Data from: Recovery of benthic marine communities from the end-Permian mass extinction at the low-latitudes of Eastern PanthalassaRichard Hofmann, Michael Hautmann, Arnaud Brayard, Alexander Nützel, Kevin Bylund, James Jenks, Emmanuelle Vennin, Nicolas Olivier & Hugo Bucher
Based on the quantitative community analysis using species-level identifications, we track the restoration of benthic ecosystems after the end-Permian mass extinction throughout the Lower Triassic of the western USA. New data on the palaeoecology of the Thaynes Group and Sinbad Formation are provided, which fill a gap between the recently studied palaeoecology of the Griesbachian–Dienerian Dinwoody Formation and the Spathian Virgin Formation. In the Sinbad Formation and Thaynes Group, 17 species (12 genera) of bivalves,...
To maximize long-term average reproductive success, individuals can diversify the phenotypes of offspring produced within a reproductive event by displaying the ‘coin-flipping’ tactic. Wild boar (Sus scrofa scrofa) females have been reported to adopt this tactic. However, whether the magnitude of developmental plasticity within a litter depends on stochasticity in food resources has not been yet investigated. From long-term monitoring, we found that juvenile females produced similar-sized fetuses within a litter independent of food availability....
A key challenge for biologists is to document and explain global patterns of diversification in a wide range of environments. Here, we explore patterns of continental-scale diversification in a groundwater species-rich clade, the superfamily Aselloidea (Pancrustacea: Isopoda). Our analyses supported a constant diversification rate during most of the course of Aselloidea evolution, until 4–15 Ma when diversification rates started to decrease. This constant accumulation of lineages challenges the view that groundwater species diversification in temperate...
Data from: Optimizing the trade-off between spatial and genetic sampling efforts in patchy populations: towards a better assessment of functional connectivity using an individual-based sampling schemeJérôme G. Prunier, Bernard Kaufmann, Serge Fenet, Damien Picard, Francois Pompanon, Pierre Joly, Jean-Paul Lena & J. P. Lena
Genetic data are increasingly used in landscape ecology for the indirect assessment of functional connectivity, i.e. the permeability of landscape to movements of organisms. Among available tools, matrix correlation analyses (e.g. Mantel tests or mixed models) are commonly used to test for the relationship between pairwise genetic distances and movement costs incurred by dispersing individuals. When organisms are spatially clustered, a population-based sampling scheme (PSS) is usually performed, so that a large number of genotypes...
Several lines of evidence such as the basal location of thermophilic lineages in large-scale phylogenetic trees and the ancestral sequence reconstruction of single enzymes or large protein concatenations support the conclusion that the ancestors of the bacterial and archaeal domains were thermophilic organisms which were adapted to hot environments during the early stages of the Earth. A parsimonious reasoning would therefore suggest that the last universal common ancestor (LUCA) was also thermophilic. Various authors have...
Data from: Phenotypic and genotypic convergences are influenced by historical contingency and environment in yeastAymé Spor, Daniel J. Kvitek, Thibault Nidelet, Juliette Martin, Judith Legrand, Christine Dillmann, Aurélie Bourgais, Dominique De Vienne, Gavin Sherlock & Delphine Sicard
Different organisms have independently and recurrently evolved similar phenotypic traits at different points throughout history. This phenotypic convergence may be caused by genotypic convergence and in addition, constrained by historical contingency. To investigate how convergence may be driven by selection in a particular environment and constrained by history, we analyzed nine life-history traits and four metabolic traits during an experimental evolution of six yeast strains in four different environments. In each of the environments, the...
The extant mammals have evolved highly diversified diets associated with many specialized morphologies. Two rare diets, termitophagy and vermivory, are characterized by unusual morphological and dental adaptations that have evolved independently in several clades. Termitophagy is known to be associated with increases in tooth number, crown simplification, enamel loss, and the appearance of intermolar diastemata. We observed similar modifications at the species level in vermivorous clades, though interestingly the vermivorous mammals lack secondarily derived tools...
Gene trees record the combination of gene-level events, such as duplication, transfer and loss, and species-level events, such as speciation and extinction. Gene tree-species tree reconciliation methods model these processes by drawing gene trees into the species tree using a series of gene and species level events. The reconstruction of gene trees based on sequence alone almost always involves choosing between statistically equivalent or weakly distinguishable relationships that could be much better resolved based on...
Data from: A branch-heterogeneous model of protein evolution for efficient inference of ancestral sequencesMathieu Groussin, Bastien Boussau & Manolo Gouy
Most models of nucleotide or amino acid substitution used in phylogenetic studies assume that the evolutionary process has been homogeneous across lineages and that composition of nucleotides or amino acids has remained the same throughout the tree. These oversimplified assumptions are refuted by the observation that compositional variability characterizes extant biological sequences. Branch-heterogeneous models of protein evolution that account for compositional variability have been developed, but are not yet in common use because of the...
University of Lyon System9
French National Centre for Scientific Research4
Claude Bernard University Lyon 13
University of California, Berkeley1
French National Institute for Agricultural Research1
Office National de la Chasse et de la Faune Sauvage1
University of Paris-Sud1
University of Zurich1
Grenoble Alpes University1