The Australian dingo is an early offshoot of modern breed dogs

Authors: FIELD, MATT - James Cook University; YADAV, SONU - University Of New South Wales; DUDCHENKO, OLGA - Baylor College Of Medicine; ESVARAN, MEERA - University Of New South Wales; Rosen, Benjamin - Ben; SKVORTSOVA, KSENIA - Garvan Institute Of Medical Research; EDWARDS, RICHARD - University Of New South Wales; KEILWAGEN, JENS - Julius Kuhn Institute; COCHRAN, BLAKE - University Of New South Wales; MANANDHAR, BIKASH - University Of New South Wales; BUSTAMANTE, SONIA - University Of New South Wales; RASMUSSEN, JACOB - University Of Copenhagen; MELVIN, RICHARD - University Of Minnesota; CHERNOFF, BARRY - Wesleyan University; OMER, ARINA - Baylor College Of Medicine; COLARIC, ZANE - Baylor College Of Medicine; CHAN, EVA - Garvan Institute Of Medical Research; MINOCHE, ANDRE - Garvan Institute Of Medical Research; Smith, Timothy - Tim; GILBERT, THOMAS - University Of Copenhagen; BOGDANOVIC, OZREN - University Of New South Wales; ZAMMIT, ROBERT - Collaborator; THOMAS, TORSTEN - University Of New South Wales; AIEN, EREZ - Baylor College Of Medicine; BALLARD, J - University Of New South Wales

Submitted to: Science Advances
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/9/2022
Publication Date: 4/22/2022
Citation: Field, M.A., Yadav, S., Dudchenko, O., Esvaran, M., Rosen, B.D., Skvortsova, K., Edwards, R.J., Keilwagen, J., Cochran, B.J., Manandhar, B., Bustamante, S., Rasmussen, J.A., Melvin, R.G., Chernoff, B., Omer, A., Colaric, Z., Chan, E.K., Minoche, A.E., Smith, T.P., Gilbert, T.P., Bogdanovic, O., Zammit, R.A., Thomas, T., Aien, E.L., Ballard, J.W. 2022. The Australian dingo is an early offshoot of modern breed dogs. Science Advances. 8(16):eabm5944. https://doi.org/10.1126/sciadv.abm5944.
DOI: https://doi.org/10.1126/sciadv.abm5944

Interpretive Summary: Apex predators are key components of ecosystem health. The dingo is Australia’s iconic top-order predator and understanding its biology is crucial to conservation efforts. We present a reference-quality genome assembly of the desert dingo to provide unbiased insight into its evolutionary history and biology. Comparison of the assembly (CanLup_DDS) to those of the Boxer (CanFam3.1) and German Shepherd (CanFam_GSD) dog breeds identified genomic variants predicted to mediate genic or regulatory changes, a unique inversion on chromosome 16 of dingo, and structural variations in genes linked with starch metabolism. Lower relative copy number of AMY2B genes in Dingo and consequent reduced serum amylase levels are linked with high serum cholesterol and LDL levels. Gut microbiome analysis revealed enrichment of family Clostridiaceae in dingo relative to GSD that may aid in digestion of complex resistant starch, consistent with the genomic indications of lower ability to digest starches. High phenylethyl alcohol concentrations in dingo scat were identified that may be linked to territory marking. Our results demonstrate that the ancient divergence of dingoes from domestic breeds and selection for feeding on native fauna has shaped its genome. We anticipate this study will be a starting point for testing chemical based methods to separate native and domesticated animals and thereby provide a novel method for biodiversity conservation.

Technical Abstract: Apex predators are key drivers of ecosystem dynamics and biodiversity conservation. The dingo is Australia’s iconic top-order predator and arrived on the continent between 5,000-8,000 years ago. We present a reference-quality genome assembly of the desert dingo (contig N50 >24 megabases) with associated epigenetic, metabolomic, and microbiome analyses to provide unbiased insight into its evolutionary history and biology. Comparison of the assembly (CanLup_DDS) to those of the Boxer (CanFam3.1) and German Shepherd (CanFam_GSD) dog breeds identified 21,483 dingo-specific and 16,595 domestic dog-specific structural variants predicted to mediate genic or regulatory changes, a unique inversion on chromosome 16 of dingo, and structural variations in genes linked with starch metabolism that included seven promoters displaying differential methylation. Comparative biochemical and faecal microbiome analyses of dingo and GSD cohorts was performed to further analyse differences in starch metabolism, indicating that the lower relative copy number of AMY2B genes and consequent reduced serum amylase levels in dingoes are linked with high serum cholesterol and LDL levels. Gut microbiome analysis revealed enrichment of family Clostridiaceae in dingo relative to GSD that may aid in digestion of complex resistant starch, consistent with the genomic indications of lower ability to digest starches. High phenylethyl alcohol concentrations in dingo scat were identified that may be linked to territory marking. Our results demonstrate that the ancient divergence of dingoes from domestic breeds and selection for feeding on native fauna has shaped its genome. We anticipate this study will be a starting point for testing chemical based methods to separate native and domesticated animals and thereby provide a novel method for biodiversity conservation.