Lei Ming, Dong Dong
Laboratory of Molecular Ecology and Evolution, Institute of Estuarine and Coastal Research, East China Normal University, Shanghai, 200062, China.
Sci Rep. 2016 Jun 13;6:27726. doi: 10.1038/srep27726.
Bats, order Chiroptera, are one of the largest monophyletic clades in mammals. Based on morphology and behaviour bats were once differentiated into two suborders Megachiroptera and Microchiroptera Recently, researchers proposed alternative views of chiropteran classification (suborders Yinpterochiroptera and Yangochiroptera) based on morphological, molecular and fossil evidence. Since genome-scale data can significantly increase the number of informative characters for analysis, transcriptome RNA-seq data for 12 bat taxa were generated in an attempt to resolve bat subordinal relationships at the genome level. Phylogenetic reconstructions were conducted using up to 1470 orthologous genes and 634,288 aligned sites. We found strong support for the Yinpterochiroptera-Yangochiroptera classification. Next, we built expression distance matrices for each species and reconstructed gene expression trees. The tree is highly consistent with sequence-based phylogeny. We also examined the influence of taxa sampling on the performance of phylogenetic methods, and found that the topology is robust to sampling. Relaxed molecular clock estimates the divergence between Yinpterochiroptera and Yangochiroptera around 63 million years ago. The most recent common ancestor of Yinpterochiroptera, corresponding to the split between Rhinolophoidea and Pteropodidae (Old World Fruit bats), is estimated to have occurred 60 million years ago. Our work provided a valuable resource to further explore the evolutionary relationship within bats.
翼手目蝙蝠是哺乳动物中最大的单系类群之一。基于形态学和行为学，蝙蝠曾被分为两个亚目：大蝙蝠亚目和小蝙蝠亚目。最近，研究人员基于形态学、分子学和化石证据，提出了关于蝙蝠分类的另一种观点（阴翼手亚目和阳翼手亚目）。由于基因组规模的数据可以显著增加用于分析的信息特征数量，因此生成了12种蝙蝠分类单元的转录组RNA测序数据，试图在基因组水平上解决蝙蝠亚目之间的关系。使用多达1470个直系同源基因和634,288个比对位点进行了系统发育重建。我们发现有力支持阴翼手亚目-阳翼手亚目分类。接下来，我们为每个物种构建了表达距离矩阵，并重建了基因表达树。该树与基于序列的系统发育高度一致。我们还研究了分类单元抽样对系统发育方法性能的影响，发现拓扑结构对抽样具有稳健性。宽松分子钟估计阴翼手亚目和阳翼手亚目之间的分歧发生在约6300万年前。阴翼手亚目的最近共同祖先，对应于菊头蝠科和狐蝠科（旧大陆果蝠）的分化，估计发生在6000万年前。我们的工作为进一步探索蝙蝠内部的进化关系提供了宝贵资源。
