Results 21 to 30 of about 17,767 (219)
Gene Tree Discord, Simplex Plots, and Statistical Tests under the Coalescent [PDF]
Systematic Biology, 2020 Abstract A simple graphical device, the simplex plot of quartet concordance factors, is introduced to aid in the exploration of a collection of gene trees on a common set of taxa. A single plot summarizes all gene tree discord and allows for visual comparison to the expected discord from the multispecies coalescent model (MSC) of ...
Allman, Elizabeth S. +2 more
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Speciation genes are more likely to have discordant gene trees [PDF]
Evolution Letters, 2018 AbstractSpeciation genes are responsible for reproductive isolation between species. By directly participating in the process of speciation, the genealogies of isolating loci have been thought to more faithfully represent species trees. The unique properties of speciation genes may provide valuable evolutionary insights and help determine the true ...
Wang, Richard J., Hahn, Matthew W.
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Gene Tree Discordance Can Generate Patterns of Diminishing Convergence over Time [PDF]
Molecular Biology and Evolution, 2016 Phenotypic convergence is an exciting outcome of adaptive evolution, occurring when different species find similar solutions to the same problem. Unraveling the molecular basis of convergence provides a way to link genotype to adaptive phenotypes, but can also shed light on the extent to which molecular evolution is repeatable and predictable.
Fábio K, Mendes +2 more
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The impact of gene-tree/species-tree discordance on diversification-rate estimation. [PDF]
Evolution; international journal of organic evolution, 2011 Molecular phylogenies are often used to test hypotheses about the tempo and mode of speciation and extinction. One commonly used statistic is Pybus and Harvey's γ, which measures the density of ordered internode distances on an ultrametric tree to infer earlier (negative γ) or later (positive γ) bursts of diversification.
Frank T, Burbrink, R Alexander, Pyron
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Frontiers in Plant Science, 2022 The economically important cotton and cacao family (Malvaceae sensu lato) have long been recognized as a monophyletic group. However, the relationships among some subfamilies are still unclear as discordant phylogenetic hypotheses keep arising when ...
Rebeca Hernández-Gutiérrez +8 more
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Gene Tree Discordance Does Not Explain Away the Temporal Decline of Convergence in Mammalian Protein Sequence Evolution. [PDF]
Mol Biol Evol, 2017 Several authors reported lower frequencies of protein sequence convergence between more distantly related evolutionary lineages and attributed this trend to epistasis, which renders the acceptable amino acids at a site more different and convergence less likely in more divergent lineages. A recent primate study, however, suggested that this trend is at
Zou Z, Zhang J.
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The dynamics of introgression across an avian radiation
Evolution Letters, 2021 Hybridization and resulting introgression can play both a destructive and a creative role in the evolution of diversity. Thus, characterizing when and where introgression is most likely to occur can help us understand the causes of diversification ...
Sonal Singhal +5 more
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Frontiers in Plant Science, 2022 We assess relationships among 192 species in all 12 monocot orders and 72 of 77 families, using 602 conserved single-copy (CSC) genes and 1375 benchmarking single-copy ortholog (BUSCO) genes extracted from genomic and transcriptomic datasets ...
Prakash Raj Timilsena +23 more
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Disk Covering Methods Improve Phylogenomic Analyses [PDF]
, 2014 Motivation: With the rapid growth rate of newly sequenced genomes, species tree inference from multiple genes has become a basic bioinformatics task in comparative and evolutionary biology.
Bayzid, Md Shamsuzzoha +2 more
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treeducken: An R package for simulating cophylogenetic systems
Methods in Ecology and Evolution, 2021 Cophylogenetic methods describe discordance between non‐independent phylogenies. Simulation is necessary for testing cophylogenetic methods, but few simulators exist that are capable of generating data under explicit and biologically meaningful models ...
Wade Dismukes, Tracy A. Heath
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