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Asymmetric and differential gene introgression at a contact zone between two highly divergent lineages of field voles (Microtus agrestis).

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TLDR
A possible demographic scenario to account for the patterns documented, and empirical extensions to further investigate the population genetics of a contact zone between two highly divergent lineages of field voles in the Swiss Jura mountains are proposed.
Abstract
Secondary contact zones have the potential to shed light on the mode and rate at which reproductive isolation accumulates during allopatric speciation. We investigated the population genetics of a contact zone between two highly divergent lineages of field voles (Microtus agrestis) in the Swiss Jura mountains. To shed light on the processes underlying introgression, we used maternally, paternally, and bi-parentally inherited markers. Though the two lineages maintained a strong genetic structure, we found some hybrids and evidence of gene flow. The extent of introgression varied with the mode of inheritance, being highest for mtDNA and absent for the Y chromosome. In addition, introgression was asymmetric, occurring only from the Northern to the Southern lineage. Both patterns seem parsimoniously explained by neutral processes linked to differences in effective sizes and sex-biased dispersal rates. The lineage with lower effective population size was also the more introgressed, and the mode-of-inheritance effect correlated with the male-biased dispersal rate of microtine rodents. We cannot exclude, however, that Haldane's effect contributed to the latter, as we found a marginally significant deficit in males (the heterogametic sex) among hybrids. We propose a possible demographic scenario to account for the patterns documented, and empirical extensions to further investigate this contact zone.

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The biogeography of mitochondrial and nuclear discordance in animals

TL;DR: In this article, the authors present a review of known cases of mito-nuclear discordance in animal systems and summarize the biogeographic patterns in each instance and identify common drivers of discordance.
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Modeling the Multiple Facets of Speciation-with-Gene-Flow toward Inferring the Divergence History of Lake Whitefish Species Pairs (Coregonus clupeaformis).

TL;DR: A new retrospective insight is provided into the historical demographic and selective processes that shaped a continuum of divergence associated with ecological speciation through the combined effects of linked selection and linked selection generating variable rates of lineage sorting across the genome during geographical isolation.
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Ignoring Heterozygous Sites Biases Phylogenomic Estimates of Divergence Times: Implications for the Evolutionary History of Microtus Voles

TL;DR: A phylogenomic reconstruction of the evolutionary history of the common vole with a focus on the influence of heterozygosity on the estimation of intraspecific divergence times concludes that the exclusion of heter zoning from evolutionary analyses may cause biased and misleading divergence time estimates in closely related taxa.
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Cryptic speciation in the field vole: a multilocus approach confirms three highly divergent lineages in Eurasia.

TL;DR: The field vole is investigated, a Eurasian mammal with little apparent morphological differentiation but which, on the basis of previous sex‐linked nuclear and mitochondrial DNA (mtDNA) analyses, is subdivided into a Northern and a Southern lineage, sufficiently divergent that they may represent two cryptic species.
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Structure and dynamics of hybrid zones at different stages of speciation in the common vole (Microtus arvalis)

TL;DR: Two secondary contact zones between three deep evolutionary lineages in the common vole are examined to provide information on the ongoing speciation process in M. arvalis and suggest a role for landscape history in the movement and shaping of geneflow profiles.
References
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Journal ArticleDOI

Clustal w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

TL;DR: The sensitivity of the commonly used progressive multiple sequence alignment method has been greatly improved and modifications are incorporated into a new program, CLUSTAL W, which is freely available.
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Inference of population structure using multilocus genotype data

TL;DR: Pritch et al. as discussed by the authors proposed a model-based clustering method for using multilocus genotype data to infer population structure and assign individuals to populations, which can be applied to most of the commonly used genetic markers, provided that they are not closely linked.
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Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study.

TL;DR: It is found that in most cases the estimated ‘log probability of data’ does not provide a correct estimation of the number of clusters, K, and using an ad hoc statistic ΔK based on the rate of change in the log probability between successive K values, structure accurately detects the uppermost hierarchical level of structure for the scenarios the authors tested.
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Arlequin (version 3.0): An integrated software package for population genetics data analysis

TL;DR: Arlequin ver 3.0 as discussed by the authors is a software package integrating several basic and advanced methods for population genetics data analysis, like the computation of standard genetic diversity indices, the estimation of allele and haplotype frequencies, tests of departure from linkage equilibrium, departure from selective neutrality and demographic equilibrium, estimation or parameters from past population expansions, and thorough analyses of population subdivision under the AMOVA framework.
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