A simple procedure to detect, test for the presence of stuttering, and cure stuttered data with spreadsheet programs

Abstract

Microsatellites are powerful markers for empirical population genetics, but may be affected by amplification problems like stuttering that produces heterozygote deficits between alleles with one repeat difference. In this paper, we present a simple procedure that aims at detecting stuttering for each locus overall subsamples and only requires the use of a spreadsheet interactive application on any operating system. We compare the performances of this procedure with the one of MicroChecker on simulations of dioecious pangamic populations, monoecious selfing populations and clonal populations with or without stuttering, and on real data of vectors and parasites. We also propose a cure for loci affected and compare the results with those expected without stuttering. In sexual populations (dioecious or selfers), the new procedure appeared more than three times more efficient than MicroChecker. Cure was able to restore Wright's FIS of stuttered data to the expected value, and particularly so in selfing simulations. In clones, lack of segregation artificially increased false stuttering detection, and only highly significant stuttering tests and loci strongly deviating from others, could be usefully cured, in which case FIS estimate could be much improved. In doubt, and whenever possible, removal of affected and not curable loci may help to shift population genetics parameter estimates towards more reliable values.

Development and characterization of microsatellite markers for population genetics of the cocoa pod borer Conopomorpha cramerella (Snellen) (Lepidoptera: Gracillaridae)

“…Given that some loci display negative values, as expected in dioecious species 35,54,55 , and other loci heterozygote de cits, locus speci c causes, unlike a Wahlund effect, probably better explain our data. This was con rmed by the substantially variable and highly signi cant F ST = 0.043 in 95% CI = [0.027, 0.06], with several loci displaying very small or very high values that ranged outside the 95% CI: loci Cpb14, Cpb55, Cpb62, Cpb84, Cpb135, Cpb139 and Cpb190 (Fig.…”

“…In case of signi cant heterozygote de cits, we used the approaches described in several papers [32][33][34][35] . For null alleles, the ratio of standard errors of F IS over F ST (r FIS/FST ) was computed, a value above 2 being a signature of probable null alleles.…”

“…Expected frequencies of null alleles followed the expectation-maximization step (EM) algorithm 36 with FreeNA and were compared to observed ones. Stuttering signatures were checked with the recently developed methods of De Meeûs and Noûs 35 and corrected by pooling alleles with one to two base differences, following rules de ned in 33 . The presence of SAD was checked using a one-sided (negative correlation) Spearman's rank correlation test between F IT and allele size 34 .…”

Development of microsatellite markers for Afrotropical Ornithodoros ticks

“…Several loci presented point mutations outside of the repeated dinucleotide or trinucleotide motifs, resulting in alleles with 1 nucleotide difference (in ms-48, ms-59, ms-73, ms-76, ms-81, ms-82, ms-90, ms-96, and ms-117). Such point mutations can increase the risk of stuttering [32], and forbid the calculation of evolutive distance between alleles according to the stepwise mutation model (SMM) which is based on the idea that microsatellite evolution happens by progressively adding or removing single repeat units [33]. The 19 selected markers were tested for linkage disequilibrium.…”

Population genetics ofGlossina palpalis gambiensisin the sleeping sickness focus of Boffa (Guinea) before and after eight years of vector control: no effect of control despite a significant decrease of human exposure to the disease

“…Stuttering detection and correction followed the procedure described elsewhere (De Meeûs et al, 2021; De Meeûs & Noûs, 2022) over all subsamples and for each locus, using the associated template “TestStutterDioecious-n1000N100-1-10%Stuttering.xlsx” available at https://zenodo.org/record/7029324, exact binomial tests and adjustment of p - values with Benjamini and Hochberg (BH) procedure with R (command “p.adjust“).…”