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 …

A practical guide to design and assess a phylogenomic study

J Lozano-Fernandez - Genome Biology and Evolution, 2022 - academic.oup.com
Over the last decade, molecular systematics has undergone a change of paradigm as high-
throughput sequencing now makes it possible to reconstruct evolutionary relationships …

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 …

Independent rediploidization masks shared whole genome duplication in the sturgeon-paddlefish ancestor

AK Redmond, D Casey, MK Gundappa… - Nature …, 2023 - nature.com
Whole genome duplication (WGD) is a dramatic evolutionary event generating many new
genes and which may play a role in survival through mass extinctions. Paddlefish and …

[PDF][PDF] Phylogenomics reveals ancient gene tree discordance in the amphibian tree of life

PM Hime, AR Lemmon, ECM Lemmon… - Systematic …, 2021 - academic.oup.com
Molecular phylogenies have yielded strong support for many parts of the amphibian Tree of
Life, but poor support for the resolution of deeper nodes, including relationships among …

PhyloFisher: a phylogenomic package for resolving eukaryotic relationships

AK Tice, D Žihala, T Pánek, RE Jones… - PLoS …, 2021 - journals.plos.org
Phylogenomic analyses of hundreds of protein-coding genes aimed at resolving
phylogenetic relationships is now a common practice. However, no software currently exists …

Successive climate crises in the deep past drove the early evolution and radiation of reptiles

TR Simões, CF Kammerer, MW Caldwell… - Science …, 2022 - science.org
Climate change–induced mass extinctions provide unique opportunities to explore the
impacts of global environmental disturbances on organismal evolution. However, their …

New approaches for inferring phylogenies in the presence of paralogs

ML Smith, MW Hahn - Trends in Genetics, 2021 - cell.com
The availability of whole genome sequences was expected to supply essentially unlimited
data for phylogenetics. However, strict reliance on single-copy genes for this purpose has …

The squamate tree of life

TR Simões, RA Pyron - Bulletin of the Museum of Comparative Zoology, 2021 - BioOne
Squamates (lizards, snakes, and their kin such as amphisbaenians, or “worm lizards”)
represent the world's most diverse clade of terrestrial vertebrates with∼ 11,000 described …

Prey shifts drive venom evolution in cone snails

TL Koch, SD Robinson, PF Salcedo… - Molecular biology …, 2024 - academic.oup.com
Venom systems are complex traits that have independently emerged multiple times in
diverse plant and animal phyla. Within each venomous lineage there typically exists …