Data from: Species-specific responses to island connectivity cycles: refined models for testing phylogeographic concordance across a Mediterranean Pleistocene Aggregate Island complex

The contribution of Pleistocene sea-level changes to diversification patterns in archipelagos around the world, and specifically whether the repeated cycles of island connectivity and isolation acted as a “species pump” is debated. The debate has been perpetuated in part because of the type of evidence used to evaluate the species pump hypothesis. Specifically, existing tests of the “Pleistocene Aggregate Island Complex” (PAIC) model of diversification interpret the lack of concordant divergence times among multiple co-distributed taxa as a rejection of the PAIC model. However the null expectation of concordance disregards taxon-specific ecological traits and geographic characteristics that may affect population persistence and gene flow among islands. Here we study the factors affecting population divergence in thirteen flightless darkling beetle species (Coleoptera: Tenebrionidae) across the PAIC system of the Cycladic plateau in the Aegean archipelago. Based on isolation-by-resistance analyses, hierarchical AMOVA and the degree of genealogical sorting on individual islands, we identify a major effect of bathymetry and habitat stability on the levels of genetic divergence across the PAIC, with island size and body size playing a secondary role as well. We subsequently use bathymetric maps and habitat association to generate predictions about the set of islands and group of taxa expected to show phylogeographic concordance. We test these predictions using hierarchical Approximate Bayesian Computation and show how our interpretations regarding the role of PAICs as drivers of divergence change when relying on a null expectation of concordance compared to a refined model that takes geography and ecological traits into account.更新世（Pleistocene）海平面变化对全球群岛物种分化格局的影响，尤其是岛屿连通与隔离的往复循环是否充当了“物种泵”，这一议题迄今仍存在广泛争议。该争议长期未能平息，部分原因在于评估“物种泵”假说所采用的证据类型存在局限。具体而言，现有针对更新世聚合岛复合体（Pleistocene Aggregate Island Complex, PAIC）分化模型的检验，均将多个共分布类群间分化时间的不一致性，解读为对PAIC模型的否定。然而，这类基于一致性的零假设，忽略了类群特异性的生态特征与地理属性——这些因素可影响种群存续及岛屿间的基因交流。本研究以爱琴海群岛基克拉迪高原PAIC系统中的13种无翅拟步甲（鞘翅目：拟步甲科Coleoptera: Tenebrionidae）为研究对象，探究影响其种群分化的关键因素。我们基于抗性隔离分析（isolation-by-resistance analyses）、分层分子方差分析（hierarchical AMOVA）以及单个岛屿的谱系排序程度，发现水深条件与生境稳定性对PAIC系统内的遗传分化水平具有显著主导效应，岛屿面积与体型大小亦起到次要辅助作用。随后，我们借助水深地图与生境关联数据，针对预期呈现系统地理一致性的岛屿集合与类群组生成预测。我们通过分层近似贝叶斯计算（hierarchical Approximate Bayesian Computation）检验上述预测，并阐明了在仅依赖一致性零假设，与纳入地理与生态特征的精细化模型两种情形下，我们对PAIC作为分化驱动因子的解读会产生何种差异。