Results 11 to 20 of about 12,359 (228)

Assessing the fit of the multi-species network coalescent to multi-locus data

Bioinformatics, 2020
Abstract Motivation With growing genome-wide molecular datasets from next-generation sequencing, phylogenetic networks can be estimated using a variety of approaches. These phylogenetic networks include events like hybridization, gene flow or horizontal gene transfer explicitly.
Ruoyi, Cai, Cécile, Ané
openaire   +2 more sources

Weighted ASTRID: fast and accurate species trees from weighted internode distances

Algorithms for Molecular Biology, 2023
Background Species tree estimation is a basic step in many biological research projects, but is complicated by the fact that gene trees can differ from the species tree due to processes such as incomplete lineage sorting (ILS), gene duplication and loss (
Baqiao Liu, Tandy Warnow
doaj   +1 more source

Transcriptome-based phylogenomic analysis reveals evidence of ancient hybridization events in the Mepraia genus (Hemiptera: Reduviidae: Triatominae)

Frontiers in Ecology and Evolution, 2023
IntroductionThe Mepraia genus is composed of three endemic species in Chile, namely Mepraia spinolai, Mepraia gajardoi, and Mepraia parapatrica, all capable of transmitting the causative agent of Chagas disease.
Tiago Belintani, Tiago Belintani, Carlos Congrains, Carlos Congrains, Heloisa Pinotti, Samira Chahad-Ehlers, Reinaldo A. de Brito, Jader Oliveira, Daniel Frias-Lasserre, Felipe Mendes Fontes, João Aristeu da Rosa   +10 more
doaj   +1 more source

STELAR: a statistically consistent coalescent-based species tree estimation method by maximizing triplet consistency

BMC Genomics, 2020
Background Species tree estimation is frequently based on phylogenomic approaches that use multiple genes from throughout the genome. However, estimating a species tree from a collection of gene trees can be complicated due to the presence of gene tree ...
Mazharul Islam, Kowshika Sarker, Trisha Das, Rezwana Reaz, Md. Shamsuzzoha Bayzid   +4 more
doaj   +1 more source

Phylogenetic Relationships Within the Hyper-Diverse Genus Eugenia (Myrtaceae: Myrteae) Based on Target Enrichment Sequencing

Frontiers in Plant Science, 2022
Eugenia is one of the most taxonomically challenging lineages of flowering plants, in which morphological delimitation has changed over the last few years resulting from recent phylogenetic study based on molecular data.
Augusto Giaretta, Augusto Giaretta, Bruce Murphy, Bruce Murphy, Olivier Maurin, Fiorella F. Mazine, Paulo Sano, Eve Lucas   +7 more
doaj   +1 more source

Inferring Species Trees Directly from Biallelic Genetic Markers: Bypassing Gene Trees in a Full Coalescent Analysis [PDF]

, 2011
The multi-species coalescent provides an elegant theoretical framework for estimating species trees and species demographics from genetic markers. Practical applications of the multi-species coalescent model are, however, limited by the need to integrate
Brumfield, Robb T., Derryberry, Elizabeth P., Graves, Gary R., Hird, Sarah M., Maley, James M., McCormack, John E.   +5 more
core   +3 more sources

Trial by phylogenetics - Evaluating the Multi-Species Coalescent for phylogenetic inference on taxa with high levels of paralogy (Gonyaulacales, Dinophyceae) [PDF]

, 2019
ABSTRACTFrom publicly available next-gen sequencing datasets of non-model organisms, such as marine protists, arise opportunities to explore their evolutionary relationships. In this study we explored the effects that dataset and model selection have on the phylogenetic inference of the Gonyaulacales, single celled marine algae of the phylum ...
Kretzschmar, Anna Liza, Verma, Arjun, Murray, Shauna, Kahlke, Tim, Fourment, Mathieu, Darling, Aaron E.   +5 more
openaire   +1 more source

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, Hunt, Tyler, Warnow, Tandy   +2 more
core   +1 more source

Supplemental Analysis, Derivations, and Results from Covariance of pairwise differences on a multi-species coalescent tree and implications for F_ST

, 2022
Further simulation comparisons, more in-depth discussion of topics presented, and more thorough derivations of theoretical ...
Guerra, Geno, Nielsen, Rasmus
openaire   +1 more source

Anchoring quartet-based phylogenetic distances and applications to species tree reconstruction

BMC Genomics, 2016
Background Inferring species trees from gene trees using the coalescent-based summary methods has been the subject of much attention, yet new scalable and accurate methods are needed.
Erfan Sayyari, Siavash Mirarab
doaj   +1 more source