[HTML][HTML] Implementing and testing the multispecies coalescent model: a valuable paradigm for phylogenomics

SV Edwards, Z **, A Janke, BC Faircloth… - Molecular phylogenetics …, 2016 - Elsevier
In recent articles published in Molecular Phylogenetics and Evolution, Mark Springer and
John Gatesy (S&G) present numerous criticisms of recent implementations and testing of the …

Major revisions in pancrustacean phylogeny and evidence of sensitivity to taxon sampling

JP Bernot, CL Owen, JM Wolfe, K Meland… - Molecular Biology …, 2023 - academic.oup.com
The clade Pancrustacea, comprising crustaceans and hexapods, is the most diverse group
of animals on earth, containing over 80% of animal species and half of animal biomass. It …

StarBEAST2 brings faster species tree inference and accurate estimates of substitution rates

HA Ogilvie, RR Bouckaert… - Molecular biology and …, 2017 - academic.oup.com
Fully Bayesian multispecies coalescent (MSC) methods like* BEAST estimate species trees
from multiple sequence alignments. Today thousands of genes can be sequenced for a …

Misconceptions on missing data in RAD-seq phylogenetics with a deep-scale example from flowering plants

DAR Eaton, EL Spriggs, B Park… - Systematic …, 2017 - academic.oup.com
Restriction-site associated DNA (RAD) sequencing and related methods rely on the
conservation of enzyme recognition sites to isolate homologous DNA fragments for …

To include or not to include: the impact of gene filtering on species tree estimation methods

EK Molloy, T Warnow - Systematic biology, 2018 - academic.oup.com
With the increasing availability of whole genome data, many species trees are being
constructed from hundreds to thousands of loci. Although concatenation analysis using …

The perfect storm: gene tree estimation error, incomplete lineage sorting, and ancient gene flow explain the most recalcitrant ancient angiosperm clade, Malpighiales

L Cai, Z **, EM Lemmon, AR Lemmon, A Mast… - Systematic …, 2021 - academic.oup.com
The genomic revolution offers renewed hope of resolving rapid radiations in the Tree of Life.
The development of the multispecies coalescent model and improved gene tree estimation …

StarBeast3: adaptive parallelized Bayesian inference under the multispecies coalescent

J Douglas, CL Jiménez-Silva, R Bouckaert - Systematic Biology, 2022 - academic.oup.com
As genomic sequence data become increasingly available, inferring the phylogeny of the
species as that of concatenated genomic data can be enticing. However, this approach …

Defining coalescent genes: theory meets practice in organelle phylogenomics

JJ Doyle - Systematic biology, 2022 - academic.oup.com
The species tree paradigm that dominates current molecular systematic practice infers
species trees from collections of sequences under assumptions of the multispecies …

RADseq dataset with 90% missing data fully resolves recent radiation of Petalidium (Acanthaceae) in the ultra‐arid deserts of Namibia

EA Tripp, YHE Tsai, Y Zhuang… - Ecology and …, 2017 - Wiley Online Library
Deserts, even those at tropical latitudes, often have strikingly low levels of plant diversity,
particularly within genera. One remarkable exception to this pattern is the genus Petalidium …

Phylogenetic trees and networks can serve as powerful and complementary approaches for analysis of genomic data

C Blair, C Ané - Systematic Biology, 2020 - academic.oup.com
Genomic data have had a profound impact on nearly every biological discipline. In
systematics and phylogenetics, the thousands of loci that are now being sequenced can be …