Divergence time estimation of Galliformes based on the best gene shopping scheme of ultraconserved elements

Abstract Background Divergence time estimation is fundamental to understanding many aspects of the evolution of organisms, such as character evolution, diversification, and biogeography. With the development of sequence technology, improved analytical methods, and knowledge of fossils for calibration, it is possible to obtain robust molecular dating results. However, while phylogenomic datasets show great promise in phylogenetic estimation, the best ways to leverage the large amounts of data for divergence time estimation has not been well explored. A potential solution is to focus on a subset of data for divergence time estimation, which can significantly reduce the computational burdens and avoid problems with data heterogeneity that may bias results. Results In this study, we obtained thousands of ultraconserved elements (UCEs) from 130 extant galliform taxa, including representatives of all genera, to determine the divergence times throughout galliform history. We tested the effects of different “gene shopping” schemes on divergence time estimation using a carefully, and previously validated, set of fossils. Our results found commonly used clock-like schemes may not be suitable for UCE dating (or other data types) where some loci have little information. We suggest use of partition (e.g., PartitionFinder) and selection of tree-like partitions, may be a good strategy to select a subset of data for divergence time estimation from UCEs. Our galliform time tree is largely consistent with other molecular clock studies of mitochondrial and nuclear loci. With our increased taxon sampling, a well-resolved topology, carefully vetted fossil calibrations, and suitable molecular dating methods, we obtained a high quality galliform time tree. Conclusions The updated galliform time tree provides a robust backbone time tree that can be combined with more fossil records to further facilitate our understanding for the evolution of Galliformes and as a resource for many comparative and biogeographic studies in this group.Abstract Background 分化时间估计是解析生物演化诸多方面（如性状演化、物种分化与生物地理学）的核心基础。随着测序技术的进步、分析方法的优化以及校准用化石知识的积累，获取稳健的分子定年结果已成为可能。尽管系统基因组数据集在系统发育估计中展现出巨大潜力，但如何充分利用海量数据开展分化时间估计的最优策略尚未得到充分探索。一种可行的解决方案是聚焦于子集数据开展分化时间估计，这可显著降低计算负担，并规避可能导致结果偏倚的数据异质性问题。 Results 本研究从130个现存鸡形目（Galliformes）类群（涵盖所有已知属的代表类群）中获取了数千个超保守元件（ultraconserved elements, UCEs），以解析鸡形目演化全程的分化时间。我们借助一套经过严格验证的前人校准化石集，测试了不同“基因筛选”策略对分化时间估计的影响。结果显示，常用的类时钟分析方案或许并不适用于部分位点信息含量较低的UCE定年（或其他类似数据类型）。我们建议采用分区策略（例如PartitionFinder）并选择类树分区，或许是从UCE数据中筛选子集数据用于分化时间估计的较佳策略。本研究构建的鸡形目时间树与既往基于线粒体和核基因位点的分子钟研究结果总体一致。得益于本研究增加的类群采样量、分辨率良好的拓扑结构、经过严格审核的化石校准点以及合适的分子定年方法，我们获得了高质量的鸡形目时间树。 Conclusions 本研究更新的鸡形目时间树提供了一个稳健的主干时间树，可结合更多化石记录进一步加深我们对鸡形目演化的理解，同时可作为该类群诸多比较生物学与生物地理学研究的参考资源。