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Population divergence and linkage disequilibrium analysis

XL Xiaolong Li
YJ Yinqiao Jian
CX Chuanxiao Xie
JW Jun Wu
YX Yunbi Xu
CZ Cheng Zou
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Genomic divergence between different populations and pairwise nucleotide diversity within a population were calculated using VCFtools version 0.1.12.0 via the Weir and Cockerham estimator59 of Fst 60 with a window size of 1 Mb. Windows with more than 30 segregating sites were analysed. Population-specific SNPs were extracted by VCFtools. Because the population size affects the number of population-specific SNPs, we randomly sampled 50 individuals from each population. The result from 10 independent runs were summarised. The r 2 of ten adjacent SNPs were calculated using PLINK 1.0761, and a boxplot of different r 2 bins in different populations was generated by ggplot2 in R. Population-specific SNPs were selected by VCFtools.

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