Restrictable DNA from sloughed cetacean skin: Its potential for use in population analysis

University of Cambridge, Cambridge, England, United Kingdom
Marine Mammal Science (Impact Factor: 1.94). 08/2006; 8(3):275 - 283. DOI: 10.1111/j.1748-7692.1992.tb00409.x


Several species of cetaceans naturally slough visible quantities of skin. We have investigated the prospect of using this material as a viable alternative to the use of biopsy darts for the collection of samples for molecular analysis. Pieces of skin were collected from free-ranging individuals of three different species—the humpback (Megaptera novaeangliae), sperm (Physeter macrocephalus) and right whales (Eubalaena glacialis). DNA was extracted from 11 pieces of sloughed skin and DNA “fingerprint” profiles prepared. All samples contained DNA of both sufficient quality and quantity for genetic analysis. The applicability of this approach is discussed generally in relation to answering problems about the population structure and breeding systems of cetaceans.

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    • "When multiple dung piles were associated with a group of elephants, efforts were made to collect samples from all the different individuals present, based on bolus size and distribution of dung piles. Approximately 10 g of dung was placed in each case into sterile tubes filled with *20 ml of Queen's College Buffer (20 % DMSO, 100 mM Tris pH 7.5, 0.25 M EDTA, saturated with NaCl; Amos et al. 1992). "
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    ABSTRACT: The Asian elephant is a flagship species for conservation in tropical Asia, but reliable population estimates are available only from a few populations. This is because the species can be elusive and occurs at low densities in dense habitat over a large part of its range. Phnom Prich Wildlife Sanctuary in the Eastern Plains, Cambodia, which is part of one of the largest protected area complexes in South-East Asia, is one such habitat that had not been systematically censused for elephants. We, therefore, used fecal-DNA based capture-mark-recapture sampling to estimate the population size for establishing a monitoring baseline. Five sampling sessions targeted all areas in and adjacent to Phnom Prich Wildlife Sanctuary believed to be used by elephants. Fresh dung was collected as the source of DNA and genotyping was carried out based on nine microsatellite loci. The 224 samples collected yielded 78 unique genotypes. Using model averaging of closed population capture-mark-recapture models, the elephant population in Phnom Prich Wildlife Sanctuary was estimated to number 136 ± 18 (SE) individuals. Our results suggest that eastern Cambodia supports a regionally important Asian elephant population.
    No preview · Article · Aug 2014 · Conservation Genetics
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    • "to reliably identify species without additional confirmation such as sequencing or cloning, offering a faster turnover time than other DNA-based methods. Speciesspecific TaqMan assays have a number of uses, including distinguishing phenotypically similar species (Fox et al. 2005), detecting exogenous DNA from rare aquatic species (Amos & Whitehead 1992; Jerde et al. 2011), as well as detection of prey in feces or gut contents (King et al. 2008; Shehzad et al. 2012; Baerwald et al. 2012). "
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    ABSTRACT: The effect of predation on native fish by introduced species in the San Francisco Estuary-Delta (SFE) has not been thoroughly studied despite its potential to impact species abundances. Species-specific quantitative PCR (qPCR) is an accurate method for identifying species from exogenous DNA samples. Quantitative PCR assays can be used for detecting prey in gut contents or feces, discriminating between cryptic species, or detecting rare aquatic species. We designed ten TaqMan qPCR assays for fish species from the SFE watershed most likely to be affected by non-native piscivores. The assays designed are highly specific, producing no signal from co-occurring or related species, and sensitive, with a limit of detection between 3.2 and 0.013 pg/μL of target DNA. These assays will be used in conjunction with a high-throughput qPCR platform to compare predation rates between native and non-native piscivores and assess the impacts of predation in the system.This article is protected by copyright. All rights reserved.
    Full-text · Article · Jul 2014 · Molecular Ecology Resources
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    • "These locations are deep within the forest zones of West and Central Africa, thus avoiding regions in which historical or contemporary hybridization may have occurred between forest and savanna elephants [51]. Approximately 20 g of dung were collected and boiled in the collection tube to prevent the transportation of pathogens, then stored in Queens College preservation buffer (20% DMSO, 0.25 M EDTA, 100 mM Tris, pH 7.5, saturated with NaCl [52]). Total genomic DNA was extracted from dung samples in a lab dedicated to noninvasive DNA extractions [53] using the Qiagen QIAmp DNA Stool Mini Kit (Qiagen, Valenica, CA, USA) with modifications as described in Archie [54]. "
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    ABSTRACT: As species evolve, they become adapted to their local environments. Detecting the genetic signature of selection and connecting that to the phenotype of the organism, however, is challenging. Here we report using an integrative approach that combines DNA sequencing with structural biology analyses to assess the effect of selection on residues in the mitochondrial DNA of the two species of African elephants. We detected evidence of positive selection acting on residues in complexes I and V, and we used homology protein structure modeling to assess the effect of the biochemical properties of the selected residues on the enzyme structure. Given the role these enzymes play in oxidative phosphorylation, we propose that the selected residues may contribute to the metabolic adaptation of forest and savanna elephants to their unique habitats.
    Full-text · Article · Apr 2014 · PLoS ONE
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