Matthew W. Hahn

The paper introduces the MSC-DL model to account for gene duplication, loss, and coalescence, showing it generates many more gene tree topologies than previous models.

The paper quantifies the evolutionary rate of sex-biased gene expression in songbird brains, finding faster evolution on the Z chromosome and increased rates in species with obligate cavity-nesting.

OOPS estimates de novo mutation rates using single parent-offspring pairs, achieving comparable accuracy to trio-based methods.

The paper introduces a new method to detect and characterize introgression in large species trees by analyzing discordant attachment frequencies of gene trees, demonstrating its application in cichlids and Drosophila.

The paper uses phyloGWAS to link genotypes to longevity in Sebastes rockfishes despite high genealogical discordance, identifying variants associated with longevity.

The paper evaluates how well variant effect predictors perform across different genetic ancestries, finding comparable performance across major groups after accounting for allele frequency.

This paper introduces Spinney, a method that estimates quantitative trait evolution rates by considering gene tree discordance, improving accuracy over species-tree-only approaches.

This paper shows that using larger gene families with multiple copies can reduce long-branch attraction errors in phylogenetic analysis, improving accuracy compared to single-copy genes.

The paper re-evaluates evidence for Muller's ratchet in mitochondrial genomes using three species pairs, finding strong selection in mtDNA and no ratchet-like mutation accumulation.

This study reports the lowest germline mutation rate in mammals and a typical male mutation bias in the gray short-tailed opossum, suggesting alternative mechanisms to cell division drive sex-specific mutation rates.

This paper shows that machine learning can estimate recombination rates using only the allele frequency spectrum, without needing individual genotype data.

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

The paper presents a haplotype-resolved genome of Quercus alba and analyzes its genetic diversity and phylogenetic relationships within oaks.

This study finds a female mutation bias in aye-ayes, contrasting the typical male mutation bias in mammals, and identifies potential genetic causes.

The paper introduces the MAST model for phylogenetic inference using concatenated alignments with multiple evolutionary histories, showing it can accurately recover tree parameters and detect incomplete lineage sorting and introgression.

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.

reconcILS improves gene tree-species tree reconciliation by incorporating incomplete lineage sorting through NNI events, outperforming existing methods on simulated and primate datasets.

CAGEE infers gene expression changes across phylogenies and tissue-specific rates, validated on simulated data and applied to Solanum species.

The paper introduces an updated site concordance factor method that reduces homoplasy and taxon sampling effects using likelihood-based ancestral state probabilities.

This paper develops a machine learning model to detect incomplete lineage sorting in species trees using genome-scale summary statistics, showing it can predict discordance and infer correct species tree topology.

The paper introduces RoC-ITS, a method for high-resolution microbial community analysis using Nanopore sequencing, and demonstrates its accuracy in quantifying species abundance and identity.

The paper analyzes the potential for an autosomal X-shredder to become a Y-linked drive element in malaria mosquitoes and concludes it is unlikely due to suppression mechanisms.

The paper estimates distinct error rates for reference and non-reference genotypes using pedigree analysis in owl monkeys, finding significant differences in error types.

The paper analyzes genome variation in 1,142 Anopheles mosquitoes to study population structure and insecticide resistance.

The paper characterizes bumblebee genomes across 17 species to identify genetic variation linked to ecological and behavioral traits, revealing insights into genome structure, evolution, and adaptation.

This study revisits the ortholog conjecture by analyzing function prediction accuracy using orthologs and paralogs across two species pairs, finding strong evidence against the conjecture.

IQ-TREE 2 implements taxon-coverage-aware gene concordance factors and introduces site concordance factors, quantifying gene- and site-level discordance that 100% bootstrap support leaves hidden.

The paper analyzes gene and protein domain content changes across 76 arthropod genomes to understand evolutionary patterns and their association with phenotypic adaptations.

The paper improves Anopheles genome assemblies using comparative genomics methods and experimental data, resulting in more contiguous and chromosomally anchored assemblies.

The paper sequences genomes of 765 malaria vector mosquitoes to study genetic diversity and insecticide resistance.