Phylogenetic patterns differ for native and exotic plant communities across a richness gradient in Northern California

Aim Increasingly, ecologists are using evolutionary relationships to infer the mechanisms of community assembly. However, modern communities are being invaded by non‐indigenous species. Since natives have been associated with one another through evolutionary time, the forces promoting character and niche divergence should be high. On the other hand, exotics have evolved elsewhere, meaning that conserved traits may be more important in their new ranges. Thus, co‐occurrence over sufficient time‐scales for reciprocal evolution may alter how phylogenetic relationships influence assembly. Here, we examined the phylogenetic structure of native and exotic plant communities across a large‐scale gradient in species richness and asked whether local assemblages are composed of more or less closely related natives and exotics and whether phylogenetic turnover among plots and among sites across this gradient is driven by turnover in close or distant relatives differentially for natives and exotics. Location Central and northern California, USA. Methods We used data from 30 to 50 replicate plots at four sites and constructed a maximum likelihood molecular phylogeny using the genes: matK, rbcl, ITS1 and 5.8s. We compared community‐level measures of native and exotic phylogenetic diversity and among‐plot phylobetadiversity. Results There were few exotic clades, but they tended to be widespread. Exotic species were phylogenetically clustered within communities and showed low phylogenetic turnover among communities. In contrast, the more species‐rich native communities showed higher phylogenetic dispersion and turnover among sites. Main conclusions The assembly of native and exotic subcommunities appears to reflect the evolutionary histories of these species and suggests that shared traits drive exotic patterns while evolutionary differentiation drives native assembly. Current invasions appear to be causing phylogenetic homogenization at regional scales.     

From plant neighbourhood to landscape scales: how grazing modifies native and exotic plant species richness in grassland

The interactive effect of grazing and soil resources on plant species richness and coexistence has been predicted to vary across spatial scales. When resources are not limiting, grazing should reduce competitive effects and increase colonisation and richness at fine scales. However, at broad scales richness is predicted to decline due to loss of grazing intolerant species. We examined these hypotheses in grasslands of southern Australia that varied in resources and ungulate grazing intensity since farming commenced 170 years ago. Fine-scale species richness was slightly greater in more intensively grazed upper slope sites with high nutrients but low water supply compared to those that were moderately grazed, largely due to a greater abundance of exotic species. At broader scales, exotic species richness declined with increasing grazing intensity whether nutrients or water supply were low or high. Native species richness declined at all scales in response to increasing grazing intensity and greater resource supply. Grazing also reduced fine-scale heterogeneity in native species richness and although exotics were also characterised by greater heterogeneity at fine scales, grazing effects varied across scales. In these grasslands patterns of plant species richness did not match predictions at all scales and this is likely to be due to differing responses of native and exotic species and their relative abundance in the regional species pool. Over the past 170 years intolerant native species have been eliminated from areas that are continually and heavily grazed, whereas transient, light grazing increases richness of both exotics and natives. The results support the observation that the processes and scales at which they operate differ between coevolved ungulate—grassland systems and those in transition due to recent invasion of herbivores and associated plant species.     

Comparison between actin filament models: coarse-graining reveals essential differences

The interconversion of actin between monomeric and polymeric forms is a fundamental process in cell biology that is incompletely understood, in part because there is no high-resolution structure for filamentous actin. Several models have been proposed recently; identifying structural and dynamic differences between them is an essential step toward understanding actin dynamics. We compare three of these models, using coarse-grained analysis of molecular dynamics simulations to analyze the differences between them and evaluate their relative stability. Based on this analysis, we identify key motions that may be associated with polymerization, including a potential energetic barrier in the process. We also find that actin subunits are polymorphic; during simulations they assume a range of configurations remarkably similar to those seen in recent cryoEM images.     

Comparison of computational models for assessing conservation of gene expression across species

Assessing conservation/divergence of gene expression across species is important for the understanding of gene regulation evolution. Although advances in microarray technology have provided massive high-dimensional gene expression data, the analysis of such data is still challenging. To date, assessing cross-species conservation of gene expression using microarray data has been mainly based on comparison of expression patterns across corresponding tissues, or comparison of co-expression of a gene with a reference set of genes. Because direct and reliable high-throughput experimental data on conservation of gene expression are often unavailable, the assessment of these two computational models is very challenging and has not been reported yet. In this study, we compared one corresponding tissue based method and three co-expression based methods for assessing conservation of gene expression, in terms of their pair-wise agreements, using a frequently used human-mouse tissue expression dataset. We find that 1) the co-expression based methods are only moderately correlated with the corresponding tissue based methods, 2) the reliability of co-expression based methods is affected by the size of the reference ortholog set, and 3) the corresponding tissue based methods may lose some information for assessing conservation of gene expression. We suggest that the use of either of these two computational models to study the evolution of a gene's expression may be subject to great uncertainty, and the investigation of changes in both gene expression patterns over corresponding tissues and co-expression of the gene with other genes is necessary.     

Exotic species richness and native species endemism increase the impact of exotic species on islands

Aim Exotic species pose one of the most significant threats to biodiversity, especially on islands. The impacts of exotic species vary in severity among islands, yet little is known about what makes some islands more susceptible than others. Here we determine which characteristics of an island influence how severely exotic species affect its native biota. Location We studied 65 islands and archipelagos from around the world, ranging from latitude 65° N to 54° S. Methods We compiled a global database of 10 island characteristics for 65 islands and determined the relative importance of each characteristic in predicting the impact of exotic species using multivariate modelling and hierarchical partitioning. We defined the impact of exotic species as the number of bird, amphibian and mammal (BAM) species listed by the International Union for Conservation of Nature (IUCN) as threatened by exotics, relative to the total number of BAM species on that island. Results We found that the impact of exotic species is more severe on islands with more exotic species and a greater proportion of native species that are endemic. Unexpectedly, the level of anthropogenic disturbance did not influence an island's susceptibility to the impacts of exotic species. Main conclusions By coupling our results with studies on the introduction and establishment of exotic species, we conclude that colonization pressure, or invasion opportunities, influences all stages of the invasion process. However, species endemism, the other important factor determining the impact of exotic species, is not known to contribute to introduction and establishment success on islands. This demonstrates that different factors correlate with the initial stages of the invasion process and the subsequent impacts of those invaders, highlighting the importance of studying the impacts of exotic species directly. Our study helps identify islands that are at risk of impact by exotics and where investment should focus on preventing further invasions.     

Opposite relationships between invasibility and native species richness at patch versus landscape scales

Using a nested plot design in oak forests in Minnesota, USA we measured the percent cover of young individuals of an exotic invading shrub, Rhamnus cathartica (common buckthorn), to assess the relationships at two scales between invasibility, propagule and light availability, and richness and cover of native species. Comparing patches (1 m²) within 17 Quercus -dominated stands (each 1 ha, within a 100 km by 150 km area), cover of young R. cathartica was negatively related to both species richness and cover of native species. In 1 m² patches, native cover was positively associated with native richness and thus cover-related competition was a likely mechanism by which richness influenced R. cathartica . At the landscape scale (comparing the aggregate stand-scale metrics among the 17 stands), native cover and richness were still positively related, but had opposite relationships with R. cathartica cover. R. cathartica cover was positively related to species richness and negatively related to native species cover. The observed switch at different scales from a positive to a negative relationship between R. cathartica cover and native richness supported the hypothesized scale dependence of these relations. Propagule pressure, which we estimated by measuring the size of nearby mature R. cathartica shrubs, had a large positive effect on R. cathartica seedling cover at the landscape scale. These results suggest that landscape patterns of invasion may be best understood in light of the combination of many factors including native diversity, native cover, and propagule pressure.     

BIODIVERSITY RESEARCH: Native‐exotic species richness relationships across spatial scales and biotic homogenization in wetland plant communities of Illinois,USA

Aim To examine native‐exotic species richness relationships across spatial scales and corresponding biotic homogenization in wetland plant communities. Location Illinois, USA. Methods We analysed the native‐exotic species richness relationship for vascular plants at three spatial scales (small, 0.25 m² of sample area; medium, 1 m² of sample area; large, 5 m² of sample area) in 103 wetlands across Illinois. At each scale, Spearman’s correlation coefficient between native and exotic richness was calculated. We also investigated the potential for biotic homogenization by comparing all species surveyed in a wetland community (from the large sample area) with the species composition in all other wetlands using paired comparisons of their Jaccard’s and Simpson’s similarity indices. Results At large and medium scales, native richness was positively correlated with exotic richness, with the strength of the correlation decreasing from the large to the medium scale; at the smallest scale, the native‐exotic richness correlation was negative. The average value for homogenization indices was 0.096 and 0.168, using Jaccard’s and Simpson’s indices, respectively, indicating that these wetland plant communities have been homogenized because of invasion by exotic species. Main Conclusions Our study demonstrated a clear shift from a positive to a negative native‐exotic species richness relationship from larger to smaller spatial scales. The negative native‐exotic richness relationship that we found is suggested to result from direct biotic interactions (competitive exclusion) between native and exotic species, whereas positive correlations likely reflect the more prominent influence of habitat heterogeneity on richness at larger scales. Our finding of homogenization at the community level extends conclusions from previous studies having found this pattern at much larger spatial scales. Furthermore, these results suggest that even while exhibiting a positive native‐exotic richness relationship, community level biotas can/are still being homogenized because of exotic species invasion.     

Grazing and an invasive grass confound spatial pattern of exotic and native grassland plant species richness

Previous work has shown exotic and native plant species richness are negatively correlated at fine spatial scales and positively correlated at broad spatial scales. Grazing and invasive plant species can influence plant species richness, but the effects of these disturbances across spatial scales remain untested. We collected species richness data for both native and exotic plants from five spatial scales (0.5–3000 m²) in a nested, modified Whittaker plot design from severely grazed and ungrazed North American tallgrass prairie. We also recorded the abundance of an abundant invasive grass, tall fescue (Schedonorus phoenix (Scop.) Holub), at the 0.5-m² scale. We used linear mixed-effect regression to test relationships between plant species richness, tall fescue abundance, and grazing history at five spatial scales. At no scale was exotic and native species richness linearly related, but exotic species richness at all scales was greater in grazed tracts than ungrazed tracts. Native species richness declined with increasing tall fescue abundance at all five spatial scales, but exotic species richness increased with tall fescue abundance at all but the broadest spatial scales. Severe grazing did not reduce native species richness at any spatial scale. We posit that invasion of tall fescue in this working landscape of originally native grassland plants modifies species richness-spatial scale relationships observed in less disturbed systems. Tall fescue invasion constitutes a unique biotic effect on plant species richness at broad spatial scales.     

Coherence of terrestrial vertebrate species richness with external drivers across scales and taxonomic groups

Aim

Understanding connections between environment and biodiversity is crucial for conservation, identifying causes of ecosystem stress, and predicting population responses to changing environments. Explaining biodiversity requires an understanding of how species richness and environment covary across scales. Here, we identify scales and locations at which biodiversity is generated and correlates with environment.

Location

Full latitudinal range per continent.

Time Period

Present day.

Major Taxa Studied

Terrestrial vertebrates: all mammals, carnivorans, bats, songbirds, hummingbirds, amphibians.

Methods

We describe the use of wavelet power spectra, cross-power and coherence for identifying scale-dependent trends across Earth's surface. Spectra reveal scale- and location-dependent coherence between species richness and topography (E), mean annual precipitation (Pn), temperature (Tm) and annual temperature range (ΔT).

Results

>97% of species richness of taxa studied is generated at large scales, that is, wavelengths $\gtrsim {10}^3$ km, with 30%–69% generated at scales $\gtrsim {10}^4$ km. At these scales, richness tends to be highly coherent and anti-correlated with E and ΔT, and positively correlated with Pn and Tm. Coherence between carnivoran richness and ΔT is low across scales, implying insensitivity to seasonal temperature variations. Conversely, amphibian richness is strongly anti-correlated with ΔT at large scales. At scales $\lesssim {10}^3$ km, examined taxa, except carnivorans, show highest richness within the tropics. Terrestrial plateaux exhibit high coherence between carnivorans and E at scales $\sim {10}^3$ km, consistent with contribution of large-scale tectonic processes to biodiversity. Results are similar across different continents and for global latitudinal averages. Spectral admittance permits derivation of rules-of-thumb relating long-wavelength environmental and species richness trends.

Main Conclusions

Sensitivities of mammal, bird and amphibian populations to environment are highly scale dependent. At large scales, carnivoran richness is largely independent of temperature and precipitation, whereas amphibian richness correlates strongly with precipitation and temperature, and anti-correlates with temperature range. These results pave the way for spectral-based calibration of models that predict biodiversity response to climate change scenarios.     

Comparative phosphoproteomics reveals evolutionary and functional conservation of phosphorylation across eukaryotes

Background  

Reversible phosphorylation of proteins is involved in a wide range of processes, ranging from signaling cascades to regulation of protein complex assembly. Little is known about the structure and evolution of phosphorylation networks. Recent high-throughput phosphoproteomics studies have resulted in the rapid accumulation of phosphopeptide datasets for many model organisms. Here, we exploit these novel data for the comparative analysis of phosphorylation events between different species of eukaryotes.     

The distribution of native and exotic plants in a naturally fragmented sagebrush-steppe landscape

We tested two general hypotheses for the diversity of native and exotic plants in an undisturbed, naturally fragmented sagebrush-steppe landscape in SE Idaho, USA, evaluating whether the MacArthur–Wilson hypothesis of island biogeography or a suite of environmental variables explained the distributions of native and exotic plants. We also tested a third hypothesis, which incorporated assumptions about the origin of exotic plants and their interaction with native plants. Of the three hypotheses we tested, the hypothesis that included exotic species best explained the diversity of the native plant community. The MacArthur–Wilson model of island biogeography did not explain the diversity of native (R ² = 0.13) or exotic plants well (R ² = 0.11), and the model fit the data poorly. A model of environmental variables better explained the diversity of native (R ² = 0.48) and exotic plants (R ² = 0.57), but it also fit the data poorly. Instead, proximity to a railroad explained the cover (R ² = 0.59) and richness of exotic plants (R ² = 0.63), which then explained the species richness of native plants (R ² = 0.34), and the model fit was adequate and had the lowest AIC value. This suggests that the transportation corridor had a significant, though indirect, effect on the native plant community, even in this undisturbed area. Moreover, explained variance, model fit, and the AIC model selection criteria favored the model with the railroad and exotic species over the M–W and environmental models. Since the habitat patches we studied were largely undisturbed by people and their activities, our results further suggest that the transportation corridor influenced the distribution of exotic plants by serving as a vector for colonization, rather than as a source of disturbance. Additionally, the results suggest that exotic plant species have had a negative effect on the diversity of the native plant community and have changed its composition. The results also support the inference that the nascent exotic plant community is influenced by source-sink (Pulliam in Am Nat 132:652–661, 1988) and assembly dynamics. In contrast, the native plant community appears to be more strongly influenced by environmental conditions associated with an elevational gradient, but there is evidence that the native community also has undergone directional change in species composition, associated with the invasion by non-native species.     

Associations between a highly invasive species and native macrophytes differ across spatial scales

The association between invasive and native species varies across spatial scales and is affected by phylogenetic relatedness, but these issues have rarely been addressed in aquatic ecosystems. In this study, we used a non-native, highly invasive species of Poaceae (tropical signalgrass) to test the hypotheses that (i) tropical signalgrass success correlates negatively with success of most native species of macrophytes at fine spatial scales, but its success correlates positively or at random with natives at coarse spatial scales, and that (ii) tropical signalgrass is less associated with native species belonging to the family Poaceae than with species belonging to other families (Darwin’s naturalization hypothesis). We used a dataset obtained at fine (0.25 m²) and coarse (ca. 1,000 m²) scales. The presence/absence of all species was recorded at both scales, and their biomass was also measured at the fine scale. We tested the association between tropical signalgrass biomass and individual native species with logistic regressions at the fine scale, and using the T-score index between tropical signalgrass and each native species at both scales. The likelihood of the occurrence of six species (submersed and free-floating) was negatively affected by tropical signalgrass biomass at the fine scale. T-scores showed that three species were less associated with tropical signalgrass than expected by chance, but 22 species co-occurred more than expected by chance at the coarse scale. Associations between species of Poaceae and tropical signalgrass were null at the fine scale, but were positive or null at the coarse scale. In addition to showing that spatial scale affects the patterns of association among the non-native and individual native species, our results indicate that phylogeny did not explain associations between the invasive and native macrophytes, at both scales.     

Resource diversity and provenance underpin spatial patterns in functional diversity across native and exotic species

Functional diversity metrics are increasingly used to augment or replace taxonomic diversity metrics to deliver more mechanistic insights into community structure and function. Metrics used to describe landscape structure and characteristics share many of the same limitations as taxonomy‐based metrics, particularly their reliance on anthropogenically defined typologies with little consideration of structure, management, or function. However, the development of alternative metrics to describe landscape characteristics has been limited. Here, we extend the functional diversity framework to characterize landscapes based on the diversity of resources available across habitats present. We then examine the influence of resource diversity and provenance on the functional diversities of native and exotic avian communities in New Zealand. Invasive species are increasingly prevalent and considered a global threat to ecosystem function, but the characteristics of and interactions between sympatric native and exotic communities remain unresolved. Understanding their comparative responses to environmental change and the mechanisms underpinning them is of growing importance in predicting community dynamics and changing ecosystem function. We use (i) matrices of resource use (species) and resource availability (habitats) and (ii) occurrence data for 62 native and 25 exotic species and 19 native and 13 exotic habitats in 2015 10 × 10 km quadrats to examine the relationship between native and exotic avian and landscape functional diversity. The numbers of species in, and functional diversities of, native and exotic communities were positively related. Each community displayed evidence of environmental filtering, but it was significantly stronger for exotic species. Less environmental filtering occurred in landscapes providing a more diverse combination of resources, with resource provenance also an influential factor. Landscape functional diversity explained a greater proportion of variance in native and exotic community characteristics than the number of habitat types present. Resource diversity and provenance should be explicitly accounted for when characterizing landscape structure and change as they offer additional mechanistic understanding of the links between environmental filtering and community structure. Manipulating resource diversity through the design and implementation of management actions could prove a powerful tool for the delivery of conservation objectives, be they to protect native species, control exotic species, or maintain ecosystem service provision.     

A stochastic model for integrating changes in species richness and community similarity across spatial scales

Human activities have elevated the extinction of natural populations as well as the invasion of new areas by non-native species. These dual processes of invasion and extinction may change the richness and similarity of communities, but the form these changes take is likely to depend on the manner in which invasions and extinctions occur and the spatial scale at which the changes are measured. Here, we explore the influence of differing patterns of extinction and invasion on the similarity and richness of a meta-community. In particular, we model simple stochastic processes analogous to realistic modes of human-mediated introduction of non-native species and range expansion by native species. We show that different modes of invasion and extinction can produce very different changes in diversity, and that the relative magnitude of these changes depends both on where in the meta-community diversity is measured and the degree of initial species aggregation. At any spatial scale of measurement, changes in the richness and similarity of communities following invasion and extinction are not necessarily strongly coupled: relatively large increases in richness may or may not also be associated with relatively large increases in similarity among communities. Thus, in real systems, the influence of human-induced invasions and extinctions on diversity will depend on both the precise mode of these processes (especially invasion), and how species populations are distributed across space.     

Environmental heterogeneity as a universal driver of species richness across taxa,biomes and spatial scales

Environmental heterogeneity is regarded as one of the most important factors governing species richness gradients. An increase in available niche space, provision of refuges and opportunities for isolation and divergent adaptation are thought to enhance species coexistence, persistence and diversification. However, the extent and generality of positive heterogeneity–richness relationships are still debated. Apart from widespread evidence supporting positive relationships, negative and hump‐shaped relationships have also been reported. In a meta‐analysis of 1148 data points from 192 studies worldwide, we examine the strength and direction of the relationship between spatial environmental heterogeneity and species richness of terrestrial plants and animals. We find that separate effects of heterogeneity in land cover, vegetation, climate, soil and topography are significantly positive, with vegetation and topographic heterogeneity showing particularly strong associations with species richness. The use of equal‐area study units, spatial grain and spatial extent emerge as key factors influencing the strength of heterogeneity–richness relationships, highlighting the pervasive influence of spatial scale in heterogeneity–richness studies. We provide the first quantitative support for the generality of positive heterogeneity–richness relationships across heterogeneity components, habitat types, taxa and spatial scales from landscape to global extents, and identify specific needs for future comparative heterogeneity–richness research.