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1
Pearson, S. K., S. S. Tobe, D. A. Fusco, C. M. Bull, and M. G. Gardner. "Piles of scats for piles of DNA: deriving DNA of lizards from their faeces." Australian Journal of Zoology 62, no. 6 (2014): 507. http://dx.doi.org/10.1071/zo14059.
Повний текст джерелаАнотація:
Non-invasive genetic sampling using scats has a well established role in conservation biology, but has rarely been applied to reptiles. Using scats from captive and wild Egernia stokesii (Squamata, Scincidae) we evaluated two storage and six DNA-extraction methods and the reliability of subsequent genotype and sequence data. Accurate genotype and sequence data were obtained from frozen and dried captive lizard scat DNA extracted using a QIAamp® DNA Stool Mini Kit and a modified Gentra® Puregene® method, but success rates were reduced for wild lizard scats. Wild E. stokesii eat more plants than their captive counterparts, possibly resulting in scat DNA extracts containing plant compounds that inhibit PCR-amplifications. Notably, reliable genotypes and sequences were obtained from wild E. stokesii scat DNA extracted using a Qiagen DNeasy® Plant Mini Kit, a method designed to remove plant inhibitory compounds. Results highlight the opportunity for using scat-derived DNA in lizard studies, particularly for species that deposit scats in piles.
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Ruibal, Monica, Rod Peakall, Andrew Claridge, and Karen Firestone. "Field-based evaluation of scat DNA methods to estimate population abundance of the spotted-tailed quoll (Dasyurus maculatus), a rare Australian marsupial." Wildlife Research 36, no. 8 (2009): 721. http://dx.doi.org/10.1071/wr09086.
Повний текст джерелаАнотація:
Context. DNA extracted non-invasively from remotely collected scat samples has been used successfully to enumerate populations of a few endangered mammal species. However, scat DNA surveys relying on scent-marking behaviours need to identify if age- or sex-specific variations or seasonal changes in scat scent-marking patterns affect population estimates. Furthermore, owing to the low quantity and quality of scat DNA, a thorough assessment of the technique is needed when it is applied to different species to ensure that individual identification is reliable. Aims. In the current study, microsatellite genetic profiles derived from 208 remotely collected scats of the spotted-tailed quoll (Dasyurus maculatus), a rare Australian marsupial carnivore, were compared with DNA profiles from tissue of 22 live-trapped individuals from the same study area to critically assess the reliability of the non-invasive method to estimate population abundance. Methods. Scat samples were collected at scent-marking sites over 4 consecutive months (April–July 2005), 7 weeks of which overlapped with the trapping program to allow direct comparisons of population estimates. Key results. Combining a multiple-tubes approach with error checking analyses provided reliable genetic tags and resulted in the detection of the majority of the live-trapped population (18 of 22 individuals). Ten additional individuals not known from trapping were also observed from scat DNA. A longer-term sampling regime was required for scats than for trapping to allow direct detection of a large proportion of the population and to provide a comparable population estimate. Critically, the 4-month scat collection period highlighted the importance of performing scat surveys during the mating season when scat scent marking is more frequent, and to avoid sex and age biases in scat marking patterns. Implications. Non-invasive scat DNA sampling methods that rely on scent-marking behaviours need to consider the duration of the sampling period and temporal differences in behaviours by the sexes and age groups to ensure that meaningful population estimates are achieved.
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Marks, Clive A., Frank Gigliotti, Steve McPhee, Maxine P. Piggott, Andrea Taylor, and Al S. Glen. "DNA genotypes reveal red fox (Vulpes vulpes) abundance, response to lethal control and limitations of contemporary survey techniques." Wildlife Research 36, no. 8 (2009): 647. http://dx.doi.org/10.1071/wr08109.
Повний текст джерелаАнотація:
Context. Scat genotyping has not been routinely used to measure fox (Vulpes vulpes) abundance and our study sought to provide a benchmark for further technique development and assessment of field methods. Aims. This study sought to provide a comparative assessment of some common methods used to determine fox density and contrast their success with scat DNA genotyping. Methods. DNA recovered from fox scats was used to genotype individual red foxes and determine their abundance at four transects. Population indices were also developed from bait take, scat counts and sand plot tracks using index-manipulation-index (IMI) procedures on the same transects. Known samples of foxes were taken from two treatment transects using cyanide delivered in the M-44 ejector to manipulate the population and to recover foxes at the end of the trial. Key results. Replicated counts on a 41-km-spotlight transect at the field site before and after the population manipulation had low variance and good correlation (r2 = 0.79, P < 0.01). Scat genotypes revealed 54 foxes in eight days and, when combined with biopsy DNA from recovered foxes, a minimum known to be alive (KTBA) density of between 1.6 and 5 foxes km–1 was calculated for the transects. Overall, 15/30 (50%) of all recovered foxes had not been detected by scat genotyping, 23/53 (49%) of KTBA genotypes were detected only once and 5/54 (9.5%) of foxes were found to have moved between two transects. Conclusions. At transects where population manipulation occurred, surviving individuals contributed significantly more scats than at the control transects and some individuals were detected at bait stations at a much greater frequency. This strongly suggested that they had contributed disproportionately to some IMI density estimates that were probably influenced by a change in the activity of some individuals rather than changes in population density alone. At one transect, eight foxes were confirmed to be present by spotlight surveys and were detected by scat and KTBA genotypes, yet were undetected by scat, bait station and sand plot indices. Implications. Scat and other DNA-based survey techniques provide a great deal of information about the identification and movement of individuals and if DNA sampling methods can be made more efficient they have the potential to provide accurate abundance estimates that are independent of the control technique.
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Davies, Chris, Wendy Wright, Faye Wedrowicz, and Fiona E. Hogan. "A DNA toolbox for non-invasive genetic studies of sambar deer (Rusa unicolor)." Australian Mammalogy 42, no. 1 (2020): 58. http://dx.doi.org/10.1071/am18032.
Повний текст джерелаАнотація:
Invasive sambar deer (Rusa unicolor) are having significant detrimental impacts on natural environments in south-eastern Australia. Little, however, is known about their ecology, limiting evidence-based management strategies directed at reducing deer impacts. Genetic data, generated from DNA isolated from deer scats, can be used to fill ecological knowledge gaps. This study outlines a non-invasive genetic sampling strategy by which good-quality DNA from a single deer scat can be used to determine (1) species of origin, (2) sex and (3) a unique DNA profile. DNA from deer tissue and sambar deer scat samples were used to develop and optimise molecular methods to collect reliable genetic information. A DNA toolbox is presented that describes how to find, collect and store scat samples, isolate DNA and use molecular markers to generate informative genetic data. Generating genetic data using this approach will support studies aimed at acquiring ecological knowledge about sambar deer. Such knowledge will be critical for developing evidence-based recommendations to improve on-ground management decisions for sambar deer.
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Pikuta, Elena V., Takashi Itoh, Paul Krader, Jane Tang, William B. Whitman, and Richard B. Hoover. "Anaerovirgula multivorans gen. nov., sp. nov., a novel spore-forming, alkaliphilic anaerobe isolated from Owens Lake, California, USA." International Journal of Systematic and Evolutionary Microbiology 56, no. 11 (November 1, 2006): 2623–29. http://dx.doi.org/10.1099/ijs.0.64198-0.
Повний текст джерелаАнотація:
A novel, alkaliphilic, obligately anaerobic bacterium, strain SCAT, was isolated from mud sediments of a soda lake in California, USA. The rod-shaped cells were motile, Gram-positive, formed spores and were 0.4–0.5×2.5–5.0 μm in size. Growth occurred within the pH range 6.7–10.0 and was optimal at pH 8.5. The temperature range for growth was 10–45 °C, with optimal growth at 35 °C. NaCl was required for growth. Growth occurred at 0.5–9.0 % (w/v) NaCl and was optimal at 1–2 % (w/v). The novel isolate was a catalase-negative chemo-organoheterotroph that fermented sugars, proteolysis products, some organic and amino acids, glycerol, d-cellobiose and cellulose. It was also capable of growth by the Stickland reaction. Strain SCAT was sensitive to tetracycline, chloramphenicol, rifampicin and gentamicin, but it was resistant to ampicillin and kanamycin. The G+C content of the genomic DNA was 34.2 mol%. Major fatty acid components were C14 : 0, iso-C15 : 0, C16 : 1 ω9c and C16 : 0. 16S rRNA gene sequence analysis of strain SCAT showed a similarity of approximately 97 % with the type strains of Clostridium formicaceticum and Clostridium aceticum in clostridial cluster XI and a similarity of less than 94.2 % to any other recognized Clostridium species and those of related genera in this cluster. Strain SCAT was clearly differentiated from C. formicaceticum and C. aceticum based on comparison of their phenotypic properties and fatty acid profiles, as well as low levels of DNA–DNA relatedness between strain SCAT and the type strains of these two species. Therefore, strain SCAT is considered to represent a novel species of a new genus, Anaerovirgula multivorans gen. nov., sp. nov., in clostridial cluster XI. The type strain is SCAT (=ATCC BAA-1084T=JCM 12857T=DSM 17722T=CIP 107910T).
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Alam, MS, MA Rahaman, RA Begum, and RM Shahjahan. "Non-invasive DNA extraction for molecular identification of royal Bengal tiger Panthera tigris tigris." Dhaka University Journal of Biological Sciences 30, no. 2 (July 9, 2021): 325–30. http://dx.doi.org/10.3329/dujbs.v30i2.54657.
Повний текст джерелаАнотація:
The flagship animal species of Sundarbans, the Royal Bengal tiger (Panthera tigris tigris) is under threat of extinction. Its natural population is declining day by day. So, to avoid killing and harming the animal, the use of non-invasive samples such as scat, hair, or scent is preferred for DNA extraction and subsequent genotyping of tiger species. DNA has been extracted from scat samples of the Bengal tiger in the present study, and a fragment of the cytochrome b gene has been sequenced after PCR with species-specific primers. DNA has been extracted manually using a previously described methodology with slight modifications. The size of the PCR product and sequence of cytochrome b gene indicates that tiger DNA is successfully extracted from scat samples using tigerspecific primers. Thus, presence of tiger DNA can be detected by using this method just by the PCR product size in the gel. This is the first report of a partial sequence of mitochondrial cytochrome b gene of P. t. tigris from Bangladesh.
Dhaka Univ. J. Biol. Sci. 30(2): 325-330, 2021 (July)
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Grueber, Catherine E., Rowena Chong, Rebecca M. Gooley, Elspeth A. McLennan, Vanessa R. Barrs, Katherine Belov, and Carolyn J. Hogg. "Genetic analysis of scat samples to inform conservation of the Tasmanian devil." Australian Zoologist 40, no. 3 (January 2020): 492–504. http://dx.doi.org/10.7882/az.2020.005.
Повний текст джерелаАнотація:
Recent advances in molecular genetics have enabled a great deal of information about species to be obtained from analysis of non-invasively collected samples such as scat. Scat provides genetic information via residual host DNA on the outside of the scat, via characterising the genetic makeup of intestinal microbes that are present in the scat, or by examining the DNA remnants of prey items that have passed through the animal’s digestive tract. In this review, we provide a case study to demonstrate how these approaches are being used to better understand the threatened Tasmanian devil in the landscape, and to support the species’ conservation. Scat analysis enables us to quantify the genetic diversity of remote populations, where trapping is logistically challenging. We are beginning to learn how conservation management impacts the microbiome of threatened species, and investigate how various management strategies may be impacting the diverse array of bacteria and viruses that devils, like all animal species, are host to. We are using scat samples to better understand the interaction between devils and other animals in their environment by learning more about what they eat. We explore the strengths and challenges of these approaches by comparing our work to that conducted in other species. Finally, we provide specific examples of how our results are being integrated into conservation strategy for the devil.
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Wang, Ya-Wen, Ji-Lei Zhang, Jian-Gang Jiao, Xiao-Xia Du, Samwel Mchele Limbu, Fang Qiao, Mei-Ling Zhang, Dong-Liang Li, and Zhen-Yu Du. "Physiological and metabolic differences between visceral and subcutaneous adipose tissues in Nile tilapia (Oreochromis niloticus)." American Journal of Physiology-Regulatory, Integrative and Comparative Physiology 313, no. 5 (November 1, 2017): R608—R619. http://dx.doi.org/10.1152/ajpregu.00071.2017.
Повний текст джерелаАнотація:
Visceral adipose tissue (VAT) and subcutaneous adipose tissue (SCAT) have different structures and metabolic functions and play different roles in the regulation of the mammal endocrine system. However, little is known about morphology and physiological and metabolic functions between VAT and SCAT in fish. We compared the morphological, physiological, and biochemical characteristics of VAT and SCAT in Nile tilapia and measured their functions in energy intake flux, lipolytic ability, and gene expression patterns. SCAT contained more large adipocytes and nonadipocytes than VAT in Nile tilapia. VAT had higher lipid content and was the primary site for lipid deposition. Conversely, SCAT had higher hormone-induced lipolytic activity. Furthermore, SCAT had a higher percentage of monounsaturated and lower polyunsaturated fatty acids than VAT. SCAT had higher mitochondrial DNA, gene expression for fatty acid β-oxidation, adipogenesis, and brown adipose tissue characteristics, but it also had a lower gene expression for inflammation and adipocyte differentiation than VAT. SCAT and VAT have different morphological structures, as well as physiological and metabolic functions in fish. VAT is the preferable lipid deposition tissue, whereas SCAT exhibits higher lipid catabolic activity than VAT. The physiological functions of SCAT in fish are commonly overlooked. The present study indicates that SCAT has specific metabolic characteristics that differ from VAT. The differences between VAT and SCAT should be considered in future metabolism studies using fish as models, either in biomedical or aquaculture studies.
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McInnes, Julie C., Rachael Alderman, Bruce E. Deagle, Mary‐Anne Lea, Ben Raymond, and Simon N. Jarman. "Optimised scat collection protocols for dietary DNA metabarcoding in vertebrates." Methods in Ecology and Evolution 8, no. 2 (November 7, 2016): 192–202. http://dx.doi.org/10.1111/2041-210x.12677.
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Vynne, C., M. R. Baker, Z. K. Breuer, and S. K. Wasser. "Factors influencing degradation of DNA and hormones in maned wolf scat." Animal Conservation 15, no. 2 (November 15, 2011): 184–94. http://dx.doi.org/10.1111/j.1469-1795.2011.00503.x.
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Ruibal, Monica, Rod Peakall, and Andrew Claridge. "Socio-seasonal changes in scent-marking habits in the carnivorous marsupial Dasyurus maculatus at communal latrines." Australian Journal of Zoology 58, no. 5 (2010): 317. http://dx.doi.org/10.1071/zo10040.
Повний текст джерелаАнотація:
Scat DNA analyses and monthly monitoring were used to elucidate patterns of latrine use in a free-ranging population of a rare Australian marsupial carnivore, the spotted-tailed quoll (Dasyurus maculatus) Kerr. In all, 132 latrines were identified at large complex outcrops and on bedrock in drainage lines, creeks and rivers at a single woodland site in south-eastern mainland Australia. Annual cyclic variation in scat deposition was found over the two years that latrines were monitored. Peaks in scat deposition on latrines coincided with seasonal social behaviours and differed between sites on outcrops and sites along drainage lines. A marked increase in scat deposition on latrines in drainage lines was recorded during the mating season and at outcrop latrines when females were nursing young. Genetic analyses of scats collected over one breeding season revealed that multiple individuals of both sexes defaecated at latrines. The communal use of latrines during the mating season along with the seasonal patterns of scat deposition demonstrates that latrines are important scent-marking sites that facilitate social communication among individuals of this solitary-living species. The collective evidence indicates that latrines play a major role in aiding reproduction and interindividual spacing.
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Miles, Kathleen A., Michelle N. Holtz, Zachary T. Lounsberry, and Benjamin N. Sacks. "A paired comparison of scat-collecting versus scat-swabbing methods for noninvasive recovery of mesocarnivore DNA from an arid environment." Wildlife Society Bulletin 39, no. 4 (November 8, 2015): 797–803. http://dx.doi.org/10.1002/wsb.600.
Повний текст джерела
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Aruge, Samreen, Hafsa Batool, Fida M. Khan, Fakhar-i-Abbas, and Safia Janjua. "A pilot study—genetic diversity and population structure of snow leopards of Gilgit-Baltistan, Pakistan, using molecular techniques." PeerJ 7 (November 4, 2019): e7672. http://dx.doi.org/10.7717/peerj.7672.
Повний текст джерелаАнотація:
Background The Hindu Kush and Karakoram mountain ranges in Pakistan’s northern areas are a natural habitat of the snow leopard (Panthera uncia syn. Uncia uncia) but the ecological studies on this animal are scarce since it is human shy by nature and lives in difficult mountainous tracts. The pilot study is conducted to exploit the genetic diversity and population structure of the snow leopard in this selected natural habitat of the member of the wildcat family in Pakistan. Method About 50 putative scat samples of snow leopard from five localities of Gilgit-Baltistan (Pakistan) along with a control sample of zoo maintained male snow leopard were collected for comparison. Significant quality and quantity of genomic DNA was extracted from scat samples using combined Zhang–phenol–chloroform method and successful amplification of cytochrome c oxidase I gene (190 bp) using mini-barcode primers, seven simple sequence repeats (SSR) markers and Y-linked AMELY gene (200 bp) was done. Results Cytochrome c oxidase I gene sequencing suggested that 33/50 (66%) scat samples were of snow leopard. AMELY primer suggested that out of 33 amplified samples, 21 (63.63%) scats were from male and 12 (36.36%) from female leopards. Through successful amplification of DNA of 25 out of 33 (75.75%) scat samples using SSR markers, a total of 68 alleles on seven SSR loci were identified, showing low heterozygosity, while high gene flow between population. Discussion The low gene flow rate among the population results in low genetic diversity causing decreased diversification. This affects the adaptability to climatic changes, thus ultimately resulting in decreased population size of the species.
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Seah, Adeline, Marisa C. W. Lim, Denise McAloose, Stefan Prost, and Tracie A. Seimon. "MinION-Based DNA Barcoding of Preserved and Non-Invasively Collected Wildlife Samples." Genes 11, no. 4 (April 18, 2020): 445. http://dx.doi.org/10.3390/genes11040445.
Повний текст джерелаАнотація:
The ability to sequence a variety of wildlife samples with portable, field-friendly equipment will have significant impacts on wildlife conservation and health applications. However, the only currently available field-friendly DNA sequencer, the MinION by Oxford Nanopore Technologies, has a high error rate compared to standard laboratory-based sequencing platforms and has not been systematically validated for DNA barcoding accuracy for preserved and non-invasively collected tissue samples. We tested whether various wildlife sample types, field-friendly methods, and our clustering-based bioinformatics pipeline, SAIGA, can be used to generate consistent and accurate consensus sequences for species identification. Here, we systematically evaluate variation in cytochrome b sequences amplified from scat, hair, feather, fresh frozen liver, and formalin-fixed paraffin-embedded (FFPE) liver. Each sample was processed by three DNA extraction protocols. For all sample types tested, the MinION consensus sequences matched the Sanger references with 99.29%–100% sequence similarity, even for samples that were difficult to amplify, such as scat and FFPE tissue extracted with Chelex resin. Sequencing errors occurred primarily in homopolymer regions, as identified in previous MinION studies. We demonstrate that it is possible to generate accurate DNA barcode sequences from preserved and non-invasively collected wildlife samples using portable MinION sequencing, creating more opportunities to apply portable sequencing technology for species identification.
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Tighe, Andrew, Robert Gandola, Bernerd Fulanda, Kiera Thurman, Sarah Overby, John Byrne, and Jens Carlsson. "Testing PCR amplification from elephant dung using silica-dried swabs." Pachyderm 59 (October 3, 2018): 56–65. http://dx.doi.org/10.69649/pachyderm.v59i.81.
Повний текст джерелаАнотація:
Swabbing scat samples is a simple, non-invasive method of obtaining DNA samples for population genetic analysis of wild elephants. In this study, swab samples were taken from the scat of African savanna elephants inhabiting the Galana Wildlife Conservancy (GWC), bordering Tsavo East National Park in south-east Kenya. The swab samples were dried with silica as opposed to traditional methods of preservation in liquid or freezing while in the field. Furthermore, this study examined the rate of DNA degradation in scat samples in semi-arid conditions, typical of the Galana Wildlife Conservancy, by repeated sampling of scat in the field following deposition at defined time intervals over a period of two weeks. Results showed that both nuclear DNA (nDNA) and mitochondrial DNA (mtDNA) could be successfully amplified from scat samples up to 128 hours (about five days) following deposition. Significantly better results were obtained from samples taken from the outside of the scat than from the centre. Mitochondrial D-loop sequence data suitable for phylogenetic analysis was obtained from three fresh samples and one sample taken 16 hours after deposition. However, the sequence from a sample collected after 128 hours was not of sufficient quality for sequencing. Further research is required to determine at which point between 16 and 128 hours the DNA becomes too degraded for analysis. The mtDNA analysis showed the presence of the Southwest savanna subclade in two of the four samples from GWC, which has previously been found in only one other sample in Kenya. By confirming the effectiveness of silica-dried scat samples for use in DNA analysis, the results of this study will facilitate genetic analysis of African elephant populations and thereby contribute to efforts to conserve the gene pool of this keystone species. The paper contributes to the literature on collecting and preserving dung specimens with potential for conservation management. Additional key words: eDNA, Polymerase chain reaction L'échantillonnage par prélèvement d’excrément est une méthode simple et non invasive d'obtention des échantillons d'ADN pour l'analyse génétique des populations d'éléphants sauvages. Dans cette étude, des échantillons ont été prélevés sur les excréments d'éléphants d’Afrique de la savane habitant le Galana Wildlife Conservancy (GWC), à la limite du Parc national de Tsavo East dans le sud-est du Kenya. Les échantillons ont été séchés avec de la silice par opposition aux méthodes traditionnelles de conservation en milieu liquide ou en congélation sur le terrain. En outre, cette étude a examiné le taux de dégradation de l'ADN des échantillons dans des conditions semi-arides, typiques du Galana Wildlife Conservancy, par échantillonnage répété sur le terrain après dépôt à des intervalles de temps définis sur une période de deux semaines. Les résultats ont montré que l'ADN nucléaire (ADNn) et l'ADN mitochondrial (ADNmt) pouvaient être amplifiés avec succès à partir d'échantillons de fragments jusqu'à 128 heures (environ cinq jours) après le dépôt. Des résultats significativement meilleurs ont été obtenus à partir d'échantillons prélevés de l'extérieur des excréments que du centre. Les données de séquence en boucle D mitochondriale appropriées pour l'analyse phylogénétique ont été obtenues à partir de trois échantillons frais et d’un échantillon prélevé 16 heures après le dépôt. Cependant, la séquence d'un échantillon recueilli après 128 heures n'était pas de qualité suffisante pour le séquençage. D'autres recherches sont nécessaires pour déterminer à quel moment entre 16 et 128 heures l'ADN devient trop dégradé pour l'analyse. L'analyse de l'ADN mitochondrial a montré la présence de la sous-espèce de l'éléphant d'Afrique de la savane du sud-ouest, dans deux sur les quatre échantillons du GWC, ce qui ne se trouvait auparavant que dans un seul autre échantillon au Kenya. En confirmant l'efficacité des échantillons d’excréments séchés à la silice pour l'analyse de l'ADN, les résultats de l'étude faciliteront l'analyse génétique des populations d'éléphants d'Afrique et contribueront ainsi aux efforts de conservation du patrimoine génétique de cette espèce clé. Le document a apporté une contribution à la littérature sur la collecte et la préservation des spécimens d’excréments sur le terrain avec un potentiel pour la gestion de la conservation. Mots-clés supplémentaires: Réaction en chaîne par polyméras, ADNe
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Rutledge, Linda Y., Joshua J. Holloway, Brent R. Patterson, and Bradley N. White. "An Improved Field Method to Obtain DNA for Individual Identification From Wolf Scat." Journal of Wildlife Management 73, no. 8 (November 2009): 1430–35. http://dx.doi.org/10.2193/2008-492.
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Balbag, Brittany S., Austen C. Thomas, Robert H. Devlin, and Dietmar Schwarz. "Can sex-specific consumption of prey be determined from DNA in predator scat?" Conservation Genetics Resources 11, no. 4 (March 27, 2018): 447–55. http://dx.doi.org/10.1007/s12686-018-1037-9.
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Wang, Rongjiang, Jodie N. Painter, and Ilkka Hanski. "Amplification of DNA markers from scat samples of the least weaselMustela nivalis nivalis." Acta Theriologica 47, no. 4 (December 2002): 425–31. http://dx.doi.org/10.1007/bf03192467.
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Thuo, David, Elise Furlan, Femke Broekhuis, Joseph Kamau, Kyle Macdonald, and Dianne M. Gleeson. "Food from faeces: Evaluating the efficacy of scat DNA metabarcoding in dietary analyses." PLOS ONE 14, no. 12 (December 18, 2019): e0225805. http://dx.doi.org/10.1371/journal.pone.0225805.
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Hacker, Charlotte. "Decoding the DNA of scat and the application of genetic methodologies to understanding carnivore diet." Science Reviews. Biology 2, no. 3 (October 31, 2023): 1–7. http://dx.doi.org/10.57098/scirevs.biology.2.3.1.
Повний текст джерелаАнотація:
Carnivore species are vital to ecosystem function and maintenance. One key component to understanding carnivore ecology and the most effective means of management is knowledge of dietary resource use. Traditional methods used to study carnivore diet, such as microhistology, have several technical and logistical shortcomings. These have hindered the quality and quantity of data that shape understanding of how carnivores exploit prey. Advances in genetic methodologies and their application to wildlife biology has transformed the manner in which information about species can be gained. DNA metabarcoding is one such example. With this approach, genetic sequences present in scat can be determined via next-generation sequencing and matched to reference databases, revealing the carnivore that deposited the scat and the prey it consumed. DNA metabarcoding has the ability to overcome many of the previous challenges associated with dietary analysis and works to advance and inform current knowledge surrounding carnivore ecology, predatorprey relationships, conflicts between carnivores and humans, and potential adaptability to large-scale landscape shifts. Its use has provided novel insights on numerous carnivore species to help inform research priorities and wildlife policies, including those living in unique fragile environments such as the Qinghai-Tibetan Plateau of China. The continued development and increased capacity of molecular dietary analysis via DNA metabarcoding has the promise to grossly improve carnivore conservation management strategies on a global scale.
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Duarte, José Maurício Barbanti, Ângela Cristina Talarico, Alexandre Vogliotti, José Eduardo Garcia, Márcio Leite Oliveira, Jesús E. Maldonado, and Susana González. "Scat detection dogs, DNA and species distribution modelling reveal a diminutive geographical range for the Vulnerable small red brocket deer Mazama bororo." Oryx 51, no. 4 (October 11, 2016): 656–64. http://dx.doi.org/10.1017/s0030605316000405.
Повний текст джерелаАнотація:
AbstractThe small red brocket deer Mazama bororo is endemic to the Brazilian Atlantic Forest, a biome that has been greatly fragmented and altered by human activities. This elusive species is morphologically similar to the red brocket deer Mazama americana and the Brazilian dwarf brocket deer Mazama nana, and genetic typing is necessary for reliable identification. To determine the geographical range of M. bororo more accurately, we conducted non-invasive genetic sampling using scat detection dogs trained to locate deer faeces. We surveyed 46 protected areas located within the species’ potential distribution and collected a total of 555 scat samples in 30 of the protected areas. Using a polymerase chain reaction–restriction fragment length polymorphism approach, we genotyped 497 scat samples (89%) and detected M. bororo in seven localities in three Brazilian states. The results support a range extension of the small red brocket deer to latitudes 23 and 28°S and longitudes 47 and 49°W. We show that the species’ distribution is associated with 37,517 km2 of the Ombrophilous Dense Forest in the Brazilian Atlantic Forest, and this conclusion is supported by species distribution modelling. The small red brocket deer is the largest endemic species in Brazil and may have the smallest geographical distribution of any Neotropical deer species. This species occupies fragmented landscapes and is threatened by human encroachment, poaching, and predation by dogs, and based on our findings we recommend policy intervention for conservation planning of the Ombrophilous Dense Forest.
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Wasser, Samuel K., Barbara Davenport, Elizabeth R. Ramage, Kathleen E. Hunt, Margaret Parker, Christine Clarke, and Gordon Stenhouse. "Scat detection dogs in wildlife research and management: application to grizzly and black bears in the Yellowhead Ecosystem, Alberta, Canada." Canadian Journal of Zoology 82, no. 3 (March 1, 2004): 475–92. http://dx.doi.org/10.1139/z04-020.
Повний текст джерелаАнотація:
We report the development and application of a method using domestic dogs (Canis familiaris Linnaeus, 1758) to systematically locate wildlife scat over large remote areas. Detection dogs are chosen for their strong object orientation, high play drive, and willingness to strive for a reward. Dogs were trained to detect grizzly bear (Ursus arctos Linnaeus, 1758) and black bear (Ursus americanus Pallas, 1780) scats over a 5200-km2 area of the Yellowhead Ecosystem, Alberta, Canada. DNA from scat provided the species and (for grizzly bears only) sex and individual identities of the animal at each location. Concentrations of fecal cortisol and progesterone metabolites from these same grizzly bear scats provided indices of physiological stress and reproductive activity (in females), respectively. Black and grizzly bears were most concentrated in the northern portion of the multiuse study area, where food is most abundant yet poaching-related mortality appears to be heaviest. Physiologic stress was also lowest and female reproductive activity correspondingly highest for grizzly bears in the north. The scat-based distributions corresponded to concurrently collected hair-snag data in 1999 and global positioning system radiotelemetry data (of grizzly bears) in 1999 and 2001. Results suggest that the scat dog detection methodology provides a promising tool for addressing a variety of management and research questions in the wildlife sciences.
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Old, Julie M., Eden M. Hermsen, and Lauren J. Young. "MHC Class II variability in bare-nosed wombats (Vombatus ursinus)." Australian Mammalogy 42, no. 2 (2020): 135. http://dx.doi.org/10.1071/am19015.
Повний текст джерелаАнотація:
Studies of gene diversity are used to investigate population dynamics, including immunological fitness. Aside from the selection of an appropriate gene target, an important factor that underpins these studies is the ability to recover viable DNA samples from native animals that are protected, threatened or difficult to sample or locate such as the bare-nosed wombat (Vombatus ursinus). In this study, we used genomic DNA extracted from muscle tissue samples and also identified the optimal method to extract DNA from fresh wombat scat samples to enable further analyses to be performed using non-invasive techniques. The DNA was probed via the polymerase chain reaction using previously targeted marsupial Major Histocompatibility Complex (MHC) gene primers. These genes are highly variable and associated with binding and presentation of pathogens in the immune system. Twenty-three unique MHC Class II DAB V. ursinus gene sequences were translated to 21 unique predicted peptide sequences from 34 individual tissue or scat samples. Vombatus ursinus MHC Class II DAB gene and peptide sequences were most similar to other marsupial DNA and peptide sequences. Further analysis also indicated the likelihood of MHC Class II DAB family membership through motif identification. Additional sampling is required to assess the full level of diversity of MHC Class II DAB genes among V. ursinus populations; however, this study is the first to identify MHC genes in a wombat and will advance immunological and disease studies of the species.
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Mukherjee, Shomita, Arati Ramdas Gawari, Kartik Pillai, Pankaj Koparde, P. V. Karunakaran, and Nayan Khanolkar. "Diet of Rusty-spotted Cat Prionailurus rubiginosus (I. Geoffroy Saint-Hilaire, 1831) (Mammalia: Carnivora: Felidae) in Sanjay Gandhi National Park, Mumbai, India." Journal of Threatened Taxa 16, no. 5 (May 26, 2024): 25129–36. http://dx.doi.org/10.11609/jott.8898.16.5.25129-25136.
Повний текст джерелаАнотація:
The 103.68 km2 Sanjay Gandhi National Park (SGNP), Mumbai, exists amidst human densities that figure among the highest in the world. The rich biodiversity of SGNP includes the Rusty-spotted Cat Prionailurus rubiginosus, endemic to India, Sri Lanka, and Nepal, and categorised as ‘Near Threatened’ on the IUCN Red List. Little is known about its ecology and the dynamics of its coexistence with the other small carnivores in SGNP. We conducted a study with citizen volunteers to explore the diet of the Rusty-spotted Cat and other sympatric small carnivores in SGNP and in the adjoining human-dominated areas of Yeur village, Shivaji Nagar, Dahisar Quarry, and Aarey Milk Colony. After initial training, the volunteers collected scat samples from all forest ranges in SGNP and the surrounding areas outside, following defined protocols. Seventy-eight scat samples were analysed for species assignments using standardised molecular techniques, felid-specific primers, and DNA sequencing, and 24 were identified as of the Rusty-spotted Cat. The contents of the samples were examined under a microscope to identify prey remains. Results were presented as the mean number of scat samples containing remains of specific taxa with 95% Confidence Intervals. Diet estimated from 22 Rusty-spotted Cat scat samples and 52 samples of other small carnivores revealed rodents to be the major prey of the entire group. However, a higher proportion of Rusty-spotted Cat scat samples had remains of rodents (95%) and reptiles (6%) as compared to samples of other small carnivores, i.e., 79% with rodent remains and none with remains of reptiles. On the other hand, a lower proportion of Rusty-spotted Cat scat samples had remains of insects (14%), plant matter (9%), and birds (5%) than samples of other small carnivores (40% plant matter, 38% insects, 17% birds). Our results highlight the role of small carnivores, especially Rusty-spotted Cat in regulatory services through pest control.
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Gani, Millawati, Frankie Thomas Sitam, Zubaidah Kamarudin, Siti Suzana Selamat, Nik Mohd Zamani Awang, Hani Nabilia Muhd-Sahimi, Michael Wong, et al. "Unveiling prey preferences of endangered wild Malayan tiger, Panthera tigris jacksoni, in Peninsular Malaysia through scat analysis via COI DNA metabarcoding." Nature Conservation 55 (May 22, 2024): 249–68. http://dx.doi.org/10.3897/natureconservation.55.114211.
Повний текст джерелаАнотація:
Understanding the prey preference of Malayan tiger (Panthera tigris jacksoni) in Malaysia is important to guide conservation planning initiatives. The utilisation of DNA metabarcoding provides valuable insights, particularly in the field of carnivora diet research. This technique has been proven to be effective for identifying various species within complex mixtures such as scat materials, where visual identification is challenging. The Cytochrome c oxidase subunit I (COI) locus has been selected as it is a widely used as an effective non-invasive approach for diet studies. Hence, given this advance approach, Malayan tiger scats were collected on the basis of existing records of their presence in two types of habitats, namely, protected areas (PA) and human–tiger conflict (HTC) areas. This study aimed to identify prey species in Peninsular Malaysia, based on Malayan tiger scat samples using DNA metabarcoding. Based on the partial mitochondrial COI region, DNA metabarcoding led to the taxonomic resolution of prey DNA remnants in scats and the identification of prey species consumed by Malayan tiger, which were predominately small-to-medium-sized prey, including livestock. The dominant DNA prey detected belongs to the family Canidae, followed by Bovidae, Vespertilionidae, Homonidae, Felidae, Phasianidae and Muridae. A significant difference (p < 0.05) was observed in alpha and beta diversity using the Shannon index and PERMANOVA with regard to prey richness and evenness in two different habitat groups, namely, PA and HTC. Our finding provides insights into Malayan tiger dietary requirements, which can be used to develop conservation plans and strategies for Malayan tiger, particularly for habitat priorities.
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Asadobay, Pacarina, Diego O. Urquía, Sven Künzel, Sebastian A. Espinoza-Ulloa, Miguel Vences, and Diego Páez-Rosas. "Time-calibrated phylogeny and full mitogenome sequence of the Galapagos sea lion (Zalophus wollebaeki) from scat DNA." PeerJ 11 (September 28, 2023): e16047. http://dx.doi.org/10.7717/peerj.16047.
Повний текст джерелаАнотація:
Background The Galapagos sea lion, Zalophus wollebaeki, is an endemic and endangered otariid, which is considered as a sentinel species of ecosystem dynamics in the Galapagos archipelago. Mitochondrial DNA is an important tool in phylogenetic and population genetic inference. In this work we use Illumina sequencing to complement the mitogenomic resources for Zalophus genus—the other two species employed Sanger sequencing—by a complete mitochondrial genome and a molecular clock of this species, which is not present in any case. Materials and Methods We used DNA obtained from a fresh scat sample of a Galapagos sea lion and shotgun-sequenced it on the Illumina NextSeq platform. The obtained raw reads were processed using the GetOrganelle software to filter the mitochondrial Zalophus DNA reads (∼16% survive the filtration), assemble them, and set up a molecular clock. Results From the obtained 3,511,116 raw reads, we were able to assemble a full mitogenome of a length of 16,676 bp, consisting of 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNA), and two ribosomal RNAs (rRNA). A time-calibrated phylogeny confirmed the phylogenetic position of Z. wollebaeki in a clade with Z. californianus, and Z. japonicus, and sister to Z. californianus; as well as establishing the divergence time for Z. wollebaeki 0.65 million years ago. Our study illustrates the possibility of seamlessly sequencing full mitochondrial genomes from fresh scat samples of marine mammals.
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Flanders, KR, ZH Olson, and KA Ono. "Utilizing next-generation sequencing to identify prey DNA in western North Atlantic grey seal Halichoerus grypus diet." Marine Ecology Progress Series 655 (November 26, 2020): 227–40. http://dx.doi.org/10.3354/meps13520.
Повний текст джерелаАнотація:
Increasing grey seal Halichoerus grypus abundance in coastal New England is leading to social, political, economic, and ecological controversies. Central to these issues is the foraging ecology and diet composition of the seals. We studied grey seal feeding habits through next-generation sequencing of prey DNA using 16S amplicons from seal scat (n = 74) collected from a breeding colony on Monomoy Island in Massachusetts, USA, and report frequency of occurrence and relative read abundance. We also assigned seal sex to scat samples using a revised PCR assay. In contrast to current understanding of grey seal diet from hard parts and fatty acid analysis, we found no significant difference between male and female diet measured by alpha and beta diversity. Overall, we detected 24 prey groups, 18 of which resolved to species. Sand lance Ammodytes spp. were the most frequently consumed prey group, with a frequency of occurrence (FO) of 97.3%, consistent with previous studies, but Atlantic menhaden Brevoortia tyrannus, the second most frequently consumed species (FO = 60.8%), has not previously been documented in US grey seal diet. Our results suggest that a metabarcoding approach to seal food habits can yield important new ecological insights, but that traditional hard parts analysis does not underestimate consumption of Atlantic cod Gadus morhua (FO = 6.7%, Gadidae spp.) and salmon Salmo salar (FO = 0%), 2 particularly valuable species of concern.
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Brown, W. E., D. S. L. Ramsey, and R. Gaffney. "Degradation and detection of fox (Vulpes vulpes) scats in Tasmania: evidence from field trials." Wildlife Research 41, no. 8 (2014): 681. http://dx.doi.org/10.1071/wr14152.
Повний текст джерелаАнотація:
Context The Tasmanian Government is attempting to eradicate foxes from Tasmania and carnivore-scat surveys using humans and dogs combined with DNA testing are the main methods of detection. Understanding the rate that scats degrade is a key component for estimating the power of monitoring for detecting cryptic predators and will contribute to a broader understanding of the use of scat monitoring for informing eradication programs. Aims To estimate the degradation rate of fox scats and derive an estimate of the abundance of scats available to observers monitoring for fox presence. Methods In total, 486 fresh fox scats were placed at nine sites within three bioregions in Tasmania and left to degrade for up to 126 days. Scats were observed periodically by both humans and dogs to determine when they became unrecognisable and/or undetectable. Key results Recognition of scats by humans declined faster in summer than in winter and did not vary systematically among bioregions. Median survival times of scats were 19 days in summer and 26 days in winter. Recognition of scats by dogs was higher in summer than in winter, with dogs recognising scats past the time they became unrecognisable to humans. Using estimates of scat degradation derived from human observers, the equilibrium abundance of detectable scats within a fox home range was estimated to be 179–243 scats. However, the abundance of detectable scats on linear features subject to monitoring was estimated to be 10–15 scats. Conclusions Using our estimate of the abundance of scats on linear features, the current distribution of fox scats detected in Tasmania may not be as anomalous as has been suggested by others. However, fox detection from scats will be highly dependent on deposition patterns and distribution of scats on linear features and this should be critically reassessed in Tasmania. Implications Fox scats are not expected to exhibit systematic regional differences in degradation rates that might have an impact on monitoring strategies. Estimates of the abundance of scats detectable by observers are critical for assessing the effectiveness of scat-monitoring programs. We advocate that a rigorous assessment of future scat-monitoring programs in Tasmania be undertaken to determine their power to detect foxes.
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Henger, Carol S., Emily Hargous, Christopher M. Nagy, Mark Weckel, Claudia Wultsch, Konstantinos Krampis, Neil Duncan, Linda Gormezano, and Jason Munshi-South. "DNA metabarcoding reveals that coyotes in New York City consume wide variety of native prey species and human food." PeerJ 10 (September 21, 2022): e13788. http://dx.doi.org/10.7717/peerj.13788.
Повний текст джерелаАнотація:
Carnivores are currently colonizing cities where they were previously absent. These urban environments are novel ecosystems characterized by habitat degradation and fragmentation, availability of human food, and different prey assemblages than surrounding areas. Coyotes (Canis latrans) established a breeding population in New York City (NYC) over the last few decades, but their ecology within NYC is poorly understood. In this study, we used non-invasive scat sampling and DNA metabarcoding to profile vertebrate, invertebrate, and plant dietary items with the goal to compare the diets of urban coyotes to those inhabiting non-urban areas. We found that both urban and non-urban coyotes consumed a variety of plants and animals as well as human food. Raccoons (Procyon lotor) were an important food item for coyotes within and outside NYC. In contrast, white-tailed deer (Odocoileus virginianus) were mainly eaten by coyotes inhabiting non-urban areas. Domestic chicken (Gallus gallus) was the human food item found in most scats from both urban and non-urban coyotes. Domestic cats (Felis catus) were consumed by urban coyotes but were detected in only a small proportion of the scats (<5%), which differs markedly from high rates of cat depredation in some other cities. In addition, we compared our genetic metabarcoding analysis to a morphological analysis of the same scat samples. We found that the detection similarity between the two methods was low and it varied depending on the type of diet item.
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McIntyre, James K., Lisa L. Wolf, Benjamin N. Sacks, Johon Koibur, and I. Lehr Brisbin Jr. "A population of free-living highland wild dogs in Indonesian Papua." Australian Mammalogy 42, no. 2 (2020): 160. http://dx.doi.org/10.1071/am18039.
Повний текст джерелаАнотація:
A 10-day rapid assessment has confirmed a small population of indigenous wild-living dogs in the highlands of Papua Province, Indonesia. The goal of the assessment was to observe, census, assess health and reproductive status, and collect biological samples or other data for this understudied canid. Trail cameras and DNA hair traps were deployed and baited with scent attractants, and game calls were used to elicit vocal responses or lure the dogs within observation range. Adults and pups of both sexes as well as a den were documented in 149 photographs. DNA testing of scat samples confirmed a canid origin with a close relationship to other oceanic canids including NGSD (New Guinea Singing Dog) and dingoes.
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Youngmann, Jordan L., Stacey L. Lance, John C. Kilgo, Charles Ruth, Jay Cantrell, and Gino J. D’Angelo. "Assessing springtime vertebrate prey of sympatric mesopredators in the southeastern United States using metabarcoding analysis." PLOS ONE 18, no. 10 (October 25, 2023): e0293270. http://dx.doi.org/10.1371/journal.pone.0293270.
Повний текст джерелаАнотація:
Coyotes (Canis latrans) colonized the eastern United States over the last century and formed a 3-species predator guild with bobcats (Lynx rufus) and gray foxes (Urocyon cinereoargenteus) across much of the southeastern United States. Diets among the three species vary along with respective impacts on game species such as white-tailed deer (Odocoileus virginianus) and wild turkeys (Meleagris gallopavo). To determine predation impacts on vertebrate prey and dietary overlap in consumption of prey items, we assessed diets of coyote, bobcat, and gray fox during spring, coinciding with white-tailed deer fawning and wild turkey nesting and brood rearing. We sampled across three sites along the Savannah River in South Carolina from mid-May through mid-June of 2020–2021. We collected 180 scat samples along 295.9 kilometers (71.1–122.4 km/site) of unpaved secondary roads and used DNA metabarcoding to determine vertebrate diet items. We identified predator species of scat using DNA metabarcoding and species-specific mtDNA fragment analysis (153 were coyote, 20 bobcat, and seven gray fox). Overall, we found evidence that two species, coyote and bobcat, consumed deer while all three consumed turkeys. Frequency of deer in the diet varied across sites for coyotes from 62–86% and wild turkey was present with a frequency of occurrence of 9% for coyotes, 5% for bobcats, and 14% for gray fox. Vertebrate diet specialization was evident across predator species with high frequency of deer in coyote diets, rabbits and small mammals in bobcat diets, and herpetofauna in gray fox diets. During deer fawning and wild turkey nesting and brood rearing, dietary overlap appears to be mediated by disparate selection of prey items, which reduced competition among coyotes, bobcats, and gray foxes. Use of DNA metabarcoding may augment our understanding of dietary preferences within this predator guild by providing increased resolution of diet composition among important game species.
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McKELVEY, KEVIN S., JEFFREY VON KIENAST, KEITH B. AUBRY, GARY M. KOEHLER, BENJAMIN T. MALETZKE, JOHN R. SQUIRES, EDWARD L. LINDQUIST, STEVE LOCH, and MICHAEL K. SCHWARTZ. "DNA Analysis of Hair and Scat Collected Along Snow Tracks to Document the Presence of Canada Lynx." Wildlife Society Bulletin 34, no. 2 (June 2006): 451–55. http://dx.doi.org/10.2193/0091-7648(2006)34[451:daohas]2.0.co;2.
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Lee, Ping-Shin, Han Ming Gan, Gopalasamy Reuben Clements, and John-James Wilson. "Field calibration of blowfly-derived DNA against traditional methods for assessing mammal diversity in tropical forests." Genome 59, no. 11 (November 2016): 1008–22. http://dx.doi.org/10.1139/gen-2015-0193.
Повний текст джерелаАнотація:
Mammal diversity assessments based on DNA derived from invertebrates have been suggested as alternatives to assessments based on traditional methods; however, no study has field-tested both approaches simultaneously. In Peninsular Malaysia, we calibrated the performance of mammal DNA derived from blowflies (Diptera: Calliphoridae) against traditional methods used to detect species. We first compared five methods (cage trapping, mist netting, hair trapping, scat collection, and blowfly-derived DNA) in a forest reserve with no recent reports of megafauna. Blowfly-derived DNA and mist netting detected the joint highest number of species (n = 6). Only one species was detected by multiple methods. Compared to the other methods, blowfly-derived DNA detected both volant and non-volant species. In another forest reserve, rich in megafauna, we calibrated blowfly-derived DNA against camera traps. Blowfly-derived DNA detected more species (n = 11) than camera traps (n = 9), with only one species detected by both methods. The rarefaction curve indicated that blowfly-derived DNA would continue to detect more species with greater sampling effort. With further calibration, blowfly-derived DNA may join the list of traditional field methods. Areas for further investigation include blowfly feeding and dispersal biology, primer biases, and the assembly of a comprehensive and taxonomically-consistent DNA barcode reference library.
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Fischer, Ella F., Romy Müller, Matthias Todte, Anja Taubert, and Carlos Hermosilla. "Role of Free-Ranging Synanthropic Egyptian Geese (Alopochen aegyptiaca) as Natural Host Reservoirs for Salmonella spp. in Germany." Animals 13, no. 21 (November 2, 2023): 3403. http://dx.doi.org/10.3390/ani13213403.
Повний текст джерелаАнотація:
Salmonella is one of the most common and pathogenic bacteria worldwide, causing severe enteritis in humans and representing a relevant intestinal illness in One Health for young, old and immunosuppressed patients. Various Salmonella serovars have been described to be responsible for human Salmonellosis. Birds represent natural carriers of different zoonotic-relevant Salmonella serovars and Anseriformes can not only transmit Salmonella spp. to humans but also manifest clinical Salmonellosis. In this study, 138 scat samples (n = 138) of free-ranging Egyptian geese (EG; Alopochen aegyptiaca) were collected in Germany, including 83 scat samples from city parks, 30 samples from 14 public swimming pools and 25 fresh caecal samples of dead EG. Collected EG scat samples were examined for the presence of Salmonella spp. according either to the ISO 6579 (2017) norm or to a combination of bacterial pre-enrichment and specific PCR for detection of Salmonella DNA. All 138 analysed EG faecal samples resulted Salmonella-negative. Furthermore, the survival of Salmonella enterica subsp. enterica Serovar Anatum in spiked EG droppings was tested in four different concentrations of chlorinated pool water. In vitro testing demonstrated that S. Anatum-spiked EG droppings were still infectious for up to six hours in chlorinated pool water according to current German regulations for public swimming pools. This study is to be considered as a baseline investigation to clarify the role of synanthropic EG as natural carriers of zoonotic Salmonella in cities; nonetheless, large-scale epidemiological studies, including higher numbers of samples as well as more urban locations, are needed for final conclusions on the occurrence of this intestinal bacteria in neozootic EG.
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Maniscalco, John M., Alan M. Springer, Katrina L. Counihan, Tuula Hollmen, Helen M. Aderman, and Moses Toyukak, Sr. "Contemporary diets of walruses in Bristol Bay, Alaska suggest temporal variability in benthic community structure." PeerJ 8 (March 19, 2020): e8735. http://dx.doi.org/10.7717/peerj.8735.
Повний текст джерелаАнотація:
Background Pacific walruses (Odobenus rosmarus divergens) are a conspicuous and important component of the Bristol Bay ecosystem and human social systems, but very little is known about walrus ecology in this region, principally their feeding ecology. The present work provides contemporary data on the diets of walruses at four haulout locations throughout Bristol Bay between 2014 and 2018. Methods We analyzed scat and gastrointestinal tract samples from these animals using quantitative polymerase chain reaction to amplify prey DNA, which allowed for diet estimates based on frequencies of prey item occurrence and on the relative importance of dietary items as determined from DNA threshold cycle scores. Results Diets were highly diverse at all locations, but with some variation in composition that may be related to the time of year that samples were collected (summer vs. autumn), or to spatial variability in the distribution of prey. Overall, polychaetes and tunicates had the highest frequencies of occurrence and relative abundances in 2014–15, but a major change in diet appears to have occurred by 2017–18. While some sample sizes were small, diets in these later years contrasted sharply, with a greater prevalence of sea cucumbers and mollusks, and reduced importance of decapods and fishes compared to the earlier years. Prey identified in scat samples from one collection site also contrasted sharply with those reported from the same location in 1981. The apparent temporal shifts in walrus prey may represent a changing benthic ecosystem due to warming waters in recent decades.
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Rosatte, Rick, Lil Anderson, Doug Campbell, Christine Ouellet, Brad White, Tasnova Khan, Paul Van Schyndel, et al. "Further evidence of Cougars (Puma concolor) in Ontario, Canada." Canadian Field-Naturalist 129, no. 3 (October 28, 2015): 277. http://dx.doi.org/10.22621/cfn.v129i3.1728.
Повний текст джерелаАнотація:
Previous studies have indicated that Cougars (Puma concolor) were present on the Ontario landscape from 1935 to 2010. During 2012 and 2014, six pieces of evidence were collected that verified that Cougars were present in Ontario at that time. (1) A scat found near Collingwood, Ontario, was confirmed as containing Cougar DNA. (2) A Cougar was photographed by a member of the public near Pefferlaw, Ontario, and the photograph was proven to be authentic. (3) A Cougar was photographed near Kenora, Ontario. (4) A Cougar was observed near Kenora, Ontario, and tracks confirmed the sighting. (5) A Cougar attacked a dog near Bracebridge, Ontario; the animal was subsequently shot by police and DNA evidence indicated that it had at one time been in captivity. (6) A Cougar was photographed and later captured near Grafton, Ontario.
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Rosatte, Rick. "Evidence Confirms the Presence of Cougars (Puma concolor) in Ontario, Canada." Canadian Field-Naturalist 125, no. 2 (April 1, 2011): 116. http://dx.doi.org/10.22621/cfn.v125i2.1194.
Повний текст джерелаАнотація:
A study was initiated to collect and collate evidence to resolve the long-standing question of whether free-ranging Cougars (Puma concolor) exist on the Ontario landscape. A total of 497 pieces of evidence confirmed that Cougars were present in Ontario during the period 1991 to 2010. That evidence included 21 pieces of class 1 evidence (scat, hair, DNA, tracks, photographs of a Cougar), 13 class 2 sightings (by qualified observers such as biologists), and 463 class 3 sightings (credible sightings by unqualified observers). The evidence presented in this paper indicates the presence in Ontario of free-ranging Cougars of unknown origin.
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Gardner, Michael G., Mina H. Ansari, Claire E. Treilibs, Angharad Johnston, Chris R. Pavey, and C. Michael Bull. "Isolation and characterisation of microsatellites for the endangered Slater’s skink, Liopholis slateri (Squamata : Scincidae), via next-generation sequencing." Australian Journal of Zoology 65, no. 3 (2017): 200. http://dx.doi.org/10.1071/zo17053.
Повний текст джерелаАнотація:
We characterised 14 new polymorphic microsatellite loci for the endangered lizard Liopholis slateri. Initially, 454 shotgun sequencing was used to identify 46 loci, which were trialled for amplification. Subsequently, 14 of these loci were screened for variation in 21 individuals from scat-derived DNA samples collected from Owen Springs Reserve in central Australia. All 14 loci were polymorphic, with observed heterozygosity ranging from 0.19 to 0.86 and the number of alleles per locus ranging from 2 to 10. These loci will be useful in understanding the genetic variation and connectivity within and among extant L. slateri populations.
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Rahman, Md Siddiqur, Yoshitaka Nagai, H. Akiko Popiel, Muzahed Uddin Ahmed, Md Jalal Uddin, and Talsushi Toda. "Genetic testing for Spinocerebellar Ataxias (SCA) in Parkinsonism." Bangladesh Journal of Neuroscience 28, no. 1 (November 30, 2013): 16–23. http://dx.doi.org/10.3329/bjn.v28i1.17188.
Повний текст джерелаАнотація:
Objective: The study was conducted to find out Spinocerebellar Ataxias (SCA) by genetic analysis from those presenting with parkinsonism in the Neurology department of Mymensingh Medical College.Materials and methods: A sample of about 5ml blood was collected by venipuncture in EDTA tube with informed consent from the patients following institutional ethics committee approval by genetic study from 7 healthy people and 9 patients. The neurological disorder along with a complete physical and/or psychological, as well as family history and demographic data was recorded with a prescribed questionnaire by the neurologists of Mymensingh Medical College. Extraction of genomic DNA from the venous blood using FlexiGene DNA kit (Qiagen, Japan) was performed in Department of Medicine, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh. The extracted DNA was stored and accumulated and then these DNA were sent to Division of Clinical Genetics, Department of Medical Genetics, Osaka University Medical School, Suita, Osaka 565 0871, Japan for PCR and further analysis. PCR amplification of the CAG repeat was performed for the SCA1, SCA2, SCA3, SCA6 loci using primers SCA1N-F1 and SCA1N-R1, SCA2-F1 and SCA2-R1, MJDF1 and MJDR1, SCA6-F1 and SCA6-R1, respectively.Results: SCA1 PCR of both healthy individual and suspected PD patients DNA is about 250 bp (no. of CAG repeats=36). SCA2 PCR products reveal the DNA products of about 150 bp (no. of CAG repeats=23) except one patient that we suspected and it was sequenced and revealed 175bp (no. of CAG repeats=30). SCA3 PCR product size of both healthy individual and patient DNA is within about 250 (no. of CAG=11) to 300 bp (no. of CAG repeats=28) except one patient which is about 320bp and its CAG repeats is about 34. SCA6 PCR product size of both healthy individual and patient DNA is about 150bp (no. of CAG=16).Conclusion: This is the first time from Bangladesh regarding the range of CAG repeats in patients as well as healthy individual.
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Williams, Sara, Sabrina Shirazi, Karissa Hughes, Chris Abin, Linda Welch, Alexis Mychajliw, and Courtney Hofman. "Metabarcoding of American Mink Scat to Explore Shifting Baselines in the Gulf of Maine." Bulletin of the Florida Museum of Natural History 60, no. 2 (February 16, 2023): 128. http://dx.doi.org/10.58782/flmnh.nkup2567.
Повний текст джерелаАнотація:
The mink (Neogale sp.) has been important species in North American ecosystems and communities for millennia; before European colonization, Indigenous families hunted and trapped mink for their pelts. As part of the euro-colonial fur trade (~1600-1900), wide-spread and intense harvest of mink and other furbearers transformed ecosystems, including the likely extinction of the sea mink (Neogale macrodon) in the Gulf of Maine. The American mink (Neogale vison) has slowly moved into areas that were previously inhabited by the sea mink in coastal and island Maine. The expansion of American mink has been implicated as a potential cause for the declining seabird populations on Maine islands. Here, we use metabarcoding of American mink scat collected in the USFWS Maine Coastal Islands National Wildlife Refuge to evaluate if American mink are predating upon seabirds. Preliminary analysis of mink scat from Petit Manan Island has not implicated mink in bird predation but we did recover host DNA and dietary components including lobster and fish (Cunner). Currently, managers remove American mink from the Refuge islands to protect nesting seabirds but perhaps the seabird populations are returning to population sizes of when sea mink was present in the area. Harvest of furbearers as part of the euro-colonial fur trade may still have implications for ecosystem form and function today.
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Akrim, Faraz, Tariq Mahmood, Tamara Max, Muhammad Sajid Nadeem, Siddiqa Qasim, and Shaista Andleeb. "Assessment of bias in morphological identification of carnivore scats confirmed with molecular scatology in north-eastern Himalayan region of Pakistan." PeerJ 6 (July 16, 2018): e5262. http://dx.doi.org/10.7717/peerj.5262.
Повний текст джерелаАнотація:
Scats are often used to study ecological parameters of carnivore species. However, field identification of carnivore scats, based on their morphological characteristics, becomes difficult if many carnivore species are distributed in the same area. We assessed error rates in morphological identification of five sympatric carnivores’ scats in north-eastern Himalayan region of Pakistan during 2013–2017. A sample of 149 scats were subjected to molecular identification using fecal DNA. We used a confusion matrix to assess different types of errors associated with carnivore scat identification. We were able to amplify DNA from 96.6% (n = 144) of scats. Based on field identification of carnivore scats, we had predicted that out of 144 scats: 11 (7.6%) scats were from common leopard, 38 (26.4%) from red fox, 29 (20.1%) from Asiatic jackal, 37 (25.7%) from yellow throated martin, 14 (9.7%) from Asian palm civet and 15 (10.4%) from small Indian civet. However, molecular identification revealed and confirmed nine were scats (6.24%) from common leopard, 40 (27.8 %) from red fox, 21 (14.6%) from Asiatic jackal, 45 (31.25%) from Asian palm civet, 12 (8.3%) scats from small Indian civet, while 11 scats (7.6%) were found from Canis lupus Spp., three (2%) from dog, one (0.7 %) scat sample from porcupine, and two (1.4%) from rhesus monkey. Misidentification rate was highest for Asian palm civet (25.7%), followed by red fox (11.1%) and Asiatic jackal (9.7%) but least for common leopard scats (4.2%). The results specific to our study area concur with previous studies that have recommended that carnivore monitoring programs utilize molecular identification of predator scats. Using only morphological identification of scats can be misleading and may result in wrong management decisions.
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Stevens, Kara, Alex Dehgan, Maria Karlstetter, Farid Rawan, Muhammad Ismail Tawhid, Stephane Ostrowski, Jan Mohammad Ali, and Rita Ali. "Large mammals surviving conflict in the eastern forests of Afghanistan." Oryx 45, no. 2 (April 2011): 265–71. http://dx.doi.org/10.1017/s0030605310000517.
Повний текст джерелаАнотація:
AbstractWe used transect and camera-trap surveys and DNA identification of scat samples to provide the first update since 1977 of large mammals in the montane forests of the conflict-ridden province of Nuristan in eastern Afghanistan. Nuristan contains a range of habitats from oak Quercus spp. forests to treeless alpine steppes that historically hosted populations of markhor Capra falconeri, Asiatic black bear Ursus thibetanus, grey wolf Canis lupus and common leopard Panthera pardus, among others. Surveys conducted in 2006–2009 in an area of 1,100 km2 by the Wildlife Conservation Society confirmed the presence of some of these species, and also recorded the common palm civet Paradoxurus hermaphroditus, previously unknown from Afghanistan; this extends the westernmost boundary for this species. The most commonly recorded species, as determined by direct sightings, scat identification or camera-trap photographs, were the Indian crested porcupine Hystrix indica, red fox Vulpes vulpes and a canid (grey wolf or golden jackal Canis aureus). Despite indications of significant habitat loss and unsustainable hunting, globally important species persist in the area and targeted conservation programmes are required for the protection of these species, the forests they inhabit and the surrounding communities who depend on both for their survival.
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Izzo, Antonio D., Marc Meyer, James M. Trappe, Malcolm North, and Thomas D. Bruns. "Hypogeous Ectomycorrhizal Fungal Species on Roots and in Small Mammal Diet in a Mixed-Conifer Forest." Forest Science 51, no. 3 (June 1, 2005): 243–54. http://dx.doi.org/10.1093/forestscience/51.3.243.
Повний текст джерелаАнотація:
Abstract The purpose of this study was to estimate the portion of an ectomycorrhizal (ECM) fungi root community with a hypogeous fruiting habit. We used molecular methods (DNA sequence analysis of the internally transcribed spacer [ITS] region of rDNA) to compare three viewpoints: ECM fungi on the roots in a southern Sierra Nevada Abies-dominated old-growth forest, fungi in scat samples collected from small mammals in the same forest, and hypogeous sporocarps found throughout the Sierra Nevada. We found that hypogeous taxa accounted for a minimum of 21% of the species and 25–40% of the dry root biomass of all samples. This estimate is two to three times greater than estimates from previous studies. This difference may be due to methodological advantages of this study, but may also be related to conditions in dry forests typical of western North America where prolonged drought may favor this form of fruiting. Although molecular analysis of scat samples did not add to our view of the ECM roots, we readily isolated sequences from Rhizopogon species. From these results we inferred that two species, R. occidentalis and R. olivaceotinctus, are represented primarily in the spore bank and may be dependent on substantial disturbance to become abundant on roots. FOR. SCI. 51(3):243–254.
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Dawson, Stuart J., Heather M. Crawford, Robert M. Huston, Peter J. Adams, and Patricia A. Fleming. "How to catch red foxes red handed: identifying predation of freshwater turtles and nests." Wildlife Research 43, no. 8 (2016): 615. http://dx.doi.org/10.1071/wr16066.
Повний текст джерелаАнотація:
Context Predation is one of the key contributors to mortality in freshwater turtles. Confirming the identity of predators is an important step towards conservation management action. Throughout Australia, the red fox (Vulpes vulpes) is suspected to apply significant and unsustainable predation pressure to turtle populations, killing adults and depredating nests; however methods for confirming this are limited. Aims The present study used a range of methods to confirm predation of oblong turtle (Chelodina colliei) nests and adults by the introduced red fox. Methods First, depredated adult carapaces, and turtle egg-shell fragments from excavated nests were swabbed and analysed for trace DNA. Second, we used artificial turtle nests, monitored by camera traps, to analyse seasonal changes in the behaviour of foxes around sites where turtle nests are present, including over the nesting season. Last, we used scat analysis to identify the prevalence of turtle remains in fox diet. Key results Predominantly fox DNA was recovered from both adult carapaces and depredated eggs. In addition, camera traps recorded only foxes depredating artificial nests. Despite this evidence that foxes kill adults and excavated nests, we found that turtle remains were only a small part of the diet of foxes at this study site (hatchling or turtle egg shell were present in only 4% of 230 scats sampled). The diet of these foxes was largely anthropogenic-sourced foods, such as fruit (e.g. figs, grapes, melons; 81% of scats), sheep carrion (41%) and rodents (36%). Conclusions We conclude that DNA analysis, camera trapping and scat analysis are effective methods of identifying foxes as predators of adult turtle, and their nests. Furthermore, we found that anthropogenic foods (orchard crops, livestock or synanthropic species) may subsidise greater fox population size than might occur in their absence, thereby increasing potential pressure on these freshwater turtles. Implications Our findings give credence to the argument that foxes are effective predators of turtle adults and nests. In addition, the high proportion of anthropogenic food sources in the diet of foxes, and potential subsidisation, is an important consideration for land managers.
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McInnes, Julie C., Louise Emmerson, Colin Southwell, Cassandra Faux, and Simon N. Jarman. "Simultaneous DNA-based diet analysis of breeding, non-breeding and chick Adélie penguins." Royal Society Open Science 3, no. 1 (January 2016): 150443. http://dx.doi.org/10.1098/rsos.150443.
Повний текст джерелаАнотація:
As central place foragers, breeding penguins are restricted in foraging range by the need to return to the colony to feed chicks. Furthermore, breeding birds must balance energetic gain from self-feeding with the costs of returning to provision young. Non-breeding birds, however, are likely to be less restricted in foraging range and lack the high energy demands of provisioning, therefore may consume different prey to breeders. We used DNA dietary analysis to determine whether there was a difference in provisioning and self-feeding diet by identifying prey DNA in scat samples from breeding and chick Adélie penguins at two locations in East Antarctica. We also investigated diet differences between breeders and non-breeders at one site. Although previous work shows changing foraging behaviour between chick provisioning and self-feeding, our results suggest no significant differences in the main prey groups consumed by chicks and breeders at either site or between breeding stages. This may reflect the inability of penguins to selectively forage when provisioning, or resources were sufficient for all foraging needs. Conversely, non-breeders were found to consume different prey groups to breeders, which may reflect less restricted foraging ranges, breeders actively selecting particular prey during breeding or reduced foraging experience of non-breeders.
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Momeni, Sogol, Mansoureh Malekian, and Mahmoud-Reza Hemami. "Molecular versus morphological approaches to diet analysis of the caracal (Caracal caracal)." Mammalia 83, no. 6 (November 26, 2019): 586–92. http://dx.doi.org/10.1515/mammalia-2017-0161.
Повний текст джерелаАнотація:
Abstract Diet analysis is an essential part in understanding the biology of a species and functioning of ecosystems. Traditional morphological identification of undigested remains in the scats and molecular analyses of prey species’ DNA have previously been used to assess diet. In the present study, caracal diet in the Abbasabad Wildlife Refuge, Central Iran, was investigated using both molecular and morphological methods. We collected 22 scat samples from caracal dens in the region. Feces were washed on sieves and their remaining components were morphologically identified. We also targeted a 307-base pair fragment of the cytochrome b gene to amplify and sequence the species’ DNA. Morphological analyses revealed that 76% of the diet comprised rodent species. We identified a total of nine prey taxa using the molecular method, including six rodents, one hare, one hedgehog and one wild goat. There was a general agreement between the molecular and morphological results; however, molecular methods tended to allow a better identification of the prey species. Therefore, the DNA-based approach acts as a valuable complement to current morphological methods in the study of a rare felid’s diet when no hair reference library exists.
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Baeza, J. Antonio, Ryan Barata, Dilani Rajapakse, Jayra Penaloza, Preston Harrison, and Adam Haberski. "Mitochondrial Genomes Assembled from Non-Invasive eDNA Metagenomic Scat Samples in Critically Endangered Mammals." Genes 14, no. 3 (March 5, 2023): 657. http://dx.doi.org/10.3390/genes14030657.
Повний текст джерелаАнотація:
The abundance of many large-bodied vertebrates, both in marine and terrestrial environments, has declined substantially due to global and regional climate stressors that define the Anthropocene. The development of genetic tools that can serve to monitor population’s health non-intrusively and inform strategies for the recovery of these species is crucial. In this study, we formally evaluate whether whole mitochondrial genomes can be assembled from environmental DNA (eDNA) metagenomics scat samples. Mitogenomes of four different large vertebrates, the panda bear (Ailuropoda melanoleuca), the moon bear (Ursus thibetanus), the Java pangolin (Manis javanica), and the the North Atlantic right whale (Eubalaena glacialis) were assembled and circularized using the pipeline GetOrganelle with a coverage ranging from 12x to 480x in 14 out of 18 different eDNA samples. Partial mitochondrial genomes were retrieved from three other eDNA samples. The complete mitochondrial genomes of the studied species were AT-rich and comprised 13 protein coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and a putative D-loop/control region. Synteny observed in all assembled mitogenomes was identical to that reported for specimens of the same and other closely related species. This study demonstrates that it is possible to assemble accurate whole mitochondrial chromosomes from eDNA samples (scats) using forthright bench and bioinformatics workflows. The retrieval of mitochondrial genomes from eDNA samples represents a tool to support bioprospecting, bio-monitoring, and other non-intrusive conservation strategies in species considered ‘vulnerable’, ‘endangered’, and/or ‘critically endangered’ by the IUCN Red List of Threatened Species.
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Quéméré, Erwan, Marie Aucourd, Valérie Troispoux, Sébastien Brosse, Jérôme Murienne, Raphaël Covain, Pierre‐Yves Le Bail, Jean Olivier, Niklas Tysklind, and Maxime Galan. "Unraveling the dietary diversity of Neotropical top predators using scat DNA metabarcoding: A case study on the elusive Giant Otter." Environmental DNA 3, no. 5 (May 4, 2021): 889–900. http://dx.doi.org/10.1002/edn3.195.
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Lin, Xiaozhan, Changxu Tian, Yang Huang, Hongjuan Shi, and Guangli Li. "Comparative Transcriptome Analysis Identifies Candidate Genes Related to Black-Spotted Pattern Formation in Spotted Scat (Scatophagus argus)." Animals 11, no. 3 (March 10, 2021): 765. http://dx.doi.org/10.3390/ani11030765.
Повний текст джерелаАнотація:
Spotted scat (Scatophagus argus) is an economically important marine aquaculture and ornamental fish species in Asia, especially in southeast China. In this study, skin transcriptomes of S. argus were obtained for three types of skin, including black-spotted skin (A), non-spotted skin (B) and caudal fin (C). A total of nine complementary DNA (cDNA) libraries were obtained by Illumina sequencing. Bioinformatics analysis revealed that 1358, 2086 and 487 genes were differentially expressed between A and B, A and C, and B and C, respectively. The results revealed that there were 134 common significantly differentially expressed genes (DEGs) and several key genes related to pigment synthesis and pigmentation, including tyrp1, mitf, pmel, slc7a2, tjp1, hsp70 and mart-1. Of these, some DEGs were associated with pigmentation-related Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, such as tyrosine metabolism, melanogenesis, the Wnt signaling pathway and the mitogen-activated protein kinase (MAPK) signaling pathway. The results will facilitate understanding the molecular mechanisms of skin pigmentation differentiation in S. argus and provide valuable information for skin coloration, especially the formation of spotted patterns on other marine fish species.
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Dufault, Michelle N., Zachary H. Olson, Dominique M. Mellone, Kelly R. Flanders, and Kathryn A. Ono. "Flatfish may be underestimated in the diet of gray seals (Halichoerus grypus)." Canadian Journal of Zoology 99, no. 3 (March 2021): 227–34. http://dx.doi.org/10.1139/cjz-2020-0145.
Повний текст джерелаАнотація:
The United States east coast population of the gray seal (Halichoerus grypus (Fabricius, 1791)) was once hunted to near extirpation, but the population has since rebounded due to protection by the Marine Mammal Protection Act of 1972. Although this population growth is seen as a success by conservationists, others are concerned about the economic and ecological impact of gray seals on New England fisheries. The study objective was to quantify flatfish presence in the diet of gray seals using an analysis of prey DNA in seal scat (molecular scatology). This may reduce a potential bias in other diet analysis methods since flatfish may not be swallowed whole, and therefore, their identifying otoliths may not be present. Scats were collected from Muskeget and Monomoy islands off Cape Cod, Massachusetts, USA, in 2016, 2017, and 2018 and analyzed for flatfish presence using species-specific polymerase chain reaction (PCR) assays and a hard parts analysis using otoliths. Frequency of occurrence for flatfish species from DNA was higher than estimated in previous literature on gray seal diet and a concurrent otolith analysis of the same samples, suggesting that previous analyses may have potentially underestimated the importance of flatfish in the diet.