Effects of Asymmetric Nuclear Introgression, Introgressive Mitochondrial Sweep, and Purifying Selection on Phylogenetic Reconstruction and Divergence Estimates in the Pacific Clade of Locustella Warblers
Sergei V. Drovetski,Georgy A. Semenov,Yaroslav A. Red'kin,Vladimir N. Sotnikov,Igor V. Fadeev,Evgeniy A. Koblik +5 more
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The multilocus nuDNA species tree resolved all inter- and intraspecific relationships despite substantial introgression, and the node ages on the species tree may be underestimated as suggested by the differences in node age estimates based on non-introgressing mtDNA and introgressing nuDNA.Abstract:
When isolated but reproductively compatible populations expand geographically and meet, simulations predict asymmetric introgression of neutral loci from a local to invading taxon. Genetic introgression may affect phylogenetic reconstruction by obscuring topology and divergence estimates. We combined phylogenetic analysis of sequences from one mtDNA and 12 nuDNA loci with analysis of gene flow among 5 species of Pacific Locustella warblers to test for presence of genetic introgression and its effects on tree topology and divergence estimates. Our data showed that nuDNA introgression was substantial and asymmetrical among all members of superspecies groups whereas mtDNA showed no introgression except a single species pair where the invader's mtDNA was swept by mtDNA of the local species. This introgressive sweep of mtDNA had the opposite direction of the nuDNA introgression and resulted in the paraphyly of the local species' mtDNA haplotypes with respect to those of the invader. Тhe multilocus nuDNA species tree resolved all inter- and intraspecific relationships despite substantial introgression. However, the node ages on the species tree may be underestimated as suggested by the differences in node age estimates based on non-introgressing mtDNA and introgressing nuDNA. In turn, the introgressive sweep and strong purifying selection appear to elongate internal branches in the mtDNA gene tree.read more
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References
More filters
Journal ArticleDOI
TCS: a computer program to estimate gene genealogies.
Journal ArticleDOI
Bayesian Phylogenetics with BEAUti and the BEAST 1.7
TL;DR: The Bayesian Evolutionary Analysis by Sampling Trees (BEAST) software package version 1.7 is presented, which implements a family of Markov chain Monte Carlo algorithms for Bayesian phylogenetic inference, divergence time dating, coalescent analysis, phylogeography and related molecular evolutionary analyses.
Journal ArticleDOI
A new statistical method for haplotype reconstruction from population data.
TL;DR: A new statistical method is presented, applicable to genotype data at linked loci from a population sample, that improves substantially on current algorithms and performs well in absolute terms, suggesting that reconstructing haplotypes experimentally or by genotyping additional family members may be an inefficient use of resources.
Journal ArticleDOI
The genetic legacy of the Quaternary ice ages
TL;DR: The present genetic structure of populations, species and communities has been mainly formed by Quaternary ice ages, and genetic, fossil and physical data combined can greatly help understanding of how organisms were so affected.