Predicting shifts in parasite distribution with climate change: a multitrophic level approach

Climate change likely will lead to increasingly favourable environmental conditions for many parasites. However, predictions regarding parasitism's impacts often fail to account for the likely variability in host distribution and how this may alter parasite occurrence. Here, we investigate potential distributional shifts in the meningeal worm, Parelaphostrongylosis tenuis, a protostrongylid nematode commonly found in white‐tailed deer in North America, whose life cycle also involves a free‐living stage and a gastropod intermediate host. We modelled the distribution of the hosts and free‐living larva as a complete assemblage to assess whether a complex trophic system will lead to an overall increase in parasite distribution with climate change, or whether divergent environmental niches may promote an ecological mismatch. Using an ensemble approach to climate modelling under two different carbon emission scenarios, we show that whereas the overall trend is for an increase in niche breadth for each species, mismatches arise in habitat suitability of the free‐living larva vs. the definitive and intermediate hosts. By incorporating these projected mismatches into a combined model, we project a shift in parasite distribution accounting for all steps in the transmission cycle, and identify that overall habitat suitability of the parasite will decline in the Great Plains and southeastern USA, but will increase in the Boreal Forest ecoregion, particularly in Alberta. These results have important implications for wildlife conservation and management due to the known pathogenicity of parelaphostrongylosis to alternate hosts including moose, caribou and elk. Our results suggest that disease risk forecasts which fail to consider biotic interactions may be overly simplistic, and that accounting for each of the parasite's life stages is key to refining predicted responses to climate change.     

Aquatic Ecosystem Responses to Rapid Recovery from Extreme Acidification and Metal Contamination in Lakes Near Wawa, Ontario

In the region northeast of Wawa, Ontario (Canada), many circumneutral lakes downwind of a nearby iron-sintering plant were strongly acidified (pH 3–4) in response to the emissions of large amounts of sulfur dioxide from 1939–1998. Following closure of the plant in 1998, lakewater pH has returned to circumneutral conditions due to the high buffering capacity of the local geological substrate. Prior paleolimnological analyses of dated sediment cores have detected some biological recovery among algal communities (diatoms and chrysophytes), although they have not returned to their pre-impact assemblages. Here we take a broader ecosystem approach, and build upon the algal analyses by examining cladoceran sedimentary assemblages, and spectrally-inferred chlorophyll a and dissolved organic carbon (DOC) from the same dated sediment cores. Similar to the algal communities, recent cladoceran sedimentary assemblages from three impacted lakes remain in an altered state relative to the pre-impact period (for example, increased relative abundances of Chydorus brevilabris and reduced cladoceran density in sediments). However, trends in the spectrally-inferred chlorophyll a and DOC were mixed, with long-term decreases in the study lake closest to the plant and long-term increases within the other lakes. Collectively, the multi-proxy paleolimnological analyses of these markedly acidified lakes demonstrate the delayed biological recovery from acidification (and differences in timing) across multiple trophic levels, despite the near-elimination of acid deposition almost a decade previously, which led to a striking recovery in lakewater pH and increased food availability.     

Wheat Zapper: a flexible online tool for colinearity studies in grass genomes

In the course of evolution, the genomes of grasses have maintained an observable degree of gene order conservation. The information available for already sequenced genomes can be used to predict the gene order of nonsequenced species by means of comparative colinearity studies. The “Wheat Zapper” application presented here performs on-demand colinearity analysis between wheat, rice, Sorghum, and Brachypodium in a simple, time efficient, and flexible manner. This application was specifically designed to provide plant scientists with a set of tools, comprising not only synteny inference, but also automated primer design, intron/exon boundaries prediction, visual representation using the graphic tool Circos 0.53, and the possibility of downloading FASTA sequences for downstream applications. Quality of the “Wheat Zapper” prediction was confirmed against the genome of maize, with good correlation (r?>?0.83) observed between the gene order predicted on the basis of synteny and their actual position on the genome. Further, the accuracy of “Wheat Zapper” was calculated at 0.65 considering the “Genome Zipper” application as the “gold” standard. The differences between these two tools are amply discussed, making the point that “Wheat Zapper” is an accurate and reliable on-demand tool that is sure to benefit the cereal scientific community. The Wheat Zapper is available at http://wge.ndsu.nodak.edu/wheatzapper/.     

The spatial patterns of directional phenotypic selection

Local adaptation, adaptive population divergence and speciation are often expected to result from populations evolving in response to spatial variation in selection. Yet, we lack a comprehensive understanding of the major features that characterise the spatial patterns of selection, namely the extent of variation among populations in the strength and direction of selection. Here, we analyse a data set of spatially replicated studies of directional phenotypic selection from natural populations. The data set includes 60 studies, consisting of 3937 estimates of selection across an average of five populations. We performed meta‐analyses to explore features characterising spatial variation in directional selection. We found that selection tends to vary mainly in strength and less in direction among populations. Although differences in the direction of selection occur among populations they do so where selection is often weakest, which may limit the potential for ongoing adaptive population divergence. Overall, we also found that spatial variation in selection appears comparable to temporal (annual) variation in selection within populations; however, several deficiencies in available data currently complicate this comparison. We discuss future research needs to further advance our understanding of spatial variation in selection.     

MetAMOS: a modular and open source metagenomic assembly and analysis pipeline

We describe MetAMOS, an open source and modular metagenomic assembly and analysis pipeline. MetAMOS represents an important step towards fully automated metagenomic analysis, starting with next-generation sequencing reads and producing genomic scaffolds, open-reading frames and taxonomic or functional annotations. MetAMOS can aid in reducing assembly errors, commonly encountered when assembling metagenomic samples, and improves taxonomic assignment accuracy while also reducing computational cost. MetAMOS can be downloaded from: https://github.com/treangen/MetAMOS.