[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 …

Gene tree discordance, phylogenetic inference and the multispecies coalescent

JH Degnan, NA Rosenberg - Trends in ecology & evolution, 2009 - cell.com
The field of phylogenetics is entering a new era in which trees of historical relationships
between species are increasingly inferred from multilocus and genomic data. A major …

Cryptic and abundant marine viruses at the evolutionary origins of Earth's RNA virome

AA Zayed, JM Wainaina, G Dominguez-Huerta… - Science, 2022 - science.org
Whereas DNA viruses are known to be abundant, diverse, and commonly key ecosystem
players, RNA viruses are insufficiently studied outside disease settings. In this study, we …

Contentious relationships in phylogenomic studies can be driven by a handful of genes

XX Shen, CT Hittinger, A Rokas - Nature ecology & evolution, 2017 - nature.com
Phylogenomic studies have resolved countless branches of the tree of life, but remain
strongly contradictory on certain, contentious relationships. Here, we use a maximum …

Genomic data provide insights into the classification of extant termites

S Hellemans, MM Rocha, M Wang… - Nature …, 2024 - nature.com
The higher classification of termites requires substantial revision as the Neoisoptera, the
most diverse termite lineage, comprise many paraphyletic and polyphyletic higher taxa …

Resolution of the ordinal phylogeny of mosses using targeted exons from organellar and nuclear genomes

Y Liu, MG Johnson, CJ Cox, R Medina, N Devos… - Nature …, 2019 - nature.com
Mosses are a highly diverse lineage of land plants, whose diversification, spanning at least
400 million years, remains phylogenetically ambiguous due to the lack of fossils, massive …

The evolutionary history of termites as inferred from 66 mitochondrial genomes

T Bourguignon, N Lo, SL Cameron… - Molecular biology …, 2014 - academic.oup.com
Termites have colonized many habitats and are among the most abundant animals in
tropical ecosystems, which they modify considerably through their actions. The timing of their …

The dynamics of incomplete lineage sorting across the ancient adaptive radiation of neoavian birds

A Suh, L Smeds, H Ellegren - PLoS biology, 2015 - journals.plos.org
The diversification of neoavian birds is one of the most rapid adaptive radiations of extant
organisms. Recent whole-genome sequence analyses have much improved the resolution …

A phylogeny of birds based on over 1,500 loci collected by target enrichment and high-throughput sequencing

JE McCormack, MG Harvey, BC Faircloth… - PloS one, 2013 - journals.plos.org
Evolutionary relationships among birds in Neoaves, the clade comprising the vast majority of
avian diversity, have vexed systematists due to the ancient, rapid radiation of numerous …

Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species-tree analysis

JE McCormack, BC Faircloth, NG Crawford… - Genome …, 2012 - genome.cshlp.org
Phylogenomics offers the potential to fully resolve the Tree of Life, but increasing genomic
coverage also reveals conflicting evolutionary histories among genes, demanding new …