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).