More Like this

1. Integrated community occupancy models: A framework to assess occurrence and biodiversity dynamics using multiple data sources

   https://doi.org/10.1111/2041-210X.13811  

   Doser, Jeffrey W. ; Leuenberger, Wendy ; Sillett, T. Scott ; Hallworth, Michael T. ; Zipkin, Elise F. ( February 2022 , Methods in Ecology and Evolution)

   1. The occurrence and distributions of wildlife populations and communities are shifting as a result of global changes. To evaluate whether these shifts are negatively impacting biodiversity processes, it is critical to monitor the status, trends and effects of environmental variables on entire communities. However, modelling the dynamics of multiple species simultaneously can require large amounts of diverse data, and few modelling approaches exist to simultaneously provide species and community‐level inferences.

   2. We present an ‘integrated community occupancy model’ (ICOM) that unites principles of data integration and hierarchical community modelling in a single framework to provide inferences on species‐specific and community occurrence dynamics using multiple data sources. The ICOM combines replicated and nonreplicated detection–nondetection data sources using a hierarchical framework that explicitly accounts for different detection and sampling processes across data sources. We use simulations to compare the ICOM to previously developed hierarchical community occupancy models and single species integrated distribution models. We then apply our model to assess the occurrence and biodiversity dynamics of foliage‐gleaning birds in the White Mountain National Forest in the northeastern USA from 2010 to 2018 using three independent data sources.

   3. Simulations reveal that integrating multiple data sources in the ICOM increased precision and accuracy of species and community‐level inferences compared to single data source models, although benefits of integration were dependent on the information content of individual data sources (e.g. amount of replication). Compared to single species models, the ICOM yielded more precise species‐level estimates. Within our case study, the ICOM had the highest out‐of‐sample predictive performance compared to single species models and models that used only a subset of the three data sources.

   4. The ICOM provides more precise estimates of occurrence dynamics compared to multi‐species models using single data sources or integrated single‐species models. We further found that the ICOM had improved predictive performance across a broad region of interest with an empirical case study of forest birds. The ICOM offers an attractive approach to estimate species and biodiversity dynamics, which is additionally valuable to inform management objectives of both individual species and their broader communities.

    

   more » « less
2. Challenges and opportunities for using natural history collections to estimate insect population trends

   https://doi.org/10.1111/1365-2656.13763  

   Davis, Courtney L. ; Guralnick, Robert P. ; Zipkin, Elise F. ( June 2022 , Journal of Animal Ecology)

   Natural history collections (NHC) provide a wealth of information that can be used to understand the impacts of global change on biodiversity. As such, there is growing interest in using NHC data to estimate changes in species' distributions and abundance trends over historic time horizons when contemporary survey data are limited or unavailable.

   However, museum specimens were not collected with the purpose of estimating population trends and thus can exhibit spatiotemporal and collector‐specific biases that can impose severe limitations to using NHC data for evaluating population trajectories.

   Here we review the challenges associated with using museum records to track long‐term insect population trends, including spatiotemporal biases in sampling effort and sparse temporal coverage within and across years. We highlight recent methodological advancements that aim to overcome these challenges and discuss emerging research opportunities.

   Specifically, we examine the potential of integrating museum records and other contemporary data sources (e.g. collected via structured, designed surveys and opportunistic citizen science programs) in a unified analytical framework that accounts for the sampling biases associated with each data source. The emerging field of integrated modelling provides a promising framework for leveraging the wealth of collections data to accurately estimate long‐term trends of insect populations and identify cases where that is not possible using existing data sources.

    

   more » « less
3. Integrating automated acoustic vocalization data and point count surveys for estimation of bird abundance

   https://doi.org/10.1111/2041-210X.13578  

   Doser, Jeffrey W. ; Finley, Andrew O. ; Weed, Aaron S. ; Zipkin, Elise F. ( March 2021 , Methods in Ecology and Evolution)

   Monitoring wildlife abundance across space and time is an essential task to study their population dynamics and inform effective management. Acoustic recording units are a promising technology for efficiently monitoring bird populations and communities. While current acoustic data models provide information on the presence/absence of individual species, new approaches are needed to monitor population abundance, ideally across large spatio‐temporal regions.

   We present an integrated modelling framework that combines high‐quality but temporally sparse bird point count survey data with acoustic recordings. Our models account for imperfect detection in both data types and false positive errors in the acoustic data. Using simulations, we compare the accuracy and precision of abundance estimates using differing amounts of acoustic vocalizations obtained from a clustering algorithm, point count data, and a subset of manually validated acoustic vocalizations. We also use our modelling framework in a case study to estimate abundance of the Eastern Wood‐Pewee (Contopus virens) in Vermont, USA.

   The simulation study reveals that combining acoustic and point count data via an integrated model improves accuracy and precision of abundance estimates compared with models informed by either acoustic or point count data alone. Improved estimates are obtained across a wide range of scenarios, with the largest gains occurring when detection probability for the point count data is low. Combining acoustic data with only a small number of point count surveys yields estimates of abundance without the need for validating any of the identified vocalizations from the acoustic data. Within our case study, the integrated models provided moderate support for a decline of the Eastern Wood‐Pewee in this region.

   Our integrated modelling approach combines dense acoustic data with few point count surveys to deliver reliable estimates of species abundance without the need for manual identification of acoustic vocalizations or a prohibitively expensive large number of repeated point count surveys. Our proposed approach offers an efficient monitoring alternative for large spatio‐temporal regions when point count data are difficult to obtain or when monitoring is focused on rare species with low detection probability.

    

   more » « less
4. Planktic diatom responses to spatiotemporal environmental variation in high‐mountain tropical lakes

   https://doi.org/10.1111/fwb.14218  

   Luethje, Melina ; Mosquera, Pablo V. ; Hampel, Henrietta ; Fritz, Sherilyn C. ; Benito, Xavier ( January 2024 , Freshwater Biology)

   Tropical lakes harbour high levels of biodiversity, but the temporal and spatial variability of biological communities are still inadequately characterised, making it difficult to predict the impact of accelerated rates of environmental change in these regions. Our goal was to identify the spatiotemporal dynamics of the planktic diatom community in the Cajas Massif in the tropical Andes.

   We analysed seasonal diatom and environmental data over a period of 1 year from 10 lakes located in geologically distinct basins and modelled community–environment relationships using multivariate ordination and variation partitioning techniques. Generalised additive models with a full‐subset information theoretic approach also were used to determine which environmental variables explain single‐species abundance.

   Although the lakes are monomictic and thus have variable thermal structure across the year, seasonal variability of water chemistry conditions was negligible, and seasonal differences in diatom community composition were small. Across space, diatom community composition was correlated primarily with ionic content (divalent cations and alkalinity), related to bedrock composition, and secondly with lake thermal structure and productivity. The ionic gradient overrode the effect of the thermal structure–productivity gradient at the diatom community level, whereas individual diatom species responded more sensitively to variables related to in‐lake and catchment productivity, including chlorophyll‐aand iron, and the proportion of wetlands in the catchment.

   Our results indicate that the spatiotemporal variability of Cajas lakes and their diatom communities is the result of multiple intertwined environmental factors. The emergence of the ionic and thermal structure–productivity gradients in a rather small tropical lake district suggests segregation of ecological niches for diatoms that also may be important in other high‐elevation lake regions. Future studies that track tropical Andean lakes under natural and anthropogenically mediated change, both in contemporary times and in palaeoenvironmental reconstructions, would benefit from the modelling approach (community and species levels) developed here.

    

   more » « less
5. Preventing a series of unfortunate events: Using qualitative models to improve conservation

   https://doi.org/10.1111/1365-2664.14231  

   Clark‐Wolf, T. J. ; Hahn, Philip G. ; Brelsford, Eric ; Francois, Jaleen ; Hayes, Nicolette ; Larkin, Beau ; Ramsey, Philip ; Pearson, Dean E. ( June 2022 , Journal of Applied Ecology)

   Biological organisms are increasingly being introduced and eradicated in an effort to maintain biodiversity and ecosystem function in the face of anthropogenic threats. However, these conservation actions can have unintended consequences to non‐target species. Careful vetting of these actions using ecological modelling tools could help predict and avoid unintended consequences.

   Qualitative modelling tools, such as fuzzy interaction webs (FIWs), allow for qualitative rankings of community properties (e.g. interaction strength = high, medium, low) in combination with quantitative information to predict management outcomes. These tools have lower data requirements than strictly quantitative models, facilitating their use for communities lacking comprehensive parameterization. However, no studies have evaluated the efficacy of FIWs for predicting unintended consequences against empirically documented outcomes. Moreover, there is no process for systematically identifying which species to incorporate in community‐level conservation assessments to overcome model structure uncertainty. Finally, there is a need to make qualitative modelling tools more accessible for conservation practitioners.

   We applied FIWs to the case study of lake trout introduction into Yellowstone Lake, Yellowstone National Park, to assess its ability to predict documented community‐level outcomes from an intentional species introduction. Next, we used the case study of the intentional red squirrel introduction to Newfoundland to show how a community assessment framework can help define the community interaction web needed for applying a FIW. Lastly, we introduced a user‐friendly web interface (https://matrix.mpgranch.com/#/) for applying FIWs to conservation questions.

   We found that the FIW predicted previously documented directional changes in the abundance of community components relatively well in the Yellowstone Lake case study, even with minimal knowledge of the system. The community assessment framework provided a formal process for identifying community components for the Newfoundland case study, and the resulting FIW predicted documented unintended consequences. The user interface predicts realistic outcomes in our study system and allows managers to build and apply FIWs for conservation planning.

   Synthesis and applications. Our community assessment framework and user interface can be used to apply FIWs to identify and avert potential unintended outcomes of species introductions and eradications for improved conservation management.

    

   more » « less