Issue 6.11

Issue 6.11 is now online!

The November issue of Methods is now online!

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

mvMORPH: A package of multivariate phylogenetic comparative methods for the R statistical environment which allows fitting a range of multivariate evolutionary models under a maximum-likelihood criterion. Its use can be extended to any biological data set with one or multiple covarying continuous traits.

Low-cost soil CO2 efflux and point concentration sensing systems: The authors use commercially available, low-cost and low-power non-dispersive infrared (NDIR) CO2 sensors to develop a soil CO2 efflux system and a point CO2 concentration system. Their methods enable terrestrial ecologists to substantially improve the characterization of CO2 fluxes and concentrations in heterogeneous environments.

This month’s Open Access article comes from Jolyon Troscianko and Martin Stevens. In ‘Image calibration and analysis toolbox – a free software suite for objectively measuring reflectance, colour and pattern‘ they introduce a toolbox that can convert images to correspond to the visual system (cone-catch values) of a wide range of animals, enabling human and non-human visual systems to be modelled. The toolbox is freely available as an addition to the open source ImageJ software and will considerably enhance the appropriate use of digital cameras across multiple areas of biology. In particular, researchers aiming to quantify animal and plant visual signals will find this useful. This article received some media attention upon Early View publication over the summer. You can read the Press Release about it here.

Our November issue also features articles on Population Genetics, Macroevolution, Modelling species turnover, Abundance modelling, Measuring stress and much more.

To begin the November issue, we have a great paper from Pierre Legendre et al. on Mantel tests. The Mantel test is widely used in biology, including landscape ecology and genetics, to detect spatial structures in data or control for spatial correlation in the relationship between two data sets, for example community composition and environment. In ‘Should the Mantel test be used in spatial analysis?‘ the authors demonstrate that this is an incorrect use of that test. They conclude that Mantel tests should be restricted to questions that, in the domain of application, only concern dissimilarity matrices, and are not derived from questions that can be formulated as the analysis of the vectors and matrices from which one can compute dissimilarity matrices.

This month’s cover image shows a fledgling kea (Nestor notabilis) calling to other members of its flock, which are foraging in the sub-alpine scrubland of New Zealand’s Southern Alps. The young parrot stands surrounded by snow tussock (Chionochloa spp.) which is the dominant vegetation there. The photo was shot early on Easter morning, in the Brewster glacier region of Mt. Aspiring National Park (c. 1,450m elevation).

The kea’s threatened status and extremely generalist diet make it unethical to restrict captive birds to one or two food types in order to determine their stable carbon and nitrogen isotope diet-to-tissue discrimination factors. In the related article, ‘Simple ways to calculate stable isotope discrimination factors and convert between tissue types‘ Greer et al. develop a methodology to determine stable isotope discrimination factors without changing an animal’s diet, by instead mathematically controlling for possible confounding variables. The article also details a technique to directly compare the stable isotope ratios of different animal tissues and describes how these simple and cost-effective methods can be adapted for use across other animal classes.

Photo © Andy Pratt

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


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