Data from: Species tree of a recent radiation: the subfamily Delphininae (Cetacea, Mammalia)

Lineages undergoing rapid radiations provide exceptional opportunities for studying speciation and adaptation, but also represent a challenge for molecular systematics because retention of ancestral polymorphisms and the occurrence of hybridization can obscure relationships among lineages. Dolphins in the subfamily Delphininae are one such case. Non-monophyly, rapid speciation events, and discordance between morphological and molecular characters have made the inference of phylogenetic relationships within this subfamily very difficult. Here we approach this problem by applying multiple methods intended to estimate species trees using a multi-gene dataset for the Delphininae (Sousa, Sotalia, Stenella, Tursiops, Delphinus and Lagenodelphis). Incongruent gene trees obtained indicate that incomplete lineage sorting and possibly hybridization are confounding the inference of species history in this group. Nonetheless, using coalescent-based methods, we have been able to extract an underlying species-tree signal from divergent histories of independent genes that supports relationships based on morphology. This is the first time a molecular study provides support for such relationships. This study further illustrates how methods of species-tree inference can be very sensitive both to the characteristics of the dataset and the evolutionary processes affecting the evolution of the group under study.

经历快速辐射演化的支系为研究物种形成与适应性演化提供了绝佳契机，但同时也给分子系统学研究带来了挑战——祖先多态性的保留与杂交事件的发生，常会模糊支系间的系统发育关系。海豚亚科（Delphininae）下的海豚类群便是典型案例之一。该类群存在非单系性、快速物种形成事件，且形态学与分子性状间存在冲突，这使得解析该亚科内部的系统发育关系极具难度。本研究针对海豚亚科（包含Sousa、Sotalia、Stenella、Tursiops、Delphinus及Lagenodelphis类群）的多基因数据集，采用多种旨在推断物种树的分析方法，以解决这一难题。我们得到的基因树存在显著不一致性，表明不完全谱系分选或（及）杂交过程正干扰该类群物种历史的推断。尽管如此，借助基于溯祖理论的分析方法，我们仍从独立基因的差异化演化历史中提取到了潜在的物种树信号，该信号支持基于形态学数据得到的类群亲缘关系。本研究首次通过分子生物学研究为该类群的系统发育关系提供了支持证据。此外，本研究还进一步印证了物种树推断方法对数据集特征以及研究类群所受演化过程的影响，均具有极高的敏感性。