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When compared with Bp chromosome II, the additional rrn locus could be the result of intrachromosomal duplication of the existing locus or due to an exchange between the two chromosomes.
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These new loci have potential use in other Dicamptodon species and combined with existing loci, will enable range-wide genetic analyses using high-resolution microsatellite data.
We suggest these new loci will complement existing loci [2], [4] for conducting analyses of population genetic structure, and the effects of habitat degradation on core and threatened peripheral populations of this stream amphibian.
Note that calibration and normalization functions may be estimated on a subset of existing loci.
Second, cstacks was used to build a catalog of all existing loci and alleles after merging loci from multiple individuals.
Genes that did not match existing loci in these cuffcompare analyses are numbered sequentially as RU1 RU572 (Additional file 2).
Since gene conversion does not actually mutate DNA but simply shuffles motifs between existing loci, we can see that this phenomenon has no intrinsic effect on increasing or decreasing heterogeneity of individual residues.
For comparison, we calculated the size range and average length of previously reported transcripts for the 13,162 existing loci, which was 671 4636 bp with an average of 2388 bp.
We describe seven new polymorphic loci specific for D. tenebrosus, complementing existing microsatellite loci developed for D. tenebrosus [2], [3] and those previously cross-amplified from D. copei [4].
If less than 80% identity at nucleotide level was found to any of the reference capsule loci then we considered there to be no match to existing capsule loci.
The new method performs well compared with existing multi-locus mapping methods.
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