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