Comparative phylogeographic inference with genome-wide data from aggregated population pairs

Evolution; International Journal of Organic Evolution
Alexander T Xue, Michael J Hickerson

Abstract

Comparing divergences across multiple sister population pairs has been a focus in phylogeography since its inception. Initial approaches used organelle genetic data and involved qualitative comparisons of phylogenetic patterns to evaluate hypotheses of shared and variable evolutionary responses. This endeavor has progressed with coalescent model-based statistical techniques and advances in next-generation sequencing, yet there remains a need for methods that can exploit aggregated genomic-scale data within a unified analytical framework. To this end, we introduce the aggregate joint site frequency spectrum (ajSFS) by validating its use within a hierarchical Bayesian framework through several in silico experiments. Subsequently, we applied our method against two published restriction site-associated DNA marker datasets consisting of eight local replicates of a lamprey species pair and six co-distributed passerine taxon pairs, respectively, with the aim of inferring variability in co-divergence and co-migration histories. We found that the lamprey population pairs exhibited temporal synchrony in both co-divergence and collective secondary contact times, yet an idiosyncratic pattern in secondary migration intensities. In contrast,...Continue Reading

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Citations

Jan 16, 2021·The Journal of Animal Ecology·Brent C EmersonDaniel Suárez
Feb 14, 2021·Molecular Ecology·Sarah P FlanaganAdam G Jones
Jul 13, 2021·Molecular Ecology·William WaltonKonrad Lohse

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