A phylogenetic approach identifies patterns of beta diversity and floristic subregions of the Qinghai-Tibet Plateau.

Patterns of taxonomic and phylogenetic beta diversity and their relationships with environmental correlates can help reveal the origin and evolutionary history of regional biota. The Qinghai-Tibet Plateau (QTP) harbors an exceptionally diverse flora, however, a phylogenetic perspective has rarely been used to investigate its beta diversity and floristic regions. In this study, we used a phylogenetic approach to identify patterns of beta diversity and quantitatively delimit floristic regions on the Qinghai-Tibet Plateau. We also examined the relationships between multifaceted beta diversity, geographical distance, and climatic difference, and evaluated the relative importance of various factors (i.e., climate, topography and history) in shaping patterns of beta diversity. Sørensen dissimilarity indices indicated that patterns of species turnover among sites dominated the QTP. We also found that patterns of both taxonomic and phylogenetic beta diversity were significantly related to geographical distance and climatic difference. The environmental factors that contributed most to these patterns of beta diversity include annual precipitation, mean annual temperature, climatic gradients and climatic instability. Hierarchical dendrograms of dissimilarity and non-metric multidimensional scaling ordination based on phylogenetic beta diversity data identified ten floristic subregions in the QTP. Our results suggest that the contemporary environment and historical climate changes have filtered species composition among sites and eventually determined beta diversity patterns of plants in the QTP.

Biotic homogenisation and differentiation as directional change in beta diversity: synthesising driver-response relationships to develop conceptual models across ecosystems.

Biotic homogenisation is defined as decreasing dissimilarity among ecological assemblages sampled within a given spatial area over time. Biotic differentiation, in turn, is defined as increasing dissimilarity over time. Overall, changes in the spatial dissimilarities among assemblages (termed 'beta diversity') is an increasingly recognised feature of broader biodiversity change in the Anthropocene. Empirical evidence of biotic homogenisation and biotic differentiation remains scattered across different ecosystems. Most meta-analyses quantify the prevalence and direction of change in beta diversity, rather than attempting to identify underlying ecological drivers of such changes. By conceptualising the mechanisms that contribute to decreasing or increasing dissimilarity in the composition of ecological assemblages across space, environmental managers and conservation practitioners can make informed decisions about what interventions may be required to sustain biodiversity and can predict potential biodiversity outcomes of future disturbances. We systematically reviewed and synthesised published empirical evidence for ecological drivers of biotic homogenisation and differentiation across terrestrial, marine, and freshwater realms to derive conceptual models that explain changes in spatial beta diversity. We pursued five key themes in our review: (i) temporal environmental change; (ii) disturbance regime; (iii) connectivity alteration and species redistribution; (iv) habitat change; and (v) biotic and trophic interactions. Our first conceptual model highlights how biotic homogenisation and differentiation can occur as a function of changes in local (alpha) diversity or regional (gamma) diversity, independently of species invasions and losses due to changes in species occurrence among assemblages. Second, the direction and magnitude of change in beta diversity depends on the interaction between spatial variation (patchiness) and temporal variation (synchronicity) of disturbance events. Third, in the context of connectivity and species redistribution, divergent beta diversity outcomes occur as different species have different dispersal characteristics, and the magnitude of beta diversity change associated with species invasions also depends strongly on alpha and gamma diversity prior to species invasion. Fourth, beta diversity is positively linked with spatial environmental variability, such that biotic homogenisation and differentiation occur when environmental heterogeneity decreases or increases, respectively. Fifth, species interactions can influence beta diversity via habitat modification, disease, consumption (trophic dynamics), competition, and by altering ecosystem productivity. Our synthesis highlights the multitude of mechanisms that cause assemblages to be more or less spatially similar in composition (taxonomically, functionally, phylogenetically) through time. We consider that future studies should aim to enhance our collective understanding of ecological systems by clarifying the underlying mechanisms driving homogenisation or differentiation, rather than focusing only on reporting the prevalence and direction of change in beta diversity, per se.

Two dominant forms of multisite similarity decline - Their origins and interpretation.

The number of species shared by two or more sites is a fundamental measure of spatial variation in species composition. As more sites are included in the comparison of species composition, the average number of species shared across them declines, with a rate increasingly dependent on only the most widespread species. In over 80% of empirical communities, models of decline in shared species across multiple sites (multisite similarity decline) follow one of two distinct forms. An exponential form is assumed to reflect stochastic assembly and a power law form niche-based sorting, yet these explanations are largely untested, and little is known of how the two forms arise in nature. Using simulations, we first show that the distribution of the most widespread species largely differentiates the two forms, with the power law increasingly favored where such species occupy more than ~75% of sites. We reasoned the less cosmopolitan distribution of widespread species within exponential communities would manifest as differences in community biodiversity properties, specifically more aggregated within-species distributions, less even relative abundance distributions, and weaker between-species spatial associations. We tested and largely confirmed these relationships using 80 empirical datasets, suggesting that the form of multisite similarity decline offers a basis to predict how landscape-scale loss or gain of widespread species is reflected in different local-scale community structures. Such understanding could, for example, be used to predict changes in local-scale competitive interactions following shifts in widespread species' distributions. We propose multiple explanations for the origin of exponential decline, including high among-site abiotic variation, sampling of highly specialized (narrow niche width) taxa, and strong dispersal limitation. We recommend these are evaluated as alternative hypotheses to stochastic assembly.

Species accumulation in small-large vs large-small order: more species but not all species?

Although groups of small habitat patches often support more species than large patches of equal total area, their biodiversity value remains controversial. An important line of evidence in this debate compares species accumulation curves, where patches are ordered from small-large and large-small (aka 'SLOSS analysis'). However, this method counts species equally and is unable to distinguish patch size dependence in species' occupancies. Moreover, because of the species-area relationship, richness differences typically only contribute to accumulation in small-large order, maximizing the probability of adding species in this direction. Using a null model to control for this, I tested 202 published datasets from archipelagos, habitat islands and fragments for patch size dependence in species accumulation and compared conclusions regarding relative species accumulation with SLOSS analysis. Relative to null model expectations, species accumulation was on average 2.7% higher in large-small than small-large order. The effect was strongest in archipelagos (5%), intermediate for fragments (1.5%) and smallest for habitat islands (1.1%). There was no difference in effect size among taxonomic groups, but each shared this same trend. Results suggest most meta-communities include species that either prefer, or depend upon, larger habitat patches. Relative to SLOSS analysis, null models found lower frequency of greater small-patch importance for species representation (e.g., for fragments: 69 vs 16% respectively) and increased frequency for large patches (fragments: 3 vs 25%). I suggest SLOSS analysis provides unreliable inference on species accumulation and the outcome largely depends on island species-area relationships, not the relative diversity value of small vs large patches.

The Effects of Species Abundance, Spatial Distribution, and Phylogeny on a Plant-Ectomycorrhizal Fungal Network.

Plant and root fungal interactions are among the most important belowground ecological interactions, however, the mechanisms underlying pairwise interactions and network patterns of rhizosphere fungi and host plants remain unknown. We tested whether neutral process or spatial constraints individually or jointly best explained quantitative plant-ectomycorrhizal fungal network assembly in a subtropical forest in southern China. Results showed that the observed plant-ectomycorrhizal fungal network had low connectivity, high interaction evenness, and an intermediate level of specialization, with nestedness and modularity both greater than random expectation. Incorporating information on the relative abundance and spatial overlap of plants and fungi well predicted network nestedness and connectance, but not necessarily explained other network metrics such as specificity. Spatial overlap better predicted pairwise species interactions of plants and ectomycorrhizal fungi than species abundance or a combination of species abundance and spatial overlap. There was a significant phylogenetic signal on species degree and interaction strength for ectomycorrhizal fungal but not for plant species. Our study suggests that neutral processes (species abundance matching) and niche/dispersal-related processes (implied by spatial overlap and phylogeny) jointly drive the shaping of a plant-ectomycorrhizal fungal network.

Rare, common, alien and native species follow different rules in an understory plant community.

Biological invasions are a leading threat to biodiversity globally. Increasingly, ecosystems experience multiple introductions, which can have significant effects on patterns of diversity. The way these communities assemble will depend partly on whether rare and common alien species respond to environmental predictors in the same manner as rare and common native species, but this is not well understood. To examine this question across four national parks in south-eastern Australia, we sampled the understory plant community of eucalypt-dominated dry forest subject to multiple plant introductions. The drivers of diversity and turnover in alien and native species of contrasting frequency of occurrence (low, intermediate, and high) were each tested individually. We found alien species diversity and turnover were both strongly associated with abiotic conditions (e.g., soil pH), while distance had little influence because of the greater extent of occurrence and more homogeneous composition of common aliens. In contrast, native species diversity was not associated with abiotic conditions and their turnover was as strongly influenced by distance as by abiotic conditions. In both alien and native species, however, the most important predictors of turnover changed with frequency of occurrence. Although local coexistence appears to be facilitated by life history trade-offs, species richness of aliens and natives was negatively correlated and native species might face greater competition in areas with more neutral soils (e.g., pH > ~5.5) where alien richness and relative frequency were both highest. We conclude that diversity and turnover in the generally more widespread alien species are mainly driven by species sorting along an environmental gradient associated with pH and nutrient availability, whereas turnover of native species is driven by more neutral processes associated with dispersal limitation. We show alien and native plant species respond to different environmental factors, as do rare and common species within each component.

Direct effects of selection on aboveground biomass contrast with indirect structure-mediated effects of complementarity in a subtropical forest.

Understanding the multiple biotic and abiotic controls of aboveground biomass (AGB) is important for projecting the consequences of global change and to effectively manage carbon storage. Although large-scale studies have identified the major environmental and biological controls of AGB, drivers of local-scale variation are less well known. Additionally, involvement of multiple causal paths and scale dependence in effect sizes potentially confounds comparisons among studies differing in methodology and sampling grain. We tested for scale dependence in evidence supporting selection, complementarity and environmental factors as the main determinants of AGB variation over a 50 ha study extent in subtropical China, modelling this at four sampling grains (0.01, 0.04, 0.25 and 1 ha). At each grain, we used piecewise structural equation models to quantify the direct and indirect effects of environmental (topographic and edaphic properties) and forest attributes (structure, diversity and functional traits) on AGB, while controlling for spatial autocorrelation. Direct scale-invariant effects on AGB were evident for structure and community-mean traits, supporting dominance of selection effects. However, diversity had strong indirect effects on AGB via forest structure, particularly at larger sampling grains (≥ 0.25 ha), while direct effects only emerged at the smallest grain size (0.01 ha). The direct and indirect effects of edaphic and topographic factors were also important for explaining both forest attributes and AGB across all scales. Although selection effects appeared to be more influential on ecosystem function, ignoring indirect causal pathways for diversity via structural attributes risks overlooking the importance of complementarity on ecosystem functioning, particularly as sampling grain increases.

Effects of host phylogeny, habitat and spatial proximity on host specificity and diversity of pathogenic and mycorrhizal fungi in a subtropical forest.

Soil plant-pathogenic (PF) and mycorrhizal fungi (MF) are both important in maintaining plant diversity, for example via host-specialized effects. However, empirical knowledge on the degree of host specificity and possible factors affecting the fungal assemblages is lacking. We identified PF and MF in fine roots of 519 individuals across 45 subtropical tree species in southern China in order to quantify the importance of host phylogeny (including via its effects on functional traits), habitat and space in determining fungal communities. We also compared host specificity in PF and MF at different host-phylogenetic scales. In both PF and MF, host phylogeny independently accounted for > 19% of the variation in fungal richness and composition, whereas environmental and spatial factors each explained no more than 4% of the variation. Over 77% of the variation explained by phylogeny was attributable to covariation in plant functional traits. Host specificity was phylogenetically scale-dependent, being stronger in PF than in MF at low host-phylogenetic scales (e.g. within genus) but similar at larger scales. Our study suggests that host-phylogenetic effects dominate the assembly of both PF and MF communities, resulting from phylogenetically clustered plant traits. The scale-dependent host specificity implies that PF were specialized at lower-level and MF at higher-level host taxa.

Loss of only the smallest patches will reduce species diversity in most discrete habitat networks.

Under many global-change scenarios, small habitat patches are the most vulnerable to destruction. For example, smaller ponds are at greater risk in a drying climate and their loss would remove any obligate aquatic individuals present. We asked what proportional loss of species diversity from metacommunities comprised of discrete habitat patches should be expected from attrition (complete loss) of only the smallest patches under such a premise. We analyzed 175 published datasets for different taxonomic groups (vertebrates, invertebrates, and plants) and habitat types (islands, habitat islands, and fragments). We simulated the destruction of only the smallest patches to an approximate 20% of total area (range: 15.2%-24.2%) and analyzed species loss. Mean [± 95% CI] species loss was 12.7% [10.8, 14.6], although 18.3% of datasets lost no species. Four broad patterns of species loss were evident, reflecting underlying differences in minimum area requirements and the degree of species turnover among patches. Regression modeling showed species loss increased with greater species turnover among patches (ßSIM ) and decreased with greater area scaling of diversity (i.e., larger power-law island species-area relationship exponents). Losses also increased with greater numbers of single-patch endemics and with increasing proportions of patches destroyed. After accounting for these predictors, neither taxonomic group nor habitat type increased explained variation in species loss. Attrition of the smallest patches removed species in >80% of metacommunities, despite all larger patches and >75% of total area remaining intact. At both 10% and 20% area reduction, median species loss across all datasets was around 50% higher than predicted from methods based on the species-area relationship. We conclude that any mechanism of global change that selectively destroys small habitat patches will lead to imminent extinctions in most discrete metacommunities.

Hydrological-niche models predict water plant functional group distributions in diverse wetland types.

Human use of water resources threatens environmental water supplies. If resource managers are to develop policies that avoid unacceptable ecological impacts, some means to predict ecosystem response to changes in water availability is necessary. This is difficult to achieve at spatial scales relevant for water resource management because of the high natural variability in ecosystem hydrology and ecology. Water plant functional groups classify species with similar hydrological niche preferences together, allowing a qualitative means to generalize community responses to changes in hydrology. We tested the potential for functional groups in making quantitative prediction of water plant functional group distributions across diverse wetland types over a large geographical extent. We sampled wetlands covering a broad range of hydrogeomorphic and salinity conditions in South Australia, collecting both hydrological and floristic data from 687 quadrats across 28 wetland hydrological gradients. We built hydrological-niche models for eight water plant functional groups using a range of candidate models combining different surface inundation metrics. We then tested the predictive performance of top-ranked individual and averaged models for each functional group. Cross validation showed that models achieved acceptable predictive performance, with correct classification rates in the range 0.68-0.95. Model predictions can be made at any spatial scale that hydrological data are available and could be implemented in a geographical information system. We show the response of water plant functional groups to inundation is consistent enough across diverse wetland types to quantify the probability of hydrological impacts over regional spatial scales.