Introduction The study of rates of speciation and extinction, and how these have changed over time, has traditionally mainly been the preserve of paleontology (Simpson 1953; Stanley 1979; Raup 1985). More recently, phylogenies of extant species have been shown to contain information on these rates and how they may have changed, under the assumption that the same rules have applied in all contemporaneous lineages (Harvey et al. 1994; Kubo & Iwasa 1995; see Nee 2006 for a recent review). The first section of this chapter contrasts the strengths and weaknesses of these two approaches – paleontological and phylogenetic – to the study of macroevolution in general. Moving to a specificmacroevolutionary hypothesis, we then outline some tests of the hypothesis that diversification rates have declined in the recent past, either in response to changed abiotic conditions or as a result of density-dependence or diversity-dependence. It has long been appreciated that incomplete specieslevel sampling can cause a bias in favour of this hypothesis at the expense of the null hypothesis of no change (Pybus & Harvey 2000), but we highlight a further sort of incompleteness that is likely to be very widespread and which is not widely appreciated – products of recent lineage splits are unlikely to be considered as distinct species. We reanalyze the data from a key early paper (Zink & Slowinski 1995) to show how this incompleteness, which is inevitable when taxonomy and phylogeny meet, is sufficiently strong to account for much (though not all) of the apparent tendency for rates to have declined through time. Attempts to infer the deeper history of diversification rates are relatively free of this problem but instead encounter others: in particular, the assumption that the underlying probabilities of speciation and extinction per unit time have changed in the same way in all lineages becomes increasingly unlikely as a wider and wider clade is considered. We explain how analyses of a nearcomplete species-level phylogeny of extant mammals show a complex pattern of temporal variation in the rate of effective cladogenesis (Bininda-Emonds et al. 2007), and compare the mammalian picture with that obtained some years previously for birds (Nee et al. 1992).
