Afrixalus fornasini, Afrixalus delicatus, Afrixalus sylvaticus, Arthroleptis xenodactyloides, Leptopelis argenteus, Leptopelis concolor, Leptopelis flavomaculatus Raw sequence reads

High-throughput sequencing data have greatly improved our ability to understand the processes that contribute to current biodiversity patterns. The “vanishing refuge” diversification model is speculated for the coastal forests of eastern Africa, whereby some taxa have persisted and diversified between forest refugia, while others have switched to becoming generalists also present in non-forest habitats. Complex arrangements of geographical barriers (hydrology and topography) and ecological gradients between forest and non-forest habitats may have further influenced the region's biodiversity, but elucidation of general diversification processes has been limited by lack of suitable data. Here, we explicitly test alternative diversification modes in the coastal forests using genome-wide single nucleotide polymorphisms, mtDNA, spatial and environmental data for three forest (Arthroleptis xenodactyloides, Leptopelis flavomaculatus and Afrixalus sylvaticus) and four generalist (Afrixalus fornasini, A. delicatus, Leptopelis concolor, L. argenteus) amphibians. Multiple analyses provide insight about divergence times, spatial population structure, dispersal barriers, environmental stability and demographic history. We reveal highly congruent intra-specific diversity and population structure across taxa, with most divergences occurring during the late Pliocene and Pleistocene. Although stability models support the existence of some forest refugia, dispersal barriers and demographic models point toward idiosyncratic diversification modes across taxa. We identify a consistent role for riverine barriers in the diversification of generalist taxa, but mechanisms of diversification are more complex for forest taxa and potentially include topographical barriers, forest refugia and ecological gradients. Our work demonstrates the complexity of diversification processes in this region, which vary between forest and generalist taxa, but also for ecologically similar species with shared population boundaries.

高通量测序（High-throughput sequencing）技术极大地提升了我们解析塑造当前生物多样性格局的核心过程的能力。"消失性避难所"多样化模型（vanishing refuge diversification model）被推测适用于东非沿海森林：部分分类单元（taxa）在森林避难所之间存续并发生多样化，而另一些分类单元则演变为可在非森林生境中存活的泛化物种。森林与非森林生境之间复杂的地理屏障（水文与地形）组合及生态梯度，可能进一步影响了该区域的生物多样性，但由于缺乏合适的数据，学界对通用多样化过程的阐释仍受局限。本研究针对3种森林栖息两栖类（*Arthroleptis xenodactyloides*、*Leptopelis flavomaculatus*及*Afrixalus sylvaticus*）与4种泛化栖息两栖类（*Afrixalus fornasini*、*A. delicatus*、*Leptopelis concolor*、*L. argenteus*），利用全基因组单核苷酸多态性（genome-wide single nucleotide polymorphisms）、线粒体DNA（mtDNA）、空间及环境数据，对沿海森林中的多种备选多样化模式进行了明确检验。多项分析为我们提供了关于分化时间、空间种群结构、扩散屏障、环境稳定性及种群历史动态的深入见解。研究结果显示，各类群的种内多样性与种群结构高度一致，多数分化事件发生于上新世晚期与更新世时期。尽管环境稳定性模型支持部分森林避难所的存在，但扩散屏障分析与种群历史模型则表明，各类群的多样化模式存在特异性差异。本研究发现，河流屏障在泛化类群的多样化过程中发挥了稳定的作用；而森林类群的多样化机制则更为复杂，可能涉及地形屏障、森林避难所及生态梯度等多种因素。本研究揭示了该区域多样化过程的复杂性：这类复杂性不仅存在于森林栖息类群与泛化类群之间，也体现在具有共同种群边界的生态相似物种之间。