Modeling the ecology and evolution of biodiversity: Biogeographical cradles, museums, and graves

Individual processes shaping geographical patterns of biodiversity are increasingly understood, but their complex interactions on broad spatial and temporal scales remain beyond the reach of analytical models and traditional experiments. To meet this challenge, we built a spatially explicit, mechanistic simulation model implementing adaptation, range shifts, fragmentation, speciation, dispersal, competition, and extinction, driven by modeled climates of the past 800,000 years in South America. Experimental topographic smoothing confirmed the impact of climate heterogeneity on diversification. The simulations identified regions and episodes of speciation (cradles), persistence (museums), and extinction (graves). Although the simulations had no target pattern and were not parameterized with empirical data, emerging richness maps closely resembled contemporary maps for major taxa, confirming powerful roles for evolution and diversification driven by topography and climate

Response of an Afro-Palearctic bird migrant to glaciation cycles

We combine tracks of a long-distance migratory bird with high–temporal resolution climate data to reconstruct habitat availability month by month for the past 120,000 y. The seasonal changes of suitable habitat in the past imply that continued seasonal migration was necessary during the glacial maxima. Genomic-based estimates of effective population size indicate that more generally migratory lifestyles can be beneficially adapted to various climatic conditions. Our results provide a major step forward in understanding how migratory species will fare in the future and have important implications for how we understand the role of migration in the distribution of species and potentially speciation

Strong altitudinal partitioning in the distributions of ectomycorrhizal fungi along a short (300 m) elevation gradient

• Changes in species richness and distributions of ectomycorrhizal (ECM) fungal communities along altitudinal gradients have been attributed to changes in both host distributions and abiotic variables. However, few studies have considered altitudinal relationships of ECM fungi associated with a single host to identify the role of abiotic drivers. To address this, ECM fungal communities associated with one host were assessed along five altitudinal transects in Scotland. • Roots of Scots pine (Pinus sylvestris) were collected from sites between 300 and 550–600 m altitude, and ECM fungal communities were identified by 454 pyrosequencing of the fungal internal transcribed spacer (ITS) region. Soil moisture, temperature, pH, carbon : nitrogen (C : N) ratio and organic matter content were measured as potential predictors of fungal species richness and community composition. • Altitude did not affect species richness of ECM fungal communities, but strongly influenced fungal community composition. Shifts in community composition along the altitudinal gradient were most clearly related to changes in soil moisture and temperature. • Our results show that a 300 m altitudinal gradient produced distinct shifts in ECM fungal communities associated with a single host, and that this pattern was strongly related to climatic variables. This finding suggests significant climatic niche partitioning among ECM fungal species

Elevational Patterns of Species Richness, Range and Body Size for Spiny Frogs

Quantifying spatial patterns of species richness is a core problem in biodiversity theory. Spiny frogs of the subfamily Painae (Anura: Dicroglossidae) are widespread, but endemic to Asia. Using spiny frog distribution and body size data, and a digital elevation model data set we explored altitudinal patterns of spiny frog richness and quantified the effect of area on the richness pattern over a large altitudinal gradient from 0–5000 m a.s.l. We also tested two hypotheses: (i) the Rapoport's altitudinal effect is valid for the Painae, and (ii) Bergmann's clines are present in spiny frogs. The species richness of Painae across four different altitudinal band widths (100 m, 200 m, 300 m and 400 m) all showed hump-shaped patterns along altitudinal gradient. The altitudinal changes in species richness of the Paini and Quasipaini tribes further confirmed this finding, while the peak of Quasipaini species richness occurred at lower elevations than the maxima of Paini. The area did not explain a significant amount of variation in total, nor Paini species richness, but it did explain variation in Quasipaini. Five distinct groups across altitudinal gradient were found. Species altitudinal ranges did not expand with an increase in the midpoints of altitudinal ranges. A significant negative correlation between body size and elevation was exhibited. Our findings demonstrate that Rapoport's altitudinal rule is not a compulsory attribute of spiny frogs and also suggest that Bergmann's rule is not generally applicable to amphibians. The study highlights a need to explore the underlying mechanisms of species richness patterns, particularly for amphibians in macroecology

The macroecology of phylogenetically structured hummingbird-plant networks

Aim To investigate the association between species richness, species' phylogenetic signal, insularity and historical and current climate with hummingbird-plant network structure. Location 54 communities along a c. 10,000 kilometer latitudinal gradient across the Americas (39ºN - 32ºS), ranging from sea level to c. 3700 m asl, located on the mainland and on islands, and covering a wide range of climate regimes. Methods We measured null-modeled corrected complementary specialization and bipartite modularity (compartmentalization) in networks of quantitative interactions between hummingbird and plant species. Using an ordinary least squares multi-model approach, we examined the influence of species richness, phylogenetic signal, insularity, and current and historical climate conditions on network structure. Results Phylogenetically-related species, especially plants, showed a tendency to interact with a similar array of partners. The spatial variation in network structure exhibited a constant association with species' phylogeny (R2=0.18-0.19). Species richness and environmental factors showed the strongest associations with network structure (R2=0.20-0.44; R2138 =0.32-0.45, respectively). Specifically, higher levels of complementary specialization and modularity were associated to species-rich communities and communities in which closely-related hummingbirds visited distinct sets of flowering species. On the mainland, warmer temperatures and higher historical temperature stability associated to higher levels of complementary specialization. Main conclusions Previous macroecological studies of interaction networks have highlighted the importance of environment and species richness in determining network structure. Here, for the first time, we report an association between species phylogenetic signal and network structure at macroecological scale. Specifically, null model corrected complementary specialization and modularity exhibited a positive association with species richness and a negative association with hummingbird phylogenetic signal, indicating that both high richness and high inter-specific competition among closely-related 150 hummingbirds exhibit important relationships with specialization in hummingbird-plant networks. Our results document how species richness, phylogenetic signal and climate associate with network structure in complex ways at macroecological scale

A roadmap for global synthesis of the plant tree of life

Providing science and society with an integrated, up-to-date, high quality, open, reproducible and sustainable plant tree of life would be a huge service that is now coming within reach. However, synthesizing the growing body of DNA sequence data in the public domain and disseminating the trees to a diverse audience are often not straightforward due to numerous informatics barriers. While big synthetic plant phylogenies are being built, they remain static and become quickly outdated as new data are published and tree-building methods improve. Moreover, the body of existing phylogenetic evidence is hard to navigate and access for non-experts. We propose that our community of botanists, tree builders, and informaticians should converge on a modular framework for data integration and phylogenetic analysis, allowing easy collaboration, updating, data sourcing and flexible analyses. With support from major institutions, this pipeline should be re-run at regular intervals, storing trees and their metadata long-term. Providing the trees to a diverse global audience through user-friendly front ends and application development interfaces should also be a priority. Interactive interfaces could be used to solicit user feedback and thus improve data quality and to coordinate the generation of new data. We conclude by outlining a number of steps that we suggest the scientific community should take to achieve global phylogenetic synthesis

Elevational Gradients in Bird Diversity in the Eastern Himalaya: An Evaluation of Distribution Patterns and Their Underlying Mechanisms

BACKGROUND: Understanding diversity patterns and the mechanisms underlying those patterns along elevational gradients is critically important for conservation efforts in montane ecosystems, especially those that are biodiversity hotspots. Despite recent advances, consensus on the underlying causes, or even the relative influence of a suite of factors on elevational diversity patterns has remained elusive. METHODS AND PRINCIPAL FINDINGS: We examined patterns of species richness, density and range size distribution of birds, and the suite of biotic and abiotic factors (primary productivity, habitat variables, climatic factors and geometric constraints) that governs diversity along a 4500-m elevational gradient in the Eastern Himalayan region, a biodiversity hotspot within the world's tallest mountains. We used point count methods for sampling birds and quadrats for estimating vegetation at 22 sites along the elevational gradient. We found that species richness increased to approximately 2000 m, then declined. We found no evidence that geometric constraints influenced this pattern, whereas actual evapotranspiration (a surrogate for primary productivity) and various habitat variables (plant species richness, shrub density and basal area of trees) accounted for most of the variation in bird species richness. We also observed that ranges of most bird species were narrow along the elevation gradient. We find little evidence to support Rapoport's rule for the birds of Sikkim region of the Himalaya. CONCLUSIONS AND SIGNIFICANCE: This study in the Eastern Himalaya indicates that species richness of birds is highest at intermediate elevations along one of the most extensive elevational gradients ever examined. Additionally, primary productivity and factors associated with habitat accounted for most of the variation in avian species richness. The diversity peak at intermediate elevations and the narrow elevational ranges of most species suggest important conservation implications: not only should mid-elevation areas be conserved, but the entire gradient requires equal conservation attention

Do Stacked Species Distribution Models Reflect Altitudinal Diversity Patterns?

The objective of this study was to evaluate the performance of stacked species distribution models in predicting the alpha and gamma species diversity patterns of two important plant clades along elevation in the Andes. We modelled the distribution of the species in the Anthurium genus (53 species) and the Bromeliaceae family (89 species) using six modelling techniques. We combined all of the predictions for the same species in ensemble models based on two different criteria: the average of the rescaled predictions by all techniques and the average of the best techniques. The rescaled predictions were then reclassified into binary predictions (presence/absence). By stacking either the original predictions or binary predictions for both ensemble procedures, we obtained four different species richness models per taxa. The gamma and alpha diversity per elevation band (500 m) was also computed. To evaluate the prediction abilities for the four predictions of species richness and gamma diversity, the models were compared with the real data along an elevation gradient that was independently compiled by specialists. Finally, we also tested whether our richness models performed better than a null model of altitudinal changes of diversity based on the literature. Stacking of the ensemble prediction of the individual species models generated richness models that proved to be well correlated with the observed alpha diversity richness patterns along elevation and with the gamma diversity derived from the literature. Overall, these models tend to overpredict species richness. The use of the ensemble predictions from the species models built with different techniques seems very promising for modelling of species assemblages. Stacking of the binary models reduced the over-prediction, although more research is needed. The randomisation test proved to be a promising method for testing the performance of the stacked models, but other implementations may still be developed