M. W. Hahn

Repeated behavioral evolution is associated with targeted convergence of gene expression in cavity-nesting songbirds

The paper investigates convergent evolution in cavity-nesting birds, finding behavioral similarities but limited gene expression convergence across species.

A comprehensive examination of Chelicerate genomes reveals no evidence for a whole genome duplication among spiders and scorpions

This study examines Chelicerate genomes to determine if whole genome duplications occurred in spiders and scorpions, finding no evidence for such events in their history.

Selection leads to false inferences of introgression using popular methods

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

Local adaptation of a marine diatom is governed by genome-wide changes in diverse metabolic processes

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.

Robust inference of historical human generation times

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

Geographic population structure and distinct population dynamics of globally abundant freshwater bacteria

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.

Phylogenetic inference using Generative Adversarial Networks

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

Phylogenomic comparative methods: accurate evolutionary inferences in the presence of gene tree discordance

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

Distinguishing between histories of speciation and introgression using genomic data

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

Evaluating methods for estimating the proportion of adaptive amino acid substitutions

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.

Using all gene families vastly expands data available for phylogenomic inference

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.

Hibernation shows no apparent effect on germline mutation rates in grizzly bears

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

Human generation times across the past 250,000 years

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.

Mutationathon: towards standardization in estimates of pedigree-based germline mutation rates

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.

The effects of introgression across thousands of quantitative traits revealed by gene expression in wild tomatoes

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

De novo mutations in domestic cat are consistent with an effect of reproductive longevity on both the rate and spectrum of mutations

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.

Species Tree Inference on Data with Paralogs is Accurate Using Methods Intended to Deal with Incomplete Lineage Sorting

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

The frequency and topology of pseudoorthologs

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.

Inferring the genetic basis of sex determination from the genome of a dioecious nightshade

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.

Determining the probability of hemiplasy in the presence of incomplete lineage sorting and introgression

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.

Primate phylogenomics uncovers multiple rapid radiations and ancient interspecific introgression

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

Paternal age in rhesus macaques is positively associated with germline mutation accumulation but not with measures of offspring sociability

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.

Origins and long-term patterns of copy-number variation in rhesus macaques

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.

A three-sample test for introgression

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 timing and direction of introgression under the multispecies network coalescent

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 perils of intralocus recombination for inferences of molecular convergence

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

Quantifying the risk of hemiplasy in phylogenetic inference

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.

Reproductive longevity predicts mutation rates in primates

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.

Three new genome assemblies support a rapid radiation in Musa acuminata (wild banana)

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

Multinucleotide mutations cause false inferences of lineage-specific positive selection

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