In D. rerio, the frequency of microsatellites was much higher in the telomeric regions of the chromosomes than elsewhere, whereas, in A. mellifera, microsatellite frequency was generally highest in region 8, but with differences between the chromosomes (see Additional file 2, Figure S1 for details).
This association is not quite significant when using the conservative Bonferroni correction for multiple hypotheses (alpha = 0.0026, see Methods section), but trinucleotide microsatellites are much scarcer than mono- or dinucleotide repeats in the yeast genome (Table 1), so statistical power to detect effects on their distribution is lower.
The rate at which microsatellites mutate is much higher than the single-base substitutions [ 45, 46], therefore greater variations are expected in the polymorphic loci than other regions of the genomes.
This value was much lower than those estimated with microsatellite markers (HE = 0.732 0.795) (Chen et al. 2010).
This average marker interval was much lower than that obtained when using only microsatellite markers, i.e. 18.7 cM (data not shown); furthermore, it covers almost all chromosomes.
Third, our sample size was much smaller than the one used for the intra-mammalian comparison due to the small number of microsatellite loci available from the Charadriiformes.
Overall, pairwise FST values for microsatellite data were much lower than mtDNA, with values among the continuous sites ranging from 0.006 to 0.022 and from 0.035 to 0.094 among the fragmented sites.
On the other hand, microsatellites are generally much longer and therefore require better DNA preservation than SNP-based research – a consideration which is most important to LCN aDNA.
Especially, we focused on the 154,677 tetranucleotide microsatellites because they were much more accurate and reliable than di- and tri-nucleotide microsatellites.
Fortunately, the availability of the giant panda complete genome sequences [ 27] provided the opportunity to carry out genome-wide scans for all types of microsatellites markers, which is much cheaper, more efficient and more successful than the previous methods.
Note that inter-genic microsatellites are thought to be much rarer in avian genomes than mammalian genomes [ 44] but there is little indication that a similar pattern holds for EST-SSRs.
