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Genome-wide data in nonoverlapping 500kb windows

By Sean Stankowski, Madeline A. Chase, Allison M. Fuiten, Murillo F. Rodrigues, Peter L. Ralph and Matthew A. Streisfeld

Abstract

This file includes population genetic statistics, measures of genomic features, and estimates of phylogenetic concordance in 500kb nonoverlapping windows across the bush monkeyflower genome, which were used in analyses of genomic landscape evolution. Fst and dxy are included for 36 pairwise comparisons between taxa, and nucleotide diversity is included for all 9 taxa. These statistics were calculated using python scripts downloaded from https://github.com/simonhmartin/genomics_general. PC1 Fst, PC1 dxy, and PC1 nucleotide diversity for each window are obtained by performing a PCA using the 36 comparisons (fst or dxy) or 9 taxa (nucleotide diversity) as variables, and provide a summary of variation across taxa or taxon comparisons in each of these statistics. Gene count is obtained from the genome annotation, recombination rate (cM/Mb) is based on the genetic map, and tree concordance is obtained by taking the correlation coefficient between the window based tree and the whole genome ‘species tree.

Topics: Speciation, Indirect selection, Introgression, Linked selection, Mimulus
Year: 2019
DOI identifier: 10.5061/dryad.18j0j5q/1
OAI identifier: oai:v1.datadryad.org:10255/dryad.219857
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