School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK.
Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, New York, USA.
Syst Biol. 2021 Oct 13;70(6):1077-1089. doi: 10.1093/sysbio/syab013.
The family Pteropodidae (Old World fruit bats) comprises $>$200 species distributed across the Old World tropics and subtropics. Most pteropodids feed on fruit, suggesting an early origin of frugivory, although several lineages have shifted to nectar-based diets. Pteropodids are of exceptional conservation concern with $>$50% of species considered threatened, yet the systematics of this group has long been debated, with uncertainty surrounding early splits attributed to an ancient rapid diversification. Resolving the relationships among the main pteropodid lineages is essential if we are to fully understand their evolutionary distinctiveness, and the extent to which these bats have transitioned to nectar-feeding. Here we generated orthologous sequences for $>$1400 nuclear protein-coding genes (2.8 million base pairs) across 114 species from 43 genera of Old World fruit bats (57% and 96% of extant species- and genus-level diversity, respectively), and combined phylogenomic inference with filtering by information content to resolve systematic relationships among the major lineages. Concatenation and coalescent-based methods recovered three distinct backbone topologies that were not able to be reconciled by filtering via phylogenetic information content. Concordance analysis and gene genealogy interrogation show that one topology is consistently the best supported, and that observed phylogenetic conflicts arise from both gene tree error and deep incomplete lineage sorting. In addition to resolving long-standing inconsistencies in the reported relationships among major lineages, we show that Old World fruit bats have likely undergone at least seven independent dietary transitions from frugivory to nectarivory. Finally, we use this phylogeny to identify and describe one new genus. [Chiroptera; coalescence; concordance; incomplete lineage sorting; nectar feeder; species tree; target enrichment.].
翼手目（旧世界果蝠）家族包括分布在旧世界热带和亚热带地区的超过 200 种物种。大多数果蝠以水果为食，表明其在早期就开始了食果行为，尽管有几个谱系已经转变为以花蜜为食的饮食。翼手目蝙蝠受到特别关注，超过 50%的物种被认为受到威胁，但该类群的系统发育长期以来一直存在争议，早期的分支不确定性归因于古老的快速多样化。如果我们要充分了解它们的进化独特性，以及这些蝙蝠向花蜜喂养转变的程度，那么解决主要翼手目谱系之间的关系至关重要。在这里，我们对来自旧世界果蝠 43 个属的 114 种蝙蝠的超过 1400 个核蛋白编码基因（280 万碱基对）进行了同源序列分析（分别代表现存物种和属水平多样性的 57%和 96%），并结合系统发育推断和信息内容过滤来解决主要谱系之间的系统关系。连接和基于合并的方法恢复了三个不同的主干拓扑结构，这些拓扑结构无法通过过滤信息内容来协调。一致性分析和基因谱系分析表明，一种拓扑结构始终得到最好的支持，并且观察到的系统发育冲突既来自基因树错误，也来自深层不完全谱系分选。除了解决主要谱系之间报告关系中的长期不一致性外，我们还表明，旧世界果蝠可能至少经历了七次从食果到食蜜的独立饮食转变。最后，我们使用这个系统发育来识别和描述一个新属。[翼手目；合并；一致性；不完全谱系分选；蜜食者；种系发生树；靶向富集。]
