Section: Evolutionary Biology
Topic: Evolution, Genetics/Genomics

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.

10.24072/pcjournal.34 - Peer Community Journal, Volume 1 (2021), article no. e40.

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Null alleles, short allele dominance (SAD), and stuttering increase the perceived relative inbreeding of individuals and subpopulations as measured by Wrights F_IS and F_ST. Ascertainment bias, due to such amplifying problems are usually caused by inaccurate primer design (if developed from a different species or a distant population), poor DNA quality, low DNA concentration, or a combination of some or all these sources of inaccuracy. When combined, these issues can increase the correlation between polymorphism at concerned loci and, consequently, of linkage disequilibrium (LD) between those. In this note, we studied an original microsatellite data set generated by analyzing nine loci in Ixodes scapularis ticks from the eastern U.S.A. To detect null alleles and SAD we used correlation methods and variation measures. To detect stuttering, we evaluated heterozygote deficit between alleles displaying a single repeat difference. We demonstrated that an important proportion of loci affected by amplification problems (one with null alleles, two with SAD and three with stuttering) lead to highly significant heterozygote deficits (F_IS=0.1, p-value<0.0001). This occurred together with an important proportion (22%) of pairs of loci in significant LD, two of which were still significant after a false discovery rate (FDR) correction, and some variation in the measurement of population subdivision across loci (Wrights F_ST). This suggested a strong Wahlund effect and/or selection at several loci. By finding small peaks corresponding to previously disregarded larger alleles in some homozygous profiles for loci with SAD and by pooling alleles close in size for loci with stuttering, we generated an amended dataset. Except for one locus with null alleles and another still displaying a modest SAD, the analyses of the corrected dataset revealed a significant excess of heterozygotes (F_IS=-0.07 as expected in dioecious and strongly subdivided populations, with a more reasonable proportion (19%) of pairs of loci characterized by significant LD, none of which stayed significant after the FDR procedure. Strong subdivision was also confirmed by the standardized F_ST corrected for null alleles (F_ST=0.19) and small effective subpopulation sizes (N_e=7).

Published online:
DOI: 10.24072/pcjournal.34
Type: Research article
De Meeûs, Thierry 1; Chan, Cynthia T. 2, 3, 4; Ludwig, John M. 5, 4; Tsao, Jean I. 6; Patel, Jaymin 7, 4; Bhagatwala, Jigar 8, 4; Beati, Lorenza 4

1 Intertryp, IRD, Cirad, Univ Montpellier, Montpellier, France
2 Boehringer Ingelheim, Athens, GA, USA
3 College of Agricultural & Environmental Sciences, University of Georgia, Athens, GA, USA
4 The U.S. National Tick Collection, Institute for Coastal Plain Science, Georgia Southern University, Statesboro, GA, USA
5 Institute of Bioinformatics, University of Georgia, Athens, GA, USA
6 Department of Fisheries and Wildlife, Department of Large Animal Clinical Sciences, Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing, MI, USA
7 Division of Hospital Medicine, College of Medicine, University of Florida, Gainesville, FL, USA
8 Medical College of Georgia, Augusta University, Augusta, GA, USA
License: CC-BY 4.0
Copyrights: The authors retain unrestricted copyrights and publishing rights
     author = {De Mee\^us, Thierry and Chan, Cynthia T. and Ludwig, John M. and Tsao, Jean I. and Patel, Jaymin and Bhagatwala, Jigar and Beati, Lorenza},
     title = {Deceptive combined effects of short allele dominance and stuttering: an example with {\protect\emph{Ixodes} scapularis}, the main vector of {Lyme} disease in the {U.S.A.}},
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De Meeûs, Thierry; Chan, Cynthia T.; Ludwig, John M.; Tsao, Jean I.; Patel, Jaymin; Bhagatwala, Jigar; Beati, Lorenza. 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.. Peer Community Journal, Volume 1 (2021), article  no. e40. doi : 10.24072/pcjournal.34.

PCI peer reviews and recommendation, and links to data, scripts, code and supplementary information: 10.24072/pci.evolbiol.100081

Conflict of interest of the recommender and peer reviewers:
The recommender in charge of the evaluation of the article and the reviewers declared that they have no conflict of interest (as defined in the code of conduct of PCI) with the authors or with the content of the article.

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