Continuous Landscape Research Articles

Continuous fitness landscape analysis using a chaos-based random walk algorithm

Extensive research on heuristic algorithms has proved their potential in solving complex optimization problems. However, it is not easy to choose the best heuristic technique for solving a particular problem. Fitness landscape analysis is used for understanding the problem characteristics based on which the best-suited algorithm for the problem can be chosen. Compared to the literature on discrete search spaces, only a few significant works have been undertaken on landscape analysis in continuous search spaces. Random walk (RW) algorithm has been used for generating sample points in the search space, and fitness landscape is created based on the relative fitness of the neighboring sample points. This paper proposes a chaos-based random walk algorithm, called as the chaotic random walk (CRW), applied in continuous search space to generate the landscape structure for a problem. The chaotic map is used to generate the chaotic pseudorandom numbers for determining variable scaled step size and direction of the proposed RW algorithm. Histogram analysis demonstrates better coverage of search space by the CRW algorithm compared to the simple and progressive random walk algorithms. In addition, we test the efficiency of the proposed method by quantifying the ruggedness and deception of a problem using entropy and fitness distance correlation measures. Experiments are conducted on the IEEE Congers on Evolutionary Computing 2013 benchmark functions in continuous search space having different levels of complexity. Extensive experiments indicate the capability for generating landscape structure on the continuous search space and efficiency of the proposed method to investigate the structural features of fitness landscapes.

Barrier Displacement on a Neutral Landscape: Toward a Theory of Continental Biogeography.

Macroevolutionary theory posits three processes leading to lineage diversification and the formation of regional biotas: dispersal (species geographic range expansion), speciation (species lineage splitting), and extinction (species lineage termination). The Theory of Island Biogeography (TIB) predicts species richness values using just two of these processes; dispersal and extinction. Yet most species on Earth live on continents or continental shelves, and the dynamics of evolutionary diversification at regional and continental scales are qualitatively different from those that govern the formation of species richness on biogeographic islands. Certain geomorphological processes operating perennially on continental platforms displace barriers to gene flow and organismal dispersal, and affect all three terms of macroevolutionary diversification. For example, uplift of a dissected landscape and river capture both merge and separate portions of adjacent areas, allowing dispersal and larger geographic ranges, vicariant speciation and smaller geographic ranges, and extinction when range sizes are subdivided below a minimum persistence threshold. The TIB also does not predict many biogeographic and phylogenetic patterns widely observed in continentally distributed taxa, including: (i) power function-like species-area relationships; (ii) log-normal distribution of species geographic range sizes, in which most species have restricted ranges (are endemic) and few species have broad ranges (are cosmopolitan); (iii) mid-domain effects with more species toward the geographic center, and more early-branching, species-poor clades toward the geographic periphery; (iv) exponential rates of net diversification with log-linear accumulation of lineages through geological time; and (v) power function-like relationships between species-richness and clade diversity, in which most clades are species-poor and few clades are species-rich. Current theory does not provide a robust mechanistic framework to connect these seemingly disparate patterns. Here we present SEAMLESS (Spatially Explicit Area Model of Landscape Evolution by SimulationS) that generates clade diversification by moving geographic barriers on a continuous, neutral landscape. SEAMLESS is a neutral Landscape Evolution Model (LEM) that treats species and barriers as functionally equivalent with respect to model parameters. SEAMLESS differs from other model-based biogeographic methods (e.g., Lagrange, GeoSSE, BayArea, and BioGeoBEARS) by modeling properties of dispersal barriers rather than areas, and by modeling the evolution of species lineages on a continuous landscape, rather than the evolution of geographic ranges along branches of a phylogeny. SEAMLESS shows how dispersal is required to maintain species richness and avoid clade-wide extinction, demonstrates that ancestral range size does not predict species richness, and provides a unified explanation for the suite of commonly observed biogeographic and phylogenetic patterns listed above. SEAMLESS explains how a simple barrier-displacement mechanism affects lineage diversification under neutral conditions, and is advanced here toward the formulation of a general theory of continental biogeography. [Diversification, extinction, geodispersal, macroevolution, river capture, vicariance.].

Human haematopoietic stem cell differentiation follows a continuous waddington-like landscape

Human haematopoietic stem cell differentiation follows a continuous waddington-like landscape

Habitat specialization predicts genetic response to fragmentation in tropical birds.

Habitat fragmentation is one of the most severe threats to biodiversity as it may lead to changes in population genetic structure, with ultimate modifications of species evolutionary potential and local extinctions. Nonetheless, fragmentation does not equally affect all species and identifying which ecological traits are related to species sensitivity to habitat fragmentation could help prioritization of conservation efforts. Despite the theoretical link between species ecology and extinction proneness, comparative studies explicitly testing the hypothesis that particular ecological traits underlies species-specific population structure are rare. Here, we used a comparative approach on eight bird species, co-occurring across the same fragmented landscape. For each species, we quantified relative levels of forest specialization and genetic differentiation among populations. To test the link between forest specialization and susceptibility to forest fragmentation, we assessed species responses to fragmentation by comparing levels of genetic differentiation between continuous and fragmented forest landscapes. Our results revealed a significant and substantial population structure at a very small spatial scale for mobile organisms such as birds. More importantly, we found that specialist species are more affected by forest fragmentation than generalist ones. Finally, our results suggest that even a simple habitat specialization index can be a satisfying predictor of genetic and demographic consequences of habitat fragmentation, providing a reliable practical and quantitative tool for conservation biology.

Pulsed exhumation of interior eastern Tibet: Implications for relief generation mechanisms and the origin of high-elevation planation surfaces

River incision into a widespread, upland low-relief landscape, and related patterns of exhumation recorded by low-temperature thermochronology, together underpin geodynamic interpretations for crustal thickening and uplift of the eastern Tibetan Plateau. We report results from a suite of 11 (U–Th–Sm)/He cooling-age samples. Eight samples comprise a 1.2 km relief section collected from elevations up to 4800 m in the Jiulong Shan, an elevated, rugged region located in the hinterland of the Yalong-Longmen Shan Thrust Belt, and surrounded on three sides by upland low-relief landscape surfaces. Zircon and apatite cooling ages record two episodes of rapid exhumation in the early Oligocene and late Miocene, that were separated by a period of stability from ∼30 to 15 Ma. The first episode is consistent with a similar pulse evident from the Longmen Shan. The second episode is ongoing, and when integrated with adjacent cooling-age data sets, shows that doming of the Jiulong Shan has resulted in 2 to 4 km of differential exhumation of the plateau interior. We show from a compilation of glacial landform-mapping that the elevation of the plateau surface closely tracks global last glacial maximum equilibrium line altitude. We hypothesize that smoothing of highlands by efficient glacial and periglacial erosion, coupled with potential river captures and conveyance of sediments via external drainage, can yield an apparently continuous low-relief plateau landscape formed diachronously at high elevation.

Appraisal of social-ecological innovation as an adaptive response by stakeholders to local conditions: Mapping stakeholder involvement in horticulture orientated green space management

Urban areas are hubs of creativity and innovation providing fertile ground for novel responses to modern environmental challenges. Previous studies have attempted to conceptualise the ecological, social and political potential of social-ecological innovation in urban green space management. However, little work has been conducted on the social-ecological conditions influencing their occurrence and distribution. Further research is therefore necessary to demonstrate whether stakeholder stewardship of green resources contributes towards adaptive capacity in social-ecological systems. The research reported here explored the extent of organised social-ecological innovations in a continuous urban landscape comprising three adjoining metropolitan areas: Manchester, Salford and Trafford (UK). Examples of horticulture orientated organised social-ecological innovation were identified using a snowball-sampling method. Their distribution, explored with GIS and remote sensing technology, was found to be significantly associated with levels of both, social and ecological, deprivation. The study presented social-ecological innovation as an adaptive response to environmental stressors, conditioned by specific social and ecological parameters in the landscape. It therefore provides empirical support for social-ecological innovation as a valid ingredient contributing to resilience in adaptive social-ecological systems. Not only do such collective community-led elements of natural resource management warrant acknowledgement in urban green space planning, but their distribution and productivity may provide a valuable social-ecological laboratory for the study of polycentric governance and adaptive capacity in the urban environment.

Effects of diffusion on total biomass in heterogeneous continuous and discrete-patch systems

Theoretical models of populations on a system of two connected patches previously have shown that when the two patches differ in maximum growth rate and carrying capacity, and in the limit of high diffusion, conditions exist for which the total population size at equilibrium exceeds that of the ideal free distribution, which predicts that the total population would equal the total carrying capacity of the two patches. However, this result has only been shown for the Pearl-Verhulst growth function on two patches and for a single-parameter growth function in continuous space. Here, we provide a general criterion for total population size to exceed total carrying capacity for three commonly used population growth rates for both heterogeneous continuous and multi-patch heterogeneous landscapes with high population diffusion. We show that a sufficient condition for this situation is that there is a convex positive relationship between the maximum growth rate and the parameter that, by itself or together with the maximum growth rate, determines the carrying capacity, as both vary across a spatial region. This relationship occurs in some biological populations, though not in others, so the result has ecological implications.

Seagrass fragmentation impacts recruitment dynamics of estuarine-dependent fish

Seagrass beds are a key component of the estuarine landscape supporting high productivity, abundant marine life, and serve as nursery areas for many estuarine-dependent species. With increasing anthropogenic activity, there is concern about overall habitat loss via fragmentation and what effects this may have on local biotas relying on seagrasses for persistence. To examine these effects, fragmented seagrass beds (Halodule wrightii, Ascherson 1868) in two different bay systems, Corpus Christi and Aransas Bay, Texas, were delineated, quantified, and mapped, and red drum (Sciaenops ocellatus, Linnaeus 1766) was used as a model species to test for impacts of fragmentation on this common estuarine-dependent species. Red drum density, growth, and movement were measured in response to varying levels of fragmentation (i.e., High, Medium, and Low). No difference in initial recruitment of red drum density was observed among fragmentation levels for newly settled arrivals. However, there was a significant size effect; larger fish were found in non-fragmented areas. Growth rates were also compared among fragmented habitats using both RNA:DNA ratios and otolith microstructure, and no significant effect of growth among fragmentation levels was found. Migration potential was measured at the landscape-level within and among fragmented seagrass meadows by tagging and releasing 200 juvenile red drum into three separate replicated fragmented networks. Within 24h, only one fish was recaptured within the original fragmented network. The vast majority of recaptured fish were found in the nearest continuous non-fragmented seagrass bed over 50m from their release point. These results suggest a temporal transition of small newly recruited red drum, where individuals settle ubiquitously among varying levels of fragmentation but over time migrate toward more continuous beds. This study provides evidence that there may be a fragmentation “threshold” for red drum, whereby once a habitat becomes too fragmented; individuals either suffer higher mortality or more likely move to more continuous landscapes. Overall, this study suggests that habitat fragmentation and loss of more continuous seagrass meadows may have negative impacts on estuarine-dependent species using these areas as their primary recruitment habitat.

VALUE OF AN URBAN FRAGMENT FOR THE CONSERVATION OF CERRADO IN THE FEDERAL DISTRICT OF BRAZIL

The Brazilian Federal District (FD) has 25% of the total woody flora of the Cerrado biodiversity hotspot, but has lost most of its vegetation cover and 30% of its plant species are considered extinct. Here we evaluate the conservation potential of an Cerrado in FD that is strategically located between key protected areas. The study was conducted in two sites within the Gama e Cabeca de Veado Environmental Protection Area: the urban fragment and a control site. We found a high floristic and structural similarity between the sites, suggesting that in the past they formed a continuous landscape. The was floristically diverse, with indices that are considered high and typical for Cerrado. The studied fragment, therefore, can help reduce the ongoing deterioration of FD's biodiversity, due to its vegetation representativeness and strategic location, potentially acting as a stepping stone between key protected areas. The study gives support to ongoing efforts to transform the studied area into a protected area.

Predictable allele frequency changes due to habitat fragmentation in the Glanville fritillary butterfly

Describing the evolutionary dynamics of now extinct populations is challenging, as their genetic composition before extinction is generally unknown. The Glanville fritillary butterfly has a large extant metapopulation in the Åland Islands in Finland, but declined to extinction in the nearby fragmented southwestern (SW) Finnish archipelago in the 20th century. We genotyped museum samples for 222 SNPs across the genome, including SNPs from candidate genes and neutral regions. SW Finnish populations had significantly reduced genetic diversity before extinction, and their allele frequencies gradually diverged from those in contemporary Åland populations over 80 y. We identified 15 outlier loci among candidate SNPs, mostly related to flight, in which allele frequencies have changed more than the neutral expectation. At outlier loci, allele frequencies in SW Finland shifted in the same direction as newly established populations deviated from old local populations in contemporary Åland. Moreover, outlier allele frequencies in SW Finland resemble those in fragmented landscapes as opposed to continuous landscapes in the Baltic region. These results indicate selection for genotypes associated with good colonization capacity in the highly fragmented landscape before the extinction of the populations. Evolutionary response to habitat fragmentation may have enhanced the viability of the populations, but it did not save the species from regional extinction in the face of severe habitat loss and fragmentation. These results highlight a potentially common situation in changing environments: evolutionary changes are not strong enough to fully compensate for the direct adverse effects of environmental change and thereby rescue populations from extinction.

Bacterial predator-prey dynamics in microscale patchy landscapes.

Soil is a microenvironment with a fragmented (patchy) spatial structure in which many bacterial species interact. Here, we explore the interaction between the predatory bacterium Bdellovibrio bacteriovorus and its prey Escherichia coli in microfabricated landscapes. We ask how fragmentation influences the prey dynamics at the microscale and compare two landscape geometries: a patchy landscape and a continuous landscape. By following the dynamics of prey populations with high spatial and temporal resolution for many generations, we found that the variation in predation rates was twice as large in the patchy landscape and the dynamics was correlated over shorter length scales. We also found that while the prey population in the continuous landscape was almost entirely driven to extinction, a significant part of the prey population in the fragmented landscape persisted over time. We observed significant surface-associated growth, especially in the fragmented landscape and we surmise that this sub-population is more resistant to predation. Our results thus show that microscale fragmentation can significantly influence bacterial interactions.

Effects of Increased Flight on the Energetics and Life History of the Butterfly Speyeria mormonia.

Movement uses resources that may otherwise be allocated to somatic maintenance or reproduction. How does increased energy expenditure affect resource allocation? Using the butterfly Speyeria mormonia, we tested whether experimentally increased flight affects fecundity, lifespan or flight capacity. We measured body mass (storage), resting metabolic rate and lifespan (repair and maintenance), flight metabolic rate (flight capacity), egg number and composition (reproduction), and food intake across the adult lifespan. The flight treatment did not affect body mass or lifespan. Food intake increased sufficiently to offset the increased energy expenditure. Total egg number did not change, but flown females had higher early-life fecundity and higher egg dry mass than control females. Egg dry mass decreased with age in both treatments. Egg protein, triglyceride or glycogen content did not change with flight or age, but some components tracked egg dry mass. Flight elevated resting metabolic rate, indicating increased maintenance costs. Flight metabolism decreased with age, with a steeper slope for flown females. This may reflect accelerated metabolic senescence from detrimental effects of flight. These effects of a drawdown of nutrients via flight contrast with studies restricting adult nutrient input. There, fecundity was reduced, but flight capacity and lifespan were unchanged. The current study showed that when food resources were abundant, wing-monomorphic butterflies living in a continuous meadow landscape resisted flight-induced stress, exhibiting no evidence of a flight-fecundity or flight-longevity trade-off. Instead, flight changed the dynamics of energy use and reproduction as butterflies adopted a faster lifestyle in early life. High investment in early reproduction may have positive fitness effects in the wild, as long as food is available. Our results help to predict the effect of stressful conditions on the life history of insects living in a changing world.

Predictive geochemical mapping using environmental correlation

The distribution of chemical elements at and near the Earth's surface, the so-called critical zone, is complex and reflects the geochemistry and mineralogy of the original substrate modified by environmental factors that include physical, chemical and biological processes over time.Geochemical data typically is illustrated in the form of plan view maps or vertical cross-sections, where the composition of regolith, soil, bedrock or any other material is represented. These are primarily point observations that frequently are interpolated to produce rasters of element distributions. Here we propose the application of environmental or covariate regression modelling to predict and better understand the controls on major and trace element geochemistry within the regolith. Available environmental covariate datasets (raster or vector) representing factors influencing regolith or soil composition are intersected with the geochemical point data in a spatial statistical correlation model to develop a system of multiple linear correlations. The spatial resolution of the environmental covariates, which typically is much finer (e.g. ∼90 m pixel) than that of geochemical surveys (e.g. 1 sample per 10-10,000 km2), carries over to the predictions. Therefore the derived predictive models of element concentrations take the form of continuous geochemical landscape representations that are potentially much more informative than geostatistical interpolations.Environmental correlation is applied to the Sir Samuel 1:250,000 scale map sheet in Western Australia to produce distribution models of individual elements describing the geochemical composition of the regolith and exposed bedrock. As an example we model the distribution of two elements – chromium and sodium. We show that the environmental correlation approach generates high resolution predictive maps that are statistically more accurate and effective than ordinary kriging and inverse distance weighting interpolation methods. Furthermore, insights can be gained into the landscape processes controlling element concentration, distribution and mobility from analysis of the covariates used in the model. This modelling approach can be extended to groups of elements (indices), element ratios, isotopes or mineralogy over a range of scales and in a variety of environments.

Landscape sequences along the urban–rural–natural gradient: A novel geospatial approach for identification and analysis

Human influence on the environment differs in terms of distribution and intensity, thus producing a gradient of landscape modifications that translates into different landscape structures. Within this variety of landscapes, fringe areas represent complex spaces where dynamic processes and instable conditions can be observed. In this research Kernel Density Estimation, multivariate spatial analysis, landscape pattern analysis, and Principal Component Analysis (PCA) were combined to model and characterise landscape gradients, and to analyse the structural features of fringe areas. This methodology was applied to a rural area of central Italy, using density indicators associated with urbanisation, agriculture, and natural elements considered to be key components for the identification of landscape gradients. The results highlight not only specific “pillar” landscapes, which are dominated by said components, but also transitional landscapes, where the most relevant forms of interaction between land uses were identified. Characterisation of landscape structures along the gradient illustrated different trends in patch density, shape complexity and landscape diversity, demonstrating greater variability in fringe areas than in pillar landscapes. PCA revealed a partial overlap between the main structural characteristics of the agro-forestry matrix and the medium intensity agricultural landscapes, whereas urban fringes and semi-natural fringes were clearly separated. The discovery of the continuous landscape gradients and an understanding of the gamut of landscape types nested along them is crucial in allowing for more effective land-use planning in which also fringe areas become a relevant part of the process.

The elastic free energy of a tandem modular protein under force

Recent studies have provided a theoretical framework for including entropic elasticity in the free energy landscape of proteins under mechanical force. Accounting for entropic elasticity using polymer physics models has helped explain the hopping behavior seen in single molecule experiments in the low force regime. Here, we expand on the construction of the free energy of a single protein domain under force proposed by Berkovich et al. to provide a free energy landscape for N tandem domains along a continuous polypeptide. Calculation of the free energy of individual domains followed by their concatenation provides a continuous free energy landscape whose curvature is dominated by the worm-like chain at forces below 20 pN. We have validated our free energy model using Brownian dynamics and reproduce key features of protein folding. This free energy model can predict the effects of changes in the elastic properties of a multidomain protein as a consequence of biological modifications such as phosphorylation or the formation of disulfide bonds. This work lays the foundations for the modeling of tissue elasticity, which is largely determined by the properties of tandem polyproteins.

Testing the relevance of binary, mosaic and continuous landscape conceptualisations to reptiles in regenerating dryland landscapes

Fauna distributions are assessed using discrete (binary and mosaic) or continuous conceptualisations of the landscape. The value of the information derived from these analyses depends on the relevance of the landscape representation (or model) used to the landscape and fauna of interest. Discrete representations dominate analyses of landscape context in disturbed and regenerating landscapes; however within-patch variation suggests that continuous representations may help explain the distribution of fauna in such landscapes. We tested the relevance of binary, mosaic, and continuous conceptualisations of landscape context to reptiles in regenerating dryland landscapes. For each of thirteen reptile groups, we compared the fit of models consisting of one landscape composition and one landscape heterogeneity variable for each of six landscape representations (2× binary, 2× mosaic, and 2× continuous), at three buffer distances. We used Akaike weights to assess the relative support for each model. Maps were created from Landsat satellite images. Reptiles varied in their response to landscape context; however, the binary landscape representation with classes ‘intact/disturbed’ was best supported overall. Species richness was best described by a binary landscape representation with classes ‘wooded/clear’, whereas reptile abundance was best described by a mosaic landscape representation with classes defined by vegetation type. Five out of ten reptile species responded strongly to a single landscape representation, with the most relevant representation and conceptualisation varying among species. Our findings support the use of multiple landscape conceptualisations and representations during analyses of landscape context for fauna in regenerating landscapes.

Exploratory Landscape Analysis of Continuous Space Optimization Problems Using Information Content

Data-driven analysis methods, such as the information content of a fitness sequence, characterize a discrete fitness landscape by quantifying its smoothness, ruggedness, or neutrality. However, enhancements to the information content method are required when dealing with continuous fitness landscapes. One typically employed adaptation is to sample the fitness landscape using random walks with variable step size. However, this adaptation has significant limitations: random walks may produce biased samples, and uncertainty is added because the distance between observations is not accounted for. In this paper, we introduce a robust information content-based method for continuous fitness landscapes, which addresses these limitations. Our method generates four measures related to the landscape features. Numerical simulations are used to evaluate the efficacy of the proposed method. We calculate the Pearson correlation coefficient between the new measures and other well-known exploratory landscape analysis measures. Significant differences on the measures between benchmark functions are subsequently identified. We then demonstrate the practical relevance of the new measures using them as class predictors on a machine learning model, which classifies the benchmark functions into five groups. Classification accuracy greater than 90% was obtained, with computational costs bounded between 1% and 10% of the maximum function evaluation budget. The results demonstrate that our method provides relevant information, at a low cost in terms of function evaluations.

Pinning time statistics for vortex lines in disordered environments.

We study the pinning dynamics of magnetic flux (vortex) lines in a disordered type-II superconductor. Using numerical simulations of a directed elastic line model, we extract the pinning time distributions of vortex line segments. We compare different model implementations for the disorder in the surrounding medium: discrete, localized pinning potential wells that are either attractive and repulsive or purely attractive, and whose strengths are drawn from a Gaussian distribution; as well as continuous Gaussian random potential landscapes. We find that both schemes yield power-law distributions in the pinned phase as predicted by extreme-event statistics, yet they differ significantly in their effective scaling exponents and their short-time behavior.

The Utility of Fisher's Geometric Model in Evolutionary Genetics.

The accumulation of data on the genomic bases of adaptation has triggered renewed interest in theoretical models of adaptation. Among these models, Fisher Geometric Model (FGM) has received a lot of attention over the last two decades. FGM is based on a continuous multidimensional phenotypic landscape, but it is for the emerging properties of individual mutation effects that it is mostly used. Despite an apparent simplicity and a limited number of parameters, FGM integrates a full model of mutation and epistatic interactions that allows the study of both beneficial and deleterious mutations, and subsequently the fate of evolving populations. In this review, I present the different properties of FGM and the qualitative and quantitative support they have received from experimental evolution data. I later discuss how to estimate the different parameters of the model and outline some future directions to connect FGM and the molecular determinants of adaptation.

Electronic tongue generating continuous recognition patterns for protein analysis.

In current protocol, a combinatorial approach has been developed to simplify the design and production of sensing materials for the construction of electronic tongues (eT) for protein analysis. By mixing a small number of simple and easily accessible molecules with different physicochemical properties, used as building blocks (BBs), in varying and controlled proportions and allowing the mixtures to self-assemble on the gold surface of a prism, an array of combinatorial surfaces featuring appropriate properties for protein sensing was created. In this way, a great number of cross-reactive receptors can be rapidly and efficiently obtained. By combining such an array of combinatorial cross-reactive receptors (CoCRRs) with an optical detection system such as surface plasmon resonance imaging (SPRi), the obtained eT can monitor the binding events in real-time and generate continuous recognition patterns including 2D continuous evolution profile (CEP) and 3D continuous evolution landscape (CEL) for samples in liquid. Such an eT system is efficient for discrimination of common purified proteins.