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Johnson, J. C.

Publications and source records attributed to Johnson, J. C..

2 recordsLinked to original sources

Cascading Effects of Shrimp Trawling: Increased Benthic Biomass and Increase in Net Primary Production

Trawling has been shown to cause high mortality of discarded species (bycatch) and short-term ecological disturbance to bottom communities in coastal systems, resulting in lowered benthic biomass. Here we report evidence of a trawling-induced trophic cascade resulting in an increase in biomass of benthic polychaetes after the end of the shrimp trawling season in areas open to trawling in North Carolina (USA). Using comparative measurements of abundance of bycatch species and benthos in open and closed trawling management areas and Ecopath network modeling, we show that trawling in the open area has led to increases in deposit-feeding polychaetes and decreases in bycatch species (fish and crabs) that are benthic predators on the polychaetes. We conclude that proposed management actions to reduce the shrimp trawl fishery effort will influence other net and trap fisheries for southern flounder and blue crabs indirectly, as revealed by our network models, and the proposed trawling ban may lead to improvements in other valuable fisheries.

ecology

Fluidigm2PURC: automated processing and haplotype inference for double-barcoded PCR amplicons

Premise of the studyTargeted enrichment strategies for phylogenomic inference are a time- and cost-efficient way to collect DNA sequence data for large numbers of individuals at multiple, independent loci. Automated and reproducible processing of these data is a crucial step for researchers conducting phylogenetic studies.\n\nMethods and ResultsWe present Fluidigm2PURC, an open source Python utility for processing paired-end Illumina data from double-barcoded PCR amplicons. In combination with the program PURC (Pipeline for Untangling Reticulate Complexes), our scripts process raw FASTQ files for analysis with PURC and use its output to infer haplotypes for diploids, polyploids, and samples with unknown ploidy. We demonstrate the use of the pipeline with an example data set from the genus Thalictrum L. (Ranunculaceae).\n\nConclusionsFluidigm2PURC is freely available for Unix-like operating systems on GitHub [https://github.com/pblischak/fluidigm2purc] and for all operating systems through Docker [https://hub.docker.com/r/pblischak/fluidigm2purc].

bioinformatics