Fig 1.
Sampling locations of house mice trapped for SNP genotyping (2019–2020).
See methods for location abbreviations.
Fig 2.
Analysis of population genetic variation based on filtered GigaMUGA genotypes (49,058 SNPs) from 70 mice sampled at five locations in southeastern Australia.
(A) Results of PCA, with axes representing the first two principal components along with percentage of total genetic variation explained. Points are individual samples with inertia ellipses shown for each population. (B) Results of DAPC, which identifies synthetic variables that maximize the differences among populations. LD1 and LD2 are the first two linear discriminants, along with respective percentage of interpopulation variation explained. Population means are connected by dashed lines representing the minimum spanning tree based on the squared distances among populations.
Fig 3.
Target SNP sequencing coverage from hybridization sequence capture.
Each curve represents a different sample (N = 317), and the observed proportion of targeted SNPs (3,651 total) that had coverage equal to or greater than the value indicated on the x-axis.
Fig 4.
Characterization of population genetic variation based on hybridization capture sequencing dataset for house mice (N = 317) sampled from two adjoining farms in Adelaide Plains, SA (AP1 and AP2).
(A) PCA, with samples plotted against first (x-axis) and second (y-axis) principal components (PCs). Percentage of total genetic variation explained by each axis provided in parentheses. (B) Density plot for individual samples (ticks on x-axis) along linear discriminant (LD) function from DAPC (25 PCs, 1 LD). (C) Posterior membership probabilities (colors) for individual mice (columns) to each population, with sampling location indicated by arrows at top of plot.
Fig 5.
Comparison of pairwise kinship values, estimated using PC-Relate for the same samples (N = 47) using both the GigaMUGA genotyping (x-axis) and custom hybridization capture sequencing SNP datasets (y-axis).
Each point represents a unique dyad, colored by the corresponding degree of kinship.