Issue 10.9: Phenotypes, Species Interactions, Biodiversity and More

The September issue of Methods is now online!

We’ve got another brilliant issue of Methods in Ecology and Evolution out today. In another bumper 250 page offering, you’ll find articles on identifying waterbird hotspots, identity metrics, capture-recapture methods (and the alternative close-kin mark-recpature) and way more.

Don’t have a subscription to the journal? No need to worry – this month’s issue has TEN articles that are free to access for absolutely anyone. You can find out about all 10 below.

Keep reading for a little more information on the September issue of Methods in Ecology and Evolution.

Featured Articles

The value of Petri nets was examined using the ecosystem of a termite colony. ©J Brew

Dynamics of an Integrated Ecosystem: Gaucherel and Pommereau propose an original family of models based on discrete systems. Their models are designed to comprehensively characterise ecosystem dynamics holistically and over the long term. The qualitative model they developed is based on Petri nets, made up of a relational graph that was then rigorously handled using transition rules.

Multivariate Comparison of Variance: Comparisons of pattern and magnitude of phenotypic variation are central to many studies in evolution and ecology. But a meaningful comparison of multivariate variance patterns can be challenging. Le Maître and Mitteroecker review an effective exploratory strategy, relative principal component analysis, for the comparison of variance–covariance matrices based on their relative eigenvalues and eigenvectors. In their Open Access article, the authors present a novel biometric justification of these approaches, along with a new implementation of these methods in R.

Improving Structured Population Models: Structured population models are among the most widely used tools in ecology and evolution. Yet, almost all of them make an important assumption that size‐dependent growth transitions are (or can be transformed to be) normally distributed. Peterson et al. develop a flexible approach to modelling skewed growth data using a modified beta regression model.

Beta and Dirichlet Regression: Proportional data are analysed in many subfields of ecology and evolution. In this Open Access paper, Douma and Weedon review and discuss the use of promising, but little used, techniques for analysing continuous proportions: beta and Dirichlet regression, and some of their most important extensions. They have also written a blog post about beta and Dirichlet regression which will give you a basic introduction to the topic. 這篇博客文章也有中文版.

What is the contribution of terrestrial carbon to an endemic cavefish? ©Chulabush Khatancharoen

Terrestrial Carbon in Freshwater Food Webs: Flow of terrestrial carbon though aquatic ecosystems is an important but underestimated component of the global carbon cycle. Liew et al. tested how effective amino acid δ13C data is as a generalizable measure of this. They found the δ13C fingerprints amino acids to be consistently distinct between terrestrial and aquatic carbon sources.

Untangling Species Associations: A wide variety of methods are now available for modelling how environmental filtering drives species distributions. Methods for studying other causes of co‐occurence are much more limited though. Popovic et al. propose Gaussian copula graphical models for studying the effect of mediator species on co‐occurence patterns.

Applications and Practical Tools

With five Applications papers and one Practical Tools article, we’ve got a lot to cover in this section. So, let’s get straight to it!

Koala wearing a GPS radio collar with an OpenDropOff device (circled) attached.

OpenDropOff: In this Practical Tools article, Rafiq et al. introduce an open‐source, low‐cost electronic drop‐off unit for remotely detaching animal‐borne sensors from individuals: OpenDropOff. Their devices provide a wider range of researchers with a reliable, cost‐effective tool for detaching animal‐borne sensors.

Anacapa Toolkit: There are a few longstanding needs of the eDNA community. They include the need for modular informatics tools, comprehensive and customisable reference databases, flexibility across high‐throughput sequencing platforms, fast multilocus metabarcode processing and accurate taxonomic assignment. Improvements in bioinformatics tools make addressing each of these demands within a single toolkit a reality. Enter the Anacapa Toolkit!

fishtrack3d: Aspillaga et al. propose a new data‐driven quantitative method to estimate 3D space use from telemetry networks. 3D space use estimations that incorporate topography will give you a more comprehensive view of the movement ecology of tracked individuals.

ThermStats: Variation in temperature at a fine spatial scale creates critically important microclimates for many organisms. Thermography is becoming an increasingly popular way of studying these variations. The R package ThermStats addresses current constraints on applying thermography in ecology

phenotools: One approach to building approximations of organismal phenomes is to combine published datasets of discrete characters assembled for phylogenetic analyses into a phenomic dataset. Eliason et al. introduce a new r package phenotools for integrating, curating and visualising phenomic datasets.

StoX: StoX was principally built to process research‐vessel survey data, and includes several standard survey estimation models. Johnsen et al. developed the software to be robust and versatile and aimed at the open source community, so you can easily build your own models.

Open Access Articles

There are two freely available papers that we have not yet mentioned, both of which are Open Access.

False detection rates for sei whales with the Baumgartner et al. method were 0%. ©Christin Khan, NOAA/NEFSC

Near Real‐Time Passive Acoustic Monitoring: Baumgartner et al.  have developed a moored passive acoustic monitoring system that provides near real‐time occurrence estimates for a number of species of whales from a single site for a year. Those occurrence estimates are made publicly available. This system been used to reduce the risk of ship strikes for right whales in a U.S. Coast Guard gunnery range, and can be applied to other mitigation applications.

Temporal Variation in Phenotypic Selection: Temporal and spatial variation in phenotypic selection due to changing environmental conditions is of great interest to evolutionary biologists. Not many existing methods estimating its magnitude take into account the temporal autocorrelation though. Cao et al. show how you can estimate additional parameters compared to previous methods, all without requiring a substantial increase in computational resources.

The Fish on the Cover

A male California sheephead swims over purple hydrocoral and southern sea palms at Farnsworth Bank, off Catalina Island. This colorful and diverse marine seascape represents a small fraction of the unique biodiversity of California that can be detected and monitored using environmental DNA (eDNA). eDNA metabarcoding is a promising method to monitor species and community diversity that is rapid, affordable and non‐invasive.

The Anacapa Toolkit enhances the bioinformatic capabilities of eDNA metabarcoding approaches for improved conservation management. It does this by improving the functionality of eDNA for taxonomic assignment thus streamlining biodiversity assessment and aiding conservation management decision making. The toolkit can generate comprehensive custom metabarcode specific databases, process multilocus data, retain a larger proportion of sequencing reads than its alternatives and expand non‐traditional eDNA targets. The tool kit also includes a module for automated results exploration using standard biodiversity statistical analysis. All the components of the Anacapa Toolkit are open source and available in a virtual container to ease installation.

Photo credit: © Zack Gold

To keep up to date with Methods newest content, have a look at our Accepted Articles and Early View articles, which will be showing up in issues later this year.

 

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