Fig 1.
Frequencies of Runs of Homozygosity (ROH) according to segment size in Mb.
ROH were calculated for 176 British Lop samples and 44,315 SNPs and classified based on their length.
Table 1.
Estimates of inbreeding for the genotyped British Lop animals.
Fig 2.
Historical effective size trend in the British Lop population.
Calculated based on a dataset of 176 genotypes and 36,048 SNPs, using the SNeP software and the mapping function of Sved & Feldman.
Fig 3.
Neighbor-joining Identity-by-State (IBS) consensus tree for 14 pig populations.
IBS genetic distances for 405 samples and 14,628 SNPs were estimated in PLINK with 100 bootstrap permutations, using PHYLIP and GraPhlAn to create the tree. Wild boar (in black) was used as outgroup.
Fig 4.
Evanno analyses (A) and maximum-likelihood consensus trees with 4 (B) and 12 (C) migration edges for 14 pig populations. For a total of 405 samples and 14,628 SNPs, allelic frequencies per breed were estimated in PLINK, using Treemix to create the trees. The Evanno method (10 bootstrap replicates per node number) was used to estimate the optimal number of migration nodes; 12 migration edges explained 99.4% of the variance, while 4 migration edges explained 98.6% of the variance.
Fig 5.
Unsupervised admixture analysis of the studied pig populations for 3, 13, 14 and 15 ancestral populations (K3, K13, K14, K15).
For a total of 405 samples and 14,628 SNPs. Admixture levels were estimated using the ADMIXTURE software. Error estimates were calculated using a 5-fold cross-validation to estimate the most likely value for the number of ancestral populations (K). The label was given a posteriori by comparing the membership coefficient with the known breed. As such, cluster codes are: Berkshire (Berk), British Saddleback (BS), Duroc (Dur), Gloucestershire Old Spots (Glou), Hampshire (Hamp), Landrace (Land), Large Black (LBl), Large White (LWh), Lop (Lop), Middle White (MWh), Pietrain (Pie), Tamworth (Tam), Welsh (Wls) and Wild boar (Wboar).
Table 2.
Average admixture in the British Lop and other pig populations (unsupervised admixture analysis).
Table 3.
Aggregate genotypes for the selected 75 SNPs per autosomal chromosome that, combined, distinguish the British Lop.