Evidence of constant diversification punctuated by a mass extinction in the African cycads

The recent evidence that extant cycads are not living fossils triggered a renewed search for a better understanding of their evolutionary history. In this study, we investigated the evolutionary diversification history of the genus Encephalartos, a monophyletic cycad endemic to Africa. We found an antisigmoidal pattern with a plateau and punctual explosive radiation. This pattern is typical of a constant radiation with mass extinction. The rate shift that we found may therefore be a result of a rapid recolonization of niches that have been emptied owing to mass extinction. Because the explosive radiation occurred during the transition Pliocene–Pleistocene, we argued that the processes might have been climatically mediated.

Phylogenetic plant community structure along elevation is lineage specific

The trend of closely related taxa to retain similar environmental preferences mediated by inherited traits suggests that several patterns observed at the community scale originate from longer evolutionary processes. While the effects of phylogenetic relatedness have been previously studied within a single genus or family, lineage-specific effects on the ecological processes governing community assembly have rarely been studied for entire communities or flora. Here, we measured how community phylogenetic structure varies across a wide elevation gradient for plant lineages represented by 35 families, using a co-occurrence index and net relatedness index (NRI). We propose a framework that analyses each lineage separately and reveals the trend of ecological assembly at tree nodes. We found prevailing phylogenetic clustering for more ancient nodes and overdispersion in more recent tree nodes. Closely related species may thus rapidly evolve new environmental tolerances to radiate into distinct communities, while older lineages likely retain inherent environmental tolerances to occupy communities in similar environments, either through efficient dispersal mechanisms or the exclusion of older lineages with more divergent environmental tolerances. Our study illustrates the importance of disentangling the patterns of community assembly among lineages to better interpret the ecological role of traits. It also sheds light on studies reporting absence of phylogenetic signal, and opens new perspectives on the analysis of niche and trait conservatism across lineages.

First evidence for a massive extinction event affecting bees close to the K-T boundary

Bees and eudicot plants both arose in the mid-late Cretaceous, and their co-evolutionary relationships have often been assumed as an important element in the rise of flowering plants. Given the near-complete dependence of bees on eudicots we would expect that major extinction events affecting the latter would have also impacted bees. However, given the very patchy distribution of bees in the fossil record, identifying any such extinctions using fossils is very problematic. Here we use molecular phylogenetic analyses to show that one bee group, the Xylocopinae, originated in the mid-Cretaceous, coinciding with the early radiation of the eudicots. Lineage through time analyses for this bee subfamily show very early diversification, followed by a long period of seemingly no radiation and then followed by rapid diversification in each of the four constituent tribes. These patterns are consistent with both a long-fuse model of radiation and a massive extinction event close to the K-T boundary. We argue that massive extinction is much more plausible than a long fuse, given the historical biogeography of these bees and the diversity of ecological niches that they occupy. Our results suggest that events near the K-T boundary would have disrupted many plant-bee relationships, with major consequences for the subsequent evolution of eudicots and their pollinators.

Carving out turf in a biodiversity hotspot: multiple, previously unrecognized shrew species co-occur on Java Island, Indonesia

In theory, competition among species in a shared habitat results in niche separation. In the case of small recondite mammals such as shrews, little is known about their autecologies, leaving open questions regarding the degree to which closely related species co-occur and how or whether ecological niches are partitioned. The extent to which species are able to coexist may depend on the degree to which they exploit different features of their habitat, which may in turn influence our ability to recognize them as species. We explored these issues in a biodiversity hotspot, by surveying shrew (genus Crocidura) diversity on the Indonesian island of Java. We sequenced portions of nine unlinked genes in 100-117 specimens of Javan shrews and incorporated homologous data from most known Crocidura species from other parts of island South-East Asia. Current taxonomy recognizes four Crocidura species on Java, including two endemics. However, our phylogenetic, population genetic and species delimitation analyses identify five species on the island, and all are endemic to Java. While the individual ranges of these species may not overlap in their entirety, we found up to four species living syntopically and all five species co-occurring on one mountain. Differences in species' body size, use of above ground-level habitats by one species and habitat partitioning along ecological gradients may have facilitated species diversification and coexistence.

Diversification rates have declined in the Malagasy herpetofauna

The evolutionary origins of Madagascar's biodiversity remain mysterious despite the fact that relative to land area, there is no other place with consistently high levels of species richness and endemism across a range of taxonomic levels. Most efforts to explain diversification on the island have focused on geographical models of speciation, but recent studies have begun to address the island's accumulation of species through time, although with conflicting results. Prevailing hypotheses for diversification on the island involve either constant diversification rates or scenarios where rates decline through time. Using relative-time-calibrated phylogenies for seven endemic vertebrate clades and a model-fitting framework, I find evidence that diversification rates have declined through time on Madagascar. I show that diversification rates have clearly declined throughout the history of each clade, and models invoking diversity-dependent reductions to diversification rates best explain the diversification histories for each clade. These results are consistent with the ecological theory of adaptive radiation, and, coupled with ancillary observations about ecomorphological and life-history evolution, strongly suggest that adaptive radiation was an important formative process for one of the most species-rich regions on the Earth. These results cast the Malagasy biota in a new light and provide macroevolutionary justification for conservation initiatives.

Predicting the loss of phylogenetic diversity under non-stationary diversification models

For many species, the current high rates of extinction are likely to result in a significant loss of biodiversity. The evolutionary heritage of biodiversity is frequently quantified by a measure called phylogenetic diversity (PD). We predict the loss of PD under a wide class of phylogenetic tree models, where speciation rates and extinction rates may be time-dependent, and assuming independent random species extinctions at the present. We study the loss of PD when K contemporary species are selected uniformly at random from the N extant species as the surviving species, while the remaining N-K become extinct (N and K being random variables). We consider two models of species sampling, the so-called field of bullets model, where each species independently survives the extinction event at the present with probability p, and a model for which the number of surviving species is fixed. We provide explicit formulae for the expected remaining PD in both models, conditional on N=n, conditional on K=k, or conditional on both events. When N=n is fixed, we show the convergence to an explicit deterministic limit of the ratio of new to initial PD, as n→∞, both under the field of bullets model, and when K=kn is fixed and depends on n in such a way that kn/n converges to p. We also prove the convergence of this ratio as T→∞ in the supercritical, time-homogeneous case, where N simultaneously goes to ∞, thereby strengthening previous results of Mooers et al. (2012).

Ecomorphological disparity in an adaptive radiation: opercular bone shape and stable isotopes in Antarctic icefishes

To assess how ecological and morphological disparity is interrelated in the adaptive radiation of Antarctic notothenioid fish we used patterns of opercle bone evolution as a model to quantify shape disparity, phylogenetic patterns of shape evolution, and ecological correlates in the form of stable isotope values. Using a sample of 25 species including representatives from four major notothenioid clades, we show that opercle shape disparity is higher in the modern fauna than would be expected under the neutral evolution Brownian motion model. Phylogenetic comparative methods indicate that opercle shape data best fit a model of directional selection (Ornstein–Uhlenbeck) and are least supported by the “early burst” model of adaptive radiation. The main evolutionary axis of opercle shape change reflects movement from a broad and more symmetrically tapered opercle to one that narrows along the distal margin, but with only slight shape change on the proximal margin. We find a trend in opercle shape change along the benthic–pelagic axis, underlining the importance of this axis for diversification in the notothenioid radiation. A major impetus for the study of adaptive radiations is to uncover generalized patterns among different groups, and the evolutionary patterns in opercle shape among notothenioids are similar to those found among other adaptive radiations (three-spined sticklebacks) promoting the utility of this approach for assessing ecomorphological interactions on a broad scale.

Recovering speciation and extinction dynamics based on phylogenies

Phylogenetic trees of only extant species contain information about the underlying speciation and extinction pattern. In this review, I provide an overview over the different methodologies that recover the speciation and extinction dynamics from phylogenetic trees. Broadly, the methods can be divided into two classes: (i) methods using the phylogenetic tree shapes (i.e. trees without branch length information) allowing us to test for speciation rate variation and (ii) methods using the phylogenetic trees with branch length information allowing us to quantify speciation and extinction rates. I end the article with an overview on limitations, open questions and challenges of the reviewed methodology.

Anthropogenic extinction threats and future loss of evolutionary history in reef corals

Extinction always results in loss of phylogenetic diversity (PD), but phylogenetically selective extinctions have long been thought to disproportionately reduce PD. Recent simulations show that tree shapes also play an important role in determining the magnitude of PD loss, potentially offsetting the effects of clustered extinctions. While patterns of PD loss under different extinction scenarios are becoming well characterized in model phylogenies, analyses of real clades that often have unbalanced tree shapes remain scarce, particularly for marine organisms. Here, we use a fossil-calibrated phylogeny of all living scleractinian reef corals in conjunction with IUCN data on extinction vulnerabilities to quantify how loss of species in different threat categories will affect the PD of this group. Our analyses reveal that predicted PD loss in corals varies substantially among different threats, with extinctions due to bleaching and disease having the largest negative effects on PD. In general, more phylogenetically clustered extinctions lead to larger losses of PD in corals, but there are notable exceptions; extinction of rare corals from distantly-related old and unique lineages can also result in substantial PD loss. Thus our results show that loss of PD in reef corals is dependent on both tree shape and the nature of extinction threats.

General patterns of diversity in major marine microeukaryote lineages

Microeukaryotes have vital roles for the functioning of marine ecosystems, but still some general characteristics of their current diversity and phylogeny remain unclear. Here we investigated both aspects in major oceanic microeukaryote lineages using 18S rDNA (V4–V5 hypervariable regions) sequences from public databases that derive from various marine environmental surveys. A very carefully and manually curated dataset of 8291 Sanger sequences was generated and subsequently split into 65 taxonomic groups (roughly to Class level based on KeyDNATools) prior to downstream analyses. First, we calculated genetic distances and clustered sequences into Operational Taxonomic Units (OTUs) using different distance cut-off levels. We found that most taxonomic groups had a maximum pairwise genetic distance of 0.25. Second, we used phylogenetic trees to study general evolutionary patterns. These trees confirmed our taxonomic classification and served to run Lineage Through Time (LTT) plots. LTT results indicated different cladogenesis dynamics across groups, with some displaying an early diversification and others a more recent one. Overall, our study provides an improved description of the microeukaryote diversity in the oceans in terms of genetic differentiation within groups as well as in the general phylogenetic structure. These results will be important to interpret the large amount of sequence data that is currently generated by High Throughput Sequencing technologies.

As Old as the hills: montane scorpions in Southwestern North America reveal ancient associations between biotic diversification and landscape history

Background

The age of lineages has become a fundamental datum in studies exploring the interaction between geological transformation and biotic diversification. However, phylogeographical studies are often biased towards lineages that are younger than the geological features of the landscapes they inhabit. A temporally deeper historical biogeography framework may be required to address episodes of biotic diversification associated with geologically older landscape changes. Signatures of such associations may be retained in the genomes of ecologically specialized (stenotopic) taxa with limited vagility. In the study presented here, genetic data from montane scorpions in the Vaejovis vorhiesi group, restricted to humid rocky habitats in mountains across southwestern North America, were used to explore the relationship between scorpion diversification and regional geological history.

Results

Strong phylogeographical signal was evident within the vorhiesi group, with 27 geographically cohesive lineages inferred from a mitochondrial phylogeny. A time-calibrated multilocus species tree revealed a pattern of Miocene and Pliocene (the Neogene period) lineage diversification. An estimated 21 out of 26 cladogenetic events probably occurred prior to the onset of the Pleistocene, 2.6 million years ago. The best-fit density-dependent model suggested diversification rate in the vorhiesi group gradually decreased through time.

Conclusions

Scorpions of the vorhiesi group have had a long history in the highlands of southwestern North America. Diversification among these stenotopic scorpions appears to have occurred almost entirely within the Neogene period, and is temporally consistent with the dynamic geological history of the Basin and Range, and Colorado Plateau physiographical provinces. The persistence of separate lineages at small spatial scales suggests that a combination of ecological stenotopy and limited vagility may make these scorpions particularly valuable indicators of geomorphological evolution.

Phylogenetic niche conservatism: what are the underlying evolutionary and ecological causes?

Phylogenetic niche conservatism (PNC) is the tendency of lineages to retain their niche-related traits through speciation events. A recent surge in the availability of well-sampled molecular phylogenies has stimulated phylogenetic approaches to understanding ecological processes at large geographical scales and through macroevolutionary time. We stress that PNC is a pattern, not a process, and is found only in some traits and some lineages. At the simplest level, a pattern of PNC is an inevitable consequence of evolution - descent with modification and divergence of lineages - but several intrinsic causes, including physicochemical, developmental and genetic constraints, can lead directly to a marked pattern of PNC. A pattern of PNC can also be caused indirectly, as a by-product of other causes, such as extinction, dispersal limitation, competition and predation. Recognition of patterns of PNC can contribute to understanding macroevolutionary processes: for example, release from constraint in traits has been hypothesized to trigger adaptive radiations such as that of the angiosperms. Given the multiple causes of patterns of PNC, tests should address explicit questions about hypothesized processes. We conclude that PNC is a scientifically useful concept with applications to the practice of ecological research.

Evidence for determinism in species diversification and contingency in phenotypic evolution during adaptive radiation

Adaptive radiation (AR) theory predicts that groups sharing the same source of ecological opportunity (EO) will experience deterministic species diversification and morphological evolution. Thus, deterministic ecological and morphological evolution should be correlated with deterministic patterns in the tempo and mode of speciation for groups in similar habitats and time periods. We test this hypothesis using well-sampled phylogenies of four squamate groups that colonized the New World (NW) in the Late Oligocene. We use both standard and coalescent models to assess species diversification, as well as likelihood models to examine morphological evolution. All squamate groups show similar early pulses of speciation, as well as diversity-dependent ecological limits on clade size at a continental scale. In contrast, processes of morphological evolution are not easily predictable and do not show similar pulses of early and rapid change. Patterns of morphological and species diversification thus appear uncoupled across these groups. This indicates that the processes that drive diversification and disparification are not mechanistically linked, even among similar groups of taxa experiencing the same sources of EO. It also suggests that processes of phenotypic diversification cannot be predicted solely from the existence of an AR or knowledge of the process of diversification.

Is regional species diversity bounded or unbounded?

Two conflicting hypotheses have been proposed to explain large-scale species diversity patterns and dynamics. The unbounded hypothesis proposes that regional diversity depends only on time and diversification rate and increases without limit. The bounded hypothesis proposes that ecological constraints place upper limits on regional diversity and that diversity is usually close to its limit. Recent evidence from the fossil record, phylogenetic analysis, biogeography, and phenotypic disparity during lineage diversification suggests that diversity is constrained by ecological processes but that it is rarely asymptotic. Niche space is often unfilled or can be more finely subdivided and still permit coexistence, and new niche space is often created before ecological limits are reached. Damped increases in diversity over time are the prevalent pattern, suggesting the need for a new 'damped increase hypothesis'. The damped increase hypothesis predicts that diversity generally increases through time but that its rate of increase is often slowed by ecological constraints. However, slowing due to niche limitation must be distinguished from other possible mechanisms creating similar patterns. These include sampling artifacts, the inability to detect extinctions or declines in clade diversity with some methods, the distorting effects of correlated speciation-extinction dynamics, the likelihood that opportunities for allopatric speciation will vary in space and time, and the role of undetected natural enemies in reducing host ranges and thus slowing speciation rates. The taxonomic scope of regional diversity studies must be broadened to include all ecologically similar species so that ecological constraints may be accurately inferred. The damped increase hypothesis suggests that information on evolutionary processes such as time-for-speciation and intrinsic diversification rates as well as ecological factors will be required to explain why regional diversity varies among times, places and taxa.

Trees of unusual size: biased inference of early bursts from large molecular phylogenies

An early burst of speciation followed by a subsequent slowdown in the rate of diversification is commonly inferred from molecular phylogenies. This pattern is consistent with some verbal theory of ecological opportunity and adaptive radiations. One often-overlooked source of bias in these studies is that of sampling at the level of whole clades, as researchers tend to choose large, speciose clades to study. In this paper, we investigate the performance of common methods across the distribution of clade sizes that can be generated by a constant-rate birth-death process. Clades which are larger than expected for a given constant-rate branching process tend to show a pattern of an early burst even when both speciation and extinction rates are constant through time. All methods evaluated were susceptible to detecting this false signature when extinction was low. Under moderate extinction, both the -statistic and diversity-dependent models did not detect such a slowdown but only because the signature of a slowdown was masked by subsequent extinction. Some models which estimate time-varying speciation rates are able to detect early bursts under higher extinction rates, but are extremely prone to sampling bias. We suggest that examining clades in isolation may result in spurious inferences that rates of diversification have changed through time.

Eco-evolutionary community dynamics: covariation between diversity and invasibility across temperature gradients

Understanding biodiversity gradients is a long-standing challenge, and progress requires theory unifying ecology and evolution. Here, we unify concepts related to the speed of evolution, the influence of species richness on diversification, and niche-based coexistence. We focus on the dynamics, through evolutionary time, of community invasibility and species richness across a broad thermal gradient. In our framework, the evolution of body size influences the ecological structure and dynamics of a trophic network, and organismal metabolism ties temperature to eco-evolutionary processes. The framework distinguishes ecological invasibility (governed by ecological interactions) from evolutionary invasibility (governed by local ecology and constraints imposed by small phenotypic effects of mutation). The model yields four primary predictions: (1) ecological invasibility declines through time and with increasing temperature; (2) average evolutionary invasibility across communities increases and then decreases through time as the richness-temperature gradient flattens; (3) in the early stages of diversification, richness and evolutionary invasibility both increase with increasing temperature; and (4) at equilibrium, richness does not vary with temperature, yet evolutionary invasibility decreases with increasing temperature. These predictions emerge from the "evolutionary-speed" hypothesis, which attempts to account for latitudinal species richness gradients by invoking faster biological rates in warmer, tropical regions. The model contrasts with predictions from other richness-gradient hypotheses, such as "niche conservatism" and "species energy." Empirically testing our model's predictions should help distinguish among these hypotheses.

A comparison of the effects of random and selective mass extinctions on erosion of evolutionary history in communities of digital organisms

The effect of mass extinctions on phylogenetic diversity and branching history of clades remains poorly understood in paleobiology. We examined the phylogenies of communities of digital organisms undergoing open-ended evolution as we subjected them to instantaneous “pulse” extinctions, choosing survivors at random, and to prolonged “press” extinctions involving a period of low resource availability. We measured age of the phylogenetic root and tree stemminess, and evaluated how branching history of the phylogenetic trees was affected by the extinction treatments. We found that strong random (pulse) and strong selective extinction (press) both left clear long-term signatures in root age distribution and tree stemminess, and eroded deep branching history to a greater degree than did weak extinction and control treatments. The widely-used Pybus-Harvey gamma statistic showed a clear short-term response to extinction and recovery, but differences between treatments diminished over time and did not show a long-term signature. The characteristics of post-extinction phylogenies were often affected as much by the recovery interval as by the extinction episode itself.

Asynchronous origins of ectomycorrhizal clades of Agaricales

The ectomycorrhizal (ECM) symbiosis is the most widespread biotrophic nutritional mode in mushroom-forming fungi. ECM fungi include, though are not limited to, about 5000 described species of Agaricales from numerous, independently evolved lineages. Two central hypotheses suggest different explanations for the origin of ECM fungal diversity: (i) dual origins, initially with the Pinaceae in the Jurassic and later with angiosperms during the Late Cretaceous, and (ii) a simultaneous and convergent radiation of ECM lineages in response to cooling climate during the Palaeogene and advancing temperate ECM plant communities. Neither of these hypotheses is supported here. While we demonstrate support for asynchronous origins of ECM Agaricales, the timing of such events appears to have occurred more recently than suggested by the first hypothesis, first during the Cretaceous and later during the Palaeogene. We are also unable to reject models of rate constancy, which suggests that the diversity of ECM Agaricales is not a consequence of convergent rapid radiations following evolutionary transitions from saprotrophic to ECM habits. ECM lineages of Agaricales differ not only in age, but also in rates of diversification and rate of substitution at nuclear ribosomal RNA loci. These results question the biological uniformity of the ECM guild.

Explosive radiation of a bacterial species group

The current diversity of life on earth is the product of macroevolutionary processes that have shaped the dynamics of diversification. Although the tempo of diversification has been studied extensively in macroorganisms, much less is known about the rates of diversification in the exceedingly diverse and species-rich microbiota. Decreases in diversification rates over time, a signature of explosive radiations, are commonly observed in plant and animal lineages. However, the few existing analyses of microbial lineages suggest that the tempo of diversification in prokaryotes may be fundamentally different. Here, we use multilocus and genomic sequence data to test hypotheses about the rate of diversification in a well-studied pathogenic bacterial lineage, Borrelia burgdorferi sensu lato (sl). Our analyses support the hypothesis that an explosive radiation of lineages occurred near the origin of the clade, followed by a sharp decay in diversification rates. These results suggest that explosive radiations may be a general feature of evolutionary history across the tree of life.

Can clade age alone explain the relationship between body size and diversity?

One of the most striking patterns observed among animals is that smaller-bodied taxa are generally much more diverse than larger-bodied taxa. This observation seems to be explained by the mere fact that smaller-bodied taxa tend to have an older evolutionary origin and have therefore had more time to diversify. A few studies, based on the prevailing null model of diversification (i.e. the stochastic constant-rate birth–death model), have suggested that this is indeed the correct explanation, and body-size dependence of speciation and extinction rates does not play a role. However, there are several potential shortcomings to these studies: a suboptimal statistical procedure and a relatively narrow range of body sizes in the analysed data. Here, we present a more coherent statistical approach, maximizing the likelihood of the constant-rate birth–death model with allometric scaling of speciation and extinction rates, given data on extant diversity, clade age and average body size in each clade. We applied our method to a dataset compiled from the literature that includes a wide range of Metazoan taxa (range from midges to elephants). We find that the higher diversity among small animals is indeed, partly, caused by higher clade age. However, it is also partly caused by the body-size dependence of speciation and extinction rates. We find that both the speciation rate and extinction rate decrease with body size such that the net diversification rate is close to 0. Even more interestingly, the allometric scaling exponent of speciation and extinction rates is approximately −0.25, which implies that the per generation speciation and extinction rates are independent of body size. This suggests that the observed relationship between diversity and body size pattern can be explained by clade age alone, but only if clade age is measured in generations rather than years. Thus, we argue that the most parsimonious explanation for the observation that smaller-bodied taxa are more diverse is that their evolutionary clock ticks faster.

The effect of a competitor on a model adaptive radiation

The ecological forces shaping adaptive radiations are of great interest to evolutionary ecologists. Here, we experimentally test the hypothesis that the diversification of a lineage should be limited in the presence of competition from another taxon. We do this by studying a model microbial adaptive radiation (the generation of phenotypic diversity in asexual lineages of the bacterium Pseudomonas fluorescens) in the presence or absence of a competitor (Pseudomonas putida). In a spatially heterogeneous environment, the competitor P. putida reduced P. fluorescens population size only slightly and had no effect on diversification. In a spatially homogeneous environment, the competitor reduced P. fuoresecens population size to a much greater extent. Again the final extent of diversification in P. fluorescens was not affected by the competitor, but early diversification was accelerated. In this environment, P. putida suppressed the growth of a common variant of P. fluorescens and directly or indirectly facilitated the growth of a rare morph. Our results suggest that competition experienced by diversifying lineages may have complex effects on adaptive radiations not fully captured by current theory.

Multiple continental radiations and correlates of diversification in Lupinus (Leguminosae): testing for key innovation with incomplete taxon sampling

Replicate radiations provide powerful comparative systems to address questions about the interplay between opportunity and innovation in driving episodes of diversification and the factors limiting their subsequent progression. However, such systems have been rarely documented at intercontinental scales. Here, we evaluate the hypothesis of multiple radiations in the genus Lupinus (Leguminosae), which exhibits some of the highest known rates of net diversification in plants. Given that incomplete taxon sampling, background extinction, and lineage-specific variation in diversification rates can confound macroevolutionary inferences regarding the timing and mechanisms of cladogenesis, we used Bayesian relaxed clock phylogenetic analyses as well as MEDUSA and BiSSE birth-death likelihood models of diversification, to evaluate the evolutionary patterns of lineage accumulation in Lupinus. We identified 3 significant shifts to increased rates of net diversification (r) relative to background levels in the genus (r = 0.18-0.48 lineages/myr). The primary shift occurred approximately 4.6 Ma (r = 0.48-1.76) in the montane regions of western North America, followed by a secondary shift approximately 2.7 Ma (r = 0.89-3.33) associated with range expansion and diversification of allopatrically distributed sister clades in the Mexican highlands and Andes. We also recovered evidence for a third independent shift approximately 6.5 Ma at the base of a lower elevation eastern South American grassland and campo rupestre clade (r = 0.36-1.33). Bayesian ancestral state reconstructions and BiSSE likelihood analyses of correlated diversification indicated that increased rates of speciation are strongly associated with the derived evolution of perennial life history and invasion of montane ecosystems. Although we currently lack hard evidence for "replicate adaptive radiations" in the sense of convergent morphological and ecological trajectories among species in different clades, these results are consistent with the hypothesis that iteroparity functioned as an adaptive key innovation, providing a mechanism for range expansion and rapid divergence in upper elevation regions across much of the New World.

The niche, biogeography and species interactions

In this paper, I review the relevance of the niche to biogeography, and what biogeography may tell us about the niche. The niche is defined as the combination of abiotic and biotic conditions where a species can persist. I argue that most biogeographic patterns are created by niche differences over space, and that even 'geographic barriers' must have an ecological basis. However, we know little about specific ecological factors underlying most biogeographic patterns. Some evidence supports the importance of abiotic factors, whereas few examples exist of large-scale patterns created by biotic interactions. I also show how incorporating biogeography may offer new perspectives on resource-related niches and species interactions. Several examples demonstrate that even after a major evolutionary radiation within a region, the region can still be invaded by ecologically similar species from another clade, countering the long-standing idea that communities and regions are generally 'saturated' with species. I also describe the somewhat paradoxical situation where competition seems to limit trait evolution in a group, but does not prevent co-occurrence of species with similar values for that trait (called here the 'competition-divergence-co-occurrence conundrum'). In general, the interface of biogeography and ecology could be a major area for research in both fields.

The shape of mammalian phylogeny: patterns, processes and scales

Mammalian phylogeny is far too asymmetric for all contemporaneous lineages to have had equal chances of diversifying. We consider this asymmetry or imbalance from four perspectives. First, we infer a minimal set of 'regime changes'-points at which net diversification rate has changed-identifying 15 significant radiations and 12 clades that may be 'downshifts'. We next show that mammalian phylogeny is similar in shape to a large set of published phylogenies of other vertebrate, arthropod and plant groups, suggesting that many clades may diversify under a largely shared set of 'rules'. Third, we simulate six simple macroevolutionary models, showing that those where speciation slows down as geographical or niche space is filled, produce more realistic phylogenies than do models involving key innovations. Lastly, an analysis of the spatial scaling of imbalance shows that the phylogeny of species within an assemblage, ecoregion or larger area always tends to be more unbalanced than expected from the phylogeny of species at the next more inclusive spatial scale. We conclude with a verbal model of mammalian macroevolution, which emphasizes the importance to diversification of accessing new regions of geographical or niche space.

How diversification rates and diversity limits combine to create large-scale species-area relationships

Species-area relationships (SARs) have mostly been treated from an ecological perspective, focusing on immigration, local extinction and resource-based limits to species coexistence. However, a full understanding across large regions is impossible without also considering speciation and global extinction. Rates of both speciation and extinction are known to be strongly affected by area and thus should contribute to spatial patterns of diversity. Here, we explore how variation in diversification rates and ecologically mediated diversity limits among regions of different sizes can result in the formation of SARs. We explain how this area-related variation in diversification can be caused by either the direct effects of area or the effects of factors that are highly correlated with area, such as habitat diversity and population size. We also review environmental, clade-specific and historical factors that affect diversification and diversity limits but are not highly correlated with region area, and thus are likely to cause scatter in observed SARs. We present new analyses using data on the distributions, ages and traits of mammalian species to illustrate these mechanisms; in doing so we provide an integrated perspective on the evolutionary processes shaping SARs.

Different processes lead to similar patterns: a test of codivergence and the role of sea level and climate changes in shaping a southern temperate freshwater assemblage

Background

Understanding how freshwater assemblages have been formed and maintained is a fundamental goal in evolutionary and ecological disciplines. Here we use a historical approach to test the hypothesis of codivergence in three clades of the Chilean freshwater species assemblage. Molecular studies of freshwater crabs (Aegla: Aeglidae: Anomura) and catfish (Trichomycterus arealatus: Trichomycteridae: Teleostei) exhibited similar levels of genetic divergences of mitochondrial lineages between species of crabs and phylogroups of the catfish, suggesting a shared evolutionary history among the three clades in this species assemblage.

Results

A phylogeny was constructed for Trichomycterus areolatus under the following best-fit molecular models of evolution GTR + I + R, HKY + I, and HKY for cytochrome b, growth hormone, and rag 1 respectively. A GTR + I + R model provided the best fit for both 28S and mitochondrial loci and was used to construct both Aegla phylogenies. Three different diversification models were observed and the three groups arose during different time periods, from 2.25 to 5.05 million years ago (Ma). Cladogenesis within Trichomycterus areolatus was initiated roughly 2.25 Ma (Late Pliocene - Early Pleistocene) some 1.7 - 2.8 million years after the basal divergences observed in both Aegla clades. These results reject the hypothesis of codivergence.

Conclusions

The similar genetic distances between terminal sister-lineages observed in these select taxa from the freshwater Chilean species assemblage were formed by different processes occurring over the last ~5.0 Ma. Dramatic changes in historic sea levels documented in the region appear to have independently shaped the evolutionary history of each group. Our study illustrates the important role that history plays in shaping a species assemblage and argues against assuming similar patterns equal a shared evolutionary history.

Vertebral evolution and the diversification of squamate reptiles

Taxonomic, morphological, and functional diversity are often discordant and independent components of diversity. A fundamental and largely unanswered question in evolutionary biology is why some clades diversify primarily in some of these components and not others. Dramatic variation in trunk vertebral numbers (14 to >300) among squamate reptiles coincides with different body shapes, and snake-like body shapes have evolved numerous times. However, whether increased evolutionary rates or numbers of vertebrae underlie body shape and taxonomic diversification is unknown. Using a supertree of squamates including 1375 species, and corresponding vertebral and body shape data, we show that increased rates of evolution in vertebral numbers have coincided with increased rates and disparity in body shape evolution, but not changes in rates of taxonomic diversification. We also show that the evolution of many vertebrae has not spurred or inhibited body shape or taxonomic diversification, suggesting that increased vertebral number is not a key innovation. Our findings demonstrate that lineage attributes such as the relaxation of constraints on vertebral number can facilitate the evolution of novel body shapes, but that different factors are responsible for body shape and taxonomic diversification.

Community assembly and diversification in Indo-Pacific coral reef fishes

Theories of species coexistence have played a central role in ecology and evolutionary studies of the origin and maintenance of biodiversity in highly diverse communities. The concept of niche and associated theories predict that competition for available ecological space leads to a ceiling in species richness that influences further diversification patterns. By contrast, the neutral theory supports that speciation is stochastic and diversity independent. We examined the phylogenetic community structure and diversification rates in three families and 14 sites within coral reef fish communities from the Indian and Pacific oceans. Using the phylogenetic relationships among 157 species estimated with 2300 bp of mitochondrial DNA, we tested predictions in terms of species coexistence from the neutral and niche theories. At the regional scale, our findings suggest that phylogenetic community structure shifts during community assembly to a pattern of dispersion as a consequence of allopatric speciation in recent times but overall, variations in diversification rates did not relate with sea level changes. At the local scale, the phylogenetic community structure is consistent with a neutral model of community assembly since no departure from a random sorting of species was observed. The present results support a neutral model of community assembly as a consequence of the stochastic and unpredictable nature of coral reefs favoring generalist and sedentary species competing for living space rather than trophic resources. As a consequence, the observed decrease in diversification rates may be seen as the result of a limited supply of living space as expected in a finite island model.

Diversity-dependence brings molecular phylogenies closer to agreement with the fossil record

The branching times of molecular phylogenies allow us to infer speciation and extinction dynamics even when fossils are absent. Troublingly, phylogenetic approaches usually return estimates of zero extinction, conflicting with fossil evidence. Phylogenies and fossils do agree, however, that there are often limits to diversity. Here, we present a general approach to evaluate the likelihood of a phylogeny under a model that accommodates diversity-dependence and extinction. We find, by likelihood maximization, that extinction is estimated most precisely if the rate of increase in the number of lineages in the phylogeny saturates towards the present or first decreases and then increases. We demonstrate the utility and limits of our approach by applying it to the phylogenies for two cases where a fossil record exists (Cetacea and Cenozoic macroperforate planktonic foraminifera) and to three radiations lacking fossil evidence (Dendroica, Plethodon and Heliconius). We propose that the diversity-dependence model with extinction be used as the standard model for macro-evolutionary dynamics because of its biological realism and flexibility.

The molecular phylogenetic signature of clades in decline

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.