The wolf and the desert: genomics and molecular ecology of the African golden wolf (Canis lupaster)

Abstract

Life in deserts is an example of resilience and adaptation. There is a plethora of challenges that animals need to endure in these places. These challenges include abiotic stresses such as scarcity of water, low or no forest cover (resulting in constant exposure to UV radiation), strong winds, airborne dust, and oxidative stresses from a variety of sources. But there are also important stresses of biotic origin: competition for meager resources, predation and parasitism, without leaving behind the tremendous impact of human-related activities. Climate change in the past was a major driver of desertification and regreening processes in deserts like Sahara, which dramatically increase the strength of the challenges presented and profoundly impacted animal populations. The strong selective pressures in these environments drive behavioral and physiological adaptation in animals, especially important for carnivores since their predatory diet is connected to larger home ranges and higher metabolic rates. The African golden wolf (Canis lupaster) lives in arid and semi-arid environments in Sahara, Sahel and the northern Mediterranean fringe of Africa and is constantly under these extreme selective pressures. In this dissertation some of their potential trophic and genetic adaptations are explored. We have optimized a field-to-lab pipeline for genetic studies with fecal material from carnivores, decreasing costs threefold and allowing an economic and efficient extraction of noninvasive DNA with highly available biochemical reagents. Using this optimized method, we genetically identified a large assemblage of feces from four carnivores from an arid, food-depleted environment in Sahara and discovered a trophic strategy of niche partitioning with African golden wolves as top predator. we used whole genome sequences from roadkills and museum material to evaluate how climate change in the Pleistocene and Holocene affected different lineages of African golden wolf, discovering a widespread genetic cluster that spans more than 4,500 km from Algeria to Senegal, and a relict lineage from the Atlas Moroccan mountains that has possibly been isolated for more than 18,000 years. Finally, we employed a set of whole genome sequences from African golden wolves to detect regions under introgression from gray wolves of the Middle East and a number of putative sites under selection in genes related to excretion and homeostasis, fat and sugar storage and metabolism, UV damage repair, response to oxidative stress, cardiac muscle, immune system and epidermal structure, and color. Altogether, this dissertation provides evidence for adaptation of African golden wolves to hot and arid environments and informs about the potential existence of different subpopulations and ecotypes of the species. The results of my work increse understanding of the genetic and molecular ecology of a very poorly studied canid that acts as top predator in one of the most threatened ecosystems in the world, the Sahara desert.