Research Article

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

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Science  20 Jul 2018:
Vol. 361, Issue 6399, eaar5452
DOI: 10.1126/science.aar5452
  • Observed species richness versus modeled (simulated) richness.

    Upper map: Contemporary South American bird richness (2967 species). Lower map: Simulated spatial pattern for the cumulative richness of persistent (museum) species, arising from the model. The map show results averaged over all parameter values for an Atlantic Rainforest founder, excluding the climate-smoothing experimental treatments. Simulated species richness is highly correlated with observed species richness for birds (r2 = 0.6337).

  • Fig. 1 Simulation model structure.

    The processes and parameters implemented in the model, all illustrated here, link climate dynamics and topography to emerging biodiversity patterns. Key entities and patterns (tables S3 and S4) appear in rectangles at the population, species, and assemblage levels. Processes are shown in ovals. Control knobs (table S1) represent the four model parameters: Dmax, maximum dispersal distance; Hmax, maximum niche evolutionary rate; Tmin, minimum time for speciation; and Cmax, maximum intensity of competition allowing coexistence, estimated as a function of phylogenetic distance. Climate change, on a realistic topographical template, drives ecological and evolutionary processes, interacting with each population’s environmental niche to determine range dynamics. Dispersal promotes range shift and range expansion. Interactions between climate change, niche, and geographic distribution may result in adaptive niche evolution, range fragmentation, or extinction. Fragments that remain isolated long enough become new species. Closely related species, in sympatry, may coexist or undergo competitive exclusion. Starting from a single, founding species (and its initial climatic niche), the simulation produces temporal and spatial patterns of biodiversity, including times and places of speciation (cradles), extinction (graves), and persistence (museums). See the Methods section, below, and “Model specification: process sequence” in (95).

  • Fig. 2 Lifetime trajectory of species.

    Initially, the species on the left (labeled “ancestral population”) is in a persistence trajectory (thick black line), as a single, viable population. Driven by climate change, the population experiences range fragmentation, yielding two, isolated descendant populations (blue and red dashed lines). These two daughter populations enter speciation trajectories. Once they have remained isolated for at least Tmin years, they are considered independent species (speciation event). Each descendant species then enters its own persistence trajectory (blue and red solid lines). In this example, after a short period of persistence, the red species enters an extinction trajectory (thin dashed red line), as its geographic range continuously contracts in a changing climate, ending in full range collapse (species extinction). The blue species will eventually give rise to two daughter species, undergo extinction, or survive to the end of the simulation.

  • Fig. 3 Simulation results for an Andean founder.

    Upper panel: Occupancy time series for speciation (cradle richness, green), extinction (grave richness, red), and mean continental temperature (blue) over the course of the simulation (time moves from left to right). The highest five to seven peaks of speciation (green dashed lines) and extinction (red dashed lines) were marked manually, but time-series cross-correlations were analyzed rigorously (table S6). Precipitation time series appear in fig. S2. Lower panel: Cumulative richness maps for cradles, graves, net diversification (cradles minus graves), and total richness. Each map is a summation over the course of the simulation. The figure shows the average of all parameter values for an Andean founder, excluding the climate-smoothing experimental treatments.

  • Fig. 4 Simulation results for an Atlantic Rainforest founder.

    See the caption for Fig. 3.

  • Fig. 5 Simulation results for an Amazon founder.

    See the caption for Fig. 3.

  • Fig. 6 Pooled simulation results for the Andean, Atlantic Rainforest, and Amazon founders of Figs. 3 to 5.

    See the caption for Fig. 3.

  • Fig. 7 The effect of topographic smoothing on rates and cumulative spatial patterns of speciation (cradles), extinction (graves), net diversification (cradles minus graves), and total richness, for Andes, Atlantic Forest, and Amazon founders, pooled.

    Upper panel: Occupancy time series for speciation (cradle richness, green), extinction (grave richness, red), and mean continental temperature (blue) over the course of the simulation (time moves from left to right). Black time series are for smoothed topographies. Red and green time series are the same as in Fig. 6. Rates of speciation (cradles) and extinction (graves) were both suppressed by smoothing.

  • Fig. 8 Observed species richness versus modeled richness.

    Left column of maps: Contemporary spatial patterns for South American bird richness (2967 species, upper map) and mammal richness (1342 species, lower map). Middle column map: The simulated spatial pattern for cumulative museum richness, arising from the model (Fig. 1), averaged over all parameter values for an Atlantic Rainforest founder. Right column of maps: The differences between observed (left maps) and simulated (middle map) richness for birds (upper map) and mammals (lower map). Red indicates that the model underestimates richness, and blue indicates overestimation. Simulated species richness is highly correlated with observed species richness for birds (r2 = 0.6337) and for mammals (r2 = 0.6548). Observed species richness was not targeted in any way by the simulations. A qualitative comparison of modeled richness with South American plants appears in “Contrasting empirical and simulated spatial patterns in species richness” in (95).

  • Movie 1. Spatial and temporal dynamics of South American climates.

    The four dynamic maps on the left display minimum and maximum annual precipitation (upper maps) and temperature (lower maps) in South America over the last 800 ka. The colored lines in the corresponding time-series plots (center) indicate, from the top to bottom, (i) maximum, (ii) third-quartile, (iii) median, (iv) first-quartile, and (v) minimum annual precipitation (upper time series) and temperature (lower time series) among map cells. For precipitation, minimum and first-quartile time series overlap. In the dynamic temperature-precipitation climate space (right), each cross corresponds to one grid cell in the map. All cells are illustrated. The width of the cross indicates the annual precipitation seasonality (difference between maximum and minimum), while the height of the cross indicates annual temperature seasonality. The gray scale of individual crosses varies to allow climatically overlapping cells to be visually distinguished.

  • Movie 2. Demonstration of simulated geographic and evolutionary dynamics for a small clade of Andean origin.

    In the temperature versus precipitation climate space diagram (top left), the climatic niche of each extant population is indicated by a rectangle, defined by the population’s maximum and minimum climatic tolerance for temperature and precipitation. As the simulation progresses, and populations become fragmented, the niche of each fragment is represented by its own rectangle. Niches of different populations of the same species share the same color, whereas different species’ niches are shown in different colors. The dynamic map (top right) shows the richness of species at each time step. The phylogeny (bottom) records the events of speciation and extinction that emerge from the interaction of climate dynamics, geographic distribution, and the evolutionary response of species.

  • Movie 3. Emerging spatial and temporal patterns of species richness, cradles, museums, and net diversification for a rapidly speciating Andean clade.

    Spatial patterns of instantaneous (top row) and cumulative (bottom row) total species richness (first column), cradle richness (second column), grave richness (third column), and net diversification (fourth column; the difference between cradle richness and grave richness). Cumulative richness is the sum of instantaneous richness over time, capturing—in a single map—an overview of historical spatial patterns.

  • Movie 4. Emerging spatial and temporal patterns in museum species richness, averaged for the Andean, Amazonian, and Atlantic Rainforest founders.

    Cumulative patterns of cradle, grave, and museum species richness (first three columns), for Andean, Atlantic Rainforest, and Amazonian founders (rows), from model simulations. Static empirical maps (on the right) show contemporary patterns of plant, bird, and mammal species richness. Simulated patterns of cumulative museum richness, over the course of 800 ka, closely resemble current patterns in species richness.

Supplementary Materials

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

    Thiago F. Rangel, Neil R. Edwards, Philip B. Holden, José Alexandre F. Diniz-Filho, William D. Gosling, Marco Túlio P. Coelho, Fernanda A. S. Cassemiro, Carsten Rahbek, Robert K. Colwell

    Materials/Methods, Supplementary Text, Tables, Figures, and/or References

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    • Supplementary Text
    • Figs. S1 to S25
    • Tables S1 to S10
    • Caption for Database S1 
    • References 

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