Incipient speciation and secondary contact in a fossorial island endemic, the São Tomé caecilian

Secondary contact of lineages in the early stages of divergence can result in lineage fusion or promote reproductive isolation through reinforcement. While these processes are well studied in many taxonomic groups, we know little about their contribution to diversification of the secretive and enigmatic caecilians (Amphibia: Gymnophiona). Here, we combine genetic (mtDNA and genome-wide SNPs) and phenotypic data to investigate the divergence history of caecilians endemic to the oceanic island of São Tomé in the Gulf of Guinea archipelago. Consistent with a previous mtDNA study, we find two phenotypically and genetically distinct lineages that occur along a north-to-south axis with extensive admixture in the centre of the island. Demographic modelling supports divergence in allopatry (~300 kya) followed by secondary contact (~95 kya). Contrary to a morphological study that interpreted latitudinal phenotypic variation in these caecilians as a cline within a single widespread species, our analyses suggest a history of allopatric lineage divergence and subsequent hybridization that may have blurred species boundaries. We propose that late Pleistocene volcanic activity favoured allopatric divergence between these lineages with local adaptation to climate maintaining a stable hybrid zone in the centre of São Tomé Island.

处于分化早期的支系若发生二次接触，既可能导致支系融合，也可能通过强化作用促进生殖隔离。尽管这类过程在诸多分类群中已得到充分研究，但我们对其在隐秘而神秘的蚓螈（Amphibia: Gymnophiona，两栖纲：无足目）物种多样化中的作用仍知之甚少。本研究结合遗传数据（线粒体DNA（mtDNA）与全基因组单核苷酸多态性（Single Nucleotide Polymorphisms，SNPs））及表型数据，探究几内亚湾群岛圣多美岛特有蚓螈的分化历史。与此前一项线粒体DNA研究结果一致，我们发现两个表型与遗传均存在显著差异的支系，二者沿南北轴分布，且在岛屿中部存在广泛的遗传混合。种群历史建模结果支持，二者先经历异域分化（约30万年前），随后发生二次接触（约9.5万年前）。与此前一项形态学研究将该类蚓螈的纬度梯度表型变异解读为单一广布物种内的渐变群不同，我们的分析结果表明，其演化历史为先经异域支系分化，随后发生杂交，这一过程或已模糊了物种界限。我们提出，更新世晚期的火山活动推动了这两个支系的异域分化，而对气候的局部适应则维持了圣多美岛中部稳定的杂交带。