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 …

Identifying and addressing methodological incongruence in phylogenomics: A review

JF Fleming, A Valero‐Gracia… - Evolutionary …, 2023 - Wiley Online Library
The availability of phylogenetic data has greatly expanded in recent years. As a result, a
new era in phylogenetic analysis is dawning—one in which the methods we use to analyse …

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 …

Error, signal, and the placement of Ctenophora sister to all other animals

NV Whelan, KM Kocot, LL Moroz… - Proceedings of the …, 2015 - pnas.org
Elucidating relationships among early animal lineages has been difficult, and recent
phylogenomic analyses place Ctenophora sister to all other extant animals, contrary to the …

Phylogenomics of Lophotrochozoa with consideration of systematic error

KM Kocot, TH Struck, J Merkel, DS Waits… - Systematic …, 2017 - academic.oup.com
Phylogenomic studies have improved understanding of deep metazoan phylogeny and
show promise for resolving incongruences among analyses based on limited numbers of …

Illuminating the base of the annelid tree using transcriptomics

A Weigert, C Helm, M Meyer, B Nickel… - Molecular biology …, 2014 - academic.oup.com
Annelida is one of three animal groups possessing segmentation and is central in
considerations about the evolution of different character traits. It has even been proposed …

A critical appraisal of the placement of **phosura (Chelicerata) with account of known sources of phylogenetic error

JA Ballesteros, PP Sharma - Systematic Biology, 2019 - academic.oup.com
Horseshoe crabs (**phosura) are traditionally regarded as sister group to the clade of
terrestrial chelicerates (Arachnida). This hypothesis has been challenged by recent …

On 20 years of Lophotrochozoa

KM Kocot - Organisms Diversity & Evolution, 2016 - Springer
Lophotrochozoa is a protostome clade that includes disparate animals such as molluscs,
annelids, bryozoans, and flatworms, giving it the distinction of including the most body plans …

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 …

An integrative phylogenomic approach to elucidate the evolutionary history and divergence times of Neuropterida (Insecta: Holometabola)

A Vasilikopoulos, B Misof, K Meusemann… - BMC Evolutionary …, 2020 - Springer
Background The latest advancements in DNA sequencing technologies have facilitated the
resolution of the phylogeny of insects, yet parts of the tree of Holometabola remain …