TreeS10 from Cryptic diversity impacts model selection and macroevolutionary inferences in diversification analyses

Species persist in landscapes through ecological dynamics but proliferate at wider spatial scales through evolutionary mechanisms. Disentangling the contribution of each dynamic is challenging, but the increasing use of dated molecular phylogenies opened new perspectives. First, the increasing use of DNA sequences in biodiversity inventory shed light on a substantial amount of cryptic diversity in species-rich ecosystems. Second, explicit diversification models accounting for various eco-evolutionary models are now available. Integrating both advances, we explored diversification trajectories among 10 lineages of freshwater fishes in Sundaland, for which time-calibrated and taxonomically rich phylogenies are available. By fitting diversification models to dated phylogenies and incorporating DNA-based species delimitation methods, the impact of cryptic diversity on diversification model selection and related inferences is explored. Eight clades display constant speciation rate model as the most likely if cryptic diversity is accounted, but nine display a signature of diversification slowdowns when cryptic diversity is ignored. Cryptic diversification occurs during the last 5 Myr for most groups, and palaeoecological models received little support. Most cryptic lineages display restricted range distribution, supporting geographical isolation across homogeneous landscapes as the main driver of diversification. These patterns question the persistence of cryptic diversity and its role during species proliferation.物种依托生态动态在局域景观中存续，却通过进化机制在更大空间尺度上实现种群扩张。厘清各类动态的相对贡献颇具挑战，但定年分子系统发育树（dated molecular phylogenies）的日益普及为相关研究打开了全新视角。其一，DNA序列在生物多样性清查中的广泛应用，揭示了物种丰富生态系统中大量的隐蔽多样性（cryptic diversity）。其二，当前已可构建适配多种生态进化模型的显式物种分化模型（diversification models）。结合上述两项研究进展，本研究针对巽他陆架（Sundaland）的10个淡水鱼类支系展开物种分化轨迹分析，该类群已具备时间校准且分类学信息丰富的系统发育树。通过将物种分化模型拟合至定年系统发育树，并结合基于DNA的物种界定方法（DNA-based species delimitation methods），本研究探究了隐蔽多样性对物种分化模型选择及相关推论的影响。若考虑隐蔽多样性，8个演化支（clades）的最优模型为恒定成种速率模型；但若忽略隐蔽多样性，则有9个演化支呈现物种分化速率放缓的特征。多数类群的隐蔽分化发生于过去5百万年（Myr），且古生态模型（palaeoecological models）的支持度极低。多数隐蔽支系的分布范围受限，这表明均质景观中的地理隔离是物种分化的主要驱动因素。上述研究结果对隐蔽多样性的存续机制及其在物种扩张过程中的作用提出了新的科学疑问。