3.4 | Local ancestry and genome-wide patterns of
introgression
Haplotypes at 27495 ddRAD loci in each chromosome were obtained from
imputation and phasing for SNP genotypes of the 224 sampled trees in
both sites. Among the sampled trees, 47 Qc trees (the Qdancestry S = 0) and 25 Qd trees (S = 1) were
selected as Qc and Qd reference individuals, respectively
(Table S1). Local ancestry (Qc homzygote, Qc and Qdheterozygote, and Qd homozygote) at ddRAD loci in each chromosome
was inferred for the remaining 152 admixed individuals based on the
haplotypes of the Qc and Qd reference individuals (Figure
6a). Genome-wide patterns of local ancestry in admixed individuals
indicated heterogeneous ancestry along chromosomes (Figure 6b).
The Patterson’s D statistics obtained at sliding windows of 101
neighboring ddRAD loci were also heterogeneous along chromosomes (Figure
S7). Genomic regions showing excessive introgression (higher Dvalues; Figures S7) were not always consistent with those with higher
local ancestry from Qd (Figure 6b).