Principal components analysis on RAD-tag genotypes. Meredith V. Everett Linda K. Park Ewann A. Berntson Anna E. Elz Curt E. Whitmire Aimee A. Keller M. Elizabeth Clarke 10.1371/journal.pone.0165279.g003 https://plos.figshare.com/articles/figure/Principal_components_analysis_on_RAD-tag_genotypes_/4166826 <p>Colors correspond to putative geographic population groupings in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0165279#pone.0165279.g001" target="_blank">Fig 1</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0165279#pone.0165279.t001" target="_blank">Table 1</a>. A. Includes all 23 individuals. The three outliers are the three individuals with the most missing loci. PC1 and PC2 explain 10.5% and 5.5% of the total variance respectively. B. PCA after removing the three individuals with excess missing markers. The separations along PC1 in both cases are driven by missing genotypes. After removal PC1 and PC2 explain 6.7% and 6.6% of the variance.</p> 2016-10-31 17:36:50 quality control RAD population structure 23 individuals Swiftia simplex Gene Flow Deep-Sea Octocoral Swiftia simplex octocoral Swiftia simplex F ST United States Deep-sea corals coordinates analysis west coast F ST values United States Large-Scale Genotyping-by-Sequencing Indicates High Levels Eastern Pacific waters West Coast population differentiation genome-wide SNPs DNA population groups species octocoral populations life history connectivity STRUCTURE analysis high-throughput restriction-site