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Minimally-invasive sampling (MIS) is widespread in wildlife studies; however, its utility for massively parallel DNA sequencing (MPS) is limited. Poor sample quality and contamination by exogenous DNA can make MIS challenging to use with modern genotyping-by-sequencing approaches, which have been traditionally developed for high-quality DNA sources. Given that MIS is often more appropriate in many contexts, there is a need to make such samples practical for harnessing MPS. Here, we test the ability for Genotyping-in-Thousands by sequencing (GT-seq), a multiplex amplicon sequencing approach, to effectively genotype minimally-invasive cloacal DNA samples collected from the Western Rattlesnake (Crotalus oreganus), a threatened species in British Columbia, Canada. As there was no previous genetic information for this species, an optimized panel of 362 SNPs was selected for use with GT-seq from a de novo restriction-site associated DNA sequencing (RADseq) assembly. Comparisons of genotypes generated within and among RADseq and GT-seq for the same individuals found low rates of genotyping error (GT-seq: 0.50%; RADseq: 0.80%) and discordance (2.57%), the latter likely due to the different genotype calling models employed. GT-seq mean genotype discordance between blood and cloacal swab samples collected from the same individuals was also minimal (1.37%). Estimates of population diversity parameters were similar across GT-seq and RADseq datasets, as were inferred patterns of population structure. Overall, GT-seq can be effectively applied to low quality DNA samples, minimizing the inefficiencies presented by exogenous DNA typically found in minimally-invasive samples and continuing the expansion of molecular ecology and conservation genetics in the genomics era. This article is protected by copyright. All rights reserved.
This article was published in the following journal.
Name: Molecular ecology resources
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Procedures that avoid use of open invasive surgery in favor of closed or local surgery. These generally involve use of laparoscopic devices and remote-control manipulation of instruments with indirect observation of the surgical field through an endoscope or similar device. With the reduced trauma associated with minimally invasive surgery, long hospital stays may be reduced with increased rates of short stay or day surgery.
The use of ultrasound to guide minimally invasive surgical procedures such as needle ASPIRATION BIOPSY; DRAINAGE; etc. Its widest application is intravascular ultrasound imaging but it is useful also in urology and intra-abdominal conditions.
Procedures that avoid use of open, invasive surgery in favor of closed or local surgery. These generally involve use of laparoscopic devices and remote-controlled manipulation of instruments with indirect observation of the surgical field through an endoscope or similar device.
Minimally invasive procedures guided with the aid of magnetic resonance imaging to visualize tissue structures.
Minimally invasive procedures, diagnostic or therapeutic, performed within the BLOOD VESSELS. They may be perfomed via ANGIOSCOPY; INTERVENTIONAL MAGNETIC RESONANCE IMAGING; INTERVENTIONAL RADIOGRAPHY; or INTERVENTIONAL ULTRASONOGRAPHY.
DNA sequencing is the process of determining the precise order of nucleotides within a DNA molecule. During DNA sequencing, the bases of a small fragment of DNA are sequentially identified from signals emitted as each fragment is re-synthesized from a ...
Bioinformatics is the application of computer software and hardware to the management of biological data to create useful information. Computers are used to gather, store, analyze and integrate biological and genetic information which can then be applied...
Food is any substance consumed to provide nutritional support for the body. It is usually of plant or animal origin, and contains essential nutrients, such as carbohydrates, fats, proteins, vitamins, or minerals. The substance is ingested by an organism ...