Choosing among types of genomic markers to be used in a phylogenomic study can have a major influence on the cost, design, and results of a study. Yet few attempts have been made to compare categories of next-generation sequence markers limiting our ability to compare the suitability of these different genomic fragment types. Here, we explore properties of different genomic markers to find if they vary in the accuracy of component phylogenetic trees and to clarify the causes of conflict obtained from different data sets or inference methods. As a test case, we explore the causes of discordance between phylogenetic hypotheses obtained using a novel data set of ultraconserved elements (UCEs) and a recently published exon data set of the cichlid tribe Heroini. Resolving relationships among heroine cichlids has historically been difficult, and the processes of colonization and diversification in Middle America and the Greater Antilles are not yet well understood. Despite differences in informativeness and levels of gene tree discordance between UCEs and exons, the resulting phylogenomic hypotheses generally agree on most relationships. The independent data sets disagreed in areas with low phylogenetic signal that were overwhelmed by incomplete lineage sorting and nonphylogenetic signals. For UCEs, high levels of incomplete lineage sorting were found to be the major cause of gene tree discordance, whereas, for exons, nonphylogenetic signal is most likely caused by a reduced number of highly informative loci. This paucity of informative loci in exons might be due to heterogeneous substitution rates that are problematic to model (i.e., computationally restrictive) resulting in systematic errors that UCEs (being less informative individually but more uniform) are less prone to. These results generally demonstrate the robustness of phylogenomic methods to accommodate genomic markers with different biological and phylogenetic properties. However, we identify common and unique pitfalls of different categories of genomic fragments when inferring enigmatic phylogenetic relationships.

中文翻译：

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比较超保守元素和外显子以进行中美洲慈鲷的系统发育分析：当数据一致与不一致时

选择用于系统发育学研究的基因组标记类型可能会对研究的成本、设计和结果产生重大影响。然而，很少有人尝试比较下一代序列标记的类别，这限制了我们比较这些不同基因组片段类型的适用性的能力。在这里，我们探索不同基因组标记的特性，以发现它们在组成系统发育树的准确性方面是否存在差异，并阐明从不同数据集或推理方法获得的冲突原因。作为一个测试案例，我们探讨了使用超保守元素（UCE）的新颖数据集和最近发布的慈鲷部落 Heroini 的外显子数据集获得的系统发育假设之间不一致的原因。从历史上看，解决英雄丽鱼之间的关系一直很困难，中美洲和大安的列斯群岛的殖民化和多样化过程尚不清楚。尽管 UCE 和外显子之间的信息量和基因树不一致程度存在差异，但由此产生的系统发育假说通常在大多数关系上是一致的。独立数据集在系统发育信号较低的区域存在分歧，这些区域被不完整的谱系排序和非系统发育信号所淹没。对于 UCE，高水平的不完整谱系排序被发现是基因树不一致的主要原因，而对于外显子，非系统发育信号很可能是由高信息基因座数量减少引起的。外显子中信息位点的缺乏可能是由于异质替代率导致模型存在问题（即计算限制），从而导致 UCE（单个信息量较少但更统一）不太容易出现系统错误。这些结果通常证明了系统发育学方法适应具有不同生物学和系统发育特性的基因组标记的稳健性。然而，在推断神秘的系统发育关系时，我们发现了不同类别的基因组片段的常见和独特的陷阱。