Issue 7.1 is now online!
As always, the first issue of the year is our sample issue. You can access all of the articles online free of charge. No subscription or membership is required!
We have two Open Access articles and two Applications papers in our January issue.
– Recognizing False Positives: Environmental DNA (eDNA) is increasingly used for surveillance and detection of species of interest in aquatic and soil samples. A significant risk associated with eDNA methods is potential false-positive results due to laboratory contamination. To minimize and quantify this risk, Chris Wilson et al. designed and validated a set of synthetic oligonucleotides for use as species-specific positive PCR controls for several high-profile aquatic invasive species.
– BiMat: An open-source MATLAB package for the study of the structure of bipartite ecological networks. BiMat enables both multiscale analysis of the structure of a bipartite ecological network – spanning global (i.e. entire network) to local (i.e. module-level) scales – and meta-analyses of many bipartite networks simultaneously. The authors have chosen to make this Applications article Open Access.
Gemma Murray et al. provide this month’s second Open Access article. In ‘The effect of genetic structure on molecular dating and tests for temporal signal‘ the authors use simulated data to investigate the performance of several tests of temporal signal, including some recently suggested modifications. The article shows that all of the standard tests of temporal signal are seriously misleading for data where temporal and genetic structures are confounded (i.e. where closely related sequences are more likely to have been sampled at similar times). This is not an artifact of genetic structure or tree shape per se, and can arise even when sequences have measurably evolved during the sampling period.
This month’s cover image depicts an adult Daphnia in the foreground, with a looming predator nearby. Daphnia zooplankton are a plentiful meal for fish predators in freshwater systems. They are not helpless, however, as they have evolved a number of mechanisms for predator avoidance, including the ability to increase rates of development and produce defensive morphologies in the presence of predators. Furthermore, these traits are sometimes passed onto their offspring. This Daphnia carries a number of eggs, and the growth rates and morphologies of these offspring may be influenced by the mother’s detection of the fish predator.
In the article associated with this image, Drew Schield et al. sought to develop a method for understanding the degree to which genome-wide epigenetic changes across generations are associated with changes in environmental variables (such as chemicals associated with predators). The resulting method, epiRADseq, which is a restriction enzyme DNA fragment associated next generation sequencing technique, allows for the detection of continuously variable methylation states throughout the genome. While applicable to many diverse questions related to epigenetic regulation, the method was demonstrated on a clonal Daphnia system. First generation Daphnia were introduced to fish predator cues and the second generation was raised in the absence of predator cues. Using epiRADseq, the authors discovered significant shifts in methylation state across several thousand genomic regions. Additionally, many of these loci were found to be in or nearby protein-coding genes. Due to a lack of genetic differences across clonal generations, differences in phenotype between first and second generation Daphnia in response to predation are likely directed by epigenetic modifications like those identified using this new method.
Photo © Drew Schield, University of Texas at Arlington
Original Images used to create the cover © Hajime Watanabe (Daphnia) and US Fish and Wildlife (Bluegill)
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