What We’re Reading- Aug 28, 2015

Congratulations to SNPits blogger Anna on her new paper (sub) on DNA barcoding for invasive red foxes (Vulpes vulpes) in Tazmania. She wrote an accompanying blog post about the paper.

From Benchtop to Desktop: Important Considerations when Designing Amplicon Sequencing Workflows
Amplicon sequencing (PCR and sequencing of specific target genes) using high throughput sequencing platforms has become an important tool for biodiversity assessments, dietary studies etc. Quite a bit of attention has been paid to the pros and cons of the different sequencing platforms used and the bioinformatic approaches to data analysis, but there has been less focus in the literature on study design and the laboratory steps leading up to and including library preparation. This is unfortunate, because, as in the words of Murray et al. “No amount of high-end bioinformatics can compensate for poorly prepared samples…”. This paper provides a great overview of amplicon library preparation, outlining some of the pitfalls for the unwary, and describing the strategies and controls needed to provide confidence in the sequences obtained.

Vive La Résistance: Reviving Resistance for 21st Century Conservation
Resilience is an important concept in ecology, that helps us to understand how ecosystems respond to changes. This paper outlines how the traditional idea of “ecological resilience” can be divided into two components: resistance, which reflects the ability of an ecosystem to persist during a disturbance; and resilience, which reflects the ability of an ecosystem to recover once the disturbance has ceased. The authors show how understanding this “resistance-resilience framework” can contribute to conservation and management by improving our understanding of ecosystem responses to disturbance.

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