Abstract
Molecular phylogenies have been used to study the diversification of many clades. However, current methods for inferring diversification dynamics from molecular phylogenies ignore the possibility that clades may be decreasing in diversity, despite the fact that the fossil record shows this to be the case for many groups. Here we investigate the molecular phylogenetic signature of decreasing diversity using the most widely used statistic for inferring diversity dynamics from molecular phylogenies, the γ statistic. We show that if a clade is in decline its molecular phylogeny may show evidence of the decrease in the diversification rate that occurred between its diversification and decline phases. The ability to detect the change in diversification rate depends largely on the ratio of the speciation rates of the diversification and decline phases, the higher the ratio the stronger the signal of the change in diversification rate. Consequently, molecular phylogenies of clades in relative rapid decline do not carry a signature of their decreasing diversification. Further, the signal of the change in diversification rate, if present, declines as the diversity drop. Unfortunately, the molecular signature of clades in decline is the same as the signature produced by diversity dependent diversification. Given this similarity, and the inability of current methods to detect declining diversity, it is likely that some of the extant clades that show a decrease in diversification rate, currently interpreted as evidence for diversity dependent diversification, are in fact in decline. Unless methods can be developed that can discriminate between the different modes of diversification, specifically diversity dependent diversification and declining diversity, we will need the fossil record, or data from some other source, to distinguish between these very different diversity trajectories.
Highlights
Understanding the controls of biodiversity is one of the main goals of ecology and evolutionary biology
When the ratio is too low, for example when jlwax=lwanej is 2.5 (Figures 1A and 3A), the null hypothesis of a constant diversification rate will not usually be rejected. In this case the exponential decline would most likely be interpreted as exponential diversification, as appears to have happened in a molecular phylogenetic analysis of the diversity dynamics of the living cetaceans [18,29], as we note above, the c statistic has low statistical power – a c value.21.645 could mean the early phases of diversity dependent growth [27]; diversity dependent growth with low a ratio between the initial speciation rate and equilibrium extinction rate [26]; or, species turn-over at equilibrium diversity [27]
The molecular signature of declining diversity Our results clearly show that molecular phylogenies of clades experiencing a decline in diversity will present a molecular signature of the decreasing diversification rate, the switch from the waxing phase to the waning phase
Summary
Understanding the controls of biodiversity is one of the main goals of ecology and evolutionary biology. Key has been the development of analytic methods for estimating speciation and extinction rates from molecular phylogenies, despite the absence of extinct species [7,8,9,10,11,12,13], and ways of investigating the tempo of diversification [1,12,14]. This is especially important given that many clades do not have a fossil record of sufficient quality (or any fossil record at all for that matter) to enable detailed diversification studies. Even though caution is warranted – overdispersed sampling commonly used by biologists [1,16] and underparameterization of the DNA models [17] might mask true diversification patterns – many phylogenies show a pattern of decreasing diversification rates, which in turn are typically attributed to diversity dependent diversification [4,5,15]
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