Cannot see the diversity for all the species: Evaluating inclusion criteria for local species lists when using abundant citizen science data

Abundant citizen science data on species occurrences are becoming increasingly available and enable identifying composition of communities occurring at multiple sites with high temporal resolution. However, for species displaying temporary patterns of local occurrences that are transient to some sites, biodiversity measures are clearly dependent on the criteria used to include species into local species lists. Using abundant opportunistic citizen science data from frequently visited wetlands, we investigated the sensitivity of α‐ and β‐diversity estimates to the use raw versus detection‐corrected data and to the use of inclusion criteria for species presence reflecting alternative site use. We tested seven inclusion criteria (with varying number of days required to be present) on time series of daily occurrence status during a breeding season of 90 days for 77 wetland bird species. We show that even when opportunistic presence‐only observation data are abundant, raw data may not produce reliable local species richness estimates and rank sites very differently in terms of species richness. Furthermore, occupancy model based α‐ and β‐diversity estimates were sensitive to the inclusion criteria used. Total species lists (all species observed at least once during a season) may therefore mask diversity differences among sites in local communities of species, by including vagrant species on potentially breeding communities and change the relative rank order of sites in terms of species richness. Very high sampling effort does not necessarily free opportunistic data from its inherent bias and can produce a pattern in which many species are observed at least once almost everywhere, thus leading to a possible paradox: The large amount of biological information may hinder its usefulness. Therefore, when prioritizing among sites to manage or preserve species diversity estimates need to be carefully related to relevant inclusion criteria depending on the diversity estimate in focus.     

One size does not fit all: Customizing MCMC methods for hierarchical models using NIMBLE

Improved efficiency of Markov chain Monte Carlo facilitates all aspects of statistical analysis with Bayesian hierarchical models. Identifying strategies to improve MCMC performance is becoming increasingly crucial as the complexity of models, and the run times to fit them, increases. We evaluate different strategies for improving MCMC efficiency using the open‐source software NIMBLE (R package nimble) using common ecological models of species occurrence and abundance as examples. We ask how MCMC efficiency depends on model formulation, model size, data, and sampling strategy. For multiseason and/or multispecies occupancy models and for N‐mixture models, we compare the efficiency of sampling discrete latent states vs. integrating over them, including more vs. fewer hierarchical model components, and univariate vs. block‐sampling methods. We include the common MCMC tool JAGS in comparisons. For simple models, there is little practical difference between computational approaches. As model complexity increases, there are strong interactions between model formulation and sampling strategy on MCMC efficiency. There is no one‐size‐fits‐all best strategy, but rather problem‐specific best strategies related to model structure and type. In all but the simplest cases, NIMBLE's default or customized performance achieves much higher efficiency than JAGS. In the two most complex examples, NIMBLE was 10–12 times more efficient than JAGS. We find NIMBLE is a valuable tool for many ecologists utilizing Bayesian inference, particularly for complex models where JAGS is prohibitively slow. Our results highlight the need for more guidelines and customizable approaches to fit hierarchical models to ensure practitioners can make the most of occupancy and other hierarchical models. By implementing model‐generic MCMC procedures in open‐source software, including the NIMBLE extensions for integrating over latent states (implemented in the R package nimbleEcology), we have made progress toward this aim.     

Will Lynx Lose Their Edge? Canada Lynx Occupancy in Washington

Populations of species located at southern range edges may be particularly vulnerable to the effects of climate change as warming temperatures and subsequent changes to ecosystems exceed species-specific tolerances. One such species is Canada lynx (Lynx canadensis), a cold-adapted mesocarnivore that maintains a large core population in Alaska, USA, and Canada but exists within several peripheral populations in the contiguous United States. Increases in temperature, declines in snow pack, and climate-influenced increases in fire frequency and intensity, could negatively affect lynx populations, threatening their long-term persistence in the continental United States. Despite these threats, our understanding of broad-scale effects on lynx occupancy and the extent of current lynx distribution in many of these peripheral populations is minimal. We conducted an occupancy survey of lynx in Washington, USA, using a spatially extensive camera-trapping array covering 7,000 km² of potential lynx habitat. We used the resulting database of detection data to develop single-season occupancy models to examine the abiotic and biotic effects on current lynx occupancy and predict future lynx distribution based on climate change forecasts. Our results show lynx occupancy across the Washington landscape is restricted and dictated largely by abiotic factors, disturbance regimes, and distance from source populations in Canada. Predictions of future distribution suggest lynx will be increasingly challenged by climatic changes, particularly at the southern and lower elevation portions of their range in Washington. Our results paint an alarming picture for lynx persistence in Washington that is relevant to current deliberations regarding lynx delisting from the Endangered Species Act. Our simple camera design was a highly effective method for surveying lynx across broad spatial scales, and could be a key monitoring tool for lynx that is easy to implement by researchers and government agencies. © 2020 The Wildlife Society.     

Occurrence of blood-feeding terrestrial leeches (Haemadipsidae) in a degraded forest ecosystem and their potential as ecological indicators

Blood-feeding invertebrates are emerging model taxa in biodiversity assessments, both as indicators of mammal abundance and also as sources of mammal DNA for identification. Among these, terrestrial leeches arguably offer the greatest promise; they are abundant and widespread in the humid tropics, and their blood meals can be easily assayed to establish diet. Unfortunately, terrestrial leeches are understudied, with little known about their ecology and behavior. Such information is needed to evaluate their utility as ecological indicators and to account for potential sampling biases that might arise from habitat preferences. By combining occupancy modeling and thermal tolerance assays, we determined the factors affecting species occurrence in the related terrestrial brown (Haemadipsa sumatrana) and tiger leech (Haemadipsa picta), both of which are widespread in tropical forests in Southeast Asia. We sampled both species across a degraded forest landscape in Sabah, Borneo, in wet and dry seasons, associating occurrence with habitat-level metrics. We found that, for both species, detection probability increased with canopy height regardless of season. Additionally, increased vegetation heterogeneity had a strong negative influence on brown leech occurrence in the dry season, implying an interaction between vegetation structure and climate. However, we found no difference in physiological thermal tolerance (CT_MAX) between the two species. Finally, using a reduced dataset, we found a small improvement in brown leech model fit when including mammal abundance. Our results suggest that the presence of terrestrial leeches may act as useful ecological indicators of habitat quality and potentially mammalian abundance. Abstract in Indonesia is available with online material.     

Assessing the effects of habitat characteristics and co-occurrence with closely related species on occupancy of resident ‘wood-warblers’ in a Neotropical working landscape

The simultaneous effects of habitat traits and interspecific interactions determine the occurrence and habitat use of wildlife populations. However, little research has been devoted to examining spatial co-occurrence among closely related species while considering the effect of habitat variation and imperfect detectability of species in the field. In this study, we focused on migratory and resident 'wood-warblers' that coexist during the winter in a Neotropical working landscape in southern Mexico to understand if habitat occupancy of resident wood-warblers is influenced by habitat characteristics and by the presence of other species of resident and migratory wood-warblers. For this purpose, we implemented two-species occupancy models, which account for the imperfect detectability of these birds in the field. Our results revealed that habitat occupancy of resident wood-warblers was positively influenced by the presence of other closely related species (both migratory and resident). These positive relationships may be explained by the fact that different species of wood-warblers frequently participate in mixed-species flocks. However, these patterns of species co-occurrence were more evident among resident species than between migratory and resident species, which may be explained by micro-habitat segregation and differences in behaviours between resident and migratory wood-warblers. We also found that some habitat characteristics may mediate the observed patterns of species co-occurrence. Specifically, sites with larger trees were associated with the co-occurrence of some species of resident wood-warblers. In addition, we discuss the possibility that species co-occurrence might be the result of shared preferences for environmental factors that we did not consider. Our study highlights the importance of the interplay between species co-occurrence and habitat traits in determining the presence and habitat use of resident birds in Neotropical working landscapes.     

Changing use of camera traps in mammalian field research: habitats,taxa and study types

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