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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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Vertebrate roadkill en Andalusia

Vertebrate roadkill en Andalusia

Although roadkill studies on a large scale are challenging, they can provide valuable information to assess the impact of road traffic on animal populations. Over 22 months, 45 road sections of 10 km within a global biodiversity hotspot in Andalusia, in southern Spain, were surveyed. The region was divided into five ecoregions differing in environmental conditions and landscape characteristics and the relative magnitude, composition and spatiotemporal patterns of vertebrate (birds, mammal, amphibians, and reptiles) mortality were recorded. Roadkill data from monthly surveys of road stretches with different speed limits, traffic volume, road design, and adjacent landscape composition were used. Roadkills varied over time and were not randomly distributed across ecoregions and road types. Overall, the groups most frequently encountered were mammals (54.4 % of total roadkills) and birds (36.2 %). Mortality rates in these two groups were higher on highways than on national or local roads, whereas those of amphibians (4.6 %) and reptiles (4.3 %) did not differ between road types. Except for mammals, the observed variation in vertebrate roadkills across ecoregions reflects the patterns of species richness previously described in the literature. Roadkills were concentrated over relatively short periods and this pattern was repeated over study periods and for all vertebrate classes. These findings provide baseline information about road types, time periods and taxa with a higher probability of roadkills across an extensive region. These data represent an essential step towards the future implementation of broad–scale mitigation measures. informacion[at]ebd.csic.es: Canal et al (2018) Magnitude, composition and spatiotemporal patterns of vertebrate roadkill at regional scales: a study in southern Spain. Anim Biodiv Conserv 41.2: 281–300


http://abc.museucienciesjournals.cat/volum-41-2-2018-abc/magnitude-composition-and-spatiotemporal-patterns-of-vertebrate-roadkill-at-regional-scales-a-study-in-southern-spain/?lang=es