Data from: Elucidating biogeographical patterns in Australian native canids using genome wide SNPs

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.

澳洲野犬（Dingo）作为澳大利亚生态系统中的顶级捕食者，在澳大利亚生态框架中发挥着关键作用，但正面临杂交与农业防控计划的双重威胁。澳大利亚政府立法将澳洲野犬保护列为重要目标，但目前对这种神秘犬科动物的生物地理学认知匮乏，导致保护工作难以有效开展。线粒体与Y染色体DNA研究已证实澳洲野犬种群内部存在种群结构。本研究提供了23只取自5个区域种群的澳洲野犬、以及5只新几内亚歌唱犬（New Guinea Singing Dogs）的Illumina HD犬类基因分型芯片基因分型数据，旨在利用全基因组数据进一步探究澳洲野犬的生物地理学分布模式。全基因组单核苷酸多态性（SNP）数据支持存在3个受地理分化影响的独立澳洲野犬种群（或进化显著单元，ESUs）：东南部（SE）种群、弗雷泽岛（FI）种群与西北部（NW）种群。这些进化显著单元应进行独立管理。弗雷泽岛种群是已知的纯种、遗传独特的澳洲野犬基因库。本研究检测到的升高的近交系数表明，该种群可能存在遗传健康受损问题，亟需救助；当前未考虑遗传信息的致死性管控策略应暂停实施，直至获取更多相关数据。D统计量证实，东南部澳洲野犬与东南亚乡村犬之间存在历史基因混合或血统共享的证据。澳大利亚大陆的保护工作应聚焦于东南部澳洲野犬种群——该种群正承受家犬杂交与高强度致死管控的双重压力。亟需获取更多关于东南部与弗雷泽岛澳洲野犬种群的遗传健康、种群动态以及杂交流行率的数据，以制定循证的保护与管理策略。