N. Salamin

Ongoing hybridisation among clownfishes: the genomic architecture of the Kimbe Bay hybrid zone

The paper examines the genomic structure of a clownfish hybrid zone, identifying first-generation hybrids and early backcrosses, and suggests adaptive introgression from one parent species.

Recurrent gene flow events shaped the diversification of the clownfish skunk complex

This study investigates the diversification mechanisms of the clownfish skunk complex, finding moderate ancestral gene flow and limited recent gene flow, with introgression and recombination disruption playing key roles.

Gene flow throughout the evolutionary history of a polymorphic and generalist clownfish

This study uses whole-genome data to show A. clarkii has a single species status with pervasive gene flow and color polymorphism not linked to population structure.

Detecting diversifying selection for a trait from within and between-species genotypes and phenotypes

This paper introduces a neutrality index combining within- and between-species variation to detect diversifying selection on quantitative traits, applied to brain and body mass in mammals.

Improved estimation of molecular evolution coupling stochastic simulations and deep learning

This paper combines stochastic simulations with deep learning to estimate molecular evolution parameters, achieving higher accuracy than traditional likelihood-based methods under complex rate variation patterns.

Estimating the proportion of beneficial mutations that are not adaptive in mammals

The paper estimates the proportion of beneficial mutations in mammals that are not adaptive, finding they account for 15-45% of all beneficial mutations in 24 of 28 populations.

Integrating Biotic Interactions In Niche Analyses Unravels Patterns Of Community Composition in Clownfishes

This study integrates biotic interactions into niche modeling to reveal how mutualistic relationships influence clownfish community composition and diversity.

Exploring the Macroevolutionary Signature of Asymmetric Inheritance at Speciation

The paper introduces an Asymmetric Brownian Motion model to study phenotypic inheritance during speciation, finding evidence of character displacement in Darwin finches.

Extensive hybridisation throughout clownfishes evolutionary history

This study investigates hybridisation in clownfishes, finding multiple past hybridisation events that support its role in adaptive radiation.

Insights into the genomics of clownfish adaptive radiation: the genomic substrate of the diversification

This study investigates the genomic features driving clownfish adaptive radiation, identifying transposable elements, accelerated evolution, and positive selection in genes related to social behavior and ecology.

A cautionary note on the use of haplotype callers in Phylogenomics

The paper compares GATK and ATLAS haplotype callers in phylogenomic studies, showing GATK underestimates variants at the phylogenetic level but not population level.

On the effect of asymmetrical trait inheritance on models of trait evolution

This study investigates how asymmetrical trait inheritance at speciation affects macroevolutionary analyses, showing that small phenotypic jumps can significantly alter model selection and parameter estimation.

Prototypic SNARE proteins are encoded in the genomes of Heimdallarchaeota, potentially bridging the gap between the prokaryotes and eukaryotes

The paper identifies SNARE-like proteins in Heimdallarchaeota, suggesting they may be ancestral to eukaryotic SNAREs, and finds evidence of lateral gene transfer in some bacteria.

Convergent changes in gene expression associated with repeated transitions between hummingbird and bee pollinated flowers

This study identifies 550 genes whose expression changes are associated with pollinator shifts in Gesneriaceae species, suggesting convergent genetic mechanisms underlie convergent floral phenotypes.

Functional diversification enabled grassy biomes to fill global climate space

The paper maps global grassy biomes and identifies key traits and lineages driving their distribution across climates.

Evolution of life cycles and reproductive traits: insights from the brown algae

This study examines the evolution of life cycle and reproductive traits in brown algae, finding diploid growth may evolve due to mutation complementation and haploid sex determination is ancestral.

Linking micro and macroevolution in the presence of migration

This paper introduces an OU model that incorporates migration during speciation to study trait evolution and phenotypic disparity across phylogenies, showing migration reduces disparity and affects inference.

Improved estimation of macroevolutionary rates from fossil data using a Bayesian framework

The paper updates PyRate, a Bayesian software for estimating macroevolutionary rates from fossil data, showing significant shifts in marine mammal origination and extinction rates.

Evolutionary history of New World monkeys revealed by molecular and fossil data

This study integrates fossil and molecular data to estimate the evolutionary history of New World monkeys, revealing earlier origins and key morphological and geographic changes.

No evidence for the radiation time lag model after whole genome duplications in Teleostei

This study tests the radiation time lag model after whole genome duplications in teleost fishes using fossil data and molecular phylogenies, finding no evidence of delayed evolutionary success.