Species selection and random drift in macroevolution

Species selection resulting from trait‐dependent speciation and extinction is increasingly recognized as an important mechanism of phenotypic macroevolution. However, the recent bloom in statistical methods quantifying this process faces a scarcity of dynamical theory for their interpretation, notably regarding the relative contributions of deterministic versus stochastic evolutionary forces. I use simple diffusion approximations of birth‐death processes to investigate how the expected and random components of macroevolutionary change depend on phenotype‐dependent speciation and extinction rates, as can be estimated empirically. I show that the species selection coefficient for a binary trait, and selection differential for a quantitative trait, depend not only on differences in net diversification rates (speciation minus extinction), but also on differences in species turnover rates (speciation plus extinction), especially in small clades. The randomness in speciation and extinction events also produces a species‐level equivalent to random genetic drift, which is stronger for higher turnover rates. I then show how microevolutionary processes including mutation, organismic selection, and random genetic drift cause state transitions at the species level, allowing comparison of evolutionary forces across levels. A key parameter that would be needed to apply this theory is the distribution and rate of origination of new optimum phenotypes along a phylogeny.     

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.     

Considering the case for biodiversity cycles: re-examining the evidence for periodicity in the fossil record

We re-examine the evidence for a 62 million year (Myr) periodicity in biodiversity throughout the Phanerozoic history of animal life reported by, as well as related questions of periodicity in origination and extinction. We find that the signal is robust against variations in methods of analysis, and is based on fluctuations in the Paleozoic and a substantial part of the Mesozoic. Examination of origination and extinction is somewhat ambiguous, with results depending upon procedure. Origination and extinction intensity as defined by may be affected by an artifact at 27 Myr in the duration of stratigraphic intervals. Nevertheless, when a procedure free of this artifact is implemented, the 27 Myr periodicity appears in origination, suggesting that the artifact may ultimately be based on a signal in the data. A 62 Myr feature appears in extinction, when this same procedure is used. We conclude that evidence for a periodicity at 62 Myr is robust, and evidence for periodicity at approximately 27 Myr is also present, albeit more ambiguous.     

Taxon age,origination, and extinction through geologic time

Changes in the taxon ages of fossil marine families that are alive and those that become extinct in each stage of the Phanerozoic reflect changes in the origination rate, differences in the extinction rate of families with different taxon ages, and mass extinction events. Extinct families are generally much younger than the population from which they were drawn. Periods dominated by higher numbers of younger families are more susceptible to larger size extinctions and greater variation in extinction size. As a result the relative size of extinction peaks must be viewed with regard to the taxon age structure of the population. Mass extinctions cause little change in the taxon age of the fauna. However, adaptive radiations cause a large drop in the average age of the families that are alive at any given time. Families must be treated as dynamic entities in macroevolutionary studies because their probabilities of extinction change over time.     

Detecting shifts in diversity limits from molecular phylogenies: what can we know?

Large complete species-level molecular phylogenies can provide the most direct information about the macroevolutionary history of clades having poor fossil records. However, extinction will ultimately erode evidence of pulses of rapid speciation in the deep past. Assessment of how well, and for how long, phylogenies retain the signature of such pulses has hitherto been based on a--probably untenable--model of ongoing diversity-independent diversification. Here, we develop two new tests for changes in diversification 'rules' and evaluate their power to detect sudden increases in equilibrium diversity in clades simulated with diversity-dependent speciation and extinction rates. Pulses of diversification are only detected easily if they occurred recently and if the rate of species turnover at equilibrium is low; rates reported for fossil mammals suggest that the power to detect a doubling of species diversity falls to 50 per cent after less than 50 Myr even with a perfect phylogeny of extant species. Extinction does eventually draw a veil over past dynamics, suggesting that some questions are beyond the limits of inference, but sudden clade-wide pulses of speciation can be detected after many millions of years, even when overall diversity is constrained. Applying our methods to existing phylogenies of mammals and angiosperms identifies intervals of elevated diversification in each.     

What is macroevolution?

Definitions of macroevolution fall into three categories: (1) evolution of taxa of supraspecific rank; (2) evolution on the grand time-scale; and (3) evolution that is guided by sorting of interspecific variation (as opposed to sorting of intraspecific variation in microevolution). Here, it is argued that only definition 3 allows for a consistent separation of macroevolution and microevolution. Using this definition, speciation has both microevolutionary and macroevolutionary aspects: the process of morphological transformation is microevolutionary, but the variation among species that it produces is macroevolutionary, as is the rate at which speciation occurs. Selective agents may have differential effects on intraspecific and interspecific variation, with three possible situations: effect at one level only, effect at both levels with the same polarity but potentially different intensity, and effects that oppose between levels. Whereas the impact of all selective agents is direct in macroevolution, microevolution requires intraspecific competition as a mediator between selective agents and evolutionary responses. This mediating role of intraspecific competition occurs in the presence of sexual reproduction and has therefore no analogue at the macroevolutionary level where species are the evolutionary units. Competition between species manifests both on the microevolutionary and macroevolutionary level, but with different effects. In microevolution, interspecific competition spurs evolutionary divergence, whereas it is a potential driver of extinction at the macroevolutionary level. Recasting the Red Queen hypothesis in a macroevolutionary framework suggests that the effects of interspecific competition result in a positive correlation between origination and extinction rates, confirming empirical observations herein referred to as Stanley's rule.     

The first 50Myr of dinosaur evolution: macroevolutionary pattern and morphological disparity

The evolutionary radiation of dinosaurs in the Late Triassic and Early Jurassic was a pivotal event in the Earth's history but is poorly understood, as previous studies have focused on vague driving mechanisms and have not untangled different macroevolutionary components (origination, diversity, abundance and disparity). We calculate the morphological disparity (morphospace occupation) of dinosaurs throughout the Late Triassic and Early Jurassic and present new measures of taxonomic diversity. Crurotarsan archosaurs, the primary dinosaur 'competitors', were significantly more disparate than dinosaurs throughout the Triassic, but underwent a devastating extinction at the Triassic-Jurassic boundary. However, dinosaur disparity showed only a slight non-significant increase after this event, arguing against the hypothesis of ecological release-driven morphospace expansion in the Early Jurassic. Instead, the main jump in dinosaur disparity occurred between the Carnian and Norian stages of the Triassic. Conversely, dinosaur diversity shows a steady increase over this time, and measures of diversification and faunal abundance indicate that the Early Jurassic was a key episode in dinosaur evolution. Thus, different aspects of the dinosaur radiation (diversity, disparity and abundance) were decoupled, and the overall macroevolutionary pattern of the first 50Myr of dinosaur evolution is more complex than often considered.     

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.     

MODES OF REPRODUCTION IN RECENT AND FOSSIL CUPULADRIID BRYOZOANS

Abstract:  Cupuladriid cheilostome bryozoans can make new colonies both sexually and asexually. Sexual (aclonal) colonies are derived from larvae while asexual (clonal) colonies result from the fragmentation or division of larger colonies. A number of specialised morphologies exist which either enhance or discourage clonality, and cupuladriids preserve these in their skeletons, meaning that it is possible to count the abundances of individual modes of reproduction in fossil assemblages, and thus measure the mode and tempo of evolution of life histories using fossil colonies. In this paper we categorise, illustrate and describe the various clonal and aclonal methods of propagation in cupuladriids through the Cenozoic. Sexual reproduction is the only aclonal method of propagation, while four clonal methods are described comprising: (1) mechanical fragmentation, (2) autofragmentation, (3) colonial budding and (4) peripheral fragmentation. The processes involved in each are discussed and we explain how their prevalence can be measured in the fossil record using preservable morphologies. Compiling a record of the occurrence and distribution of the various modes of propagation through time and space we discover a general trend of evolution towards more complex modes in all three cupuladriid genera, but a geologically recent extinction of some modes of propagation that has left the present-day assemblage relatively depauperate. We see striking similarities in the general timing of expansion of modes of reproduction between the two most important genera, Cupuladria and Discoporella , although it is clear that Discoporella evolved a much wider range of special morphologies either to enhance or to discourage clonality than did Cupuladria .     

SCALE AND HIERARCHY IN MACROEVOLUTION

Abstract: Scale and hierarchy must be incorporated into any conceptual framework for the study of macroevolution, i.e. evolution above the species level. Expansion of temporal and spatial scales reveals evolutionary patterns and processes that are virtually inaccessible to, and unpredictable from, short‐term, localized observations. These larger‐scale phenomena range from evolutionary stasis at the species level and the mosaic assembly of complex morphologies in ancestral forms to the non‐random distribution in time and space of the origin of major evolutionary novelties, as exemplified by the Cambrian explosion and post‐extinction recoveries of metazoans, and the preferential origin of major marine groups in onshore environments and tropical waters. Virtually all of these phenomena probably involve both ecological and developmental factors, but the integration of these components with macroevolutionary theory has only just begun. Differential survival and reproduction of units can occur at several levels within a biological hierarchy that includes DNA sequences, organisms, species and clades. Evolution by natural selection can occur at any level where there is heritable variation that affects birth and death of units by virtue of interaction with the environment. This dynamic can occur when selfish DNA sequences replicate disproportionately within genomes, when organisms enjoy fitness advantages within populations (classical Darwinian selection), when differential speciation or extinction occurs within clades owing to organismic properties (effect macroevolution), and when differential speciation or extinction occurs within clades owing to emergent, species‐level properties (in the strict sense species selection). Operationally, emergent species‐level properties such as geographical range can be recognized by testing whether their macroevolutionary effects are similar regardless of the different lower‐level factors that produce them. Large‐scale evolutionary trends can be driven by transformation of species, preferential production of species in a given direction, differential origination or extinction, or any combination of these; the potential for organismic traits to hitch‐hike on other factors that promote speciation or damp extinction is high. Additional key attributes of macroevolutionary dynamics within biological hierarchies are that (1) hierarchical levels are linked by upward and downward causation, so that emergent properties at a focal level do not impart complete independence; (2) hierarchical effects are asymmetrical, so that dynamics at a given focal level need not propagate upwards, but will always cascade downwards; and (3) rates are generally, although not always, faster at lower hierarchical levels. Temporal and spatial patterns in the origin of major novelties and higher taxa are significantly discordant from those at the species and genus levels, suggesting complex hierarchical effects that remain poorly understood. Not only are many of the features promoting survivorship during background times ineffective during mass extinctions, but also they are replaced in at least some cases by higher‐level, irreducible attributes such as clade‐level geographical range. The incorporation of processes that operate across hierarchical levels and a range of temporal and spatial scales has expanded and enriched our understanding of evolution.     

Ten years in the library: new data confirm paleontological patterns

A comparison is made between compilations of times of origination and extinction of fossil marine animal families published in 1982 and 1992. As a result of ten years of library research, half of the information in the compendia has changed: families have been added and deleted, low-resolution stratigraphic data been improved, and intervals of origination and extinction have been altered. Despite these changes, apparent macroevolutionary patterns for the entire marine fauna have remained constant. Diversity curves compiled from the two data bases are very similar, with a goodness-of-fit of 99%; the principal difference is that the 1992 curve averages 13% higher than the older curve. Both numbers and percentages of origination and extinction also match well, with fits ranging from 83% to 95%. All major events of radiation and extinction are identical. Therefore, errors in large paleontological data bases and arbitrariness of included taxa are not necessarily impediments to the analysis of pattern in the fossil record, so long as the data are sufficiently numerous.     

地层古生物研究辅助绘图软件StratDraw 1.0

为了减少绘制化石延限图的误差和工作量,设计了StratDraw1.0,自动对化石延限资料进行汇总,并借助于专业矢量绘图软件CorelDraw,自动生成初始延限图。在此基础上,可利用CorelDraw做各种编辑和修饰,获得可直接出版的化石延限图。该软件也可根据用户的选择对化石种级、属级或更高分类单元的地质延限进行自动绘制,借助于这一功能,用户可以直观地进行生物宏演化方面的数据统计。     

The ecology of lizard reproductive output

Aim We provide a new quantitative analysis of lizard reproductive ecology. Comparative studies of lizard reproduction to date have usually considered life‐history components separately. Instead, we examine the rate of production (productivity hereafter) calculated as the total mass of offspring produced in a year. We test whether productivity is influenced by proxies of adult mortality rates such as insularity and fossorial habits, by measures of temperature such as environmental and body temperatures, mode of reproduction and activity times, and by environmental productivity and diet. We further examine whether low productivity is linked to high extinction risk. Location World‐wide. Methods We assembled a database containing 551 lizard species, their phylogenetic relationships and multiple life history and ecological variables from the literature. We use phylogenetically informed statistical models to estimate the factors related to lizard productivity. Results Some, but not all, predictions of metabolic and life‐history theories are supported. When analysed separately, clutch size, relative clutch mass and brood frequency are poorly correlated with body mass, but their product – productivity – is well correlated with mass. The allometry of productivity scales similarly to metabolic rate, suggesting that a constant fraction of assimilated energy is allocated to production irrespective of body size. Island species were less productive than continental species. Mass‐specific productivity was positively correlated with environmental temperature, but not with body temperature. Viviparous lizards were less productive than egg‐laying species. Diet and primary productivity were not associated with productivity in any model. Other effects, including lower productivity of fossorial, nocturnal and active foraging species were confounded with phylogeny. Productivity was not lower in species at risk of extinction. Main conclusions Our analyses show the value of focusing on the rate of annual biomass production (productivity), and generally supported associations between productivity and environmental temperature, factors that affect mortality and the number of broods a lizard can produce in a year, but not with measures of body temperature, environmental productivity or diet.     

Origination, extinction, and dispersal: integrative models for understanding present-day diversity gradients

Species diversity gradients seen today are, to a large degree, a product of history. Spatially nonrandom originations, extinctions, and changes in geographic distributions can create gradients in species and higher-taxon richness, but the relative roles of each of these processes remain poorly documented. Existing explanations of diversity gradients have tended to focus on either macroevolutionary or biogeographic processes; integrative models that include both are largely lacking. We used simple models that incorporate origination and extinction rates along with dispersal of taxa between regions to show that dispersal not only affects regional richness patterns but also has a strong influence on the average age of taxa present in a region. Failure to take into account the effects of dispersal can, in principle, lead to biased estimates of diversification rates and potentially wrong conclusions regarding processes driving latitudinal and other gradients in diversity. Thus, it is critical to include the effects of dispersal when formulating and testing hypotheses about the causes of large-scale gradients in diversity. Finally, the model results, in conjunction with the results of existing empirical studies, suggest that the nature of macroevolutionary and biogeographic processes may differ between terrestrial and marine diversity gradients.     

A 450 million years long latitudinal gradient in age‐dependent extinction

Leigh Van Valen famously stated that under constant conditions extinction probability is independent of species age. To test this 'law of constant extinction', we developed a new method using deep learning to infer age‐dependent extinction and analysed 450 myr of marine life across 21 invertebrate clades. We show that extinction rate significantly decreases with age in > 90% of the cases, indicating that most species died out soon after their appearance while those which survived experienced ever decreasing extinction risk. This age‐dependent extinction pattern is stronger towards the Equator and holds true when the potential effects of mass extinctions and taxonomic inflation are accounted for. These results suggest that the effect of biological interactions on age‐dependent extinction rate is more intense towards the tropics. We propose that the latitudinal diversity gradient and selection at the species level account for this exceptional, yet little recognised, macroevolutionary and macroecological pattern.     

Onshore–offshore gradient in metacommunity turnover emerges only over macroevolutionary time-scales

Invertebrate lineages tend to originate and become extinct at a higher rate in onshore than in offshore habitats over long temporal durations (more than 10 Myr), but it remains unclear whether this pattern scales down to durations of stages (less than 5 Myr) or even sequences (less than 0.5 Myr). We assess whether onshore–offshore gradients in long-term turnover between the tropical Eocene and the warm-temperate Plio-Pleistocene can be extrapolated from gradients in short-term turnover, using abundances of molluscan species from bulk samples in the northeast Atlantic Province. We find that temporal turnover of metacommunities does not significantly decline with depth over short durations (less than 5 Myr), but significantly declines with depth between the Eocene and Plio-Pleistocene (approx. 50 Myr). This decline is determined by a higher onshore extinction of Eocene genera and families, by a higher onshore variability in abundances of genera and families, and by an onshore expansion of genera and families that were frequent offshore in the Eocene. Onshore–offshore decline in turnover thus emerges only over long temporal durations. We suggest that this emergence is triggered by abrupt and spatially extensive climatic or oceanographic perturbations that occurred between the Eocene and Plio-Pleistocene. Plio-Pleistocene metacommunities show a high proportion of bathymetric generalists, in contrast to Eocene metacommunities. Accordingly, the net cooling and weaker thermal gradients may have allowed offshore specialists to expand into onshore habitats and maintain their presence in offshore habitats.     

Key stages in the evolution of the Antarctic marine fauna

We are beginning to appreciate that the origin of the modern Antarctic marine fauna is related to a series of key events throughout the Cenozoic era. In the first of these, the mass extinction at the Cretaceous–Palaeogene boundary (66 Ma) reset the evolutionary stage and led to a major radiation of modern taxa in the benthic realm. Although this took place in a greenhouse world, there is evidence to suggest that the radiation was tempered by the seasonality of primary productivity, and this may be a time‐invariant feature of the polar regions. Although there could well have been a single, abrupt extinction event at c. 34 Ma, there is also evidence to suggest a phased extinction of various taxa over a period of millions of years. Important new molecular phylogenetic data are indicating that a wide variety of both benthic and pelagic taxa radiated shortly after a second major phase of cooling at c. 14 Ma. Such a phenomenon is linked to a series of major palaeoceanographic changes, which in turn led to a proliferation of diatom‐based ecosystems. Although the modern benthic marine fauna can be traced back some 45–50 Myr, a substantial component of the modern pelagic one may be less than 14 Myr old. The latter is also characterized by assemblages of high abundance but comparatively low species richness and evenness. A distinctive signature of low diversity but high dominance within Antarctic marine assemblages was maintained by the interplay between temperature and primary productivity throughout the Cenozoic.     

Planktonic foraminiferal turnover, diversity fluctuations and geochemical signals across the Eocene/Oligocene boundary in Tanzania

A major turnover in planktonic foraminifera occurred across the Eocene/Oligocene (E/O) boundary. New drill holes through the E/O boundary in southern Tanzania contain extremely well-preserved and diverse assemblages of planktonic foraminifera. Here we document a 1.2 million year record of assemblages, diversity and stable isotope fluctuations through this critical interval, which is often dissolved and/or recrystallised in carbonate-rich facies. The E/O boundary is marked by the abrupt extinction of all five remaining species of the family Hantkeninidae and a distinct size reduction in the genus Pseudohastigerina. The boundary is preceded over a short stratigraphic interval by the extinction of Turborotalia cerroazulensis, Turborotalia cocoaensis and Turborotalia cunialensis. Quantitative analysis of planktonic foraminiferal assemblages reveals significant changes in the abundance of certain species and the composition of the assemblages. We compare diversity fluctuations to the stable isotope record of Pseudohastigerina naguewichiensis and use multispecies stable isotope analyses to determine the life habitats of the most important species. A major shift in the evenness occurs at ~ 33.8 Ma associated with the extinction of the T cerroazulensis group suggesting acute ecological disturbance. We propose that the extinction of the T. cerroazulensis group at ~ 33.8 Ma was directly related to cooling of sea surface temperatures, while the extinction of Hantkeninidae was due to modifications in the thermal structure of the oceans and associated productivity changes. After the extinctions, renewed origination and diversification occurred, leading to a characteristic Oligocene planktonic foraminifer assemblage.     

Diversity dynamics of Miocene mammals in relation to the history of tectonism and climate

Continental biodiversity gradients result not only from ecological processes, but also from evolutionary and geohistorical processes involving biotic turnover in landscape and climatic history over millions of years. Here, we investigate the evolutionary and historical contributions to the gradient of increasing species richness with topographic complexity. We analysed a dataset of 418 fossil rodent species from western North America spanning 25 to 5 Ma. We compared diversification histories between tectonically active (Intermontane West) and quiescent (Great Plains) regions. Although diversification histories differed between the two regions, species richness, origination rate and extinction rate per million years were not systematically different over the 20 Myr interval. In the tectonically active region, the greatest increase in originations coincided with a Middle Miocene episode of intensified tectonic activity and global warming. During subsequent global cooling, species richness declined in the montane region and increased on the Great Plains. These results suggest that interactions between tectonic activity and climate change stimulate diversification in mammals. The elevational diversity gradient characteristic of modern mammalian faunas was not a persistent feature over geologic time. Rather, the Miocene rodent record suggests that the elevational diversity gradient is a transient feature arising during particular episodes of Earth''s history.     

End‐Triassic bivalve extinction: Lombardian Alps,Italy

A major biotic crisis affecting virtually all major marine invertebrate clades occurred at the close of the Triassic. Species‐level data on bivalves from the Lombardian Alps of Italy record the extinction and suggest a possible causal mechanism. A significant decline in species richness is observed during the lower Rhaetian, where 51% of bivalve species, equally distributed among infaunal and epifaunal filter‐feeders, went extinct. The taxonomic loss at the middle Rhaetian was more severe, where 71% of the bivalve species were eliminated, including all infaunal and 50% of the epifaunal species. The data indicate that the extinction selectively eliminated infaunal bivalves.

An initial loss of bivalve species richness during the middle and upper Rhaetian correlates with changes in sedimentary facies related to a fall in relative sea level. This sea level fall is marked by the onset of peritidal micrites and shifting ooid shoals which may have rendered substrates unsuitable for both epifaunal and infaunal bivalves. The possible influences of temperature and salinity fluctuations are difficult to assess, but they may also have had a deleterious effect on the local bivalve fauna. The loss due to peritidal conditions is not consistent with the selective survivorship of epifaunal taxa recurring in overlying Jurassic rocks.

We propose that physiologic differences and selective resistance to physical stress are consistent with the pattern of selective extinction. Facies shifts associated with the marine regression are not sufficient to account for the extremely high magnitude of infaunal extinction. This selection against infaunal bivalves is probably caused by their decreased capacity to filter feed relative to their metabolic demands. A decrease in primary productivity could have selectively eliminated the infauna. Oceanographic processes or atmospheric darkening, perhaps caused by an extraterrestrial impact, could drastically limit food resources (primary productivity) and is consistent with the selective extinction at the end of the Triassic.