Abstract

Allelic dropouts (ADO) are an important
source of genotyping error and because of their negative
impact on non-invasive sampling techniques, have become
the focus of considerable attention. Previous studies have
noted that ADO rates are greater with increasing allele size
and in tetranucleotides. It has also been suggested, but not
tested, that ADO rates may be higher in studies using crossspecies
microsatellites and that mutations may play a role
in ADO rates. Here we examine the relationship between
ADO rates and the relationship between evolutionary distance
since divergence time between species for which the
microsatellite was designed for and species on which it was
used (divergence times), and how this may interact with
median allele size. In addition, as the adenosine (A) and
thymine (T) content of the primer may increase mutation
rates, we also included total % AT content of the primer in
the analyses. Finally, we examined whether other commonly
associated causes of ADO (i.e. repeat motif length,
median allele size and allele number) co-varied. We found
that ADO rates were positively associated to divergence
time and median allele size. Repeat motif length, median
allele size and allele number positively covaried suggesting
a link between mutability and these parameters. Results
from previous studies that did not correct for co-variation
among these parameters may have been confounded. AT
content of the primer was positively associated with ADO
rates. The best linear regression model contained divergence
time, median allele size and total % AT content,
explaining 21% of the variation in ADO rates. The available
evidence suggests that mutations partly cause ADO
and that studies using cross-species microsatellites may be
at higher risk of ADO. Based on our results we highlight
some important considerations in the selection of microsatellites
for all conservation genetic studies.