The papers we discussed were Sen: Yang JR, Maclean CJ, Park C, Zhao H, & Zhang J (2017) Intra and Interspecific Variations of Gene Expression Levels in Yeast Are Largely Neutral: (Nei Lecture, SMBE 2016, Gold Coast). Mol Biol Evol 34:2125-2139. Swatantra: Heier CR & Dudycha JL (2009) Ecological speciation in a cyclic parthenogen: sexual capability of experimental hybrids between…
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Estimating within population/species PI (nucleotide diversity)
Learned a new bioinformatics trick today while using VCFtools to analyze nucleotide diversity for the Amazon molly (Poecilia formosa), an intriguing asexually reproducing (gynogenesis) fish. To calculate withing species/population Pi from a big vcf file containing multiple populations, provide a list containing all the individuals’ names from one population in a file (e.g., LIST), and use the following command “vcftools…