John K. Kelly

This study investigates how soil microbiomes influence flowering traits in Mimulus guttatus, finding that plant genotype primarily drives flowering traits rather than the microbiome.

GCM improves gene module detection by directly optimizing correlation-based metrics using a genetic algorithm, outperforming standard methods in synthetic and real data.

The paper shows that a male-limited color polymorphism in Anolis distichus is maintained by a neo-sex chromosome, with additive genetic contributions from neo-Y haplotypes and autosomal variants.

The paper examines codon usage bias and linked selection in Mimulus guttatus, finding weak codon selection for most genes and strong selection for specific functional genes, with linked selection affecting nucleotide diversity.

The paper tests if neighbor density experienced by parents affects offspring traits through transgenerational plasticity, finding that offspring perform better when their environment matches parental conditions.

The paper uses experimental evolution to study micro-evolution in Mimulus guttatus under different mating systems and identifies genomic regions and candidate genes associated with selfing.

The paper studies secondary contact and gene flow in whistler birds in Fiji, identifying a genomic region linked to phenotypic differences and proposing rapid plumage evolution and post-divergence gene flow as key factors.

The paper maps transcriptome variation in Mimulus guttatus to cis- and trans-acting mutations, finding differing patterns of selection and showing that gene expression modules predict allele frequencies and traits.

The paper develops a statistical method to detect genomic structural variation using genetic mapping data from Mimulus guttatus crosses, correcting reference genome errors and identifying chromosomal inversions.

This study maps flowering time loci in Mimulus guttatus across space and time, finding significant genetic variation and genotype-by-environment interactions.

The paper uses whole genome sequencing of 56 Mimulus individuals to study population structure and local selection, finding high polymorphism, positive Tajima's D, and distinctive haplotype structure.

The paper shows adaptation to copper-contaminated environments in Mimulus guttatus occurs through selection on pre-existing genetic variation rather than new mutations.

The paper identifies a segregating inversion in Mimulus guttatus that has mixed fitness effects, contributing to genetic variation and inbreeding depression.