Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

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.

View ORCID ProfileThierry De Meeûs, Cynthia T. Chan, John M. Ludwig, Jean I. Tsao, Jaymin Patel, Jigar Bhagatwala, Lorenza Beati
doi: https://doi.org/10.1101/622373
Thierry De Meeûs
1Intertryp, IRD, Cirad, Univ Montpellier, Montpellier, France
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Thierry De Meeûs
  • For correspondence: thierry.demeeus@ird.fr
Cynthia T. Chan
2The U.S. National Tick Collection, Institute for Coastal Plain Science, Georgia Southern University, Statesboro, GA, USA
3College of Agricultural & Environmental Sciences, University of Georgia, Athens, GA, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
John M. Ludwig
2The U.S. National Tick Collection, Institute for Coastal Plain Science, Georgia Southern University, Statesboro, GA, USA
4Institute of Bioinformatics, University of Georgia, Athens, GA, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Jean I. Tsao
5Department of Fisheries and Wildlife, Department of Large Animal Clinical Sciences, Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing, MI, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Jaymin Patel
2The U.S. National Tick Collection, Institute for Coastal Plain Science, Georgia Southern University, Statesboro, GA, USA
6Division of Hospital Medicine, College of Medicine, University of Florida, Gainesville, FL, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Jigar Bhagatwala
2The U.S. National Tick Collection, Institute for Coastal Plain Science, Georgia Southern University, Statesboro, GA, USA
7Medical College of Georgia, Augusta University, Augusta, GA, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Lorenza Beati
2The U.S. National Tick Collection, Institute for Coastal Plain Science, Georgia Southern University, Statesboro, GA, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Data/Code
  • Preview PDF
Loading

ABSTRACT

Null alleles, short allele dominance (SAD), and stuttering increase the perceived relative inbreeding of individuals and subpopulations as measured by Wright’s FIS and FST. 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 (FIS=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 (Wright’s FST). 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 (FIS=-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 FST’ corrected for null alleles (FST’=0.19) and small effective subpopulation sizes (Ne=7).

Footnotes

  • http://www.t-de-meeus.fr/Data/DeMeeus-et-al-SAD&StutteringI-scapularisUSA-PCI-EvolBiol-TableS1.xlsx

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
Back to top
PreviousNext
Posted September 09, 2019.
Download PDF
Data/Code
Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
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.
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
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.
Thierry De Meeûs, Cynthia T. Chan, John M. Ludwig, Jean I. Tsao, Jaymin Patel, Jigar Bhagatwala, Lorenza Beati
bioRxiv 622373; doi: https://doi.org/10.1101/622373
Digg logo Reddit logo Twitter logo CiteULike logo Facebook logo Google logo Mendeley logo
Citation Tools
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.
Thierry De Meeûs, Cynthia T. Chan, John M. Ludwig, Jean I. Tsao, Jaymin Patel, Jigar Bhagatwala, Lorenza Beati
bioRxiv 622373; doi: https://doi.org/10.1101/622373

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Evolutionary Biology
Subject Areas
All Articles
  • Animal Behavior and Cognition (2533)
  • Biochemistry (4977)
  • Bioengineering (3486)
  • Bioinformatics (15232)
  • Biophysics (6910)
  • Cancer Biology (5395)
  • Cell Biology (7753)
  • Clinical Trials (138)
  • Developmental Biology (4539)
  • Ecology (7159)
  • Epidemiology (2059)
  • Evolutionary Biology (10234)
  • Genetics (7517)
  • Genomics (9794)
  • Immunology (4863)
  • Microbiology (13234)
  • Molecular Biology (5144)
  • Neuroscience (29465)
  • Paleontology (203)
  • Pathology (838)
  • Pharmacology and Toxicology (1466)
  • Physiology (2142)
  • Plant Biology (4756)
  • Scientific Communication and Education (1013)
  • Synthetic Biology (1338)
  • Systems Biology (4014)
  • Zoology (768)