Jérôme Goudet

MONET: A model for neutral evolution of traits

The paper introduces MONET, a neutral evolution model for traits, and presents two tests to distinguish selection from neutral differentiation in quantitative traits.

Widespread but cryptic introgression shapes genetic diversity in natural populations

The paper quantifies introgression in 4126 ant colonies, finding 23% of species show introgression, more than double previous estimates, and suggests postzygotic barriers constrain it.

Growth effects and the underlying genetic architecture of inbreeding depression in a wild raptor

This study investigates inbreeding depression in wild barn owls using whole-genome sequences, showing its presence in growth and adult traits, and identifying genomic regions with significant effects.

Allelic Association Analyses: Estimation Recommendations

The paper reviews methods for estimating inbreeding, relatedness, and population structure and proposes five recommendations for improving allele-sharing statistics.

Benchmarking imputation accuracy in the presence or absence of a reference panel

This study benchmarks imputation accuracy for low-coverage whole-genome sequencing data with and without a reference panel, showing that large datasets can achieve sufficient accuracy without one.

The effect of age and sex on the rate of de novo mutations in barn owls

This study estimates de novo mutation rates in barn owls, showing paternal age effects and sex-specific mutation patterns.

A chromosome-level, haplotype-resolved genome assembly for the barn owl, Tyto alba

The paper presents a chromosome-level, haplotype-resolved genome assembly for the barn owl, resolving microchromosomes and enabling structural variation studies.

Genomic bases of short-term evolution in the wild revealed by long-term monitoring and population-scale sequencing

The paper uses long-term genomic data from Swiss barn owls to show that selection on few loci drives rapid phenotypic evolution in response to environmental change.

A method for identifying spatially divergent selection in structured populations.

The paper introduces a method to detect spatially divergent selection by incorporating population structure into genetic variance comparisons, showing improved performance over traditional methods.

The recombination landscape of the barn owl, from families to populations

This study combines family and population data to analyze recombination patterns in the barn owl, revealing sex-specific and chromosomal differences in crossover placement and recombination rates.

Estimation of Jacquard's genetic identity coefficients with bi-allelic variants by constrained least-squares

This paper proposes a constrained least squares method to estimate Jacquard's genetic identity coefficients and related parameters, showing computational efficiency comparable to maximum likelihood methods.

Detecting inbreeding depression in structured populations

This study compares methods for quantifying inbreeding depression in structured populations using simulated and empirical data, finding that weighted gamete correlation and specific GRM matrices improve estimation.

The genomic architecture of a continuous color polymorphism in the European barn owl (Tyto alba)

The paper identifies two new genomic regions associated with a continuous color polymorphism in European barn owls, explaining most of the color variation along with a known mutation.

Effect of reduced genomic representation on using runs of homozygosity for inbreeding characterization

The paper evaluates how reduced genomic representation affects ROH-based inbreeding estimates and shows that RZooRoH outperforms PLINK with smaller genomic fractions.

Population structure in the MHC region

The paper examines genetic diversity at HLA loci in the MHC region, showing that while SNPs show low FST values, haplotype frequencies vary geographically, impacting bone-marrow transplantation.

Assessing natural selection during range expansions: Insights from a spatially explicit ABC study

This study uses spatially explicit ABC simulations to assess natural selection during range expansions, finding that isolation-by-distance statistics reliably estimate selection strength despite genetic and demographic noise.

Population Differentiation at the HLA Genes

The paper examines population differentiation at HLA genes under balancing selection, finding reduced differentiation globally but higher differentiation in closely related populations.

Complex genetic patterns in human arise from a simple range-expansion model over continental landmasses

The paper uses simulations and Bayesian methods to show a simple range-expansion model explains much of human genetic diversity.

A Unified Characterization ofPopulation Structure and Relatedness

The paper redefines population structure and relatedness by introducing parameters based on differences in identity by descent probabilities, providing new estimates sensitive to rare variants and suitable for association studies.

Mapping bias overestimates reference allele frequencies at the HLA genes in the 1000 Genomes Project phase I data

The paper evaluates genotype calls and allele frequency estimates at HLA genes in 1000 Genomes Project data, finding significant overestimation of reference allele frequencies due to mapping bias.