Data from: Leap-frog dispersal and mitochondrial introgression: phylogenomics and biogeography of Limnonectes fanged frogs in the Lesser Sundas Archipelago of Wallacea

Aim: The Lesser Sunda Islands are situated between the Sunda and Sahul Shelves, with a linear arrangement that has functioned as a two-way filter for taxa dispersing between the Asian and Australo-Papuan biogeographic realms. Distributional patterns of many terrestrial vertebrates suggest a stepping-stone model of island colonization. Here we investigate the timing and sequence of island colonization in Asian-origin fanged frogs from the volcanic Sunda Arc islands with the goal of testing the stepping-stone model of island colonization. Location: The Indonesian islands of Java, Lombok, Sumbawa, Flores, and Lembata. Taxon: Limnonectes dammermani and L. kadarsani (Family: Dicroglossidae) Methods: Mitochondrial DNA was sequenced from 153 frogs to identify major lineages and to select samples for an exon-capture experiment. We designed probes to capture sequence data from 974 exonic loci (1,235,981 bp) from 48 frogs including the outgroup species, L. microdiscus. The resulting data were analyzed using phylogenetic, population genetic, and biogeographical model testing methods. Results: The mtDNA phylogeny finds L. kadarsani paraphyletic with respect to L. dammermani, with a pectinate topology consistent with the stepping-stone model. Phylogenomic analyses of 974 exons recovered the two species as monophyletic sister taxa that diverged ~7.6 Ma with no detectable contemporary gene flow, suggesting introgression of the L. dammermani mitochondrion into L. kadarsani on Lombok resulting from an isolated ancient hybridization event ~4 Ma. Within L. kadarsani, the Lombok lineage diverged first while the Sumbawa and Lembata lineages are nested within a Flores assemblage composed of two parapatrically distributed lineages meeting in central Flores. Biogeographical model comparison found strict stepping-stone dispersal to be less likely than models involving leap-frog dispersal events. Main conclusions: These results suggest that the currently accepted stepping-stone model of island colonization might not best explain the current patterns of diversity in the archipelago. The high degree of genetic structure, large divergence times, and absent or low levels of migration between lineages suggests that L. kadarsani represents five distinct species.

研究目的：小巽他群岛地处巽他陆架（Sunda Shelves）与萨乌鲁陆架（Sahul Shelves）之间，呈线性分布格局，长期扮演着连接亚洲与澳大拉西亚-巴布亚生物地理界的生物类群双向扩散过滤器的角色。诸多陆生脊椎动物的分布格局均印证了岛屿殖民的踏脚石扩散模型。本研究以火山弧巽他群岛上源自亚洲的棘蛙属（Limnonectes）物种为研究对象，旨在探究岛屿殖民的时间与序列，以验证岛屿殖民踏脚石扩散模型。
研究区域：印度尼西亚的爪哇岛、龙目岛、松巴哇岛、弗洛勒斯岛与伦巴塔岛。
研究类群：达姆曼棘蛙（Limnonectes dammermani）与卡达尔桑棘蛙（Limnonectes kadarsani，隶属于叉舌蛙科（Dicroglossidae））。
研究方法：本研究对153号蛙类样本的线粒体DNA（mitochondrial DNA, mtDNA）进行测序，以鉴定主要支系并为外显子捕获（exon-capture）实验筛选样本。我们设计了探针，用于捕获48号蛙类（包含外类群物种微盘棘蛙（Limnonectes microdiscus））的974个外显子位点（共计1,235,981 bp）的序列数据。随后采用系统发育（phylogenetic）、群体遗传学及生物地理模型检验方法对所得数据进行分析。
研究结果：线粒体DNA系统发育分析显示，卡达尔桑棘蛙为并系群，与达姆曼棘蛙构成栉状拓扑结构，契合踏脚石扩散模型。基于974个外显子的系统基因组学（phylogenomic）分析则将两个物种恢复为单系姊妹群，二者的分化时间约为7.6百万年前，且未检测到当代基因流，这表明约4百万年前龙目岛上发生的一次孤立的古代杂交事件，导致达姆曼棘蛙的线粒体基因渐渗至卡达尔桑棘蛙群体中。在卡达尔桑棘蛙内部，龙目岛支系最先分化，松巴哇岛与伦巴塔岛支系嵌套于弗洛勒斯岛类群中，该类群包含两个邻域分布的支系，二者在弗洛勒斯中部区域交汇。生物地理模型比较分析显示，严格踏脚石扩散模型的支持度劣于包含跳跃扩散事件的模型。
主要结论：本研究结果表明，当前广为接受的岛屿殖民踏脚石扩散模型，或许无法最佳解释该群岛现有的生物多样性分布格局。卡达尔桑棘蛙群体内极高的遗传结构分化、漫长的支系分化时间，以及支系间极低甚至缺失的迁移水平，暗示该类群实际上包含5个独立物种。