Maximum likelihood tree based upon 4,913 ancestry informative markers in 23 dingoes and 5 NGSD (‘Dataset A’).

<p>The tree was constructed via the SNPhylo pipeline [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0198754#pone.0198754.ref082" target="_blank">82</a>], 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 [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0198754#pone.0198754.ref062" target="_blank">62</a>]. Squares depict Y chromosome haplogroup with; green for H1, blue for H3 and red for H60 [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0198754#pone.0198754.ref067" target="_blank">67</a>].</p

Sample file for CanineHD array from 24 dingoes (fam)

.fam file for CanineHD array from 24 dingoes. Created in PLINK

Elucidating biogeographical patterns in Australian native canids using genome wide SNPs

<div><p>Dingoes play a strong role in Australia’s ecological framework as the apex predator but are under threat from hybridization and agricultural control programs. Government legislation lists the conservation of the dingo as an important aim, yet little is known about the biogeography of this enigmatic canine, making conservation difficult. Mitochondrial and Y chromosome DNA studies show evidence of population structure within the dingo. Here, we present the data from Illumina HD canine chip genotyping for 23 dingoes from five regional populations, and five New Guinea Singing Dogs to further explore patterns of biogeography using genome-wide data. Whole genome single nucleotide polymorphism (SNP) data supported the presence of three distinct dingo populations (or ESUs) subject to geographical subdivision: southeastern (SE), Fraser Island (FI) and northwestern (NW). These ESUs should be managed discretely. The FI dingoes are a known reservoir of pure, genetically distinct dingoes. Elevated inbreeding coefficients identified here suggest this population may be genetically compromised and in need of rescue; current lethal management strategies that do not consider genetic information should be suspended until further data can be gathered. D statistics identify evidence of historical admixture or ancestry sharing between southeastern dingoes and South East Asian village dogs. Conservation efforts on mainland Australia should focus on the SE dingo population that is under pressure from domestic dog hybridization and high levels of lethal control. Further data concerning the genetic health, demographics and prevalence of hybridization in the SE and FI dingo populations is urgently needed to develop evidence based conservation and management strategies.</p></div

Geographical map depicting sampling location of each sample from ‘Dataset A’ and its majority population cluster identity.

<p>NGSD samples (plotted in Papua New Guinea) are from a captive North American population.</p

Distribution of Fraser Island dingo samples and natal pack territories.

<p>The location of dingo samples is indicated by enclosed grey circles and the boundaries of estimated natal pack territories adapted from Allen et al. [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0198754#pone.0198754.ref089" target="_blank">89</a>] are drawn in dark grey.</p

Maximum likelihood population clustering analysis on ‘Dataset A’ (23 dingoes and 5 NGSD) at 58,512 SNP loci.

<p>Average Q-plot for K = 4 constructed in Distruct v1.1 [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0198754#pone.0198754.ref077" target="_blank">77</a>]. 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.</p

Genotype file for Canine HD array from 24 dingoes (bed)

Illumina CanineHD SNP data from 24 dingoes. In PLINK binary format (.bed, .bim and .fam)

Description of datasets and samples used in analyses.

<p>Description of datasets and samples used in analyses.</p

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.

<p>Average Q-plots constructed in Distruct v1.1 [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0198754#pone.0198754.ref077" target="_blank">77</a>]. 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. <b>(A)</b> Average Q-plot for K = 5. <b>(B)</b> Average Q-plot for K = 7.</p

Maximum likelihood tree constructed based upon 6,288 informative SNPs in 23 dingoes, 5 NGSD and 12 wolves (‘Dataset C’).

<p>The 12 wolf samples [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0198754#pone.0198754.ref074" target="_blank">74</a>] were added as outgroup taxa. Tree constructed in raxmlGUI [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0198754#pone.0198754.ref087" target="_blank">87</a>] 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.</p