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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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Identified the main introduction routes of the red swamp crayfish Procambarus clarkii during its global-scale invasion

Identified the main introduction routes of the red swamp crayfish Procambarus clarkii during its global-scale invasion

This North American species is the most widely spread freshwater crayfish worldwide, and is one of the worst invasive species due to its severe impacts on the structure and functioning of freshwater ecosystems. The results of the study may help to prevent the further expansion of the red swamp crayfish and to avoid potential future invasions. The invasion routes followed by the red swamp crayfish during its human-driven expansion were reconstructed based on the analysis of a mitochondrial gene (COI), which was sequenced for 1,412 crayfish from 122 populations across the Northern Hemisphere. The article describes how different invasion scenarios have produced different genetic patterns among invasive populations. For example, in the US there are two main invasion routes, west- and east-wards from the native area. The invasive populations in the west are genetically more diverse, because they have received more introductions, which probably involved more individual crayfish, starting in the 1920s. The genetic results show that western US (California), itself an invaded area, was the source of the crayfish populations established in Hawaii and a probable source of the crayfish introduced to Japan, and from there to China, in the late 1920s. The low genetic diversity of all red swamp crayfish populations studied in Asia supports documentary evidence that a small group of some 20 individuals may have been the origin of the Japanese and Chinese red swamp crayfish populations which now number into the millions. The red swamp crayfish was introduced twice from Louisiana to south-western Spain, in 1973 (near the city of Badajoz) and 1974 (in the Guadalquivir River marshes). These introductions were promoted by the aristocrat Andrés Salvador de Habsburgo-Lorena. Until now, it has been assumed that these introductions were the sole origin of all red swamp crayfish populations established across Europe, but the new study finds evidence of a separate, later introduction. The large number of individuals involved in the two introduction events (around 500 in Badajoz and 6,000 in the Guadalquivir marshes) has led to the high genetic diversity levels observed in Iberian populations, although diversity values tend to be lower as populations are further away from the introduction foci. However, in this study a genetic profile in central-western Europe that is not present in the Iberian Peninsula was also unexpectedly detected, a finding that suggests that additional unrecorded introductions of the red swamp crayfish into Europe may have occurred, either from the US or from other invaded territories. información[at]ebd.csic.es: Oficialdegui et al (2019) Unravelling the global invasion routes of a worldwide invader, the red swamp crayfish (Procambarus clarkii). Freshwater Biol https://doi.org/10.1111/fwb.13312 


https://onlinelibrary.wiley.com/doi/full/10.1111/fwb.13312