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 little skate genome and the evolutionary emergence of wing-like fins

F Marlétaz, E de la Calle-Mustienes, RD Acemel… - Nature, 2023 - nature.com
Skates are cartilaginous fish whose body plan features enlarged wing-like pectoral fins,
enabling them to thrive in benthic environments,. However, the molecular underpinnings of …

The hagfish genome and the evolution of vertebrates

F Marlétaz, N Timoshevskaya, VA Timoshevskiy… - Nature, 2024 - nature.com
As the only surviving lineages of jawless fishes, hagfishes and lampreys provide a crucial
window into early vertebrate evolution,–. Here we investigate the complex history, timing …

The monoaminergic system is a bilaterian innovation

M Goulty, G Botton-Amiot, E Rosato… - Nature …, 2023 - nature.com
Monoamines like serotonin, dopamine, and adrenaline/noradrenaline (epinephrine/
norepinephrine) act as neuromodulators in the nervous system. They play a role in complex …

Reconciling gene trees with species trees

B Boussau, C Scornavacca - Phylogenetics in the genomic era, 2020 - hal.science
In the last decade, we witnessed the ascent of reconciliations as an important tool to model
and study the evolution of gene families. Reconciliations model discordance between gene …

Key processes required for the different stages of fungal carnivory by a nematode-trap** fungus

HC Lin, GVD de Ulzurrun, SA Chen, CT Yang… - PLoS …, 2023 - journals.plos.org
Nutritional deprivation triggers a switch from a saprotrophic to predatory lifestyle in soil-
dwelling nematode-trap** fungi (NTF). In particular, the NTF Arthrobotrys oligospora …

Analysis of the P. lividus sea urchin genome highlights contrasting trends of genomic and regulatory evolution in deuterostomes

F Marlétaz, A Couloux, J Poulain, K Labadie… - Cell Genomics, 2023 - cell.com
Sea urchins are emblematic models in developmental biology and display several
characteristics that set them apart from other deuterostomes. To uncover the genomic cues …

Phylogenetic analyses of seven protein families refine the evolution of small RNA pathways in green plants

S Bélanger, J Zhan, BC Meyers - Plant physiology, 2023 - academic.oup.com
Several protein families participate in the biogenesis and function of small RNAs (sRNAs) in
plants. Those with primary roles include Dicer-like (DCL), RNA-dependent RNA polymerase …

Detecting macroevolutionary genotype–phenotype associations using error-corrected rates of protein convergence

K Fukushima, DD Pollock - Nature Ecology & Evolution, 2023 - nature.com
On macroevolutionary timescales, extensive mutations and phylogenetic uncertainty mask
the signals of genotype–phenotype associations underlying convergent evolution. To …

Order of amino acid recruitment into the genetic code resolved by Last Universal Common Ancestor's protein domains

S Wehbi, A Wheeler, B Morel, N Manepalli… - Proceedings of the …, 2024 - pnas.org
The current “consensus” order in which amino acids were added to the genetic code is
based on potentially biased criteria, such as the absence of sulfur-containing amino acids …