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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.
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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.
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.
Additionally, notion of inverse kinematics singularity (IKS) is defined and existing IKS loci in workspace for the two operational modes are determined.
Although commercial kits now combine the five new STRs with existing core loci, we found the ESS-pentaplex we developed in-house performed better than both MiniFiler (comprising eight miniaturized STRs) and the NGM kit that includes the new STRs in a 15-marker multiplex.
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