Members of the family Pteropodidae, also known as Old World fruit bats, are represented in Africa by 14 genera and 44 species. Here, we sequenced 67 complete mitochondrial genomes from African and Asian pteropodids to better understand the evolutionary history of the subfamily Rousettinae, which includes most of the African species. An increased frequency of guanine to adenine transitions is detected in the mtDNA genomes of Macroglossus sobrinus and all species of Casinycteris and Scotonycteris. Our phylogenetic and molecular dating analyses based on 126 taxa and 15,448 characters indicate a low signal for deep relationships within the family, suggesting a rapid diversification during the Late Oligocene period of “warming.” Within the subfamily Rousettinae, most nodes are highly supported by our different analyses (all nucleotide sites, SuperTRI analyses of a sliding window, transversions only, coding genes only, and amino acid sequences). The results indicate the existence of four tribes: Rousettini—distributed from Africa through Mediterranean region and South Asia to South‐East Asia; Eonycterini—found in Asia; and Epomophorini and Scotonycterini—restricted to sub‐Saharan Africa. Although most interspecies relationships are highly supported, three parts of the Rousettinae mitochondrial tree are still unresolved, suggesting rapid diversification: (a) among the three subtribes Epomophorina (Epomophorus sensu lato, i.e., including Micropteropus, Epomops, Hypsignathus, Nanonycteris), Plerotina (Plerotes), and Myonycterina (Myonycteris, Megaloglossus) in the Late Miocene; (b) among Epomops, Hypsignathus, and other species of Epomophorina at the Pliocene–Pleistocene boundary; and (c) among Myonycteris species in the Early Pleistocene. Within the Epomophorini, Stenonycteris lanosus emerged first, suggesting that lingual echolocation may have appeared in the common ancestor of Epomophorini and Rousettini. Our analyses suggest that multiple events of mtDNA introgression occurred within the Epomophorus species complex during the Pleistocene.

中文翻译：

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基于完整线粒体基因组的非洲果蝠（鳞翅目，翼足类）的系统发育

翼龙科的成员，也被称为旧世界果蝠，在非洲有14属和44种。在这里，我们对来自非洲和亚洲翼足类动物的67个完整的线粒体基因组进行了测序，以更好地了解包括大多数非洲物种的Rousettinae亚科的进化历史。在巨大Macgloglosus sobrinus和所有种类的Casinycteris和Scotonycteris的mtDNA基因组中检测到鸟嘌呤向腺嘌呤转变的频率增加。我们基于126个分类单元和15448个字符的系统发育和分子测年分析表明，该家族内部深层关系的信号很小，这表明在渐新世晚期“变暖”期间迅速多样化。在Rousettinae家族中，大多数节点得到我们不同分析（所有核苷酸位点，SuperTRI滑动窗分析，仅转化，仅编码基因和氨基酸序列）的大力支持。结果表明存在四个部落：Rousettini-从非洲通过地中海地区和南亚分布到东南亚；Eonycterini-位于亚洲；Epomophorini和Scotonycterini –仅限撒哈拉以南非洲。尽管大多数种间关系都得到了高度支持，但Rousettinae线粒体树的三个部分仍未解析，颈囊果蝠属意义上拉托，即，包括小狐蝠属，饰肩果蝠属，Hypsignathus，Nanonycteris），Plerotina（Plerotes），和Myonycterina（领果蝠属，Megaloglossus）在晚中新世; （b）在上新世-更新世边界的埃波莫普斯，海马以及其他物种的埃波莫菲纳；（c）在早更新世的Myonycteris物种中。在Epomophorini中，Stenonycteris lanosus首先出现，表明舌部回声定位可能已经出现在Epomophorini和Rousettini的共同祖先中。我们的分析表明，在更新世期间，轮虫物种复合体内发生了多个mtDNA渗入事件。