Did hard substrate taxa diversify prior to the Great Ordovician Biodiversification Event?

The Great Ordovician Biodiversification Event (GOBE) refers to one of the greatest increases in biodiversity during the Phanerozoic. Recent studies have shown that this taxonomic increase can be attributed to elevated origination rates around the Dapingian–Darriwilian boundary in the Middle Ordovician, while extinction rates stayed relatively constant throughout the Ordovician. Even though this global pattern of origination and extinction appears similar across diverse groups and geographical areas, earlier studies suggested that hard substrate taxa may have diversified prior to the GOBE, during the Early Ordovician. Here, we quantify Ordovician diversification dynamics of hard substrate taxa while simultaneously accounting for temporally varying sampling probabilities. Diversification rates of hard substrate taxa, both as a whole and when analysed as separate groups, appear to be very similar to those of free-living benthic taxa. The observation that the diversification dynamics of many different taxonomic and ecological groups show the same temporal pattern, suggests a common cause of Ordovician diversification dynamics.     

Rates of speciation in the fossil record

Data from palaeontology and biodiversity suggest that the global biota should produce an average of three new species per year. However, the fossil record shows large variation around this mean. Rates of origination have declined through the Phanerozoic. This appears to have been largely a function of sorting among higher taxa (especially classes), which exhibit characteristic rates of speciation (and extinction) that differ among them by nearly an order of magnitude. Secular decline of origination rates is hardly constant, however; many positive deviations reflect accelerated speciation during rebounds from mass extinctions. There has also been general decline in rates of speciation within major taxa through their histories, although rates have tended to remain higher among members in tropical regions. Finally, pulses of speciation appear sometimes to be associated with climate change, although moderate oscillations of climate do not necessarily promote speciation despite forcing changes in species' geographical ranges.     

Present day risk of extinction may exacerbate the lower species richness of dioecious clades

Dioecious clades have been observed to have lower species richness than their non‐dioecious sister groups indicating that dioecious species experience higher extinction rates and (or) lower speciation rates. To determine whether current threats to biodiversity may exacerbate this pattern, we examined the threat to exclusively dioecious families of angiosperms among the 13,013 species of threatened plants included in the IUCN Red List of Threatened Species. When examined phylogenetically, dioecious families had proportionally more species listed than their sister groups. We then examined whether ecological traits correlated with dioecy, namely tropical distribution, woody growth form, and fleshy fruits, are associated with having higher proportions of threatened species. Ignoring breeding system, woody growth form was the only trait that was associated with a greater than expected proportion of threatened species per family. Red‐Listed dioecious families were more likely to have a woody growth form than non‐dioecious families. Woody growth habit is likely contributing to the higher incidence of dioecious species being at risk of extinction but is not solely responsible for the pattern because higher risk within dioecious groups was also apparent in a comparison of exclusively woody sister‐group pairs. Our results indicate that dioecious plants may warrant special attention in conservation practices.     

Molecular phylogenies and historical biogeography of a circumtropical group of gastropods (Genus: Nerita): implications for regional diversity patterns in the marine tropics

To determine how historical processes, namely speciation, extinction, and dispersal, have contributed to regional species diversity patterns across the marine tropics, we examined the biogeographical history of a circumtropical genus of intertidal gastropods. A species-level phylogeny of Nerita, representing approximately 87% of extant species, was developed from 1608bp of mitochondrial (COI and 16S) and nuclear (ATPSalpha) markers. Phylogenetic relationships generally corresponded to prior classifications; however, comprehensive sampling revealed a number of previously undetected ESUs. Using the resulting tree as a framework, we combined geographical distributions and fossil evidence to reconstruct ancestral ranges, produce a time-calibrated chronogram, and estimate diversification rates. Analyses revealed two monophyletic eastern Pacific+Atlantic (EPA) clades, each of which likely split from an Indo-West Pacific (IWP) sister clade prior to an early Miocene Tethys Seaway closure. More recent diversification throughout the IWP appears to have been driven by both vicariance and dispersal events; EPA diversity has been further shaped by speciation across the Central American Seaway prior to its closure and dispersal across the Atlantic. Despite the latter, inter-regional dispersal has been rare, and likely contributes little to regional diversity patterns. Similarly, infrequent transitions into temperate regions combined with reduced diversification rates may explain low diversity in West and South Pacific clades. Since origination, Nerita diversification appears remarkably constant, with the exception of a lag in the late Eocene-early Oligocene and elevated rates in the late Oligocene-early Miocene. However, a comparison among regions suggested that IWP clades have experienced, on average, higher rates of speciation. Fossil evidence indicates that the EPA likely witnessed greater extinction relative to the IWP. We propose that regional differences in species diversity in Nerita have been largely shaped by differential rates of speciation and extinction.     

Evolution and the latitudinal diversity gradient: speciation, extinction and biogeography

A latitudinal gradient in biodiversity has existed since before the time of the dinosaurs, yet how and why this gradient arose remains unresolved. Here we review two major hypotheses for the origin of the latitudinal diversity gradient. The time and area hypothesis holds that tropical climates are older and historically larger, allowing more opportunity for diversification. This hypothesis is supported by observations that temperate taxa are often younger than, and nested within, tropical taxa, and that diversity is positively correlated with the age and area of geographical regions. The diversification rate hypothesis holds that tropical regions diversify faster due to higher rates of speciation (caused by increased opportunities for the evolution of reproductive isolation, or faster molecular evolution, or the increased importance of biotic interactions), or due to lower extinction rates. There is phylogenetic evidence for higher rates of diversification in tropical clades, and palaeontological data demonstrate higher rates of origination for tropical taxa, but mixed evidence for latitudinal differences in extinction rates. Studies of latitudinal variation in incipient speciation also suggest faster speciation in the tropics. Distinguishing the roles of history, speciation and extinction in the origin of the latitudinal gradient represents a major challenge to future research.     

EXTINCTION RATES SHOULD NOT BE ESTIMATED FROM MOLECULAR PHYLOGENIES

Molecular phylogenies contain information about the tempo and mode of species diversification through time. Because extinction leaves a characteristic signature in the shape of molecular phylogenetic trees, many studies have used data from extant taxa only to infer extinction rates. This is a promising approach for the large number of taxa for which extinction rates cannot be estimated from the fossil record. Here, I explore the consequences of violating a common assumption made by studies of extinction from phylogenetic data. I show that when diversification rates vary among lineages, simple estimators based on the birth–death process are unable to recover true extinction rates. This is problematic for phylogenetic trees with complete taxon sampling as well as for the simpler case of clades with known age and species richness. Given the ubiquity of variation in diversification rates among lineages and clades, these results suggest that extinction rates should not be estimated in the absence of fossil data.     

The identification of fossil angiosperm pollen and its bearing on the time and place of the origin of angiosperms

Studies in the 1970's reporting the occurrence of fossil pollen types in the Cretaceous, coupled with surveys of extant pollen morphology of primitive flowering plants, laid the foundation for proposing a Lower Cretaceous origin of angiosperms. Over the last 30 years, morphological, ultrastructural, and ontogenetic studies of both extant and fossil pollen have provided an array of new characters, as well as greater resolution in defining character polarities. Moreover, a range of fossil pollen types exhibiting angiosperm characters occur in low frequency within Triassic and Jurassic sediments. The pollen data provide evidence of a pre-Cretaceous origin of angiosperms. Speciation and extinction rates were likely equal during the Triassic and Jurassic, resulting in the paucity of angiosperm pollen types from different geographic areas in the Atlantic – South American/African rift zone. It was not until the Lower Cretaceous that origination rates exceed extinction rates, resulting in the subsequent diversification of angiosperms and the origin of the eudicots.     

Geographic range size, life history and rates of diversification in Australian mammals

Abstract What causes species richness to vary among different groups of organisms? Two hypotheses are that large geographical ranges and fast life history either reduce extinction rates or raise speciation rates, elevating a clade's rate of diversification. Here we present a comparative analysis of these hypotheses using data on the phylogenetic relationships, geographical ranges and life history of the terrestrial mammal fauna of Australia. By comparing species richness patterns to null models, we show that species are distributed nonrandomly among genera. Using sister‐clade comparisons to control for clade age, we then find that faster diversification is significantly associated with larger geographical ranges and larger litters, but there is no evidence for an effect of body size or age at first breeding on diversification rates. We believe the most likely explanation for these patterns is that larger litters and geographical ranges increase diversification rates because they buffer species from extinction. We also discuss the possibility that positive effects of litter size and range size on diversification rates result from elevated speciation rates.     

Correlations in fossil extinction and origination rates through geological time

Recent analyses have suggested that extinction and origination rates exhibit long-range correlations, implying that the fossil record may be controlled by self-organized criticality or other scale-free internal dynamics of the biosphere. Here we directly test for correlations in the fossil record by calculating the autocorrelation of extinction [corrected] and origination rates through time. Our results show that extinction rates are uncorrelated beyond the average duration of a stratigraphic interval. Thus, they lack the long-range correlations predicted by the self-organized criticality hypothesis. In contrast, origination rates show strong autocorrelations due to long-term trends. After detrending, origination rates generally show weak positive correlations at lags of 5-10 million years (Myr) and weak negative correlations at lags of 10-30 Myr, consistent with aperiodic oscillations around their long-term trends. We hypothesize that origination rates are more correlated than extinction rates because originations of new taxa create new ecological niches and new evolutionary pathways for reaching them, thus creating conditions that favour further diversification.     

Angiosperm growth habit,dispersal and diversification reconsidered

Summary Previous studies have sought to elucidate the relationship between dispersal mode (biotic versus abiotic) and the taxonomic diversification of angiosperm families, but with ambiguous results. In this study, we propose the hypothesis that the combination of (1) the large seed size required of plants germinating in closed, light-poor environments and (2) the necessity to move disseminules away from the maternal plant in order to avoid intraspecific competition, predation and pathogens should favour biotically-dispersed relative to abiotically-dispersed woody arborescent angiosperms, resulting in higher diversification of the former. In this paper, we seek patterns of diversification that support this hypothesis. We examine the association between dispersal mode, growth habit and taxonomic richness of monocotyledon and dicotyledon families using (1) contingency table analyses to detect the effect of dispersal mode on the relative abundances and diversification of woody versus herbaceous taxa and (2) non-parametric analyses of variance to detect the statistical effect of dispersal mode on taxonomic diversification (mean number of species per genus, genera per family and species per family) in monocot and dicot families dominated by biotic or abiotic dispersal. We found a clear statistical effect of dispersal mode on diversification. Among families of woody dicots, dispersal by vertebrates is associated with significantly higher levels of species per genus, genera per family and species per family than is abiotic dispersal. The same pattern is observed among woody monocots, but is not significant at the 0.05 level. Among families of herbaceous monocots and dicots, the situation is reversed, with abiotically-dispersed families exhibiting higher levels of diversification than vertebrate-dispersed families. When woody and herbaceous families are pooled, there is no association between dispersal mode and diversification. These data coincide with evidence from the fossil record to suggest vertebrate dispersal has positively contributed to the diversification of woody angiosperms. We suggest that vertebrate dispersal may have promoted the diversity of extant taxa by reducing the probability of extinction over evolutionary time, rather than by elevating speciation rates. Our results suggest vertebrate dispersal has contributed to, but does not explainin toto, the diversity of living angiosperms.     

Heterostyly accelerates diversification via reduced extinction in primroses

The exceptional species diversity of flowering plants, exceeding that of their sister group more than 250-fold, is especially evident in floral innovations, interactions with pollinators and sexual systems. Multiple theories, emphasizing flower–pollinator interactions, genetic effects of mating systems or high evolvability, predict that floral evolution profoundly affects angiosperm diversification. However, consequences for speciation and extinction dynamics remain poorly understood. Here, we investigate trajectories of species diversification focusing on heterostyly, a remarkable floral syndrome where outcrossing is enforced via cross-compatible floral morphs differing in placement of their respective sexual organs. Heterostyly evolved at least 20 times independently in angiosperms. Using Darwin''s model for heterostyly, the primrose family, we show that heterostyly accelerates species diversification via decreasing extinction rates rather than increasing speciation rates, probably owing to avoidance of the negative genetic effects of selfing. However, impact of heterostyly appears to differ over short and long evolutionary time-scales: the accelerating effect of heterostyly on lineage diversification is manifest only over long evolutionary time-scales, whereas recent losses of heterostyly may prompt ephemeral bursts of speciation. Our results suggest that temporal or clade-specific conditions may ultimately determine the net effects of specific traits on patterns of species diversification.     

ABSOLUTE DIVERSIFICATION RATES IN ANGIOSPERM CLADES

Abstract The extraordinary contemporary species richness and ecological predominance of flowering plants (angiosperms) are even more remarkable when considering the relatively recent onset of their evolutionary diversification. We examine the evolutionary diversification of angiosperms and the observed differential distribution of species in angiosperm clades by estimating the rate of diversification for angiosperms as a whole and for a large set of angiosperm clades. We also identify angiosperm clades with a standing diversity that is either much higher or lower than expected, given the estimated background diversification rate. Recognition of angiosperm clades, the phylogenetic relationships among them, and their taxonomic composition are based on an empirical compilation of primary phylogenetic studies. By making an integrative and critical use of the paleobotanical record, we obtain reasonably secure approximations for the age of a large set of angiosperm clades. Diversification was modeled as a stochastic, time‐homogeneous birth‐and‐death process that depends on the diversification rate (r) and the relative extinction rate (∈). A statistical analysis of the birth and death process was then used to obtain 95% confidence intervals for the expected number of species through time in a clade that diversifies at a rate equal to that of angiosperms as a whole. Confidence intervals were obtained for stem group and for crown group ages in the absence of extinction (∈= 0.0) and under a high relative extinction rate (∈= 0.9). The standing diversity of angiosperm clades was then compared to expected species diversity according to the background rate of diversification, and, depending on their placement with respect to the calculated confidence intervals, exceedingly species‐rich or exceedingly species‐poor clades were identified. The rate of diversification for angiosperms as a whole ranges from 0.077 (∈= 0.9) to 0.089 (∈= 0.0) net speciation events per million years. Ten clades fall above the confidence intervals of expected species diversity, and 13 clades were found to be unexpectedly species poor. The phylogenetic distribution of clades with an exceedingly high number of species suggests that traits that confer high rates of diversification evolved independently in different instances and do not characterize the angiosperms as a whole.     

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.     

Evolutionary dynamics of taxonomic structure

The distribution of species among genera and higher taxa has largely untapped potential to reveal among-clade variation in rates of origination and extinction. The probability distribution of the number of species within a genus is modelled with a stochastic, time-homogeneous birth-death model having two parameters: the rate of species extinction, μ, and the rate of genus origination, γ, each scaled as a multiple of the rate of within-genus speciation, λ. The distribution is more sensitive to γ than to μ, although μ affects the size of the largest genera. The species : genus ratio depends strongly on both γ and μ, and so is not a good diagnostic of evolutionary dynamics. The proportion of monotypic genera, however, depends mainly on γ, and so may provide an index of the genus origination rate. Application to living marine molluscs of New Zealand shows that bivalves have a higher relative rate of genus origination than gastropods. This is supported by the analysis of palaeontological data. This concordance suggests that analysis of living taxonomic distributions may allow inference of macroevolutionary dynamics even without a fossil record.     

A model of onshore-offshore change in faunal diversity

Onshore-offshore patterns of faunal change occurred at many taxonomic scales during the Paleozoic Era, ranging from replacement of the Cambrian evolutionary fauna by the Paleozoic fauna to the environmental expansion of many orders and classes. A simple mathematical model is constructed to investigate such change. The environmental gradient across the marine shelf-slope is treated as a linear array of discrete habitats, each of which holds a set number of species, as observed in the fossil record. During any interval of time, some portion of the species in each habitat becomes extinct by background processes, with rates of extinction varying among both clades and habitats, as also observed in the record. After extinction, species are replaced from within the habitat and from immediately adjacent habitats, with proportions dependent on surviving species. This model leads to the prediction that extinction-resistant clades will always diversify at the expense of extinction-prone clades. But if extinction intensity is highest in nearshore habitats, extinction-resistant clades will expand preferentially in the onshore direction, build up diversity there, and then diversify outward toward the offshore. Thus, onshore-offshore patterns of diversification may be the expectation for faunal change quite independently of whether or not clades originate onshore. When the model is parameterized for Paleozoic trilobites and brachiopods, numerical solutions exhibit both a pattern of faunal change and a time span for diversification similar to that seen in the fossil record. They also generate structure similar to that seen in global diversification, including logistic patterns of growth, declining origination but constant extinction within clades through time, and declining overall extinction across clades through time.     

Different timing of the adaptive radiations of North American and Asian warblers

The timing of speciation events among warblers (small insectivorous woodland birds) in the Himalayas of India and in the White Mountains of New Hampshire, USA, is compared. Sequence divergence in the mitochondrial cytochrome b gene for 13 New World species in six genera averages 2.6%, which according to standard calibrations places most of the diversification in the early Pleistocene. In contrast, eight Himalayan species in the single genus Phylloscopus differ by an average of 10.7% in the same gene sequence. The New Hampshire warblers appear to have undergone a relatively recent burst of speciation and morphological evolution, but there is a detectable slowing of speciation rates (or increase in extinction rates) within the community towards the present. Other North American passerine groups that have been studied show no signs of explosive diversification in the Pleistocene. In these groups, pairs of sister species are often older than the entire warbler radiation. Boreal forest migrated south from very high latitudes towards the end of the Pliocene and this apparently created conditions ripe for explosive diversification among the warblers, but not for many other groups.     

BODY SIZE DIVERSIFICATION IN ANOLIS: NOVEL ENVIRONMENT AND ISLAND EFFECTS

Extreme morphologies of many insular taxa suggest that islands have unusual properties that influence the tempo and mode of evolution. Yet whether insularity per se promotes rapid phenotypic evolution remains largely untested. We extend a phylogenetic comparative approach to test the influence of novel environments versus insularity on rates of body size and sexual size dimorphism diversification in Anolis . Rates of body size diversification among small-island and mainland species were similar to those of anole species on the Greater Antilles. However, the Greater Antilles taxa that colonized small islands and the mainland are ecologically nonrandom: rates of body size diversification among small-island and mainland species are high compared to their large-island sister taxa. Furthermore, rates of diversification in sexual size dimorphism on small islands are high compared to all large-island and mainland lineages. We suggest that elevated diversifying selection, particularly as a result of ecological release, may drive high rates of body size diversification in both small-island and mainland novel environments. In contrast, high abundance (prevalent among small-island lizard communities) mediating intraspecific resource competition and male–male competition may explain why sexual size dimorphism diversifies faster among small-island lineages than among their mainland and large-island relatives.     

Global diversification rates of passerine birds

The distribution of species richness in families of passerine birds suggests that the net rate of diversification was significantly higher than average in as many as 7 out of 47 families. However, the absence of excess species richness among the 106 tribes within these families indicates that these high rates were transient, perhaps associated in some cases with tectonic movements or dispersal events that extended geographical ranges. Thus, large clade size among passerine birds need not represent intrinsic key innovations that influence the rate of diversification. Approximately 17 families and 30 tribes have too few species relative to other passerine taxa. Many of these are ecologically or geographically marginal, being especially overrepresented in the Australasian region. Observed intervals between lineage splitting suggest that extinction has occurred ca. 90% as frequently as speciation (waiting times of 1.03 and 0.93 Myr) and that the 47 modern families comprising 5712 species descended from approximately 430 passerine lineages extant 24 Myr ago. Speciation and extinction rates among small, marginal families might be 1-2 orders of magnitude lower.