Divergent timing and patterns of species accumulation in lowland and highland neotropical birds

Late Pliocene and Pleistocene climatic instability has been invoked to explain the buildup of Neotropical biodiversity, although other theories date Neotropical diversification to earlier periods. If these climatic fluctuations drove Neotropical diversification, then a large proportion of species should date to this period and faunas should exhibit accelerated rates of speciation. However, the unique role of recent climatic fluctuations in promoting diversification could be rejected if late Pliocene and Pleistocene rates declined. To test these temporal predictions, dateable molecular phylogenies for 27 avian taxa were used to contrast the timing and rates of diversification in lowland and highland Neotropical faunas. Trends in diversification rates were analyzed in two ways. First, rates within taxa were analyzed for increasing or decreasing speciation rates through time. There was a significant trend within lowland taxa towards decreasing speciation rates, but no significant trend was observed within most highland taxa. Second, fauna wide diversification rates through time were estimated during one-million-year intervals by combining rates across taxa. In the lowlands, rates were highest during the late Miocene and then decreased towards the present. The decline in rates observed both within taxa and for the fauna as a whole probably resulted from density dependent cladogenesis. In the highlands, faunawide rates did not vary greatly before the Pleistocene but did increase significantly during the last one million years of the Pleistocene following the onset of severe glacial cycles in the Andes. These contrasting patterns of species accumulation suggest that lowland and highland regions were affected differently by recent climatic fluctuations. Evidently, habitat alterations associated with global climate change were not enough to promote an increase in the rate of diversification in lowland faunas. In contrast, direct fragmentation of habitats by glaciers and severe altitudinal migration of montane vegetation zones during climatic cycles may have resulted in the late Pleistocene increase in highland diversification rates. This increase resulted in a fauna with one third of its species dating to the last one million years.     

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.     

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.     

Differences between subfamilies in diversification process of the Early and Middle Permian fusulinid fauna in South China

Based on the fusulinid occurrence records from a computerized database of stratigraphic distribution, statistic comparisons have been conducted to disclose the differences among six subfamilies (constituting the major part of the fusulinid fauna) in generic and specific diversities, rates of speciation and extinction, and changes in the rates and others during the diversification process of the fusulinid fauna in Early and Middle Permian in South China. Our results reveal that: (1) significant differences exist in the diversification pattern of different taxa and (2) the rates of speciation and extinction in Schwagerininae are statistically higher than those in the others. Furthermore, the high rate of speciation in Schwagerininae contributed to the higher rate of diversification of the fusulinid fauna in Early Permian, whereas the lower rate of diversification in the Middle Permian has resulted from the ubiquitous low rates of speciation in all major taxa in the fauna, such as Schwagerininae, Neoschwagerininae, Verbeekininae, Sumatrininae, and Misellininae.     

Extinction,diversity and survivorship of taxa in the fossil record

Using data drawn from large-scale databases, a number of interesting trends in the fossil record have been observed in recent years. These include the average decline in extinction rates throughout the Phanerozoic, the average increase in standing diversity, correlations between rates of origination and extinction, and simple laws governing the form of survivorship curves and the distribution of the lifetimes of taxa. In this paper we derive a number of mathematical relationships between these quantities and show how these different trends are interrelated. We also derive a variety of constraints on the possible forms of these trends, such as limits on the rate at which extinction may decline and limits on the allowed difference between extinction and origination rates at any given time.     

Song evolution,speciation, and vocal learning in passerine birds

Phenotypic divergence can promote reproductive isolation and speciation, suggesting a possible link between rates of phenotypic evolution and the tempo of speciation at multiple evolutionary scales. To date, most macroevolutionary studies of diversification have focused on morphological traits, whereas behavioral traits─including vocal signals─are rarely considered. Thus, although behavioral traits often mediate mate choice and gene flow, we have a limited understanding of how behavioral evolution contributes to diversification. Furthermore, the developmental mode by which behavioral traits are acquired may affect rates of behavioral evolution, although this hypothesis is seldom tested in a phylogenetic framework. Here, we examine evidence for rate shifts in vocal evolution and speciation across two major radiations of codistributed passerines: one oscine clade with learned songs (Thraupidae) and one suboscine clade with innate songs (Furnariidae). We find that evolutionary bursts in rates of speciation and song evolution are coincident in both thraupids and furnariids. Further, overall rates of vocal evolution are higher among taxa with learned rather than innate songs. Taken together, these findings suggest an association between macroevolutionary bursts in speciation and vocal evolution, and that the tempo of behavioral evolution can be influenced by variation in developmental modes among lineages.     

From success to persistence: Identifying an evolutionary regime shift in the diverse Paleozoic aquatic arthropod group Eurypterida,driven by the Devonian biotic crisis

Mass extinctions have altered the trajectory of evolution a number of times over the Phanerozoic. During these periods of biotic upheaval a different selective regime appears to operate, although it is still unclear whether consistent survivorship rules apply across different extinction events. We compare variations in diversity and disparity across the evolutionary history of a major Paleozoic arthropod group, the Eurypterida. Using these data, we explore the group's transition from a successful, dynamic clade to a stagnant persistent lineage, pinpointing the Devonian as the period during which this evolutionary regime shift occurred. The late Devonian biotic crisis is potentially unique among the “Big Five” mass extinctions in exhibiting a drop in speciation rates rather than an increase in extinction. Our study reveals eurypterids show depressed speciation rates throughout the Devonian but no abnormal peaks in extinction. Loss of morphospace occupation is random across all Paleozoic extinction events; however, differential origination during the Devonian results in a migration and subsequent stagnation of occupied morphospace. This shift appears linked to an ecological transition from euryhaline taxa to freshwater species with low morphological diversity alongside a decrease in endemism. These results demonstrate the importance of the Devonian biotic crisis in reshaping Paleozoic ecosystems.     

Testing the link between the latitudinal gradient in species richness and rates of molecular evolution

Numerous hypotheses have been proposed to explain latitudinal gradients in species richness, but all are subject to ongoing debate. Here we examine Rohde's (1978, 1992) hypothesis, which proposes that climatic conditions at low latitudes lead to elevated rates of speciation. This hypothesis predicts that rates of molecular evolution should increase towards lower latitudes, but this prediction has never been tested. We discuss potential links between rates of molecular evolution and latitudinal diversity gradients, and present the first test of latitudinal variation in rates of molecular evolution. Using 45 phylogenetically independent, latitudinally separated pairs of bird species and higher taxa, we compare rates of evolution of two mitochondrial genes and DNA-DNA hybridization distances. We find no support for an effect of latitude on rate of molecular evolution. This result casts doubt on the generality of a key component of Rohde's hypothesis linking climate and speciation.     

Mechanisms of speciation and faunal enrichment in Atlantic parrotfishes

Relationships based on mtDNA and nDNA sequences were used to assess effects of two major geographic barriers (the >30 myo Atlantic ocean and the approximately 11 myo Amazon-Orinoco outflow) on speciation among Atlantic parrotfishes (Sparisoma and Nicholsina). Allopatric distributions of sister taxa implicate isolating actions of both barriers in all recent speciation in these fishes, with no clear indications that any speciation resulted from other mechanisms. Molecular clock estimates of the timing of lineage splits indicate that both barriers acted by limiting dispersal well after they formed, although the Amazon barrier also may have been a vicariance agent. Fluctuations in sealevel, climate, and ocean-current dynamics over the past approximately 10 my likely produced marked variation in the effectiveness of both barriers, but particularly the Amazon barrier, allowing intermittent dispersal leading to establishment and allopatric speciation. A dynamic Amazon barrier represents a major engine of West Atlantic faunal enrichment that has repeatedly facilitated bidirectional dispersal, allopatric speciation, and remixing of the Caribbean and Brazilian faunas.     

Nonstochastic variation of species-level diversification rates within angiosperms

Variations in the origination and extinction rates of species over geological time often are linked with a range of factors, including the evolution of key innovations, changes in ecosystem structure, and environmental factors such as shifts in climate and physical geography. Before hypothesizing causality of a single factor, it is critical to demonstrate that the observed variation in diversification is significantly greater than one would expect due to natural stochasticity in the evolutionary branching process. Here, we use a likelihood-ratio test to compare taxonomic rate heterogeneity to a neutral birth-death model, using data on well-supported sister pairs of taxa and their species richness. We test the likelihood that the distribution of extant species among angiosperm genera and families could be the result of constant diversification rates. Results strongly support the conclusion that there is significantly more heterogeneity in diversity at the species level within angiosperms than would be expected due to stochastic processes. This result is consistent in datasets of genus pairs and family pairs and is not affected significantly by degrading pairs to simulate inaccuracy in the assumption of simultaneous origin of sister taxa. When we parse taxon pairs among higher groups of angiosperms, results indicate that a constant rates model is not rejected by rosid and basal eudicot pairs but is rejected by asterid and eumagnoliid pairs. These results provide strong support for the hypothesis that species-level rates of origination and/or extinction have varied nonrandomly within angiosperms and that the magnitude of heterogeneity varies among major groups within angiosperms.     

Global Taxonomic Diversity of Anomodonts (Tetrapoda,Therapsida) and the Terrestrial Rock Record Across the Permian-Triassic Boundary

The end-Permian biotic crisis (∼252.5 Ma) represents the most severe extinction event in Earth''s history. This paper investigates diversity patterns in Anomodontia, an extinct group of therapsid synapsids (‘mammal-like reptiles’), through time and in particular across this event. As herbivores and the dominant terrestrial tetrapods of their time, anomodonts play a central role in assessing the impact of the end-Permian extinction on terrestrial ecosystems. Taxonomic diversity analysis reveals that anomodonts experienced three distinct phases of diversification interrupted by the same number of extinctions, i.e. an end-Guadalupian, an end-Permian, and a mid-Triassic extinction. A positive correlation between the number of taxa and the number of formations per time interval shows that anomodont diversity is biased by the Permian-Triassic terrestrial rock record. Normalized diversity curves indicate that anomodont richness continuously declines from the Middle Permian to the Late Triassic, but also reveals all three extinction events. Taxonomic rates (origination and extinction) indicate that the end-Guadalupian and end-Permian extinctions were driven by increased rates of extinction as well as low origination rates. However, this pattern is not evident at the final decline of anomodont diversity during the Middle Triassic. Therefore, it remains unclear whether the Middle Triassic extinction represents a gradual or abrupt event that is unique to anomodonts or more common among terrestrial tetrapods. The end-Permian extinction represents the most distinct event in terms of decline in anomodont richness and turnover rates.     

Coupled evolutionary rates and the fossil record

A model for speciation is given in which a taxon’s phenotypic variation and concomitant variation in fitness are related to gradients within the environment. Phenotypic expressions within the population are shown to undergo abrupt transitions as a result of discontinuous fitness-functions. Evidence for rapid and abrupt phenotypic variation is explored by analyses of speciation (= origination) rates within the fossil record. In general, a high correlation exists among the area/volume changes of sedimentary rocks known for each geologic period and the apparent speciation rates seen in selected vascular/non-vascular plant groups. Regressions of speciation rates on rock area/volume plots indicate that the Devonian, Carboniferous, and Permian show significant divergences (= residual) rates from predicted origination rates. The Cretaceous shows the highest residual value as a consequence of the rapid appearance of angiosperm fossils. A similar pattern in diversity changes for the mandibulate terrestrial invertebrates is also apparent. The coupled evolution of the angiosperms with specific insect groups appears to be the most tenable explanation for the residual Cretaceous origination rate of the former group. It is postulated that the angiospems have evolved in part as the result of a phytochemical cost-function such that phytophagous insects are warded off, while potential pollinators are favored. Quantitative/qualitative differences observed in the distribution of secondary metabolites may be evidence for coupled evolution. A “predatorprey mediated co-existence” between phytophagous insects and angiosperms may have served as a factor in allowing the co-existence of less than optimal plant species providing an impetus for relatively rapid speciation turnover.     

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.     

Two decades of interaction between the MacArthur-Wilson model and the complexities of mammalian distributions

More than two decades after its publication, MacArthur and Wilson's equilibrium model of insular biogeography continues to provide the conceptual foundation for investigating the distribution of species on islands and the composition of insular biotas. During this period, studies of the distributions of mammals among insular habitats have tested, modified, and extended MacArthur and Wilson's simple formalism to enhance greatly our understanding of the complexities of biogeographic patterns and processes. The papers in this symposium summarize many of the past contributions of mammalian biogeographers and introduce important new data and ideas. The diversity of biological characteristics and associated distributional patterns exhibited by mammals has facilitated this endeavour. Some insular mammalian faunas appear to represent approximate equilibria between opposing rates of contemporary colonization and extinction. Other faunas are currently decreasing in diversity because of extinctions, owing either to natural habitat fragmentation that has occurred since the Pleistocene or to human activities within the last few centuries. Still other faunas have been increasing in diversity (at least until recent human impacts) because limiting rates of origination, both colonization and speciation, have been extremely low. The questions and analyses of island biogeography can also be applied to continents with comparable overall results: the distributions of continental faunas reflect the consequences of similar processes of colonization, speciation and extinction. Analyses of insular distributions show unequivocally that probabilities of extinction, colonization and speciation are highly deterministic and vary in predictable ways among different taxa and archipelagos. These findings have important implications for applying the theory and data of insular biogeography to the pressing practical problems of designing natural reserves to preserve native species.     

Invasive species and biodiversity crises: testing the link in the late devonian

During the Late Devonian Biodiversity Crisis, the primary driver of biodiversity decline was the dramatic reduction in speciation rates, not elevated extinction rates; however, the causes of speciation decline have been previously unstudied. Speciation, the formation of new species from ancestral populations, occurs by two primary allopatric mechanisms: vicariance, where the ancestral population is passively divided into two large subpopulations that later diverge and form two daughter species, and dispersal, in which a small subset of the ancestral population actively migrates then diverges to form a new species. Studies of modern and fossil clades typically document speciation by vicariance in much higher frequencies than speciation by dispersal. To assess the mechanism behind Late Devonian speciation reduction, speciation rates were calculated within stratigraphically constrained species-level phylogenetic hypotheses for three representative clades and mode of speciation at cladogenetic events was assessed across four clades in three phyla: Arthropoda, Brachiopoda, and Mollusca. In all cases, Devonian taxa exhibited a congruent reduction in speciation rate between the Middle Devonian pre-crisis interval and the Late Devonian crisis interval. Furthermore, speciation via vicariance is almost entirely absent during the crisis interval; most episodes of speciation during this time were due to dispersal. The shutdown of speciation by vicariance during this interval was related to widespread interbasinal species invasions. The lack of Late Devonian vicariance is diametrically opposed to the pattern observed in other geologic intervals, which suggests the loss of vicariant speciation attributable to species invasions during the Late Devonian was a causal factor in the biodiversity crisis. Similarly, modern ecosystems, in which invasive species are rampant, may be expected to exhibit similar shutdown of speciation by vicariance as an outcome of the modern biodiversity crisis.     

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.     

Continental faunal exchange and the asymmetrical radiation of carnivores

Lineages arriving on islands may undergo explosive evolutionary radiations owing to the wealth of ecological opportunities. Although studies on insular taxa have improved our understanding of macroevolutionary phenomena, we know little about the macroevolutionary dynamics of continental exchanges. Here we study the evolution of eight Carnivora families that have migrated across the Northern Hemisphere to investigate if continental invasions also result in explosive diversification dynamics. We used a Bayesian approach to estimate speciation and extinction rates from a substantial dataset of fossil occurrences while accounting for the incompleteness of the fossil record. Our analyses revealed a strongly asymmetrical pattern in which North American lineages invading Eurasia underwent explosive radiations, whereas lineages invading North America maintained uniform diversification dynamics. These invasions into Eurasia were characterized by high rates of speciation and extinction. The radiation of the arriving lineages in Eurasia coincide with the decline of established lineages or phases of climate change, suggesting differences in the ecological settings between the continents may be responsible for the disparity in diversification dynamics. These results reveal long-term outcomes of biological invasions and show that the importance of explosive radiations in shaping diversity extends beyond insular systems and have significant impact at continental scales.     

The effect of habitat on modern shark diversification

Sharks occupy marine habitats ranging from shallow, inshore environments to pelagic, and deepwaters, and thus provide a model system for testing how gross habitat differences have shaped vertebrate macroevolution. Palaeontological studies have shown that onshore lineages diversify more quickly than offshore taxa. Among onshore habitats, coral reef‐association has been shown to increase speciation rates in several groups of fishes and invertebrates. In this study, we investigated whether speciation rates are habitat dependent by generating the first comprehensive molecular timescale for shark divergence. Using phylogenetic comparative methods, we rejected the hypothesis that shelf (i.e. onshore) lineages have higher speciation rates compared to those occupying deepwater and oceanic (i.e. offshore) habitats. Our results, however, support the hypothesis of increased speciation rates in coral reef‐associated lineages within the Carcharhinidae. Our new timetree suggests that the two major shark lineages leading to the extant shark diversity began diversifying mostly after the end‐Permian mass extinction: the squalimorphs into deepwater and the galeomorphs into shelf habitats. We suggest that the breakdown of the onshore–offshore speciation rate pattern in sharks is mediated by success in deepwater environments through ecological partitioning, and in some cases, the evolution of morphological novelty.     

The impact of Quaternary Ice Ages on mammalian evolution

The Quaternary was a time of extensive evolution among mammals. Most living species arose at this time, and many of them show adaptations to peculiarly Quaternary environments. The latter include continental northern steppe and tundra, and the formation of lakes and offshore islands. Although some species evolved fixed adaptations to specialist habitats, others developed flexible adaptations enabling them to inhabit broad niches and to survive major environmental changes. Adaptation to short-term (migratory and seasonal) habitat change probably played a part in pre-adapting mammal species to the longer-term cyclical changes of the Quaternary. Fossil evidence indicates that environmental changes of the order of thousands of years have been sufficient to produce subspeciation, but speciation has typically required one hundred thousand to a few hundred thousand years, although there are both shorter and longer exceptions. The persistence of taxa in environments imposing strong selective regimes may have been important in forcing major adaptive change. Individual Milankovitch cycles are not necessarily implicated in this process, but nor did they generally inhibit evolutionary change among mammals: many evolutionary divergences built over multiple climatic cycles. Deduction of speciation timing requires input from fossils and modern phenotypic and breeding data, to complement and constrain mitochondrial DNA coalescence dates which appear commonly to overestimate taxic divergence dates and durations of speciation. Migrational and evolutionary responses to climate change are not mutually exclusive but, on the contrary, may be synergistic. Finally, preliminary analysis suggests that faunal turnover, including an important element of speciation, was elevated in the Quaternary compared with the Neogene, at least in some biomes. Macroevolutionary species selection or sorting has apparently resulted in a modern mammalian fauna enriched with fast-reproducing and/or adaptively generalist species.     

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.