R. Corbett-Detig

Mixed Wolbachia infections resolve rapidly during in vitro evolution

This study shows that the wMel Wolbachia strain outcompetes the promiscuous wRi strain in vitro across different host cell types, suggesting a deterministic outcome that may explain low natural mixed infections.

Limited genomic signatures of population collapse in the critically endangered black abalone (Haliotis cracherodii)

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.

Automated Agnostic Designation of Pathogen Lineages

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

Mutational spectra distinguish SARS-CoV-2 replication niches

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.

Ecological differences among hydrothermal vent symbioses may drive contrasting patterns of symbiont population differentiation

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.

Sex-linked gene traffic underlies the acquisition of sexually dimorphic UV color vision in Heliconius butterflies

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: Scalable Neighbour-Joining for the Genomic Era

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

matOptimize: A parallel tree optimization method enables online phylogenetics for SARS-CoV-2

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

Pandemic-Scale Phylogenomics Reveals Elevated Recombination Rates in the SARS-CoV-2 Spike Region

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.

A Lethal Genetic Incompatibility between Naturally Hybridizing Species in Mitochondrial Complex I

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.

Evolutionary rates of testes-expressed genes differ in monogamous and promiscuous Peromyscus species

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

Mutation rates and selection on synonymous mutations in SARS-CoV-2

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.

Deep data mining reveals variable abundance and distribution of microbial reproductive manipulators within and among diverse host species

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.

Inferring Adaptive Introgression Using Hidden Markov Models

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.

Horizontal transmission and recombination maintain forever young bacterial symbiont genomes

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

Fine-scale position effects shape the distribution of inversion breakpoints in Drosophila melanogaster

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

Estimating the timing of multiple admixture pulses during local ancestry inference.

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.

A hidden Markov model approach for simultaneously estimating local ancestry and admixture time using next generation sequence data in samples of arbitrary ploidy

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.