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

• Published in: Peer community journal Vol. 1
• Main Authors: De Meeûs, Thierry, Chan, Cynthia T., Ludwig, John M., Tsao, Jean I., Patel, Jaymin, Bhagatwala, Jigar, Beati, Lorenza
• Format: Journal Article
• Language: English
• Published: Peer Community In 29.11.2021
• Subjects: Emerging diseases; Human health and pathology; Life Sciences; ETATS UNIS
• ISSN: 2804-3871; 2804-3871
• DOI: 10.24072/pcjournal.34

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