Abstract
Using presence/absence data from over 10,000 Ves SINE insertions, we reconstructed a phylogeny for 11 Myotis species. With nearly one-third of individual Ves gene trees discordant with the overall species tree, phylogenetic conflict appears to be rampant in this genus. From the observed conflict, we infer that ILS is likely a major contributor to the discordance. Much of the discordance can be attributed to the hypothesized split between the Old World and New World Myotis clades and with the first radiation of Myotis within the New World. Quartet asymmetry tests reveal signs of introgression between Old and New World taxa that may have persisted until approximately 8 MYA. Our introgression tests also revealed evidence of both historic and more recent, perhaps even contemporary, gene flow among Myotis species of the New World. Our findings suggest that hybridization likely played an important role in the evolutionary history of Myotis and may still be happening in areas of sympatry. Despite limitations arising from extreme discordance, our SINE-based phylogeny better resolved deeper relationships (particularly the positioning of M. brandtii) and was able to identify potential introgression pathways among the Myotis species sampled.
Highlights
Two key factors have been identified as drivers of discordance when inferring phylogenies of rapidly diverged taxa: Incomplete Lineage Sorting (ILS) and gene flow between species
Our results indicate that both ILS and gene flow among species are abundant within Myotis
For phylogenomic analyses of the transposable elements (TEs) dataset, we only examined Ves insertions where genotypes were determined for all 11 species and a matrix of binary genotypes was constructed
Summary
Two key factors have been identified as drivers of discordance when inferring phylogenies of rapidly diverged taxa: Incomplete Lineage Sorting (ILS) and gene flow between species (hybridization or introgression). ILS is expected to be more prevalent in species with histories of rapid adaptive radiations since there is less time for polymorphic insertions to become fixed. This inconsistent sorting often confounds efforts to reconstruct an accurate species tree. The relationships recovered by analyses relying on nucleotide sequences can recover radically different topologies if the evolutionary history of the selected genes or regions are sufficiently distinct. Efforts have been made to overcome this shortcoming by analyzing multiple genes and analyzing the concatenated genic sequences, increasing the number of loci and genomic regions used to infer the phylogenies
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