From cacti to carnivores: Improved phylotranscriptomic sampling and hierarchical homology inference provide further insight into the evolution of Caryophyllales.
Sign Up to like & getrecommendations! Published in 2018 at "American journal of botany"
DOI: 10.1002/ajb2.1069
Abstract: PREMISE OF THE STUDY The Caryophyllales contain ~12,500 species and are known for their cosmopolitan distribution, convergence of trait evolution, and extreme adaptations. Some relationships within the Caryophyllales, like those of many large plant clades,… read more here.
Keywords: tree inference; evolution; gene tree; species tree ... See more keywords
Identifiability and Reconstructibility of Species Phylogenies Under a Modified Coalescent
Sign Up to like & getrecommendations! Published in 2019 at "Bulletin of Mathematical Biology"
DOI: 10.1007/s11538-018-0456-9
Abstract: Coalescent models of evolution account for incomplete lineage sorting by specifying a species tree parameter which determines a distribution on gene trees, and consequently, a site pattern probability distribution. It has been shown that the… read more here.
Keywords: identifiability reconstructibility; reconstructibility species; topology; species tree ... See more keywords
Expected pairwise congruence among gene trees under the coalescent model.
Sign Up to like & getrecommendations! Published in 2017 at "Molecular phylogenetics and evolution"
DOI: 10.1016/j.ympev.2016.09.023
Abstract: Although it is widely appreciated that gene trees may differ from the overall species tree and from one another due to various evolutionary processes (e.g., incomplete lineage sorting (ILS), horizontal gene transfer, etc.), the extent… read more here.
Keywords: species tree; coalescent model; expected pairwise; gene ... See more keywords
Complex biogeographic scenarios revealed in the diversification of the largest woodpecker radiation in the New World.
Sign Up to like & getrecommendations! Published in 2017 at "Molecular phylogenetics and evolution"
DOI: 10.1016/j.ympev.2017.04.013
Abstract: Phylogenetic relationships and patterns of evolution within Melanerpes, one of the most diverse groups of New World woodpeckers (22-23 lineages), have been complicated due to complex plumages and morphological adaptations. In an attempt to resolve… read more here.
Keywords: new world; species tree; diversification largest; world ... 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
Completing gene trees without species trees in sub-quadratic time
Sign Up to like & getrecommendations! Published in 2022 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btab875
Abstract: MOTIVATION As genome-wide reconstruction of phylogenetic trees becomes more widespread, limitations of available data are being appreciated more than ever before. One issue is that phylogenomic datasets are riddled with missing data, and gene trees,… read more here.
Keywords: complete gene; time; gene trees; trees without ... See more keywords
STELLS2: fast and accurate coalescent‐based maximum likelihood inference of species trees from gene tree topologies
Sign Up to like & getrecommendations! Published in 2017 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btx079
Abstract: Motivation: It is well known that gene trees and species trees may have different topologies. One explanation is incomplete lineage sorting, which is commonly modeled by the coalescent process. In multispecies coalescent, a gene tree… read more here.
Keywords: probability; maximum likelihood; gene tree; 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
Filtration of Gene Trees From 9,000 Exons, Introns, and UCEs Disentangles Conflicting Phylogenomic Relationships in Tree Frogs (Hylidae)
Sign Up to like & getrecommendations! Published in 2023 at "Genome Biology and Evolution"
DOI: 10.1093/gbe/evad070
Abstract: Abstract An emerging challenge in interpreting phylogenomic data sets is that concatenation and multi-species coalescent summary species tree approaches may produce conflicting results. Concatenation is problematic because it can strongly support an incorrect topology when… read more here.
Keywords: topology; 000 exons; gene trees; tree frogs ... See more keywords
STRIDE: Species Tree Root Inference from Gene Duplication Events
Sign Up to like & getrecommendations! Published in 2017 at "Molecular Biology and Evolution"
DOI: 10.1093/molbev/msx259
Abstract: Abstract The correct interpretation of any phylogenetic tree is dependent on that tree being correctly rooted. We present STRIDE, a fast, effective, and outgroup-free method for identification of gene duplication events and species tree root… read more here.
Keywords: tree root; duplication events; gene duplication; species tree ... See more keywords
Species Tree Inference with BPP Using Genomic Sequences and the Multispecies Coalescent
Sign Up to like & getrecommendations! Published in 2018 at "Molecular Biology and Evolution"
DOI: 10.1093/molbev/msy147
Abstract: Abstract The multispecies coalescent provides a natural framework for accommodating ancestral genetic polymorphism and coalescent processes that can cause different genomic regions to have different genealogical histories. The Bayesian program BPP includes a full-likelihood implementation… read more here.
Keywords: tree inference; inference bpp; bpp using; species tree ... See more keywords