School of BioSciences, University of Melbourne, Victoria, Australia.
School of BioSciences, University of Melbourne, Victoria, Australia; CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal.
Mol Phylogenet Evol. 2024 Dec;201:108197. doi: 10.1016/j.ympev.2024.108197. Epub 2024 Sep 11.
Phylogenomics has enriched our understanding that the Tree of Life can have network-like or reticulate structures among some taxa and genes. Two non-vertical modes of evolution - hybridization/introgression and horizontal gene transfer - deviate from a strictly bifurcating tree model, causing non-treelike patterns. However, these reticulate processes can produce similar patterns to incomplete lineage sorting or recombination, potentially leading to ambiguity. Here, we present a brief overview of a phylogenomic workflow for inferring organismal histories and compare methods for distinguishing modes of reticulate evolution. We discuss how the timing of coalescent events can help disentangle introgression from incomplete lineage sorting and how horizontal gene transfer events can help determine the relative timing of speciation events. In doing so, we identify pitfalls of certain methods and discuss how to extend their utility across the Tree of Life. Workflows, methods, and future directions discussed herein underscore the need to embrace reticulate evolutionary patterns for understanding the timing and rates of evolutionary events, providing a clearer view of life's history.
系统发生基因组学丰富了我们的认识，即生命之树在一些分类群和基因之间可能具有网状或网状结构。两种非垂直进化模式——杂交/渗入和水平基因转移——偏离了严格的分支树模型，导致非树状模式。然而，这些网状过程可以产生类似于不完全谱系分选或重组的模式，可能导致模糊性。在这里，我们简要概述了一种推断生物历史的系统发生基因组学工作流程，并比较了区分网状进化模式的方法。我们讨论了合并事件的时间如何帮助区分渗入与不完全谱系分选，以及水平基因转移事件如何帮助确定物种形成事件的相对时间。通过这样做，我们确定了某些方法的陷阱，并讨论了如何在整个生命之树上扩展它们的用途。本文讨论的工作流程、方法和未来方向强调了需要接受网状进化模式，以了解进化事件的时间和速度，从而更清晰地了解生命的历史。
