Results 11 to 20 of about 17,767 (219)

Phylogenetic Discordance between Species Tree and Functional Gene Trees of Fagaceous Genera

Environmental Sciences Proceedings, 2022
Fagaceae species predominate a diverse range of habitats in the northern hemisphere and are critical to the ecosystem and economy. The high morphological and genetic diversity of these species serves as the foundation for adaptation to environmental ...
Min-Xin Luo, Chien-Ti Chao, Jui-Tse Chang, Pei-Chun Liao   +3 more
doaj   +2 more sources

Widespread discordance of gene trees with species tree in Drosophila: evidence for incomplete lineage sorting.

PLoS Genetics, 2006
The phylogenetic relationship of the now fully sequenced species Drosophila erecta and D. yakuba with respect to the D. melanogaster species complex has been a subject of controversy.
Daniel A Pollard, Venky N Iyer, Alan M Moses, Michael B Eisen   +3 more
doaj   +5 more sources

Phylogenomics Reveals Ancient Gene Tree Discordance in the Amphibian Tree of Life. [PDF]

Syst Biol, 2021
AbstractMolecular phylogenies have yielded strong support for many parts of the amphibian Tree of Life, but poor support for the resolution of deeper nodes, including relationships among families and orders. To clarify these relationships, we provide a phylogenomic perspective on amphibian relationships by developing a taxon-specific Anchored Hybrid ...
Hime PM, Lemmon AR, Lemmon ECM, Prendini E, Brown JM, Thomson RC, Kratovil JD, Noonan BP, Pyron RA, Peloso PLV, Kortyna ML, Keogh JS, Donnellan SC, Mueller RL, Raxworthy CJ, Kunte K, Ron SR, Das S, Gaitonde N, Green DM, Labisko J, Che J, Weisrock DW.   +22 more
europepmc   +5 more sources

Phylogenomic comparative methods: Accurate evolutionary inferences in the presence of gene tree discordance. [PDF]

Proc Natl Acad Sci U S A, 2023
Phylogenetic comparative methods have long been a mainstay of evolutionary biology, allowing for the study of trait evolution across species while accounting for their common ancestry. These analyses typically assume a single, bifurcating phylogenetic tree describing the shared history among species.
Hibbins MS, Breithaupt LC, Hahn MW.
europepmc   +3 more sources

Phylogenomic analyses in Phrymaceae reveal extensive gene tree discordance in relationships among major clades. [PDF]

Am J Bot, 2022
Abstract Premise Phylogenomic datasets using genomes and transcriptomes provide rich opportunities beyond resolving bifurcating phylogenetic relationships. Monkeyflower (Phrymaceae) is a model system for evolutionary ecology.
Morales-Briones DF, Lin N, Huang EY, Grossenbacher DL, Sobel JM, Gilmore CD, Tank DC, Yang Y.   +7 more
europepmc   +3 more sources

Disentangling Sources of Gene Tree Discordance in Phylogenomic Data Sets: Testing Ancient Hybridizations in Amaranthaceae s.l. [PDF]

Syst Biol, 2021
Abstract Gene tree discordance in large genomic data sets can be caused by evolutionary processes such as incomplete lineage sorting and hybridization, as well as model violation, and errors in data processing, orthology inference, and gene tree estimation. Species tree methods that identify and accommodate all sources of conflict are
Morales-Briones DF, Kadereit G, Tefarikis DT, Moore MJ, Smith SA, Brockington SF, Timoneda A, Yim WC, Cushman JC, Yang Y.   +9 more
europepmc   +4 more sources

Extensive gene tree discordance and hemiplasy shaped the genomes of North American columnar cacti. [PDF]

Proc Natl Acad Sci U S A, 2017
Significance Convergent and parallel evolution (homoplasy) is widespread in the tree of life and can obscure evidence about phylogenetic relationships. Homoplasy can be elevated in genomes because individual loci may have independent evolutionary histories different from the species history.
Copetti D, Búrquez A, Bustamante E, Charboneau JLM, Childs KL, Eguiarte LE, Lee S, Liu TL, McMahon MM, Whiteman NK, Wing RA, Wojciechowski MF, Sanderson MJ.   +12 more
europepmc   +6 more sources

Refining discordant gene trees [PDF]

BMC Bioinformatics, 2014
Evolutionary studies are complicated by discordance between gene trees and the species tree in which they evolved. Dealing with discordant trees often relies on comparison costs between gene and species trees, including the well-established Robinson-Foulds, gene duplication, and deep coalescence costs.
Górecki, Pawel, Eulenstein, Oliver
openaire   +2 more sources

DiscoVista: Interpretable visualizations of gene tree discordance [PDF]

Molecular Phylogenetics and Evolution, 2018
Phylogenomics has ushered in an age of discordance. Analyses often reveal abundant discordances among phylogenies of different parts of genomes, as well as incongruences between species trees obtained using different methods or data partitions. Researchers are often left trying to make sense of such incongruences.
Sayyari, Erfan, Whitfield, James B., Mirarab, Siavash   +2 more
openaire   +3 more sources

Gene Tree Discordance Causes Apparent Substitution Rate Variation [PDF]

Systematic Biology, 2015
AbstractSubstitution rates are known to be variable among genes, chromosomes, species, and lineages due to multifarious biological processes. Here we consider another source of substitution rate variation due to a technical bias associated with gene tree discordance, which has been found to be rampant in genome-wide datasets, often due to incomplete ...
Mendes, Fabio K., Hahn, Matthew W.
openaire   +2 more sources