Data from: Conflicting evolutionary histories of the mitochondrial and nuclear genomes in New World Myotis bats

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 3,648
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.

鼠耳蝠属（Myotis）快速分化出超过100个物种，是目前可用于研究的最广泛的哺乳动物辐射演化事件之一。此前学界对鼠耳蝠属内物种亲缘关系的研究，主要依赖线粒体标记，而基于核标记构建的系统发育树分辨率不足。因此，当前学界对鼠耳蝠属内亲缘关系的认知，偏向于依赖一组可能无法反映核基因组演化历史的系统发育标记。
为解决这一问题，本研究对37个代表性鼠耳蝠物种的完整线粒体基因组进行了测序（样本主要采自新大陆），同时对3648个超保守元件（UCEs）开展靶向测序。我们构建了系统发育树，并探究了串联法、总结式系统发育分析方法，以及基于标记信息含量或缺失数据水平组合的标记子集，对分析结果的影响。
在基于核UCE数据生成的294套系统发育树中，所有结果均与基于线粒体基因组构建的系统发育树存在显著差异。即便在核UCE数据内部，四分体频率分析结果显示，约半数的UCE基因座与推断出的物种树存在冲突。
这类冲突可由多种因素导致，包括不完全谱系分选、渐渗杂交，甚至系统发育分析误差。尽管核UCE基因座与线粒体基因组之间、以及核UCE基因座彼此之间均存在较高程度的不一致，但在四分之一的分析中可得到最常见的核基因组拓扑结构，且该结构的节点支持度极强。
基于上述结果，我们重新审视了鼠耳蝠属的演化历史，以更好地理解驱动其独特的核基因组、线粒体基因组及生物地理演化历程的相关现象。