Computational protocol: Clonality Despite Sex: The Evolution of Host-Associated Sexual Neighborhoods in the Pathogenic Fungus Penicillium marneffei

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Protocol publication

[…] Genotypes were analysed using GenAlex 6.0 to determine allelic diversity, genotypic diversity and spatial correlation across regions and the global distribution of P. marneffei. We used the package adegenet and its dependencies in R to conduct spatial PCA and DAPC analyses . To compare our inferred results against a model of a single continuous population structured by a dingle dispersal kernel and mutation rate we used the coalescent based program IBDsim . Additional distribution data for bamboo rats were collected from specimen databases AMNH, FMNH, NMNH, and the GBIF. We used the bioclim layers 1–21 at 30 sec from the world clim database in MAXENT to generate predicted distributions for bamboo rats and P. marneffei genetic clusters. We measured distributional overlap using Schoener's D and a resampling approach . We compared the relative overlap of genetic clusters to host distributions by generating null distributions of D based on resampling of R. sumatrensis and Cannomys (). Possible parental distances were compared to null distributions generated by choosing isolates randomly that met the genetic distance criteria from the population that met the parental criteria. […]

Pipeline specifications

Software tools GenAlEx, adegenet, IBDsim
Application Population genetic analysis
Organisms Talaromyces marneffei, Homo sapiens, Rattus norvegicus
Diseases Acquired Immunodeficiency Syndrome, Sexual Infantilism