| Summary: | Additional file 7. Results from parameter optimization for de novo assembly and genotyping. Eight parameter optimization series were conducted following Rochette & Catchen (2017) [45] to identify optimal parameters to genotype reduced representation sequencing (RRS) data with Stacks v2.4 (Rochette et al. 2019) [21]; one test series for each species/species complex. The Stacks parameter m was kept constant (m = 3), while parameters M and n were varied together from 1 to 9. Subsequently, only loci present in 80% of the samples were retained and for each M = n parameter the number of loci and polymorphic loci was plotted, as well as the proportion of these loci containing 0 to 10 or > 10 SNPs. In ostracods, the library contained DNA from a species-complex, resulting in very few shared loci across 80% of the samples. Therefore, in this case results based on loci shared by 50% of samples are shown. Optimal M = n values were decided in all cases with this information (and reported in Table 5). Note, however, that it is impossible to make absolute calls regarding the ideal value.
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