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African Wild Dog De Novo Genome Assembly

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African wild dogs are one of the most endangered carnivores in Africa and as such, are the subject of close monitoring and conservation efforts in many parks. They live in cooperative packs where usually only an alpha male and female breed, a social behavior that limits their potential for population growth. Because they are so endangered, reintroductions across Africa have been a key part of their conservation plan for many years. For this project, our conservation partners looked closer to gain better insight into the following questions:

  • What are they eating? 
  • What intestinal parasites are they carrying? 
  • Is the microbiome of translocated individuals different from locals? 
  • Do dogs closer to human settlements have higher stress levels? 
  • Which dogs are reproducing? Is it always really just the alpha pair? 
  • What is the genomics diversity of African wild dogs? How genetically distinct are the different populations? How inbred are they?

To answer these questions, the Petrov lab in partnership with Painted Dog Conservation is working to create a reference genome to facilitate future studies of this species. Fecal metabarcoding will answer to the diet and any pursuant intestinal parasites present, as well as differences in microbiomes between local and translocated individuals. Fecal enzyme immunoassays will be applied to compare stress levels of packs depending on proximity to humans. SNP panels will speak to the reproductive question, and whole genome sequencing of tissue samples from across the range revealed the overall genomics diversity of the species. From these methods and the resulting insights combined, a high quality reference genome will emerge to aid in genetic monitoring of other threatened species by other conservationists. Gongorosa National Park and the Pringle Lab at Princeton are additional partners in this project.

 

Fig 1 from the completed study published in GigaScience