Incongruence in the phylogenomics era
Genome-scale data and the development of novel statistical phylogenetic approaches have
greatly aided the reconstruction of a broad sketch of the tree of life and resolved many of its …
greatly aided the reconstruction of a broad sketch of the tree of life and resolved many of its …
Phylogenomics and the flowering plant tree of life
The advances accelerated by next‐generation sequencing and long‐read sequencing
technologies continue to provide an impetus for plant phylogenetic study. In the past …
technologies continue to provide an impetus for plant phylogenetic study. In the past …
[HTML][HTML] Plastid phylogenomic insights into relationships of all flowering plant families
Background Flowering plants (angiosperms) are dominant components of global terrestrial
ecosystems, but phylogenetic relationships at the familial level and above remain only …
ecosystems, but phylogenetic relationships at the familial level and above remain only …
New methods to calculate concordance factors for phylogenomic datasets
We implement two measures for quantifying genealogical concordance in phylogenomic
data sets: the gene concordance factor (gCF) and the novel site concordance factor (sCF) …
data sets: the gene concordance factor (gCF) and the novel site concordance factor (sCF) …
[HTML][HTML] Widespread introgression across a phylogeny of 155 Drosophila genomes
Genome-scale sequence data have invigorated the study of hybridization and introgression,
particularly in animals. However, outside of a few notable cases, we lack systematic tests for …
particularly in animals. However, outside of a few notable cases, we lack systematic tests for …
Disentangling sources of gene tree discordance in phylogenomic data sets: testing ancient hybridizations in Amaranthaceae sl
DF Morales-Briones, G Kadereit, DT Tefarikis… - Systematic …, 2021 - academic.oup.com
Gene tree discordance in large genomic data sets can be caused by evolutionary processes
such as incomplete lineage sorting and hybridization, as well as model violation, and errors …
such as incomplete lineage sorting and hybridization, as well as model violation, and errors …
Phylogenomics resolves the deep phylogeny of seed plants and indicates partial convergent or homoplastic evolution between Gnetales and angiosperms
JH Ran, TT Shen, MM Wang… - Proceedings of the …, 2018 - royalsocietypublishing.org
After decades of molecular phylogenetic studies, the deep phylogeny of gymnosperms has
not been resolved, and the phylogenetic placement of Gnetales remains one of the most …
not been resolved, and the phylogenetic placement of Gnetales remains one of the most …
[HTML][HTML] Phylogenomic analysis of 997 nuclear genes reveals the need for extensive generic re-delimitation in Caesalpinioideae (Leguminosae)
Abstract Subfamily Caesalpinioideae with ca. 4,600 species in 152 genera is the second-
largest subfamily of legumes (Leguminosae) and forms an ecologically and economically …
largest subfamily of legumes (Leguminosae) and forms an ecologically and economically …
[HTML][HTML] Phylotranscriptomics unveil a Paleoproterozoic-Mesoproterozoic origin and deep relationships of the Viridiplantae
Z Yang, X Ma, Q Wang, X Tian, J Sun, Z Zhang… - Nature …, 2023 - nature.com
The Viridiplantae comprise two main clades, the Chlorophyta (including a diverse array of
marine and freshwater green algae) and the Streptophyta (consisting of the freshwater …
marine and freshwater green algae) and the Streptophyta (consisting of the freshwater …
[HTML][HTML] Incongruence between gene trees and species trees and phylogenetic signal variation in plastid genes
The current classification of angiosperms is based primarily on concatenated plastid
markers and maximum likelihood (ML) inference. This approach has been justified by the …
markers and maximum likelihood (ML) inference. This approach has been justified by the …