Inter-specific comparison of the NR1D1 cTNR
We have previously reported a non-overlapping allelic range between Canada lynx and bobcat individuals (excluding introgressed individuals) and signatures of positive selection in Canada lynx using FST outlier-based analysis (Prentice et al. 2017a). Here, across a much larger-scale screening of lynx and bobcat individuals, we identified the same 7 alleles at the NR1D1 locus with the same non-overlapping patternAll identified bobcat samples had genotypes comprising the smaller 3 NR1D1 alleles and all identified Canada lynx samples had genotypes comprising the larger 4NR1D1 alleles with the exception of 10 putatively introgressed individuals (described below). Gradients in allele frequencies were observed in both lynx and bobcat (Fig., 2). In lynx, allele frequencies were largely similar across the range we surveyed, with the exception of the most southern population sampled (New Brunswick lynx and Quebec lynx sampled south of the St. Lawrence River), which showed a substantial increase in the frequency of the smallest allele observed in lynx (Fig., 2B). Insular populations of lynx (Newfoundland and Cape Breton Island) were fixed for the most common lynx allele (Fig., 2B). Of the 3 alleles identified in bobcats, the intermediate allele was found most prevalently across the range we surveyed whereas the smallest and largest allele were observed most prevalently (although not exclusively) in western and eastern bobcat, respectively (Fig., 2B). In comparison, neutral microsatellite markers were found to have largely overlapping allelic ranges across the two sister species; on average, 42.7% of alleles per locus overlapped, across all 14 presumably neutral loci. We note however, that the range of overlap was variable across loci (from 0-83.3%), with 2/14 loci showing no overlap in alleles between lynx and bobcat.
We further identified 10 putative Canada lynx samples with mixed genotypes (i.e., 1 “bobcat” and 1 “lynx” allele; Fig 1B). These samples were all visually identified as Canada lynx, and contained neutral microsatellite profiles and control region mtDNA sequences consistent with Canada lynx. In addition, we evaluated samples from introgressed animals previously identify by Koen et al., (2014). Of the 5 samples they identified as introgressed bobcats, 4 had genotype profiles consistent with bobcats at the NR1D1 locus (i.e., they had 2 “bobcat” alleles), and 1 individual failed to amplify. Of the 2 samples identified by Koen et al., (2014) as introgressed lynx, 1 had a genotype profile consistent with lynx at the NR1D1 locus (2 “lynx” alleles), and the other had a mixed profile (1 “lynx” and 1 “bobcat” allele).