The Old World insectivorous bat genus Rhinolophus is highly speciose. Over the last 15 years, the number of its recognized species has grown from 77 to 106, but knowledge of their interrelationships has not kept pace. Species limits and phylogenetic relationships of this morphologically conservative group remain problematic due both to poor sampling across the Afrotropics and to repeated instances of mitochondrial-nuclear discordance. Recent intensive surveys in East Africa and neighboring regions, coupled with parallel studies by others in West Africa and in Southern Africa, offer a new basis for understanding its evolutionary history. We investigated phylogenetic relationships and intraspecific genetic variation in the Afro-Palearctic clade of Rhinolophidae using broad sampling. We sequenced mitochondrial cytochrome-b (1140 bp) and four independent and informative nuclear introns (2611 bp) for 213 individuals and incorporated sequence data from 210 additional individuals on GenBank that together represent 24 of the 33 currently recognized Afrotropical Rhinolophus species. We addressed the widespread occurrence of mito-nuclear discordance in Rhinolophus by inferring concatenated and species tree phylogenies using only the nuclear data. Well resolved mitochondrial, concatenated nuclear, and species trees revealed phylogenetic relationships and population structure of the Afrotropical species and species groups. Multiple well-supported and deeply divergent lineages were resolved in each of the six African Rhinolophus species groups analyzed, suggesting as many as 12 undescribed cryptic species; these include several instances of sympatry among close relatives. Coalescent lineage delimitation offered support for new undescribed lineages in four of the six African groups in this study. On the other hand, two to five currently recognized species may be invalid based on combined mitochondrial and/or nuclear phylogenetic analyses. Validation of these cryptic lineages as species and formal relegation of current names to synonymy will require integrative taxonomic assessments involving morphology, ecology, acoustics, distribution, and behavior. The resulting phylogenetic framework offers a powerful basis for addressing questions regarding their ecology and evolution.

中文翻译：

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非洲马蹄蝙蝠的分子系统发育（鳞翅目：Rhinoolophidae）：扩大了非洲地区的地理和分类学采样

旧世界的食虫蝙蝠属Rhinolophus非常特殊。在过去的15年中，其公认的物种数量已从77个增加到106个，但是对它们之间的相互关系的了解并没有跟上发展的步伐。由于整个非洲地区的采样不佳以及线粒体-核不和谐的反复出现，这种形态上保守的种群的种类限制和系统发育关系仍然存在问题。最近在东非和周边地区进行的深入调查，再加上西非和南部非洲其他国家的平行研究，为了解其演化历史提供了新的基础。我们使用广泛的抽样调查了犀科的非洲古生物进化枝的系统发生关系和种内遗传变异。我们对213个个体的线粒体细胞色素b（1140 bp）和四个独立的信息性内含子（2611 bp）进行了测序，并整合了来自GenBank上210个其他个体的序列数据，这些数据共同代表了33种目前公认的非洲Rhinolophus物种中的24个。我们通过仅使用核数据来推断级联和物种树的系统发育，从而解决了犀牛中广泛存在的核-核不和谐现象。线粒体，级联核树和种树的解析良好，揭示了非热带种和种组的系统发生关系和种群结构。在所分析的六个非洲犀牛物种组中，每个物种都解析出了多个受到良好支持和高度分歧的世系，表明多达12种未描述的隐性物种。其中包括近亲之间的一些共谋行为。联盟谱系划分为这项研究中的六个非洲组中的四个中的新的未描述谱系提供了支持。另一方面，基于线粒体和/或核系统发育分析的组合，目前已知的2至5个物种可能无效。要验证这些隐性谱系是否为物种并将当前名称正式降级为同义词，将需要对形态，生态，声学，分布和行为进行综合分类学评估。由此形成的系统发育框架为解决有关其生态和进化的问题提供了强大的基础。根据线粒体和/或核系统发育分析的组合，目前公认的2至5个物种可能无效。要验证这些隐性谱系是否为物种并将当前名称正式降级为同义词，将需要对形态，生态，声学，分布和行为进行综合分类学评估。由此形成的系统发育框架为解决有关其生态和进化的问题提供了强大的基础。根据线粒体和/或核系统发育分析的组合，目前公认的2至5个物种可能无效。要验证这些隐性谱系是否为物种并将当前名称正式降级为同义词，将需要对形态，生态，声学，分布和行为进行综合分类学评估。由此形成的系统发育框架为解决有关其生态和进化的问题提供了强大的基础。