Testing for recombination in a short nuclear DNA sequence of the European meadow grasshopper, Chorthippus parallelus

Single-copy nuclear DNA sequences have high potential as a source of genetic markers for population analyses. However, the difficulties that arise when haplotypes that are the product of recombinational rearrangements are present require additional consideration. Two statistical methods for identifying potential recombinants by detecting anomalies in the distribution of variable sites along sequences were used to screen sequences from a single-copy nuclear DNA fragment, cpnl-1, of the European meadow grasshopper (Chorthippus parallelus). Five of the 71 haplotypes in the cpnl-1 data set showed nonrandom distribution of polymorphic sites using both methods. The second method pinpointed an additional four haplotypes. Estimates of the rate of recombination in the entire data set were obtained using standard methods. It is concluded that cpnl-1 haplotypes have been involved in recombination or gene conversion events at a rate more than twice the mutation rate. This confirms that recombination and gene conversion are significant factors in the generation of haplotype variation in nuclear gene sequences. The cpnl-1 haplotypes identified by the tests were present only in populations that have had recent contact; the Balkan and Turkish refugial populations and their post-glacial colonies to the north. This is discussed in relation to the phylogenetic inferences drawn from the same data in a previous report.