To examine phylogenetic heterogeneity in turtle evolution, we collected thousands of high-confidence single-copy orthologs from 19 genome assemblies representative of extant turtle diversity and estimated a phylogeny with multispecies coalescent and concatenated partitioned methods. We also collected next-generation sequences from 26 turtle species and assembled millions of biallelic markers to reconstruct phylogenies based on annotated regions from the western painted turtle (Chrysemys picta bellii) genome (coding regions, introns, untranslated regions, intergenic, and others). We then measured gene tree-species tree discordance, as well as gene and site heterogeneity at each node in the inferred trees, and tested for temporal patterns in phylogenomic conflict across turtle evolution. We found strong and consistent support for all bifurcations in the inferred turtle species phylogenies. However, a number of genes, sites, and genomic features supported alternate relationships between turtle taxa. Our results suggest that gene tree-species tree discordance in these datasets is likely driven by population-level processes such as incomplete lineage sorting. We found very little effect of substitutional saturation on species tree topologies, and no clear phylogenetic patterns in codon usage bias and compositional heterogeneity. There was no correlation between gene and site concordance, node age, and DNA substitution rate across most annotated genomic regions. Our study demonstrates that heterogeneity is to be expected even in well resolved clades such as turtles, and that future phylogenomic studies should aim to sample as much of the genome as possible in order to obtain accurate phylogenies for assessing conservation priorities in turtles.

中文翻译：

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海龟进化多样化的基因组学观点

为了检查海龟进化中的系统发育异质性，我们从代表现存海龟多样性的 19 个基因组组件中收集了数千个高置信度的单拷贝直系同源物，并使用多物种合并和级联分区方法估计了系统发育。我们还收集了来自 26 个海龟物种的下一代序列，并组装了数百万个双等位基因标记，以根据西部彩龟 (Chrysemys picta bellii) 基因组的注释区域（编码区、内含子、非翻译区、基因间等）重建系统发育。然后，我们测量了基因树种树的不一致，以及推断树中每个节点的基因和位点异质性，并测试了龟进化过程中系统发育冲突的时间模式。我们发现对推断的海龟物种系统发育中的所有分叉的强烈和一致的支持。然而，许多基因、位点和基因组特征支持龟类群之间的交替关系。我们的研究结果表明，这些数据集中的基因树种树不一致可能是由种群水平的过程驱动的，例如不完整的谱系分类。我们发现替代饱和对物种树拓扑的影响很小，并且在密码子使用偏差和组成异质性方面没有明确的系统发育模式。在大多数带注释的基因组区域中，基因和位点一致性、节点年龄和 DNA 替代率之间没有相关性。我们的研究表明，即使在海龟等分辨良好的进化枝中，异质性也是可以预料的，