Population viability analysis with species occurrence data from museum collections

The most comprehensive data on many species come from scientific collections. Thus, we developed a method of population viability analysis (PVA) in which this type of occurrence data can be used. In contrast to classical PVA, our approach accounts for the inherent observation error in occurrence data and allows the estimation of the population parameters needed for viability analysis. We tested the sensitivity of the approach to spatial resolution of the data, length of the time series, sampling effort, and detection probability with simulated data and conducted PVAs for common, rare, and threatened species. We compared the results of these PVAs with results of standard method PVAs in which observation error is ignored. Our method provided realistic estimates of population growth terms and quasi-extinction risk in cases in which the standard method without observation error could not. For low values of any of the sampling variables we tested, precision decreased, and in some cases biased estimates resulted. The results of our PVAs with the example species were consistent with information in the literature on these species. Our approach may facilitate PVA for a wide range of species of conservation concern for which demographic data are lacking but occurrence data are readily available.

Distribution pattern of plant species diversity in the mountainous region of Ili River Valley, Xinjiang

In this paper, detrended canonical correspondence analysis was performed to analyze the relationships between diversity indices and environmental gradients, generalized additive model was employed to modal the response curves of diversity indices to the elevation, based on data from field investigation in the mountainous region of the Ili River Valley and a survey of 94 sample plots. Two hundred fifty-nine plant species were recorded in the 94 sample plots investigated, up to 235 species all appeared in the herb layer, and the species of woody plants were very limited. The communities with a complicated vertical structure presented higher values of indices. The distribution pattern of plant species diversity on the northern slope was affected by such factors as elevation, slope aspect, slope gradient, total nitrogen, total potassium, soil water content, organic matter, and that on the southern slope was mainly affected by such factors as slope gradient, elevation, available phosphorus, and soil water content. On the northern slope, Patrick index and Shannon-Wiener index of the plant communities presented a bimodality pattern along altitude; Simpson index and Pielou index showed a partially unimodal pattern. On the southern slope all the distribution pattern of species diversity indices showed two peaks, though Patrick index's bimodality pattern was not an obvious one. These altitudinal patterns were formed by the synthetic action of a variety of environmental factors with elevation playing an important role.

An ecological genomic approach challenging the paradigm of differential plant responses to specialist versus generalist insect herbivores

A general prediction of the specialist/generalist paradigm indicates that plant responses to insect herbivores may depend on the degree of ecological specialization of the insect attacker. However, results from a single greenhouse experiment evaluating the responses of the model plant Arabidopsis thaliana to three specialist (Plutella xylostella, Pieris rapae, and Brevicoryne brassicae) and three generalist (Trichoplusia ni, Spodoptera exigua, and Myzus persicae) insect species did not support the previous prediction. Using an ecological genomic approach, we assessed plant responses in terms of herbivore-induced changes in genome-wide gene expression, defense-related pathways, and concentrations of glucosinolates (i.e., secondary metabolites that are ubiquitously present in cruciferous plants). Our results showed that plant responses were not influenced by the degree of specialization of insect herbivores. In contrast, responses were more strongly shaped by insect taxa (i.e., aphid vs. lepidopteran species), likely due to their different feeding modes. Interestingly, similar patterns of plant responses were induced by the same insect herbivore species in terms of defense signaling (jasmonic acid pathway), aliphatic glucosinolate metabolism (at both the gene expression and phenotypic levels) and genome-wide responses. Furthermore, plant responses to insect herbivores belonging to the same taxon (i.e., four lepidopteran species) were not explained by herbivore specialization or phylogenetic history. Overall, this study suggests that different feeding modes of insect taxa as well as herbivore-specific plant responses, which may result from distinct ecological/evolutionary interactions between A. thaliana (or a close relative) and each of the lepidopteran species, may explain why observed responses deviate from those predicted by the specialist/generalist paradigm.

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.

Phylogenetic inference of reciprocal effects between geographic range evolution and diversification

Geographic characters--traits describing the spatial distribution of a species-may both affect and be affected by processes associated with lineage birth and death. This is potentially confounding to comparative analyses of species distributions because current models do not allow reciprocal interactions between the evolution of ranges and the growth of phylogenetic trees. Here, we introduce a likelihood-based approach to estimating region-dependent rates of speciation, extinction, and range evolution from a phylogeny, using a new model in which these processes are interdependent. We demonstrate the method with simulation tests that accurately recover parameters relating to the mode of speciation and source-sink dynamics. We then apply it to the evolution of habitat occupancy in Californian plant communities, where we find higher rates of speciation in chaparral than in forests and evidence for expanding habitat tolerances.

Equilibrium of vegetation and climate at the European rear edge. A reference for climate change planning in mountainous Mediterranean regions

Mediterranean mountains harbour some of Europe's highest floristic richness. This is accounted for largely by the mesoclimatic variety in these areas, along with the co-occurrence of a small area of Eurosiberian, Boreal and Mediterranean species, and those of Tertiary Subtropical origin. Throughout the twenty-first century, we are likely to witness a climate change-related modification of the biogeographic scenario in these mountains, and there is therefore a need for accurate climate regionalisations to serve as a reference of the abundance and distribution of species and communities, particularly those of a relictic nature. This paper presents an objective mapping method focussing on climate regions in a mountain range. The procedure was tested in the Cordillera Central Mountains of the Iberian Peninsula, in the western Mediterranean, one of the ranges occupying the largest area of the Mediterranean Basin. This regionalisation is based upon multivariate analyses and upon detailed cartography employing 27 climatic variables. We used spatial interpolation of data based on geographic information. We detected high climatic diversity in the mountain range studied. We identified 13 climatic regions, all of which form a varying mosaic throughout the annual temperature and rainfall cycle. This heterogeneity results from two geographically opposed gradients. The first one is the Mediterranean-Euro-Siberian variation of the mountain range. The second gradient involves the degree of oceanicity, which is negatively related to distance from the Atlantic Ocean. The existing correlation between the climatic regions detected and the flora existing therein enables the results to be situated within the projected trends of global warming, and their biogeographic and ecological consequences to be analysed.

[Effects of highway on the vegetation species composition along a distance gradient from road edge in southeastern margin of Tengeer Desert]

Aimed to examine the effects of highway on the vegetation species composition in arid desert area, forty-eight transects perpendicular to the provincial highway 201 from Shapotou to Jing-tai in the southeastern margin of Tengger Desert were installed, with the vegetation species distribution along a distance gradient from the road edge investigated. The results showed that with increasing distance from the road edge, the species number, coverage, biomass, and alpha-diversity of herbaceous plants declined, but had no significant differences with the control beyond 5 m. Within 0-6 m to the road edge, the herbaceous plant height was greater than that of the control, but their density had less change. Within 0-2 m to the road edge, the species turnover rate of herbaceous plants was lower; at 2-5m, this rate was the highest; while beyond 10 m, the species composition of herbaceous plants was similar to that of the control. The herbaceous plant community at the road edge was dominated by gramineous plants, with the disturbance-tolerant species Pennisetum centrasiaticum, Chloris virgata, and Agropyron cristatum accounting for 68.6% of the total. C. virgata beyond 1 m to the road edge had a rapid decrease in its individual number and presence frequency, P. centrasiaticum and A. cristatum beyond 2 m also showed a similar trend, while the composite plants Artemisia capillaris and A. frigida beyond 2 m from the road edge had a rapid increase in its individual number, accounting for 70% of the herbaceous plants. At the road edge, the coverage and density of shrubs were significantly lower than those of the control, but the species composition had no significant difference.

Extinction risk and diversification are linked in a plant biodiversity hotspot

It is widely recognized that we are entering an extinction event on a scale approaching the mass extinctions seen in the fossil record. Present-day rates of extinction are estimated to be several orders of magnitude greater than background rates and are projected to increase further if current trends continue. In vertebrates, species traits, such as body size, fecundity, and geographic range, are important predictors of vulnerability. Although plants are the basis for life on Earth, our knowledge of plant extinctions and vulnerabilities is lagging. Here, we disentangle the underlying drivers of extinction risk in plants, focusing on the Cape of South Africa, a global biodiversity hotspot. By comparing Red List data for the British and South African floras, we demonstrate that the taxonomic distribution of extinction risk differs significantly between regions, inconsistent with a simple, trait-based model of extinction. Using a comprehensive phylogenetic tree for the Cape, we reveal a phylogenetic signal in the distribution of plant extinction risks but show that the most threatened species cluster within short branches at the tips of the phylogeny--opposite to trends in mammals. From analyzing the distribution of threatened species across 11 exemplar clades, we suggest that mode of speciation best explains the unusual phylogenetic structure of extinction risks in plants of the Cape. Our results demonstrate that explanations for elevated extinction risk in plants of the Cape flora differ dramatically from those recognized for vertebrates. In the Cape, extinction risk is higher for young and fast-evolving plant lineages and cannot be explained by correlations with simple biological traits. Critically, we find that the most vulnerable plant species are nonetheless marching towards extinction at a more rapid pace but, surprisingly, independently from anthropogenic effects. Our results have important implications for conservation priorities and cast doubts on the utility of current Red List criteria for plants in regions such as the Cape, where speciation has been rapid, if our aim is to maximize the preservation of the tree-of-life.

[Specific features of plants at early stages of the colonization of loose volcanic matter]

Plant morphology and seed germination have been studied in several species joining monodominant beds of pioneer plant species on loose volcanic matter on the Kamchatka Peninsula and Kuril Islands. The competition of these species is discussed.

Why are some plant genera more invasive than others?

Determining how biological traits are related to the ability of groups of organisms to become economically damaging when established outside of their native ranges is a major goal of population biology, and important in the management of invasive species. Little is known about why some taxonomic groups are more likely to become pests than others among plants. We investigated traits that discriminate vascular plant genera, a level of taxonomic generality at which risk assessment and screening could be more effectively performed, according to the proportion of naturalized species which are pests. We focused on the United States and Canada, and, because our purpose is ultimately regulatory, considered species classified as weeds or noxious. Using contingency tables, we identified 11 genera of vascular plants that are disproportionately represented by invasive species. Results from boosted regression tree analyses show that these categories reflect biological differences. In summary, approximately 25% of variation in genus proportions of weeds or noxious species was explained by biological covariates. Key explanatory traits included genus means for wetland habitat affinity, chromosome number, and seed mass.

The repeatability of vegetation classification and mapping

The mapping of habitats as defined by plant communities is a common component of the planning and monitoring of conservation management. However, there are major concerns about the subjectivity and risk of observer bias in most commonly used plant community mapping protocols. This study provides the first test of the consistency of habitat maps based on the mapping units defined by the National Vegetation Classification (NVC), the most widely used classification of plant communities used for habitat mapping on conservation sites in the UK. Seven surveyors mapped the same upland site within five weeks in summer 2008 and the spatial correspondence of the resulting maps was assessed. The NVC is a hierarchical classification and pair-wise spatial agreement between maps decreased with lower levels of sub-classification. The average area of agreement between maps was 77.6% at the habitat level, 34.2% at the community level and 18.5% at the sub-community level. Spatial disparity in the location of mapped boundaries between vegetation types only made a small contribution to overall differences; the majority of variation between maps was due to discrepancies in classification, with vegetation types containing similar species composition most often confused. Factors relating to surveyor effort (cost, time taken and length of route) were not able to explain the substantial differences between maps. However, the methods used to assign areas to vegetation type did seem to have an effect, with surveyors who relied primarily on their own experience having the highest levels of mean agreement with other maps. The study raises serious concerns with current practice of using the NVC for site description and monitoring/surveillance. Since this is just a single case study, we recommend that further work is carried out with the aim of determining the degree and source of variation between surveyors and how consistency can be increased.

Regional and decadal patterns of native and exotic plant coexistence in California grasslands

Coexistence through a variety of mechanisms is possible for species with differential responses to environmental conditions. Understanding the role of environmental heterogeneity in mediating coexistence of species of different provenance (i.e., native vs. exotic) has important implications for theory and management. We used two California grassland data sets, one spanning seven years at three reserves along a 500-km latitudinal gradient and one spanning 47 years at 11 sites within a single 1000-ha reserve, to determine how environmental heterogeneity in space and time contributes to variability in provenance group abundance and diversity, and whether native and exotic species respond similarly to spatial and temporal variability. We found that temporal environmental heterogeneity is the primary determinant of provenance group abundance, while spatial and temporal environmental heterogeneity both contribute to community diversity. Spatial and temporal heterogeneity must therefore be considered simultaneously when examining community dynamics and species coexistence. Provenance was a poor general predictor of species response; native and exotic species exhibit similar spatiotemporal patterns in some cases but not others. Plant persistence may depend more upon the abiotic environment than competition from the other provenance group as native and exotic diversity were generally positively correlated. Furthermore, mesoscale (10(2)-10(3) m) spatial heterogeneity may be a greater mediator of provenance group coexistence than temporal heterogeneity or spatial heterogeneity at other scales.

Landscape connectivity and seed dispersal characteristics inform the best management strategy for exotic plants

Exotic plant invasions have triggered environmental and economic problems throughout the world. Our ability to manage these invasions is hindered by the difficulty of predicting spread in fragmented landscapes. Because the spatial pattern of invasions depends on the dispersal characteristics of the invasive species and the configuration of suitable habitat within the landscape, a universal management strategy is unlikely to succeed for any particular species. We suggest that the most effective management strategy may be an adaptive one that shifts from local control to landscape management depending on the specific invader and landscape. In particular, we addressed the question of where management activities should be focused to minimize spread of the invading species. By simulating an invasion across a real landscape (Antietam National Battlefield in Maryland, USA), we examined the importance of patch size and connectivity to management success. We found that the best management strategy depended on the dispersal characteristics of the exotic species. Species with a high probability of random long-distance dispersal were best managed by focusing on the largest patches, while species with a lower probability of random long-distance dispersal were best managed by considering landscape configuration and connectivity of the patches. Connectivity metrics from network analysis were useful for identifying the most effective places to focus management efforts. These results provide insight into invasion patterns of various species and suggest a general rule for managers in National Parks and other places where invasive species are a concern.

[Variation trends of natural vegetation net primary productivity in China under climate change scenario]

Based on the widely used Lund-Potsdam-Jena Dynamic Global Vegetation Model (LPJ) for climate change study, and according to the features of natural environment in China, the operation mechanism of the model was adjusted, and the parameters were modified. With the modified LPJ model and taking 1961-1990 as baseline period, the responses of natural vegetation net primary productivity (NPP) in China to climate change in 1991-2080 were simulated under the Special Report on Emissions Scenarios (SRES) B2 scenario. In 1961-1990, the total NPP of natural vegetation in China was about 3.06 Pg C a(-1); in 1961-2080, the total NPP showed a fluctuant decreasing trend, with an accelerated decreasing rate. Under the condition of slight precipitation change, the increase of mean air temperature would have definite adverse impact on the NPP. Spatially, the NPP decreased from southeast coast to northwest inland, and this pattern would have less variation under climate change. In eastern China with higher NPP, especially in Northeast China, east of North China, and Loess Plateau, the NPP would mainly have a decreasing trend; while in western China with lower NPP, especially in the Tibetan Plateau and Tarim Basin, the NPP would be increased. With the intensive climate change, such a variation trend of NPP would be more obvious.

More closely related species are more ecologically similar in an experimental test

The relationship between phylogenetic distance and ecological similarity is key to understanding mechanisms of community assembly, a central goal of ecology. The field of community phylogenetics uses phylogenetic information to infer mechanisms of community assembly; we explore, the underlying relationship between phylogenetic similarity and the niche. We combined a field experiment using 32 native plant species with a molecular phylogeny and found that closely related plant species shared similar germination and early survival niches. Species also competed more with close relatives than with distant relatives in field soils; however, in potting soil this pattern reversed, and close relatives might even have more mutalistic relationships than distant relatives in these soils. Our results suggest that niche conservatism (habitat filtering) and species interactions (competition or facilitation) structure community composition, that phylogenetic relationships influence the strength of species' interactions, and that conserved aspects of plant niches include soil attributes.

Assessing the performance of sampling designs for measuring the abundance of understory plants

Accurate estimation of responses of understory plants to disturbance is essential for understanding the efficacy of management activities. However, the ability to assess changes in the abundance of plants may be hampered by inappropriate sampling methodologies. Conventional methods for sampling understory plants may be precise for common species but may fail to adequately characterize abundance of less common species. We tested conventional (modified Whittaker plots and Daubenmire and point-line intercept transects) and novel (strip adaptive cluster sampling [SACS]) approaches to sampling understory plants to determine their efficacy for quantifying abundance on control and thinned-and-burned treatment units in Pinus ponderosa forests in western Montana, USA. For species grouped by growth-form and for common species, all three conventional designs were capable of estimating cover with a 50% relative margin of error with reasonable sample sizes (3-36 replicates for growth-form groups; 8-14 replicates for common species); however, increasing precision to 25% relative margin of error required sample sizes that may be infeasible (11-143 replicates for growth-form groups; 28-54 replicates for common species). All three conventional designs required enormous sample sizes to estimate cover of nonnative species as a group (29-60 replicates) and of individual less common species (62-118 replicates), even with a 50% relative margin of error. SACS was the only design that efficiently sampled less common species, requiring only 6-11% as many replicates relative to conventional designs. Conventional designs may not be effective for estimating abundance of the majority of forest understory plants, which are typically patchily distributed with low abundance, or of newly establishing nonnative plants. Novel methods such as SACS should be considered in investigations when cover of these species is of concern.

Native plant communities in an abandoned Pb-Zn mining area of northern Spain: implications for phytoremediation and germplasm preservation

Plants growing on metalliferous soils from abandoned mines are unique because of their ability to cope with high metal levels in soil. In this study, we characterized plants and soils from an abandoned Pb-Zn mine in the Basque Country (northern Spain). Soil in this area proved to be deficient in major macronutrients and to contain toxic levels of Cd, Pb, and Zn. Spontaneously growing native plants (belonging to 31 species, 28 genera, and 15 families) were botanically identified. Plant shoots and rhizosphere soil were sampled at several sites in the mine, and analyzed for Pb, Zn and Cd concentration. Zinc showed the highest concentrations in shoots, followed by Pb and Cd. Highest Zn concentrations in shoots were found in the Zn-Cd hyperaccumulator Thlaspi caerulescens (mean = 18,254 mg Zn kg(-1) DW). Different metal tolerance and accumulation patterns were observed among the studied plant species, thus offering a wide germplasm assortment for the suitable selection of phytoremediation technologies. This study highlights the importance of preserving metalliferous environments as they shelter a unique and highly valuable metallicolous biodiversity.

Genome-scale phylogenetics: inferring the plant tree of life from 18,896 gene trees

Phylogenetic analyses using genome-scale data sets must confront incongruence among gene trees, which in plants is exacerbated by frequent gene duplications and losses. Gene tree parsimony (GTP) is a phylogenetic optimization criterion in which a species tree that minimizes the number of gene duplications induced among a set of gene trees is selected. The run time performance of previous implementations has limited its use on large-scale data sets. We used new software that incorporates recent algorithmic advances to examine the performance of GTP on a plant data set consisting of 18,896 gene trees containing 510,922 protein sequences from 136 plant taxa (giving a combined alignment length of >2.9 million characters). The relationships inferred from the GTP analysis were largely consistent with previous large-scale studies of backbone plant phylogeny and resolved some controversial nodes. The placement of taxa that were present in few gene trees generally varied the most among GTP bootstrap replicates. Excluding these taxa either before or after the GTP analysis revealed high levels of phylogenetic support across plants. The analyses supported magnoliids sister to a eudicot + monocot clade and did not support the eurosid I and II clades. This study presents a nuclear genomic perspective on the broad-scale phylogenic relationships among plants, and it demonstrates that nuclear genes with a history of duplication and loss can be phylogenetically informative for resolving the plant tree of life.

Managing soil nitrogen to restore annual grass-infested plant communities: effective strategy or incomplete framework?

Theoretical and empirical work has established a positive relationship between resource availability and habitat invasibility. For nonnative invasive annual grasses, similar to other invasive species, invader success has been tied most often to increased nitrogen (N) availability. These observations have led to the logical assumption that managing soils for low N availability will facilitate restoration of invasive plant-dominated systems. Although invasive annual grasses pose a serious threat to a number of perennial-dominated ecosystems worldwide, there has been no quantitative synthesis evaluating the degree to which soil N management may facilitate restoration efforts. We used meta-analysis to evaluate the degree to which soil N management impacts growth and competitive ability of annual and perennial grass seedlings. We then link our analysis to current theories of plant ecological strategies and community assembly to improve our ability to understand how soil N management may be used to restore annual grass-dominated communities. Across studies, annual grasses maintained higher growth rates and greater biomass and tiller production than perennials under low and high N availability. We found no evidence that lowering N availability fundamentally alters competitive interactions between annual and perennial grass seedlings. Competitive effects of annual neighbors on perennial targets were similar under low and high N availability. Moreover, in most cases perennials grown under competition in high-N soils produced more biomass than perennials grown under competition in low-N soils. While these findings counter current restoration and soil N management assumptions, these results are consistent with current plant ecological strategy and community assembly theory. Based on our results and these theories we argue that, in restoration scenarios in which the native plant community is being reassembled from seed, soil N management will have no direct positive effect on native plant establishment unless invasive plant propagule pools and priority effects are controlled the first growing season.

The age and diversification of terrestrial New World ecosystems through Cretaceous and Cenozoic time

Eight ecosystems that were present in the Cretaceous about 100 Ma (million years ago) in the New World eventually developed into the 12 recognized for the modern Earth. Among the forcing mechanisms that drove biotic change during this interval was a decline in global temperatures toward the end of the Cretaceous, augmented by the asteroid impact at 65 Ma and drainage of seas from continental margins and interiors; separation of South America from Africa beginning in the south at ca. 120 Ma and progressing northward until completed 90-100 Ma; the possible emission of 1500 gigatons of methane and CO(2) attributed to explosive vents in the Norwegian Sea at ca. 55 Ma, resulting in a temperature rise of 5°-6°C in an already warm world; disruption of the North Atlantic land bridge at ca. 45 Ma at a time when temperatures were falling; rise of the Andes Mountains beginning at ca. 40 Ma; opening of the Drake Passage between South America and Antarctica at ca. 32 Ma with formation of the cold Humboldt at ca. 30 Ma; union of North and South America at ca. 3.5 Ma; and all within the overlay of evolutionary processes. These processes generated a sequence of elements (e.g., species growing in moist habitats within an overall dry environment; gallery forests), early versions (e.g., mangrove communities without Rhizophora until the middle Eocene), and essentially modern versions of present-day New World ecosystems. As a first approximation, the fossil record suggests that early versions of aquatic communities (in the sense of including a prominent angiosperm component) appeared early in the Middle to Late Cretaceous, the lowland neotropical rainforest at 64 Ma (well developed by 58-55 Ma), shrubland/chaparral-woodland-savanna and grasslands around the middle Miocene climatic optimum at ca. 15-13 Ma, deserts in the middle Miocene/early Pliocene at ca. 10 Ma, significant tundra at ca. 7-5 Ma, and alpine tundra (páramo) shortly thereafter when cooling temperatures were augmented by high elevations attained, for example, in the Andes<10 Ma and especially after 7-6 Ma.

Deer browsing and soil disturbance induce cascading effects on plant communities: a multilevel path analysis

Understanding how large herbivores shape plant diversity patterns is an important challenge in community ecology, especially because many ungulate populations in the northern hemisphere have recently expanded. Because species within plant communities can exhibit strong interactions (e.g., competition, facilitation), selective foraging by large herbivores is likely not only to affect the abundance of palatable species, but also to induce cascading effects across entire plant communities. To investigate these possibilities, we first tested the effects of deer browsing and soil disturbance on herbaceous plant diversity patterns in boreal forest, using standard analyses of variance. Second, we evaluated direct and indirect effects of deer browsing and soil disturbance on the small-scale richness of herbaceous taxa using a multilevel path analysis approach. The first set of analyses showed that deer browsing and soil disturbance influenced herb richness. Path analyses revealed that deer browsing and soil disturbance influenced richness via complex chains of interactions, involving dominant (i.e., the most abundant) browsing-tolerant (DBT) taxa and white birch (Betula papyrifera), a species highly preferred by white-tailed deer (Odocoileus virginianus). We found no evidence that an increase of white birch in fenced quadrats was the direct cause of a decrease in herb richness. However, we found strong evidence that a higher abundance of DBT taxa (i.e., graminoids and Circium arvense), both in fenced and unfenced quadrats, increased herb layer richness. We propose an empirical model in which competitive interactions between white birch and DBT taxa regulate the strength of facilitative relationships between the abundance of DBT taxa and herb richness. In this model, deer browsing and the intensity of soil disturbance initiate a complex chain of cascading effects in boreal plant communities by controlling the abundance of white birch.

Floristic composition, beta diversity, and nestedness of reference sites for restoration of xeroriparian areas

In restoration ecology, reference sites serve as models for areas to be restored and can provide a standard of comparison for restoration project outcomes. When reference sites are located a relatively long distance from associated restoration projects, differences in climate, disturbance history, and biogeography can increase beta diversity and may decrease the relevance of reference sites. Variation in factors at the scale of individual reference sites such as patch size, microclimate, barriers to dispersal, or soil chemistry can result in reference site species composition that is a nested subset of the regional species pool. In the Western United States, restoration of riparian areas, particularly those occupied by Tamarix spp., has become a priority; however, little is known about suitable native replacement vegetation communities for relatively dry and saline riparian terraces that comprise many of the sites where Tamarix is removed prior to restoration activities. We studied plant communities on riparian terraces along five rivers in New Mexico, USA, to (1) determine whether the floristic composition of reference sites can be predicted by easily measured soil variables such as pH, salinity (electric conductivity), and texture; (2) examine the extent of distance decay in the compositional similarity of xeroriparian plant communities in the southwestern United States; and (3) determine the degree of nestedness in xeroriparian plant communities in relationship to soil variables. We found that sites clustered into groups based largely on variation in soil salinity and texture. Vegetation across all sites was highly nested with dominant, salt-tolerant species found on most soil groups and salt-intolerant subordinate species restricted to low-salinity soils. The identity of subordinate species was largely site dependent, causing all sites to have the same low degree of similarity regardless of the distance between them. We conclude that, when planning restoration projects on dry and saline riparian sites, soil salinity and texture are good predictors of which species will be most suited to the area being restored, but a candidate species pool should be developed from the nearest possible reference sites, particularly for subordinate species.

Manipulative lowering of the water table during summer does not affect CO2 emissions and uptake in a fen in Germany

We simulated the effect of prolonged dry summer periods by lowering the water table on three manipulation plots (D(1-3)) in a minerotrophic fen in southeastern Germany in three years (2006-2008). The water table at this site was lowered by drainage and by excluding precipitation; three nonmanipulated control plots (C(1-3)) served as a reference. We found no significant differences in soil respiration (R(Soil)), gross primary production (GPP), or aboveground respiration (R(AG)) between the C(1-3) and D(1-3) plots in any of the measurement years. The water table on the control plots was naturally low, with a median water table (2006-2008) of 8 cm below the surface, and even lower during summer when respiratory activity was highest, with median values (C(1-3)) between 11 and 19 cm below the surface. If it is assumed that oxygen availability in the uppermost 10 cm was not limited by the location of the water table, manipulative lowering of the water table most likely increased oxygen availability only in deeper peat layers where we expect R(Soil) to be limited by poor substrate quality rather than anoxia. This could explain the lack of a manipulation effect. In a second approach, we estimated the influence of the water table on R(Soil) irrespective of treatment. The results showed a significant correlation between R(Soil) and water table, but with R(Soil) decreasing at lower water tables rather than increasing. We thus conclude that decomposition in the litter layer is not limited by waterlogging in summer, and deeper peat layers bear no significant decomposition potential due to poor substrate quality. Consequently, we do not expect enhanced C losses from this site due to increasing frequency of dry summers. Assimilation and respiration of aboveground vegetation were not affected by water table fluctuations between 10 and >60 cm depth, indicating the lack of stress resulting from either anoxia (high water table) or drought (low water table).

Plant species richness, identity and productivity differentially influence key groups of microbes in grassland soils of contrasting fertility

The abundance of microbes in soil is thought to be strongly influenced by plant productivity rather than by plant species richness per se. However, whether this holds true for different microbial groups and under different soil conditions is unresolved. We tested how plant species richness, identity and biomass influence the abundances of arbuscular mycorrhizal fungi (AMF), saprophytic bacteria and fungi, and actinomycetes, in model plant communities in soil of low and high fertility using phospholipid fatty acid analysis. Abundances of saprophytic fungi and bacteria were driven by larger plant biomass in high diversity treatments. In contrast, increased AMF abundance with larger plant species richness was not explained by plant biomass, but responded to plant species identity and was stimulated by Anthoxantum odoratum. Our results indicate that the abundance of saprophytic soil microbes is influenced more by resource quantity, as driven by plant production, while AMF respond more strongly to resource composition, driven by variation in plant species richness and identity. This suggests that AMF abundance in soil is more sensitive to changes in plant species diversity per se and plant species composition than are abundances of saprophytic microbes.