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Therefore we were hesitant to use these loci for population genetic analysis.
Although these markers proved to be useful loci for population studies in P. alba Griseb.
To use EST-SSR loci for population genetics, it is thus essential that Mendelian segregation be verified in controlled crosses.
Second, we wanted to test the utility of randomly identified SNP loci for population genetic analysis compared with STR loci.
De novo assemblies were used to characterize the repeat structure of the genome and to develop nuclear markers consisting of low-copy nuclear loci for phylogenetics and microsatellite loci for population genetics.
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Due to low genetic diversity, this is the maximum number of marker loci for population-specific linkage maps, although >6000 SSR markers have been developed for mapping.
We detected deviation from HWE (P < 0.05) at some of the microsatellite loci as a result of heterozygote excess, e.g., three (Scin1, 4, 8), one (Scin7), two (Scin1, 2), and two (Scin7, 9) loci for populations MZ, GD, ZY, and QL, respectively (Table 2); five (Scin1, 2, 3, 8, 9), two (Scin5, 7), and nine (Scin1, 2, 4, 5, 7, 8, 10, 11, 12) loci for populations RK, WS, and TS, respectively (Table 3).
For each value, we first generate allele frequencies, Φ(1) and Φ(2), at all 343 loci for populations 1 and 2. Next, we draw genotypes separately for each population according to the genotype frequencies in Equation 5, with the same value of the inbreeding coefficient ρ.
Linkage disequilibrium among all pairs of loci for each population and all populations in the Western Pacific and the Indian Ocean was also tested by Genepop'007 [ 47].
Microsatellites were not used, as loci usable for population genetic studies are generally few and difficult to identify in Lepidoptera [ 39, 40].
Additionally, RS, HO and gene diversity are averaged over all loci (for each population) and FIS is averaged over all populations (for each locus).
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