Researchers in ecology and evolutionary biology are increasingly dependent on computational code to conduct research, and the use of efficient methods to share, reproduce, and collaborate on code as well as any research-related documentation has become fundamental. GitHub is an online, cloud-based service that can help researchers track, organize, discuss, share, and collaborate on software and other materials related to research production, including data, code for analyses, and protocols.Despite these benefits, the use of GitHub by EEB researchers is not widespread due to the lack of domain-specific information and guidelines. To help EEB researchers adopt useful features from GitHub in their own workflows, we review twelve practical ways to use the platform. We outline features ranging from low to high technical difficulty: storing code, managing projects, coding collaboratively, conducting peer review, and writing a manuscript. Given that members of a research team may have different technical skills and responsibilities, we describe how the optimal use of GitHub features may vary among members of a research collaboration. As more ecologists and evolutionary biologists establish their workflows using GitHub, the field can continue to push the boundaries of collaborative, transparent, and open research.

Mediterranean maquis vegetation is highly biodiverse, but widespread grazing poses a challenge for management and conservation. We sampled woody and herbaceous plants separately on a limestone mountain with strong mesic-xeric gradients in Tunisia’s Parc National de L’Ichkeul, assessed grazing pressure (on a scale of 1–3), and asked whether grazing had a significant effect on plant compositional abundance before and after controlling for environmental covariates. Sites on the more mesic lakeside face of the mountain were most compositionally unique, and forbs contributed most to the herbaceous beta-diversity on the mountain. We used variance partitioning to separate the collective and individual effects of the abiotic environment, grazing, human activity, and space on herbaceous and woody beta-diversity. However, the individual effect of grazing on overall plant community composition was confounded with space, due to the spatially autocorrelated grazing pressure on the mountain. Importantly, we found that herbaceous and woody communities responded differently to increasing levels of grazing intensity: herbaceous beta-diversity was highest between sites with no grazing pressure, while woody beta-diversity peaked under light grazing. Herbaceous community composition was sensitive to any intensity of grazing pressure, and biotic homogenization occured under moderate-to-high grazing pressure. On the other hand, woody community composition remained relatively similar under no to light grazing pressure, but differed under moderate-to-heavy grazing. Using a one-way permutational analysis of variance analysis, we showed that grazing had a significant effect when controlling for abiotic and spatial covariates. Our findings offer insight into the effects of grazing on maquis vegetation at Jebel Ichkeul, acting as a microcosm of similar conservation and management issues elsewhere in the Mediterranean. We suggest that a combination of monitoring and carefully controlled grazing may enhance plant diversity and maintain the region’s biodiverse maquis vegetation, potentially maintaining a key climate refugium for vulnerable endemic species. Importantly, our study provides a useful baseline of the plant assemblages at Jebel Ichkeul with which to compare future vegetation changes.

Aim: Islands have been the test bed of several theories in community ecology, biogeography, and evolutionary biology. Progress within these disciplines has given a more comprehensive and mechanistic understanding of the processes governing variation in species richness among islands. However, it remains unclear whether these same processes also explain variation in species and phylogenetic composition among islands. Integrating theory from ecology and biogeography, we infer the roles of dispersal, selection, and stochasticity on the composition of insular assemblages within archipelagos. We further assess the influence of source pool diversity and connectivity on the compositional uniqueness of insular assemblages.Location: Island systems worldwide. Taxon: Mammals.Methods: We compiled data on species composition of nonvolant mammals on ~200 islands in nine archipelagos distributed worldwide from the literature. We used variation partitioning to quantify the relative influence of the environment (selection) and geographic distance (dispersal) relative to a null model (stochasticity, randomness) on taxonomic and phylogenetic compositional turnover within archipelagos. We then used a linear mixed model to gain further insight into the underlying mechanisms shaping variation in assemblage composition among islands at a global scale. Specifically, we assessed the influence of source pool diversity, isolation from the source pool, and island characteristics on compositional uniqueness. Results:Our results suggest that within-archipelago variation in the composition of insular mammal assemblages is associated with stochastic or unmeasured processes rather than abiotic selection or dispersal limitation. The diversity and proximity of the source pool, as well as some island characteristics, explained variation in phylogenetic, but not taxonomic, compositional uniqueness globally. Globally, isolated islands associated with phylogenetically diverse source pools exhibit high phylogenetic uniqueness whereas well-connected islands associated with phylogenetically clustered source pools show the opposite trend. Phylogenetically unique assemblages also tend occur on islands with a small elevational span and low annual temperature variation.Main conclusions: Taken together, our results suggest that source pool diversity, along with the potential for colonization from those pools, has a strong influence on the composition of insular mammal assemblages worldwide.

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Researchers in ecology and evolutionary biology are increasingly dependent on computational code to conduct research. Hence, the use of efficient methods to share, reproduce, and collaborate on code as well as document research is fundamental. GitHub is an online, cloud‐based service that can help researchers track, organize, discuss, share, and collaborate on software and other materials related to research production, including data, code for analyses, and protocols. Despite these benefits, the use of GitHub in ecology and evolution is not widespread. To help researchers in ecology and evolution adopt useful features from GitHub to improve their research workflows, we review 12 practical ways to use the platform. We outline features ranging from low to high technical difficulty, including storing code, managing projects, coding collaboratively, conducting peer review, writing a manuscript, and using automated and continuous integration to streamline analyses. Given that members of a research team may have different technical skills and responsibilities, we describe how the optimal use of GitHub features may vary among members of a research collaboration. As more ecologists and evolutionary biologists establish their workflows using GitHub, the field can continue to push the boundaries of collaborative, transparent, and open research.

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To effectively combat the biodiversity crisis, we need ambitious targets and reliable indicators to accurately track trends and measure conservation impact. In Canada, the Living Planet Index (LPI) has been adapted to produce a national indicator by both World Wildlife Fund-Canada (Canadian Living Planet Index; C-LPI) and Environment and Climate Change Canada (Canadian Species Index) to provide insight into the status of Canadian wildlife, by evaluating temporal trends in vertebrate population abundance. The indicator includes data for just over 50% of Canadian vertebrate species. To assess whether the current dataset is representative of the distribution of life history characteristics of Canadian wildlife, we analyzed the representation of species-specific biotic variables (i.e., body size, trophic level, lifespan) for vertebrates within the C-LPI compared to native vertebrates lacking LPI data. Generally, there was considerable overlap in the distribution of biotic variables for species in the C-LPI compared to native Canadian vertebrate species lacking LPI data. Nevertheless, some differences among distributions were found, driven in large part by discrepancy in the representation of fishes—where the C-LPI included larger-bodied and longer-lived species. We provide recommendations for targeted data collection and additional analyses to further strengthen the applicability, accuracy, and representativity of biodiversity indicators.