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
Gene tree and species tree reconciliation with endosymbiotic gene transfer
Sign Up to like & getrecommendations! Published in 2021 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btab328
Abstract: Abstract Motivation It is largely established that all extant mitochondria originated from a unique endosymbiotic event integrating an α−proteobacterial genome into an eukaryotic cell. Subsequently, eukaryote evolution has been marked by episodes of gene transfer,… read more here.
Keywords: gene tree; endosymbiotic gene; transfer; gene transfer ... 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
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
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
Phylogenomic analysis of the parrots of the world distinguishes artifactual from biological sources of gene tree discordance.
Sign Up to like & getrecommendations! Published in 2022 at "Systematic biology"
DOI: 10.1093/sysbio/syac055
Abstract: Gene tree discordance is expected in phylogenomic trees and biological processes are often invoked to explain it. However, heterogeneous levels of phylogenetic signal among individuals within datasets may cause artifactual sources of topological discordance. We… read more here.
Keywords: topology; gene tree; tree discordance; sources gene ... 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
Unconstrained Diameters for Deep Coalescence
Sign Up to like & getrecommendations! Published in 2017 at "IEEE/ACM Transactions on Computational Biology and Bioinformatics"
DOI: 10.1109/tcbb.2016.2520937
Abstract: The minimizing-deep-coalescence (MDC) approach infers a median (species) tree for a given set of gene trees under the deep coalescence cost. This cost accounts for the minimum number of deep coalescences needed to reconcile a… read more here.
Keywords: gene tree; coalescence; deep coalescence; species tree ... See more keywords
Utilizing paralogues for phylogenetic reconstruction has the potential to increase species tree support and reduce gene tree discordance in target enrichment data
Sign Up to like & getrecommendations! Published in 2022 at "Molecular Ecology Resources"
DOI: 10.1111/1755-0998.13684
Abstract: The analysis of target enrichment data in phylogenetics lacks optimization toward using paralogues for phylogenetic reconstruction. We developed a novel approach of detecting paralogues and utilizing them for phylogenetic tree inference, by retrieving both ortho‐… read more here.
Keywords: gene tree; paralogues phylogenetic; enrichment data; gene ... See more keywords
Detecting hybridization by likelihood calculation of gene tree extra lineages given explicit models
Sign Up to like & getrecommendations! Published in 2018 at "Methods in Ecology and Evolution"
DOI: 10.1111/2041-210x.12846
Abstract: Explanations for gene tree discordance with respect to a species tree are commonly attributed to deep coalescence (also known as incomplete lineage sorting [ILS]), as well as different evolutionary processes such as hybridization, horizontal gene… read more here.
Keywords: hybridization; extra lineages; gene tree; gene ... See more keywords
Assessing the accuracy of phylogenetic rooting methods on prokaryotic gene families
Sign Up to like & getrecommendations! Published in 2020 at "PLoS ONE"
DOI: 10.1371/journal.pone.0232950
Abstract: Almost all standard phylogenetic methods for reconstructing gene trees result in unrooted trees; yet, many of the most useful applications of gene trees require that the gene trees be correctly rooted. As a result, several… read more here.
Keywords: gene families; gene tree; prokaryotic gene; gene ... See more keywords