However, alleles at commonly used nuclear markers such as autosomal microsatellites are often shared between closely related taxa see [23], [24], so inferences are to a large degree based on allele frequency differences.
For example, microsatellites are often more variable, requiring amplification of fewer loci to achieve a high level of insight, whereas any given SNP can only have a maximum of four states.
Given their source, gene-based microsatellites are often called genic microsatellites or alternatively cDNA or EST-derived simple sequence repeats.
Rationale for choosing the small cutoff value was that, the microsatellites are often disrupted by single base substitution.
The minisatellites are also called 'Variable Number Tandem Repeats' or VNTRs and the microsatellites are often referred to as 'Short Tandem Repeats' or STRs.
Genic microsatellites are often located in introns, and un-translated regions of sequenced cDNAs but can also be located in exons and in translated regions of ORFs [ 2].
Because estimates of FST depend on how much variation there is in a population, estimates based on microsatellites are often biased downward due to the large number of alleles per locus and high amount of heterozygosity (Hedrick 2005a).
Although proving that such structures form in vivo is difficult, microsatellites are often sites of chromosome fragility, a phenomenon typically attributed to secondary structure formation and replication fork collapse (reviewed in Freudenreich 2007; Fungtammasan et al. 2012).
Fortunately, chloroplast microsatellites are often quite short in length, and NGS methods are available that use reads long enough to capture repeat tracts as well as flanking sequences in their entirety.
At present, markers such as microsatellites are often used for defining movement patterns among populations of invasive pest mammals (e.g. Hampton et al. 2004; Abdelkrim et al. 2005; Berry et al. 2012; Adams et al. 2014).
