Extinction, diversity and survivorship of taxa in the fossil record

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.

Recent Fourier analyses of fossil extinction data have indicated that the power spectrum of extinction during the Phanerozoic may take the form of 1/f noise, a result which, it has been suggested, could be indicative of the presence of `critical dynamics' in the processes giving rise to extinction. In this paper we examine extinction power spectra in some detail, using family-level data from two widely available compilations. We find that although the average form of the power spectrum roughly obeys the 1/f law, the spectrum can be represented more accurately by dividing it into two regimes: a low-frequency one which is well fit by an exponential, and a high-frequency one in which it follows a power law with a 1/f2 form. We give explanations for the occurrence of each of these behaviours and for the position of the crossover between them.

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.

Rates of Evolution

Extinction in the Anthropocene.

For mammals today, mountains are diverse ecosystems globally, yet the strong relationship between species richness and topographic complexity is not a persistent feature of the fossil record. Based on fossil-occurrence data, diversity and diversification rates in the intermontane western North America varied through time, increasing significantly during an interval of global warming and regional intensification of tectonic activity from 18 to 14 Ma. However, our ability to infer origination and extinction rates reliably from the fossil record is affected by variation in preservation history. To investigate the influence of preservation on estimates of diversification rates, I simulated fossil records under four alternative diversification hypotheses and six preservation scenarios. Diversification hypotheses included tectonically controlled speciation pulses, while preservation scenarios were based on common trends (e.g., increasing rock record toward the present) or derived from fossil occurrences and the continental rock record. For each scenario, I estimated origination, extinction, and diversification rates using three standard methods—per capita, three-timer, and capture–mark–recapture (CMR) metrics—and evaluated the ability of the simulated fossil records to accurately recover the underlying diversification dynamics. Despite variable and low preservation probabilities, simulated fossil records retained the signal of true rates in several of the scenarios. The three metrics did not exhibit similar behavior under each preservation scenario: while three-timer and CMR metrics produced more accurate rate estimates, per capita rates tended to better reproduce true shifts in origination rates. All metrics suffered from spurious peaks in origination and extinction rates when highly volatile preservation impacted the simulated record. Results from these simulations indicate that elevated diversification rates in relation to tectonic activity during the middle Miocene are likely to be evident in the fossil record, even if preservation in the North American fossil record was variable. Input from the past is necessary to evaluate the ultimate mechanisms underlying speciation and extinction dynamics.

Understanding evolutionary transitions in scleractinian corals is fundamental to predicting responses of coral reefs to climate change. We examine transitions between solitary and colonial corals in the fossil record, focusing on the Caribbean solitary reef coral Scolymia and members of the subfamily Mussinae. Fossil specimens are selected from a large well-documented collection of Neogene Caribbean corals, and a total of 23 species are distinguished using 15 morphological features. Ten of the 23 species are extant Caribbean species, seven are previously described extinct Neogene species, and six other extinct species are formally described as new. The 7 + 6 extinct species are added to a morphological data set consisting of 30 extant molecularly characterized species plus seven additional extinct (five Eocene, two Neogene) species. In addition to the Caribbean subfamily Mussinae, the extant species include the Indo-Pacific families Merulinidae and Lobophylliidae, and the Caribbean subfamily Faviinae. Phylogenetic analysis was performed on the data using maximum parsimony, and the results reveal four clades, which correspond with previously reported molecular clades. Solitary corals group most closely with Caribbean Mussinae and Indo-Pacific Lobophylliidae, whereas colonial corals are present in all four clades. Within Caribbean Mussinae, members of the colonial genera Mycetophyllia and Isophyllia form distinct subclades, as do the extinct solitary genera Antillia and Antillophyllia. The relationships within Scolymia are less well defined but its members appear more closely related to extinct solitary genera dating back to the Eocene. These results indicate that evolutionary transitions between solitary and colonial corals have been rare within the Mussinae. Except Antillophyllia, most Mussinae genera are restricted to the Caribbean. During the late Miocene, Mycetophyllia diversified and three other modern Mussinae genera (Mussa, Scolymia, Isophyllia) originated in association with increased Caribbean productivity. Mussinae that were more likely to survive Plio–Pleistocene extinction may have taken refuge in deep forereef habitats.

Biases in the per-taxon origination and extinction rates of fossil taxa

One of the goals of paleoprimatology is to provide adaptive explanations for the origins of evolutionary novelties of the order and its major groups. For such scenarios to be more than,“just-so stories,” like Kipling’s story of how the leopard got its spots, we need to develop and test ideas about the adaptive significance of particular morphological character states that are likely to be preserved in the fossil record. Once the adaptive context of the morphology is fully appreciated, we can go on to make inferences about the behavior of extinct primate species that possessed similar character states. But even when we know with some confidence the adaptive “meaning” of a particular morphological character state and use it to infer the behavior of an extinct species, we must be able to place that extinct species into its phylogenetic context. What is the distribution of the newly identified morphological peculiarity? Is it found in just one extinct species or does it characterize some larger group of species? And what does the distribution of the character state tell us about the ancestral morphological (and inferred behavioral) pattern of primate clades? Therefore, in parallel with the effort to understand adaptation of character states, there must be an effort to reconstruct the phylogenetic pattern of primates.

Evolutionary history of the devilrays (Chondrichthyes: Myliobatiformes) from fossil and morphological inference

The discipline-wide effort to database the fossil record at the occurrence level has made it possible to estimate marine invertebrate extinction and origination rates with much greater accuracy. The new data show that two biotic mechanisms have hastened recoveries from mass extinctions and confined diversity to a relatively narrow range over the past 500 million years (Myr). First, a drop in diversity of any size correlates with low extinction rates immediately afterward, so much so that extinction would almost come to a halt if diversity dropped by 90%. Second, very high extinction rates are followed by equally high origination rates. The two relationships predict that the rebound from the current mass extinction will take at least 10 Myr, and perhaps 40 Myr if it rivals the Permo-Triassic catastrophe. Regardless, any large event will result in a dramatic ecological and taxonomic restructuring of the biosphere. The data also confirm that extinction and origination rates both declined through the Phanerozoic and that several extinctions in addition to the Permo-Triassic event were particularly severe. However, the trend may be driven by taxonomic biases and the rates vary in accord with a simple log normal distribution, so there is no sharp distinction between background and mass extinctions. Furthermore, the lack of any significant autocorrelation in the data is inconsistent with macroevolutionary theories of periodicity or self-organized criticality.

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.

Understanding spatial variation in origination and extinction can help to unravel the mechanisms underlying macroevolutionary patterns. Although methods have been developed for estimating global origination and extinction rates from the fossil record, no framework exists for applying these methods to restricted spatial regions. Here, we test the efficacy of three metrics for regional analysis, using simulated fossil occurrences. These metrics are then applied to the marine invertebrate record of the Permian and Triassic to examine variation in extinction and origination rates across latitudes. Extinction and origination rates were generally uniform across latitudes for these time intervals, including during the Capitanian and Permian–Triassic mass extinctions. The small magnitude of this variation, combined with the possibility of its attribution to sampling bias, cautions against linking any observed differences to contrasting evolutionary dynamics. Our results indicate that origination and extinction levels were more variable across clades than across latitudes.

How quickly does biodiversity rebound after extinctions? Palaeobiologists have examined the temporal, taxonomic and geographic patterns of recovery following individual mass extinctions in detail, but have not analysed recoveries from extinctions throughout the fossil record as a whole. Here, we measure how fast biodiversity rebounds after extinctions in general, rather than after individual mass extinctions, by calculating the cross-correlation between extinction and origination rates across the entire Phanerozoic marine fossil record. Our results show that extinction rates are not significantly correlated with contemporaneous origination rates, but instead are correlated with origination rates roughly 10 million years later. This lagged correlation persists when we remove the 'Big Five' major mass extinctions, indicating that recovery times following mass extinctions and background extinctions are similar. Our results suggest that there are intrinsic limits to how quickly global biodiversity can recover after extinction events, regardless of their magnitude. They also imply that today's anthropogenic extinctions will diminish biodiversity for millions of years to come.

Some molecular clock estimates of divergence times of taxonomic groups undergoing evolutionary radiation are much older than the groups' first observed fossil record. Mathematical models of branching evolution are used to estimate the maximal rate of fossil preservation consistent with a postulated missing history, given the sum of species durations implied by early origins under a range of species origination and extinction rates. The plausibility of postulated divergence times depends on origination, extinction, and preservation rates estimated from the fossil record. For eutherian mammals, this approach suggests that it is unlikely that many modern orders arose much earlier than their oldest fossil records.