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van Bleijswijk, J.

Publications and source records attributed to van Bleijswijk, J..

2 recordsLinked to original sources

Disentangling the diet composition of chicks of Arctic shorebirds provides a new perspective on trophic mismatches

With rapid climatic changes over the past decades, organisms living in seasonal environments are suggested to increasingly face trophic mismatches: the disruption of synchrony between different trophic levels due to a different phenological response to increasing temperatures. Strong effects of mismatches are especially expected in the Arctic region, where climatic changes are most rapid. Nevertheless, relatively few studies have found strong evidence for trophic mismatches between the breeding period of Arctic-breeding shorebirds and the arthropod prey on which they rely. Here we argue that this is potentially caused by a generalisation of trophic interactions. While many studies have measured the mismatch relative to the peak in abundance of all available arthropod species, we use metabarcoding of prey items in faeces to show that chicks of four different shorebird species (red knot, curlew sandpiper, little stint, and red phalarope) strongly differ in their arthropod diet. Three out of the four species feed on arthropods peaking in availability five-ten days before the overall arthropod peak which had implications for the calculations of trophic mismatches. We conclude that ignoring diet selectivity hampers our understanding of phenological mismatches.

ecology↗

Cascabel: a flexible, scalable and easy-to-use amplicon sequence data analysis pipeline

Marker gene sequencing of the rRNA operon (16S, 18S, ITS) or cytochrome c oxidase I (CO1) is a popular means to assess microbial communities of the environment, microbiomes associated with plants and animals, as well as communities of multicellular organisms via environmental DNA sequencing. Since this technique is based on sequencing a single gene rather than the entire genome, the number of reads needed per sample is lower than that required for metagenome sequencing, making marker gene sequencing affordable to nearly any laboratory. Despite the relative ease and cost-efficiency of data generation, analyzing the resulting sequence data requires computational skills that may go beyond the standard repertoire of a current molecular biologist/ecologist. We have developed Cascabel, a flexible and easy-to-use amplicon sequence data analysis pipeline, which uses Snakemake and a combination of existing and newly developed solutions for its computational steps. Cascabel takes the raw data as input and delivers a table of operational taxonomic units (OTUs) and a representative sequence tree. Our pipeline allows customizing the analyses by offering several choices for most of the steps, for example different OTU generating methods. The pipeline can make use of multiple computing nodes and scales from personal computers to computing servers. The analyses and results are fully reproducible and documented in an HTML and optional pdf report. Cascabel is freely available at Github: https://github.com/AlejandroAb/CASCABEL and licensed under GNU GPLv3.

bioinformatics↗