Comparative analysis of variables across phylogenetically linked observations can reveal mechanisms and insights in evolutionary biology. As the taxonomic breadth of the sample of interest increases, challenges of data sparsity, poor phylogenetic resolution, and complicated evolutionary dynamics emerge. Here, we investigate a cross-eukaryotic question where all these problems exist: which organismal ecology features are correlated with gene retention in mitochondrial and chloroplast DNA (organelle DNA or oDNA). Through a wide palette of synthetic control studies, we first characterize the specificity and sensitivity of a collection of parametric and non-parametric phylogenetic comparative approaches to identify relationships in the face of such sparse and awkward datasets. This analysis is not directly focused on oDNA, and so provides generalizable insights into comparative approaches with challenging data. We then combine and curate ecological data coupled to oDNA genome information across eukaryotes, including a new semi-automated approach for gathering data on organismal traits from less systematized open-access resources including encyclopedia articles on species and taxa. The curation process also involved resolving several issues with existing datasets, including enforcing clade-specificity of several ecological features and fixing incorrect annotations. Combining this unique dataset with our benchmarked comparative approaches, we confirm support for several known links between organismal ecology and organelle gene retention, identify several previously unidentified relationships constituting possible ecological contributors to oDNA genome evolution, and provide support for a recently hypothesized link between environmental demand and oDNA retention. We, with caution, discuss the implications of these findings for organelle evolution and of this pipeline for broad comparative analyses in other fields.

中文翻译：

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细胞器基因组进化的生态预测因子：与分类学广泛、稀疏、非系统化数据的系统发育相关性


对系统发育相关观察中的变量进行比较分析可以揭示进化生物学的机制和见解。随着感兴趣样本的分类广度增加，出现了数据稀疏、系统发育分辨率差和复杂的进化动力学等挑战。在这里，我们研究了所有这些问题都存在的跨真核问题：哪些生物体生态特征与线粒体和叶绿体 DNA（细胞器 DNA 或 oDNA）中的基因保留相关。通过广泛的综合控制研究，我们首先描述了一系列参数和非参数系统发育比较方法的特异性和敏感性，以识别面对如此稀疏和尴尬的数据集的关系。该分析并不直接关注 oDNA，因此提供了具有挑战性数据的比较方法的普遍见解。然后，我们将生态数据与真核生物的 oDNA 基因组信息相结合并进行整理，包括一种新的半自动化方法，用于从不太系统化的开放获取资源（包括有关物种和类群的百科全书文章）收集生物性状的数据。管理过程还涉及解决现有数据集的几个问题，包括加强几个生态特征的进化枝特异性以及修复不正确的注释。将这个独特的数据集与我们的基准比较方法相结合，我们确认了对有机体生态学和细胞器基因保留之间的几个已知联系的支持，确定了构成oDNA基因组进化的可能生态贡献者的几个先前未识别的关系，并为最近假设的环境需求之间的联系提供了支持和 oDNA 保留。 我们谨慎地讨论这些发现对细胞器进化的影响以及该管道对其他领域广泛比较分析的影响。