Identifying the minimum number of microsatellite loci needed to assess population genetic structure: A case study in fly culturing

Abstract

Small, isolated populations are constantly threatened by loss of genetic diversity due to drift. Such situations are found, for instance, in laboratory culturing. In guarding against diversity loss, monitoring of potential changes in population structure is paramount; this monitoring is most often achieved using microsatellite markers, which can be costly in terms of time and money when many loci are scored in large numbers of individuals. Here, we present a case study reducing the number of microsatellites to the minimum necessary to correctly detect the population structure of two Drosophila nigrosparsa populations. The number of loci was gradually reduced from 11 to 1, using the Allelic Richness (AR) and Private Allelic Richness (PAR) as criteria for locus removal. The effect of each reduction step was evaluated by the number of genetic clusters detectable from the data and by the allocation of individuals to the clusters; in the latter, excluding ambiguous individuals was tested to reduce the rate of incorrect assignments. We demonstrate that more than 95% of the individuals can still be correctly assigned when using eight loci and that the major population structure is still visible when using two highly polymorphic loci. The differences between sorting the loci by AR and PAR were negligible. The method presented here will most efficiently reduce genotyping costs when small sets of loci ("core sets") for long-time use in large-scale population screenings are compiled.

Keywords: Drosophila nigrosparsa; genetic drift; genetic monitoring; loss of genetic variation; microsatellite markers; population genetics; population structure.

Figure 1.

Allelic and Private Allelic Richness of populations Kaserstattalm (K) and Pfitscherjoch (P) in Generation 0 and Generation 5. Pairwise comparisons by two-sided t-tests are indicated by squared brackets. Significant differences (α = 0.05) are indicated by an asterisk.

Figure 2.

STRUCTURE results of the populations Kaserstattalm (K) and Pfitscherjoch (P) in Generation 0 and Generation 5. K = 2 was the most probable number of clusters. Loss of different alleles due to genetic drift during five generations laboratory rearing lead to increasing population differentiation.

Figure 3.

STRUCTURE results after sequential removal of loci, sorted according to Allelic (AR) and Private Allelic Richness (PAR). Plots in which the estimate for the best K deviated from 2 are printed in grey. While the separation quality gradually deteriorated, the major population structure was still visible when only the two loci with highest AR or PAR are used.

Figure 4.

Based on the STRUCTURE results, individuals genotyped at one to ten loci were assigned to two clusters. Individuals with intermediate probabilities to belong to one cluster were excluded using a variable threshold x; x = 0 results in no exclusions, x = 0.5 excludes all individuals. The cluster assignment with 11 loci was used as a benchmark. Each individual could be either correctly assigned (i. e., in the same cluster as with 11 loci; upper row of plots), incorrectly assigned (i.e., in the other cluster than with 11 loci; middle row), or excluded from assignment based on the threshold value (lower row). High thresholds minimize incorrect assignments at the cost of many excluded individuals.