Our third issue of the year is now online!
This month we have five Applications and two Practical Tools articles, all of which are completely free to read!
Senior Editor Rob Freckleton has selected six featured articles, including methods for defining and evaluating predictions of joint species distribution models, inferring extinction date of a species and choosing cost‐effective indicators for conservation decisions. Find out all about them below.
Joint species distribution models Despite increasing adoption of joint species distribution models (JSDMs) in the literature, the question of how to define and evaluate JSDM predictions has only begun to be explored. Here, Wilkinson et al. define four different JSDM prediction types that correspond to different aspects of species distribution and community assemblage processes. They illustrate different prediction types and evaluation metrics by fitting a JSDM to a frog occurrence dataset from Australia.
Acoustic indices perform better when applied at ecologically meaningful time and frequency scales Acoustic indices are increasingly employed in the analysis of soundscapes to ascertain biodiversity value, but may be negatively impacted by signal masking. Here, Metcalf et al. show that signal masking has a large impact on the sensitivity of acoustic indices to forest disturbance classes, using a large acoustic dataset from Eastern Amazonia spanning a disturbance gradient. Calculating acoustic indices at a range of narrower time–frequency bins substantially increases the classification accuracy of forest classes by random forest models.
NicheMapR Body size affects the body temperature of an ectotherm by altering both heating rates and the microclimate experienced, but these joint effects are rarely considered in the analyses of climatic constraints on ectotherms. Here, Kearney et al. develop and test transient heat‐budget models that use height‐specific microclimatic forcing to compute the dynamics of size‐dependent body temperatures of ectotherms in sun and in shade. Their simulations show that the behavioural and ecological consequences of size can be strongly biased when joint effects of body size and size‐imposed microclimate are ignored. All functions are integrated into the biophysical modelling R package NicheMapR and as a Shiny app.
Generalized Hidden Markov Models for Phylogenetic Comparative Datasets Hidden Markov models (HMMs) have emerged as an important tool for understanding the evolution of characters that take on discrete states. Previously available packages placed unnecessary limits on the number of observed and hidden states that can be considered when estimating transition rates and inferring ancestral states on a phylogeny. To address these issues, Boyko & Beaulieu expand the capabilities of the R package corHMM to handle n‐state and n‐character problems and provide users with a streamlined set of functions to create custom HMMs for any biological question of arbitrary complexity.
A cost‐effective indicator to trigger conservation decisions *open access* Most ecological systems face multiple threats, so monitoring to assess the impacts of threats on biodiversity is a complex task. Indicators help simplify the challenge of monitoring but choosing the best indicators to inform management is not straightforward. Here, Bal et al. provide a decision framework that can help identify optimal indicators to trigger management in a system faced with multiple threats. The approach evaluates indicators based on criteria spanning monitoring efficiency, management outcomes and the economic constraints for decision‐making. Critical decision factors are identified and detailed in a six‐step process to estimate the cost‐effectiveness of alternate indicators.
Inferring extinction date of a species Bayesian methods have been developed for inferring the true year of extinction of a species from sighting records that have both certain and uncertain sightings. These methods typically make the restrictive assumption that all sighting types (i.e. certain, valid uncertain, invalid uncertain) derive from constant rate Poisson processes. In this study, Kodikara et al. present a new Bayesian method for inferring species extinction date based on a temporally non-homogeneous Poisson process. The proposed method is applied to the sighting records of the black‐footed ferret and the ivory‐billed woodpecker.
The Butterflies on the Cover
Pictured are 14 migratory monarch butterflies feeding on blooming butterfly milkweed in Ames, IA USA. Because the size of the eastern North American monarch butterfly population has significantly declined over the past two decades, observations captured in the photograph are becoming uncommon. In December 2020, the North American monarch was determined to be a candidate species for listing under the U.S. Endangered Species Act due, in part, to the loss of breeding habitat in agricultural landscapes of the Midwest United States. The female monarch is not a habitat patch resident, but instead flies extensively across the landscape, laying eggs in numerous patches. Consequently, monarch egg densities in a landscape are influenced by the amount of habitat and the size and spatial patterns of patches. Understanding monarch movement behavior is critical to employing biologically relevant conservation strategies. Limitations in the ability to directly track flight paths of large insects, like the monarch, was the motivation for the study in this issue by Fisher et al., describing an automated radio telemetry system to track female monarchs beyond human visual range on a fine temporal scale. As technology improves, this system provides a benchmark for automated systems to track insects. Photo credit: ©K. E. Fisher.