A time-lagged effect of conspecific density on habitat selection by snowshoe hare

A computational reproducibility study of PLOS ONE articles featuring longitudinal data analyses

Computational reproducibility is a corner stone for sound and credible research. Especially in complex statistical analyses-such as the analysis of longitudinal data-reproducing results is far from simple, especially if no source code is available. In this work we aimed to reproduce analyses of longitudinal data of 11 articles published in PLOS ONE. Inclusion criteria were the availability of data and author consent. We investigated the types of methods and software used and whether we were able to reproduce the data analysis using open source software. Most articles provided overview tables and simple visualisations. Generalised Estimating Equations (GEEs) were the most popular statistical models among the selected articles. Only one article used open source software and only one published part of the analysis code. Replication was difficult in most cases and required reverse engineering of results or contacting the authors. For three articles we were not able to reproduce the results, for another two only parts of them. For all but two articles we had to contact the authors to be able to reproduce the results. Our main learning is that reproducing papers is difficult if no code is supplied and leads to a high burden for those conducting the reproductions. Open data policies in journals are good, but to truly boost reproducibility we suggest adding open code policies.

Naturalness Assessment of Forest Management Scenarios in Abies balsamea–Betula papyrifera Forests

Research Highlights: This research provides an application of a model assessing the naturalness of the forest ecosystem to demonstrate its capacity to assess either the deterioration or the rehabilitation of the ecosystem through different forest management scenarios. Background and Objectives: The model allows the assessment of the quality of ecosystems at the landscape level based on the condition of the forest and the proportion of different forest management practices to precisely characterize a given strategy. The present work aims to: (1) verify the capacity of the Naturalness Assessment Model to perform bi-directional assessments, allowing not only the evaluation of the deterioration of naturalness characteristics, but also its improvement related to enhanced ecological management or restoration strategies; (2) identify forest management strategies prone to improving ecosystem quality; (3) analyze the model’s capacity to summarize the effect of different practices along a single alteration gradient. Materials and Methods: The Naturalness Assessment Model was adapted to the Abies balsamea–Betula papyrifera forest of Quebec (Canada), and a naturalness assessment of two sectors with different historical management strategies was performed. Fictive forest management scenarios were evaluated using different mixes of forestry practices. The sensitivity of the reference data set used for the naturalness assessment has been evaluated by comparing the results using data from old management plans with those based on Quebec’s reference state registry. Results: The model makes it possible to identify forest management strategies capable of improving ecosystem quality compared to the current situation. The model’s most sensitive variables are regeneration process, dead wood, closed forest and cover type. Conclusions: In the Abies balsamea–Betula papyrifera forest, scenarios with enhanced protection and inclusion of irregular shelterwood cuttings could play an important role in improving ecosystem quality. Conversely, scenarios with short rotation (50 years) could lead to further degradation of the ecosystem quality.

Advances in population ecology and species interactions in mammals

The study of mammals has promoted the development and testing of many ideas in contemporary ecology. Here we address recent developments in foraging and habitat selection, source–sink dynamics, competition (both within and between species), population cycles, predation (including apparent competition), mutualism, and biological invasions. Because mammals are appealing to the public, ecological insight gleaned from the study of mammals has disproportionate potential in educating the public about ecological principles and their application to wise management. Mammals have been central to many computational and statistical developments in recent years, including refinements to traditional approaches and metrics (e.g., capture-recapture) as well as advancements of novel and developing fields (e.g., spatial capture-recapture, occupancy modeling, integrated population models). The study of mammals also poses challenges in terms of fully characterizing dynamics in natural conditions. Ongoing climate change threatens to affect global ecosystems, and mammals provide visible and charismatic subjects for research on local and regional effects of such change as well as predictive modeling of the long-term effects on ecosystem function and stability. Although much remains to be done, the population ecology of mammals continues to be a vibrant and rapidly developing field. We anticipate that the next quarter century will prove as exciting and productive for the study of mammals as has the recent one.