Plastome phylogenomic study of Gentianeae (Gentianaceae): widespread gene tree discordance and its association with evolutionary rate heterogeneity of plastid genes [PDF]
BMC Plant Biology, 2020 Background Plastome-scale data have been prevalent in reconstructing the plant Tree of Life. However, phylogenomic studies currently based on plastomes rely primarily on maximum likelihood inference of concatenated alignments of plastid genes, and thus ...
Xu Zhang +11 more
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Discordance of species trees with their most likely gene trees. [PDF]
PLoS Genetics, 2006 Because of the stochastic way in which lineages sort during speciation, gene trees may differ in topology from each other and from species trees. Surprisingly, assuming that genetic lineages follow a coalescent model of within-species evolution, we find ...
James H Degnan, Noah A Rosenberg
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Concatenation fails to describe the anomalous radiation of giant cockroaches (Blattodea: Blaberidae) despite moderate to low discordance [PDF]
BMC Ecology and EvolutionBackground Patterns of discordance between gene trees and the species trees they reside in are crucial to the coalescent vs. concatenation debate and may be key to resolving rapid radiations.
Dominic A. Evangelista +3 more
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Teasing apart the sources of phylogenetic tree discordance across three genomes in the oak family (Fagaceae) [PDF]
BMC Plant BiologyBackground Gene tree incongruence is a well-documented, but the biological and analytical factors driving phylogenetic discordance remains incompletely understood. In this study, we investigated how different factors contribute to incongruence among gene
Zhao Shen +12 more
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Phylogenomics of East Asian lineage within subgenus Anguinum (Allium, Amaryllidaceae): insights into its taxonomic puzzles and phylogenetic conflicts [PDF]
BMC Plant BiologyPhylogenomic data enriched with informative loci have significantly improved phylogenetic resolution and facilitated the elucidation of evolutionary mechanisms underlying phylogenetic discordance. Species of the East Asian lineage (EAL) within the Allium
Rui-Yu Cheng +7 more
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Frontiers in Plant Science, 2022 A major challenge in phylogenetics and -genomics is to resolve young rapidly radiating groups. The fast succession of species increases the probability of incomplete lineage sorting (ILS), and different topologies of the gene trees are expected, leading ...
Martha Kandziora +5 more
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Conflicting phylogenetic signals in plastomes of the tribe Laureae (Lauraceae) [PDF]
PeerJ, 2020 Background Gene tree discordance is common in phylogenetic analyses. Many phylogenetic studies have excluded non-coding regions of the plastome without evaluating their impact on tree topology. In general, plastid loci have often been treated as a single
Tian-Wen Xiao +5 more
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Minimum variance rooting of phylogenetic trees and implications for species tree reconstruction. [PDF]
PLoS ONE, 2017 Phylogenetic trees inferred using commonly-used models of sequence evolution are unrooted, but the root position matters both for interpretation and downstream applications.
Uyen Mai, Erfan Sayyari, Siavash Mirarab
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Frontiers in Plant Science, 2021 Next-generation sequencing technologies have facilitated new phylogenomic approaches to help clarify previously intractable relationships while simultaneously highlighting the pervasive nature of incongruence within and among genomes that can complicate ...
Jeffrey P. Rose +10 more
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Fine-scale phylogenetic discordance across the house mouse genome. [PDF]
PLoS Genetics, 2009 Population genetic theory predicts discordance in the true phylogeny of different genomic regions when studying recently diverged species. Despite this expectation, genome-wide discordance in young species groups has rarely been statistically quantified.
Michael A White +4 more
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