[HTML][HTML] Incongruence between gene trees and species trees and phylogenetic signal variation in plastid genes

DJP Goncalves, BB Simpson, EM Ortiz… - Molecular phylogenetics …, 2019 - Elsevier
The current classification of angiosperms is based primarily on concatenated plastid
markers and maximum likelihood (ML) inference. This approach has been justified by the …

Characterizing gene tree conflict in plastome-inferred phylogenies

JF Walker, N Walker-Hale, OM Vargas, DA Larson… - PeerJ, 2019 - peerj.com
Evolutionary relationships among plants have been inferred primarily using chloroplast data.
To date, no study has comprehensively examined the plastome for gene tree conflict. Using …

Plastome phylogenetics: 30 years of inferences into plant evolution

MA Gitzendanner, PS Soltis, TS Yi, DZ Li… - Advances in botanical …, 2018 - Elsevier
From restriction site analyses to whole plastid genome sequences, our understanding of
green plant (Viridiplantae;~ 500,000 extant species) evolutionary relationships over the past …

Plastid genomes and deep relationships among the commelinid monocot angiosperms

CF Barrett, JI Davis, J Leebens‐Mack, JG Conran… - …, 2013 - Wiley Online Library
The commelinid monocots comprise the orders Arecales (A), Commelinales (C), Poales
sensu Angiosperm Phylogeny Group III (APGIII)(P), Zingiberales (Z), plus the unplaced …

Plastid genome sequencing, comparative genomics, and phylogenomics: current status and prospects

L Gao, YJ SU, T Wang - Journal of Systematics and Evolution, 2010 - Wiley Online Library
More than 190 plastid genomes have been completely sequenced during the past two
decades due to advances in DNA sequencing technologies. Based on this unprecedented …

Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns

RK Jansen, Z Cai, LA Raubeson… - Proceedings of the …, 2007 - National Acad Sciences
Angiosperms are the largest and most successful clade of land plants with> 250,000 species
distributed in nearly every terrestrial habitat. Many phylogenetic studies have been based on …

Inferring the higher‐order phylogeny of mosses (Bryophyta) and relatives using a large, multigene plastid data set

Y Chang, SW Graham - American journal of botany, 2011 - Wiley Online Library
• Premise of the study: Investigating the early diversification of major clades requires well‐
corroborated and accurate phylogenetic inferences. We examined the performance of a …

Plastid phylogenomics and green plant phylogeny: almost full circle but not quite there

CC Davis, Z Xi, S Mathews - BMC biology, 2014 - Springer
A study in BMC Evolutionary Biology represents the most comprehensive effort to clarify the
phylogeny of green plants using sequences from the plastid genome. This study highlights …

Plastid phylogenomic insights into relationships of all flowering plant families

HT Li, Y Luo, L Gan, PF Ma, LM Gao, JB Yang, J Cai… - BMC biology, 2021 - Springer
Background Flowering plants (angiosperms) are dominant components of global terrestrial
ecosystems, but phylogenetic relationships at the familial level and above remain only …

Using plastid genome-scale data to resolve enigmatic relationships among basal angiosperms

MJ Moore, CD Bell, PS Soltis… - Proceedings of the …, 2007 - National Acad Sciences
Although great progress has been made in clarifying deep-level angiosperm relationships,
several early nodes in the angiosperm branch of the Tree of Life have proved difficult to …