D. A. Duchene

Bayesian inference of phylogenetic distances: revisiting the eigenvalue approach

The paper develops a Bayesian method to infer phylogenetic distances incorporating heterotachy and rate variation, finding evidence for a two-domain theory of eukaryotic origins.

Blue turns to grey - Paleogenomic insights into the evolutionary history and extinction of the blue antelope (Hippotragus leucophaeus)

This study recovers the first draft genomes of the extinct blue antelope, revealing its evolutionary relationships and low genetic diversity, suggesting human impact contributed to its extinction.

Multiple types of genomic variation contribute to adaptive traits in the mustelid subfamily Guloninae

The paper identifies candidate loci associated with adaptive traits in mustelids by analyzing genomic variation across species.

Excluding loci with substitution saturation improves inferences from phylogenomic data

The paper introduces a test to detect substitution saturation in phylogenomic data and shows that excluding saturated loci improves phylogenetic inference.

A genomic assessment of the marine-speciation paradox within the toothed whale superfamily Delphinoidea

This study investigates post-divergence gene flow in Delphinoidea toothed whales using phylogenomics, allele distribution, and demographic analysis, revealing complex speciation involving ancient gene flow and limited contemporary hybridization.

Ecological specialisation and evolutionary reticulation in extant Hyaenidae

This study generates an aardwolf genome and analyzes it with other hyena genomes to explore evolutionary relationships, dietary adaptations, and genetic diversity patterns in Hyaenidae.

Phylogenetic signal is associated with the degree of variation in root-to-tip distances

The paper examines the relationship between phylogenetic inference accuracy and branch length characteristics in phylogenomic data, finding that variation in root-to-tip distances is associated with accuracy.

Urban colonization is driven by a mixture of evolutionarily conserved and labile traits

The paper analyzes passerine bird data to show urban colonization involves both conserved and labile traits, leading to faster speciation and trait transitions.

Flight demand and environmental niche are associated with molecular evolutionary rates in a large avian radiation

The paper examines how flight-related metabolic demands and environmental factors influence molecular evolutionary rates in Furnariidae birds, finding associations between flight traits and mutation rates, and interactions between temperature and UV radiation with selection pressures.

Linking Branch Lengths Across Loci Provides the Best Fit for Phylogenetic Inference

This study finds that proportionally linking branch lengths across loci provides the best fit for phylogenetic inference compared to other models.

A Comparison of Methods for Estimating Substitution Rates from Ancient DNA Sequence Data

This study compares three methods for estimating substitution rates from ancient DNA data and finds they perform reliably under specific conditions but vary when rate variation and phylo-temporal clustering are present.