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Methods in Ecology and Evolution

Matthew M Guzzo, Travis E Van Leeuwen, Jack Hollins, Barbara Koeck, Matthew Newton, Dale M Webber, Frank I Smith, David M Bailey, Shaun S Killen
Acoustic telemetry is an important tool for studying the behaviour of aquatic organisms in the wild.VEMCO high residence (HR) tags and receivers are a recent introduction in the field of acoustic telemetry and can be paired with existing algorithms (e.g. VEMCO positioning system [VPS]) to obtain high-resolution two-dimensional positioning data.Here, we present results of the first documented field test of a VPS composed of HR receivers (hereafter, HR-VPS). We performed a series of stationary and moving trials with HR tags (mean HR transmission period = 1...
June 2018: Methods in Ecology and Evolution
Martin J P Sullivan, Simon L Lewis, Wannes Hubau, Lan Qie, Timothy R Baker, Lindsay F Banin, Jerôme Chave, Aida Cuni-Sanchez, Ted R Feldpausch, Gabriela Lopez-Gonzalez, Eric Arets, Peter Ashton, Jean-François Bastin, Nicholas J Berry, Jan Bogaert, Rene Boot, Francis Q Brearley, Roel Brienen, David F R P Burslem, Charles de Canniere, Markéta Chudomelová, Martin Dančák, Corneille Ewango, Radim Hédl, Jon Lloyd, Jean-Remy Makana, Yadvinder Malhi, Beatriz S Marimon, Ben Hur Marimon Junior, Faizah Metali, Sam Moore, Laszlo Nagy, Percy Nuñez Vargas, Colin A Pendry, Hirma Ramírez-Angulo, Jan Reitsma, Ervan Rutishauser, Kamariah Abu Salim, Bonaventure Sonké, Rahayu S Sukri, Terry Sunderland, Martin Svátek, Peter M Umunay, Rodolfo Vasquez Martinez, Ronald R E Vernimmen, Emilio Vilanova Torre, Jason Vleminckx, Vincent Vos, Oliver L Phillips
Quantifying the relationship between tree diameter and height is a key component of efforts to estimate biomass and carbon stocks in tropical forests. Although substantial site-to-site variation in height-diameter allometries has been documented, the time consuming nature of measuring all tree heights in an inventory plot means that most studies do not include height, or else use generic pan-tropical or regional allometric equations to estimate height.Using a pan-tropical dataset of 73 plots where at least 150 trees had in-field ground-based height measurements, we examined how the number of trees sampled affects the performance of locally derived height-diameter allometries, and evaluated the performance of different methods for sampling trees for height measurement...
May 2018: Methods in Ecology and Evolution
Topaz Halperin, Michael Kalyuzhny, Dror Hawlena
Movement-based indices such as moves per minute (MPM) and proportion time moving (PTM) are common methodologies to quantify foraging behaviour. We explore fundamental drawbacks of these indices that question the ways scientists have been using them and propose new solutions.To do so, we combined analytical and simulation models with lizards foraging data at the individual and species levels.We found that the maximal value of MPM is constrained by the minimal durations of moves and stops. As a result, foragers that rarely move and those that rarely stop are bounded to similar low MPM values...
April 2018: Methods in Ecology and Evolution
Marie-Pauline Beugin, Thibault Gayet, Dominique Pontier, Sébastien Devillard, Thibaut Jombart
The investigation of genetic clusters in natural populations is an ubiquitous problem in a range of fields relying on the analysis of genetic data, such as molecular ecology, conservation biology and microbiology. Typically, genetic clusters are defined as distinct panmictic populations, or parental groups in the context of hybridisation. Two types of methods have been developed for identifying such clusters: model-based methods, which are usually computer-intensive but yield results which can be interpreted in the light of an explicit population genetic model, and geometric approaches, which are less interpretable but remarkably faster...
April 2018: Methods in Ecology and Evolution
William E Stutz, Andrew R Blaustein, Cheryl J Briggs, Jason T Hoverman, Jason R Rohr, Pieter T J Johnson
Associations among parasites affect many aspects of host-parasite dynamics, but a lack of analytical tools has limited investigations of parasite correlations in observational data that are often nested across spatial and biological scales.Here we illustrate how hierarchical, multiresponse modeling can characterize parasite associations by allowing for hierarchical structuring, offering estimates of uncertainty, and incorporating correlational model structures. After introducing the general approach, we apply this framework to investigate coinfections among four amphibian parasites (the trematodes Ribeiroia ondatrae and Echinostoma spp...
April 2018: Methods in Ecology and Evolution
Oskar Hagen, Tanja Stadler
Understanding macroevolutionary processes using phylogenetic trees is a challenging and complex process that draws on mathematics, computer science and biology. Given the development of complex mathematical models and the growing computational processing power, simulation tools are becoming increasingly popular.In order to simulate phylogenetic trees, most evolutionary biologists are forced to build their own algorithms or use existing tools built on different platforms and/or as standalone programmes. The absence of a simulation tool accommodating for user-chosen model specifications limits, amongst others, model testing and pipelining with approximate Bayesian computation methods or other subsequent statistical analysis...
March 2018: Methods in Ecology and Evolution
Eileen F Power, Daniel Stabler, Anne M Borland, Jeremy Barnes, Geraldine A Wright
Floral nectar is a reward offered by flowering plants to visiting pollinators. Nectar chemistry is important for understanding plant nutrient allocation and plant-pollinator interactions. However, many plant species are difficult to sample as their flowers are small and produce low amounts of nectar.We compared the effects of different methods of nectar collection on the amino acid composition of flowers with low volumes of nectar. We used five methods to collect nectar from 60 (5 × 12) Calluna vulgaris flowers: microcapillary tubes, a low-volume flower rinse (the micro-rinse method, using 2 μl water), filter paper, a high-volume flower rinse (2 ml water) and a flower wash (2 ml water)...
March 2018: Methods in Ecology and Evolution
C Patrick Doncaster, Rebecca Spake
Meta-analyses conventionally weight study estimates on the inverse of their error variance, in order to maximize precision. Unbiased variability in the estimates of these study-level error variances increases with the inverse of study-level replication. Here, we demonstrate how this variability accumulates asymmetrically across studies in precision-weighted meta-analysis, to cause undervaluation of the meta-level effect size or its error variance (the meta-effect and meta-variance).Small samples, typical of the ecological literature, induce big sampling errors in variance estimation, which substantially bias precision-weighted meta-analysis...
March 2018: Methods in Ecology and Evolution
Ian Paynter, Daniel Genest, Edward Saenz, Francesco Peri, Peter Boucher, Zhan Li, Alan Strahler, Crystal Schaaf
In this study, we introduce metaproperty analysis of terrestrial laser scanner (TLS) data, and demonstrate its application through several ecological classification problems. Metaproperty analysis considers pulse level and spatial metrics derived from the hundreds of thousands to millions of lidar pulses present in a single scan from a typical contemporary instrument. In such large aggregations, properties of the populations of lidar data reflect attributes of the underlying ecological conditions of the ecosystems...
February 2018: Methods in Ecology and Evolution
Juan Pablo Gomez, Scott K Robinson, Jason K Blackburn, José Miguel Ponciano
In this study we propose an extension of the N-mixture family of models that targets an improvement of the statistical properties of rare species abundance estimators when sample sizes are low, yet typical for tropical studies. The proposed method harnesses information from other species in an ecological community to correct each species' estimator. We provide guidance to determine the sample size required to estimate accurately the abundance of rare tropical species when attempting to estimate the abundance of single species...
February 2018: Methods in Ecology and Evolution
Steven M Van Belleghem, Riccardo Papa, Humberto Ortiz-Zuazaga, Frederik Hendrickx, Chris D Jiggins, W Owen McMillan, Brian A Counterman
The use of image data to quantify, study and compare variation in the colors and patterns of organisms requires the alignment of images to establish homology, followed by color-based segmentation of images. Here we describe an R package for image alignment and segmentation that has applications to quantify color patterns in a wide range of organisms. patternize is an R package that quantifies variation in color patterns obtained from image data. patternize first defines homology between pattern positions across specimens either through manually placed homologous landmarks or automated image registration...
February 2018: Methods in Ecology and Evolution
Daniel Stabler, Eileen F Power, Anne M Borland, Jeremy D Barnes, Geraldine A Wright
Pollen provides floral visitors with essential nutrients including proteins, lipids, vitamins and minerals. As an important nutrient resource for pollinators, including honeybees and bumblebees, pollen quality is of growing interest in assessing available nutrition to foraging bees. To date, quantifying the protein-bound amino acids in pollen has been difficult and methods rely on large amounts of pollen, typically more than 1 g. More usual is to estimate a crude protein value based on the nitrogen content of pollen, however, such methods provide no information on the distribution of essential and non-essential amino acids constituting the proteins...
February 2018: Methods in Ecology and Evolution
Sam L Cox, Florian Orgeret, Mathieu Gesta, Charles Rodde, Isaac Heizer, Henri Weimerskirch, Christophe Guinet
Biologging technologies are changing the way in which the marine environment is observed and monitored. However, because device retrieval is typically required to access the high-resolution data they collect, their use is generally restricted to those animals that predictably return to land. Data abstraction and transmission techniques aim to address this, although currently these are limited in scope and do not incorporate, for example, acceleration measurements which can quantify animal behaviours and movement patterns over fine-scales...
January 2018: Methods in Ecology and Evolution
R Axel W Wiberg, Oscar E Gaggiotti, Michael B Morrissey, Michael G Ritchie
With increasing application of pooled-sequencing approaches to population genomics robust methods are needed to accurately quantify allele frequency differences between populations. Identifying consistent differences across stratified populations can allow us to detect genomic regions under selection and that differ between populations with different histories or attributes. Current popular statistical tests are easily implemented in widely available software tools which make them simple for researchers to apply...
December 2017: Methods in Ecology and Evolution
Damien R Farine
Null models are an important component of the social network analysis toolbox. However, their use in hypothesis testing is still not widespread. Furthermore, several different approaches for constructing null models exist, each with their relative strengths and weaknesses, and often testing different hypotheses.In this study, I highlight why null models are important for robust hypothesis testing in studies of animal social networks. Using simulated data containing a known observation bias, I test how different statistical tests and null models perform if such a bias was unknown...
October 2017: Methods in Ecology and Evolution
Luis Lopez-Sangil, Charles George, Eduardo Medina-Barcenas, Ali J Birkett, Catherine Baxendale, Laëtitia M Bréchet, Eduard Estradera-Gumbau, Emma J Sayer
Root exudation is a key component of nutrient and carbon dynamics in terrestrial ecosystems. Exudation rates vary widely by plant species and environmental conditions, but our understanding of how root exudates affect soil functioning is incomplete, in part because there are few viable methods to manipulate root exudates in situ. To address this, we devised the Automated Root Exudate System (ARES), which simulates increased root exudation by applying small amounts of labile solutes at regular intervals in the field...
September 2017: Methods in Ecology and Evolution
Thomas O Richardson, Luca Giuggioli, Nigel R Franks, Ana B Sendova-Franks
Animals often display a marked tendency to return to previously visited locations that contain important resources, such as water, food, or developing brood that must be provisioned. A considerable body of work has demonstrated that this tendency is strongly expressed in ants, which exhibit fidelity to particular sites both inside and outside the nest. However, thus far many studies of this phenomena have taken the approach of reducing an animal's trajectory to a summary statistic, such as the area it covers...
August 2017: Methods in Ecology and Evolution
Mark Grabowski, Arthur Porto
1. The variational properties of living organisms are an important component of current evolutionary theory. As a consequence, researchers working on the field of multivariate evolution have increasingly used integration and evolvability statistics as a way of capturing the potentially complex patterns of trait association and their effects over evolutionary trajectories. Little attention has been paid, however, to the cascading effects that inaccurate estimates of trait covariance have on these widely used evolutionary statistics...
May 2017: Methods in Ecology and Evolution
Mark Q Wilber, Kate E Langwig, A Marm Kilpatrick, Hamish I McCallum, Cheryl J Briggs
Host parasite models are typically constructed under either a microparasite or macroparasite paradigm. However, this has long been recognized as a false dichotomy because many infectious disease agents, including most fungal pathogens, have attributes of both microparasites and macroparasites.We illustrate how Integral Projection Models (IPM)s provide a novel, elegant modeling framework to represent both types of pathogens. We build a simple host-parasite IPM that tracks both the number of susceptible and infected hosts and the distribution of parasite burdens in infected hosts...
October 2016: Methods in Ecology and Evolution
Michele Dalponte, David A Coomes
Forests are a major component of the global carbon cycle, and accurate estimation of forest carbon stocks and fluxes is important in the context of anthropogenic global change. Airborne laser scanning (ALS) data sets are increasingly recognized as outstanding data sources for high-fidelity mapping of carbon stocks at regional scales.We develop a tree-centric approach to carbon mapping, based on identifying individual tree crowns (ITCs) and species from airborne remote sensing data, from which individual tree carbon stocks are calculated...
October 2016: Methods in Ecology and Evolution
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