Heterogeneous Matrix Habitat Drives Species Occurrences in Complex, Fragmented Landscapes

A well-connected Earth: The science and conservation of organismal movement

Global biodiversity targets focus on landscape and seascape connectivity as a foundational component of biodiversity conservation, including networks of connected protected areas. Recent advances allow the measurement and prediction of organismal movements at multiple scales. We provide a definition of connectivity that links movement to persistence and ecological function. Connectivity science can guide planning for biodiversity, ecosystem services, ecological restoration, and climate adaptation. Ongoing climate change and land and sea use are closing the window of opportunity for connectivity conservation. A coordinated global effort is required to implement scientific knowledge and to monitor, map, protect, and restore areas that promote movement and maintain well-connected ecosystems for biodiversity in the long term.

Community metabarcoding reveals the relative role of environmental filtering and spatial processes in metacommunity dynamics of soil microarthropods across a mosaic of montane forests

Disentangling the relative role of environmental filtering and spatial processes in driving metacommunity structure across mountainous regions remains challenging, as the way we quantify spatial connectivity in topographically and environmentally heterogeneous landscapes can influence our perception of which process predominates. More empirical data sets are required to account for taxon- and context-dependency, but relevant research in understudied areas is often compromised by the taxonomic impediment. Here we used haplotype-level community DNA metabarcoding, enabled by stringent filtering of amplicon sequence variants (ASVs), to characterize metacommunity structure of soil microarthropod assemblages across a mosaic of five forest habitats on the Troodos mountain range in Cyprus. We found similar β diversity patterns at ASV and species (OTU, operational taxonomic unit) levels, which pointed to a primary role of habitat filtering resulting in the existence of largely distinct metacommunities linked to different forest types. Within-habitat turnover was correlated to topoclimatic heterogeneity, again emphasizing the role of environmental filtering. However, when integrating landscape matrix information for the highly fragmented Quercus alnifolia habitat, we also detected a major role of spatial isolation determined by patch connectivity, indicating that stochastic and niche-based processes synergistically govern community assembly. Alpha diversity patterns varied between ASV and OTU levels, with OTU richness decreasing with elevation and ASV richness following a longitudinal gradient, potentially reflecting a decline of genetic diversity eastwards due to historical pressures. Our study demonstrates the utility of haplotype-level community metabarcoding for characterizing metacommunity structure of complex assemblages and improving our understanding of biodiversity dynamics across mountainous landscapes worldwide.

Sensitivity of habitat network models to changes in maximum dispersal distance

Predicting the presence or absence (occurrence-state) of species in a certain area is highly important for conservation. Occurrence-state can be assessed by network models that take suitable habitat patches as nodes, connected by potential dispersal of species. To determine connections, a connectivity threshold is set at the species' maximum dispersal distance. However, this requires field observations prone to underestimation, so for most animal species there are no trustable maximum dispersal distance estimations. This limits the development of accurate network models to predict species occurrence-state. In this study, we performed a sensitivity analysis of the performance of network models to different settings of maximum dispersal distance. Our approach, applied on six amphibian species in Switzerland, used habitat suitability modelling to define habitat patches, which were linked within a dispersal distance threshold to form habitat networks. We used network topological measures, patch suitability, and patch size to explain species occurrence-state in habitat patches through boosted regression trees. These modelling steps were repeated on each species for different maximum dispersal distances, including a species-specific value from literature. We evaluated mainly the predictive performance and predictor importance among the network models. We found that predictive performance had a positive relation with the distance threshold, and that almost none of the species-specific values from literature yielded the best performance across tested thresholds. With increasing dispersal distance, the importance of the habitat-quality-related variable decreased, whereas that of the topology-related predictors increased. We conclude that the sensitivity of these models to the dispersal distance parameter stems from the very different topologies formed with different movement assumptions. Most reported maximum dispersal distances are underestimated, presumably due to leptokurtic dispersal distribution. Our results imply that caution should be taken when selecting a dispersal distance threshold, considering higher values than those derived from field reports, to account for long-distance dispersers.

Modeling effects of matrix heterogeneity on population persistence at the patch-level

Habitat loss and fragmentation is the largest contributing factor to species extinction and declining biodiversity. Landscapes are becoming highly spatially heterogeneous with varying degrees of human modification. Much theoretical study of habitat fragmentation has historically focused on a simple theoretical landscape with patches of habitat surrounded by a spatially homogeneous hostile matrix. However, terrestrial habitat patches are often surrounded by complex mosaics of many different land cover types, which are rarely ecologically neutral or completely inhospitable environments. We employ an extension of a reaction diffusion model to explore effects of heterogeneity in the matrix immediately surrounding a patch in a one-dimensional theoretical landscape. Exact dynamics of a population exhibiting logistic growth, an unbiased random walk in the patch and matrix, habitat preference at the patch/matrix interface, and two functionally different matrix types for the one-dimensional landscape is obtained. These results show existence of a minimum patch size (MPS), below which population persistence is not possible. This MPS can be estimated via empirically derived estimates of patch intrinsic growth rate and diffusion rate, habitat preference, and matrix death and diffusion rates. We conclude that local matrix heterogeneity can greatly change model predictions, and argue that conservation strategies should not only consider patch size, configuration, and quality, but also quality and spatial structure of the surrounding matrix.

Understanding the distribution of bushmeat hunting effort across landscapes by testing hypotheses about human foraging

Mitigating the massive impacts of defaunation on natural ecosystems requires understanding and predicting hunting effort across the landscape. But such understanding has been hindered by the difficulty of assessing the movement patterns of hunters in thick forests and across complex terrain. We statistically tested hypotheses about the spatial distribution of hunting with circuit theory and structural equation models. We used a data set of >7000 known kill locations in Guyana and hunter movement models to test these methods. Comparing models with different resistance layers (i.e., different estimates of how terrain and land cover influence human movement speed) showed that rivers, on average, limited movement rather than serving as transport arteries. Moreover, far more kills occurred close to villages than in remote areas. This, combined with the lack of support for structural equation models that included latent terms for prey depletion driven by past overhunting, suggests that kill locations in this system tended to be driven by where hunters were currently foraging rather than by influences of historical harvest. These analyses are generalizable to a variety of ecosystems, species, and data types, providing a powerful way of enhancing maps and predictions of hunting effort across complex landscapes.

Temperature-associated decreases in demographic rates of Afrotropical bird species over 30 years

Tropical mountains harbor globally significant levels of biodiversity and endemism. Climate change threatens many tropical montane species, yet little research has assessed the effects of climate change on the demographic rates of tropical species, particularly in the Afrotropics. Here, we report on the demographic rates of 21 Afrotropical bird species over 30 years in montane forests in Tanzania. We used mark-recapture analyses to model rates of population growth, recruitment, and apparent survival as functions of annual mean temperature and annual precipitation. For over one-half of focal species, decreasing population growth rates were associated with increasing temperature. Due to the trend in temperature over time, we substituted a time covariate for the temperature covariate in top-ranked population growth rate models. Temperature was a better explanatory covariate than time for 6 of the 12 species, or 29% of all focal species. Population growth rates were also lower for species found further below their elevational midpoint and for smaller-bodied species. Changes in population growth rates were more closely tied to changes in recruitment than to changes in apparent survival. There were no consistent associations between demographic rates and precipitation. This study demonstrates temperature-associated demographic impacts for 6 (29%) of 21 focal species in an Afrotropical understory bird community and highlights the need to incorporate the impacts of climate change on demographic rates into conservation planning across the tropics.

Afrotropical montane birds experience upslope shifts and range contractions along a fragmented elevational gradient in response to global warming

Global warming is predicted to result in upslope shifts in the elevational ranges of bird species in montane habitats. Yet few studies have examined changes over time in the elevational distribution of species along fragmented gradients in response to global warming. Here, we report on a resurvey of an understory bird community in the Usambara Mountains in Tanzania, along a forested elevational gradient that has been fragmented over the last 200 years. In 2019, we resurveyed seven sites, ranging in elevation from 360 m to 2110 m, that were originally surveyed between 1979 and 1981. We calculated differences in mean elevation and lower and upper range limits for 29 species between the two time periods and corrected for possible differences in elevation due to chance. Over four decades, we documented a significant mean upslope shift across species of 93 m. This shift was smaller than the 125 m expected shift due to local climate warming. Of the 29 focal species, 19 shifted upslope, eight downslope, and two remained unchanged. Mean upslope shifts in species were driven largely by contracting lower range limits which moved significantly upslope on average across species by 183 m, while upper range limits shifted non-significantly upslope by 72 m, leading to a mean range contraction of 114 m across species. Community composition of understory bird species also shifted over time, with current communities resembling communities found historically at lower elevations. Past forest fragmentation in combination with the limited gap-crossing ability of many tropical understory bird species are very likely important contributory factors to the observed asymmetrical shifts in lower and upper elevational range limits. Re-establishing forested linkages among the largest and closest forest fragments in the Eastern Arc Mountains are critical to permitting species to shift upslope and to reduce further elevational range contractions over time.

Circuitscape in Julia: Empowering Dynamic Approaches to Connectivity Assessment

The conservation field is experiencing a rapid increase in the amount, variety, and quality of spatial data that can help us understand species movement and landscape connectivity patterns. As interest grows in more dynamic representations of movement potential, modelers are often limited by the capacity of their analytic tools to handle these datasets. Technology developments in software and high-performance computing are rapidly emerging in many fields, but uptake within conservation may lag, as our tools or our choice of computing language can constrain our ability to keep pace. We recently updated Circuitscape, a widely used connectivity analysis tool developed by Brad McRae and Viral Shah, by implementing it in Julia, a high-performance computing language. In this initial re-code (Circuitscape 5.0) and later updates, we improved computational efficiency and parallelism, achieving major speed improvements, and enabling assessments across larger extents or with higher resolution data. Here, we reflect on the benefits to conservation of strengthening collaborations with computer scientists, and extract examples from a collection of 572 Circuitscape applications to illustrate how through a decade of repeated investment in the software, applications have been many, varied, and increasingly dynamic. Beyond empowering continued innovations in dynamic connectivity, we expect that faster run times will play an important role in facilitating co-production of connectivity assessments with stakeholders, increasing the likelihood that connectivity science will be incorporated in land use decisions.

Habitat Fragmentation Increases Overall Richness, but Not of Habitat-Dependent Species

Debate rages as to whether habitat fragmentation leads to the decline of biodiversity once habitat loss is accounted for. Previous studies have defined fragmentation variously, but research needs to address “fragmentation per se,” which excludes confounding effects of habitat loss. Our study controls for habitat area and employs a mechanistic multi-species simulation to explore processes that may lead some species groups to be more or less sensitive to fragmentation per se. Our multi-land-cover, landscape-scale, individual-based model incorporates the movement of generic species, each with different land cover preferences. We investigate how fragmentation per se changes diversity patterns; within (alpha), between (beta) and across (gamma) patches of a focal-land-cover, and if this differs among species groups according to their specialism and dependency on this focal-land-cover. We defined specialism as the increased competitive ability of specialists in suitable habitat and decreased ability in less suitable land covers compared to generalist species. We found fragmentation per se caused an increase in gamma diversity in the focal-land-cover if we considered all species regardless of focal-land-cover preference. However, critically for conservation, the gamma diversity of species for whom the focal land cover is suitable habitat declined under fragmentation per se. An exception to this finding occurred when these species were specialists, who were unaffected by fragmentation per se. In general, focal-land-cover species were under pressure from the influx of other species, with fragmentation per se leading to a loss of alpha diversity not compensated for by increases in beta diversity and, therefore, gamma diversity fell. The specialist species, which were more competitive, were less affected by the influx of species and therefore alpha diversity decreased less with fragmentation per se and beta diversity compensated for this loss, meaning gamma diversity did not decrease. Our findings help to inform the fragmentation per se debate, showing that effects on biodiversity can be negative or positive, depending on species’ competitive abilities and dependency on the fragmented land cover. Such differences in the effect of fragmentation per se would have important consequences for conservation. Focusing conservation efforts on reducing or preventing fragmentation in areas with species vulnerable to fragmentation.