$ : chr "observed eigenvalues" "variance explained" "cumulative variance explained" #>. “…There is a lack of clear population structure, suggesting that the world’s mallards, perhaps with minor exceptions, form a single large, mainly interbreeding population”.Ĭlass ( pcaR ) #> "list" names ( pcaR ) #> "pca.snp_loadings" "pca.eigenvalues" "pca.sample_coordinates" str ( pcaR ) #> List of 3 #> $ pca.snp_loadings :'ame': 363 obs. “…Only Greenland is genetically differentiated from the remaining mallard population, and to a lesser extent, slight differentiation is observed between flyways in Europe and North America”.
The study supports panmixia in cosmopolitan bird species (see Kraus et al. 2013): SNP names (mallard_snps_Kraus2013.txt) = 695 rows x 1 column.Group names (mallard_samples_Kraus2013.txt) = 695 rows x 3 columns, column 1 = flyway names, column 2 = population name, column 3 = indvidual names comprise 55 populations and 10 flyways.Genotypes are 0, 1, 2 or (for missing values) 9 Genotype data (mallard_genotype_Kraus2012.txt) = 364 SNPs (rows) x 695 individuals (columns), individuals comprise 55 populations and 10 flyways.
#Permanova normalize or rarify download
They are part of the smartsnp package, you don’t need to download or process the data from dryad: Populations GBAB, GBFE and GBNM (British Isles) removed from dataset as these individuals might have mixed with captive/feral mallards (Robert Kraus, pers. Population SEAP removed from dataset as its geographic background is unclear (Robert Kraus, pers. Multivariate analysis of mallard genotypes using the dataset published by Kraus et al. 2013.
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