Detecting shifts in diversification rates without fossils

Studies of shifts in diversification rates and adaptive radiations are difficult when there are no fossils because past events cannot be inferred. The phylogenies of recent species, however, allow one to infer the patterns of past diversifications. I present a new method for estimating the diversification rate of a lineage, provided that a phylogeny of recent species, constructed, for instance, with molecular data, is available. This method was inspired by survival models and takes into account species that are not included in detailed phylogenetic data, provided that approximate dates of origin of these species are known. Likelihood ratio tests and Akaike Information Criterion make it possible to test for differences in diversification among lineages or groups of lineages and, thus, to evaluate adaptive radiation hypotheses. The present modeling approach can easily be extended to include temporal variations in diversification rates. A simulation study showed that the method is statistically consistent, avoiding Type I and Type II errors, and that it is robust to periodic or random fluctuations in the speciation rate. An example is presented with a composite phylogeny of primates.     

Likelihood methods for detecting temporal shifts in diversification rates

Maximum likelihood is a potentially powerful approach for investigating the tempo of diversification using molecular phylogenetic data. Likelihood methods distinguish between rate-constant and rate-variable models of diversification by fitting birth-death models to phylogenetic data. Because model selection in this context is a test of the null hypothesis that diversification rates have been constant over time, strategies for selecting best-fit models must minimize Type I error rates while retaining power to detect rate variation when it is present. Here I examine model selection, parameter estimation, and power to reject the null hypothesis using likelihood models based on the birth-death process. The Akaike information criterion (AIC) has often been used to select among diversification models; however, I find that selecting models based on the lowest AIC score leads to a dramatic inflation of the Type I error rate. When appropriately corrected to reduce Type I error rates, the birth-death likelihood approach performs as well or better than the widely used gamma statistic, at least when diversification rates have shifted abruptly over time. Analyses of datasets simulated under a range of rate-variable diversification scenarios indicate that the birth-death likelihood method has much greater power to detect variation in diversification rates when extinction is present. Furthermore, this method appears to be the only approach available that can distinguish between a temporal increase in diversification rates and a rate-constant model with nonzero extinction. I illustrate use of the method by analyzing a published phylogeny for Australian agamid lizards.     

A new method for handling missing species in diversification analysis applicable to randomly or nonrandomly sampled phylogenies

Chronograms from molecular dating are increasingly being used to infer rates of diversification and their change over time. A major limitation in such analyses is incomplete species sampling that moreover is usually nonrandom. While the widely used γ statistic with the Monte Carlo constant-rates test or the birth-death likelihood analysis with the δ AICrc test statistic are appropriate for comparing the fit of different diversification models in phylogenies with random species sampling, no objective automated method has been developed for fitting diversification models to nonrandomly sampled phylogenies. Here, we introduce a novel approach, CorSiM, which involves simulating missing splits under a constant rate birth-death model and allows the user to specify whether species sampling in the phylogeny being analyzed is random or nonrandom. The completed trees can be used in subsequent model-fitting analyses. This is fundamentally different from previous diversification rate estimation methods, which were based on null distributions derived from the incomplete trees. CorSiM is automated in an R package and can easily be applied to large data sets. We illustrate the approach in two Araceae clades, one with a random species sampling of 52% and one with a nonrandom sampling of 55%. In the latter clade, the CorSiM approach detects and quantifies an increase in diversification rate, whereas classic approaches prefer a constant rate model; in the former clade, results do not differ among methods (as indeed expected since the classic approaches are valid only for randomly sampled phylogenies). The CorSiM method greatly reduces the type I error in diversification analysis, but type II error remains a methodological problem.     

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.     

Detecting local diversity‐dependence in diversification

Whether there are ecological limits to species diversification is a hotly debated topic. Molecular phylogenies show slowdowns in lineage accumulation, suggesting that speciation rates decline with increasing diversity. A maximum‐likelihood (ML) method to detect diversity‐dependent (DD) diversification from phylogenetic branching times exists, but it assumes that diversity‐dependence is a global phenomenon and therefore ignores that the underlying species interactions are mostly local, and not all species in the phylogeny co‐occur locally. Here, we explore whether this ML method based on the nonspatial diversity‐dependence model can detect local diversity‐dependence, by applying it to phylogenies, simulated with a spatial stochastic model of local DD speciation, extinction, and dispersal between two local communities. We find that type I errors (falsely detecting diversity‐dependence) are low, and the power to detect diversity‐dependence is high when dispersal rates are not too low. Interestingly, when dispersal is high the power to detect diversity‐dependence is even higher than in the nonspatial model. Moreover, estimates of intrinsic speciation rate, extinction rate, and ecological limit strongly depend on dispersal rate. We conclude that the nonspatial DD approach can be used to detect diversity‐dependence in clades of species that live in not too disconnected areas, but parameter estimates must be interpreted cautiously.     

Niche evolution and diversification in a Neotropical radiation of birds (Aves: Furnariidae)

Rapid diversification may be caused by ecological adaptive radiation via niche divergence. In this model, speciation is coupled with niche divergence and lineage diversification is predicted to be correlated with rates of niche evolution. Studies of the role of niche evolution in diversification have generally focused on ecomorphological diversification but climatic‐niche evolution may also be important. We tested these alternatives using a phylogeny of 298 species of ovenbirds (Aves: Furnariidae). We found that within Furnariidae, variation in species richness and diversification rates of subclades were best predicted by rate of climatic‐niche evolution than ecomorphological evolution. Although both are clearly important, univariate regression and multivariate model averaging more consistently supported the climatic‐niche as the best predictor of lineage diversification. Our study adds to the growing body of evidence, suggesting that climatic‐niche divergence may be an important driver of rapid diversification in addition to ecomorphological evolution. However, this pattern may depend on the phylogenetic scale at which rate heterogeneity is examined.     

Testing for temporal variation in diversification rates when sampling is incomplete and nonrandom

A common pattern found in phylogeny-based empirical studies of diversification is a decrease in the rate of lineage accumulation toward the present. This early-burst pattern of cladogenesis is often interpreted as a signal of adaptive radiation or density-dependent processes of diversification. However, incomplete taxonomic sampling is also known to artifactually produce patterns of rapid initial diversification. The Monte Carlo constant rates (MCCR) test, based upon Pybus and Harvey's gamma (γ)-statistic, is commonly used to accommodate incomplete sampling, but this test assumes that missing taxa have been randomly pruned from the phylogeny. Here we use simulations to show that preferentially sampling disparate lineages within a clade can produce severely inflated type-I error rates of the MCCR test, especially when taxon sampling drops below 75%. We first propose two corrections for the standard MCCR test, the proportionally deeper splits that assumes missing taxa are more likely to be recently diverged, and the deepest splits only MCCR that assumes that all missing taxa are the youngest lineages in the clade, and assess their statistical properties. We then extend these two tests into a generalized form that allows the degree of nonrandom sampling (NRS)to be controlled by a scaling parameter, α. This generalized test is then applied to two recent studies. This new test allows systematists to account for nonrandom taxonomic sampling when assessing temporal patterns of lineage diversification in empirical trees. Given the dramatic affect NRS can have on the behavior of the MCCR test, we argue that evaluating the sensitivity of this test to NRS should become the norm when investigating patterns of cladogenesis in incompletely sampled phylogenies.     

High tropical net diversification drives the New World latitudinal gradient in palm (Arecaceae) species richness

Aim Species richness exhibits striking geographical variation, but the processes that drive this variation are unresolved. We investigated the relative importance of two hypothesized evolutionary causes for the variation in palm species richness across the New World: time for diversification and evolutionary (net diversification) rate. Palms have a long history in the region, with the major clades diversifying during the Tertiary (65–2 Ma). Location Tropical and subtropical America (34° N–34° S; 33–120° W). Methods Using range maps, palm species richness was estimated in a 1° × 1° grid. Mean lineage net diversification was estimated by the mean phylogenetic root distance (MRD), the average number of nodes separating a species from the base of the palm phylogeny for the species in each grid cell. If evolutionary rate limits richness, then richness should increase with MRD. If time limits richness, then old, relict species (with low root distance) should predominantly occur in long‐inhabited and therefore species‐rich areas. Hence, richness should decrease with MRD. To determine the influence of net diversification across different time frames, MRD was computed for subtribe, genus and species levels within the phylogeny, and supplemented with the purely tip‐level measure, mean number of species per genus (MS/G). Correlations and regressions, in combination with eigenvector‐based spatial filtering, were used to assess the relationship between species richness, the net diversification measures, and potential environmental and geographical drivers. Results Species richness increased with all net diversification measures. The regression models showed that richness and the net diversification measures increased with decreasing (absolute) latitude and, less strongly, with increasing energy/temperature and water availability. These patterns therefore reflect net diversification at both deep and shallow levels in the phylogeny. Richness also increased with range in elevation, but this was only reflected in the MS/G pattern and therefore reflects recent diversification. Main conclusions The geographical patterns in palm species richness appear to be predominantly the result of elevated net diversification rates towards the equator and in warm, wet climates, sustained throughout most of the Tertiary. Late‐Tertiary orogeny has caused localized increases in net diversification rates that have also made a mark on the richness pattern.     

When are adaptive radiations replicated in areas? Ecological opportunity and unexceptional diversification in West Indian dipsadine snakes (Colubridae: Alsophiini)

Aim We examine diversification in Caribbean alsophiine snakes and hypothesize that, given the ecological opportunity presented by colonization of the West Indies, alsophiines should show the signature of an early burst of diversification and associated low within‐clade ecological and morphological disparification. We also test whether changes in morphology and ecology are associated with changes in diversification rate, as trait‐dependent diversification is hypothesized to affect historical inferences of diversification and disparification. Finally, as replicated radiations are found across the West Indies in the anoles, we test for significant differences in ecological and morphological assemblages and rates among the major island groups. Location The West Indies. Methods A time‐calibrated phylogeny produced from six genes using relaxed clock methods in beast was constructed to estimate ancestral areas using Lagrange . Maximum body size and ecological niche were scored for all species in the phylogeny, and comparative phylogenetic methods in R using geiger , laser , ape and our own code were used to examine diversification through time, disparification and trait‐dependent diversification from this dated phylogeny. Results The pattern of species diversification did not differ significantly from the Yule model of diversification. Morphology and ecology fitted a Brownian and white noise model of diversification, respectively. Although not significantly different, morphological disparification was lower than the Brownian null model, whereas ecological disparification was significantly greater than the null. Trait‐dependent diversification analyses suggested that the constant null models provided the best fit to these data. There was no significant signal of rate variation among the major island groups for size, but moderate evidence for niche. Main conclusions Although ecological opportunity was similarly present for alsophiines as it was for anoles, the snakes fail to show an early burst of speciation. Potential reasons for this include the young age of the group, and staggered diversification due to waiting times between island colonization. In turn, ecological and morphological disparities do not necessarily follow predictable patterns related to species diversification. Thus, the presence of ecological opportunity alone is not necessarily sufficient to trigger replicated adaptive radiations in areas.     

Heterogeneity in the rate of molecular sequence evolution substantially impacts the accuracy of detecting shifts in diversification rates

As species richness varies along the tree of life, there is a great interest in identifying factors that affect the rates by which lineages speciate or go extinct. To this end, theoretical biologists have developed a suite of phylogenetic comparative methods that aim to identify where shifts in diversification rates had occurred along a phylogeny and whether they are associated with some traits. Using these methods, numerous studies have predicted that speciation and extinction rates vary across the tree of life. In this study, we show that asymmetric rates of sequence evolution lead to systematic biases in the inferred phylogeny, which in turn lead to erroneous inferences regarding lineage diversification patterns. The results demonstrate that as the asymmetry in sequence evolution rates increases, so does the tendency to select more complicated models that include the possibility of diversification rate shifts. These results thus suggest that any inference regarding shifts in diversification pattern should be treated with great caution, at least until any biases regarding the molecular substitution rate have been ruled out.     

SYNDROME‐DRIVEN DIVERSIFICATION IN A MEDITERRANEAN ECOSYSTEM

Phylogenetic methods to detect lineage diversification have been traditionally used within a particular taxonomic clade, but rarely applied to detect local diversification. For understanding in situ diversification triggered by novel conditions it is necessary to focus on the time slice where such conditions occur. These new conditions may differentially affect the diversification rate of lineages with different morpho‐functional syndromes. A prominent example of these processes occurs in the Mediterranean Basin, where climate arising along the Tertiary/Quaternary transition acted as an environmental filter. In this context, lineages with different syndromes (sclerophyllous and nonsclerophyllous) are hypothesized to have different local diversification rates after the rise of the Mediterranean conditions. We used macroevolutionary methods of time‐dependent diversification on a calibrated local phylogeny accommodating topological and chronological uncertainty to test syndrome‐driven diversification in Mediterranean shrublands from the eastern Iberian Peninsula. We found phylogenetic evidence of higher speciation associated with the nonsclerophyllous syndrome, although extinction rates were similar between syndromes. Consequently a syndrome‐driven local diversification has occurred in shrublands under Mediterranean conditions. The results provide an example of how the integration of the environmental filter in a dated phylogeny may recreate the local history of lineages and help to explain assembly processes in Mediterranean ecosystems.     

Phylogenetics of the Antopocerus-Modified Tarsus Clade of Hawaiian Drosophila: Diversification across the Hawaiian Islands

The Hawaiian Drosophilidae radiation is an ecologically and morphologically diverse clade of almost 700 described species. A phylogenetic approach is key to understanding the evolutionary forces that have given rise to this diverse lineage. Here we infer the phylogeny for the antopocerus, modified tarsus and ciliated tarsus (AMC) clade, a lineage comprising 16% (91 of 687 species) of the described Hawaiian Drosophilidae. To improve on previous analyses we constructed the largest dataset to date for the AMC, including a matrix of 15 genes for 68 species. Results strongly support most of the morphologically defined species groups as monophyletic. We explore the correlation of increased diversity in biogeography, sexual selection and ecology on the present day diversity seen in this lineage using a combination of dating methods, rearing records, and distributional data. Molecular dating analyses indicate that AMC lineage started diversifying about 4.4 million years ago, culminating in the present day AMC diversity. We do not find evidence that ecological speciation or sexual selection played a part in generating this diversity, but given the limited number of described larval substrates and secondary sexual characters analyzed we can not rule these factors out entirely. An increased rate of diversification in the AMC is found to overlap with the emergence of multiple islands in the current chain of high islands, specifically Oahu and Kauai.     

Influence of sexual selection and feeding functional morphology on diversification rate of parrotfishes (Scaridae)

Scaridae (parrotfishes) is a prominent clade of 96 species that shape coral reef communities worldwide through their actions as grazing herbivores. Phylogenetically nested within Labridae, the profound ecological impact and high species richness of parrotfishes suggest that their diversification and ecological success may be linked. Here, we ask whether parrotfish evolution is characterized by a significant burst of lineage diversification and whether parrotfish diversity is shaped more strongly by sexual selection or modifications of the feeding mechanism. We first examined scarid diversification within the greater context of labrid diversity. We used a supermatrix approach for 252 species to propose the most extensive phylogenetic hypothesis of Labridae to date, and time-calibrated the phylogeny with fossil and biogeographical data. Using divergence date estimates, we find that several parrotfish clades exhibit the highest diversification rates among all labrid lineages. Furthermore, we pinpoint a rate shift at the shared ancestor of Scarus and Chlorurus, a scarid subclade characterized by territorial behaviour and strong sexual dichromatism, suggesting that sexual selection was a major factor in parrotfish diversification. Modifications of the pharyngeal and oral jaws that happened earlier in parrotfish evolution may have contributed to this diversity by establishing parrotfishes as uniquely capable reef herbivores.     

The effect of environmental diversification on species diversification in New Caledonian caddisflies (Insecta: Trichoptera: Hydropsychidae)

Aim To test whether environmental diversification played a role in the diversification of the New Caledonian Hydropsychinae caddisflies. Location New Caledonia, south‐west Pacific. Methods The phylogeny of the New Caledonian Hydropsychinae caddisflies was hypothesized using parsimony and Bayesian methods on molecular characters. The Bayesian analysis was the basis for a comparative analysis of the correlation between phylogeny and three environmental factors: geological substrate (ultrabasic, non‐ultrabasic), elevation and precipitation. Phylogenetic divergence times were estimated using a relaxed clock method, and environmental factors were mapped onto a lineage‐through‐time plot to investigate the timing of environmental diversification in relation to species radiation. The correlation between rainfall and elevation was tested using independent contrasts, and the gamma statistic was calculated to infer the diversification pattern of the group. Results The diversification of extant Orthopsyche–Caledopsyche species began in the Middle–Late Oligocene, when much of the island of New Caledonia was covered by ultrabasic substrate and mountain forming was prevalent. Most lineages originated in the Middle–Late Miocene, a period associated with long‐term climate oscillation. Optimization of environmental factors on the phylogeny demonstrated that the New Caledonian Hydropsychinae group adapted to ultrabasic substrate early in its evolutionary history. The clade living mostly on ultrabasic substrate was far more species‐rich than the clade living mostly on non‐ultrabasic substrate. Elevation and rainfall were significantly correlated with each other. The lineage‐through‐time plot revealed that the main environmental diversification preceded species diversification. A constant speciation through time was rejected, and the negative gamma indicates that most of the diversification occurred early in the history of the clade. According to the inferred phylogeny, the genus Orthopsyche McFarlane is a synonym under Caledopsyche Kimmins, and Abacaria caledona Oláh & Barnard should also be included in Caledopsyche. Main conclusions The age of the radiation does not support a vicariance origin of New Caledonian Hydropsychinae caddisflies. Environmental diversification pre‐dates lineage diversification, and thus environmental heterogeneity potentially played a role in the diversification of the group, by providing a variety of fragmented habitats to disperse into, promoting speciation. The negative gamma indicates that the speciation rate slowed as niches started to fill.     

Speciation dynamics during the global radiation of extant bats

Species richness varies widely across extant clades, but the causes of this variation remain poorly understood. We investigate the role of diversification rate heterogeneity in shaping patterns of diversity across families of extant bats. To provide a robust framework for macroevolutionary inference, we assemble a time‐calibrated, species‐level phylogeny using a supermatrix of mitochondrial and nuclear sequence data. We analyze the phylogeny using a Bayesian method for modeling complex evolutionary dynamics. Surprisingly, we find that variation in family richness can largely be explained without invoking heterogeneous diversification dynamics. We document only a single well‐supported shift in diversification dynamics across bats, occurring at the base of the subfamily Stenodermatinae. Bat diversity is phylogenetically imbalanced, but—contrary to previous hypotheses—this pattern is unexplained by any simple patterns of diversification rate heterogeneity. This discordance may indicate that diversification dynamics are more complex than can be captured using the statistical tools available for modeling data at this scale. We infer that bats as a whole are almost entirely united into one macroevolutionary cohort, with decelerating speciation through time. There is also a significant relationship between clade age and richness, suggesting that global bat diversity may still be expanding.     

A Dated Phylogeny Complements Macroecological Analysis to Explain the Diversity Patterns in Geonoma (Arecaceae)

Integrating phylogenetic data into macroecological studies of biodiversity patterns may complement the information provided by present‐day spatial patterns. In the present study, we used range map data for all Geonoma (Arecaceae) species to assess whether Geonoma species composition forms spatially coherent floristic clusters. We then evaluated the extent to which the spatial variation in species composition reflects present‐day environmental variation vs. nonenvironmental spatial effects, as expected if the pattern reflects historical biogeography. We also examined the degree of geographic structure in the Geonoma phylogeny. Finally, we used a dated phylogeny to assess whether species richness within the floristic clusters was constrained by a specific historical biogeographic driver, namely time‐for‐diversification. A cluster analysis identified six spatially coherent floristic clusters, four of which were used to reveal a significant geographic phylogenetic structure. Variation partitioning analysis showed that 56 percent of the variation in species composition could be explained by spatial variables alone, consistent with historical factors having played a major role in generating the Geonoma diversity pattern. To test for a time‐for‐diversification effect, we correlated four different species richness measures with the diversification time of the earliest large lineage that is characteristic of each cluster. In support of this hypothesis, we found that geographic areas with higher richness contained older radiations. We conclude that current geographic diversity patterns in Geonoma reflect the present‐day climate, but to a larger extent are related to nonenvironmental spatial constraints linked to colonization time, dispersal limitation, and geological history, followed by within‐area evolutionary diversification. Abstract in Spanish is available at http://www.blackwell‐synergy.com/loi/btp .     

Speciation and radiations track climate transitions since the Miocene Climatic Optimum: a case study of southern African chameleons

Aim The high amount of species diversity concentrated in southern Africa has been attributed to palaeoclimatic factors, and the timing of radiations in some taxa corresponds to global palaeoclimatic trends. Using dwarf chameleons (Bradypodion: Chamaeleonidae) as a model system, we explored the relationship between palaeoclimatic fluctuations and cladogenesis with respect to both temporal and spatial patterns in an effort to understand the process of speciation in southern Africa. Location South Africa, with particular emphasis on the Cape Floristic Region and the Maputaland–Pondoland–Albany hotspot. Methods Mitochondrial sequence data (ND2 and 16S) were used to estimate the timing of major radiations and to examine the number of lineages through time. A dated phylogeny was constructed using Bayesian phylogenetic reconstruction, and a Bayesian relaxed molecular clock was used to estimate divergence times. Spatial data and lineage‐through‐time plots were used to identify geographic regions that underwent diversification in connection with major climatic events. Both parsimony and likelihood optimizations of habitat type on the phylogeny were used to determine whether major habitat shifts have occurred. On a coarse scale (half‐degree grid cells), phylogenetic diversity (sum of the branch lengths linking terminals) was compared with species richness (absolute number of species) to identify areas of conservation importance. Results The complete species phylogeny of dwarf chameleons shows that the timing and mode of diversification exhibit spatio‐temporal patterns that link to phases in the evolution of southern Africa’s climate over the last 14 Myr. Optimizations of habitat on the phylogenetic tree show a progression from closed to open habitats since the Mid‐Miocene, corresponding to the shift from C₃ to C₄ environments, and later with the development of south‐western Africa’s winter‐rainfall regime. These shifts are not simultaneous across the region, with different geographic centres of diversity generated during different time periods. Main conclusions Regions that are prominent centres of chameleon diversification are encompassed by the current biodiversity hotspots as shown by chameleon species richness and phylogenetic diversity. Diversity within the Cape Floristic Region appears to be the result of a Late Pliocene radiation, whereas the diversity encompassed within the Maputaland–Pondoland–Albany hotspot is an aggregate of asynchronous radiation events, probably influenced by lineage losses. Overall, dwarf chameleons have experienced a shift in habitat types, with recent radiations occupying open habitats, and older lineages persisting in relictual forested habitats, corresponding to the continental shift of vegetation types since the Miocene Climatic Optimum.     

Tightly congruent bursts of lineage and phenotypic diversification identified in a continental ant radiation

Adaptive diversification is thought to be shaped by ecological opportunity. A prediction of this ecological process of diversification is that it should result in congruent bursts of lineage and phenotypic diversification, but few studies have found this expected association. Here, we study the relationship between rates of lineage diversification and body size evolution in the turtle ants, a diverse Neotropical clade. Using a near complete, time‐calibrated phylogeny we investigated lineage diversification dynamics and body size disparity through model fitting analyses and estimation of per‐lineage rates of cladogenesis and phenotypic evolution. We identify an exceptionally high degree of congruence between the high rates of lineage and body size diversification in a young clade undergoing renewed diversification in the ecologically distinct Chacoan biogeographical region of South America. It is likely that the region presented turtle ants with novel ecological opportunity, which facilitated a nested burst of diversification and phenotypic evolution within the group. Our results provide a compelling quantitative example of tight congruence between rates of lineage and phenotypic diversification, meeting the key predicted pattern of adaptive diversification shaped by ecological opportunity.     

Late Miocene diversification of the genus Hydrochus (Coleoptera, Hydrochidae) in the west Mediterranean area

We provide a reconstruction of the phylogenetic relationships, the geographical and temporal origin, and the mode of diversification of the Mediterranean species of the aquatic beetle family Hydrochidae (Coleoptera, Hydrophiloidea). A total of ca. 3KB of sequence data of three mitochondrial and two nuclear genes were used to reconstruct the phylogeny of 62 specimens of 21 species of Hydrochus, including all western Mediterranean species but one. We estimated the times of divergence using Bayesian methods and an evolutionary rate of 0.0115 substitutions/site/MY, and used an ultrametric calibrated tree to construct a Lineage Through Time (LTT) plot to test alternative models of diversification. A well resolved, well supported phylogeny showed that all western Mediterranean Hydrochus formed a clade, sister to a group including species with a central and eastern European distribution. The origin of the western Mediterranean clade was estimated to be at ca. 13MY, and the speciation events took place between this time and the end of the Messinian, at about 5.3MY. The LTT plot best fitted a model with a shift in the rate of diversification at ca. 8 MY, with a single speciation event (originating two Iberian endemics) subsequent to this period. We conclude that most of the western Mediterranean species of Hydrochidae, including the Ibero-Maghrebian endemics, are ancient elements likely to have remained in the same geographical area since their Miocene origin. Our results add to a growing body of evidence showing the importance of Mediterranean long-term, Tertiary refugia as both cradles and museums of diversity.