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).