Abstract
The rapid diversification of Myotis bats into more than 100 species is one of the most extensive mammalian radiations available for study. Efforts to understand relationships within Myotis have primarily utilized mitochondrial markers and trees inferred from nuclear markers lacked resolution. Our current understanding of relationships within Myotis is therefore biased towards a set of phylogenetic markers that may not reflect the history of the nuclear genome. To resolve this, we sequenced the full mitochondrial genomes of 37 representative Myotis, primarily from the New World, in conjunction with targeted sequencing of 3648 ultraconserved elements (UCEs). We inferred the phylogeny and explored the effects of concatenation and summary phylogenetic methods, as well as combinations of markers based on informativeness or levels of missing data, on our results. Of the 294 phylogenies generated from the nuclear UCE data, all are significantly different from phylogenies inferred using mitochondrial genomes. Even within the nuclear data, quartet frequencies indicate that around half of all UCE loci conflict with the estimated species tree. Several factors can drive such conflict, including incomplete lineage sorting, introgressive hybridization, or even phylogenetic error. Despite the degree of discordance between nuclear UCE loci and the mitochondrial genome and among UCE loci themselves, the most common nuclear topology is recovered in one quarter of all analyses with strong nodal support. Based on these results, we re-examine the evolutionary history of Myotis to better understand the phenomena driving their unique nuclear, mitochondrial, and biogeographic histories.
Highlights
The bat genus Myotis (Order Chiroptera, Family Vespertilionidae) comprises more than 100 species that originated during the last 10-15 million years (Stadelmann et al 2007), making it one of the most successful, extant, mammalian radiations
Specimens identified as M. nigricans and M. albescens form multiple paraphyletic lineages distributed throughout the phylogeny of Neotropical Myotis (Larsen et al 2012)
Previous work with ultraconserved elements (UCEs) loci demonstrated that support for deep divergences varied based on the number of loci examined (McCormack et al 2013)
Summary
The bat genus Myotis (Order Chiroptera, Family Vespertilionidae) comprises more than 100 species that originated during the last 10-15 million years (Stadelmann et al 2007), making it one of the most successful, extant, mammalian radiations. Subsequent phylogenetic analyses of the mitochondrial cytochrome-b (cytb) gene demonstrated paraphyletic origins of each morphotype, suggesting frequent convergent evolution (Ruedi et al 2001). These same analyses demonstrated that geography was a better predictor of phylogenetic relationship than morphology (Ruedi et al 2001, Stadelmann et al 2007). For example alignments of the nuclear RAG2 and mitochondrial cytb contained 162 and 560 variable characters, respectively (Stadelmann et al 2007) Despite these concerns, we find ourselves in a situation where our understanding of evolutionary relationships, our basis for conservation strategies, and our biogeographic hypotheses are all founded, almost entirely, on mitochondrial phylogenies. Given that the nuclear and mitochondrial trees are distinct from one another it is necessary to reevaluate hypotheses made based solely on the mitochondrial phylogeny
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