The end of the adaptive landscape metaphor?

The concepts of adaptive/fitness landscapes and adaptive peaks are a central part of much of contemporary evolutionary biology; the concepts are introduced in introductory texts, developed in more detail in graduate-level treatments, and are used extensively in papers published in the major journals in the field. The appeal of visualizing the process of evolution in terms of the movement of populations on such landscapes is very strong; as one becomes familiar with the metaphor, one often develops the feeling that it is possible to gain deep insights into evolution by thinking about the movement of populations on landscapes consisting of adaptive valleys and peaks. But, since Wright first introduced the metaphor in 1932, the metaphor has been the subject of persistent confusion, from equivocation over just what the features of the landscape are meant to represent to how we ought to expect the landscapes to look. Recent advances—conceptual, empirical, and computational—have pointed towards the inadequacy and indeed incoherence of the landscapes as usually pictured. I argue that attempts to reform the metaphor are misguided; it is time to give up the pictorial metaphor of the landscape entirely and rely instead on the results of formal modeling, however difficult such results are to understand in ‘intuitive’ terms.

Dual energy landscape: the functional state of the β-barrel outer membrane protein G molds its unfolding energy landscape

We applied dynamic single-molecule force spectroscopy to quantify the parameters (free energy of activation and distance of the transition state from the folded state) characterizing the energy barriers in the unfolding energy landscape of the outer membrane protein G (OmpG) from Escherichia coli. The pH-dependent functional switching of OmpG directs the protein along different regions on the unfolding energy landscape. The two functional states of OmpG take the same unfolding pathway during the sequential unfolding of β-hairpins I-IV. After the initial unfolding events, the unfolding pathways diverge. In the open state, the unfolding of β-hairpin V in one step precedes the unfolding of β-hairpin VI. In the closed state, β-hairpin V and β-strand S11 with a part of extracellular loop L6 unfold cooperatively, and subsequently β-strand S12 unfolds with the remaining loop L6. These two unfolding pathways in the open and closed states join again in the last unfolding step of β-hairpin VII. Also, the conformational change from the open to the closed state witnesses a rigidified extracellular gating loop L6. Thus, a change in the conformational state of OmpG not only bifurcates its unfolding pathways but also tunes its mechanical properties for optimum function.     

Is there such a thing as landscape genetics?

For a scientific discipline to be interdisciplinary, it must satisfy two conditions; it must consist of contributions from at least two existing disciplines, and it must be able to provide insights, through this interaction, that neither progenitor discipline could address. In this study, I examine the complete body of peer‐reviewed literature self‐identified as landscape genetics (LG) using the statistical approaches of text mining and natural language processing. The goal here was to quantify the kinds of questions being addressed in LG studies, the ways in which questions are evaluated mechanistically, and how they are differentiated from the progenitor disciplines of landscape ecology and population genetics. I then circumscribe the main factions within published LG studies examining the extent to which emergent questions are being addressed and highlighting a deep bifurcation between existing individual‐ and population‐based approaches. I close by providing some suggestions on where theoretical and analytical work is needed if LGs is to serve as a real bridge connecting evolution and ecology sensu lato.     

Do forest-dwelling plant species disperse along landscape corridors?

Woody corridors in fragmented landscapes have been proposed as alternative habitats for forest plants, but the great variation in species-specific responses blurs the overall assessment. The aim of this study was to estimate the dispersal success of forest-dwelling plants from a stand into and along an attached woody corridor, and to explain the observed patterns from the point of view of species’ dispersal traits and corridor properties. We sampled 47 forest–corridor transects in the agricultural landscapes of southeastern Estonia. Regionally common forest-dwelling species (observed in at least 10 % of seed-source forests) were classified on the basis of their ecological response profile—forest-restricted species (F-type) and forest-dwelling generalists (G-type). Species richness and the proportion of F-type species decreased sharply from the seed-source forest core to the forest edge and to the first 10–15 m of the corridor, while G-type species richness remained constant throughout the transect. Corridor structure had a species-specific effect—F species were promoted by old (≥50 years) and wide (≥10 m) corridors, while G species were supported by young and narrow corridors with ditch-related soil disturbances. Moderate shade (canopy cover <75 %) was optimal for all forest-dwelling species. Large dispersule weight, and not seed weight, dispersal vector or Ellenberg’s indicator values, was the trait that differentiated F species from G species. We conclude that most woody corridors are only dispersal stepping-stone habitats for habitat generalist species, and not for specialists. Only century old corridors can relieve the dispersal limitation of forest-restricted species.     

The rise and fall of the adaptive landscape?

The discussion of the adaptive landscape in the philosophical literature appears to be divided along the following lines. On the one hand, some claim that the adaptive landscape is either “uninterpretable” or incoherent. On the other hand, some argue that the adaptive landscape has been an important heuristic, or tool in the service of explaining, as well as proposing and testing hypotheses about evolutionary change. This paper attempts to reconcile these two views.

From spatial form to system and process through pattern making in the landscape: can landscape design contribute to nature restoration?

This study presents a scenario in which recent development of landscape design based on modernism and modernists works is depicted in conjunction with its possible contribution toward nature restoration. Spatial pattern found in modernists works enhanced the designers understanding of landscape pattern underlying the land and environment at an extensive scale. In search of solid ground for pattern making, landscape designers further investigated the environmental system and its structure. A morphological approach employed in the discourse of landscape ecology gives a theoretical foundation to those endeavors. Also, the process through which the environmental system functions and is maintained becomes another potential field of design expression in landscape. Detailed studies of several works and p landscape design projects, which have already indicated a direction of development, will promote a productive and creative co-relationship between landscape design and nature restoration.This revised version was published online in April 2005 with corrections to keywords.     

Can landscape ecology untangle the complexity of antibiotic resistance?

Bacterial resistance to antibiotics continues to pose a serious threat to human and animal health. Given the considerable spatial and temporal heterogeneity in the distribution of resistance and the factors that affect its evolution, dissemination and persistence, we argue that antibiotic resistance must be viewed as an ecological problem. A fundamental difficulty in assessing the causal relationship between antibiotic use and resistance is the confounding influence of geography: the co-localization of resistant bacterial species with antibiotic use does not necessarily imply causation and could represent the presence of environmental conditions and factors that have independently contributed to the occurrence of resistance. Here, we show how landscape ecology, which links the biotic and abiotic factors of an ecosystem, might help to untangle the complexity of antibiotic resistance and improve the interpretation of ecological studies.     

The effect of landscape heterogeneity on host–parasite dynamics

Environmental heterogeneity has been shown to have a profound effect on population dynamics and biological invasions, yet the effect of its spatial structure on the dynamics of disease invasion in a spatial host–parasite system has received little attention. Here we explore the effect of environment heterogeneity using the pair approximation and the stochastic spatially explicit simulation in which the lost patches are clustered in a fragmented landscape. The intensity of fragmentation is defined by the amount and spatial autocorrelation of the lost habitat. More fragmented landscape (high amount of habitat loss, low clustering of lost patches) was shown to be detrimental to the parasitic disease invasion and transmission, which implies that the potential of using artificial disturbances as a disease-control agency in biological conservation and management. Two components of the spatial heterogeneity (the amount and spatial autocorrelation of the lost habitat) formed a trade-off in determining the host–parasite dynamics. An extremely high degree of habitat loss was, counter-intuitively, harmful to the host. These results enrich our understanding of eco-epidemiological, host–parasite systems, and suggest the possibility of using the spatial arrangement of habitat patches as a conservation tool for guarding focal species against parasitic infection and transmission.     

How to localize epigenetics in the landscape of biological research?

Today, epigenetics is a very fashionable field of research. Modification of DNA by methylation, and of chromatin by histone modification or substitution represents a major fraction of the studies; but this special issue shows that epigenetic studies are very diverse, and not limited to the study of chromatin. What is common behind these different uses of the word epigenetics? A brief historical survey shows that epigenetics was invented twice, with different meanings: in the 1940s, by Conrad Waddington, as the study of the relations between the genotype and the phenotype; in the 1960s, as the global mechanisms of gene regulation involved in differentiation and development; what is common is that an approach distinct from genetics was in both cases considered as necessary because genetic models were incapable to address these problems. A good way to appreciate the relations between genetics and epigenetics is to realize that the main aim of organisms is to reproduce, and to consider the way organisms perform this task. Genetics is the precise means organisms have invented to reproduce the structure of their macromolecular components; the genome is also used to control the level and place of this reproduction. All the other means organisms have used to reproduce were more or less the result of tinkering, and constitute the field of epigenetics, with its diversity and richness.     

Plant–microbe interactions at multiple scales across a high-elevation landscape

Here we review the numerous studies of plant–microbe interactions conducted at the Niwot Ridge LTER site in Colorado, USA. By synthesising work at scales ranging from the rhizosphere to the landscape, we offer a mechanistic view of how these interactions are essential to understanding the spatial and temporal structuring of plant and microbial communities across this diverse and changing landscape. These new insights are also important for making predictions about how both plant and microbial communities and populations will respond to future changes in this environment, especially with regard to the potential uphill movement of plants and microbes in response to climate change and nitrogen deposition. We predict that the uphill movement of plants and microbes will be especially apparent, and have the most impact, in areas of the alpine that are now mostly plant free. These areas are currently undergoing a shift from a microbe-dominated ecosystem to one where microbe–plant interactions will play a critical role in reducing nutrient losses to downstream ecosystems.     

What is the required minimum landscape size for dispersal studies?

Among small animals dispersal parameters are mainly obtained by traditional methods using population studies of marked individuals. Dispersal studies may underestimate the rate and distance of dispersal, and be biased because of aggregated habitat patches and a small study area. The probability of observing long distance dispersal events decreases with distance travelled by the organisms. In this study a new approach is presented to solve this methodological problem. An extensive mark-release-recapture programme was performed in an area of 81 km(2) in southern Sweden. To estimate the required size of the study area for adequate dispersal measures we examined the effect of study area size on dispersal distance using empirical data and a repeated subsampling procedure. In 2003 and 2004, two species of diurnal burnet moths (Zygaenidae) were studied to explore dispersal patterns. The longest confirmed dispersal distance was 5600 m and in total 100 dispersal events were found between habitat patches for the two species. The estimated dispersal distance was strongly affected by the size of the study area and the number of marked individuals. For areas less than 10 km(2) most of the dispersal events were undetected. Realistic estimates of dispersal distance require a study area of at least 50 km(2). To obtain adequate measures of dispersal, the marked population should be large, preferably over 500 recaptured individuals. This result was evident for the mean moved distance, mean dispersal distance and maximum dispersal distance. In general, traditional dispersal studies are performed in small study areas and based on few individuals and should therefore be interpreted with care. Adequate dispersal measures for insects obtained by radio-tracking and genetic estimates (gene flow) is still a challenge for the future.     

Do landscape processes predict phylogeographic patterns in the wood frog?

Understanding factors that influence population connectivity and the spatial distribution of genetic variation is a major goal in molecular ecology. Improvements in the availability of high-resolution geographic data have made it increasingly possible to quantify the effects of landscape features on dispersal and genetic structure. However, most studies examining such landscape effects have been conducted at very fine (e.g. landscape genetics) or broad (e.g. phylogeography) spatial scales. Thus, the extent to which processes operating at fine spatial scales are linked to patterns at larger scales remains unclear. Here, we test whether factors impacting wood frog dispersal at fine spatial scales are correlated with genetic structure at regional scales. Using recently developed methods borrowed from electrical circuit theory, we generated landscape resistance matrices among wood frog populations in eastern North America based on slope, a wetness index, land cover and absolute barriers to wood frog dispersal. We then determined whether these matrices are correlated with genetic structure based on six microsatellite markers and whether such correlations outperform a landscape-free model of isolation by resistance. We observed significant genetic structure at regional spatial scales. However, topography and landscape variables associated with the intervening habitat between sites provide little explanation for patterns of genetic structure. Instead, absolute dispersal barriers appear to be the best predictor of regional genetic structure in this species. Our results suggest that landscape variables that influence dispersal, microhabitat selection and population structure at fine spatial scales do not necessarily explain patterns of genetic structure at broader scales.     

Redox and Lewis acid–base activities through an electronegativity-hardness landscape diagram

Chemistry is the science of bond making and bond breaking which requires redistribution of electron density among the reactant partners. Accordingly acid–base and redox reactions form cardinal components in all branches of chemistry, e.g., inorganic, organic, physical or biochemistry. That is the reason it forms an integral part of the undergraduate curriculum all throughout the globe. In an electronegativity (χ)- hardness (η) landscape diagram the diagonal χ?=?η line separates reducing agents from oxidizing agents as well as Lewis acids from Lewis bases. While electronegativity is related to the degree of electron transfer between two reactants, hardness is related to the resistance to that process. Accordingly the electronegativities of oxidizing agents/Lewis acids are generally greater than the corresponding hardness values and the reverse is true for reducing agents/Lewis bases. Electrophiles and nucleophiles are also expected to follow similar trends.     

Eradication of rabbits from landscape scale exclosures: pipedream or possibility?

Summary High densities of the European Rabbit (Oryctolagus cuniculus) were eradicated from 60 km² of the Arid Recovery Reserve between 1996 and 2001. Eradication was possible due to an initial knockdown caused by rabbit haemorrhagic disease, followed by effective exclusion fencing, broadscale poison baiting, targeted shooting, warren destruction and trapping on rabbit burrows and buckheaps. The efficacy of different broadscale control and intensive rabbit eradication techniques was subsequently estimated in a 26 km² expansion to the Reserve from 2002 to 2006. Non‐target implications of these control techniques were also assessed where possible. An estimated 8000 rabbits were removed in total from both areas and results suggest that rabbit eradication is possible at a landscape scale. Strategies for eliminating rabbits from confined areas are suggested.     

Do wooded streets provide connectivity for bats in an urban landscape?

The effects of urbanization on bats are poorly understood, but published data suggests it might be detrimental to them. Even though urban parks provide refuge to native biota, the nature of the urban landscape exacerbates the insularization process. In order to evaluate if wooded streets in an urban landscape provide connectivity for bats, we compared bat community structure in three different types of habitats: urban parks, wooded streets and non-wooded streets. Sampling occurred monthly from August 2006 to July 2007 in the city of Vitória, southeastern Brazil. Richness, relative abundance and diversity were higher in urban parks and lower in non-wooded streets. Jaccard’s similarity index showed that the wooded streets are more similar to non-wooded streets than to urban parks. Urbanization may benefit generalist species by providing new resources, but for specialist species critical resources may be lost and persistence endangered. There is evidence that wooded streets may provide some degree of connectivity for birds in urban landscapes, but our results suggest that this is not the case, with wooded streets being used by few individuals of a few species. Vegetation cover is important to maintain bat diversity in urban centers. Activities like landscape planning and gardening should include biodiversity data in their outputs in order to better design a landscape that improves the likelihood of persistence of bats.     

Modeling landscape condition for biodiversity assessment—Application in temperate North America

Conservation decisions are well supported by predictive spatial models that indicate the relative ecological condition of a given place. The intent of this 90 m pixel landscape condition model is to use nationally available spatial data from the USA, Mexico, and Canada to express assumptions regarding the relative ecological effects of land uses on terrestrial natural communities and species. This approach emphasizes and updateable and transparent design which takes advantage of empirical biodiversity data from the USA to both calibrate and validate the model. Map layers depicting infrastructure, land use, and modified vegetation were each scored for site impact and distance decay, and then combined into one map surface. Field observations from Natural Heritage Programs, each scored for relative ecological condition (in categories A = excellent to D = poor), were used to calibrate distance decay parameters. Some 90,000 observations for at-risk species, invasive plant species, and natural communities were used for model validation. Statistically significant distinctions in ecological condition among validation samples were predicted by the resultant spatial model. Variation in landscape condition was then summarized by regional U.S. Landscape Conservation Cooperatives (LCCs) in terms of areas approximating A–D condition. Montane and desert LCCs scored on average much higher in area approximating “A” and “B” landscape condition, while LCCs with more substantial agricultural and urban footprints scored overwhelmingly within the “D” range of condition. Similar analyses illustrated range-wide scoring of landscape condition for major vegetation types across temperate North America.     

Enhanced sampling simulations to construct free-energy landscape of protein–partner substrate interaction

Molecular dynamics (MD) simulations using all-atom and explicit solvent models provide valuable information on the detailed behavior of protein–partner substrate binding at the atomic level. As the power of computational resources increase, MD simulations are being used more widely and easily. However, it is still difficult to investigate the thermodynamic properties of protein–partner substrate binding and protein folding with conventional MD simulations. Enhanced sampling methods have been developed to sample conformations that reflect equilibrium conditions in a more efficient manner than conventional MD simulations, thereby allowing the construction of accurate free-energy landscapes. In this review, we discuss these enhanced sampling methods using a series of case-by-case examples. In particular, we review enhanced sampling methods conforming to trivial trajectory parallelization, virtual-system coupled multicanonical MD, and adaptive lambda square dynamics. These methods have been recently developed based on the existing method of multicanonical MD simulation. Their applications are reviewed with an emphasis on describing their practical implementation. In our concluding remarks we explore extensions of the enhanced sampling methods that may allow for even more efficient sampling.     

Mammalian predator–prey interaction in a fragmented landscape: weasels and voles

The relationship between predators and prey is thought to change due to habitat loss and fragmentation, but patterns regarding the direction of the effect are lacking. The common prediction is that specialized predators, often more dependent on a certain habitat type, should be more vulnerable to habitat loss compared to generalist predators, but actual fragmentation effects are unknown. If a predator is small and vulnerable to predation by other larger predators through intra-guild predation, habitat fragmentation will similarly affect both the prey and the small predator. In this case, the predator is predicted to behave similarly to the prey and avoid open and risky areas. We studied a specialist predator’s, the least weasel, Mustela nivalis nivalis, spacing behavior and hunting efficiency on bank voles, Myodes glareolus, in an experimentally fragmented habitat. The habitat consisted of either one large habitat patch (non-fragmented) or four small habitat patches (fragmented) with the same total area. The study was replicated in summer and autumn during a year with high avian predation risk for both voles and weasels. As predicted, weasels under radio-surveillance killed more voles in the non-fragmented habitat which also provided cover from avian predators during their prey search. However, this was only during autumn, when the killing rate was also generally high due to cold weather. The movement areas were the same for both sexes and both fragmentation treatments, but weasels of both sexes were more prone to take risks in crossing the open matrix in the fragmented treatment. Our results support the hypothesis that habitat fragmentation may increase the persistence of specialist predator and prey populations if predators are limited in the same habitat as their prey and they share the same risk from avian predation.     

Effects of perturbation on the predator–prey system in a heterogeneous landscape

Environmental perturbations occur in ecosystems as the result of disturbance, which is closely related to ecosystem stability and resilience. To understand how perturbations can affect ecosystems, we constructed a spatially explicit lattice model to simulate the integrative predator–prey–grass relationships. In this model, a predator (or prey) gives birth to offspring, according to a specific birth probability, when it is able to feed on prey (or grass). When a predator or prey animal was initially introduced or newly born, its health state was set at a given high value. This state decreased by 1 with each time step. When the state of an animal decreased to zero, the animal was considered dead and was removed from the system. In this model, the perturbation was defined as the sudden death of some portion of the population. The heterogeneous landscape was characterized by a parameter, H, which controlled the degree of heterogeneity. When H ≥ 0.6, the predator population size was positively influenced by the perturbation. However, the perturbation had little effect upon the population sizes of prey or grass, regardless of the value of H.