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.
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.
There was a strong concordance between the MLST data and the existing multi-locus enzyme electrophoresis and ribotyping data.
Six new sequence markers (loci 3968, 3972, 4081, 6512, 5437, and 6549) were developed in this study (Tables 1 and 2), which were utilized in combination with the existing 3-locus system [ 21, 24, 45].
These included 13 of the 19 loci previously used in the existing genetic database and two loci newly incorporated in order to improve the power of analyses (Muniz and Widdig, unpublished data).
