The causes of species richness patterns among clades

Abstract

Two major types of species richness patterns are spatial (e.g. the latitudinal diversity gradient) and clade-based (e.g. the dominance of angiosperms among plants). Studies have debated whether clade-based richness patterns are explained primarily by larger clades having faster rates of species accumulation (speciation minus extinction over time; diversification-rate hypothesis) or by simply being older (clade-age hypothesis). However, these studies typically compared named clades of the same taxonomic rank, such as phyla and families. This study design is potentially biased against the clade-age hypothesis, since clades of the same rank may be more similar in age than randomly selected clades. Here, we analyse the causes of clade-based richness patterns across the tree of life using a large-scale, time-calibrated, species-level phylogeny and random sampling of clades. We find that within major groups of organisms (animals, plants, fungi, bacteria, archaeans), richness patterns are most strongly related to clade age. Nevertheless, weaker relationships with diversification rates are present in animals and plants. These overall results contrast with similar large-scale analyses across life based on named clades, which showed little effect of clade age on richness. More broadly, these results help support the overall importance of time for explaining diverse types of species richness patterns.

Keywords: clade age; diversification; macroevolution; phylogeny; species richness.

Figure 1.

Hypothetical example and workflow for selecting clades and analysing the relationships among variables. (a) A time-calibrated phylogeny for a hypothetical group of organisms, illustrating the consequences of using named clades as opposed to randomly selected clades. If clades are randomly selected, they can be of almost any age. Here, the four randomly selected clades range in age from 26 to 2 million years old. By contrast, clades of the same taxonomic rank may be constrained to be of similar ages, or older ages. Here the three genera range in age from 17 to 23 million years old. Note that random clade 4 is highlighted in red because it is nested inside random clade 1. We excluded such nested clades. (b) Illustration of the overall workflow used in this study. For a given group of organisms (e.g. animals, plants, bacteria), we obtained a time-calibrated, species-level phylogeny. We then generated a list of all the nodes in that tree. We next randomly selected 50 clades. Clades that were nested inside of other selected clades were deleted, as were those that were extremely young (e.g. zero-length branches, and when different species in the clade had almost identical sequences). We then estimated clade ages and diversification rates for each clade. Clades with very high diversification rates (greater than 1 species per million years) were also excluded. Finally, we used phylogenetic generalized least-squares regression (PGLS) to test whether species richness (dependent variable) was related to clade age or to diversification (independent variables) among these 50 clades, testing the clade-age and diversification rate hypotheses. We also tested whether diversification rates were related to clade age. This overall procedure was repeated 10 times (each with a different random selection of 50 clades) for each major group of organisms.

Figure 2.

Pairwise relationships between species richness and clade age, species richness and diversification rate, and diversification rate and clade age. Species richness is log10-transformed. Clade age is the crown-group age. Diversification rate is inferred from the MS crown-group estimator with an ε of 0.5. For each group, we show the mean r² from PGLS regression analyses. Full results are in table 1. We present species richness, clade age and diversification rate for each clade in electronic supplementary material, dataset S1.