Species trees from consensus single nucleotide polymorphism (SNP) data: Testing phylogenetic approaches with simulated and empirical data.
Sign Up to like & getrecommendations! Published in 2017 at "Molecular phylogenetics and evolution"
DOI: 10.1016/j.ympev.2017.07.018
Abstract: Datasets of hundreds or thousands of SNPs (Single Nucleotide Polymorphisms) from multiple individuals per species are increasingly used to study population structure, species delimitation and shallow phylogenetics. The principal software tool to infer species or… read more here.
Keywords: snp data; analysis; simulated empirical; topology ... See more keywords
SVDquest: Improving SVDquartets species tree estimation using exact optimization within a constrained search space.
Sign Up to like & getrecommendations! Published in 2018 at "Molecular phylogenetics and evolution"
DOI: 10.1016/j.ympev.2018.03.006
Abstract: Species tree estimation from multi-locus datasets is complicated by processes such as incomplete lineage sorting (ILS) that result in different loci having different trees. Summary methods, which estimate species trees by combining gene trees, are… read more here.
Keywords: estimation; quartet trees; tree estimation; species tree ... See more keywords
QuCo: quartet-based co-estimation of species trees and gene trees
Sign Up to like & getrecommendations! Published in 2022 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btac265
Abstract: Abstract Motivation Phylogenomics faces a dilemma: on the one hand, most accurate species and gene tree estimation methods are those that co-estimate them; on the other hand, these co-estimation methods do not scale to moderately… read more here.
Keywords: gene tree; species trees; gene trees; quartet ... See more keywords
Polymorphism-Aware Species Trees with Advanced Mutation Models, Bootstrap, and Rate Heterogeneity
Sign Up to like & getrecommendations! Published in 2019 at "Molecular Biology and Evolution"
DOI: 10.1093/molbev/msz043
Abstract: Abstract Molecular phylogenetics has neglected polymorphisms within present and ancestral populations for a long time. Recently, multispecies coalescent based methods have increased in popularity, however, their application is limited to a small number of species… read more here.
Keywords: aware species; rate; species trees; mutation ... See more keywords
Bayesian Inference of Species Trees using Diffusion Models.
Sign Up to like & getrecommendations! Published in 2020 at "Systematic biology"
DOI: 10.1093/sysbio/syaa051
Abstract: We describe a new and computationally efficient Bayesian methodology for inferring species trees and demographics from unlinked binary markers. Likelihood calculations are carried out using diffusion models of allele frequency dynamics combined with novel numerical… read more here.
Keywords: bayesian inference; diffusion; diffusion models; species trees ... See more keywords
Theoretical and practical considerations when using retroelement insertions to estimate species trees in the anomaly zone.
Sign Up to like & getrecommendations! Published in 2021 at "Systematic biology"
DOI: 10.1093/sysbio/syab086
Abstract: A potential shortcoming of concatenation methods for species tree estimation is their failure to account for incomplete lineage sorting. Coalescent methods address this problem but make various assumptions that, if violated, can result in worse… read more here.
Keywords: anomaly zone; tree topology; ris; topology ... See more keywords
Weighting by Gene Tree Uncertainty Improves Accuracy of Quartet-based Species Trees
Sign Up to like & getrecommendations! Published in 2022 at "Molecular Biology and Evolution"
DOI: 10.1101/2022.02.19.481132
Abstract: Phylogenomic analyses routinely estimate species trees using methods that account for gene tree discordance. However, the most scalable species tree inference methods, which summarize independently inferred gene trees to obtain a species tree, are sensitive… read more here.
Keywords: gene tree; species trees; summary methods; quartet based ... See more keywords