Genetic variation of wildlife in a human-dominated landscape : Genome-wide SNP analysis of wild boar (Sus scrofa) and red deer (Cervus elaphus) from the European continent

Jong, Joost F. de


In human-dominated landscapes, the genetic variation of present-day wildlife populations is shaped by historical and contemporary processes of natural and anthropogenic origin. Relatively recent, human-induced local extinction, fragmentation, hybridization and translocation of wildlife has impacted the intrinsic genetic variation such as formed by the spatiotemporal geographic dynamics of the physical landscape. In this thesis, I assessed the anthropogenic impact on the genetic variation of wildlife of human-dominated landscapes, relative to the variation caused by physical geography. I studied genome-wide Single Nucleotide Polymorphisms (SNP) of wild boar (Sus scrofa) and red deer (Cervus elaphus) from the European continent, with emphasis on Northwestern Europe. To capture the diversity of demographic histories of wildlife in human-dominated landscapes, the study populations covered a large spatial extent, and had contrasting histories and management regimes. Using genotypes of >20K SNPs, I was able to accurately examine genetic structure, and to estimate inbreeding and relatedness using genomic segments that are identical-by-descent (IBD). I showed that the spatial genetic structure of wild boar of Europe is a continental-wide cline that extends from Southwestern Europe via Northeastern Europe to Eastern Europe. Based on a simulation approach, I argue that this structure is caused by the topography of the European continent, rather than historical glaciations or recent anthropogenic impact. At regional and local scale, however, anthropogenic impact – in the form of local eradication, fragmentation, pig hybridization, and translocation – has caused the spatial genetic structure of wild boar and red deer to become a mosaic of high and low variation. I found that the red deer and wild boar populations with the lowest variation are isolated, relic populations. In these populations, long and frequent IBD segments evidenced that animals are as inbred and related as 2nd and 3rd order relatives. My findings on wild boar and red deer populations indicate that the genetic variation of wildlife populations in human-dominated landscapes is the product of specific, local demographic history. An effective genetic management requires regular monitoring with next generation sequencing, most critically to alleviate potential high realized inbreeding and relatedness.