Managing biodiversity under climate change: challenges,frameworks, and tools for adaptation

The myriad challenges facing biodiversity under climate change are reflected in the challenges facing managers planning for these impacts. An ever-expanding number of recommendations and tools for climate change adaptation exist to aid managers in these efforts, yet navigating these various resources can lead to information overload and paralysis in decision-making. Here we provide a synthesis of the key considerations, approaches, and available tools for integrating climate change adaptation into management plans. We discuss principal elements in climate change adaptation—incorporating uncertainty through scenario planning and adaptive management—and review three leading frameworks for incorporating climate change adaptation into place-based biodiversity conservation planning. Finally, we identify the following key questions needed for long-term conservation planning and review the associated tools and techniques needed to address them: (1) How is the climate projected to change in my study area?; (2) How are non-climatic stressors projected to change?; (3) How vulnerable are species to climate change impacts?; (4) How are species ranges likely to respond?; and (5) How are management strategies expected to affect outcomes? In doing so, we aim to aid natural resource managers in navigating the burgeoning field of climate change adaptation planning and provide managers a roadmap for managing biodiversity under climate change.     

Latent learning,shortcuts and detours: a computational model

Voicu and Schmajuk (Rob. Auto. Syst. 35 (2001a) 23) described a model of spatial navigation and exploration that includes an action system capable of guiding, with the help of a cognitive system, the search for specific goals as determined by a motivation system. Whereas in the original model the cognitive map stores information about the connectivity between places in the environment, in the present version the cognitive map also stores information about the paths traversed by the agent. Computer simulations show that the network correctly describes experimental results including latent learning in a maze, detours in a maze, and shortcuts in an open field. In addition, the model generates novel predictions about detours and shortcuts in an open field.     

Sampling the rarest: threatened beetles in boreal forest biodiversity inventories

Presence or absence of threatened species in samples is information that is widely used in designing and implementing conservation actions. We explored the effectiveness of beetle (Coleoptera) inventories and contribution of different sampling methods in revealing occurrences of threatened and near threatened species in boreal forests. The number of species caught using traps in a particular area proved to be a useful indicator of the representativeness of data, the relationship between total number of species and the number of threatened and near threatened species being almost exponential. Samples containing less than 200 trapped species (or 2000 individuals) are almost useless in surveying threatened and near threatened species. The probability of finding such species increases considerably when the number of trapped species exceeds 400. Window traps attached directly on the trunks of dead trees proved to be the most efficient sampling method in trapping threatened beetles, whereas many other standard methods gave relatively poor results. We suggest that the best alternative in surveying threatened species in boreal forests is a combination of intensive direct searching and trunk window traps. Finding threatened beetles with rigorous probability requires very large sample sizes, even if the most effective sampling methods are used. For example, ranking 10 boreal forest areas to be protected according to the occurrence of threatened species with some reliability may require trapping of over 100000 beetle individuals. Collecting and identifying these large samples routinely in conservation actions is not feasible, which means that shortcuts (indicators etc.) are necessary. However, a lot of good-quality inventories with appropriate sampling efforts are needed before these shortcuts can be identified and elaborated. Such inventories are also crucial for the improvement of the classification of threatened species and full assessment on how past forest management has eventually affected the biota.     

The comparative method in conservation biology

The phylogenetic comparative approach is a statistical method for analyzing correlations between traits across species. Whilst it has revolutionized evolutionary biology, can it work for conservation biology? Although it is correlative, advocates of the comparative method hope that it will reveal general mechanisms in conservation, provide shortcuts for prioritizing conservation research, and enable us to predict which species will experience (or create) problems in the future. Here, we ask whether these stated management goals are being achieved. We conclude that comparative methods are stimulating research into the ecological mechanisms underlying conservation, and are providing information for preemptive screening of problem species. But comparative analyses of extinction risk to date have tended to be too broad in scope to provide shortcuts to conserving particular endangered species. Correlates of vulnerability to conservation problems are often taxon, region and threat specific, so models must be narrowly focused to be of maximum practical use.     

Ant Navigation: Fractional Use of the Home Vector

Home is a special location for many animals, offering shelter from the elements, protection from predation, and a common place for gathering of the same species. Not surprisingly, many species have evolved efficient, robust homing strategies, which are used as part of each and every foraging journey. A basic strategy used by most animals is to take the shortest possible route home by accruing the net distances and directions travelled during foraging, a strategy well known as path integration. This strategy is part of the navigation toolbox of ants occupying different landscapes. However, when there is a visual discrepancy between test and training conditions, the distance travelled by animals relying on the path integrator varies dramatically between species: from 90% of the home vector to an absolute distance of only 50 cm. We here ask what the theoretically optimal balance between PI-driven and landmark-driven navigation should be. In combination with well-established results from optimal search theory, we show analytically that this fractional use of the home vector is an optimal homing strategy under a variety of circumstances. Assuming there is a familiar route that an ant recognizes, theoretically optimal search should always begin at some fraction of the home vector, depending on the region of familiarity. These results are shown to be largely independent of the search algorithm used. Ant species from different habitats appear to have optimized their navigation strategy based on the availability and nature of navigational information content in their environment.     

Probabilistic path ranking based on adjacent pairwise coexpression for metabolic transcripts analysis

MOTIVATION: Pathway knowledge in public databases enables us to examine how individual metabolites are connected via chemical reactions and what genes are implicated in those processes. For two given (sets of) compounds, the number of possible paths between them in a metabolic network can be intractably large. It would be informative to rank these paths in order to differentiate between them. RESULTS: Focusing on adjacent pairwise coexpression, we developed an algorithm which, for a specified k, efficiently outputs the top k paths based on a probabilistic scoring mechanism, using a given metabolic network and microarray datasets. Our idea of using adjacent pairwise coexpression is supported by recent studies that local coregulation is predominant in metabolism. We first evaluated this idea by examining to what extent highly correlated gene pairs are adjacent and how often they are consecutive in a metabolic network. We then applied our algorithm to two examples of path ranking: the paths from glucose to pyruvate in the entire metabolic network of yeast and the paths from phenylalanine to sinapyl alcohol in monolignols pathways of arabidopsis under several different microarray conditions, to confirm and discuss the performance analysis of our method.     

Tree Diversity,Environmental Heterogeneity,and Productivity in a Mexican Tropical Dry Forest1

Species diversity–environmental heterogeneity (D–EH) and species diversity–productivity (D–P) relationships have seldom been analyzed simultaneously even though such analyses could help to understand the processes underlying contrasts in species diversity among sites. Here we analyzed both relationships at a local scale for a highly diverse tropical dry forest of Mexico. We posed the following questions: (1) are environmental heterogeneity and productivity related?; (2) what are the shapes of D–EH and D–P relationships?; (3) what are individual, and interactive, contributions of these two variables to the observed variance in species diversity?; and (4) are patterns affected by sample size, or by partitioning into average local diversity and spatial species turnover? All trees (diameter at breast height ≥5 cm) within twenty‐six 0.2‐ha transects were censused; four environmental variables associated with water availability were combined into an environmental heterogeneity index; aboveground standing biomass was used as a productivity estimator. Simple and multiple linear and nonlinear regression models were run. Environmental heterogeneity and productivity were not correlated. We found consistently positive log‐linear D–EH and D–P relationships. Productivity explained a larger fraction of among‐transect variance in species diversity than did environmental heterogeneity. No effects of sample size were found. Different components of diversity varied in sensitivity to environmental heterogeneity and productivity. Our results suggest that species' differentiation along water availability gradients and species exclusion at the lowest productivity (driest) sites occur simultaneously, independently, and in a scale‐dependent fashion on the tree community of this forest.     

Ecological Theory and Community Restoration Ecology

Community ecological theory may play an important role in the development of a science of restoration ecology. Not only will the practice of restoration benefit from an increased focus on theory, but basic research in community ecology will also benefit. We pose several major thematic questions that are relevant to restoration from the perspective of community ecological theory and, for each, identify specific areas that are in critical need of further research to advance the science of restoration ecology. We ask, what are appropriate restoration endpoints from a community ecology perspective? The problem of measuring restoration at the community level, particularly given the high amount of variability inherent in most natural communities, is not easy, and may require a focus on restoration of community function (e.g., trophic structure) rather than a focus on the restoration of particular species. We ask, what are the benefits and limitations of using species composition or biodiversity measures as endpoints in restoration ecology? Since reestablishing all native species may rarely be possible, research is needed on the relationship between species richness and community stability of restored sites and on functional redundancy among species in regional colonist “pools.” Efforts targeted at restoring system function must take into account the role of individual species, particularly if some species play a disproportionate role in processing material or are strong interactors. We ask, is restoration of habitat a sufficient approach to reestablish species and function? Many untested assumptions concerning the relationship between physical habitat structure and restoration ecology are being made in practical restoration efforts. We need rigorous testing of these assumptions, particularly to determine how generally they apply to different taxa and habitats. We ask, to what extent can empirical and theoretical work on community succession and dispersal contribute to restoration ecology? We distinguish systems in which succession theory may be broadly applicable from those in which it is probably not. If community development is highly predictable, it may be feasible to manipulate natural succession processes to accelerate restoration. We close by stressing that the science of restoration ecology is so intertwined with basic ecological theory that practical restoration efforts should rely heavily on what is known from theoretical and empirical research on how communities develop and are structured over time.     

A network perspective on the topological importance of enzymes and their phylogenetic conservation

Background  

A metabolic network is the sum of all chemical transformations or reactions in the cell, with the metabolites being interconnected by enzyme-catalyzed reactions. Many enzymes exist in numerous species while others occur only in a few. We ask if there are relationships between the phylogenetic profile of an enzyme, or the number of different bacterial species that contain it, and its topological importance in the metabolic network. Our null hypothesis is that phylogenetic profile is independent of topological importance. To test our null hypothesis we constructed an enzyme network from the KEGG (Kyoto Encyclopedia of Genes and Genomes) database. We calculated three network indices of topological importance: the degree or the number of connections of a network node; closeness centrality, which measures how close a node is to others; and betweenness centrality measuring how frequently a node appears on all shortest paths between two other nodes.     

Understanding predator densities for successful co‐existence of alien predators and threatened prey

The high failure rate of threatened species translocations has prompted many managers to fence areas to protect wildlife from introduced predators. However, conservation fencing is expensive, restrictive and exacerbates prey naïveté reducing the chance of future co‐existence between native prey and introduced predators. Here, we ask whether two globally threatened mammal species protected in fenced reserves, with a history of predation‐driven decline and reintroduction failure, could co‐exist with introduced predators. We defined co‐existence as population persistence for at least 3 years and successful recruitment. We manipulated the density of feral cats within a large fenced paddock and measured the impact on abundance and reproduction of 353 reintroduced burrowing bettongs and 47 greater bilbies over 3 years. We increased cat densities from 0.038 to 0.46 per square km and both threatened species survived, reproduced and increased their population size. However, a previous reintroduction trial of 66 bettongs into the same paddock found one red fox (Vulpes vulpes), at a density of 0.027 per square km, drove the bettong population extinct within 12 months. Our results show that different predator species vary in their impact and that despite a history of reintroduction failure, threatened mammal species can co‐exist with low densities of feral cats. There may be a threshold density below which it is possible to maintain unfenced populations of reintroduced marsupials. Understanding the numerical relationships between population densities of introduced predators and threatened species is urgently needed if these species are to be re‐established at landscape scales. Such knowledge will enable a priori assessment of the risk of reintroduction failure thereby increasing the likelihood of reintroduction success and reducing the financial and ethical cost of failed translocations.     

生物磁学在鸟类定向研究中的进展

地球上广泛存在的地磁场能够为导航提供可靠的信息,因此很多鸟类在迁徙和归巢过程中都使用地磁信息来保证航行方向的正确,在迁徙的鸟类中已经发现有18种是利用地磁罗盘进行定向和导航的。本文从鸟类使用的磁罗盘、航行地图以及磁感应机制等几方面阐述了目前在鸟类生物磁学方面的研究进展。     

From richer to poorer: successful invasion by freshwater fishes depends on species richness of donor and recipient basins

Evidence for the theory of biotic resistance is equivocal, with experiments often finding a negative relationship between invasion success and native species richness, and large‐scale comparative studies finding a positive relationship. Biotic resistance derives from local species interactions, yet global and regional studies often analyze data at coarse spatial grains. In addition, differences in competitive environments across regions may confound tests of biotic resistance based solely on native species richness of the invaded community. Using global and regional data sets for fishes in river and stream reaches, we ask two questions: (1) does a negative relationship exist between native and non‐native species richness and (2) do non‐native species originate from higher diversity systems. A negative relationship between native and non‐native species richness in local assemblages was found at the global scale, while regional patterns revealed the opposite trend. At both spatial scales, however, nearly all non‐native species originated from river basins with higher native species richness than the basin of the invaded community. Together, these findings imply that coevolved ecological interactions in species‐rich systems inhibit establishment of generalist non‐native species from less diverse communities. Consideration of both the ecological and evolutionary aspects of community assembly is critical to understanding invasion patterns. Distinct evolutionary histories in different regions strongly influence invasion of intact communities that are relatively unimpacted by human actions, and may explain the conflicting relationship between native and non‐native species richness found at different spatial scales.     

Extinction debt of cities and ways to minimise their realisation: a focus on Melbourne

The formation and growth of cities sets in train a slow process of local species extinction, although it can take a long time for that extinction to be realised. Using Melbourne as an example, the authors ask ‘What plant species are potentially at risk and what strategies and actions could minimise the predicted negative outcomes?’     

Hommel's procedure in linear time

Hommel's and Hochberg's procedures for familywise error control are both derived as shortcuts in a closed testing procedure with the Simes local test. Hommel's shortcut is exact but takes quadratic time in the number of hypotheses. Hochberg's shortcut takes only linear time after the P‐values are sorted, but is conservative. In this paper, we present an exact shortcut in linear time on sorted P‐values, combining the strengths of both procedures. The novel shortcut also applies to a robust variant of Hommel's procedure that does not require the assumption of the Simes inequality.     

Behavior influences range limits and patterns of coexistence across an elevational gradient in tropical birds

Does competition influence patterns of coexistence between closely related taxa? Here we address this question by analyzing patterns of range overlap between related species of birds (‘sister pairs’) co‐occurring on a tropical elevational gradient. We explicitly contrast the behavioral dimension of interspecific competition (interference competition) with similarity in resource acquisition traits (exploitative competition). Specifically, we ask whether elevational range overlap in 118 sister pairs that live along the Manu Transect in southeastern Peru is predicted by proxies for competition (intraspecific territorial behavior) or niche divergence (beak divergence and divergence times, an estimate of evolutionary age). We find that close relatives that defend year‐round territories tend to live in non‐overlapping elevational distributions, while close relatives that do not defend territories tend to broadly overlap in elevational distribution. In contrast, neither beak divergence nor evolutionary age was associated with patterns of range limitation. We interpret these findings as evidence that behavioral interactions – particularly direct territorial aggression – can be important in setting elevational range limits and preventing coexistence of closely related species, though this depends upon the extent to which intraspecific territorial behavior can be extended to territorial interactions between species. Our results suggest that interference competition can be an important driver of species range limits in diverse assemblages, and thus highlight the importance of considering behavioral dimensions of the niche in macroecological studies.     

A primer of community ecology using the R language

Community ecology beginners often struggle to understand theories expressed in complex mathematical formulas and to master computer programming. To remedy this situation, this article provides a practical, R-based introduction to community ecology by illustrating core concepts (vital rates, carrying capacity, and density dependence) and models that can be used to explore the patterns of species abundance and diversity. The structure of this article consists of three modeling exercises, each asking a general question that can be answered by a combination of theory and R programming: (1) what determines the abundance of species, and what makes a population persist and go extinct?; (2) what determines the distribution of species and species diversity?; (3) what determines the relative abundance of species and what allows species to coexist? Through the exercises, I discuss the following five concepts and ideas that provide valuable insights into the questions: (i) the tragedy of the commons, (ii) the theory of island biogeography, (iii) competitive exclusion, (iv) the neutral theory of biodiversity, and (v) frequency dependence. These materials are thus designed to guide the reader in developing an intuition for ecological thinking that will help capture the essence of the global environmental and biodiversity crisis. Although this article does not delineate the scope and depth of the vast field of community ecology, I hope that it will motivate the reader to step up to a more formal introduction to community ecology.     

Birds of a Feather: Neanderthal Exploitation of Raptors and Corvids

The hypothesis that Neanderthals exploited birds for the use of their feathers or claws as personal ornaments in symbolic behaviour is revolutionary as it assigns unprecedented cognitive abilities to these hominins. This inference, however, is based on modest faunal samples and thus may not represent a regular or systematic behaviour. Here we address this issue by looking for evidence of such behaviour across a large temporal and geographical framework. Our analyses try to answer four main questions: 1) does a Neanderthal to raptor-corvid connection exist at a large scale, thus avoiding associations that might be regarded as local in space or time?; 2) did Middle (associated with Neanderthals) and Upper Palaeolithic (associated with modern humans) sites contain a greater range of these species than Late Pleistocene paleontological sites?; 3) is there a taphonomic association between Neanderthals and corvids-raptors at Middle Palaeolithic sites on Gibraltar, specifically Gorham''s, Vanguard and Ibex Caves? and; 4) was the extraction of wing feathers a local phenomenon exclusive to the Neanderthals at these sites or was it a geographically wider phenomenon?. We compiled a database of 1699 Pleistocene Palearctic sites based on fossil bird sites. We also compiled a taphonomical database from the Middle Palaeolithic assemblages of Gibraltar. We establish a clear, previously unknown and widespread, association between Neanderthals, raptors and corvids. We show that the association involved the direct intervention of Neanderthals on the bones of these birds, which we interpret as evidence of extraction of large flight feathers. The large number of bones, the variety of species processed and the different temporal periods when the behaviour is observed, indicate that this was a systematic, geographically and temporally broad, activity that the Neanderthals undertook. Our results, providing clear evidence that Neanderthal cognitive capacities were comparable to those of Modern Humans, constitute a major advance in the study of human evolution.     

Applying stable isotopes to examine food‐web structure: an overview of analytical tools

Stable isotope analysis has emerged as one of the primary means for examining the structure and dynamics of food webs, and numerous analytical approaches are now commonly used in the field. Techniques range from simple, qualitative inferences based on the isotopic niche, to Bayesian mixing models that can be used to characterize food‐web structure at multiple hierarchical levels. We provide a comprehensive review of these techniques, and thus a single reference source to help identify the most useful approaches to apply to a given data set. We structure the review around four general questions: (1) what is the trophic position of an organism in a food web?; (2) which resource pools support consumers?; (3) what additional information does relative position of consumers in isotopic space reveal about food‐web structure?; and (4) what is the degree of trophic variability at the intrapopulation level? For each general question, we detail different approaches that have been applied, discussing the strengths and weaknesses of each. We conclude with a set of suggestions that transcend individual analytical approaches, and provide guidance for future applications in the field.     

Nestedness,SLOSS and conservation networks of boreal herb‐rich forests

Question: Herb‐rich patches are biodiversity hotspots for vascular plants in boreal forests. We ask: Do species occurrences on herb‐rich patches show a non‐random, nested structure?; Does patch size relate to richness of edaphically demanding and red‐listed species?; Does a set of small patches support more edaphically demanding and red‐listed species than a few large patches of the equal area? Location: Eastern Finland (63°04′N, 29°52′E), boreal vegetation zone. Data: Vegetation mapping of 90 herb‐rich sites, varying from 0.05 to 6.93 ha in size and belonging to six different, predetermined forest site types. Results: Using the RANDNEST procedure, only one site type showed a significantly nested pattern, and patch area was not related to “nestedness” in any of the site types. The number of edaphically demanding and red‐listed plant species was positively correlated with a patch size in three forest site types. In all site types, a set of small patches had more edaphically demanding and red‐listed species than did a few large patches of the equal total area. Conclusions: For conservation, it is essential to protect representative sets of different herb‐rich forest site types because flora varies between the site types. Within herb‐rich forest site types, several small areas may support representative species composition. However, successful conservation requires thorough species inventories, because of the high level of heterogeneity between the herb‐rich patches.