Population divergence time estimation using individual lineage label switching

Beerli, Peter; Ashki, Haleh; Mashayekhi, Somayeh; Palczewski, Michal

doi:10.1093/g3journal/jkac040

Cited by 4 publications

(2 citation statements)

References 24 publications

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“…To assess the direction and magnitude of migration across five replicate contact zones within the broader hybrid zone, MIGRATE‐n v4.4 (Beerli et al, 2022 ) was used to analyze Anchored Hybrid Enrichment (AHE) sequence data of P . feriarum from a previous study (Banker et al, 2020 ).…”

Section: Methodsmentioning

confidence: 99%

“…To assess the direction and magnitude of migration across five replicate contact zones within the broader hybrid zone, MIGRATE-n v4.4 (Beerli et al, 2022) was used to analyze Anchored Hybrid Enrichment (AHE) sequence data of P. feriarum from a previous study (Banker et al, 2020). MIGRATE-n is a Bayesian coalescent-based algorithm that estimates the mutation-scaled population sizes (θ) and mutationscaled gene flow rates (M) among populations (Beerli et al, 2019); θ is 4 times the effective population size times the mutation rate per site and generation, M is a ratio between the immigration rate and the mutation rate, we assume that the mutation rate is the same among all species and we use θ and M instead of absolute numbers.…”

Section: Directionality Of Gene Flowmentioning

confidence: 99%

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The population genetics of speciation by cascade reinforcement

Anderson

Ospina

Beerli

et al. 2023

Ecology and Evolution

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Species interactions drive diverse evolutionary outcomes. Speciation by cascade reinforcement represents one example of how species interactions can contribute to the proliferation of species. This process occurs when the divergence of mating traits in response to selection against interspecific hybridization incidentally leads to reproductive isolation among populations of the same species. Here, we investigated the population genetic outcomes of cascade reinforcement in North American chorus frogs (Hylidae: Pseudacris ). Specifically, we estimated the frequency of hybridization among three taxa, assessed genetic structure within the focal species, P . feriarum , and ascertained the directionality of gene flow within P . feriarum across replicated contact zones via coalescent modeling. Through field observations and preliminary experimental crosses, we assessed whether hybridization is possible under natural and laboratory conditions. We found that hybridization occurs among P . feriarum and two conspecifics at a low rate in multiple contact zones, and that gene flow within the former species is unidirectional from allopatry into sympatry with these other species in three of four contact zones studied. We found evidence of substantial genetic structuring within P . feriarum including a divergent western allopatric cluster, a behaviorally‐distinct sympatric South Carolina cluster, and several genetically‐overlapping clusters from the remainder of the distribution. Furthermore, we found sub‐structuring between reinforced and nonreinforced populations in the two most intensely‐sampled contact zones. Our literature review indicated that P . feriarum hybridizes with at least five heterospecifics at the periphery of its range providing a mechanism for further intraspecific diversification. This work strengthens the evidence for cascade reinforcement in this clade, revealing the geographic and genetic landscape upon which this process can contribute to the proliferation of species.

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Section: Methodsmentioning

confidence: 99%

Section: Directionality Of Gene Flowmentioning

confidence: 99%

The population genetics of speciation by cascade reinforcement

Anderson

Ospina

Beerli

et al. 2023

Ecology and Evolution

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Efficient Bayesian inference under the multispecies coalescent with migration

Flouri,

Jiao,

Huang

et al. 2023

Proc. Natl. Acad. Sci. U.S.A.

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Analyses of genome sequence data have revealed pervasive interspecific gene flow and enriched our understanding of the role of gene flow in speciation and adaptation. Inference of gene flow using genomic data requires powerful statistical methods. Yet current likelihood-based methods involve heavy computation and are feasible for small datasets only. Here, we implement the multispecies-coalescent-with-migration model in the Bayesian program bpp , which can be used to test for gene flow and estimate migration rates, as well as species divergence times and population sizes. We develop Markov chain Monte Carlo algorithms for efficient sampling from the posterior, enabling the analysis of genome-scale datasets with thousands of loci. Implementation of both introgression and migration models in the same program allows us to test whether gene flow occurred continuously over time or in pulses. Analyses of genomic data from Anopheles mosquitoes demonstrate rich information in typical genomic datasets about the mode and rate of gene flow.

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Multilocus phylogeography, population genetics and niche evolution of Australian brown and black-tailed treecreepers (Aves:Climacteris)

Edwards

Tonini

McInerney

et al. 2023

Biological Journal of the Linnean Society

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The Carpentarian barrier across north-eastern Australia is a major biogeographic barrier and a generator of biodiversity within the Australian Monsoonal Tropics. Here we present a continent-wide analysis of mitochondrial (control region) and autosomal (14 anonymous loci) sequence and indel variation and niche modelling of brown and black-tailed treecreepers (Climacteris picumnus and Climacteris melanurus), a clade with a classic distribution on either side of the Carpentarian barrier. mtDNA control region sequences exhibited reciprocal monophyly and strong differentiation (Fst = 0.91), and revealed a signature of a recent selective sweep in C. picumnus. A variety of tests support an isolation-with-migration model of divergence, albeit with low levels of gene flow across the Carpentarian barrier and a divergence time between species of ~1.7–2.8 Mya. Palaeoecological niche models show that both range size as measured by available habitat and estimated historical population sizes of both species declined in the past ~600 kyr and that the area of interspecific range overlap was never historically large, perhaps decreasing opportunities for extensive gene flow. The relatively long divergence time and low opportunity for gene flow may have facilitated speciation more so than in other co-distributed bird taxa across the Australian Monsoonal Tropics.

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Population divergence time estimation using individual lineage label switching

Cited by 4 publications

References 24 publications

The population genetics of speciation by cascade reinforcement

The population genetics of speciation by cascade reinforcement

Efficient Bayesian inference under the multispecies coalescent with migration

Multilocus phylogeography, population genetics and niche evolution of Australian brown and black-tailed treecreepers (Aves:Climacteris)

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