The influence of evolutionary distance between cross-species microsatellites and primer base-pair composition on allelic dropout rates

Soulsbury, Carl and Iossa, Graziella and Edwards, Keith (2009) The influence of evolutionary distance between cross-species microsatellites and primer base-pair composition on allelic dropout rates. Conservation Genetics, 10 (3). pp. 797-802. ISSN 1566-0621

Documents
Soulsbury_et_al._2009_(allelic_droput_phylo).pdf
pdf of manuscript
[img]
[Download]
Request a copy
[img] PDF
Soulsbury_et_al._2009_(allelic_droput_phylo).pdf - Whole Document
Restricted to Repository staff only

213kB

Full text URL: http://dx.doi.org/10.1007/s10592-008-9665-3

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.

Item Type:Article
Additional Information: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.
Keywords:allelic dropout, conservation genetics, DNA
Subjects:C Biological Sciences > C120 Behavioural Biology
Divisions:College of Science > School of Life Sciences
ID Code:6731
Deposited By: Carl Soulsbury
Deposited On:30 Oct 2012 20:45
Last Modified:13 Mar 2013 09:18

Repository Staff Only: item control page