Evolutionary dynamics are shaped by a variety of fundamental, generic drivers, including spatial structure, ecology, and selection pressure. These drivers impact the trajectory of evolution, and have been hypothesized to influence phylogenetic structure. Here, we set out to assess (1) if spatial structure, ecology, and selection pressure leave detectable signatures in phylogenetic structure, (2) the extent, in particular, to which ecology can be detected and discerned in the presence of spatial structure, and (3) the extent to which these phylogenetic signatures generalize across evolutionary systems. To this end, we analyze phylogenies generated by manipulating spatial structure, ecology, and selection pressure within three computational models of varied scope and sophistication. We find that selection pressure, spatial structure, and ecology have characteristic effects on phylogenetic metrics, although these effects are complex and not always intuitive. Signatures have some consistency across systems when using equivalent taxonomic unit definitions (e.g., individual, genotype, species). Further, we find that sufficiently strong ecology can be detected in the presence of spatial structure. We also find that, while low-resolution phylogenetic reconstructions can bias some phylogenetic metrics, high-resolution reconstructions recapitulate them faithfully. Although our results suggest potential for evolutionary inference of spatial structure, ecology, and selection pressure through phylogenetic analysis, further methods development is needed to distinguish these drivers' phylometric signatures from each other and to appropriately normalize phylogenetic metrics. With such work, phylogenetic analysis could provide a versatile toolkit to study large-scale evolving populations.

翻译：进化动态受多种基本且通用的驱动因素影响，包括空间结构、生态和选择压力。这些驱动因素影响进化轨迹，并被认为对系统发育结构产生影响。本研究旨在评估：（1）空间结构、生态和选择压力是否在系统发育结构中留下可检测的特征；（2）尤其在存在空间结构的情况下，生态因素被检测和辨识的程度；（3）这些系统发育特征在进化系统中的泛化程度。为此，我们通过三种不同范围与复杂度的计算模型，操控空间结构、生态和选择压力，分析由此产生的系统发育树。研究发现，选择压力、空间结构与生态对系统发育指标具有特征性影响，尽管这些影响复杂且并非总是直观。当使用等效的分类单元定义（例如个体、基因型、物种）时，特征在不同系统中具有一定的一致性。此外，我们发现在存在空间结构的情况下，足够强的生态信号仍可被检测。研究还表明，低分辨率的系统发育重建可能使部分指标产生偏差，而高分辨率重建则能准确再现这些指标。尽管我们的结果暗示通过系统发育分析推断空间结构、生态和选择压力具有潜力，但需进一步发展方法以区分这些驱动因素的系统发育特征，并对相关指标进行适当标准化。通过此类工作，系统发育分析有望成为研究大规模进化群体的通用工具。