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）与萨赫尔陆架（Sahul Shelves）之间，呈线性展布，长期作为亚洲与澳大拉西亚-巴布亚生物地理界之间物种扩散的双向过滤屏障。多数陆生脊椎动物的分布模式支持岛屿定殖的踏脚石模型（stepping-stone model）。本研究以巽他火山弧岛屿上源自亚洲的拳蛙属（Limnonectes）蛙类为研究对象，探究其岛屿定殖的时间序列与过程，旨在验证岛屿定殖的踏脚石模型（stepping-stone model）。

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：达默曼拳蛙（Limnonectes dammermani）与卡达尔桑尼拳蛙（Limnonectes kadarsani）（叉舌蛙科Dicroglossidae）

研究方法：对153份蛙类样本的线粒体DNA（mitochondrial DNA）进行测序，以鉴定主要演化支并筛选样本用于外显子捕获（exon-capture）实验。我们设计探针以捕获包括外类群微盘拳蛙（Limnonectes microdiscus）在内的48份样本的974个外显子位点（总长度1,235,981 bp）的序列数据。后续采用系统发育（phylogenetic）、群体遗传（population genetic）及生物地理（biogeographical）模型检验方法对所得数据开展分析。

研究结果：线粒体DNA系统发育树显示，卡达尔桑尼拳蛙相对于达默曼拳蛙为并系类群（paraphyletic），其梳状拓扑结构符合踏脚石模型（stepping-stone model）。对974个外显子的系统基因组学（phylogenomic）分析将两个物种恢复为单系类群（monophyletic）姊妹群（sister taxa），二者的分化时间约为7.6百万年，未检测到现代基因交流，提示约4百万年前龙目岛上一次孤立的古代杂交事件导致达默曼拳蛙的线粒体渐渗（introgression）入卡达尔桑尼拳蛙。在卡达尔桑尼拳蛙内部，龙目岛谱系最先分化，松巴哇岛与伦巴塔岛谱系嵌套于由两个邻域分布（parapatric）的谱系组成的弗洛勒斯类群中，二者在弗洛勒斯岛中部形成接触带。生物地理模型比较发现，严格踏脚石模型（stepping-stone model）的支持度低于涉及跳跃扩散事件的模型。

主要结论：本研究结果表明，当前被广泛接受的岛屿定殖踏脚石模型（stepping-stone model）或许无法最佳解释该群岛现存的物种多样性格局。类群间高度的遗传结构、漫长的分化时间以及极低甚至缺失的迁移水平，提示卡达尔桑尼拳蛙复合群实际上包含5个独立物种。