Restriction fragment length polymorphisms (RFLPs) of mitochondrial (mt) DNA were used for investigating genetic differentiation in chamois (genus Rupicapra). Digestion of the mtDNAs of 58 individuals from 6 populations with a battery of 16 six-base cutting (restriction endonucleases yielded a total of 67 restriction sites. Based on the presence and absence of these restriction sites a total of 8 haplotypes could be defined. Six of them served for assessing genetic diversity within and among 4 local populations of R. rupicapra rupicapra. Estimates of nucleotide divergence among those haplotypes ranged from 0.05% to 0.25%. One chamois from the High Tatra (subspecies R. r. tatrica) was examined and showed the standard haplotype found in R. r. rupicapra. MtDNA in chamois from Catalunya, belonging to R. pyrenaica pyrenaica, was polymorphic for two haplotypes not found in any population of R. rupicapra. Mean nucleotide divergence among haplotypes found in R. rupicapra and R. pyrenaica was 0.56% (SD = 0.16%). Based on this value, an estimated divergence time of about 280 000 years suggests that the mtDNA lineages of R. rupicapra and R. pyrenaica separated prior to the Riss glacial in the later Pleistocene.
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