@article{fdi:010088322,
  title = {{D}eceptive combined effects of short allele dominance and stuttering : an example with {I}xodes scapularis, the main vector of {L}yme disease in the {U}.{S}.{A}.},
  author = {{D}e {M}eeûs, {T}hierry and {C}han, {C}.{T}. and {L}udwig, {J}.{M}. and {T}sao, {J}.{I}. and {P}atel, {J}. and {B}hagatwala, {J}. and {B}eati, {L}.},
  editor = {},
  language = {{ENG}},
  abstract = {{N}ull alleles, short allele dominance ({SAD}), and stuttering increase the perceived relative inbreeding of individuals and subpopulations as measured by {W}rights {F}_{IS} and {F}_{ST}. {A}scertainment 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. {W}hen combined, these issues can increase the correlation between polymorphism at concerned loci and, consequently, of linkage disequilibrium ({LD}) between those. {I}n this note, we studied an original microsatellite data set generated by analyzing nine loci in {I}xodes scapularis ticks from the eastern {U}.{S}.{A}. {T}o detect null alleles and {SAD} we used correlation methods and variation measures. {T}o detect stuttering, we evaluated heterozygote deficit between alleles displaying a single repeat difference. {W}e 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). {T}his 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 ({W}rights {F}_{ST}). {T}his suggested a strong {W}ahlund effect and/or selection at several loci. {B}y 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. {E}xcept 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. {S}trong 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).},
  keywords = {{ETATS} {UNIS}},
  booktitle = {},
  journal = {{P}eer {C}ommunity {J}ournal},
  volume = {1},
  numero = {},
  pages = {e40 [16 ]},
  ISSN = {2804-3871},
  year = {2021},
  DOI = {10.24072/pcjournal.34},
  URL = {https://www.documentation.ird.fr/hor/fdi:010088322},
}