Integrating patterns across multiple genetic markers to infer spatial processes

Landscape geneticists can take considerable advantage of differences in the action of evolutionary forces (mutation, migration, selection, and drift) on different loci within the genome. Appropriate comparisons among loci allow researchers to isolate and study the effects of these processes. For example, the organelles are typically inherited maternally (but occasionally paternally), and so will experience migration only when females or seeds disperse (males or pollen in the paternally inherited organelles). Thus, the comparison with biparentally inherited loci allows inferences about the differential migration rates of male vs. female animals or of seeds vs. pollen in plants. Conversely, all biparentally inherited nuclear loci should experience the same levels of migration and drift. Thus, loci that show unusually large levels of variation across the landscape (as compared with the bulk of loci) may be reflecting the action of spatially varying natural selection (local adaptation). Such comparisons are conceptually straightforward, but are complicated by the high intrinsic variability of stochastic neutral processes. Careful statistical analysis is needed to avoid over-interpreting differences among loci. Inferences will be most robust when both genetic and non-genetic data can be integrated, and the collaboration of landscape ecologists with geneticists promises to be particularly fruitful.     

Surface metrics for landscape ecology: a comparison of landscape models across ecoregions and scales

Context

The patch-mosaic model is lauded for its conceptual simplicity and ease with which conventional landscape metrics can be computed from categorical maps, yet many argue it is inconsistent with ecological theory. Gradient surface models (GSMs) are an alternative for representing landscapes, but adoption of surface metrics for analyzing spatial patterns in GSMs is hindered by several factors including a lack of meaningful interpretations.

Objectives

We investigate the performance and applicability of surface metrics across a range of ecoregions and scales to strengthen theoretical foundations for their adoption in landscape ecology.

Methods

We examine metric clustering across scales and ecoregions, test correlations with patch-based metrics, and provide ecological interpretations for a variety of surface metrics with respect to forest cover to support the basis for selecting surface metrics for ecological analyses.

Results

We identify several factors complicating the interpretation of surface metrics from a landscape perspective. First, not all surface metrics are appropriate for landscape analyses. Second, true analogs between surface metrics and patch-based, landscape metrics are rare. Researchers should focus instead on how surface measures can uniquely measure spatial patterns. Lastly, scale dependencies exist for surface metrics, but relationships between metrics do not appear to change considerably with scale.

Conclusions

Incorporating gradient surfaces into landscape ecological analyses is challenging, and many surface metrics may not have patch analogs or be ecologically relevant. For this reason, surface metrics should be considered in terms of the set of pattern elements they represent that can then be linked to landscape characteristics.

     

Spatial and temporal analysis of landscape patterns

A variety of ecological questions now require the study of large regions and the understanding of spatial heterogeneity. Methods for spatial-temporal analyses are becoming increasingly important for ecological studies. A grid cell based spatial analysis program (SPAN) is described and results of landscape pattern analysis using SPAN are presentedd. Several ecological topics in which geographic information systems (GIS) can play an important role (landscape pattern analysis, neutral models of pattern and process, and extrapolation across spatial scales) are reviewed. To study the relationship between observed landscape patterns and ecological processes, a neutral model approach is recommended. For example, the expected pattern (i.e., neutral model) of the spread of disturbance across a landscape can be generated and then tested using actual landscape data that are stored in a GIS. Observed spatial or temporal patterns in ecological data may also be influenced by scale. Creating a spatial data base frequently requires integrating data at different scales. Spatial is shown to influence landscape pattern analyses, but extrapolation of data across spatial scales may be possible if the grain and extent of the data are specified. The continued development and testing of new methods for spatial-temporal analysis will contribute to a general understanding of landscape dynamics.     

The impact of shifting cultivation on a rainforest landscape in West Kalimantan: spatial and temporal dynamics

To assess the role of shifting cultivation in the loss of rainforests in Indonesia, we examined the spatial and temporal dynamics of traditional land-use north of Gunung Palung National Park in West Kalimantan. We analyzed the abundance, size, frequency, and stature (by tree size) of discrete management units (patches) as a function of land-use category and distance from the village. Data were gathered from point samples along six 1.5-km transects through the landscape surrounding the Dayak village of Kembera. Most land was managed for rice, with 5% in current production, 12% in wet-rice fallows (regenerating swamp forest), and 62% in dry-rice fallows (regenerating upland forest). The proportion of land in dry-rice increased with distance from the village; rubber gardens (17% of the total area), dominated close to the village. The size of rubber trees declined with distance, reflecting the recent establishment of rubber gardens far from the village. Fruit gardens accounted for only 4% of the area. From interviews in Kembera and three other villages, we estimated rates of primary forest clearing and documented changes in land-use. Most rice fields were cleared from secondary forest fallows. However, 17% of dry-rice fields and 9% of wet-rice fields were cleared from primary forest in 1990, resulting in the loss of approximately 12 ha of primary forest per village. Almost all dry-rice fields cleared from primary forest were immediately converted to rubber gardens, as were 39% of all dry-rice fields cleared from fallows. The rate of primary forest conversion increased dramatically from 1990 to 1995, due not to soil degradation or population growth but rather to changes in the socio-economic and political environment faced by shifting cultivators. Although the loss of primary forest is appreciable under shifting cultivation, the impact is less than that of the major alternative land-uses in the region: timber extraction and oil palm plantations.     

Influence of landscape structure and stand age on species density and biomass of a tropical dry forest across spatial scales

Three central related issues in ecology are to identify spatial variation of ecological processes, to understand the relative influence of environmental and spatial variables, and to investigate the response of environmental variables at different spatial scales. These issues are particularly important for tropical dry forests, which have been comparatively less studied and are more threatened than other terrestrial ecosystems. This study aims to characterize relationships between community structure and landscape configuration and habitat type (stand age) considering different spatial scales for a tropical dry forest in Yucatan. Species density and above ground biomass were calculated from 276 sampling sites, while land cover classes were obtained from multi-spectral classification of a Spot 5 satellite imagery. Species density and biomass were related to stand age, landscape metrics of patch types (area, edge, shape, similarity and contrast) and principal coordinate of neighbor matrices (PCNM) variables using regression analysis. PCNM analysis was performed to interpret results in terms of spatial scales as well as to decompose variation into spatial, stand age and landscape structure components. Stand age was the most important variable for biomass, whereas landscape structure and spatial dependence had a comparable or even stronger influence on species density than stand age. At the very broad scale (8,000–10,500 m), stand age contributed most to biomass and landscape structure to species density. At the broad scale (2,000–8,000 m), stand age was the most important variable predicting both species density and biomass. Our results shed light on which landscape configurations could enhance plant diversity and above ground biomass.     

Responses of Chilean forest birds to anthropogenic habitat fragmentation across spatial scales

Although it is recognized that anthropogenic forest fragmentation affects habitat use by organisms across multiple spatial scales, there is uncertainty about these effects. We used a hierarchical sampling design spanning three spatial scales of habitat variability (landscape > patch > within-patch) and generalized mixed-effect models to assess the scale-dependent responses of bird species to fragmentation in temperate forests of southern Chile. The abundances of nine of 20 bird species were affected by interactions across spatial scales. These interactions resulted in a limited effect of within-patch habitat structure on the abundance of birds in landscapes with low forest cover, suggesting that suitable local habitats, such as sites with dense understory cover or large trees, are underutilized or remain unused in highly fragmented landscapes. Habitat specialists and cavity-nesters, such as tree-trunk foragers and tapaculos, were most likely to exhibit interactions across spatial scales. Because providing additional sites with dense understory vegetation or large habitat trees does not compensate the negative effect of the loss of forest area on bird species, conservation strategies should ensure the retention of native forest patches in the mixed-use landscapes.     

Butterflies in Swedish grasslands benefit from forest and respond to landscape composition at different spatial scales

Context

Loss and fragmentation of semi-natural grasslands has critically affected many butterfly species in Europe. Habitat area and isolation can have strong effects on the local biodiversity but species may also be strongly affected by the surrounding matrix.

Objectives

We explored how different land cover types in the landscape explained the occurrence of butterfly species in semi-natural grasslands.

Methods

Using data from 476 semi-natural grasslands in Sweden, we analysed the effect of matrix composition on species richness and occurrence. Additionally, we analysed at which spatial scales butterflies responded to matrix types (forests, semi-natural grasslands, arable land and water).

Results

Forest cover showed the strongest positive effect on species richness, followed by semi-natural grasslands. Forest also had a positive effect on red-listed species at local scales. Responses to matrix composition were highly species-specific. The majority of the 30 most common species showed strong positive responses to the amount of forest cover within 200–500 m. There was a smaller group of species showing a positive response to arable land cover within 500–2000 m. Thirteen species showed positive responses to the amount of semi-natural grasslands, generally at larger scales (10–30 km).

Conclusions

Our study showed that surrounding forest is beneficial for many grassland butterfly species and that forests might mitigate the negative effects of habitat loss caused by agricultural intensification. Also, semi-natural grasslands were an important factor for species richness at larger spatial scales, indicating that a landscape consisting mainly of supporting habitats (i.e. forests) are insufficient to sustain a rich butterfly fauna.

     

Landscape patterns and diversity of meadow plants and flower-visitors in a mountain landscape

Context

Wild flowering plants and their wild insect visitors are of great importance for pollination. Montane meadows are biodiversity hotspots for flowering plants and pollinators, but they are contracting due to tree invasion.

Objectives

This study quantified flowering plants and their flower-visitor species in montane meadows in the western Cascade Range of Oregon. Species diversity in small, isolated meadows was expected to be lower and nested relative to large meadows. Alternatively, landform features may influence richness and spatial turnover.

Methods

Flowering plants and their visitors were sampled in summers of 2011–2017 in twelve montane meadows with varying soil moisture. All flowering plants and all flower-visitors were recorded during five to seven 15 min watches in ten 3?×?3 m plots in each meadow and year.

Results

A total of 178 flowering plant species, 688 flower-visitor species and 137,916 interactions were identified. Richness of flower-visitors was related to meadow patch size, but neither plant nor flower-visitor richness was related to isolation measured as meadow area within 1000 m. Species in small meadows were not nested subsets of those in large meadows. Species replacement accounted for more than 78% of dissimilarity between meadows and was positively related to differences in soil moisture.

Conclusions

Although larger meadows contained more species, landform features have influenced meadow configuration, persistence, and soil moisture, contributing to high plant and insect species diversity. Hence, conservation and restoration of a variety of meadow types may promote landscape diversity of wild plants and pollinators.

     

Occupancy pattern of a long-horned beetle in a variegated forest landscape: linkages between tree quality and forest cover across spatial scales

Context

Interactions between landscape-scale processes and fine-grained habitat heterogeneity are usually invoked to explain species occupancy in fragmented landscapes. In variegated landscapes, however, organisms face continuous variation in micro-habitat features, which makes necessary to consider ecologically meaningful estimates of habitat quality at different spatial scales.

Objectives

We evaluated the spatial scales at which forest cover and tree quality make the greatest contribution to the occupancy of the long-horned beetle Microplophorus magellanicus (Coleoptera: Cerambycidae) in a variegated forest landscape.

Methods

We used averaged data of tree quality (as derived from remote sensing estimates of the decay stage of single trees) and spatially independent pheromone-baited traps to model the occurrence probability as a function of multiple cross-scale combinations between forest cover and tree quality (with scales ranging between 50 and 400 m).

Results

Model support and performance increased monotonically with the increasing scale at which tree quality was measured. Forest cover was not significant, and did not exhibit scale-specific effects on the occurrence probability of M. magellanicus. The interactive effect between tree quality and forest cover was stronger than the independent (additive) effects of tree quality and particularly forest cover. Significant interactions included tree quality measured at spatial scales ≥200 m, but cross-scale interactions occurred only in four of the seven best-supported models.

Conclusions

M. magellanicus respond to the high-quality trees available in the landscape rather than to the amount of forest per se. Conservation of viable metapopulations of M. magellanicus should consider the quality of trees at spatial scales >200 m.

     

Quantifying patch distribution at multiple spatial scales: Applications to wildlife-habitat models

Multiscale analyses are widely employed for wildlife-habitat studies. In most cases, however, each scale is considered discrete and little emphasis is placed on incorporating or measuring the responses of wildlife to resources across multiple scales. We modeled the responses of three Arctic wildlife species to vegetative resources distributed at two spatial scales: patches and collections of patches aggregated across a regional area. We defined a patch as a single or homogeneous collection of pixels representing 1 of 10 unique vegetation types. We employed a spatial pattern technique, three-term local quadrat variance, to quantify the distribution of patches at a larger regional scale. We used the distance at which the variance for each of 10 vegetation types peaked to define a moving window for calculating the density of patches. When measures of vegetation patch and density were applied to resource selection functions, the most parsimonious models for wolves and grizzly bears included covariates recorded at both scales. Seasonal resource selection by caribou was best described using a model consisting of only regional scale covariates. Our results suggest that for some species and environments simple patch-scale models may not capture the full range of spatial variation in resources to which wildlife may respond. For mobile animals that range across heterogeneous areas we recommend selection models that integrate resources occurring at a number of spatial scales. Patch density is a simple technique for representing such higher-order spatial patterns.     

Quantifying patch distribution at multiple spatial scales: Applications to wildlife-habitat models

Multiscale analyses are widely employed for wildlife-habitat studies. In most cases, however, each scale is considered discrete and little emphasis is placed on incorporating or measuring the responses of wildlife to resources across multiple scales. We modeled the responses of three Arctic wildlife species to vegetative resources distributed at two spatial scales: patches and collections of patches aggregated across a regional area. We defined a patch as a single or homogeneous collection of pixels representing 1 of 10 unique vegetation types. We employed a spatial pattern technique, three-term local quadrat variance, to quantify the distribution of patches at a larger regional scale. We used the distance at which the variance for each of 10 vegetation types peaked to define a moving window for calculating the density of patches. When measures of vegetation patch and density were applied to resource selection functions, the most parsimonious models for wolves and grizzly bears included covariates recorded at both scales. Seasonal resource selection by caribou was best described using a model consisting of only regional scale covariates. Our results suggest that for some species and environments simple patch-scale models may not capture the full range of spatial variation in resources to which wildlife may respond. For mobile animals that range across heterogeneous areas we recommend selection models that integrate resources occurring at a number of spatial scales. Patch density is a simple technique for representing such higher-order spatial patterns.     

An integrative approach for analysing landscape dynamics in diverse cultivated and natural mountain areas

Our landscape can be regarded as a development process that is affected and subsequently shaped by a series of different environmental and human-induced factors. However, to date, concrete data about the impact of each of these factors are still missing. One key reason for this is that methods of acquisition and evaluation of these factors inherently have differences, thereby preventing meaningful comparative analyses. This study presents an integrative methodical approach that bridges many of these gaps. Our approach also has the advantages of being generally applicable while delivering easily interpretable results that also allow comparisons between diverse geographical regions. The indicators used enable all major features of landscape change, e.g. changes in land use, landscape structuring, habitat settings, and urban sprawl, to be accurately monitored and provide high-quality realistic results that were validated in our study site, South Tyrol (North Italy). Indicators were selected for both their further subdivision, e.g. monocrops and different features of mixed crops, and their easy to ascertain hierarchically structured feature classification, e.g. land cover. Furthermore, our use of ecoregions enables better comparison of aspects of landscape development for geographical regions having diverse socio-economic and ecological conditions. Our methodical approach can be used as a basis not only for creating landscape change scenarios, but also for determining the environmental and human-induced factors involved and being able to list them in order of importance. Further the detected striking difference between the mapped land-use data and the official census data suggests a validation of the methodical approach in context of the national agriculture census.     

Integrating airborne lidar and satellite imagery to model habitat connectivity dynamics for spatial conservation prioritization

Context

The application of regional-level airborne lidar (light detection and ranging) data to characterize habitat patches and model habitat connectivity over large landscapes has not been well explored. Maintaining a connected network of habitat in the presence of anthropogenic disturbances is essential for regional-level conservation planning and the maintenance of biodiversity values.

Objectives

We quantified variation in connectivity following simulated changes in land cover and contrasted outcomes when different conservation priorities were emphasized.

Methods

First, we defined habitat patches using vegetation structural attributes identified via lidar. Second, habitat networks were constructed for different forest types and assessed using network connectivity metrics. And finally, land cover change scenarios were simulated using a series of habitat patch removals, representing the impact of implementing different spatial prioritization schemes.

Results

Networks for different forest structure types produced very different patch distributions. Conservation scenarios based on different schemes led to contrasting changes during land cover change simulations: the scheme prioritizing only habitat area resulted in immediate near-term losses in connectivity, whereas the scheme considering both habitat area and their spatial configurations maintained the overall connectivity most effectively. Adding climate constraints did not diminish or improve overall connectivity.

Conclusions

Both habitat area and habitat configuration should be considered in dynamic modeling of habitat connectivity under changing landscapes. This research provides a framework for integrating forest structure and cover attributes obtained from remote sensing data into network connectivity modeling, and may serve as a prototype for multi-criteria forest management and conservation planning.

     

Effects of landscape structure and temporal habitat dynamics on wintering mallard abundance

Context

Management of wintering waterfowl in North America requires adaptability because constant landscape and environmental change challenges existing management strategies regarding waterfowl habitat use at large spatial scales. Migratory waterfowl including mallards (Anas platyrhynchos) use the lower Mississippi Alluvial Valley (MAV) for wintering habitat, making this an important area of emphasis for improving wetland conservation strategies, while enhancing the understanding of landscape-use patterns.

Objectives

We used aerial survey data collected in the Arkansas portion of the MAV (ARMAV) to explain the abundance and distribution of mallards in relation to variable landscape conditions.

Methods

We used two-stage, hierarchical spatio-temporal models with a random spatial effect to identify covariates related to changes in mallard abundance and distribution within and among years.

Results

We found distinct spatio-temporal patterns existed for mallard distributions across the ARMAV and these distributions are dependent on the surrounding landscape structure and changing environmental conditions. Models performing best indicated seasonal surface water extent, rice field, wetland and fallow (uncultivated) fields positively influenced mallard presence. Rice fields, surface water and weather were found to influence mallard abundance. Additionally, the results suggest weather and changing surface water affects mallard presence and abundance throughout the winter.

Conclusions

Using novel datasets to identify which environmental factors drive changes in regional wildlife distribution and abundance can improve management by providing managers additional information to manage land over landscapes spanning private and public lands. We suggest our analytical approach may be informative in other areas and for other wildlife species.

     

Scaling Aspen-FACE experimental results to century and landscape scales

The Aspen-FACE experiment generated 11 years of empirical data on the effect of CO₂ enrichment and elevated ozone on the growth of field-grown trees (maple, birch and six aspen clones) in northern Wisconsin, but it is not known how these short-term plot-level responses might play out at the landscape scale over multiple decades where competition, succession and disturbances interact with tree-level responses. In this study we used a forest landscape model (LANDIS-II) to scale these site level results to broader temporal and spatial scales. These general principles emerged from the results. (1) The productivity of taxa under future conditions is the primary determinant of short-term taxon dominance. (2) Longer-term, longevity and shade tolerance may supersede productivity as the determinant of importance, depending on the disturbance regime. This result offers hope that, even in the face of atmospheric changes, managers may have some control over future forest composition and carbon sequestration through modification of disturbance regimes. (3) Changes in the abundance of taxa were mostly gradual and none of the taxa were extirpated from the landscape, even under treatments for which they were poorly adapted. This suggests that as atmospheric conditions change, abrupt extirpations are expected to be rare. (4) Similarly, different taxa fared relatively well under different treatments. This suggests that maintaining species and genetic diversity is a prudent forest management strategy in the face of global change. (5) Accounting for spatial processes is important because seed dispersal and establishment may limit the ability of some species to colonize available habitat.     

Associations between soil carbon and ecological landscape variables at escalating spatial scales in Florida,USA

The spatial distribution of soil carbon (C) is controlled by ecological processes that evolve and interact over a range of spatial scales across the landscape. The relationships between hydrologic and biotic processes and soil C patterns and spatial behavior are still poorly understood. Our objectives were to (i) identify the appropriate spatial scale to observe soil total C (TC) in a subtropical landscape with pronounced hydrologic and biotic variation, and (ii) investigate the spatial behavior and relationships between TC and ecological landscape variables which aggregate various hydrologic and biotic processes. The study was conducted in Florida, USA, characterized by extreme hydrologic (poorly to excessively drained soils), and vegetation/land use gradients ranging from natural uplands and wetlands to intensively managed forest, agricultural, and urban systems. We used semivariogram and landscape indices to compare the spatial dependence structures of TC and 19 ecological landscape variables, identifying similarities and establishing pattern–process relationships. Soil, hydrologic, and biotic ecological variables mirrored the spatial behavior of TC at fine (few kilometers), and coarse (hundreds of kilometers) spatial scales. Specifically, soil available water capacity resembled the spatial dependence structure of TC at escalating scales, supporting a multi-scale soil hydrology-soil C process–pattern relationship in Florida. Our findings suggest two appropriate scales to observe TC, one at a short range (autocorrelation range of 5.6 km), representing local soil-landscape variation, and another at a longer range (119 km), accounting for regional variation. Moreover, our results provide further guidance to measure ecological variables influencing C dynamics.     

How to assess the temporal dynamics of landscape connectivity in ever-changing landscapes: a literature review

Landscape Ecology - Landscape connectivity plays a key role in determining the persistence of species inhabiting fragmented habitat patches. In dynamic landscapes, most studies measure connectivity...     

Saproxylic species are linked to the amount and isolation of dead wood across spatial scales in a beech forest

Context

Dead wood is a key habitat for saproxylic species, which are often used as indicators of habitat quality in forests. Understanding how the amount and spatial distribution of dead wood in the landscape affects saproxylic communities is therefore important for maintaining high forest biodiversity.

Objectives

We investigated effects of the amount and isolation of dead wood on the alpha and beta diversity of four saproxylic species groups, with a focus on how the spatial scale influences results.

Methods

We inventoried saproxylic beetles, wood-inhabiting fungi, and epixylic bryophytes and lichens on 62 plots in the Sihlwald forest reserve in Switzerland. We used GLMs to relate plot-level species richness to dead wood amount and isolation on spatial scales of 20–200 m radius. Further, we used GDMs to determine how dead wood amount and isolation affected beta diversity.

Results

A larger amount of dead wood increased beetle richness on all spatial scales, while isolation had no effect. For fungi, bryophytes and lichens this was only true on small spatial scales. On larger scales of our study, dead wood amount had no effect, while greater isolation decreased species richness. Further, we found no strong consistent patterns explaining beta diversity.

Conclusions

Our multi-taxon study shows that habitat amount and isolation can strongly differ in the spatial scale on which they influence local species richness. To generally support the species richness of different saproxylic groups, dead wood must primarily be available in large amounts but should also be evenly distributed because negative effects of isolation already showed at scales under 100 m.