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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] 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
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Cities may save some threatened species but not their ecological functions

Cities may save some threatened species but not their ecological functions

Urbanization is one of the main causes of biodiversity loss worldwide. Wildlife responses to urbanization, however, are greatly variable and, paradoxically, some threatened species may achieve much larger populations in urban than in natural habitats. Urban conservation hotspots may therefore help some species avoid regional or even global extinctions, but not conserve their often overlooked ecological functions in the wild. This issue is being addressed in this study by using two species of globally threatened parrots occurring in the Dominican Republic: the Hispaniolan amazon (Amazona ventralis) and the Hispaniolan parakeet (Psittacara chloropterus). A large-scale roadside survey was conducted in June 2017 across the country to estimate the relative abundance of parrots in natural habitats, rural habitats, and cities. Relative abundances of both parrot species were negligible in rural areas and very low in natural habitats. They were generally between one and two orders of magnitude lower than that of congeneric species inhabiting other Neotropical ecosystems. Relative abundances were six times higher in cities than in natural habitats in the case of the Hispaniolan parakeet and three times higher in the case of the Hispaniolan amazon. People indicated hunting for a source food and to mitigate crop damage as causes of parrot population declines, and a vigorous illegal trade for parrots (131 individuals recorded, 75% of them poached very recently), mostly obtained from protected areas where the last small wild populations remain. Parrots were observed foraging on 19 plant species from 11 families, dispersing the fruits of 14 species by carrying them in their beaks and consuming them in distant perching trees. They discarded undamaged mature seeds, with the potential to germinate, in 99.5% of cases (n = 306), and minimum dispersal distances ranged from 8 to 155 m (median = 37 m).The loss of ecological functions provided by some species when they disappear from natural habitats and only persist in cities may have long-term, unexpected effects on ecosystems. This study demonstrates how two cities may soon be the last refuges for two endemic parrots if overharvesting continues, in which case their overlooked role as seed dispersers would be completely lost in nature. The functional extinction of these species could strongly affect vegetation communities in an island environment where seed-dispersal species are naturally scarce. While conservation plans must include urban populations of threatened species, greater efforts are needed to restore their populations in natural habitats to conserve ecological functions. informacion[at] Luna et al (2018) Cities may save some threatened species but not their ecological functions. PeerJ 6:e4908 Doi 10.7717/peerj.4908