaries: The Hybrid Histories of the True Geese. PhD thesis, Wageningen University, the Netherlands. Hybridization, the interbreeding of different species, is a common phenomenon in birds: about 16% of bird species is known to have hybridized with at least one other species. Numerous avian hybrid zones have been studied from a morphological or genetic perspective, often documenting the interspecific exchange of genetic material by hybridization and backcrossing (i.e. introgression). The incidence of hybridization varies among bird orders with the Anseriformes (waterfowl: ducks, geese and swans) showing the highest propensity to hybridize. In this thesis, I provide a genomic perspective on the role of hybridization in the evolutionary history of one particular anseriform tribe, the Anserini or "True Geese", which comprises 17 species divided over two genera: Anser and Branta . The diversification of this bird group took place in the late Pliocene and the early Pleistocene (between four and two million years ago), conceivably driven by a global cooling trend that led to the establishment of a circumpolar tundra belt and the emergence of temperate grasslands. Most species show a steady population increase during this period, followed by population subdivision during the Last Glacial Maximum about 110,000 to 12,000 years ago. The combination of large effective population sizes and occasional range shifts facilitated contact between the diverging goose species, resulting in high levels of interspecific gene flow. Introgressive hybridization might have enabled these goose populations to quickly adapt to changing environments by transferring of advantageous alleles across species boundaries, increasing standing genetic variation or expanding phenotypic variation of certain traits (e.g., beak morphology). Hybridization seems to be a common and integral component in the evolution and diversification of geese. The pervasiveness of rapid speciation and hybridization in geese complicates the attempt to capture their evolutionary history in a phylogenetic tree, therefore I advocate a phylogenetic network approach. Indeed, trying to capture the complex diversification of the True Geese in a branching tree can be regarded as a wild goose chase. Abstract TABLE OF CONTENTS

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The distribution of the coalescence time and the number of pairwise nucleotide differences in the “isolation with migration” model

Cited by 61 publications

References 24 publications

The Impact of Sampling Schemes on the Site Frequency Spectrum in Nonequilibrium Subdivided Populations

The Impact of Sampling Schemes on the Site Frequency Spectrum in Nonequilibrium Subdivided Populations

Biogeography of Flowering Plants: A Case Study in Mignonettes (Resedaceae) and Sedges (Carex, Cyperaceae)

Crossing species boundaries : the hybrid histories of the true geese

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