Primate diversification inferred from phylogenies and fossils

Biodiversity arises from the balance between speciation and extinction. Fossils record the origins and disappearance of organisms, and the branching patterns of molecular phylogenies allow estimation of speciation and extinction rates, but the patterns of diversification are frequently incongruent between these two data sources. I tested two hypotheses about the diversification of primates based on ～600 fossil species and 90% complete phylogenies of living species: (1) diversification rates increased through time; (2) a significant extinction event occurred in the Oligocene. Consistent with the first hypothesis, analyses of phylogenies supported increasing speciation rates and negligible extinction rates. In contrast, fossils showed that while speciation rates increased, speciation and extinction rates tended to be nearly equal, resulting in zero net diversification. Partially supporting the second hypothesis, the fossil data recorded a clear pattern of diversity decline in the Oligocene, although diversification rates were near zero. The phylogeny supported increased extinction ～34 Ma, but also elevated extinction ～10 Ma, coinciding with diversity declines in some fossil clades. The results demonstrated that estimates of speciation and extinction ignoring fossils are insufficient to infer diversification and information on extinct lineages should be incorporated into phylogenetic analyses.     

Numerical experiments with model monophyletic and paraphyletic taxa

The problem of how accurately paraphyletic taxa versus monophyletic (i.e., holophyletic) groups (clades) capture underlying species patterns of diversity and extinction is explored with Monte Carlo simulations. Phylogenies are modeled as stochastic trees. Paraphyletic taxa are defined in an arbitrary manner by randomly choosing progenitors and clustering all descendants not belonging to other taxa. These taxa are then examined to determine which are clades, and the remaining paraphyletic groups are dissected to discover monophyletic subgroups. Comparisons of diversity patterns and extinction rates between modeled taxa and lineages indicate that paraphyletic groups can adequately capture lineage information under a variety of conditions of diversification and mass extinction. This suggests that these groups constitute more than mere "taxonomic noise" in this context. But, strictly monophyletic groups perform somewhat better, especially with regard to mass extinctions. However, when low levels of paleontologic sampling are simulated, the veracity of clades deteriorates, especially with respect to diversity, and modeled paraphyletic taxa often capture more information about underlying lineages. Thus, for studies of diversity and taxic evolution in the fossil record, traditional paleontologic genera and families need not be rejected in favor of cladistically-defined taxa.     

Ecological limits and diversification rate: alternative paradigms to explain the variation in species richness among clades and regions

Diversification rate is one of the most important metrics in macroecological and macroevolutionary studies. Here I demonstrate that diversification analyses can be misleading when researchers assume that diversity increases unbounded through time, as is typical in molecular phylogenetic studies. If clade diversity is regulated by ecological factors, then species richness may be independent of clade age and it may not be possible to infer the rate at which diversity arose. This has substantial consequences for the interpretation of many studies that have contrasted rates of diversification among clades and regions. Often, it is possible to estimate the total diversification experienced by a clade but not diversification rate itself. I show that the evidence for ecological limits on diversity in higher taxa is widespread. Finally, I explore the implications of ecological limits for a variety of ecological and evolutionary questions that involve inferences about speciation and extinction rates from phylogenetic data.     

CENTRAL MOMENTS AND PROBABILITY DISTRIBUTION OF COLLESS'S COEFFICIENT OF TREE IMBALANCE

The great increase in the number of phylogenetic studies of a wide variety of organisms in recent decades has focused considerable attention on the balance of phylogenetic trees—the degree to which sister clades within a tree tend to be of equal size—for at least two reasons: (1) the degree of balance of a tree may affect the accuracy of estimates of it; (2) the degree of balance, or imbalance, of a tree may reveal something about the macroevolutionary processes that produced it. In particular, variation among lineages in rates of speciation or extinction is expected to produce trees that are less balanced than those that result from phylogenetic evolution in which each extant species of a group has the same probability of speciation or extinction. Several coefficients for measuring the balance or imbalance of phylogenetic trees have been proposed. I focused on Colless's coefficient of imbalance (7) for its mathematical tractability and ease of interpretation. Earlier work on this statistic produced exact methods only for calculating the expected value. In those studies, the variance and confidence limits, which are necessary for testing the departure of observed values of I from the expected, were estimated by Monte Carlo simulation. I developed recursion equations that allow exact calculation of the mean, variance, skewness, and complete probability distribution of I for two different probability-generating models for bifurcating tree shapes. The Equal-Rates Markov (ERM) model assumes that trees grow by the random speciation and extinction of extant species, with all species that are extant at a given time having the same probability of speciation or extinction. The Equal Probability (EP) model assumes that all possible labeled trees for a given number of terminal taxa have the same probability of occurring. Examples illustrate how these theoretically derived probabilities and parameters may be used to test whether the evolution of a monophyletic group or set of monophyletic groups has proceeded according to a Markov model with equal rates of speciation and extinction among species, that is, whether there has been significant variation among lineages in expected rates of speciation or extinction.     

Congruent phylogenetic and fossil signatures of mammalian diversification dynamics driven by Tertiary abiotic change

Computational methods for estimating diversification rates from extant species phylogenetic trees have become abundant in evolutionary research. However, little evidence exists about how their outcome compares to a complementary and direct source of information: the fossil record. Furthermore, there is virtually no direct test for the congruence of evolutionary rates based on these two sources. This task is only achievable in clades with both a well‐known fossil record and a complete phylogenetic tree. Here, we compare the evolutionary rates of ruminant mammals as estimated from their vast paleontological record—over 1200 species spanning 50 myr—and their living‐species phylogeny. Significantly, our results revealed that the ruminant's fossil record and phylogeny reflect congruent evolutionary processes. The concordance is especially strong for the last 25 myr, when living groups became a dominant part of ruminant diversity. We found empirical support for previous hypotheses based on simulations and neontological data: The pattern captured by the tree depends on how clade specific the processes are and which clades are involved. Also, we report fossil evidence for a postradiation speciation slowdown coupled with constant, moderate extinction in the Miocene. The recent deceleration in phylogenetic rates is connected to rapid extinction triggered by recent climatic fluctuations.     

Extinction, ecological opportunity, and the origins of global snake diversity

Snake diversity varies by at least two orders of magnitude among extant lineages, with numerous groups containing only one or two species, and several young clades exhibiting exceptional richness (>700 taxa). With a phylogeny containing all known families and subfamilies, we find that these patterns cannot be explained by background rates of speciation and extinction. The majority of diversity appears to derive from a radiation within the superfamily Colubroidea, potentially stemming from the colonization of new areas and the evolution of advanced venom-delivery systems. In contrast, negative relationships between clade age, clade size, and diversification rate suggest the potential for possible bias in estimated diversification rates, interpreted by some recent authors as support for ecologically mediated limits on diversity. However, evidence from the fossil record indicates that numerous lineages were far more diverse in the past, and that extinction has had an important impact on extant diversity patterns. Thus, failure to adequately account for extinction appears to prevent both rate- and diversity-limited models from fully characterizing richness dynamics in snakes. We suggest that clade-level extinction may provide a key mechanism for explaining negative or hump-shaped relationships between clade age and diversity, and the prevalence of ancient, species-poor lineages in numerous groups.     

Exploring the tempo of species diversification in legumes

Whatever criteria are used to measure evolutionary success – species numbers, geographic range, ecological abundance, ecological and life history diversity, background diversification rates, or the presence of rapidly evolving clades – the legume family is one of the most successful lineages of flowering plants. Despite this, we still know rather little about the dynamics of lineage and species diversification across the family through the Cenozoic, or about the underlying drivers of diversification. There have been few attempts to estimate net species diversification rates or underlying speciation and extinction rates for legume clades, to test whether among-lineage variation in diversification rates deviates from null expectations, or to locate species diversification rate shifts on specific branches of the legume phylogenetic tree. In this study, time-calibrated phylogenetic trees for a set of species-rich legume clades – Calliandra, Indigofereae, Lupinus, Mimosa and Robinieae – and for the legume family as a whole, are used to explore how we might approach these questions. These clades are analysed using recently developed maximum likelihood and Bayesian methods to detect species diversification rate shifts and test for among-lineage variation in speciation, extinction and net diversification rates. Possible explanations for rate shifts in terms of extrinsic factors and/or intrinsic trait evolution are discussed. In addition, several methodological issues and limitations associated with these analyses are highlighted emphasizing the potential to improve our understanding of the evolutionary dynamics of legume diversification by using much more densely sampled phylogenetic trees that integrate information across broad taxonomic, geographical and temporal levels.     

Diversity and Evolution of Body Size in Fishes

The diversity of body sizes observed among species of a clade is a combined result of microevolutionary processes (i.e. natural selection and genetic drift) that cause size changes within phylogenetic lineages, and macroevolutionary processes (i.e. speciation and extinction) that affect net rates of diversification among lineages. Here we assess trends of size diversity and evolution in fishes (non-tetrapod craniates), employing paleontological, macroecological, and phylogenetic information. Fishes are well suited to studies of size diversity and evolution, as they are highly diverse, representing more than 50% of all living vertebrate species, and many fish taxa are well represented in the fossil record from throughout the Phanerozoic. Further, the frequency distributions of sizes among fish lineages resemble those of most other animal taxa, in being right-skewed, even on a log scale. Using an approach that measures rates of size evolution (in darwins) within a formal phylogenetic framework, we interpret the shape of size distributions as a balance between the competing forces of diversification, pushing taxa away from ancestral values, and of conservation, drawing taxa closer to a central tendency. Within this context we show how non-directional mechanisms of evolution (i.e. passive diffusion processes) can produce an hitherto unperceived bias to larger size, when size is measured on the conventional log scale. These results demonstrate how the interpretation of macroecological datasets can be enriched from an historical perspective, and document the ways in which macroevolutionary and microevolutionary processes may be decoupled in the production of size diversity.     

The phylogenetic signal of diversification rates

Hypotheses to explain the causes of diversity gradients have increasingly focused on the factors that actually change species numbers, namely speciation, extinction and dispersal. A common assumption of many of these hypotheses is that there should be phylogenetic signal in diversification rates, yet this assumption has rarely been tested explicitly. In this study, we compile a large data set including 328,219 species of plants, mammals, amphibians and squamates to assess the level of phylogenetic signal in their diversification rates. Significant phylogenetic signal was detected in all data sets, except for squamates, suggesting not only that closely related clades indeed might share similar diversification rates, but also that the level of phylogenetic signal might vary considerably between them. Moreover, there were intriguing differences among taxa in the rate of decay in phylogenetic autocorrelation over time, underscoring the existence of taxon-specific patterns of phylogenetic autocorrelation. These results have important implications for the development of more realistic models of species diversification.     

Dealing with incomplete taxon sampling and diversification of a large clade of mushroom-forming fungi

The absence of an adequate fossil record can hinder understanding the process of diversification that underlies the evolutionary history of a given group. In such cases, investigators have used ultrametric trees derived from molecular data from extant taxa to gain insights into processes of speciation and extinction over time. Inadequate taxon sampling, however, impairs such inferences. In this study, we use simulations to investigate the effect of incomplete taxon sampling on the accumulation of lineages through time for a clade of mushroom-forming fungi, the Hebelomateae. To achieve complete taxon sampling, we use a new Bayesian approach that incorporates substitute lineages to estimate diversification rates. Unlike many studies of animals and plants, we find no evidence of a slowdown in speciation. This indicates the Hebelomateae has not undergone an adaptive radiation. Rather, these fungi have evolved under a relatively constant rate of diversification since their most recent common ancestor, which we date back to the Eocene. The estimated net diversification rate (0.08-0.19 spp./lineage/Ma) is comparable with that of many plants and animals. We suggest that continuous diversification in the Hebelomateae has been facilitated by climatic and vegetation changes throughout the Cenozoic. We also caution against modeling multiple genes as a single partition when performing phylogenetic dating analyses.     

Clade age and not diversification rate explains species richness among animal taxa

Animal taxa show remarkable variability in species richness across phylogenetic groups. Most explanations for this disparity postulate that taxa with more species have phenotypes or ecologies that cause higher diversification rates (i.e., higher speciation rates or lower extinction rates). Here we show that clade longevity, and not diversification rate, has primarily shaped patterns of species richness across major animal clades: more diverse taxa are older and thus have had more time to accumulate species. Diversification rates calculated from 163 species-level molecular phylogenies were highly consistent within and among three major animal phyla (Arthropoda, Chordata, Mollusca) and did not correlate with species richness. Clades with higher estimated diversification rates were younger, but species numbers increased with increasing clade age. A fossil-based data set also revealed a strong, positive relationship between total extant species richness and crown group age across the orders of insects and vertebrates. These findings do not negate the importance of ecology or phenotype in influencing diversification rates, but they do show that clade longevity is the dominant signal in major animal biodiversity patterns. Thus, some key innovations may have acted through fostering clade longevity and not by heightening diversification rate.     

Bias in phylogenetic measurements of extinction and a case study of end‐Permian tetrapods

Extinction risk in the modern world and extinction in the geological past are often linked to aspects of life history or other facets of biology that are phylogenetically conserved within clades. These links can result in phylogenetic clustering of extinction, a measurement comparable across different clades and time periods that can be made in the absence of detailed trait data. This phylogenetic approach is particularly suitable for vertebrate taxa, which often have fragmentary fossil records, but robust, cladistically‐inferred trees. Here we use simulations to investigate the adequacy of measures of phylogenetic clustering of extinction when applied to phylogenies of fossil taxa while assuming a Brownian motion model of trait evolution. We characterize expected biases under a variety of evolutionary and analytical scenarios. Recovery of accurate estimates of extinction clustering depends heavily on the sampling rate, and results can be highly variable across topologies. Clustering is often underestimated at low sampling rates, whereas at high sampling rates it is always overestimated. Sampling rate dictates which cladogram timescaling method will produce the most accurate results, as well as how much of a bias ancestor–descendant pairs introduce. We illustrate this approach by applying two phylogenetic metrics of extinction clustering (Fritz and Purvis's D and Moran's I) to three tetrapod clades across an interval including the Permo‐Triassic mass extinction event. These groups consistently show phylogenetic clustering of extinction, unrelated to change in other quantitative metrics such as taxonomic diversity or extinction intensity.     

Do Mediterranean‐type ecosystems have a common history?—Insights from the Buckthorn family (Rhamnaceae)

Mediterranean‐type ecosystems (MTEs) are remarkable in their species richness and endemism, but the processes that have led to this diversity remain enigmatic. Here, we hypothesize that continent‐dependent speciation and extinction rates have led to disparity in diversity between the five MTEs of the world: the Cape, California, Mediterranean Basin, Chile, and Western Australia. To test this hypothesis, we built a phylogenetic tree for 280 Rhamnaceae species, estimated divergence times using eight fossil calibrations, and used Bayesian methods and simulations to test for differences in diversification rates. Rhamnaceae lineages in MTEs generally show higher diversification rates than elsewhere, but speciation and extinction dynamics show a pattern of continent‐dependence. We detected high speciation and extinction rates in California and significantly lower extinction rates in the Cape and Western Australia. The independent colonization of four of five MTEs may have occurred conterminously in the Oligocene/Early Miocene, but colonization of the Mediterranean Basin happened later, in the Late Miocene. This suggests that the in situ radiations of these clades were initiated before the onset of winter rainfall in these regions. These results indicate independent evolutionary histories of Rhamnaceae in MTEs, possibly related to the intensity of climate oscillations and the geological history of the regions.     

High species diversity in fleshy-fruited tropical understory plants

Key innovations may increase the number of taxa in a clade that possesses the proposed innovation in comparison to its sister group that lacks the trait through either increased speciation or reduced extinction rates. Comparing sister clades across several independent lineages provides statistical support that the trait has increased species diversity. Previous studies have indicated that there may not be a relationship between biotic dispersal and higher species diversity, but only a few of these studies specified habit, habitat, or type of disperser. No previous study has specified all of the above parameters and used a phylogenetic approach. This article examines species diversity in numerous lineages of tropical understory plants with small, fleshy, bird-dispersed fruits for which a reliable estimate of phylogenetic relationships is available. Clades with fleshy fruits are significantly more diverse than sister clades with dry fruits.     

A mitogenomic timescale for birds detects variable phylogenetic rates of molecular evolution and refutes the standard molecular clock

Current understanding of the diversification of birds is hindered by their incomplete fossil record and uncertainty in phylogenetic relationships and phylogenetic rates of molecular evolution. Here we performed the first comprehensive analysis of mitogenomic data of 48 vertebrates, including 35 birds, to derive a Bayesian timescale for avian evolution and to estimate rates of DNA evolution. Our approach used multiple fossil time constraints scattered throughout the phylogenetic tree and accounts for uncertainties in time constraints, branch lengths, and heterogeneity of rates of DNA evolution. We estimated that the major vertebrate lineages originated in the Permian; the 95% credible intervals of our estimated ages of the origin of archosaurs (258 MYA), the amniote-amphibian split (356 MYA), and the archosaur-lizard divergence (278 MYA) bracket estimates from the fossil record. The origin of modern orders of birds was estimated to have occurred throughout the Cretaceous beginning about 139 MYA, arguing against a cataclysmic extinction of lineages at the Cretaceous/Tertiary boundary. We identified fossils that are useful as time constraints within vertebrates. Our timescale reveals that rates of molecular evolution vary across genes and among taxa through time, thereby refuting the widely used mitogenomic or cytochrome b molecular clock in birds. Moreover, the 5-Myr divergence time assumed between 2 genera of geese (Branta and Anser) to originally calibrate the standard mitochondrial clock rate of 0.01 substitutions per site per lineage per Myr (s/s/l/Myr) in birds was shown to be underestimated by about 9.5 Myr. Phylogenetic rates in birds vary between 0.0009 and 0.012 s/s/l/Myr, indicating that many phylogenetic splits among avian taxa also have been underestimated and need to be revised. We found no support for the hypothesis that the molecular clock in birds "ticks" according to a constant rate of substitution per unit of mass-specific metabolic energy rather than per unit of time, as recently suggested. Our analysis advances knowledge of rates of DNA evolution across birds and other vertebrates and will, therefore, aid comparative biology studies that seek to infer the origin and timing of major adaptive shifts in vertebrates.     

The role of frugivory in the diversification of bats in the Neotropics

Aim Ecological interactions are among the most important biotic factors influencing the processes of speciation and extinction. Our aim was to test whether diversification rates of New World Noctilionoidea bats are associated with specialization for frugivory, and how this pattern differs between the mainland and the West Indies. Location The New World. Methods We reconstructed a time‐calibrated molecular phylogenetic hypothesis for the New World genera of the superfamily Noctilionoidea. We compiled data on diet, morphology, geographical distribution and number of ecoregions in which each genus occurs. Then, using the phylogenetic tree constructed, we tested whether diversification was driven by diet (animalivorous and sanguinivorous versus nectarivorous and frugivorous) and specialization for frugivory. Afterwards, we conducted phylogenetic comparative analyses to identify correlates of species richness and net diversification rates. Results The diversification rate was higher in mutualistic than in antagonistic clades in mainland and Antillean biogeographical scenarios, but only strictly frugivorous clades showed a markedly higher diversification rate than the rest of the genera. Geographical range and number of ecoregions were positively associated with species richness and diversification rate in continental and insular lineages. Lower body mass, lower forearm length and specialization for frugivory were significantly positively correlated with higher diversification rates in continental lineages, whereas these parameters were negatively correlated in Antillean lineages. Main conclusions The direction of the relationship of intrinsic factors (specialization for frugivory and body size) with diversification of noctilionoid bats depends on the biogeographical context, whereas the direction of the relationship of extrinsic factors (geographical range and number of ecoregions) with diversification is consistent in both mainland and the West Indian lineages.     

Angiosperm diversification through time

The extraordinary diversity of angiosperms is the ultimate outcome of the interplay of speciation and extinction, which determine the net diversification of different lineages. We document the temporal trends of angiosperm diversification rates during their early history. Absolute diversification rates were estimated for order-level clades using ages derived from relaxed molecular clock analyses that included or excluded a maximal constraint to angiosperm age. Diversification rates for angiosperms as a whole ranged from 0.0781 to 0.0909 net speciation events per million years, with dates from the constrained analysis. Diversification through time plots show an inverse relationship between clade age and rate, where the younger clades tend to have the highest rates. Angiosperm diversity is found to have mixed origins: slightly less than half of the living species belong to lineages with low to moderate diversification rates, which appeared between 130 and 102 Mya (Barremian-uppermost Albian; Lower Cretaceous). Slightly over half of the living species belong to lineages with moderate to high diversification rates, which appeared between 102 and 77 Mya (Cenomanian-mid Campanian; Upper Cretaceous). Terminal lineages leading to living angiosperm species, however, may have originated soon or long after the phylogenetic differentiation of the clade to which they belong.     

When Can Clades Be Potentially Resolved with Morphology?

Morphology-based phylogenetic analyses are the only option for reconstructing relationships among extinct lineages, but often find support for conflicting hypotheses of relationships. The resulting lack of phylogenetic resolution is generally explained in terms of data quality and methodological issues, such as character selection. A previous suggestion is that sampling ancestral morphotaxa or sampling multiple taxa descended from a long-lived, unchanging lineage can also yield clades which have no opportunity to share synapomorphies. This lack of character information leads to a lack of ‘intrinsic’ resolution, an issue that cannot be solved with additional morphological data. It is unclear how often we should expect clades to be intrinsically resolvable in realistic circumstances, as intrinsic resolution must increase as taxonomic sampling decreases. Using branching simulations, I quantify intrinsic resolution across several models of morphological differentiation and taxonomic sampling. Intrinsically unresolvable clades are found to be relatively frequent in simulations of both extinct and living taxa under realistic sampling scenarios, implying that intrinsic resolution is an issue for morphology-based analyses of phylogeny. Simulations which vary the rates of sampling and differentiation were tested for their agreement to observed distributions of durations from well-sampled fossil records and also having high intrinsic resolution. This combination only occurs in those datasets when differentiation and sampling rates are both unrealistically high relative to branching and extinction rates. Thus, the poor phylogenetic resolution occasionally observed in morphological phylogenetics may result from a lack of intrinsic resolvability within groups.     

The shape and temporal dynamics of phylogenetic trees arising from geographic speciation

Phylogenetic trees often depart from the expectations of stochastic models, exhibiting imbalance in diversification among lineages and slowdowns in the rate of lineage accumulation through time. Such departures have led to a widespread perception that ecological differences among species or adaptation and subsequent niche filling are required to explain patterns of diversification. However, a key element missing from models of diversification is the geographical context of speciation and extinction. In this study, we develop a spatially explicit model of geographic range evolution and cladogenesis, where speciation arises via vicariance or peripatry, and explore the effects of these processes on patterns of diversification. We compare the results with those observed in 41 reconstructed avian trees. Our model shows that nonconstant rates of speciation and extinction are emergent properties of the apportioning of geographic ranges that accompanies speciation. The dynamics of diversification exhibit wide variation, depending on the mode of speciation, tendency for range expansion, and rate of range evolution. By varying these parameters, the model is able to capture many, but not all, of the features exhibited by birth-death trees and extant bird clades. Under scenarios with relatively stable geographic ranges, strong slowdowns in diversification rates are produced, with faster rates of range dynamics leading to constant or accelerating rates of apparent diversification. A peripatric model of speciation with stable ranges also generates highly unbalanced trees typical of bird phylogenies but fails to produce realistic range size distributions among the extant species. Results most similar to those of a birth-death process are reached under a peripatric speciation scenario with highly volatile range dynamics. Taken together, our results demonstrate that considering the geographical context of speciation and extinction provides a more conservative null model of diversification and offers a very different perspective on the phylogenetic patterns expected in the absence of ecology.     

Exploring the phylogenetic history of mammal species richness

Aim At broad geographical scales, species richness is a product of three basic processes: speciation, extinction and migration. However, determining which of these processes predominates is a major challenge. Whilst palaeontological studies can provide information on speciation and extinction rates, data are frequently lacking. Here we use a recent dated phylogenetic tree of mammals to explore the relative importance of these three processes in structuring present‐day richness gradients. Location The global terrestrial biosphere. Methods We combine macroecological data with phylogenetic methods more typically used in community ecology to describe the phylogenetic history of regional faunas. Using simulations, we explore two simple phylogenetic metrics, the mean and variance in the pairwise distances between taxa, and describe their relationship to phylogenetic tree topology. We then use these two metrics to characterize the evolutionary relationships among mammal species assemblages across the terrestrial biome. Results We show that the mean and variance in the pairwise distances describe phylogenetic tree topology well, but are less sensitive to phylogenetic uncertainty than more direct measures of tree shape. We find the phylogeny for South American mammals is imbalanced and ‘stemmy’ (long branches towards the root), consistent with recent diversification within evolutionarily disparate lineages. In contrast, the phylogeny for African mammals is balanced and ‘tippy’ (long branches towards the tips), more consistent with the slow accumulation of diversity over long times, reflecting the Old World origin of many mammal clades. Main conclusions We show that phylogeny can accurately capture biogeographical processes operating at broad spatial scales and over long time periods. Our results support inferences from the fossil record – that the New World tropics are a diversity cradle whereas the Old World tropics are a museum of old diversity.