Understanding and accurately modeling species distributions lies at the heart of many problems in ecology, evolution, and conservation. Multiple sources of data are increasingly available for ...modeling species distributions, such as data from citizen science programs, atlases, museums, and planned surveys. Yet reliably combining data sources can be challenging because data sources can vary considerably in their design, gradients covered, and potential sampling biases. We review, synthesize, and illustrate recent developments in combining multiple sources of data for species distribution modeling. We identify five ways in which multiple sources of data are typically combined for modeling species distributions. These approaches vary in their ability to accommodate sampling design, bias, and uncertainty when quantifying environmental relationships in species distribution models. Many of the challenges for combining data are solved through the prudent use of integrated species distribution models: models that simultaneously combine different data sources on species locations to quantify environmental relationships for explaining species distribution. We illustrate these approaches using planned survey data on 24 species of birds coupled with opportunistically collected eBird data in the southeastern United States. This example illustrates some of the benefits of data integration, such as increased precision in environmental relationships, greater predictive accuracy, and accounting for sample bias. Yet it also illustrates challenges of combining data sources with vastly different sampling methodologies and amounts of data. We provide one solution to this challenge through the use of weighted joint likelihoods. Weighted joint likelihoods provide a means to emphasize data sources based on different criteria (e.g., sample size), and we find that weighting improves predictions for all species considered. We conclude by providing practical guidance on combining multiple sources of data for modeling species distributions.
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Deleterious effects of habitat fragmentation and benefits of connecting fragments could be significantly underestimated because changes in colonization and extinction rates that drive changes in ...biodiversity can take decades to accrue. In a large and well-replicated habitat fragmentation experiment, we find that annual colonization rates for 239 plant species in connected fragments are 5% higher and annual extinction rates 2% lower than in unconnected fragments. This has resulted in a steady, nonasymptotic increase in diversity, with nearly 14% more species in connected fragments after almost two decades. Our results show that the full biodiversity value of connectivity is much greater than previously estimated, cannot be effectively evaluated at short time scales, and can be maximized by connecting habitat sooner rather than later.
Connectivity plays a crucial role in determining the spread, viability, and persistence of populations across space. Dispersal across landscapes, or the movement of individuals or genes among ...resource patches, is critical for functional connectivity. Yet current connectivity modelling typically uses information on species location or habitat preference rather than movement, which unfortunately may not capture key dispersal limitations. We argue that recent developments in species distribution modelling provide insightful lessons for addressing this gap and advancing our understanding of connectivity. We suggest shifting the focus of connectivity modelling from locating where animals potentially disperse to a process-based approach directed towards understanding and mapping factors that limit successful dispersal. To do so, we propose defining species dispersal requirements through identifying spatial, environmental and intrinsic constraints to successful dispersal, analogous to identifying environmental dimensions that define niches. We discuss the benefits of this constraint-based framework for understanding the distribution of species, predicting species responses to climate change, and connectivity conservation practice. We illustrate how the framework can aid in identifying potential detrimental effects of human activities on connectivity and species persistence, and can spur the implementation of innovative conservation strategies. The proposed framework clarifies the validity and contextual utility of objectives and measures in existing connectivity models, and identifies gaps that may impede our understanding of connectivity and its integration into successful conservation strategies. We expect that this framework will facilitate a mechanistic approach to understanding and conserving connectivity, which will aid in effectively predicting and mitigating effects of ongoing environmental change.
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Habitat loss is often considered the greatest near-term threat to biodiversity. Yet the impact of habitat fragmentation, or the change in habitat configuration for a given amount of habitat loss, has ...been intensely debated. We isolated effects of habitat loss from fragmentation on the demography, movement, and abundance of wild populations of a specialist herbivore, Chelinidea vittiger, by removing 2,088 patches across 15 landscapes. We compared fragmentation resulting from random loss, which is often considered in theory, to aggregated loss, which is often observed in the real world. When quantifying fragmentation caused by random vs. aggregated loss, aggregated loss led to less fragmented landscapes than random loss based on patch isolation, but more fragmented landscapes when based on isolation at a larger mesoscale scale defined by dispersal distances of C. vittiger. Overall, habitat loss decreased population size and demographic parameters, with thresholds occurring at approximately 70–80% patch loss. Synergistic effects also occurred, where an aggregated pattern of loss had negative effects at low, but not high, amounts of habitat loss. Effects on population size of C. vittiger were driven by reductions in movement and subsequent reproduction. The direction of habitat fragmentation effects from random and aggregated loss treatments, for a given habitat amount, was conflictingly positive or negative depending on the scale at which fragmentation was quantified. Fragmentation quantified at the scale of dispersal for this species best explained population size and highlighted that fragmentation had negative effects at a mesoscale. Our results emphasize the importance of quantifying habitat fragmentation at biologically appropriate scales.
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Although matrix improvement in fragmented landscapes is a promising conservation measure, matrix permeability (willingness of an organism to enter the matrix) and movement survival in the matrix are ...usually aggregated. Consequently, it is unknown which matrix property needs to be improved. It also remains unclear whether matrix upgrading from dispersal passage to providing reproduction opportunities has large conservation benefits and whether there are interactive effects between habitat and matrix management.
We examined matrix effects on regional populations across a gradient of habitat loss and fragmentation using simulation experiments that integrated demographic processes and movement modelling based on circuit theory. We separately modified the levels of matrix permeability and movement survival to evaluate their individual effects. We also altered the amount and configuration of not only habitat but also improved matrix to assess their effects on population vital rates (size, survival and density).
In binary landscapes comprising habitat and unimproved matrix, matrix movement survival had larger effects on population vital rates than matrix permeability. Increasing movement survival increased vital rates, yet, increasing matrix permeability decreased vital rates. Increased permeability required corresponding increased movement survival to offset potential negative population outcomes.
When subsets of the matrix functioning as dispersal passage only (where no reproduction opportunities existed) were improved, increasing matrix permeability but holding movement survival constant reduced all vital rates, especially with increasing habitat fragmentation. In contrast, when movement survival increased, vital rates increased given strong habitat fragmentation. The benefits of upgrading dispersal passage to provide reproduction opportunities for population survival were greatest when habitat amount was moderate. We also found synergetic effects between amounts of habitat and improved matrix, and the benefits of matrix improvement were promoted when improvement was achieved in a spatially aggregated manner.
Synthesis and applications. Matrix improvement and connectivity modelling aimed at increasing movement survival will likely bring larger conservation benefits than those for improving permeability alone. Buffering and connecting habitat remnants with improved matrix could provide benefits as long as movement survival is increased. Simultaneous implementation of habitat management and matrix improvement would yield synergistic conservation benefits.
日本語要旨
分断化景観でのマトリックスの改善は有望な保全手法だが、マトリックスの透過性（生物がマトリックスに入る確率）とマトリックスでの移動生存率は通常まとめて扱われ、いずれのマトリックスの属性を改善すべきか不明である。また、マトリックスを移動通路から繁殖の機会を提供するまで改善すると大きな保全上の便益が得られるのか、生息地とマトリックスの管理の間に交互作用があるのかも明らかになっていない。
私たちは、人口統計学的過程とサーキット理論に基づいた移動モデルを統合したシミュレーション実験を行ない、生息地の消失と分断化の傾度上で、地域個体群にマトリックスが及ぼす影響を調査した。ここで異なるマトリックスの属性としてマトリックスの透過性と移動生存率を個別に変化させ、個々の影響を評価した。また生息地だけでなく改善したマトリックスの量と配置も変化させ、個体群統計量（サイズ、生存、密度）に及ぼす影響を調査した。
生息地と改善されていないマトリックスからなる二値の景観では、マトリックスの移動生存率は透過性よりも個体群統計量に大きな影響を及ぼしていた。移動生存率の増加は個体群統計量を増加させたが、透過性の増加は個体群統計量を減少させた。透過性の増加が個体群に及ぼす潜在的な負の影響を相殺するためには、移動生存率の増加が必要とされた。
移動通路としてのみ機能するマトリックス（繁殖の機会は存在しない）の一部を改善する場合、移動生存率を一定にしてマトリックスの透過性を増加させるとすべての個体群統計量が特に生息地が分断化した場合に大きく減少した。対照的に、移動生存率が増加すると、個体群統計量は強度の生息地の分断化下で増加した。マトリックスを移動通路から繁殖の機会を提供するまで改善すると、生息地の量が中程度の際に個体群生存率への便益は最も大きかった。生息地と改善マトリックスの量の間には相乗効果があり、マトリックス改善は空間的にまとめて実施すると便益が大きくなった。
まとめと応用：マトリックスの改善と連結性のモデリングは移動生存率の増加を目指して行なうと、透過性のみを改善する場合に比べて保全上の便益が大きいだろう。改善マトリックスで残存生息地の緩衝帯を設け、残存生息地間を連結させることは、移動生存率が増加するならば便益を生むだろう。生息地の管理とマトリックスの改善を同時に実施すれば、相乗的な保全上の便益がもたらされるだろう。
Matrix improvement and connectivity modelling aimed at increasing movement survival will likely bring larger conservation benefits than those for improving permeability alone. Buffering and connecting habitat remnants with improved matrix could provide benefits as long as movement survival is increased. Simultaneous implementation of habitat management and matrix improvement would yield synergistic conservation benefits.
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A key goal of chemistry is to develop synthetic systems that mimic biology, such as self-assembling, self-replicating models of minimal life forms. Oscillations are often observed in complex ...biological networks, but oscillating, self-replicating species are unknown, and how to control autonomous supramolecular-level oscillating systems is also not yet established. Here we show how a population of self-assembling self-replicators can autonomously oscillate, so that simple micellar species repeatedly appear and disappear in time. The interplay of molecular and supramolecular events is key to observing oscillations: the repeated formation and disappearance of compartments is connected to a reaction network where molecular-level species are formed and broken down. The dynamic behaviour of our system across different length scales offers the opportunities for mass transport, as we demonstrate via reversible dye uptake. We believe these findings will inspire new biomimetic systems and may unlock nanotechnology systems such as (supra)molecular pumps, where compartment formation is controlled in time and space.
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Balancing the competing, and often conflicting, needs of people and wildlife in shared landscapes is a major challenge for conservation science and policy worldwide. Connectivity is critical for ...wildlife persistence, but dispersing animals may come into conflict with people, leading to severe costs for humans and animals and impeding connectivity. Thus, conflict mitigation and connectivity present an apparent dilemma for conservation. We present a framework to address this dilemma and disentangle the effects of barriers to animal movement and conflict-induced mortality of dispersers on connectivity. We extend random-walk theory to map the connectivity-conflict interface, or areas where frequent animal movement may lead to conflict and conflict in turn impedes connectivity. We illustrate this framework with the endangered Asian elephant
, a species that frequently disperses out of protected areas and comes into conflict with humans. We mapped expected movement across a human-dominated landscape over the short- and long-term, accounting for conflict mortality. Natural and conflict-induced mortality together reduced expected movement and connectivity among populations. Based on model validation, our conflict predictions that explicitly captured animal movement better explained observed conflict than a model that considered distribution alone. Our work highlights the interaction between connectivity and conflict and enables identification of location-specific conflict mitigation strategies that minimize losses to people, while ensuring critical wildlife movement between habitats. By predicting where animal movement and humans collide, we provide a basis to plan for broad-scale conservation and the mutual well-being of wildlife and people in shared landscapes.
Occupancy estimation and the closure assumption Rota, Christopher T; Fletcher Jr, Robert J; Dorazio, Robert M ...
Journal of applied ecology,
December 2009, Volume:
46, Issue:
6
Journal Article
Peer reviewed
Open access
1. Recent advances in occupancy estimation that adjust for imperfect detection have provided substantial improvements over traditional approaches and are receiving considerable use in applied ...ecology. To estimate and adjust for detectability, occupancy modelling requires multiple surveys at a site and requires the assumption of 'closure' between surveys, i.e. no changes in occupancy between surveys. Violations of this assumption could bias parameter estimates; however, little work has assessed model sensitivity to violations of this assumption or how commonly such violations occur in nature. 2. We apply a modelling procedure that can test for closure to two avian point-count data sets in Montana and New Hampshire, USA, that exemplify time-scales at which closure is often assumed. These data sets illustrate different sampling designs that allow testing for closure but are currently rarely employed in field investigations. Using a simulation study, we then evaluate the sensitivity of parameter estimates to changes in site occupancy and evaluate a power analysis developed for sampling designs that is aimed at limiting the likelihood of closure. 3. Application of our approach to point-count data indicates that habitats may frequently be open to changes in site occupancy at time-scales typical of many occupancy investigations, with 71% and 100% of species investigated in Montana and New Hampshire respectively, showing violation of closure across time periods of 3 weeks and 8 days respectively. 4. Simulations suggest that models assuming closure are sensitive to changes in occupancy. Power analyses further suggest that the modelling procedure we apply can effectively test for closure. 5. Synthesis and applications. Our demonstration that sites may be open to changes in site occupancy over time-scales typical of many occupancy investigations, combined with the sensitivity of models to violations of the closure assumption, highlights the importance of properly addressing the closure assumption in both sampling designs and analysis. Furthermore, inappropriately applying closed models could have negative consequences when monitoring rare or declining species for conservation and management decisions, because violations of closure typically lead to overestimates of the probability of occurrence.
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Animal behaviour in a changing world Candolin, Ulrika; Fletcher, Robert J.; Stephens, Andrea E.A.
Trends in ecology & evolution,
April 2023, 2023-04-00, 20230401, Volume:
38, Issue:
4
Journal Article
Peer reviewed
Open access
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Understanding how species composition varies across space and time is fundamental to ecology. While multiple methods having been created to characterize this variation through the identification of ...groups of species that tend to co‐occur, most of these methods unfortunately are not able to represent gradual variation in species composition. The Latent Dirichlet Allocation (LDA) model is a mixed‐membership method that can represent gradual changes in community structure by delineating overlapping groups of species, but its use has been limited because it requires abundance data and requires users to a priori set the number of groups. We substantially extend LDA to accommodate widely available presence/absence data and to simultaneously determine the optimal number of groups. Using simulated data, we show that this model is able to accurately determine the true number of groups, estimate the underlying parameters, and fit with the data. We illustrate this method with data from the North American Breeding Bird Survey (BBS). Overall, our model identified 18 main bird groups, revealing striking spatial patterns for each group, many of which were closely associated with temperature and precipitation gradients. Furthermore, by comparing the estimated proportion of each group for two time periods (1997–2002 and 2010–2015), our results indicate that nine (of 18) breeding bird groups exhibited an expansion northward and contraction southward of their ranges, revealing subtle but important community‐level biodiversity changes at a continental scale that are consistent with those expected under climate change. Our proposed method is likely to find multiple uses in ecology, being a valuable addition to the toolkit of ecologists.
This article describes a new statistical method that can be used to understand the effect of global change phenomena on biodiversity based on high‐dimensional multivariate presence/absence data. We show how this method is able to automatically determine the number of species groups and fit the data well. Our case study reveals striking spatial patterns of breeding birds, some of which seem to be strongly constrained by temperature and rainfall, and subtle but important community‐level range shifts at a continental scale that may be associated with climate change.
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