Incongruence in the phylogenomics era

JL Steenwyk, Y Li, X Zhou, XX Shen… - Nature Reviews Genetics, 2023 - nature.com
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 …

Diversification of Neotropical freshwater fishes

JS Albert, VA Tagliacollo… - Annual Review of Ecology …, 2020 - annualreviews.org
Neotropical freshwater fishes (NFFs) constitute the most diverse continental vertebrate fauna
on Earth, with more than 6,200 named species compressed into an aquatic footprint< 0.5 …

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 …

Phylogenomic subsampling and the search for phylogenetically reliable loci

N Mongiardino Koch - Molecular biology and evolution, 2021 - academic.oup.com
Phylogenomic subsampling is a procedure by which small sets of loci are selected from
large genome-scale data sets and used for phylogenetic inference. This step is often …

[HTML][HTML] A genomic perspective on an old question: Salmo trouts or Salmo trutta (Teleostei: Salmonidae)?

IH Segherloo, J Freyhof, P Berrebi, AL Ferchaud… - Molecular Phylogenetics …, 2021 - Elsevier
There are particular challenges in defining the taxonomic status of recently radiated groups
due to the low level of phylogenetic signal. Members of the Salmo trutta species-complex …

Phylogenomic analysis of trichomycterid catfishes (Teleostei: Siluriformes) inferred from ultraconserved elements

LE Ochoa, A Datovo, C DoNascimiento, FF Roxo… - Scientific reports, 2020 - nature.com
The family Trichomycteridae is one of the most diverse groups of freshwater catfishes in
South and Central America with eight subfamilies, 41 genera and more than 300 valid …

Congruence between ultraconserved element‐based matrices and phylotranscriptomic datasets in the scorpion Tree of Life

CE Santibáñez‐López, AA Ojanguren‐Affilastro… - …, 2023 - Wiley Online Library
Scorpions are ancient and historically renowned for their potent venom. Traditionally, the
systematics of this group of arthropods was supported by morphological characters, until …

[HTML][HTML] Evolution of Amazonian biodiversity: A review

JM Guayasamin, CC Ribas, AC Carnaval… - Acta …, 2024 - SciELO Brasil
Amazonia (defined herein as the Amazon basin) is home to the greatest concentration of
biodiversity on Earth, providing unique genetic resources and ecological functions that …

Understanding UCEs: a comprehensive primer on using ultraconserved elements for arthropod phylogenomics

YM Zhang, JL Williams, A Lucky - Insect Systematics and …, 2019 - academic.oup.com
Targeted enrichment of ultraconserved elements (UCEs) has emerged as a promising tool
for inferring evolutionary history in many taxa, with utility ranging from phylogenetic and …

Accelerated diversification explains the exceptional species richness of tropical characoid fishes

BF Melo, BL Sidlauskas, TJ Near, FF Roxo… - Systematic …, 2022 - academic.oup.com
The Neotropics harbor the most species-rich freshwater fish fauna on the planet, but the
timing of that exceptional diversification remains unclear. Did the Neotropics accumulate …