Differential colonization causing non-random forest plant community structure in a fragmented agricultural landscape

We investigated forest plant community structure of recent forest patches in a highly fragmented agricultural landscape, A nestedness analysis has been performed at The community level and at the individual species level. We tested the hypothesis that plant species composition showed a nested structure and whether this was generated by isolation and differential colonization. Alternative hypotheses formulated in the past, such as nested habitats and patch area dependent species relaxation, are verified. Isolation measures were calculated between clearly defined source and target patches. At the community level target patches are defined as forest patches < 35 yr old while older patches are considered as source patches. At the individual species level we distinguished between actually occupied and potentially suitable target patches based on a habitat space model and only occupied source patches are taken into account.
All results point out that the nested community pattern in recent forest patches is generated primarily by isolation and differential colonization. These findings are confirmed at the species level, since the degree of nestedness of the individual species is highly correlated with their isolation sensitivity.
Logistic regression analyses prove that many forest plant species are sensitive to isolation. The probability of occurrence of the isolation sensitive species drops almost to zero, when the nearest source patch is situated further than 200 m. Probabilities of colonization increase significantly when source patches are situated adjacent to target patches.     

Generalist predator's niche shifts reveal ecosystem changes in an experimentally fragmented landscape

Habitat fragmentation can alter the trophic structure of communities and environmental conditions, thus driving changes in biodiversity and ecosystem functions. Quantifying niches of generalist predators can reveal how fragmentation alters ecosystems. In a habitat fragmentation experiment, we used stable isotopes of a generalist predator skink to test predictions from spatial theory on trophic structure and to quantify abiotic changes associated with fragmentation among continuous forest, fragments, and matrix habitats. We predicted that in fragments and the matrix, isotopic niches would shift due to decreases in skink trophic positions (δ¹⁵N) from reductions in trophic structure of arthropod food webs and abiotic changes over time (δ¹³C) relative to continuous forest. Contrary to theoretical predictions, we did not find evidence of reductions in trophic structure with fragmentation. In fact, skink δ¹⁵N values were higher in the matrix and fragments than continuous forest, likely due to changes in distributions of a detritivorous prey species. In addition, δ¹³C values in the matrix decreased over years since fragmentation due to abiotic changes associated with matrix tree maturation. We show how isotopic niches are influenced by fragmentation via shifts in biotic and abiotic processes. The potential for either or both spatial and abiotic effects of fragmentation present a challenge for theory to better predict ecological changes in fragmented landscapes.     

Host-parasitoid extinction and colonization in a fragmented prairie landscape

Few field studies of natural populations have examined the factors influencing local extinctions and colonization of empty habitat patches for a prey species and its predator. In this study, I carried out a census of planthopper (Prokelisia crocea; Hemiptera: Delphacidae) and egg parasitoid (Anagrus columbi; Hymenoptera: Mymaridae) incidence and densities in 147 host-plant patches (Spartina pectinata; Poaceae) over seven planthopper generations in a tall-grass prairie landscape. For both species, the likelihood of going extinct in a patch was related to a number of patch-specific variables: density, temporal variability in density, proportion of hosts parasitized (planthopper only), host-plant density, patch size, patch isolation, and composition of the surrounding matrix. Colonization likelihood was related only to the physical attributes of the patch. There was high patch turnover in this prairie landscape. On average, planthoppers went extinct in 23% of the patches and A. columbi went extinct in 51% of the patches in each generation. For the planthopper, extinction likelihood increased with a decrease in patch size and the proportion of the matrix composed of mudflat. Parasitism of eggs had no effect on the extinction likelihood of local P. crocea populations, suggesting that A. columbi may not play a major role in the patch dynamics of its host. The likelihood of extinction for A. columbi was dependent on factors that spanned three trophic levels. An increase in plant density, decrease in host density and decrease in parasitoid density all increased the likelihood of A. columbi extinction within a patch. The dependency on multiple trophic levels may explain the higher extinction risk for the parasitoid than its host. A. columbi extinction was also affected by the matrix habitat surrounding the patch—the effect was the opposite of that for P. crocea. Finally, vacant patches were colonized at rates of 53% and 34% per generation for the planthopper and parasitoid, respectively. For both species, colonization probabilities decreased with an increase in patch isolation. High host densities in a patch also favored high rates of colonization by A. columbi. I discuss how anthropogenic changes to the prairie landscape can affect the metapopulation dynamics and persistence time of this host-parasitoid interaction.     

Cross-scale drivers of plant trait distributions in a fragmented forest landscape

During community assembly, plant functional traits are under selective pressure from processes operating at multiple spatial scales. However, in fragmented landscapes, there is little understanding of the relative importance of local-, patch- and landscape-scale processes in shaping trait distributions. Here, we investigate cross-scale influences of landscape change on traits that dictate plant life history strategies in re-assembling plant communities in a fragmented landscape in eastern China. Using forest dynamics plots (FDPs) on 29 land-bridge islands in which all woody plants have been georeferenced and identified to species, we characterized and derived two composite measures of trait variation, representing variation across the leaf economics spectrum and plant size. We then tested for trait shifts in response to local-, patch- and landscape-scale factors, and their potential cross-scale interactions. We found substantial community-wide trait changes along local-scale gradients (i.e. forest edge to interior): more acquisitive leaf economic traits and larger sized species occurred at edges, with a significant increase in trait means and trait range. Moreover, there were significant cross-scale interaction effects of patch and landscape variables on local-scale edge effects. Altered spatial arrangement of habitat in the surrounding landscape (i.e. declining habitat amount and increasing patch density), as well as decreasing area at the patch level, exacerbated edge effects on traits distributions. We suggest that synergistic interactions of landscape- and patch-scale processes, such as dispersal limitation, on local-scale environmental filtering at edges, together shape the spatial distributions of plant life history strategies in fragmented plant communities.     

Phylogenetic patterns of colonization and extinction in experimentally assembled plant communities

Background

Evolutionary history has provided insights into the assembly and functioning of plant communities, yet patterns of phylogenetic community structure have largely been based on non-dynamic observations of natural communities. We examined phylogenetic patterns of natural colonization, extinction and biomass production in experimentally assembled communities.

Methodology/Principal Findings

We used plant community phylogenetic patterns two years after experimental diversity treatments (1, 2, 4, 8 or 32 species) were discontinued. We constructed a 5-gene molecular phylogeny and statistically compared relatedness of species that colonized or went extinct to remaining community members and patterns of aboveground productivity. Phylogenetic relatedness converged as species-poor plots were colonized and speciose plots experienced extinctions, but plots maintained more differences in composition than in phylogenetic diversity. Successful colonists tended to either be closely or distantly related to community residents. Extinctions did not exhibit any strong relatedness patterns. Finally, plots that increased in phylogenetic diversity also increased in community productivity, though this effect was inseparable from legume colonization, since these colonists tended to be phylogenetically distantly related.

Conclusions

We found that successful non-legume colonists were typically found where close relatives already existed in the sown community; in contrast, successful legume colonists (on their own long branch in the phylogeny) resulted in plots that were colonized by distant relatives. While extinctions exhibited no pattern with respect to relatedness to sown plotmates, extinction plus colonization resulted in communities that converged to similar phylogenetic diversity values, while maintaining differences in species composition.     

Application of a semi-automated vocal fingerprinting approach to monitor Bornean gibbon females in an experimentally fragmented landscape in Sabah,Malaysia

Vocal individuality has been documented in a variety of mammalian species and it has been proposed that this individuality can be used as a vocal fingerprint to monitor individuals. Here we provide and test a classification method using Mel-frequency cepstral coefficients (MFCCs) to extract features from Bornean gibbon female calls. Our method is semi-automated as it requires manual pre-processing to identify and extract calls from the original recordings. We compared two methods of MFCC feature extraction: (1) averaging across all time windows and (2) creating a standardized number of time windows for each call. We analysed 376 calls from 33 gibbon females and, using linear discriminant analysis, found that we were able to improve female identification accuracy from 95.7% with spectrogram features to 98.4% accuracy when averaging MFCCs across time windows, and 98.9% accuracy when using a standardized number of windows. We divided our data randomly into training and test data-sets, and tested the accuracy of support vector machine (SVM) predictions over 100 iterations. We found that we could predict female identity in the test data-set with a 98.8% accuracy. Using SVM on our entire data-set, we were able to predict female identity with 99.5% accuracy (validated by leave-one-out cross-validation). Lastly, we used the method presented here to classify four females recorded during three or more recording seasons using SVM with limited success. We provide evidence that MFCC feature extraction is effective for distinguishing between female Bornean gibbons, and make suggestions for future vocal fingerprinting applications.     

Dynamic effects of ground-layer plant communities on beetles in a fragmented farming landscape

Vegetation effects on arthropods are well recognized, but it is unclear how different vegetation attributes might influence arthropod assemblages across mixed-agricultural landscapes. Understanding how plant communities influence arthropods under different habitat and seasonal contexts can identify vegetation management options for arthropod biodiversity. We examined relationships between vegetation structure, plant species richness and plant species composition, and the diversity and composition of beetles in different habitats and time periods. We asked: (1) What is the relative importance of plant species richness, vegetation structure and plant composition in explaining beetle species richness, activity-density and composition? (2) How do plant-beetle relationships vary between different habitats over time? We sampled beetles using pitfall traps and surveyed vegetation in three habitats (woodland, farmland, their edges) during peak crop growth in spring and post-harvest in summer. Plant composition better predicted beetle composition than vegetation structure. Both plant richness and vegetation structure significantly and positively affected beetle activity-density. The influence of all vegetation attributes often varied in strength and direction between habitats and seasons for all trophic groups. The variable nature of plant-beetle relationships suggests that vegetation management could be targeted at specific habitats and time periods to maximize positive outcomes for beetle diversity. In particular, management that promotes plant richness at edges, and promotes herbaceous cover during summer, can support beetle diversity. Conserving ground cover in all habitats may improve activity-density of all beetle trophic groups. The impacts of existing weed control strategies in Australian crop margins on arthropod biodiversity require further study.     

Woody plant diversity in relation to environmental factors in a seasonally dry tropical forest landscape

Questions

Water availability is known to be a first‐order driver of plant diversity; yet water also affects fire regimes and soil fertility, which, in turn, affect plant diversity. We examined how precipitation, fire and soil properties jointly determine woody plant diversity. Specifically, we asked how woody plant diversity varies along a sharp precipitation gradient (about 600–1,800 mm mean annual precipitation [MAP ]within a ~45‐km distance) exhibiting considerable variation in long‐term fire burn frequency and soil fertility, in a southern Indian seasonally dry tropical forest (SDTF ) landscape.

Location

Mudumalai, Western Ghats, India.

Methods

Woody plants ≥1‐cm DBH were enumerated in 19 1‐ha permanent plots spanning a range of tropical vegetation types from dry thorn forest, through dry and moist deciduous forest to semi‐evergreen forest. Burn frequencies were derived from annual fire maps. Six measures of surface soil properties – total exchangeable bases (Ca + Mg + K), organic carbon (OC ), total N, pH , plant available P and micronutrients (Fe + Cu + Zn + Mn) were used in the analyses. Five measures of diversity – species richness, Shannon diversity, the rarefied/extrapolated versions of these two measures, and Fisher's α – were modelled as functions of MAP , annual fire burn frequency and the principal components of soil properties.

Results

Most soil nutrients and OC increased with MAP , except in the wettest sites. Woody productivity increased with MAP , while fire frequency was highest at intermediate values of MAP . Woody plant diversity increased with MAP but decreased with increasing fire frequency, resulting in two local diversity maxima along the MAP gradient – in the semi‐evergreen and dry thorn forest – separated by a low‐diversity central region in dry deciduous forest where fire frequency was highest. Soil variables were, on the whole, less strongly correlated with diversity than MAP .

Conclusions

Although woody plant diversity in this landscape, representative of regional SDTF s, is primarily limited by water availability, our study emphasizes the role of fire as a potentially important second‐order driver that acts to reduce diversity in this landscape.

     

Extinction,turnover and species diversity in an experimentally fragmented California annual grassland

Summary Many natural populations are subdivided among partially isolated habitat patches, but the influence of habitat patchiness per se on species immigration, extinction, and the resulting patterns of species diversity, has received virtually no experimental study. In an experiment designed to test the effects of habitat subdivision on local community structure, we compare the diversity and annual turnover of flowering plant species in 3 treatments of the same total area, but subdivided to different degrees. We experimentally fragmented a California winter annual grassland into isolated plots, two of 32 m², eight of 8 m², and 32 of 2 m², each treatment representing a combined area of 64 m². Insularization of the experimental habitat fragments is provided by grazing sheep. The effects of plot area on species diversity, extinction, and turnover are consistent with the MacArthur-Wilson model. Species richness increases with the degree of habitat subdivision. Extinction, immigration, and turnover, however, are relatively independent of the degree of subdivision. These experimental results contrast with predictions that habitat subdivision necessarily results in greater rates of extinction accompanied by reduced species diversity.     

Distribution of an increasing roe deer population in a fragmented Mediterranean landscape

This paper describes roe deer Capreolus capreolus distribution in central Spain, where the species has spread from the mountains into peripheral agricultural areas In this region, it is more abundant in forest fragments near the mountains than in those further away, in pine and oak woodlands than in sclerophyllous forests, and in forests with open water than in those lacking this resource The paper also analyzes whether habitat quality and geographic location of forests with respect to roe deer source areas are the two basic causes of its distribution, as predicted by some models of the species distribution in fragmented landscapes The results corroborate this hypothesis revealing that roe deer abundance is linked negatively to sclerophyllous forest cover and distance from mountains We conclude that this type of farmland seems to be sub-optimal for roe deer in comparison with forested, moist mountains     

Species dynamics and colonization patterns in an abandoned forest in an urban landscape

Species dynamics in an abandoned urban forest of Central Japan is described in this paper. The dominant species in the urban plantation were Cryptomeria japonica and Chamaecyparis obtusa. A variety of eight patches of the canopy was produced by previous forest management practices. Progressive and retrogressive species dynamics within these eight patches are investigated in this paper. The study elucidates the deterministic role of patchiness in the nature of species colonization and the maintenance of species diversity in an urban forest. Altogether 139 native and/or naturalized species, including 23 shrub and 35 tree species, were recorded in the study area of 3.2 ha. The performance of species varied according to their successional attributes indicating a selective canopy influence. Twenty percent of the tree species were shade-intolerant pioneers (e.g. Cornus spp., Rhus javanica var. roxburghii) re-established under selective tree-felling. Thirty percent were shade-tolerant climax species (e.g. Neolitsea sericea, Persea thunbergii) dominant in remnant closed patches. The remaining 50% belonged to various seral types with aggressive deciduous species (e.g. Aphananthe aspera, Celtis sinensis) in most of the patches. Some ruderal herbaceous species dominated heavily disturbed clear-felled patches. This study suggests that canopy modification influences the subsequent colonization pattern. Furthermore, heterogeneous patches contribute to greater species diversity and dynamics in isolated woodlands.     

Range shifting on a fragmented landscape

Projected responses of species' to climate change have so far included few of the factors that are important determinants of species' distributions within its range. In this paper we utilise a spatially explicit cellular lattice, colonisation–extinction model to investigate the effect of habitat loss, fragmentation and species characteristics on range shifting in response to climate change. Contrary to the predictions of patch occupancy in static climate models we show that fragmentation can have a positive effect on species survival when species have high colonisation rates. For species with low colonisation rates aggregative behaviours prevent success on fragmented landscapes at high levels of habitat loss, and range shifting is more successfully achieved where habitat is correlated. At levels of habitat loss near the extinction threshold, less fragmented landscapes can facilitate range shifting even for the best colonisers. We discuss how imposing a climate window may reduce percolation routes and have implications for the area of usable habitat at any given level of habitat availability. We demonstrate the importance of landscape structure for range shifting dynamics and argue that management of reserve networks needs to consider the requirements of species with different life history characteristics.     

Sexual segregation occurs in bats within fragmented remnant woodlands in an agricultural landscape

Species‐specific responses to landscape configuration and landscape composition have been studied extensively. However, little work has been done to compare intraspecific differences in habitat preferences. Bats have potential as good bioindicator taxa in woodland habitats. Therefore, studying sex differences in responses to woodland and the wider landscape can allow us to gain insight into the relative importance of these habitats for both bats and other taxa. In this study, we aimed to test the predictions that (i) habitat type and connectivity will influence the probability of recording female bats in woodlands and (ii) sex differences in response to habitat type and connectivity will be species‐specific. Bat capture data was collected in 206 woodlands over 3 years in England. The probability of detecting females relative to males was modeled in response to a range of woodland characteristics and landscape metrics for six bat species. We recorded sex differences in responses to landscape features in three species. We found a higher probability of capturing female Myotis nattereri in woodlands that were surrounded by a higher proportion of improved grasslands, whereas female Myotis mystacinus were less likely to be recorded in woodlands surrounded by semi‐natural vegetation. Female Plecotus auritus were more likely to be recorded in isolated woodlands with less connectivity to other woodlands and where agriculture dominated the surrounding landscape. Our findings indicate that sexual segregation occurs across several UK bat species in response to landscape connectivity and composition. Sexual segregation in response to landscape characteristics in bats should therefore be an important consideration in the management of fragmented agricultural landscapes.     

Woody riparian plant distributions in western Oregon,USA: comparing landscape and local scale factors

We studied riparian forests along mountain streams in four large watersheds of western Oregon and far northern California, USA, to better understand the multiscale controls on woody riparian vegetation in a geographically complex region. In each of the four-study watersheds, we sampled woody riparian vegetation in161-ha sampling reaches that straddled the stream channel. Within each hectare, we sampled riparian vegetation and local environmental factors in 40 m² sampling plots arrayed along topographic transects. We also surveyed natural disturbance gaps in 6 ha in each watershed to explore the effects of fine scale disturbance on species distributions. We compared species composition across our study watersheds and used Nonmetric Multidimensional Scaling (NMS) and chi-squared analyses to compare the relative importance of landscape scale climate variables and local topographic and disturbance variables in explaining species distributions at sampling plot and hectare scales. We noted substantial turnover in the riparian flora across the region, with greatest numbers of unique species in watersheds at the ends of the regional gradient. In NMS ordinations at both scales, variation in woody riparian species composition showed strongest correlations with climatic variables and Rubus spectabilis cover, but the latter was only an important factor in the two northern watersheds. At the smaller scale, topographic variables were also important. Chi-squared analyses confirmed that more species showed landscape scale habitat preferences (watershed associations) than associations with topographic position (94.7% vs. 42.7% of species tested) or gap versus forest setting (94.7% vs. 24.6% of species tested). The woody riparian flora of western Oregon shows important biogeographic variation; species distributions showed strong associations with climatic variables, which were the primary correlates of compositional change between riparian sites at both scales analyzed. Additional local variation in composition was explained by measures of topography and disturbance.