Stephens, D. (2011). The molecular ecology of Australian wild dogs: hybridisation, gene flow and genetic structure at multiple geographic scales. PhD, The University of Western Australia, Perth.
Advances in molecular ecology, particularly over the past two decades, have allowed studies of populations to extend to increasingly broad geographic and temporal scales without sacrificing detail. Limitations on sample numbers and types are decreasing, as efficiency and techniques for extracting DNA from suboptimal sources (such as hair or scats) improve. In this thesis I use microsatellite DNA markers to produce the first study of population genetics in Australian wild dogs, including dingoes (Canis lupus dingo), feral domestic dogs (C. l. familiaris) and their hybrids. Dingoes are unique among the Australian vertebrate fauna because they were transported to the continent approximately 5,000 years ago.
They have therefore not been in the ecosystem on evolutionary timescales, but have been present much longer than other introduced species. Dingoes are Australia’s apex predator, and have spread across habitats from deserts to tropical forests, but are currently under threat of extinction due to widespread hybridisation with domestic dogs. The conservation of dingoes is a management priority in some areas, but in others they are actively persecuted to protect livestock from predation.
The research areas addressed in this thesis are: the type of genetic samples best suited to different questions in research on wild dogs; the locations of pure dingoes; the patterns of gene flow among individuals and groups; and the degree of variability in spatial ecology across their range. Research outcomes are also placed into the context of how they can inform the management of wild dogs. Comparison of three non-invasively collected DNA sources with each other and with an invasively collected source (DNA swabs) showed that non-invasive samples, particularly scats, can be an appropriate source of DNA for monitoring based on
identification of individual. The costs and time involved in quality control of noninvasive samples, however, make them a less attractive option for large-scale or population-level studies, which require more genetic markers. I therefore employed tissue samples sourced from culling programs to examine aspects of
gene flow at four geographic scales. At the continental scale, I assessed the level of interbreeding between dingoes and domestic dogs, using both established methodology and a Bayesian clustering approach. Both methods provided similar results, showing increased hybridisation in coastal areas, particularly the
southeast of Australia, but fewer hybrids in the inland areas with lower densities of human settlement. Because population structure may affect approaches to control of wild dogs and conservation of dingoes, I then examined the scale and pattern of genetic subdivision and relatedness in three regions: the Tanami desert in the northern central region of Australia; south Queensland on the east coast; and across the western third of the continent. Wild dogs showed unexpected patterns of population structure, with variations in the geographical extent and separation of clusters. Relationships and spatial ecology of wild dogs in the Tanami desert appeared to be strongly affected by human activity, particularly the presence of artificially abundant food resources. The wild dogs sampled in south Queensland and Western Australia showed distinct genetic clusters in the absence of geographic barriers, showing that Australian wild dogs display cryptic genetic
subdivision at a similar scale found in wolves in vastly different habitats. The findings of this study reinforce the variability found in Australian wild dogs previously demonstrated by studies of diet and movements, and provide a novel and comprehensive overview of gene flow both among wild dogs and between dingoes and domestic dogs.
See more about wild canid hybridisation with dogs
Advances in molecular ecology, particularly over the past two decades, have allowed studies of populations to extend to increasingly broad geographic and temporal scales without sacrificing detail. Limitations on sample numbers and types are decreasing, as efficiency and techniques for extracting DNA from suboptimal sources (such as hair or scats) improve. In this thesis I use microsatellite DNA markers to produce the first study of population genetics in Australian wild dogs, including dingoes (Canis lupus dingo), feral domestic dogs (C. l. familiaris) and their hybrids. Dingoes are unique among the Australian vertebrate fauna because they were transported to the continent approximately 5,000 years ago.
They have therefore not been in the ecosystem on evolutionary timescales, but have been present much longer than other introduced species. Dingoes are Australia’s apex predator, and have spread across habitats from deserts to tropical forests, but are currently under threat of extinction due to widespread hybridisation with domestic dogs. The conservation of dingoes is a management priority in some areas, but in others they are actively persecuted to protect livestock from predation.
The research areas addressed in this thesis are: the type of genetic samples best suited to different questions in research on wild dogs; the locations of pure dingoes; the patterns of gene flow among individuals and groups; and the degree of variability in spatial ecology across their range. Research outcomes are also placed into the context of how they can inform the management of wild dogs. Comparison of three non-invasively collected DNA sources with each other and with an invasively collected source (DNA swabs) showed that non-invasive samples, particularly scats, can be an appropriate source of DNA for monitoring based on
identification of individual. The costs and time involved in quality control of noninvasive samples, however, make them a less attractive option for large-scale or population-level studies, which require more genetic markers. I therefore employed tissue samples sourced from culling programs to examine aspects of
gene flow at four geographic scales. At the continental scale, I assessed the level of interbreeding between dingoes and domestic dogs, using both established methodology and a Bayesian clustering approach. Both methods provided similar results, showing increased hybridisation in coastal areas, particularly the
southeast of Australia, but fewer hybrids in the inland areas with lower densities of human settlement. Because population structure may affect approaches to control of wild dogs and conservation of dingoes, I then examined the scale and pattern of genetic subdivision and relatedness in three regions: the Tanami desert in the northern central region of Australia; south Queensland on the east coast; and across the western third of the continent. Wild dogs showed unexpected patterns of population structure, with variations in the geographical extent and separation of clusters. Relationships and spatial ecology of wild dogs in the Tanami desert appeared to be strongly affected by human activity, particularly the presence of artificially abundant food resources. The wild dogs sampled in south Queensland and Western Australia showed distinct genetic clusters in the absence of geographic barriers, showing that Australian wild dogs display cryptic genetic
subdivision at a similar scale found in wolves in vastly different habitats. The findings of this study reinforce the variability found in Australian wild dogs previously demonstrated by studies of diet and movements, and provide a novel and comprehensive overview of gene flow both among wild dogs and between dingoes and domestic dogs.
See more about wild canid hybridisation with dogs
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