Signatures of selection in the red fox (Vulpes vulpes) in Europe using genotype-by-sequencing

Roberts, L

Abstract

Evolution acts on variations in individuals via the mechanisms of natural selection, genetic drift, and gene flow. Using genomic sequencing methods such as genotype-by-sequencing (GBS) to detect single nucleotide polymorphisms (SNPs) can lead to a better understanding of a species evolutionary history and identify patterns of local adaptations. Abiotic and biotic factors can cause selective pressures that may be seen in the red fox’s genome. Additionally, debate continues to whether red foxes remained in isolated refugia or existed as a continuous population in southern Europe. Regardless, previous studies highlight the importance of refugia of the Last Glacial Maximum period in shaping genetic variation and differentiation in many taxa. This study aims to provide additional evidence to this dispute while also uncovering signatures of selection in genes related to the new conditions faced as red foxes pushed northwards in a warming climate. To test these predictions, recently generated GBS data from over 500 red foxes (Vulpes vulpes) in Eurasia was utilized. First, I formed a population criterion based on the sample’s location and the fox’s ecological habits. This resulted in 436 samples in which I identified 30,708 SNPs after bioinformatic filtering. I then ascertained population structure using principal component analysis (PCA). This provided consistencies with red foxes living outside of proposed refugia’s during the Pleistocene. To detect candidate genes for diversifying selection I used outlier loci that overlapped from both PCAdapt and BayeScan methods. This revealed candidate genes relating to immunity, vision, and other phenotypic traits. A particularly interesting result found a significant allele frequency change in just four Nordic fox populations in the innate immune MUC19 gene which may have responded to a parasitic selective force. Further investigation into these findings may elucidate clearer, more detailed adaptive processes in the wild red fox within Eurasia.

Citation

Roberts, L. Signatures of selection in the red fox (Vulpes vulpes) in Europe using genotype-by-sequencing. (Dissertation). University of Salford

• Thesis Type: Dissertation
• Deposit Date: Nov 12, 2019
• Publicly Available Date: Nov 12, 2019
• Additional Information: Additional Information : There are excel links in the Appendix