Reticulate evolution: Detection and utility in the phylogenomics era

• Published in: Molecular phylogenetics and evolution Vol. 201; p. 108197
• Main Authors: Bjornson, Saelin, Verbruggen, Heroen, Upham, Nathan S., Steenwyk, Jacob L.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.12.2024
• Subjects: Animals; Biological Evolution; Divergence time estimation; Evolution, Molecular; Gene Transfer, Horizontal; Gene-tree-species-tree discordance; Genetic Speciation; Genomics; Horizontal gene transfer; Hybridization; Hybridization, Genetic; Introgression; Lateral gene transfer; Models, Genetic; Phylogenetic incongruence; Phylogenetics; Phylogeny; Phylogenetics; Lateral gene transfer; Divergence time estimation; Hybridization; Introgression; Phylogenetic incongruence; Horizontal gene transfer; Gene-tree-species-tree discordance
• ISSN: 1055-7903; 1095-9513; 1095-9513
• DOI: 10.1016/j.ympev.2024.108197

[Display omitted] •An overview of a comprehensive phylogenomic workflow.•Discussion of methods for detecting reticulate evolution.•Reticulate evolution can elucidate the timing of events.•Identification of future research avenues throughout. 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.