M. W. Hahn

This study shows that popular methods for detecting migration can falsely infer introgression when selection is present, highlighting the need for more robust methods.

This study identifies genome-wide metabolic changes driving local adaptation of a marine diatom to the Baltic Sea's environmental gradients over 8,000 years.

The paper addresses concerns about historical human generation time estimates, showing their robustness despite methodological critiques.

The paper examines geographic population structure and dynamics of freshwater bacteria using metagenomes and genomes, finding significant spatial differentiation and contrasting population dynamics across species.

This paper introduces phyloGAN, a GAN for phylogenetic inference, and evaluates its performance on small-scale datasets.

This paper develops new phylogenomic methods to account for gene tree discordance in evolutionary trait analysis, showing improved accuracy in estimating trait evolution rates.

This study uses supervised machine learning to distinguish between speciation and introgression histories using genomic data, showing high accuracy in simulated datasets.

This study evaluates nine methods for estimating adaptive amino acid substitutions, finding that DFE models are most accurate and reporting varying proportions across species and genomic regions.

The paper evaluates the impact of using all gene families instead of single-copy orthologs in phylogenomic analysis, finding increased data availability and consistent results across methods and datasets.

This study finds no difference in male mutation bias or per-generation mutation rates between hibernating grizzly bears and non-hibernating species.

The paper estimates human generation times over 250,000 years using mutation spectrum changes, finding an average of 26.9 years with fathers older than mothers.

The paper evaluates variation in germline mutation rate estimates across labs using a standardized pedigree of rhesus macaques, highlighting methodological differences and the need for standardization.

This study uses gene expression data from wild tomatoes to show introgression affects quantitative trait evolution by generating convergent patterns across thousands of traits.

This study estimates the mutation rate in domestic cats and finds a paternal age effect, suggesting reproductive longevity influences mutation rate and spectrum across species.

This study shows that species tree inference methods can accurately handle data with paralogs, even when incomplete lineage sorting is present.

This paper models the probabilities and topologies of pseudoorthologs in a three-taxon species tree, showing they are rare and unlikely to mislead phylogenetic inference.

The paper generates the first genome sequence of a dioecious Solanum species and identifies the genetic basis of sex determination, finding males are the heterogametic sex and sex-specific genes are involved in pectin degradation.

The paper develops a method to estimate hemiplasy probabilities in the presence of ILS and introgression, showing introgression increases hemiplasy likelihood and presents a tool for statistical inference.

This study uses genome-wide data to resolve primate phylogenetic relationships, identifying multiple radiations and ancient introgression events.

This study estimates the de novo mutation rate in rhesus macaques and finds it is lower than in humans, but paternal age still correlates with increased mutations. No association is found between paternal age and offspring sociability.

This study examines CNV mutation patterns in rhesus macaques, finding low mutation rates, no age correlation, and more segregating deletions than duplications compared to humans.

The paper introduces a new test for introgression, D3, which uses single sequences from three taxa and shows comparable statistical power to existing methods.

The paper develops statistical methods to test hypotheses about introgression timing and direction using the multispecies network coalescent framework and applies them to yeast genomic data.

The paper examines how intralocus recombination leads to false convergence inferences (hemiplasy) when analyzing molecular data from single loci in primates and Drosophila.

The paper quantifies the risk of hemiplasy in phylogenetic inference by comparing its likelihood to homoplasy and introducing a method to calculate the hemiplasy risk factor across phylogenies.

The paper shows that paternal age determines de novo mutation rates in owl monkeys and proposes a model linking reproductive longevity to mutation rates across primates.

This study presents three new genome assemblies of Musa acuminata subspecies to investigate their rapid radiation and evolutionary relationships with M. balbisiana.

The paper shows that multinucleotide mutations can falsely indicate positive selection in phylogenetic tests, suggesting many published findings may be artifacts.

The paper finds that speciation genes following the Dobzhansky-Muller model are more likely to have discordant gene trees due to incomplete lineage sorting.

The paper investigates trait evolution in Jaltomata, finding gene tree discordance affects floral trait inferences but not fruit color, and identifies candidate loci for adaptive evolution.