Results 51 to 60 of about 17,767 (219)

Discordance of Species Trees with Their Most Likely Gene Trees: A Unifying Principle [PDF]

Molecular Biology and Evolution, 2013
A labeled gene tree topology that disagrees with a labeled species tree topology is said to be anomalous if it is more probable under a coalescent model for gene lineage evolution than the labeled gene tree topology that matches the species tree. It has previously been shown that as a consequence of short internal branches of the species tree, for ...
openaire   +2 more sources

Determining the probability of hemiplasy in the presence of incomplete lineage sorting and introgression

eLife, 2020
The incongruence of character states with phylogenetic relationships is often interpreted as evidence of convergent evolution. However, trait evolution along discordant gene trees can also generate these incongruences – a phenomenon known as hemiplasy ...
Mark S Hibbins, Matthew JS Gibson, Matthew W Hahn   +2 more
doaj   +1 more source

Testing for polytomies in phylogenetic species trees using quartet frequencies

, 2018
Phylogenetic species trees typically represent the speciation history as a bifurcating tree. Speciation events that simultaneously create more than two descendants, thereby creating polytomies in the phylogeny, are possible.
Mirarab, Siavash, Sayyari, Erfan
core   +2 more sources

Plasmodium vivax-like genome sequences shed new insights into Plasmodium vivax biology and evolution [PDF]

, 2018
Although Plasmodium vivax is responsible for the majority of malaria infections outside Africa, little is known about its evolution and pathway to humans. Its closest genetic relative, P.
Arnathau, Céline, Boundenga, Larson, Durand, Patrick, Franzon, Blaise, Gilabert, Aude, Makanga, Boris, Moukodoum, Nancy D., Ngoubangoye, Barthélémy, Okouga, Alain-Prince, Ollomo, Benjamin, Otto, Thomas D., Paupy, Christophe, Prugnolle, Franck, Renaud, François, Rougeron, Virginie, Rutledge, Gavin G.   +15 more
core   +5 more sources

Specimens at the Center: An Informatics Workflow and Toolkit for Specimen-level analysis of Public DNA database data [PDF]

, 2016
Major public DNA databases — NCBI GenBank, the DNA DataBank of Japan (DDBJ), and the European Molecular Biology Laboratory (EMBL) — are invaluable biodiversity libraries. Systematists and other biodiversity scientists commonly mine these databases for
Brown, Bethany H., Bruederle, Leo P., Escudero Lirio, Marcial, Global Carex Group, Hahn, Marlene, Jiménez Mejías, Pedro, Lueders, Kate, Maguilla Salado, Enrique, Pham, Kasey K.   +8 more
core   +1 more source

Phenotypic and Genetic Structure Support Gene Flow Generating Gene Tree Discordances in an Amazonian Floodplain Endemic Species [PDF]

Systematic Biology, 2018
Before populations become independent evolutionary lineages, the effects of micro evolutionary processes tend to generate complex scenarios of diversification that may affect phylogenetic reconstruction. Not accounting for gene flow in species tree estimates can directly impact topology, effective population sizes and branch lengths, and the resulting ...
Thom, Gregory, Amaral, Fábio Raposo do, Hickerson, Michael J., Aleixo, Alexandre, Araújo-Silva, Lucas Eduardo, Ribas, Camila Cherem, Choueri, Érik Lacerda, Miyaki, Cristina Yumi   +7 more
openaire   +3 more sources

A Phylogenomic Perspective on Evolution and Discordance in the Alpine-Arctic Plant Clade Micranthes (Saxifragaceae)

Frontiers in Plant Science, 2020
The increased availability of large phylogenomic datasets is often accompanied by difficulties in disentangling and harnessing the data. These difficulties may be enhanced for species resulting from reticulate evolution and/or rapid radiations producing ...
Rebecca L. Stubbs, Ryan A. Folk, Chun-Lei Xiang, Shichao Chen, Douglas E. Soltis, Douglas E. Soltis, Douglas E. Soltis, Douglas E. Soltis, Nico Cellinese, Nico Cellinese   +9 more
doaj   +1 more source

Restricted trees: simplifying networks with bottlenecks [PDF]

, 2010
Suppose N is a phylogenetic network indicating a complicated relationship among individuals and taxa. Often of interest is a much simpler network, for example, a species tree T, that summarizes the most fundamental relationships. The meaning of a species
Willson, Stephen J.
core   +4 more sources

Disentangling Methodological and Biological Sources of Gene Tree Discordance on Oryza (Poaceae) Chromosome 3 [PDF]

Systematic Biology, 2014
We describe new methods for characterizing gene tree discordance in phylogenomic data sets, which screen for deviations from neutral expectations, summarize variation in statistical support among gene trees, and allow comparison of the patterns of discordance induced by various analysis choices.
Zwickl, Derrick J., Stein, Joshua C., Wing, Rod A., Ware, Doreen, Sanderson, Michael J.   +4 more
openaire   +3 more sources

Evaluating evolutionary history in the face of high gene tree discordance in Australian Gehyra (Reptilia: Gekkonidae). [PDF]

Heredity (Edinb), 2014
Species tree methods have provided improvements for estimating species relationships and the timing of diversification in recent radiations by allowing for gene tree discordance. Although gene tree discordance is often observed, most discordance is attributed to incomplete lineage sorting rather than other biological phenomena, and the causes of ...
Sistrom M, Hutchinson M, Bertozzi T, Donnellan S.   +3 more
europepmc   +5 more sources