Ecology and Evolution
 2018
DOI: 10.1002/ece3.4302
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CHIIMP: An automated high‐throughput microsatellite genotyping platform reveals greater allelic diversity in wild chimpanzees

Hannah J. Barbian
1
,
Andrew Connell
2
,
Alexa N. Avitto
3
et al.

Abstract: Short tandem repeats (STRs), also known as microsatellites, are commonly used to noninvasively genotype wild‐living endangered species, including African apes. Until recently, capillary electrophoresis has been the method of choice to determine the length of polymorphic STR loci. However, this technique is labor intensive, difficult to compare across platforms, and notoriously imprecise. Here we developed a MiSeq‐based approach and tested its performance using previously genotyped fecal samples from long‐term … Show more

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Cited by 48 publications

(100 citation statements)
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“…MicroDrop allelic dropout rates in the LCMS (average of 19.6%) conformed to rates reported for various studies of avian fecal allelic dropout (mean of 21%, Regnaut et al 2006) but was much higher than rates reported from chimpanzee fecal samples via GBS (7%, Barbian et al 2018). This may be due to the fact that Barbian et al (2018) only genotyped samples at loci that had over 500 reads (counts. min = 500).…”
Section: Allelic Dropout Ratessupporting
confidence: 80%
Exaggerated anticipatory anxiety is common in social anxiety disorder (SAD). Neuroimaging studies have revealed altered neural activity in response to social stimuli in SAD, but fewer studies have examined neural activity during anticipation of feared social stimuli in SAD. The current study examined the time course and magnitude of activity in threat processing brain regions during speech anticipation in socially anxious individuals and healthy controls (HC). Method Participants (SAD n = 58; HC n = 16) underwent functional magnetic resonance imaging (fMRI) during which they completed a 90s control anticipation task and 90s speech anticipation task.
“…MicroDrop allelic dropout rates in the LCMS (average of 19.6%) conformed to rates reported for various studies of avian fecal allelic dropout (mean of 21%, Regnaut et al 2006) but was much higher than rates reported from chimpanzee fecal samples via GBS (7%, Barbian et al 2018). This may be due to the fact that Barbian et al (2018) only genotyped samples at loci that had over 500 reads (counts. min = 500).…”
Section: Allelic Dropout Ratessupporting
confidence: 80%
Exaggerated anticipatory anxiety is common in social anxiety disorder (SAD). Neuroimaging studies have revealed altered neural activity in response to social stimuli in SAD, but fewer studies have examined neural activity during anticipation of feared social stimuli in SAD. The current study examined the time course and magnitude of activity in threat processing brain regions during speech anticipation in socially anxious individuals and healthy controls (HC). Method Participants (SAD n = 58; HC n = 16) underwent functional magnetic resonance imaging (fMRI) during which they completed a 90s control anticipation task and 90s speech anticipation task.
“…When we applied our 'best practices' method from this study the average rate of allelic dropout was reduced to 9.8% across all loci and including the LQMS. When data from the pooled run was evaluated, our rates of allelic dropout in the LQMS (average of 19.6%) conformed to rates reported for various studies of avian fecal allelic dropout (mean of 21%, Regnaut, Lucas, & Fumagalli, 2006) but was much higher than rates reported from chimpanzee fecal samples via GBS (7% rate of allelic dropout; Barbian et al, 2018). This may be due to the fact that Barbian et al, (2018) only genotyped samples at loci that had over 500 reads (counts.min = 500).…”
Section: Allelic Dropout Ratessupporting
confidence: 80%
“…When data from the pooled run was evaluated, our rates of allelic dropout in the LQMS (average of 19.6%) conformed to rates reported for various studies of avian fecal allelic dropout (mean of 21%, Regnaut, Lucas, & Fumagalli, 2006) but was much higher than rates reported from chimpanzee fecal samples via GBS (7% rate of allelic dropout; Barbian et al, 2018). This may be due to the fact that Barbian et al, (2018) only genotyped samples at loci that had over 500 reads (counts.min = 500). After manually processing genotypes from all the a priori information ( the replicates, pooled run, and bioinformatically pooled data) the rates of dropout in the LQMS increased dramatically following processing to 79%.…”
Section: Allelic Dropout Ratessupporting
confidence: 80%
Exaggerated anticipatory anxiety is common in social anxiety disorder (SAD). Neuroimaging studies have revealed altered neural activity in response to social stimuli in SAD, but fewer studies have examined neural activity during anticipation of feared social stimuli in SAD. The current study examined the time course and magnitude of activity in threat processing brain regions during speech anticipation in socially anxious individuals and healthy controls (HC). Method Participants (SAD n = 58; HC n = 16) underwent functional magnetic resonance imaging (fMRI) during which they completed a 90s control anticipation task and 90s speech anticipation task.
“…We additionally showed the applicability of the 3-pool approach to degraded DNA samples such as fecal samples, which is a common material in many noninvasive wildlife studies (Carroll et al, 2018;Waits & Paetkau, 2005). The results for fecal samples were similar to the results of the high-quality samples with respect to the mean number of loci and alleles amplified per sample ( Barbian et al, 2018). Additionally, multiple samples per individual can be analyzed or the number of PCR replicates per sample can be increased.…”
Section: Discussionsupporting
confidence: 61%
Exaggerated anticipatory anxiety is common in social anxiety disorder (SAD). Neuroimaging studies have revealed altered neural activity in response to social stimuli in SAD, but fewer studies have examined neural activity during anticipation of feared social stimuli in SAD. The current study examined the time course and magnitude of activity in threat processing brain regions during speech anticipation in socially anxious individuals and healthy controls (HC). Method Participants (SAD n = 58; HC n = 16) underwent functional magnetic resonance imaging (fMRI) during which they completed a 90s control anticipation task and 90s speech anticipation task.
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