The genetic distance between two individuals was calculated as the mean genetic distance over all loci genotyped in both individuals.
The framework integrated map contained 1307 markers (110 SNPs, 588 SSRs, 252 AFLPs, 236 RFLPs, 89 RAPDs, 6 indels, 15 IMAs, and 11 morphological traits) spanning 1150 cM that were distributed across 12 LGs with a mean genetic distance between adjacent loci of 0.88 cM.
Genetic diversity of the loci and mean genetic diversity were calculated from the digitized nine-locus STs using LIAN [ 52] accessed at (http://pubmlst.org).org
The group of exons that were successfully amplified by this method did not differ from "unsuccessful" loci in mean genetic distance (0.154 vs. 0.155, respectively; [see Additional File 2], indicating that PCR success did not heavily bias the inference of genetic distance and substitution rates.
In total, these SSR loci covered 2,631.3 cM with a mean genetic distance of 5.1 cM between adjacent loci (Table S3).
This distance does not differ significantly from our synonymous divergence estimates (p = 0.34), but it is significantly higher than the mean genetic distance at our 66 intergenic loci (p = 0.006).
In contrast, the R genome chromosomes containing 451.7 loci (279.3 unique) and a map length of on average 879.3 cM featured the highest marker density with a mean genetic map distance of 3.1 cM between unique loci (Table 3).
This association is crucial for distinguishing the mean genetic divergence between species (the mean coalescent time between loci) from speciation time (Edwards and Beerli 2000).
The association of evolutionary variation with the distribution of gene trees within proposed phylogenies is crucial for distinguishing the mean genetic divergence between species (the mean coalescent time between loci) from speciation time.
Our results indicate that mean genetic distances vary between data types and also that genetic distances vary among loci.
