Timing the extant avian radiation: The rise of modern birds, and the importance of modeling molecular rate variation
Timing the extant avian radiation: The rise of modern birds, and the importance of modeling molecular rate variation
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DOI：
10.7287/peerj.preprints.27521v1
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发表时间：
2019-02
期刊：
影响因子：
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通讯作者：
D. Field;Jacob S. Berv;Allison Y. Hsiang;R. Lanfear;Michael J. Landis;A. Dornburg
中科院分区：
文献类型：
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作者：
D. Field;Jacob S. Berv;Allison Y. Hsiang;R. Lanfear;Michael J. Landis;A. Dornburg
解开现存鸟类主要类群之间的系统发育关系被认为是恐龙系统学中最突出的问题。最近的工作已经确定了鸟类生命树的一些部分，这些部分特别具有挑战性，可能是由于冠状鸟进化史早期（特别是白垩纪末期大灭绝之后的一段时间）的快速枝进化。从表面上看，这一假设得到了冠鸟化石记录的支持，该记录记录了大多数主要冠鸟谱系在新生代早期的首次出现，这与存活的鸟类谱系在灭绝后迅速填补生态位的模型一致。然而，分子钟分析对冠鸟的年龄得出了惊人的不同估计，并且对白垩纪末期大灭绝对现存鸟类辐射的影响产生了相互矛盾的推断。这种不确定性通常归因于不完整的鸟类化石记录，但分子分化时间分析中模型规范错误的可能性代表了一个重要的、相对未被充分探索的替代假设。在这里，我们强调了进一步开发和使用模型的必要性，这些模型可以解释跨系统发育的分子进化速率的协调变化（例如分子早期爆发），作为评估冠鸟在白垩纪后快速辐射的支持的一种手段。我们讨论了生活史和取代率之间的关系如何会误导发散时间研究，这些研究没有考虑到取代率随时间的方向性变化，并提出这些影响可能导致鸟类现有分子日期估计的一些变化。我们提出了多种途径，可以帮助解决这一问题，并在其他主要真核进化枝类似的冲突。
Unravelling the phylogenetic relationships among the major groups of living birds has been described as the greatest outstanding problem in dinosaur systematics. Recent work has identified portions of the avian tree of life that are particularly challenging to reconstruct, perhaps as a result of rapid cladogenesis early in crown bird evolutionary history (specifically, the interval immediately following the end-Cretaceous mass extinction). At face value this hypothesis enjoys support from the crown bird fossil record, which documents the first appearances of most major crown bird lineages in the early Cenozoic—in line with a model of rapid post-extinction niche filling among surviving avian lineages. However, molecular-clock analyses have yielded strikingly variable estimates for the age of crown birds, and conflicting inferences on the impact of the end-Cretaceous mass extinction on the extant bird radiation. This uncertainty has often been ascribed to a patchy avian fossil record, but the possibility of model misspecification in molecular divergence time analyses represents an important and relatively underexplored alternative hypothesis. Here, we highlight the necessity of further developing and using models that account for coordinated variation in rates of molecular evolution across a phylogeny (e.g. molecular early bursts) as a means of assessing support for a rapid post-Cretaceous radiation of crown birds. We discuss how relationships between life-history and substitution rates can mislead divergence time studies that do not account for directional changes in substitution rates over time, and suggest that these effects might have caused some of the variation in existing molecular date estimates for birds. We suggest multiple paths forward that could help resolve this and similar conflicts within other major eukaryotic clades.