Clade diversification dynamics and the biotic and abiotic controls of speciation and extinction rates

Abstract

How ecological interactions, genetic processes, and environmental variability jointly shape the evolution of species diversity remains a challenging problem in biology. We developed an individual-based model of clade diversification to predict macroevolutionary dynamics when resource competition, genetic differentiation, and landscape fluctuations interact. Diversification begins with a phase of geographic adaptive radiation. Extinction rates rise sharply at the onset of the next phase. In this phase of niche self-structuring, speciation and extinction processes, albeit driven by biotic mechanisms (competition and hybridization), have essentially constant rates, determined primarily by the abiotic pace of landscape dynamics. The final phase of diversification begins when intense competition prevents dispersing individuals from establishing new populations. Species' ranges shrink, causing negative diversity-dependence of speciation rates. These results show how ecological and microevolutionary processes shape macroevolutionary dynamics and rates; they caution against the notion of ecological limits to diversity, and suggest new directions for the phylogenetic analysis of diversification.

Fig. 1

Macroevolutionary dynamics in silico. a, b Example of diversification in space and time. Color-coded phenotypes vary continuously across a two-dimensional phenotypic space (a); black dots indicate the phenotypic optimum in each of the nine geographic sites. Panel b shows the populations (vertical bars, height measures abundance, and color indicates phenotype) of all species at three different times (t), across the nine geographical sites into which the landscape (horizontal plane) is subdivided. The color of each site indicates the corresponding phenotypic optimum. c Phylogenetic tree of extant and extinct species, with colors showing the average phenotype along each branch. d Species diversity through time, measured in the number of generations from the common ancestor’s introduction in the landscape. e Speciation rate as a function of diversity. f Extinction rate as a function of diversity. In d–f black lines give median values over 50 simulation replicates, purple areas give 95% (dark purple) and 50% (light purple) confidence intervals, and the three stages of diversification (1–3) are highlighted by gray shadings. Parameter values as in Supplementary Table 1

Fig. 2

Effects of different biotic and abiotic factors on macroevolutionary rates and species diversity. a Diversification rate in stage 1. b Diversification rate in stage 2. c Stationary turnover rate. d Stationary species diversity. Values are medians over 50 simulation replicates. See text and Methods for factor definitions. The range of parameter values used for each factor was rescaled between 0 and 1, with 0 (respectively 1) corresponding to the smallest (respectively highest) parameter value used for that factor (see Methods). Black open circles correspond to default parameter values (Supplementary Table 1). Other parameter values as in Supplementary Table 1

Fig. 3

Diversity dependence of key ecological and genetic variables. Simulations were replicated 50 times with default parameter values (Supplementary Table 1). For each variable (see Methods, section “Numerical simulations” for details about the computation of each variable), the left column (a, c, e, g, i, k, m) shows median values (black lines), 95% and 50% confidence intervals (purple areas), computed across all species (as in Fig. 1d–f); the right column (b, d, f, h, j, l, n) shows median values for species about to speciate (within the next 200 generations; blue), about to go extinct (within the next 200 generations; red), and for “static” species (neither speciation nor extinction within the next 2000 generations; orange). The three stages of diversification (1–3) are highlighted by gray shadings, as in Fig. 1. A sensitivity analysis of these results is reported in Supplementary Figs. 6 and 8

Fig. 4

Effect of biotic and abiotic factors on the evolutionary emergence of macroecological patterns. a–f Relationship between species diversity and metacommunity size. g–l Species rank-abundance distributions. For each biotic and abiotic factor, the median values of the macroecological variables of interest (over 50 simulation replicates) are shown at different stages of diversification: at the end of stage 1 (light color), mid-way through stage 2 (medium), and at a stationary state (dark). Factor values are scaled from blue (leading to the lowest stationary species diversity) to red (leading to the highest stationary species diversity), with the corresponding values indicated above each column. Other parameter values as in Supplementary Table 1. In a–f the size of dots is proportional to the median value of species abundances. See text and Methods for the definition of each factor

Fig. 5

Effect of sites distribution and distance between ecological optima on diversification dynamics. We generated 84 landscapes for which the environmental optima of the nine sites are randomly chosen in uniform distributions of various widths. The phenotypic distance between the optima of adjacent sites (and thus the degree of resource distributions overlap of adjacent sites) is different for each pair of sites, and there is no correlation between geographical proximity and ecological similarity (Supplementary Fig. 1). a Stationary species diversity as a function of the mean phenotypic distance between ecological optima of adjacent sites. b Speciation rate as a function of diversity. c Extinction rate as a function of diversity. d–f Diversification rate in stage 1 (d), in stage 2 (e), and stationary turnover rate (f) as a function of mean phenotypic distance between environmental optima of adjacent sites. The vertical dashed line indicates the phenotypic distance between environmental optima of adjacent sites in the baseline version of the model. The results are based on 50 simulation replicates for each landscape. Parameter values as in Supplementary Table 1