Nicolas Salamin

The paper quantifies recombination landscape divergence across percomorph fish species using PRDI and finds divergence increases with genetic differentiation and divergence time, with variation among species pairs.

This study characterizes structural variation across 16 clownfish species, identifying extensive SVs and clarifying inversion events on chromosomes 18 and 9.

This study uses whole genome re-sequencing to reveal deep divergence within the Amphiprion clarkii species complex, identifying five lineages and challenging the taxonomic status of A. tricinctus.

The paper identifies a new wild clownfish hybrid in the Philippines and characterizes its genomic and phenotypic traits, showing it is a backcrossed descendant of A. sandaracinos and A. perideraion.

The paper investigates whether color polymorphism in the saddleback clownfish represents intraspecific variation or multiple species using genomic and image data.

This study examines colour and shape evolution in damselfishes, finding that ecological factors drive morphological and colour diversification, with convergent patterns indicating deterministic evolutionary trends.

The paper argues for using phylograms over chronograms when assessing neutral trait evolution, showing simulations support better model fit with phylograms for neutral traits.

This study uses simulations to show that environmental instability increases extinction rates and phenotypic evolution, affecting species with limited adaptability.

This study identifies sea anemone host use as the driver of convergent evolution in clownfish color and morphology, resolving a long-standing mystery in adaptive radiation.

This study investigates the genetic basis of vertical bar evolution in clownfish by analyzing changes in selective pressure on pigmentation-related genes.

The paper investigates selection relaxation in aquatic mammals and finds it occurs in 20% of genes across both semiaquatic and fully aquatic species.

The paper examines how clownfish demographic responses to Pleistocene sea level changes are influenced by their host specialization, revealing resilience in generalists and bottlenecks in specialists.

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.

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.

This study quantifies sialic acid and its precursors in skin mucus of clownfish and damselfish to test if their absence explains protection from anemone nematocysts.

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.

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.

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.

The paper evaluates the impact of three simplistic assumptions in codon evolution models and shows that relaxing them improves the accuracy of estimating evolutionary parameters.

The paper compares codon models that account for substitution rate variation and finds that ignoring rate variation leads to many false positives in positive selection detection.

This study investigates the genomic changes associated with the evolution of CAM photosynthesis in Tillandsioid bromeliads using phylogenomic and transcriptomic analyses.

The paper presents the first draft genome assembly of the tomato clownfish (Amphiprion frenatus), providing a resource for studying its life history traits and adaptive radiation.

This study improves divergence time estimates in Pinus by integrating more fossils and novel dating methods, finding older divergence times than previous studies.