A Genome-Wide SNP Analysis of Admixture Between Canada Lynx (Lynx canadensis) and Bobcats (Lynx rufus) in a Canadian Hybrid Zone

Abstract

Interspecific hybridization is an important phenomenon to study for conservation management because it can facilitate introgression or gene flow between species. Although introgression can increase genetic diversity, it also has the potential of introducing deleterious alleles, and thus may pose a risk to stable populations. Hybrid zones between Canada lynxes (Lynx canadensis) and bobcats (Lynx rufus) have been documented where the southern range of lynxes and northern range of bobcats overlap near the US-Canadian border. Previous studies have confirmed that the two species naturally hybridize in the wild and evidence of lynxes introgressed with bobcat genes has been found in a few provinces in central Canada. Canada lynxes are a conservation concern in 14 contiguous states US as well as in the Canadian provinces of New Brunswick and Nova Scotia, where they are listed as threatened or endangered. The lynx range has contracted about 40% from its historical range in North America due to the warming climate and habitat degradation. Therefore, studies on admixture between lynxes and bobcats can better inform our understanding of the relative risk that hybridization may also pose to lynx populations. Here, we aimed to further investigate hybridization between lynxes and bobcats by studying populations inhabiting a hybrid zone in New Brunswick, Canada. We performed ancestry and introgression analyses on genome-wide Single Nucleotide Polymorphisms (SNPs) obtained by restriction-site associated DNA sequencing (RADseq) to determine whether genetic admixture has occurred in this easternmost part of the hybrid zone. We also assessed measures of population structure and genetic diversity. Although we expected to find admixture signals due to the potential climate-driven expansion of the hybrid zone, we found no compelling evidence of admixed genomes. Further, we discovered evidence of panmixia in lynxes and population substructure in bobcats. Lynxes also had significantly lower heterozygosity estimates and higher inbreeding coefficients than bobcats. Our findings therefore support the theory that hybridization is relatively rare and may not pose a major risk to either species and highlight the importance of protecting and ensuring the connectivity of lynx habitats.