Fig 1.
Distribution of dingoes across Australia.
Map adapted from data in Fleming et al. [7] and Fleming et al. [36]. The bold black line indicates the position of the dingo fence; dingoes south of the dingo fence are particularly subject to high levels of lethal control and may have a higher prevalence of hybridization. Broad geographic sampling regions are noted on the map: the Kimberley, the Gibson Desert, the Simpson Desert, Fraser Island and the Australian Alpine region.
Table 1.
Description of datasets and samples used in analyses.
Table 2.
Gender and individual inbreeding coefficients for 23a dingoes and 5 NGSD (‘Dataset A’).
Fig 2.
Distribution of Fraser Island dingo samples and natal pack territories.
The location of dingo samples is indicated by enclosed grey circles and the boundaries of estimated natal pack territories adapted from Allen et al. [89] are drawn in dark grey.
Fig 3.
Maximum likelihood population clustering analysis on ‘Dataset A’ (23 dingoes and 5 NGSD) at 58,512 SNP loci.
Average Q-plot for K = 4 constructed in Distruct v1.1 [77]. Each column represents an individual and the proportion population cluster identity. Population clusters are represented by colours: green for New Guinea Singing Dog, red for southeastern, purple for Fraser Island and blue for northwestern.
Fig 4.
Geographical map depicting sampling location of each sample from ‘Dataset A’ and its majority population cluster identity.
NGSD samples (plotted in Papua New Guinea) are from a captive North American population.
Table 3.
FST values between dingo and NGSD populations (‘Dataset A’).
Calculated by ADMIXTURE (v1.23) based on 58,512 SNP loci.
Fig 5.
Maximum likelihood population clustering analysis on 23 dingoes, 5 NGSD, 8 Borneo village dogs, 9 Vietnam village dogs, 10 Portugal village dogs and 8 Australian cattle dogs (‘Dataset B’) at 58,512 SNP loci.
Average Q-plots constructed in Distruct v1.1 [77]. Each column represents an individual and the proportion population cluster identity. Abbreviations represent populations: NGSD for New Guinea Singing Dog; NW for northwestern dingoes; FI for Fraser Island dingoes; and SE for southeastern (Alpine) dingoes; BVD for Borneo village dogs; VVD for Vietnam village dogs; PVD for Portugal village dogs and ACD for Australian cattle dogs. (A) Average Q-plot for K = 5. (B) Average Q-plot for K = 7.
Fig 6.
Principal components analysis (PCA) based upon filtered whole genome SNP genotypes (58,512 sites) for 23 dingoes and 5 NGSD.
Colours represent population clusters: red for SE dingoes, purple for FI dingoes, blue for NW dingoes and green for NGSD. (A) PC 1 versus PC 2. (B) PC 1 versus PC 3.
Fig 7.
Principal components analysis (PCA) based upon filtered whole genome SNP genotypes (58,512 sites) for 23 dingoes, 5 NGSD, 8 Borneo village dogs, 9 Vietnam village dogs, 10 Portugal village dogs and 8 Australian cattle dogs (‘Dataset B’).
Colours represent population clusters: red for SE dingoes, purple for FI dingoes, blue for NW dingoes, dark green for NGSD, light green for Borneo village dogs, orange for Vietnam village dogs, yellow for Portugal village dogs and grey for Australian cattle dogs. (A) PC 1 versus PC 2. (B) PC 1 versus PC 3.
Fig 8.
Maximum likelihood tree based upon 4,913 ancestry informative markers in 23 dingoes and 5 NGSD (‘Dataset A’).
The tree was constructed via the SNPhylo pipeline [82], with 6,000 non-parametric bootstrap replicates. Bootstrap values located above nodes, values below 60 not shown. Colours represent population clusters: red for SE dingoes, purple for FI dingoes, blue for NW dingoes and green for NGSD. Circles indicate mitochondrial lineage with; black for NW and orange for SE [62]. Squares depict Y chromosome haplogroup with; green for H1, blue for H3 and red for H60 [67].
Fig 9.
Maximum likelihood tree constructed based upon 6,288 informative SNPs in 23 dingoes, 5 NGSD and 12 wolves (‘Dataset C’).
The 12 wolf samples [74] were added as outgroup taxa. Tree constructed in raxmlGUI [87] using a GTR + G substitution model and 2000 bootstrap replicates. Bootstrap values located above nodes, values below 70 not shown. Colours represent population clusters: red for SE dingoes, purple for FI dingoes, blue for NW dingoes, green for NGSD and gray for wolves.
Fig 10.
Introgression testing using D statistics based on 58,512 SNP sites for 23 dingoes, 5 NGSD, 8 Borneo village dogs, 9 Vietnam village dogs, 10 Portugal village dogs, 8 Australian cattle dogs and 12 wolves (‘Dataset D’).
The topology tested was W (wolves), X (dogs), Y (Alpine dingoes) and Z (non-Alpine dingoes). The non-Alpine dingo populations (Z population) are represented as pink dots for Fraser Island dingoes and black dots for northwestern dingoes. Values next to dots indicate the range of D statistic values with error; italics indicate negative D statistic values.