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Optimization of protocols for DNA extraction from fecal samples

High-throughput sequencing offers new possibilities in molecular ecology and conservation studies. However, its potential has not yet become fully exploited for noninvasive studies of free–ranging animals, such as those based on feces. High–throughput sequencing allows sequencing of short DNA fragments and could allow simultaneous genotyping of a very large number of samples and markers at a low cost. The application of high throughput genotyping to fecal samples from wildlife has been hindered by several labor intensive steps. Alternative protocols which could allow higher throughput were evaluated for two of these steps: sample collection and DNA extraction. Two different field sampling and seven different DNA extraction methods were tested on grey wolf (Canis lupus) feces. There was high variation in genotyping success rates. The field sampling method based on surface swabbing performed much worse than the extraction from a fecal fragment. In addition, there is a lot of room for improvement in the DNA extraction step. Optimization of protocols can lead to very much more efficient, cheaper and higher throughput noninvasive monitoring. Selection of appropriate markers is still of paramount importance to increase genotyping success. informacion[at]ebd.csic.es: Sarabia et al (2020) Towards high-throughput analyses of fecal samples from wildlife. Animal Biodiver Conserv 43.2: 271–283 Doi 10.32800/abc.2020.43.0271


http://abc.museucienciesjournals.cat/volum-43-2-2020/towards-high-throughput-analyses-of-fecal-samples-from-wildlife/?lang=en
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SpotEgg: a tool to analyse colour in digital images

SpotEgg: a tool to analyse colour in digital images

A user-friendly tool, called SpotEgg, has been developed to analyse colour and pattering in digital images. The tool, operated through a Graphical User Interface, runs over Matlab 2012b or latter and was primarily aimed to analyse colouration in bird´s eggs. Nevertheless it can also measure reflectances and spottiness in any other type of objects as insects, feathers, frogs, etc. SpotEgg's main advantage is a custom designed spot detection algorithm. Additionally, it allows to reduce time-consuming routinary tasks when analysing digital images. The tool is available for downloading at the following webpage: https://www2.imse-cnm.csic.es/~linan/SPOTEGG/SpotEgg_Web_Site/main.html. informacion[at]ebd.csic.es: Gomez & Liñan-Cembrano (2016) SpotEgg: An image-processing tool for automatised analysis of colouration and spottiness. J Avian Biol doi: [10.1111/jav.01117]


http://onlinelibrary.wiley.com/wol1/doi/10.1111/jav.01117/abstract