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
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
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
Resolution and reconciliation of non‐binary gene trees with transfers, duplications and losses
Sign Up to like & getrecommendations! Published in 2017 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btw778
Abstract: Summary: Gene trees reconstructed from sequence alignments contain poorly supported branches when the phylogenetic signal in the sequences is insufficient to determine them all. When a species tree is available, the signal of gains and… read more here.
Keywords: mbb; resolution reconciliation; gene; non binary ... 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
Special Care Is Needed in Applying Phylogenetic Comparative Methods to Gene Trees with Speciation and Duplication Nodes
Sign Up to like & getrecommendations! Published in 2020 at "Molecular Biology and Evolution"
DOI: 10.1093/molbev/msaa288
Abstract: Abstract How gene function evolves is a central question of evolutionary biology. It can be investigated by comparing functional genomics results between species and between genes. Most comparative studies of functional genomics have used pairwise… read more here.
Keywords: duplication nodes; phylogenetic comparative; comparative methods; biology ... See more keywords
Orthology clusters from gene trees with Possvm.
Sign Up to like & getrecommendations! Published in 2021 at "Molecular biology and evolution"
DOI: 10.1093/molbev/msab234
Abstract: Possvm (Phylogenetic Ortholog Sorting with Species oVerlap and MCL) is a tool that automates the process of identifying clusters of orthologous genes from precomputed phylogenetic trees and classifying gene families. It identifies orthology relationships between… read more here.
Keywords: clusters gene; trees possvm; orthology clusters; gene ... See more keywords
Ancient Rapid Radiation Explains Most Conflicts Among Gene Trees and Well-supported Phylogenomic Trees of Nostocalean Cyanobacteria.
Sign Up to like & getrecommendations! Published in 2023 at "Systematic biology"
DOI: 10.1093/sysbio/syad008
Abstract: Prokaryotic genomes are often considered to be mosaics of genes that do not necessarily share the same evolutionary history due to widespread Horizontal Gene Transfers (HGTs). Consequently, representing evolutionary relationships of prokaryotes as bifurcating trees… read more here.
Keywords: among gene; gene trees; well supported; radiation ... See more keywords
On the independent gene trees assumption in phylogenomic studies
Sign Up to like & getrecommendations! Published in 2017 at "Molecular Ecology"
DOI: 10.1111/mec.14274
Abstract: Multilocus coalescent methods for inferring species trees or historical demographic parameters typically require the assumption that gene trees for sampled SNPs or DNA sequence loci are conditionally independent given their species tree. In practice, researchers… read more here.
Keywords: independent gene; criterion; phylogenomic studies; ecology ... 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
Phylogenetic Signal of Indels and the Neoavian Radiation
Sign Up to like & getrecommendations! Published in 2019 at "Diversity"
DOI: 10.3390/d11070108
Abstract: The early radiation of Neoaves has been hypothesized to be an intractable “hard polytomy”. We explore the fundamental properties of insertion/deletion alleles (indels), an under-utilized form of genomic data with the potential to help solve… read more here.
Keywords: signal indels; astral trees; gene trees; radiation ... See more keywords