Detecting Wahlund effects together with amplification problems: Cryptic species, null alleles and short allele dominance in Glossina pallidipes populations from Tanzania

Abstract

Population genetics is a convenient tool to study the population biology of non‐model and hard to sample species. This is particularly true for parasites and vectors. Heterozygote deficits and/or linkage disequilibrium often occur in such studies and detecting the origin of those (Wahlund effect, reproductive system or amplification problems) is uneasy. We used new tools (correlation between the number of times a locus is found in significant linkage disequilibrium and its genetic diversity, correlations between Wright's FIS and FST, FIS and number of missing data, FIT and allele size and standard errors comparisons) for the first time on a real data set of tsetse flies, a vector of dangerous diseases to humans and domestic animals in sub‐Saharan Africa. With these new tools, and cleaning data from null allele, temporal heterogeneity and short allele dominance effects, we unveiled the coexistence of two highly divergent cryptic clades in the same sites. These results are in line with other studies suggesting that the biodiversity of many taxa still largely remain undescribed, in particular pathogenic agents and their vectors. Our results also advocate that including individuals from different cohorts tends to bias subdivision measures and that keeping loci with short allele dominance and/or too frequent missing data seriously jeopardize parameter's estimations. Finally, separated analyses of the two clades suggest very small tsetse densities and relatively large dispersal.

Parasite‐mediated selection in a natural metapopulation of Daphnia magna

“…We used the software micro‐checker v. 2.2.3 (Van Oosterhout, Hutchinson, Wills, & Shipley, ) to assess the microsatellite data for the presence of null‐alleles, large allele dropout, and stutter peaks, as well as for typographic errors. We additionally conducted further assessment for the presence of null alleles following the recommendations of Manangwa et al (; see Appendix for details). The fstat v. 2.9.3.2 program (Goudet, ) was used to test for deviations from the Hardy–Weinberg Equilibrium (HWE) within populations and to estimate F ST between infected and uninfected populations, F ST and F IS over all loci and subpopulations and Nei's estimator of within‐population gene diversity ( H s; Nei, ).…”

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

“…Nevertheless, MicroDrop did not entirely cure the data from SAD and stuttering, which does not advocate for the efficacy of the algorithm used in this software. As far as our I. scapularis data set is concerned, the cures proposed provided satisfactory results and additional useful tools to those already proposed in recently published papers on the detection and identification of causes of heterozygote deficits (Waples, 2015;De Meeûs, 2018b;Waples, 2018;Manangwa et al, 2019).…”

“…This test is more powerful than with F IS as was proposed earlier (Wattier et al, 1998;De Meeûs et al, 2004). If previous tests are not significant and if StrdErrFIS > StrdErrFST, then a Wahlund effect better explains the data (De Meeûs, 2018a), this is especially true in instances of significant LD (Manangwa et al, 2019). In these cases, a positive correlation between the number of times a locus is found in significant LD (NLD) and its total genetic diversity as measured by Nei's H T (Nei and Chesser, 1983) (Spearman's correlation above 0.1) suggests an admixture of individuals from several subpopulations of the same species but with an important degree of genetic differentiation between admixed subpopulations (i.e.…”

“…Stuttering was admitted when two out of three tests supported it. The occurrence of SAD was also checked with an unilateral (ρ<0) Spearman's rank correlation test between allele size and F IT as proposed by (Manangwa et al, 2019). This test is more powerful than with F IS as was proposed earlier (Wattier et al, 1998;De Meeûs et al, 2004).…”

“…These problems, like all others associated with amplification, are locus specific (Van Oosterhout et al, 2004;De Meeûs et al, 2007;De Meeûs, 2018a) and thus lead to locus specific variation (namely, an increase) of F IS . A less well known, though well documented (Chapuis and Estoup, 2007;Séré et al, 2017b;Manangwa et al, 2019) effect of such amplification problems consists of an increase of Wright's F ST (Wright, 1965) that is commonly used to measure the degree of genetic differentiation between subpopulations.…”