An integrative phylogenomic approach illuminates the evolutionary history of Old World tree frogs (Anura: Rhacophoridae)

Rhacophoridae is one of the most speciose and ecologically diverse families of amphibians. Resolution of its evolutionary relationships is key to understanding the accumulation of biodiversity, yet previous hypotheses based on Sanger sequencing exhibit much discordance amongst generic relationships. This conflict precludes the making of sound macroevolutionary conclusions. Herein, we conduct the first phylogenomic study using broad-scale sampling and sequences of 352 nuclear DNA loci obtained using anchored hybrid enrichment targeted sequencing. The robust time-calibrated phylogenetic hypothesis clarifies several long-disputed relationships and facilitates the testing of evolutionary hypotheses on spatiotemporal diversification and reproductive modes. The major extant lineages of Rhacophoridae appear to have radiated in mainland Asia, and the spatiotemporal process corresponds with several common accumulations of biodiversity in Asia. Analyses do not detect any case of “Out of Himalayas” in Rhacophoridae. All transitions of reproductive modes appear to have evolved in an ordered, gradual sequence associated with gaining independence of standing water for larval development. The different reproductive modes are phylogenetically conserved and the completion of their transitions appear to have occurred over a period of ~30 Ma, which does not fit a pattern of a rapid burst of diversification. Innovations in reproductive modes associate statistically with the uneven distribution of species-richness between clades, where higher diversification is linked to increased terrestrial modes of reproduction. These results strengthen the hypothesis that breeding innovations drive diversification by providing new opportunities for ecological release and dispersion.

树蛙科（Rhacophoridae）是物种丰富度与生态多样性均位居前列的两栖动物科之一。厘清其演化关系是理解生物多样性累积机制的关键，但此前基于桑格测序（Sanger sequencing）提出的各类假说在属级亲缘关系上存在大量冲突，这一问题阻碍了可靠宏观演化结论的得出。本研究首次借助大范围采样与锚定杂交富集靶向测序（anchored hybrid enrichment targeted sequencing）获得的352个核DNA基因座序列，开展系统发育基因组学研究。本研究得到的稳健时间校准系统发育假说澄清了多项长期存在争议的演化关系，为验证时空分化与繁殖模式的演化假说提供了支撑。树蛙科的主要现存支系似乎在亚洲大陆发生了辐射演化，其时空演化过程与亚洲境内多次典型的生物多样性累积事件相契合。分析结果未在树蛙科中发现任何“走出喜马拉雅（Out of Himalayas）”的演化案例。所有繁殖模式的转变均遵循有序且渐进的序列，该序列与幼体发育摆脱对静水的依赖密切相关。不同繁殖模式在系统发育上具有保守性，其转变的完成耗时约3000万年，这一结果并不符合快速爆发式物种分化的模式。繁殖模式的创新与支系间物种丰富度的不均衡分布存在统计学关联，更高的分化速率与陆生繁殖模式的增强显著相关。上述结果进一步强化了“繁殖创新通过为生态释放和扩散提供新机遇，从而推动物种分化”这一假说。