An integrative phylogenomic approach illuminates the evolutionary history of Old World tree frogs (Anura: Rhacophoridae).,Molecular Phylogenetics and Evolution

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An integrative phylogenomic approach illuminates the evolutionary history of Old World tree frogs (Anura: Rhacophoridae).
Molecular Phylogenetics and Evolution ( IF 3.6 ) Pub Date : 2019-12-24 , DOI: 10.1016/j.ympev.2019.106724
Jin-Min Chen ₁ , Elizabeth Prendini ₂ , Yun-He Wu ₃ , Bao-Lin Zhang ₄ , Chatmongkon Suwannapoom ₅ , Hong-Man Chen ₄ , Jie-Qiong Jin ₄ , Emily Moriarty Lemmon ₆ , Alan R Lemmon ₇ , Bryan L Stuart ₈ , Christopher J Raxworthy ₂ , Robert W Murphy ₉ , Zhi-Yong Yuan ₁₀ , Jing Che ₁₁

Affiliation

State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, Nay Pyi Taw 05282, Myanmar.
Department of Herpetology, American Museum of Natural History, New York, NY 10024, USA.
State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, Nay Pyi Taw 05282, Myanmar; Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming 650204, China.
State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.
School of Agriculture and Natural Resources, University of Phayao, Phayao 56000, Thailand.
Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA.
Department of Scientific Computing, Florida State University, Tallahassee, FL 32306, USA.
North Carolina Museum of Natural Sciences, Raleigh, NC 27601, USA.
State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, 100 Queen's Park, Toronto, Ontario M5S 2C6, Canada.
Key Laboratory for Conserving Wildlife with Small Populations in Yunnan, Southwest Forestry University, Kunming 650224, Yunnan, China.
State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, Nay Pyi Taw 05282, Myanmar; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 650223 Kunming, China.

Rhacophoridae are one of the most speciose and ecologically diverse families of amphibians. Resolution of their 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 Himalaya" 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.

中文翻译：

综合的植物学方法阐明了旧世界树蛙（Anura：Rhacophoridae）的进化历史。

鼠科是两栖动物中最特殊和生态最多样化的家族之一。解决它们之间的进化关系是理解生物多样性积累的关键，但是基于Sanger测序的先前假设在一般关系之间显示出很大的不一致。这种冲突排除了做出合理的宏观进化论结论的可能性。在这里，我们进行了首次系统发育研究，使用大规模采样和使用锚定杂交富集靶向测序获得的352个核DNA基因座的序列。可靠的经过时间校准的系统发育假说阐明了一些长期存在的争议，并促进了关于时空多样化和生殖方式的进化假说的检验。现存的Rhacophoridae主要血统似乎已在亚洲大陆辐射，而时空过程与亚洲生物多样性的几种常见积累相对应。分析未发现Rhacophoridae中有“ Out of Himalaya”的情况。生殖方式的所有转变似乎都按照有序的，渐进的顺序进行，与获得幼体发育所需的死水独立性有关。不同的生殖方式在系统发育上是保守的，并且它们的过渡完成似乎发生在大约30 Ma的时期内，这与多样化迅速爆发的模式不符。生殖方式的创新在统计上与进化枝之间物种丰富度分布的不均匀相关，在进化枝中，更高的多样化与陆地生殖方式的增加有关。

更新日期：2019-12-25

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