There is an increasing call for prioritizing efforts towards the conservation of phylogenetic diversity (Mace et al. 2003; Forest et al. 2007; Davies et al. 2008). Implicit within this conservation agenda is an assumption that species diverge in their ecological and morphological traits more or less linearly through time, and thus that the evolutionary distance between species captures their functional differences. We (Davies and Yessoufou 2013) explored scenarios where this assumption is violated, and feature diversity occurs in bursts at speciation, matching to a punctuated model of trait evolution. Our results illustrate that projected extinctions might prune more branches from the tree-of-life than predicted from the same number of extinctions randomly distributed across the phylogeny; however, the loss of summed branch length might be no greater than expected by chance.
We do not suggest that punctuated evolution is necessarily a better model of trait change, but rather we emphasise the need for a more explicit consideration of evolutionary models if our aim is to maximize feature diversity. Recent advances in comparative methods have allowed comparisons between alternative evolutionary models, and frequently find strict Brownian motion to be a poor fit to observed trait
Fig. 4 Results from simulated extinctions with varying levels of phylogenetic clustering (Lambda) across 100 random birth–death trees (see Fig. 1c) assuming p(ext) = 0.75 for the top 25 % of species. Light grey boxes = expected loss of PD for empirical branch lengths (assuming phylogenetic gradualism or a Brownian motion model of trait change); dark grey boxes = expected loss of PD assuming equal branch lengths (matching to a punctuated model of trait change). Simulations with Lambda = 0 are equivalent to random extinctions. This figure is similar to that in Davies and Yessoufou (2013), but presents a new set of stochastic simulations
data (e.g. Blomberg et al. 2003; O'Meara et al. 2006; Harmon et al. 2010). It remains possible that Brownian motion might still best capture aggregate species differences even when individual traits diverge from a Brownian motion model, assuming traits are evolving independently or when selective regimes fluctuate over time (Felsenstein 1988). However, this expectation has rarely been evaluated using empirical data.
Finally, we note that our understanding of the distribution of phylogenetic diversity across space and among communities might also be informed by further consideration of evolutionary models. For example, traditional metrics of phylogenetic diversity tend to correlate very closely with species richness (Rodrigues et al. 2005), although it is possible to identify regions of greater or lower phylogenetic diversity than predicted from species richness alone, for example, by looking at residual variation (e.g. Forest et al. 2007; Davies et al. 2008). The covariation between evolutionary history and species richness might exhibit very different properties under alternative evolutionary models, but as far as we are aware, there have not yet been any equivalent studies exploring such models in geographical space.
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