Mating System Evolution in Cryptococcus neoformans

Cryptococcus neoformans is a deadly fungal pathogen responsible for over 180,000 deaths annually, primarily in immunocompromised individuals. While the species is capable of both sexual and unisexual reproduction, the relative contribution of each mating mode in natural populations remains poorly understood.

Overview

My dissertation’s first aim addresses whether C. neoformans VNI populations have undergone a transition toward unisexual (same-sex) mating, which would leave characteristic genomic fingerprints distinct from outcrossing or clonal reproduction.

Approach

Using population genomic data from ~100 VNI isolates, I apply a multi-pronged inference framework:

• Allele frequency spectrum (AFS): Deviations from neutral expectations signal selfing or clonality
• • Linkage disequilibrium (LD) decay: Slower LD decay indicates reduced recombination, consistent with inbreeding
  • • Identity-by-descent (IBD) tract lengths: Long IBD tracts are a hallmark of recent inbreeding

    • • Forward simulations: Using msprime and SLiM, I simulate competing reproductive models and use ABC-SMC to compare posterior model probabilities against observed summary statistics

      • Tools

      • Python (scikit-allel, tskit, msprime), SLiM, VCFtools, pixy, GATK, Snakemake, bash

      • Status

      • Active dissertation project — Magwene Lab, Duke University Department of Biology.