A kinetic model of Phanerozoic taxonomic diversity II. Early Phanerozoic families and multiple equilibria

According to when they attained high diversity, major taxa of marine animals have been clustered into three groups, the Cambrian, Paleozoic, and Modern Faunas. Because the Cambrian Fauna was a relatively minor component of the total fauna after mid-Ordovician time, the Phanerozoic history of marine animal diversity is largely a matter of the fates of the Paleozoic and Modern Faunas. The fact that most late Cenozoic genera belong to taxa that have been radiating for tens of millions of years indicates that the post-Paleozoic increase in diversity indicated by fossil data is real, rather than an artifact of improvement of the fossil record toward the present.Assuming that ecological crowding produced the so-called Paleozoic plateau for family diversity, various workers have used the logistic equation of ecology to model marine animal diversification as damped exponential increase. Several lines of evidence indicate that this procedure is inappropriate. A plot of the diversity of marine animal genera through time provides better resolution than the plot for families and has a more jagged appearance. Generic diversity generally increased rapidly during the Paleozoic, except when set back by pulses of mass extinction. In fact, an analysis of the history of the Paleozoic Fauna during the Paleozoic Era reveals no general correlation between rate of increase for this fauna and total marine animal diversity. Furthermore, realistically scaled logistic simulations do not mimic the empirical pattern. In addition, it is difficult to imagine how some fixed limit for diversity could have persisted throughout the Paleozoic Era, when the ecological structure of the marine ecosystem was constantly changing. More fundamentally, the basic idea that competition can set a limit for marine animal diversity is incompatible with basic tenets of marine ecology: predation, disturbance, and vagaries of recruitment determine local population sizes for most marine species. Sparseness of predators probably played a larger role than weak competition in elevating rates of diversification during the initial (Ordovician) radiation of marine animals and during recoveries from mass extinctions. A plot of diversification against total diversity for these intervals yields a band of points above the one representing background intervals, and yet this band also displays no significant trend (if the two earliest intervals of the initial Ordovician are excluded as times of exceptional evolutionary innovation). Thus, a distinctive structure characterized the marine ecosystem during intervals of evolutionary radiation—one in which rates of diversification were exceptionally high and yet increases in diversity did not depress rates of diversification.Particular marine taxa exhibit background rates of origination and extinction that rank similarly when compared with those of other taxa. Rates are correlated in this way because certain heritable traits influence probability of speciation and probability of extinction in similar ways. Background rates of origination and extinction were depressed during the late Paleozoic ice age for all major marine invertebrate taxa, but remained correlated. Also, taxa with relatively high background rates of extinction experienced exceptionally heavy losses during biotic crises because background rates of extinction were intensified in a multiplicative manner; decimation of a large group of taxa of this kind in the two Permian mass extinctions established their collective identity as the Paleozoic Fauna.Characteristic rates of origination and extinction for major taxa persisted from Paleozoic into post-Paleozoic time. Because of the causal linkage between rates of origination and extinction, pulses of extinction tended to drag down overall rates of origination as well as overall rates of extinction by preferentially eliminating higher taxa having relatively high background rates of extinction. This extinction/origination ratchet depressed turnover rates for the residual Paleozoic Fauna during the Mesozoic Era. A decline of this fauna's extinction rate to approximately that of the Modern Fauna accounts for the nearly equal fractional losses experienced by the two faunas in the terminal Cretaceous mass extinction.Viewed arithmetically, the fossil record indicates slow diversification for the Modern Fauna during Paleozoic time, followed by much more rapid expansion during Mesozoic and Cenozoic time. When viewed more appropriately as depicting geometric—or exponential—increase, however, the empirical pattern exhibits no fundamental secular change: the background rate of increase for the Modern Fauna—the fauna that dominated post-Paleozoic marine diversity—simply persisted, reflecting the intrinsic origination and extinction rates of constituent taxa. Persistence of this overall background rate supports other evidence that the empirical record of diversification for marine animal life since Paleozoic time represents actual exponential increase. This enduring rate makes it unnecessary to invoke environmental change to explain the post-Paleozoic increase of marine diversity.Because of the resilience of intrinsic rates, an empirically based simulation that entails intervals of exponential increase for the Paleozoic and Modern Faunas, punctuated by mass extinctions, yields a pattern that is remarkably similar to the empirical pattern. It follows that marine animal genera and species will continue to diversify exponentially long into the future, barring disruption of the marine ecosystem by human-induced or natural environmental changes.

There are essentially three major crinoid faunas of the Paleozoic: 1) the lower Paleozoic (Ordovician) fauna dominated by disparids and diplobathrid camerates; 2) the middle Paleozoic (Silurian-middle Mississippian) fauna dominated by monobathrid camerates, cladids, and flexibles; and 3) the upper Paleozoic (middle Mississippian-Permian) fauna dominated by cladids. Change from the middle Paleozoic fauna to the late Paleozoic fauna, at or near the Osagean-Meramecian boundary, was characterized by Laudon (1948) as “one of the most remarkable faunal breaks in the entire Paleozoic era”. The monobathrids that had reached their zenith in the Osagean (Tournaisian-Visean) became a very minor component of late Paleozoic faunas. Conventional thinking has implied that a mass extinction of crinoids occurred at the Osagean-Meramecian boundary.We have biostratigraphically subdivided the late Osagean and early Meramecian into four zones (times A-D, oldest to youngest, all within the Gnathodustexanus zone) in order to study the origination and extinction of all crinoid species during the changeover from the middle to upper Paleozoic faunas. Rather than a mass extinction, a monotonic turnover of species fits a pattern of gradual extinction as extinctions outpaced originations. Data are based on 216 species (taxonomically updated) from 69 localities and are as follows:The pattern of originations and extinctions for monobathrids is very similar to the pattern for all crinoid species.The above data have maximum diversity during Time B of the late Osagean followed by declining diversity in times C and D into the early Meramecian. Late Meramecian crinoid faunas (after time D) were less diverse with a maximum of about 45 species. The gradual decline of crinoids across the Osagean-Meramecian boundary cannot be explained as sampling bias (Signor-Lipps effect), because ranges of crinoids thought to be extinct at the boundary are extended into the early Meramecian as well as disappearing at various tinles prior to the boundary.The decline in diversity and the monotonic turnover of species are hypothesized to be the result of habitat reduction as the Eastern Interior Basin of North America was gradually infilled with clastic sediments at the end of the Acadian Orogeny. Most notable in this regard was the smothering of the Keokuk Limestone carbonate bank. Changes in sea level also contributed to habitat reduction. Lowering of sea level at the end of the Osagean caused restriction of open marine environments. A transgression in the early Meramecian was followed by shoaling and restriction during deposition of the late Meramecian Salem and St. Louis limestones.

The evolution of biodiversity among the Southwest European Neogene rodent (Mammalia, Rodentia) communities: pattern and process of diversification and extinction

Brachiopods are a key group in Phanerozoic marine diversity analyses for their excellent fossil record and distinctive evolutionary history. A genus-level survey of raw diversity trajectories allows the identification of the Brachiopod Big Five, episodes of major genus losses in the phylum which are compared with the established Big Five mass extinctions of Phanerozoic marine invertebrates. The two lists differ in that the end-Cretaceous extinction appears subdued for brachiopods, whereas the mid-Carboniferous is recognized as an event with significant loss of brachiopod genera. At a higher taxonomic level, a review of temporal ranges of rhynchonelliform orders reveals episodes of synchronous termination of multiple orders, here termed clade extinctions. The end-Ordovician, Late Devonian and end-Permian events are registered as both mass extinctions and clade extinctions. The Late Cambrian and the Early Jurassic are identified as the other two clade extinction events. Coincident with the Early Toarcian oceanic anoxic event, the last clade extinction of brachiopods is defined by the disappearance of the last two spire-bearing orders, Athyridida and Spiriferinida. Their diversity trajectory through the recovery after the end-Permian crisis parallels that of the extant terebratulides and rhynchonellides until a Late Triassic peak but diverge afterwards. The end-Triassic diversity decline and Toarcian vanishing of spire-bearers correspond with contraction in their spatial distribution. The observed patterns and extinction selectivity may be explained both ecologically and physiologically. The specialized adaptation of morphologically diverse spire-bearers, as well as their fixed lophophore and passive feeding put them at a disadvantage at times of environmental crises, manifest in their end-Triassic near-extinction and Toarcian demise. Similar analyses of other clade extinctions may further improve our understanding of drivers and processes of extinction.

The stratigraphic record of the Frasnian-Famennian mass extinction in the eastern United States indicates that a reversal in the magnitude of extinction and speciation rates was the driving mechanism forcing the decline in species diversity in this region. Extinction rates increased sharply during the deposition of the West Falls Group in New York State, and remained high for the remainder of the Frasnian, a period of approximately 4.5 Myr. Sharp reductions in species diversity, however, only occurred during deposition of the Java Group at the very end of the Frasnian. The period of diversity loss was much more abrupt and short term than the period elevated extinction rates, and was more a function of a drop in speciation rate than a direct function of an increase in extinction rate.

Comments on: Periodicity in the extinction rate and possible astronomical causes – comment on mass extinctions over the last 500 myr: an astronomical cause? (Erlykin <i>et al</i>.)

A simple equilibrial model for the growth and maintenance of Phanerozoic global marine taxonomic diversity can be constructed from considerations of the behavior of origination and extinction rates with respect to diversity. An initial postulate that total rate of diversification is proportional to number of taxa extant leads to an exponential model for early phases of diversification. This model appears to describe adequately the “explosive” diversification of known metazoan orders across the Precambrian-Cambrian Boundary, suggesting that no special event, other than the initial appearance of Metazoa, is necessary to explain this phenomenon. As numbers of taxa increase, the rate of diversification should become “diversity dependent.” Ecological factors should cause the per taxon rate of origination to decline and the per taxon rate of extinction to increase. If these relationships are modeled as simple linear functions, a logistic description of the behavior of taxonomic diversity through time results. This model appears remarkably consistent with the known pattern of Phanerozoic marine ordinal diversity as a whole. Analysis of observed rates of ordinal origination also indicates these are to a large extent diversity dependent; however, diversity dependence is not immediately evident in rates of ordinal extinction. Possible explanations for this pattern are derived from considerations of the size of higher taxa and from simulations of their diversification. These suggest that both the standing diversity and the pattern of origination of orders may adequately reflect the behavior of species diversity through time; however, correspondence between rates of ordinal and species extinction may deteriorate with progressive loss of information resulting from incomplete sampling of the fossil record.

Aim Resolving the spatio‐temporal diversification patterns and systematic relationships of endemic Australian land snails against the backdrop of Neogene aridification through analyses of a combined nuclear and mitochondrial DNA sequence dataset. Location Western Australia. Taxon Mollusca, Stylommatophora, Bothriembryontidae, Bothriembryon. Methods We employed Bayesian Inference and Maximum Likelihood to reconstruct the phylogenetic relationships in a group of Australian land snails using mitochondrial (COI, 16S) and nuclear (ANT) DNA sequences. Divergence times have been estimated by employing optimised molecular clocks using BEAST2, and RelTime in MEGA12. Speciation and net‐diversification rates have been modelled using revBayes to visualise diversification dynamics in lineage‐through‐time (LTT) plots. We employed automated species delimitation methods ASAP and bPTP to estimate taxonomic diversity. Results Our final sequence dataset contained 1052 new DNA sequences from 374 individuals, representing 97% of all accepted species plus 26 putatively new species based on morphology and distribution. Recognizing almost three times as many candidate species, both DNA‐based species delimitation methods have excessively inflated diversity estimates, casting doubt on the usefulness of these methods in groups with marked phylogeographic structure. Nine well‐supported principal clades were recovered. Fossil‐calibrated chronograms revealed an early bifurcation of Bothriembryon followed by an accumulation of lineages over time. LTT plots revealed a relative flattening of the speciation curve from 15 to 10 Ma on. However, we also detected a steep increase in intraspecific lineage diversification during the last approx. 1 Ma. The modeled speciation and net diversification rates have continuously declined over the last 25 Ma, while extinction rates have remained relatively steady until about 5 Ma, when they also started to climb. Main Conclusions Declining diversification rates during much of the Neogene, followed by increasing extinction rates, coincided with increasing aridity throughout Western Australia. A more recent increase in lineage diversification rates, driven by intraspecific differentiation, coincides with the rise of mesic conditions since the end of the Pleistocene. Both trends imply that through influencing extinction and diversification rates, historical climate change has likely contributed to shaping the current distribution patterns in Bothriembryon land snails that are characterised by fragmentation. Moreover, by uncovering many undescribed taxa, including multiple short‐range endemics, this study highlights the importance of continued conservation efforts in this globally important biodiversity hotspot. Key habitats, such as lithorefugia, in an otherwise harsh and exposed landscape are important strongholds for Bothriembryon to weather the impact of aridification.

AimDuring the late Oligocene (23 mya) the New Zealand landmass was reduced to approximately 18% of its current area. It has been hypothesized that this event, known as the Oligocene Drowning, caused population bottlenecking and mass extinction. Using phylogenetic methods, we examine the effect of this and other environmental events on the hyper‐diverse Zopheridae beetles (162 morphospecies), which largely inhabit leaf litter and dead wood.LocationNew Zealand.TaxonZopheridae, Coleoptera.MethodsHere we use a fossil‐calibrated phylogenetic tree estimated from mitochondrial cytochrome c oxidase subunit I and nuclear large subunit rRNA genes to identify monophyletic New Zealand zopherid lineages and date the age of these lineages. We used Bayesian diversification models (compound Poisson process on mass extinction times) to test the hypothesis that the New Zealand zopherids underwent a mass extinction in the late Oligocene followed by an increase in speciation rate in the Miocene. We also used these data to estimate the age of these lineages in New Zealand.ResultsWe demonstrate that 15–20 zopherid lineages survived the Oligocene Drowning depending on the calibration scheme. Of these lineages from 3 to 11 have posterior intervals that encompass the rifting of New Zealand from Gondwana in the late Cretaceous, again depending on the calibration scheme. The diversification model shows no evidence of an increase in extinction rate during the Oligocene Drowning or during any other period since the Cretaceous. Furthermore, rather than recovering an increase in speciation rate during the Miocene and Pliocene, due to environmental changes, we instead recovered a large drop in the speciation rate during this time.Main conclusionsThe New Zealand zopherid fauna is a combination of lineages, some of which may have existed on New Zealand since the rifting from Gondwana and other more recent arrivals. The late Oligocene reduction in land area was insufficient to cause a mass extinction in the Zopheridae. This suggests the amount of emergent land was great enough to support a diverse invertebrate fauna. Our study demonstrates the different biogeographic patterns evident in cryptic, hyper‐diverse, and poorly dispersing invertebrate species relative to more mobile plants and animals.

Mass extinction events (MEEs), defined as significant losses of species diversity in significantly short time periods, have attracted the attention of biologists because of their link to major environmental change. MEEs have traditionally been studied through the fossil record, but the development of birth‐death models has made it possible to detect their signature based on extant‐taxa phylogenies. Most birth‐death models consider MEEs as instantaneous events where a high proportion of species are simultaneously removed from the tree (“single pulse” approach), in contrast to the paleontological record, where MEEs have a time duration. Here, we explore the power of a Bayesian Birth‐Death Skyline (BDSKY) model to detect the signature of MEEs through changes in extinction rates under a “time‐slice” approach. In this approach, MEEs are time intervals where the extinction rate is greater than the speciation rate. Results showed BDSKY can detect and locate MEEs but that precision and accuracy depend on the phylogeny's size and MEE intensity. Comparisons of BDSKY with the single‐pulse Bayesian model, CoMET, showed a similar frequency of Type II error and neither model exhibited Type I error. However, while CoMET performed better in detecting and locating MEEs for smaller phylogenies, BDSKY showed higher accuracy in estimating extinction and speciation rates.

Asian-Western Pacific Permian brachiopoda in space and time: biogeography and extinction patterns

Extinction in the Anthropocene.

A common pattern in time-calibrated molecular phylogenies is a signal of rapid diversification early in the history of a radiation. Because the net rate of diversification is the difference between speciation and extinction rates, such "explosive-early" diversification could result either from temporally declining speciation rates or from increasing extinction rates through time. Distinguishing between these alternatives is challenging but important, because these processes likely result from different ecological drivers of diversification. Here we develop a method for estimating speciation and extinction rates that vary continuously through time. By applying this approach to real phylogenies with explosive-early diversification and by modeling features of lineage-accumulation curves under both declining speciation and increasing extinction scenarios, we show that a signal of explosive-early diversification in phylogenies of extant taxa cannot result from increasing extinction and can only be explained by temporally declining speciation rates. Moreover, whenever extinction rates are high, "explosive early" patterns become unobservable, because high extinction quickly erases the signature of even large declines in speciation rates. Although extinction may obscure patterns of evolutionary diversification, these results show that decreasing speciation is often distinguishable from increasing extinction in the numerous molecular phylogenies of radiations that retain a preponderance of early lineages.

Are there limits to the number of species on Earth? If resources on the planet are finite, it is reasonable to think that there must be a limit to the number of individuals (and species) it can sustain. Yet life on Earth is, and has been, extremely diverse and dynamic, shedding doubts on whether species diversity is, or has ever been, close to this limit. The concept of diversity-dependent diversification (DDD) is at the heart of this debate and postulates there is an ecological limit regulating and constraining species diversification. The term “diversity-dependence” was first used in the field of paleontology as an analogy to “density-dependence” in population ecology. The hypothesis is that diversification slows down as communities fill with species because of competition among species for limited resources. The resulting DDD patterns are a logistic increase in the number of taxa through geological time and/or a negative relationship between the standing diversity and the net diversification rate (via decrease in speciation rate and/or increase in extinction rate). In the past decades, many studies have tested the DDD predictions. These studies have often found support for a bounded diversification pattern, although they differ in temporal, taxonomic, and geographical scales, and use either paleontological (fossil diversity over time) or neontological (molecular phylogenies of extant species) data. Interspecific competition is the main mechanism used to explain observed DDD patterns; however, other processes can generate DDD-like patterns, and theoretical models have aided in generating more mechanistic and testable predictions. This article outlines empirical paleontological and neontological studies supporting (and opposing) the DDD hypotheses, as well as the models and mechanisms underlying the observed patterns.

Estimating how the number of species in a given group varied in the deep past is of key interest to evolutionary biologists. However, current phylogenetic approaches for obtaining such estimates have limitations, such as providing unrealistic diversity estimates at the origin of the group. Here, we develop a robust probabilistic approach for estimating diversity through time curves and uncertainty around these estimates from phylogenetic data. We show with simulations that under various realistic scenarios of diversification, this approach performs better than previously proposed approaches. We also characterize the effect of tree size and undersampling on the performance of the approach. We apply our method to understand patterns of species diversity in anurans (frogs and toads). We find that Archaeobatrachia-a species-poor group of old frog clades often found in temperate regions-formerly had much higher diversity and net diversification rate, but the group declined in diversity as younger, nested clades diversified. This diversity decline seems to be linked to a decline in speciation rate rather than an increase in extinction rate. Our approach, implemented in the R package RPANDA, should be useful for evolutionary biologists interested in understanding how past diversity dynamics have shaped present-day diversity. It could also be useful in other contexts, such as for analyzing clade-clade competitive effects or the effect of species richness on phenotypic divergence.