Reticulate Evolution: Detection and Utility in the Phylogenomics Era

Published: May 14, 2024

Phylogenomics has enriched our understanding that the Tree of Life can have network-like or reticulate structures among some taxa and genes. Non-vertical modes evolution—such as hybridization/introgression horizontal gene transfer—deviate from a strictly bifurcating tree model, causing non-treelike patterns. Here, we present brief overview phylogenomic workflow for inferring organismal histories compare methods detecting evolution. We discuss how timing coalescent events help disentangle introgression incomplete lineage sorting transfer determine relative speciation events. In doing so, identify pitfalls certain to extend their utility across Life. Workflows, methods, future directions discussed herein underscore need embrace evolutionary patterns rates events, providing clearer life’s history.

Language: Английский

Chronospaces: An R package for the statistical exploration of divergence times promotes the assessment of methodological sensitivity

Methods in Ecology and Evolution, Journal Year: 2024, Volume and Issue: 15(10), P. 1822 - 1833

Published: Aug. 20, 2024

Abstract Much of our understanding the history life hinges upon time calibration, process assigning absolute times to cladogenetic events. Bayesian approaches time‐scaling phylogenetic trees have dramatically grown in complexity, and depend today numerous methodological choices. Arriving at objective justifications for all these is difficult time‐consuming. Thus, divergence are routinely inferred under only one or a handful parametric conditions, often chosen arbitrarily. Progress towards building robust biological timescales necessitates development better methods visualize quantify sensitivity results decisions. Here, we present an R package that assists this endeavour through use chronospaces, is, graphical representations summarizing variation node ages contained time‐calibrated trees. We further test approach by estimating three empirical datasets—spanning widely differing evolutionary timeframes—using software PhyloBayes. Our reveal large differences impact many common decisions, with choice clock (uncorrelated vs autocorrelated) loci having strong effects on ages. Other decisions comparatively minor consequences, including computationally intensive site‐heterogeneous model CAT‐GTR, whose effect might be discernible exceedingly old divergences (e.g. deepest eukaryote nodes). The chronospace implements range analytical tools assist exploration prioritization computational resources inference times.

Language: Английский

Genomic Innovation and Virulence Evolution in the Emerging Human Fungal Pathogen Candida auris

Published: Jan. 1, 2024

Language: Английский