Deceptive combined effects of short allele dominance and stuttering: an example with Ixodes scapularis, the main vector of Lyme disease in the U.S.A.

Abstract

Deceptive combined effects of short allele dominance and stuttering: an example with Ixodes scapularis, the main vector of Lyme disease in the U.S.A.

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

“…We compare the performances of this new procedure with the one implemented in MicroCheker on simulated data without (null hypothesis) or with (alternative hypothesis) stuttering, in dioecious populations of various sizes with random mating, hermaphrodites with selfing or clonal populations. We also checked how the cure of loci with stuttering signature, as proposed in a previous work (De Meeûs et al, 2021), restore the values expected for some parameters. We finally reanalyzed four real data sets on vectors and/or their parasite: the tick Ixodes scapularis in North America (De Meeûs et al, 2021); Glossina palpalis palpalis, vector of African trypnosomiasis in Côte d'Ivoire (Berté, De Meeus et al, 2019); the snail Galba truncatula and the fluke it transmits, Fasciola hepatica in France (Correa, De Meeûs et al, 2017); and Trypanosoma brucei gambiense, the agent of sleeping sickness in Guinea and Côte d'Ivoire (Koffi, De Meeûs et al, 2009).…”

“…Simulations were undertaken with EASYPOP (v. 2.0.1) (Balloux, 2001). We simulated random mating dioecious populations (pangamy), like what probably occurs in the wild for ticks (De Meeûs et al, 2021), Nematocera flies (Prudhomme, De Meeûs et al, 2020), Hemipteran bugs (Gomez-Palacio, Triana et al, 2013), or tsetse flies (Berté et al, 2019). We also simulated selfing monoecious populations, as flukes and water snails (Correa et al, 2017).…”

“…However, researchers began to detect the different problems that can arise, as null alleles, allelic dropout, short allele dominance or stuttering (Wattier, Engel et al, 1998;De Meeûs, Humair et al, 2004;Chapuis & Estoup, 2007;Guichoux, Lagache et al, 2011). The last kind of detection tools and possible cures only arose very recently (Wang, Schroeder et al, 2012;De Meeûs, 2018;Manangwa, De Meeûs et al, 2019;De Meeûs, Chan et al, 2021).…”

“…This generates several PCR products that differ from each other by one repeat and can cause difficulties when discriminating between fake and true homozygotes, such as heterozygous individuals for dinucleotide microsatellite allele sequences with a single repeat difference (De Meeûs et al, 2021). Stuttering produces heterozygote deficits as compared to Castle-Weinberg (CW) expected genotypic proportions (Castle, 1903;Weinberg, 1908), also known as Hardy-Weinberg (HW) expectations (please have a glance at (De Meeûs et al, 2021) for an explanation why we prefer using CW instead of HW). This phenomenon is locus specific and the deviation produced, as measured by wright's FIS (Wright, 1965), proportional to the intensity with which each locus is affected.…”

“…We finally reanalyzed four real data sets on vectors and/or their parasite: the tick Ixodes scapularis in North America (De Meeûs et al, 2021); Glossina palpalis palpalis, vector of African trypnosomiasis in Côte d'Ivoire (Berté, De Meeus et al, 2019); the snail Galba truncatula and the fluke it transmits, Fasciola hepatica in France (Correa, De Meeûs et al, 2017); and Trypanosoma brucei gambiense, the agent of sleeping sickness in Guinea and Côte d'Ivoire (Koffi, De Meeûs et al, 2009). On these datasets, we checked if more loci with stuttering could be diagnosed, cured the loci with suspicion of stuttering, following the technique proposed recently (De Meeûs et al, 2021) to verify if some conclusions could be changed.…”