Population structure and local adaptation in red foxes across an environmental gradient

Moodley, YoshanProst, StefanSekhwela, Blessing2025-08-202025-08-202025-05-16Sekhwela, B. 2025. Population structure and local adaptation in red foxes across an environmental gradient. . .https://univendspace.univen.ac.za/handle/11602/2881M. Sc. (Zoology)Department of Biological SciencesThe red fox (Vulpes vulpes) is one of the most successful species across the globe, found on five continents and in diverse habitats across various climatic and environmental conditions. Increasing Arctic warming has allowed the red fox to expand and occupy the Arctic environment. This new environment presents unique selective pressures, characterised by long, dark winters and short, continuous light summers. Arctic animals must endure extended periods of food scarcity, extremely cold conditions, and very short periods of resource abundance. Although red foxes do not exhibit physical adaptations specialized for surviving in the Arctic conditions, they continue to thrive despite these challenges. To investigate whether there are genetic adaptations in the red fox populations in the Arctic region, I used whole genome sequencing to detect signatures of positive selection across the whole genome. To achieve this, I used population branch statistics (PBS). PBS is a three-population test that identifies loci under selection by comparing the pairwise FST between the focal group (here the Arctic population) and a sister population (here Central Europe), controlling for ancestral polymorphisms using an outgroup population (here Israel). The regions found to have unusually high Fst in the focal population are potential candidates for selection. Because only low coverage genomes were available for this project, the test was conducted at two different depths (-setMinDepthInd 1 and -setMinDepthInd 3) to test whether the results were reliable with more or fewer SNPs. The two tests combined identified 123 candidate genes. Among them were genes involved in lipid metabolism, fertility, olfaction, circadian rhythm, response to hypoxia, thermogenesis and some were disease-related. I found that the Arctic population of red foxes exhibited a high genetic diversity and there was clear genetic structuring among populations. However, significant genetic contact remained between the Arctic and Central European populations. Gene-flow analysis also indicated potential signatures of ancient gene-flow between Central Europe and Israel. Despite the relatively low coverage of the available genomes, this study has identified several genes that could play a role in cold adaptation in red foxes. These genes and some of their orthologs, such as those involved in fatty acid metabolism, thermogenesis, circadian rhythm and response to hypoxia, have been identified in other arctic species like polar bears, reindeer, muskox and marmots as adaptive.1 online resource (83 leaves): color illustrations, color mapsenUniversity of VendaCold adaptationUCTDPopulation branch statisticGenetic diversityPopulation structurePositive selectionVulpes VulpesWhole genome sequencingPopulation structure and local adaptation in red foxes across an environmental gradientDissertationSekhwela B. Population structure and local adaptation in red foxes across an environmental gradient. []. , 2025 [cited yyyy month dd]. Available from:Sekhwela, B. (2025). <i>Population structure and local adaptation in red foxes across an environmental gradient</i>. (). . Retrieved fromSekhwela, Blessing. <i>"Population structure and local adaptation in red foxes across an environmental gradient."</i> ., , 2025.TY - Dissertation AU - Sekhwela, Blessing AB - The red fox (Vulpes vulpes) is one of the most successful species across the globe, found on five continents and in diverse habitats across various climatic and environmental conditions. Increasing Arctic warming has allowed the red fox to expand and occupy the Arctic environment. This new environment presents unique selective pressures, characterised by long, dark winters and short, continuous light summers. Arctic animals must endure extended periods of food scarcity, extremely cold conditions, and very short periods of resource abundance. Although red foxes do not exhibit physical adaptations specialized for surviving in the Arctic conditions, they continue to thrive despite these challenges. To investigate whether there are genetic adaptations in the red fox populations in the Arctic region, I used whole genome sequencing to detect signatures of positive selection across the whole genome. To achieve this, I used population branch statistics (PBS). PBS is a three-population test that identifies loci under selection by comparing the pairwise FST between the focal group (here the Arctic population) and a sister population (here Central Europe), controlling for ancestral polymorphisms using an outgroup population (here Israel). The regions found to have unusually high Fst in the focal population are potential candidates for selection. Because only low coverage genomes were available for this project, the test was conducted at two different depths (-setMinDepthInd 1 and -setMinDepthInd 3) to test whether the results were reliable with more or fewer SNPs. The two tests combined identified 123 candidate genes. Among them were genes involved in lipid metabolism, fertility, olfaction, circadian rhythm, response to hypoxia, thermogenesis and some were disease-related. I found that the Arctic population of red foxes exhibited a high genetic diversity and there was clear genetic structuring among populations. However, significant genetic contact remained between the Arctic and Central European populations. Gene-flow analysis also indicated potential signatures of ancient gene-flow between Central Europe and Israel. Despite the relatively low coverage of the available genomes, this study has identified several genes that could play a role in cold adaptation in red foxes. These genes and some of their orthologs, such as those involved in fatty acid metabolism, thermogenesis, circadian rhythm and response to hypoxia, have been identified in other arctic species like polar bears, reindeer, muskox and marmots as adaptive. DA - 2025-05-16 DB - ResearchSpace DP - Univen KW - Cold adaptation KW - Population branch statistic KW - Genetic diversity KW - Population structure KW - Positive selection KW - Vulpes Vulpes KW - Whole genome sequencing LK - https://univendspace.univen.ac.za PY - 2025 T1 - Population structure and local adaptation in red foxes across an environmental gradient TI - Population structure and local adaptation in red foxes across an environmental gradient UR - ER -