2.3 | Genomic composition
To summarize genetic structure of sampled trees in the inland and
coastal sites and to obtain allele frequencies in ancestral populations
that represent Qc and Qd , we conducted Bayesian clustering
for SNP genotypes at ddRAD loci using Admixture 1.3 (Alexander and Lange
2011). The log-likelihood was obtained, when the number (K ) of
ancestral populations (clusters) was 1, 2, or 3. Allele frequencies at
ddRAD loci in each cluster (P ) and ancestry proportions of each
cluster in individual trees (Q ) were estimated for each K .
Genetic differentiation between clusters (pairwiseF ST) was also estimated. We regarded two clusters
(K = 2) as ancestral populations that represented Qc andQd and estimated allele frequencies P for the two
clusters.
To describe genomic compositions of sampled trees in both sites, we
estimated the proportion of alleles derived from Qd ancestral
population (S ) and the proportion of heterozygous loci with both
alleles derived from Qc and Qd ancestral populations
(H ) using the package HIest 2.0 (Fitzpatrick 2012) in R 3.3.2
(R_Core_Team 2019). We regarded allele frequencies P for the
two clusters obtained from the Bayesian clustering asP 1 and P 2 allele
frequencies of ancestral populations of Qc and Qd ,
respectively, and estimated S (Qd ancestry) and H(inter-ancestry heterozygosity) of individual trees using the function
HIest with the options, method = SANN, iterations = 10000.