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 …

The evolution of insect biodiversity

E Tihelka, C Cai, M Giacomelli, J Lozano-Fernandez… - Current Biology, 2021 - cell.com
Insects comprise over half of all described animal species. Together with the Protura
(coneheads), Collembola (springtails) and Diplura (two-pronged bristletails), insects form …

AlphaFold predictions are valuable hypotheses and accelerate but do not replace experimental structure determination

TC Terwilliger, D Liebschner, TI Croll, CJ Williams… - Nature …, 2024 - nature.com
Artificial intelligence-based protein structure prediction methods such as AlphaFold have
revolutionized structural biology. The accuracies of these predictions vary, however, and …

Revisiting metazoan phylogeny with genomic sampling of all phyla

CE Laumer, R Fernández, S Lemer… - … of the royal …, 2019 - royalsocietypublishing.org
Proper biological interpretation of a phylogeny can sometimes hinge on the placement of
key taxa—or fail when such key taxa are not sampled. In this light, we here present the first …

A large and consistent phylogenomic dataset supports sponges as the sister group to all other animals

P Simion, H Philippe, D Baurain, M Jager, DJ Richter… - Current biology, 2017 - cell.com
Resolving the early diversification of animal lineages has proven difficult, even using
genome-scale datasets. Several phylogenomic studies have supported the classical …

Modeling site heterogeneity with posterior mean site frequency profiles accelerates accurate phylogenomic estimation

HC Wang, BQ Minh, E Susko, AJ Roger - Systematic biology, 2018 - academic.oup.com
Proteins have distinct structural and functional constraints at different sites that lead to site-
specific preferences for particular amino acid residues as the sequences evolve …

Improved modeling of compositional heterogeneity supports sponges as sister to all other animals

R Feuda, M Dohrmann, W Pett, H Philippe… - Current Biology, 2017 - cell.com
The relationships at the root of the animal tree have proven difficult to resolve, with the
current debate focusing on whether sponges (phylum Porifera) or comb jellies (phylum …

Topology-dependent asymmetry in systematic errors affects phylogenetic placement of Ctenophora and Xenacoelomorpha

P Kapli, MJ Telford - Science advances, 2020 - science.org
The evolutionary relationships of two animal phyla, Ctenophora and Xenacoelomorpha,
have proved highly contentious. Ctenophora have been proposed as the most distant …

Evidence for sponges as sister to all other animals from partitioned phylogenomics with mixture models and recoding

AK Redmond, A McLysaght - Nature communications, 2021 - nature.com
Resolving the relationships between the major lineages in the animal tree of life is
necessary to understand the origin and evolution of key animal traits. Sponges …

Ctenophore relationships and their placement as the sister group to all other animals

NV Whelan, KM Kocot, TP Moroz, K Mukherjee… - Nature ecology & …, 2017 - nature.com
Ctenophora, comprising approximately 200 described species, is an important lineage for
understanding metazoan evolution and is of great ecological and economic importance …