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.     

Disentangling the drivers of continental mammalian endemism

Endemic species and species with small ranges are ecologically and evolutionarily distinct and are vulnerable to extinction. Determining which abiotic and biotic factors structure patterns of endemism on continents can advance our understanding of global biogeographic processes, but spatial patterns of mammalian endemism have not yet been effectively predicted and reconstructed. Using novel null model techniques, we reconstruct trends in mammalian endemism and describe the isolated and combined effects of physiographic, ecological, and evolutionary factors on endemism. We calculated weighted endemism for global continental ecoregions and compared the spatial distribution of endemism to niche-based, geographic null models of endemism. These null models distribute species randomly across continents, simulating their range sizes from their degree of climatic specialization. They isolate the effects of physiography (topography and climate) and species richness on endemism. We then ran linear and structural models to determine how topography and historical climate stability influence endemism. The highest rates of mammalian endemism were found in topographically rough, climatically stable ecoregions with many species. The null model that isolated physiography did not closely approximate the observed distribution of endemism (r² = .09), whereas the null model that incorporated both physiography and species richness did (r² = .59). The linear models demonstrate that topography and climatic stability both influenced endemism values, but that average climatic niche breadth was not highly correlated with endemism. Climate stability and topography both influence weighted endemism in mammals, but the spatial distribution of mammalian endemism is driven by a combination of physiography and species richness. Despite its relationship to individual range size, average climate niche breadth has only a weak influence on endemism. The results highlight the importance of historical biogeographic processes (e.g. centers of speciation) and geography in driving endemism patterns, and disentangle the mechanisms structuring species ranges worldwide.     

Regional pools and environmental controls of vertebrate richness

Abstract The species richness of local communities depends on the richness of the regional pool and the filtering processes that preclude some regional species from occurring locally. These filters may include absolute attributes of the local environment and also how representative the local environment is of the surrounding region. The latter is consistent with a species-sorting perspective, in which regional species only occupy the local habitats to which they are adapted. Here we evaluate the relative effects of local environmental conditions, environmental representativeness, and environment-independent processes on the probability of local species occurrence, given their regional presence, of birds, mammals, and amphibians worldwide. In multipredictor models, environmental representativeness is a strong independent predictor of local species occurrence probability, with a relative contribution greater than that of absolute local environmental conditions. Furthermore, we find that local occurrence probability diminishes with increased regional richness independent of the local environment. This is consistent with reduced local occupancy in richer regions, which is a pattern that could stem from a largely neutral community assembly process. Our results support the importance of both environment-independent and species-sorting processes and suggest that regional richness and environmental representativeness should be jointly used for understanding richness gradients across scales.     

Determinants of bird species richness: role of climate and vegetation structure at a regional scale

We examined the respective roles of climate and vegetation structure on geographical variation in bird species richness. The Province of Buenos Aires (central-eastern Argentina) was divided into 146 squares of 50 km on a side. For each square we evaluated the number of bird species, the value of thirteen climatic variables, and the value of a vegetation strata index. The climatic matrix was analyzed by Principal Component Analysis (PCA), and the first factors resulting from PCA were considered as multifactorial climatic gradients. Simple and Partial Correlation Analysis among bird species richness, vegetation strata, and the first two factors derived from PCA (65% of total variation) indicated that bird richness distribution was determined by the availability of vegetation strata, associated with different vegetation types that, at the same time, were influenced by the climatic conditions summarized in the first climatic factor (a gradient of precipitation, relative humidity, annual termical amplitude, and frost occurrence). This relationships reflect the complexity of factors that can act directly as well as indirectly on the geographical patterns in species richness. Also, we evaluated the importance of study scale comparing our results with previous studies at macrogeographic and local scales, found out that the vegetation structure was the principal determinant of bird species richness at this three geographical scales.     

Global drivers of human pathogen richness and prevalence

The differences in the richness and prevalence of human pathogens among different geographical locations have ramifying consequences for societies and individuals. The relative contributions of different factors to these patterns, however, have not been fully resolved. We conduct a global analysis of the relative influence of climate, alternative host diversity and spending on disease prevention on modern patterns in the richness and prevalence of human pathogens. Pathogen richness (number of kinds) is largely explained by the number of birds and mammal species in a region. The most diverse countries with respect to birds and mammals are also the most diverse with respect to pathogens. Importantly, for human health, the prevalence of key human pathogens (number of cases) is strongly influenced by disease control efforts. As a consequence, even where disease richness is high, we might still control prevalence, particularly if we spend money in those regions where current spending is low, prevalence is high and populations are large.     

Sample richness and genetic diversity as drivers of chimera formation in nSSU metagenetic analyses

Eukaryotic diversity in environmental samples is often assessed via PCR-based amplification of nSSU genes. However, estimates of diversity derived from pyrosequencing environmental data sets are often inflated, mainly because of the formation of chimeric sequences during PCR amplification. Chimeras are hybrid products composed of distinct parental sequences that can lead to the misinterpretation of diversity estimates. We have analyzed the effect of sample richness, evenness and phylogenetic diversity on the formation of chimeras using a nSSU data set derived from 454 Roche pyrosequencing of replicated, large control pools of closely and distantly related nematode mock communities, of known intragenomic identity and richness. To further investigate how chimeric molecules are formed, the nSSU gene secondary structure was analyzed in several individuals. For the first time in eukaryotes, chimera formation proved to be higher in both richer and more genetically diverse samples, thus providing a novel perspective of chimera formation in pyrosequenced environmental data sets. Findings contribute to a better understanding of the nature and mechanisms involved in chimera formation during PCR amplification of environmentally derived DNA. Moreover, given the similarities between biodiversity analyses using amplicon sequencing and those used to assess genomic variation, our findings have potential broad application for identifying genetic variation in homologous loci or multigene families in general.     

Species richness of Colorado riparian vegetation

Abstract. The probable causes of spatial variation in the diversity of plant communities on a global and local scale have been widely investigated, but the regional scale has received little attention. It remains unclear how disturbance affects diversity in wetlands andriparian vegetation. This study examines the hypothesis that regional variation in the richness of riparian wetlands is related to variation in macro-environment and flood potential. Vascular plant species richness was sampled in 0.1 ha plots at 115 riparian sites scattered over a 300 km length of the western slope of the Rocky Mountains in western Colorado, USA. The relationship between macro-environmental variables (e.g. drainage basin area), disturbance indicators, and species richness was analyzed using correlation analysis and multiple regression analysis. Total richness varied between 20 and 87 species (average 50.6) per 0.1 ha, and was highest in subalpine riparian forests from 2600–3650 m a.s.l. (57.8 species / 0.1 ha). Tree and shrub richness were highest in lower elevation, larger drainage basins, forb and graminoid richness were highest in higher elevation, smaller drainage basins. These opposing trends resulted in no net trend in total richness with elevation. Regression models for total richness were poor, suggesting that other variables must be important. The intermediate disturbance hypothesis and other single-factor hypotheses are not supported as explanations of the regional pattern of variation in richness.     

Disentangling drivers of spatial autocorrelation in species distribution models

Species distribution models (SDMs) are frequently used to understand the influence of site properties on species occurrence. For robust model inference, SDMs need to account for the spatial autocorrelation of virtually all species occurrence data. Current methods do not routinely distinguish between extrinsic and intrinsic drivers of spatial autocorrelation, although these may have different implications for conservation. Here, we present and test a method that disentangles extrinsic and intrinsic drivers of spatial autocorrelation using repeated observations of a species. We focus on unknown habitat characteristics and conspecific interactions as extrinsic and intrinsic drivers, respectively. We model the former with spatially correlated random effects and the latter with an autocovariate, such that the spatially correlated random effects are constant across the repeated observations whereas the autocovariate may change. We tested the performance of our model on virtual species data and applied it to observations of the corncrake Crex crex in the Netherlands. Applying our model to virtual species data revealed that it was well able to distinguish between the two different drivers of spatial autocorrelation, outperforming models with no or a single component for spatial autocorrelation. This finding was independent of the direction of the conspecific interactions (i.e. conspecific attraction versus competitive exclusion). The simulations confirmed that the ability of our model to disentangle both drivers of autocorrelation depends on repeated observations. In the case study, we discovered that the corncrake has a stronger response to habitat characteristics compared to a model that did not include spatially correlated random effects, whereas conspecific interactions appeared to be less important. This implies that future conservation efforts should primarily focus on maximizing habitat availability. Our study shows how to systematically disentangle extrinsic and intrinsic drivers of spatial autocorrelation. The method we propose can help to correctly identify the main drivers of species distributions.     

Invasion legacy effects versus sediment deposition as drivers of riparian vegetation

Riparian zones are formed by interactions between fluvio-geomorphological processes, such as sediment deposition, and biota, such as vegetation. Establishment of invasive alien plant (IAP) species along rivers may influence vegetation dynamics, evidenced as higher seasonal or inter-annual fluctuations in native plant diversity when IAP cover is high. This could impact the overall functioning of riparian ecosystems. Conversely, fine sediment deposited in riparian zones after floods may replenish propagule banks, thus supporting recruitment of native species. The interactive effects of invasion and fine sediment deposition have hitherto, however, been ignored. Vegetation surveys across rivers varying in flow regime were carried out over 2 years to assess changes in community composition and diversity. Artificial turf mats were used to quantify over-winter sediment deposition. The viable propagule bank in soil and freshly deposited sediment was then quantified by germination trials. Structural Equation Models were used to assess causal pathways between environmental variables, IAPs and native vegetation. Greater variation in flow increased the cover of IAPs along riverbanks. An increased in high flow events and sediment deposition were positively associated with the diversity of propagules deposited. However, greater diversity of propagules did not result in a more diverse plant community at invaded sites, as greater cover of IAPs in summer reduced native plant diversity. Seasonal turnover in the above-ground vegetation was also accentuated at previously invaded sites, suggesting that a legacy of increased competition in previous years, not recent sediment deposition, drives above-ground vegetation structure at invaded sites. The interaction between fluvial disturbance via sediment deposition and invasion pressure is of growing importance in the management of riparian habitats. Our results suggest that invasion can uncouple the processes that contribute to resilience in dynamic habitats making already invaded habitats vulnerable to further invasions.     

Disentangling multiple drivers of pollination in a landscape-scale experiment

Animal pollination is essential for the reproductive success of many wild and crop plants. Loss and isolation of (semi-)natural habitats in agricultural landscapes can cause declines of plants and pollinators and endanger pollination services. We investigated the independent effects of these drivers on pollination of young cherry trees in a landscape-scale experiment. We included (i) isolation of study trees from other cherry trees (up to 350 m), (ii) the amount of cherry trees in the landscape, (iii) the isolation from other woody habitats (up to 200 m) and (iv) the amount of woody habitats providing nesting and floral resources for pollinators. At the local scale, we considered effects of (v) cherry flower density and (vi) heterospecific flower density. Pollinators visited flowers more often in landscapes with high amount of woody habitat and at sites with lower isolation from the next cherry tree. Fruit set was reduced by isolation from the next cherry tree and by a high local density of heterospecific flowers but did not directly depend on pollinator visitation. These results reveal the importance of considering the plant''s need for conspecific pollen and its pollen competition with co-flowering species rather than focusing only on pollinators’ habitat requirements and flower visitation. It proved to be important to disentangle habitat isolation from habitat loss, local from landscape-scale effects, and direct effects of pollen availability on fruit set from indirect effects via pollinator visitation to understand the delivery of an agriculturally important ecosystem service.     

Partitioning sources of variation in vertebrate species richness

Aim To explore biogeographic patterns of terrestrial vertebrates in Maine, USA using techniques that would describe local and spatial correlations with the environment. Location Maine, USA. Methods We delineated the ranges within Maine (86,156 km²) of 275 species using literature and expert review. Ranges were combined into species richness maps, and compared to geomorphology, climate, and woody plant distributions. Methods were adapted that compared richness of all vertebrate classes to each environmental correlate, rather than assessing a single explanatory theory. We partitioned variation in species richness into components using tree and multiple linear regression. Methods were used that allowed for useful comparisons between tree and linear regression results. For both methods we partitioned variation into broad‐scale (spatially autocorrelated) and fine‐scale (spatially uncorrelated) explained and unexplained components. By partitioning variance, and using both tree and linear regression in analyses, we explored the degree of variation in species richness for each vertebrate group that could be explained by the relative contribution of each environmental variable. Results In tree regression, climate variation explained richness better (92% of mean deviance explained for all species) than woody plant variation (87%) and geomorphology (86%). Reptiles were highly correlated with environmental variation (93%), followed by mammals, amphibians, and birds (each with 84–82% deviance explained). In multiple linear regression, climate was most closely associated with total vertebrate richness (78%), followed by woody plants (67%) and geomorphology (56%). Again, reptiles were closely correlated with the environment (95%), followed by mammals (73%), amphibians (63%) and birds (57%). Main conclusions Comparing variation explained using tree and multiple linear regression quantified the importance of nonlinear relationships and local interactions between species richness and environmental variation, identifying the importance of linear relationships between reptiles and the environment, and nonlinear relationships between birds and woody plants, for example. Conservation planners should capture climatic variation in broad‐scale designs; temperatures may shift during climate change, but the underlying correlations between the environment and species richness will presumably remain.     

Human appropriation of net primary production as driver of change in landscape-scale vertebrate richness

Aim

Land use is the most pervasive driver of biodiversity loss. Predicting its impact on species richness (SR) is often based on indicators of habitat loss. However, the degradation of habitats, especially through land-use intensification, also affects species. Here, we evaluate whether an integrative metric of land-use intensity, the human appropriation of net primary production, is correlated with the decline of SR in used landscapes across the globe.

Location

Global.

Time period

Present.

Major taxa studied

Birds, mammals and amphibians.

Methods

Based on species range maps (spatial resolution: 20 km × 20 km) and an area-of-habitat approach, we calibrated a “species–energy model” by correlating the SR of three groups of vertebrates with net primary production and biogeographical covariables in “wilderness” areas (i.e., those where available energy is assumed to be still at pristine levels). We used this model to project the difference between pristine SR and the SR corresponding to the energy remaining in used landscapes (i.e., SR loss expected owing to human energy extraction outside wilderness areas). We validated the projected species loss by comparison with the realized and impending loss reconstructed from habitat conversion and documented by national Red Lists.

Results

Species–energy models largely explained landscape-scale variation of mapped SR in wilderness areas (adjusted R²-values: 0.79–0.93). Model-based projections of SR loss were lower, on average, than reconstructed and documented ones, but the spatial patterns were correlated significantly, with stronger correlation in mammals (Pearson's r = 0.68) than in amphibians (r = 0.60) and birds (r = 0.57).

Main conclusions

Our results suggest that the human appropriation of net primary production is a useful indicator of heterotrophic species loss in used landscapes, hence we recommend its inclusion in models based on species–area relationships to improve predictions of land-use-driven biodiversity loss.     

Forest patch size and isolation as drivers of bird species richness in Maputaland,Mozambique

Aim To examine the response of forest‐dependent and generalist bird assemblages and feeding guilds to patch characteristics of forest fragments in the context of island biogeography and metapopulation theories in an area that supports high levels of species diversity and endemism. Location Dune, riverine, sand and swamp forest fragments in southern Mozambique’s Maputaland. Methods We recorded 20 forest‐dependent and 69 generalist bird species at 220 survey points in 30 forest fragments that ranged in size from 5 to 7432 ha and that were 100 to 5100 m apart. We used linear regressions to relate the number of species to forest fragment size, isolation, perimeter, fractal dimension, shape and core area for frugivores, insectivores, granivores, nectarivores, carnivores and omnivores separately for forest‐dependent and generalist bird assemblages. We tested for modality in occupancy frequency distributions of species in forest fragments and used the binary matrix temperature calculator to determine whether the assemblages had a nested structure separately for forest‐dependent and generalist bird species. Results The number of forest‐dependent and generalist bird species categorized into the feeding guilds varied independently from forest patch parameter values. Occupancy models showed a random distribution for forest‐dependent birds, and generalists had a unimodal distribution. Both the forest‐dependent and generalist bird assemblages had a non‐nested structure. The presence of eight rare forest‐dependent and four endemic bird species in 22 of the 30 fragments contributed to the non‐nested structure of these bird assemblages. Main conclusions Fragmented forests did not induce the expected responses of the forest bird assemblages in that the number of species was not explained by patch characteristics, nor could we find evidence for metapopulation dynamics. Non‐nestedness may be caused by the few rare and endemic species occupying forest fragments with a wide range of patch characteristics. Knowledge of the response of species to forest fragmentation can benefit conservation planning catering for rare and endemic species. Our study suggests that all forest fragments in the region may have to be included in a conservation network to complement existing landscape‐based plans to protect the region.     

Relative influence of habitat heterogeneity, climate, human disturbance, and spatial structure on vertebrate species richness in Spain

Many factors affect the distribution of species richness. This study examines the relative influence of habitat heterogeneity, climate, human disturbance, and spatial structure on the species-richness distribution of terrestrial vertebrates (amphibians, reptiles, birds and mammals) in mainland Spain. The results indicate that spatial structure and environment exert similar influences on species richness. For all four taxa, species richness increases southward and northward, being lower in the center of the country, when controlled for other variables. This may be the result of a peninsular effect, as found in other studies, and reflect the importance of historical events on species richness in the Iberian Peninsula. Climate is more important than habitat heterogeneity in determining species richness. Temperature is positively correlated with amphibian, reptile, and bird species richness, while mammalian species richness is highest at intermediate temperatures. This effect is stronger in ectotherms than among endotherms, perhaps reflecting physiological differences. Precipitation positively correlates with bird and mammalian species richness, but has no effect on ectotherm species richness. Amphibian species richness increases with altitudinal range, and bird species richness with habitat diversity. Human population density is positively correlated with bird and mammalian species richness, but does not affect ectotherm species richness, while amphibian and bird species richness is highest at moderate levels of human land alteration (farmland). However, unexplained variance remains, and we discuss that the effects of environmental variables on species richness may vary geographically, causing different effects to be obscured on a national scale, diminishing the explanatory power of environmental variables.