Daniel Charlton Jeffares

The paper analyzes Leishmania guyanensis population genomics to show human-driven emergence of a city-proximal population distinct from ancestral sylvatic lineage.

The paper identifies a Leishmania infantum strain suitable for genetic studies and provides its genome sequence and CRISPR-Cas9 tools for visceral leishmaniasis research.

This study shows that the Leishmania donovani species complex dispersed globally within the last 2,000 years, aligning with human migration and colonization.

The paper estimates the rate of sexual reproduction and inbreeding rate in Leishmania using population genomic data and a Moran model approach.

The paper presents genome assemblies for two Nepetoideae species and provides a species tree using genome-derived gene models.

The paper analyzes aneuploidy patterns across 866 Trypanosomatid isolates, finding aneuploidies are ancestral and an ancient duplication is maintained in some species.

This study resolves the complex phylogenetic relationships within Galdieria by analyzing genome-scale data from multiple strains, revealing divergent lineages and incongruent interlineage relationships across organellar and nuclear genomes.

The paper compares whole-genome sequences of three Galdieria sulphuraria strains, revealing structural rearrangements and a high number of nuclear chromosomes associated with adaptability in extreme environments.

The paper sequences the genome of Plasmodium simium to study its evolutionary history and identify genetic adaptations enabling host-switching to humans.

The paper identifies age-related genome rearrangements in non-dividing fission yeast cells, linking them to R-loops and regulatory changes, and finds similar patterns in human brain cells.

The paper investigates factors determining sequence evolution rates in fission yeast and finds network centrality is the most important variable.

The paper uses long-read sequencing to accurately identify root-knot nematode species from individual samples.

PoolHapX reconstructs microbial haplotypes by integrating genetic sharing and genomic sequencing, outperforming existing tools and revealing new insights into HIV evolution.

The paper uses transposon mutagenesis and a hidden Markov model to identify functional elements in the fission yeast genome, finding that 90% of the genome has fitness consequences.

The paper identifies natural genetic variants associated with longevity in fission yeast by analyzing segregant pools and genome sequencing during aging.

The paper investigates how structural variations in yeast genomes affect gene expression and quantitative traits, finding that copy number variants significantly influence phenotypes and reproductive isolation.