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：进化动力学受到一系列基本且普适驱动因素的塑造，包括空间结构、生态学和选择压力。这些驱动因素影响着进化轨迹，并被认为会影响系统发育结构。本文旨在评估：（1）空间结构、生态学和选择压力是否会在系统发育结构中留下可检测的信号；（2）特别是在空间结构存在的情况下，生态学信号能被检测和区分的程度；（3）这些系统发育信号在不同进化系统中的普适性程度。为此，我们通过操控三个不同范围和复杂度的计算模型中的空间结构、生态学和选择压力，对生成的系统发育树进行分析。我们发现选择压力、空间结构和生态学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的。在使用等效分类单元定义（例如个体、基因型、物种）时，不同系统间的信号具有一定的一致性。此外，我们发现足够强的生态学信号在空间结构存在的情况下仍可被检测。我们还发现，尽管低分辨率的系统发育重建可能使某些系统发育指标产生偏差，但高分辨率重建能忠实地复现它们。虽然我们的结果表明通过系统发育分析推断空间结构、生态学和选择压力具有潜力，但仍需进一步的方法开发以区分这些驱动因素的系统发育计量学信号，并对系统发育指标进行适当标准化。通过此类工作，系统发育分析可成为研究大规模进化种群的通用工具包。