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
Nucleotide Usage Biases Distort Inferences of the Species Tree
Sign Up to like & getrecommendations! Published in 2022 at "Genome Biology and Evolution"
DOI: 10.1093/gbe/evab290
Abstract: Despite the importance of natural selection in species’ evolutionary history, phylogenetic methods that take into account population-level processes typically ignore selection. The assumption of neutrality is often based on the idea that selection occurs at… read more here.
Keywords: usage biases; tree estimation; selection species; selection ... See more keywords
The Impact of Cross-Species Gene Flow on Species Tree Estimation.
Sign Up to like & getrecommendations! Published in 2020 at "Systematic biology"
DOI: 10.1093/sysbio/syaa001
Abstract: Recent analyses of genomic sequence data suggest cross-species gene flow is common in both plants and animals, posing challenges to species tree estimation. We examine the levels of gene flow needed to mislead species tree… read more here.
Keywords: cross species; tree estimation; species tree; gene ... See more keywords
The Perfect Storm: Gene Tree Estimation Error, Incomplete Lineage Sorting, and Ancient Gene Flow Explain the Most Recalcitrant Ancient Angiosperm Clade, Malpighiales.
Sign Up to like & getrecommendations! Published in 2020 at "Systematic biology"
DOI: 10.1093/sysbio/syaa083
Abstract: The genomic revolution offers renewed hope of resolving rapid radiations in the Tree of Life. The development of the multispecies coalescent (MSC) model and improved gene tree estimation methods can better accommodate gene tree heterogeneity… read more here.
Keywords: gene; estimation error; tree estimation; gene tree ... See more keywords
Assessing the Impacts of Positive Selection on Coalescent‐Based Species Tree Estimation and Species Delimitation
Sign Up to like & getrecommendations! Published in 2018 at "Systematic Biology"
DOI: 10.1093/sysbio/syy034
Abstract: Abstract. The assumption of strictly neutral evolution is fundamental to the multispecies coalescent model and permits the derivation of gene tree distributions and coalescent times conditioned on a given species tree. In this study, we… read more here.
Keywords: positive selection; tree estimation; selection; species delimitation ... See more keywords
Disjoint Tree Mergers for Large-Scale Maximum Likelihood Tree Estimation
Sign Up to like & getrecommendations! Published in 2021 at "Algorithms"
DOI: 10.3390/a14050148
Abstract: The estimation of phylogenetic trees for individual genes or multi-locus datasets is a basic part of considerable biological research In order to enable large trees to be computed, Disjoint Tree Mergers (DTMs) have been developed;these… read more here.
Keywords: estimation; tree mergers; tree estimation; maximum likelihood ... See more keywords