Issue 11.4: Population Dynamics, Machine Learning, Morphometrics and More

The April issue of Methods is now online!

The latest issue of Methods in Ecology and Evolution is now online! This month’s issue is a little shorter than our last few. But, as they say, good things come in small packages!

Senior Editor Lee Hsiang Liow has selected six Featured Articles this month. You can find out about all of them below. We’ve also got five Applications articles and a Practical Tools article in the April issue that we’re going to cover. Those six papers are freely available to everyone – no subscription required!

On top of all that, the April issue includes articles on camera traps, land cover classification, presence-absence sampling and more.

Featured Articles

Parasite Transmission and Host Density: Hopkins et al. systematically reviewed 262 studies containing host-parasite models that contained linear and/or nonlinear transmission functions to quantify existing modelling practices. They found that most experimental and observational studies reported that nonlinear transmission-density functions outperformed simple linear transmission-density functions. In contrast, most studies containing host-parasite models assumed that host density was constant and/or used a single, linear transmission function to explain how transmission rates changed with density.

ML-morph: Porto and Voje propose a machine‐learning‐based high‐throughput pipeline to collect high‐dimensional morphometric data in two‐dimensional images of semi‐rigid biological structures. Their pipeline allows for dense phenotyping with minimal impact on specimens, presents landmarking accuracy comparable to manual annotators, performs data collection at speeds several orders of magnitude higher than manual annotators and is of general applicability (i.e. not tied to a specific study system).

Functional and Phylogenetic Redundancy: A necessary condition to get a meaningful index of beta redundancy is that for a given pair of plots, the functional or phylogenetic dissimilarity is always lower or equal to the corresponding species dissimilarity. Many of the existing indices of functional or phylogenetic dissimilarity can lead to values greater than for species dissimilarity though. Ricotta et al. introduce a new family of tree‐based measures of phylogenetic and functional dissimilarity that conform to this requirement.

©Greg Jordan

hyperoverlap: Brown et al. discuss the weaknesses of using existing methods to analyse patterns of phenotypic overlap and present a novel method to analyse co‐occurrence in multidimensional space. Their ‘hyperoverlap’ framework detects qualitative overlap (or divergence) between point datasets. The hyperoverlap r package implement this framework, and includes functions for visualization.

steps: Species population dynamics are driven by spatial and temporal changes in the environment, anthropogenic activities and conservation management actions. Visintin et al. introduce an open‐source, multi‐platform r package, steps, that models spatial changes in species populations as a function of drivers of distribution and abundance, such as climate, disturbance, landscape dynamics and species ecological and physiological requirements.

Visual TreeCmp: Visual TreeCmp is a package of applications for comparing phylogenetic tree sets. It includes a graphical web interface allowing the visualization of compared trees and command line application extended by comparison methods recently proposed in the literature.

Applications and Practical Tools

We’ve got five applications articles and one Practical Tools article in this month’s issue of Methods in Ecology and Evolution. Two of them have been covered in our featured articles above, so let’s dive into the other four, starting with the Practical Tools paper:

GPS Collars: For many field projects, commercially available tracking devices can be expensive and may not always be ideally suited for collecting the desired monitoring data. Foley and Sillero‐Zubiri present a low‐cost solution of customizable tracking devices based on the open‐source Arduino system. These devices can be custom designed for specific studies and easily programmed to collect desired data.

Chipper: Chipper is a Python‐based software to semi‐automate both the segmentation of acoustic signals and the subsequent analysis of their frequencies and durations. Chipper provides an effective way to quickly generate quantitative, reproducible measures of birdsong. The cross‐platform graphical user interface allows the user to adjust parameters and visualise the resulting spectrogram and signal segmentation, providing a simplified method for analysing field recordings.

©Walter Siegmund

Marxan Connect: ‘Marxan Connect’ is a new open source, open access Graphical User Interface (GUI) tool designed to assist conservation planners with the appropriate use of data on ecological connectivity in protected area network planning. It can facilitate the use of estimates of demographic connectivity (e.g. derived from animal tracking data, dispersal models, or genetic tools) or structural landscape connectivity (e.g. isolation by resistance). This is accomplished by calculating metapopulation‐relevant connectivity metrics (e.g. eigenvector centrality) and treating those as conservation features or by including the connectivity data as a spatial dependency amongst sites in the prioritisation process.

grainscape: Networks are widely used for modelling landscape connectivity and have many ecological and conservation applications. The nodes in these models describe geographic locations (such as habitat patches or protected areas) and links describe the potential for organisms (or their propagules) to move among nodes. Chubaty et al. present the r package grainscape which facilitates working with these networks within a spatially explicit framework.

The Sparrow on the Cover

This month’s cover image is of an adult male chipping sparrow with his characteristic rufous cap. The photograph was taken by Jerry Webb, an avid birder, member of the Nashville chapter of the Tennessee Ornithological Society, and citizen scientist. He captured this photo in Adams County, Wisconsin on July 19, 2009 using a Canon 40D with an L Series 70‐200 lens and a 2X extender.

Citizen scientists are not only actively capturing and contributing photographs of birds, but also recordings of their songs. The curation of these recordings of various species, by such databases as Macaulay Library and Xeno‐canto, has created a valuable resource of geographically welldistributed datasets for researchers. In the article Chipper: Open‐source software for semi‐automated segmentation and analysis of birdsong and other natural sounds”, Searfoss et al. have developed a tool to streamline the use of citizen‐science data collected with various recording devices and of various species.

The first study published using this software – ‘Geographically well‐distributed citizen science data reveals range‐wide variation in the chipping sparrow’s simple song’ – was conducted on citizen science recordings of the chipping sparrow. Together, the chipping sparrow name and the software’s primary function of ‘chipping’ songs into parts (syllables) provided the namesake for Chipper.

Photo credit: © Jerry Webb 2009

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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