Results 1 to 10 of about 12,359 (228)

Quintet Rooting: rooting species trees under the multi-species coalescent model. [PDF]

Bioinformatics, 2022
AbstractMotivationRooted species trees are a basic model with multiple applications throughout biology, including understanding adaptation, biodiversity, phylogeography and co-evolution. Because most species tree estimation methods produce unrooted trees, methods for rooting these trees have been developed.
Tabatabaee Y, Sarker K, Warnow T.
europepmc   +3 more sources

Covariance of pairwise differences on a multi-species coalescent tree and implications for F_ST. [PDF]

Philos Trans R Soc Lond B Biol Sci, 2022
The multi-species coalescent (MSC) provides a theoretical foundation for modern phylogenetics and comparative population genetics. Its theoretical properties have been heavily studied but there are still aspects of the MSC that are largely unknown, including the covariances in pairwise coalescence times, which are fundamental for understanding the ...
Guerra G, Nielsen R.
europepmc   +6 more sources

Coalescent-based genome analyses resolve the early branches of the euarchontoglires [PDF]

, 2013
Despite numerous large-scale phylogenomic studies, certain parts of the mammalian tree are extraordinarily difficult to resolve. We used the coding regions from 19 completely sequenced genomes to study the relationships within the super-clade ...
A Criscuolo, Axel Janke, B Rannala, Björn M. Hallström, BM Hallström, BM Hallström, BM Hallström, BM Hallström, C Lanave, CA Russo, D Curnoe, DE Pumo, DE Wildman, DH Huson, G Churakov, G Jobb, H Shimodaira, H Shimodaira, Hans Ellegren, J Schmitz, JA van Dam, JC Avise, JE Janecka, JE McCormack, JFC Kingman, JH Degnan, JJ Fong, JO Kriegs, JP Townsend, K Katoh, KM Kjer, L Liu, L Liu, L Liu, LS Kubatko, M Dos Reis, MJ Novacek, MP Simmons, NM Jameson, PJ Waddell, RJ Asher, S Guindon, S Kumar, S Song, S Whelan, SV Edwards, TH Ogden, TK Seo, U Arnason, U Arnason, Vikas Kumar, WJ Murphy, WP Maddison   +52 more
core   +15 more sources

Estimating Waiting Distances Between Genealogy Changes under a Multi-Species Extension of the Sequentially Markov Coalescent

Systematic Biology, 2022
AbstractGenomes are composed of a mosaic of segments inherited from different ancestors, each separated by past recombination events. Consequently, genealogical relationships among multiple genomes vary spatially across different genomic regions. Expectations for the amount of genealogical variation among unlinked (uncorrelated) genomic regions is well
Patrick F. McKenzie, Deren A. R. Eaton
openaire   +1 more source

Weighted Statistical Binning: Enabling Statistically Consistent Genome-Scale Phylogenetic Analyses. [PDF]

PLoS ONE, 2015
Because biological processes can result in different loci having different evolutionary histories, species tree estimation requires multiple loci from across multiple genomes.
Md Shamsuzzoha Bayzid, Siavash Mirarab, Bastien Boussau, Tandy Warnow   +3 more
doaj   +1 more source

Spatial coalescent connectivity through multi-generation dispersal modelling predicts gene flow across marine phyla

Nature Communications, 2022
This study uses a compilation of 58 population genetic studies of 47 phylogenetically divergent marine sedentary species over the Mediterranean basin to assess how genetic differentiation is predicted by different dispersal models.
Térence Legrand, Anne Chenuil, Enrico Ser-Giacomi, Sophie Arnaud-Haond, Nicolas Bierne, Vincent Rossi   +5 more
doaj   +1 more source

A taxonomic revision of the ecologically important Ochna holstii (Ochnaceae) complex using molecular and morphological data [PDF]

Plant Ecology and Evolution, 2023
Background and aims – Ochna holstii and its allies represent an ecologically important group in a variety of lowland to montane habitats in tropical eastern and southern Africa.
Toral Shah, Fandey H. Mashimba, Haji. O. Suleiman, Yahya S. Mbailwa, Vincent Savolainen, Isabel Larridon, Iain Darbyshire   +6 more
doaj   +3 more sources

Using phylogenetic and coalescent methods to understand the species diversity in the Cladia aggregata complex (Ascomycota, Lecanorales). [PDF]

PLoS ONE, 2012
The Cladia aggregata complex is one of the phenotypically most variable groups in lichenized fungi, making species determination difficult and resulting in different classifications accepting between one to eight species.
Sittiporn Parnmen, Achariya Rangsiruji, Pachara Mongkolsuk, Kansri Boonpragob, Aparna Nutakki, H Thorsten Lumbsch   +5 more
doaj   +1 more source

Efficient Bayesian Species Tree Inference under the Multispecies Coalescent [PDF]

Systematic Biology, 2017
Abstract We develop a Bayesian method for inferring the species phylogeny under the multispecies coalescent (MSC) model. To improve the mixing properties of the Markov chain Monte Carlo (MCMC) algorithm that traverses the space of species trees, we implement two efficient MCMC proposals: the first is based on the Subtree Pruning and ...
Rannala, Bruce, Yang, Ziheng
openaire   +6 more sources

Phylogeny and species delimitations in the entomopathogenic genus Beauveria (Hypocreales, Ascomycota), including the description of B. peruviensis sp. nov. [PDF]

MycoKeys, 2019
The genus Beauveria is considered a cosmopolitan anamorphic and teleomorphic genus of soilborne necrotrophic arthropod-pathogenic fungi that includes ecologically and economically important species.
Danilo E. Bustamante, Manuel Oliva, Santos Leiva, Jani E. Mendoza, Leidy Bobadilla, Geysen Angulo, Martha S. Calderon   +6 more
doaj   +3 more sources