R. Corbett-Detig

The paper analyzes the genomes of black abalone to assess genetic impacts of a population collapse and finds no spatial genetic structure, high genetic diversity, and low WS prevalence, suggesting translocation could aid recovery.

The paper introduces an automated method for pathogen lineage designation using phylogenetic trees, offering a consistent alternative to manual curation.

The paper analyzes SARS-CoV-2 mutational spectra to infer replication niches, finding reduced G>T mutations in Omicron linked to upper respiratory tract replication.

This study compares symbiont population differentiation in deep-sea mussels with different ecological niches, finding that habitat homogeneity and mixotrophy reduce geographic structuring of symbiont strains.

The paper identifies that sex-specific UV color vision in Heliconius butterflies evolved through gene duplication and movement to the W chromosome, leading to female-specific UVRh1 expression.

DecentTree improves Neighbour-Joining phylogenetic inference scalability, handling large datasets up to 64,000 SARS-CoV-2 genomes faster than existing methods.

matOptimize improves runtime and memory efficiency for SARS-CoV-2 phylogenetic tree optimization, enabling daily maintenance of large-scale phylogenies during the pandemic.

The paper develops a novel phylogenomic method to detect recombination events in SARS-CoV-2 genomes, identifying 606 recombination events across 1.6M samples with 2.7% of genomes showing recombinant ancestry, primarily in the Spike protein region.

The paper identifies a lethal mitonuclear incompatibility in swordtail fish hybrids involving three Complex I genes, showing non-additive genetic effects and inter-species transfer of incompatibility.

The paper compares evolutionary rates of testes-expressed genes between monogamous and promiscuous Peromyscus species, finding differences linked to mating system and selective pressures.

The paper analyzes mutation rates and selection pressures in SARS-CoV-2 genomes, identifying elevated G→U and C→U mutations and challenging previous findings on synonymous site selection.

The paper uses data mining to analyze microbial reproductive manipulators in host species, finding Wolbachia infects most arthropods and nematodes, with host species explaining significant variation in bacterial density.

This paper introduces Ancestry_HMM-S, a Hidden Markov Model method for detecting adaptive introgression, and applies it to a Drosophila population to identify 17 loci with adaptive introgression signatures.

The paper examines how horizontal transmission and recombination sustain genome size and genetic diversity in marine bacterial symbionts despite expected degradation.

The paper examines the fine-scale distribution of inversion breakpoints in Drosophila melanogaster and identifies factors influencing their fitness impacts.

This paper introduces a method to estimate multiple admixture events using coalescent theory and applies it to Drosophila melanogaster data, finding evidence for both recent and ancient admixture pulses.

This paper introduces a hidden Markov model for estimating local ancestry and admixture time using next-generation sequence data in samples of arbitrary ploidy, demonstrating its accuracy on high-ploidy samples and applying it to Drosophila melanogaster populations.