Genetic Research May Help Trace Chum Salmon to Home Rivers

Below is a press release about the Methods paper ‘Potentially adaptive mitochondrial haplotypes as a tool to identify divergent nuclear loci‘ taken from the University of Alaska Fairbanks.

Michael Garvin sails through Auke Bay, just north of Juneau in Southeast Alaska. ©Chris Lunsford

Michael Garvin sails through Auke Bay, just north of Juneau in Southeast Alaska. ©Chris Lunsford

University of Alaska Fairbanks researchers have uncovered genetic markers that can help trace chum salmon to the rivers in which they hatched, according to a new paper published in the journal Methods in Ecology and Evolution.

Mapping out chum salmon pathways could help improve management of the species in Western Alaska, according to Oregon State University Department of Integrative Biology postdoctoral fellow Michael Garvin.

“In some years, chum salmon are frequently the bycatch of pollock fishermen” in the Bering Sea, Garvin explained. “Genetically, chum salmon that originate in Western Alaska tend to look very similar. This makes it difficult for stakeholders because management and conservation efforts to address this bycatch can differ among these regions, but the ability to identify them with genetics is not possible.” Continue reading

Scat Collection Protocols for Dietary DNA Metabarcoding

DNA dietary analysis is a non-invasive tool used to identify the food consumed by vertebrates. The method relies on identifying prey DNA in the target animals’ scats. It’s especially useful for marine animals such as seals and seabirds as it is difficult to watch their feeding events.

In the video below, Julie McInnes describes scat collection protocols that she (along with Rachael Alderman, Bruce Deagle, Mary-Anne Lea, Ben Raymond and Simon Jarman) developed to optimise the detection of food DNA in vertebrate scat samples. The authors use the shy albatross to demonstrate their new methods.

Continue reading

Issue 6.8

Issue 6.8 is now online!

The August issue of Methods is now online!

This month’s issue contains two Applications article and one Open Access article, all of which are freely available.

LEA: This R package enables users to run ecological association studies from the R command line. It can perform analyses of population structure and genome scans for adaptive alleles from large genomic data sets. The package derives advantages from R programming functionalities to adjust significance values for multiple testing issues and to visualize results.

PIPITS: An open-source stand-alone suite of software for automated processing of Illumina MiSeq sequences for fungal community analysis. PIPITS exploits a number of state of the art applications to process paired-end reads from quality filtering to producing OTU abundance tables.

Giovanni Strona and Joseph Veech provide this month’s Open Access article. Many studies have focused on nestedness, a pattern reflecting the tendency of network nodes to share interaction partners, as a method of measuring the structure of ecological networks. In ‘A new measure of ecological network structure based on node overlap and segregation‘ the authors introduce a new statistical procedure to measure both this kind of structure and the opposite one (i.e. species’ tendency against sharing interacting partners).

In addition to this, our August issue features articles on Estimating Diversity, Ecological Communities and Networks, Genetic Distances and Immunology. Continue reading

‘Bee soup’ could help understand declines and test remedies

Below is a press release about the Methods paper ‘High-throughput monitoring of wild bee diversity and abundance via mitogenomics‘ taken from the University of East Anglia:

It may sound counter-intuitive, but crushing up bees into a ‘DNA soup’ could help conservationists understand and even reverse their decline – according to University of East Anglia scientists.

Research published today in the journal Methods in Ecology and Evolution shows that collecting wild bees, extracting their DNA, and directly reading the DNA of the resultant ‘soup’ could finally make large-scale bee monitoring programmes feasible.

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©Mibby23 (click image to see original version)

This would allow conservationists to detect where and when bee species are being lost, and importantly, whether conservation interventions are working.

The UK’s National Pollinator Strategy outlines plans for a large-scale bee monitoring programme. Traditional monitoring involves pinning individual bees and identifying them under a microscope. But the number of bees needed to track populations reliably over the whole country makes traditional methods infeasible.

This new research shows how the process could become quicker, cheaper and more accurate. Continue reading

Biodiversity estimates from DNA sequences

The complexity of new methodologies can present a challenging barrier towards their uptake. Recognising this, Jeff Powell,  author of Accounting for uncertainty in species delineation during the analysis of environmental DNA sequence data, has put together an excellent tutorial to guide people through the implementation of his objective, theory-based method for predicting species boundaries, which explicitly incorporates uncertainty in the classification system into biodiversity estimation.

The tutorial is available to view and download from Slideshare, and the relevant R code can be found as supplementary material on Wiley Online Library.

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