Data from: Joint reconstruction of divergence times and life-history evolution in placental mammals using a phylogenetic covariance model

Violation of the molecular clock has been amply documented, and is now routinely taken into account by molecular dating methods. Comparative analyses have revealed a systematic component in rate variation, relating it to the evolution of life-history traits, such as body size or generation time. Life-history evolution can be reconstructed using Brownian models. However, the resulting estimates are typically uncertain, and potentially sensitive to the underlying assumptions. As a way of obtaining more accurate ancestral trait and divergence time reconstructions, correlations between life-history traits and substitution rates could be used as an additional source of information. In this direction, a Bayesian framework for jointly reconstructing rates, traits, and dates was previously introduced. Here, we apply this model to a 17 protein-coding gene alignment for 73 placental taxa. Our analysis indicates that the coupling between molecules and life history can lead to a reevaluation of ancestral life-history profiles, in particular for groups displaying convergent evolution in body size. However, reconstructions are sensitive to fossil calibrations and to the Brownian assumption. Altogether, our analysis suggests that further integrating inference of rates and traits might be particularly useful for neontological macroevolutionary comparative studies.

分子钟（molecular clock）违背现象已有充分文献记载，如今分子定年（molecular dating）方法在常规分析中已将其纳入考量。比较分析揭示了速率变异中的系统性组分，该组分与诸如体型大小、世代时长等生活史特征（life-history traits）的演化相关联。生活史演化可通过布朗模型（Brownian models）进行重建。然而，所得估计值通常存在不确定性，且可能对底层假设具有敏感性。为获得更精准的祖先特征与分化时间重建结果，可将生活史特征与替换速率之间的相关性作为额外信息来源。此前已有研究提出了一种可联合重建速率、特征及分化时间的贝叶斯框架（Bayesian framework）。本研究将该模型应用于涵盖73个胎盘类类群（placental taxa）的17个蛋白编码基因比对（protein-coding gene alignment）数据集。分析结果表明，分子特征与生活史之间的耦合关联，可促使我们重新评估祖先生活史特征谱，尤其针对那些在体型大小上呈现趋同演化（convergent evolution）的类群。不过，重建结果对化石校准（fossil calibrations）以及布朗模型假设具有敏感性。综上，本研究表明，进一步整合速率与特征的推断过程，或可在现生生物宏观演化比较研究（neontological macroevolutionary comparative studies）中发挥显著效用。