Dinosaur diversity and the rock record

Palaeobiodiversity analysis underpins macroevolutionary investigations, allowing identification of mass extinctions and adaptive radiations. However, recent large-scale studies on marine invertebrates indicate that geological factors play a central role in moulding the shape of diversity curves and imply that many features of such curves represent sampling artefacts, rather than genuine evolutionary events. In order to test whether similar biases affect diversity estimates for terrestrial taxa, we compiled genus-richness estimates for three Mesozoic dinosaur clades (Ornithischia, Sauropodomorpha and Theropoda). Linear models of expected genus richness were constructed for each clade, using the number of dinosaur-bearing formations available through time as a proxy for the amount of fossiliferous rock outcrop. Modelled diversity estimates were then compared with observed patterns. Strong statistically robust correlations demonstrate that almost all aspects of ornithischian and theropod diversity curves can be explained by geological megabiases, whereas the sauropodomorph record diverges from modelled predictions and may be a stronger contender for identifying evolutionary signals. In contrast to other recent studies, we identify a marked decline in dinosaur genus richness during the closing stages of the Cretaceous Period, indicating that the clade decreased in diversity for several million years prior to the final extinction of non-avian dinosaurs at the Cretaceous–Palaeocene boundary.     

Phanerozoic marine diversity: rock record modelling provides an independent test of large-scale trends

Sampling bias created by a heterogeneous rock record can seriously distort estimates of marine diversity and makes a direct reading of the fossil record unreliable. Here we compare two independent estimates of Phanerozoic marine diversity that explicitly take account of variation in sampling—a subsampling approach that standardizes for differences in fossil collection intensity, and a rock area modelling approach that takes account of differences in rock availability. Using the fossil records of North America and Western Europe, we demonstrate that a modelling approach applied to the combined data produces results that are significantly correlated with those derived from subsampling. This concordance between independent approaches argues strongly for the reality of the large-scale trends in diversity we identify from both approaches.     

Geographical,environmental and intrinsic biotic controls on Phanerozoic marine diversification

Abstract: The Paleobiology Database now includes enough data on fossil collections to produce useful time series of geographical and environmental variables in addition to a robust global Phanerozoic marine diversity curve. The curve is produced by a new ‘shareholder quorum’ method of sampling standardization that removes biases but avoids overcompensating for them by imposing entirely uniform data quotas. It involves drawing fossil collections until the taxa that have been sampled at least once (the ‘shareholders’) have a summed total of frequencies (i.e. coverage) that meets a target (the ‘quorum’). Coverage of each interval’s entire data set is estimated prior to subsampling using a variant of a standard index, Good’s u. This variant employs counts of occurrences of taxa described in only one publication instead of taxa found in only one collection. Each taxon’s frequency within an interval is multiplied by the interval’s index value, which limits the maximum possible sampling level and thereby creates the need for subsampling. Analyses focus on a global diversity curve and curves for northern, southern and ‘tropical’ (30°N to 30°S) palaeolatitudinal belts. Tropical genus richness is remarkably static, so most large shifts in the curve reflect trends at higher latitudes. Changes in diversity are analysed as a function of standing diversity; the number, spacing and palaeolatitudinal position of sampled geographical cells; the mean onshore–offshore position of cells; and proportions of cells from carbonate, onshore and reefal environments. Redundancy among the variables is eliminated by performing a principal components analysis of each data set and using the axis scores in multiple regressions. The key factors are standing diversity and the dominance of onshore environments such as reefs. These factors combine to produce logistic growth patterns with slowly changing equilibrium values. There is no evidence of unregulated exponential growth across any long stretch of the Phanerozoic, and in particular there was no large Cenozoic radiation beyond the Eocene. The end‐Ordovician, Permo–Triassic and Cretaceous–Palaeogene mass extinctions had relatively short‐term albeit severe effects. However, reef collapse was involved in these events and also may have caused large, longer term global diversity decreases in the mid‐Devonian and across the Triassic/Jurassic boundary. Conversely, the expansion of reef ecosystems may explain newly recognized major radiations in the mid‐Permian and mid‐Jurassic. Reef ecosystems are particularly vulnerable to current environmental disturbances such as ocean acidification, and their decimation might prolong the recovery from today’s mass extinction by millions or even tens of millions of years.     

古生物多样性统计中的偏差及其校正

地质历史时期生物多样性统计中的偏差是普遍存在的。文中以奥陶纪海洋生物和二叠纪腕足动物分异度为例介绍和讨论古生物多样性统计中的偏差问题。认为在研究某些时段分异度时不能依靠单一的种、属或科的数量来建立分异度模式,而需要用生物分异度、灭绝率和新生率等多种计算方法来综合分析。同时古生物分异度的研究受到化石记录的完整性、研究、保存和采集程度、时间段的不均一性等多种因素影响,因此,大多需要应用稀疏标准化法等对不同时段或化石群在同等量化标准的基础上进行比较和校正后,才能得到比较符合实际的分异度模式。     

A refined modelling approach to assess the influence of sampling on palaeobiodiversity curves: new support for declining Cretaceous dinosaur richness

Modelling has been underdeveloped with respect to constructing palaeobiodiversity curves, but it offers an additional tool for removing sampling from their estimation. Here, an alternative to subsampling approaches, which often require large sample sizes, is explored by the extension and refinement of a pre-existing modelling technique that uses a geological proxy for sampling. Application of the model to the three main clades of dinosaurs suggests that much of their diversity fluctuations cannot be explained by sampling alone. Furthermore, there is new support for a long-term decline in their diversity leading up to the Cretaceous–Paleogene (K–Pg) extinction event. At present, use of this method with data that includes either Lagerstätten or ‘Pull of the Recent’ biases is inappropriate, although partial solutions are offered.     

Mesozoic marine tetrapod diversity: mass extinctions and temporal heterogeneity in geological megabiases affecting vertebrates

The fossil record is our only direct means for evaluating shifts in biodiversity through Earth''s history. However, analyses of fossil marine invertebrates have demonstrated that geological megabiases profoundly influence fossil preservation and discovery, obscuring true diversity signals. Comparable studies of vertebrate palaeodiversity patterns remain in their infancy. A new species-level dataset of Mesozoic marine tetrapod occurrences was compared with a proxy for temporal variation in the volume and facies diversity of fossiliferous rock (number of marine fossiliferous formations: FMF). A strong correlation between taxic diversity and FMF is present during the Cretaceous. Weak or no correlation of Jurassic data suggests a qualitatively different sampling regime resulting from five apparent peaks in Triassic–Jurassic diversity. These correspond to a small number of European formations that have been the subject of intensive collecting, and represent ‘Lagerstätten effects’. Consideration of sampling biases allows re-evaluation of proposed mass extinction events. Marine tetrapod diversity declined during the Carnian or Norian. However, the proposed end-Triassic extinction event cannot be recognized with confidence. Some evidence supports an extinction event near the Jurassic/Cretaceous boundary, but the proposed end-Cenomanian extinction is probably an artefact of poor sampling. Marine tetrapod diversity underwent a long-term decline prior to the Cretaceous–Palaeogene extinction.     

Sea level,dinosaur diversity and sampling biases: investigating the ‘common cause’ hypothesis in the terrestrial realm

The fossil record is our primary window onto the diversification of ancient life, but there are widespread concerns that sampling biases may distort observed palaeodiversity counts. Such concerns have been reinforced by numerous studies that found correlations between measures of sampling intensity and observed diversity. However, correlation does not necessarily mean that sampling controls observed diversity: an alternative view is that both sampling and diversity may be driven by some common factor (e.g. variation in continental flooding driven by sea level). The latter is known as the ‘common cause’ hypothesis. Here, we present quantitative analyses of the relationships between dinosaur diversity, sampling of the dinosaur fossil record, and changes in continental flooding and sea level, providing new insights into terrestrial common cause. Although raw data show significant correlations between continental flooding/sea level and both observed diversity and sampling, these correlations do not survive detrending or removal of short-term autocorrelation. By contrast, the strong correlation between diversity and sampling is robust to various data transformations. Correlations between continental flooding/sea level and taxic diversity/sampling result from a shared upward trend in all data series, and short-term changes in continental flooding/sea level and diversity/sampling do not correlate. The hypothesis that global dinosaur diversity is tied to sea-level fluctuations is poorly supported, and terrestrial common cause is unsubstantiated as currently conceived. Instead, we consider variation in sampling to be the preferred null hypothesis for short-term diversity variation in the Mesozoic terrestrial realm.     

Fossil biogeography: a new model to infer dispersal,extinction and sampling from palaeontological data

Methods in historical biogeography have revolutionized our ability to infer the evolution of ancestral geographical ranges from phylogenies of extant taxa, the rates of dispersals, and biotic connectivity among areas. However, extant taxa are likely to provide limited and potentially biased information about past biogeographic processes, due to extinction, asymmetrical dispersals and variable connectivity among areas. Fossil data hold considerable information about past distribution of lineages, but suffer from largely incomplete sampling. Here we present a new dispersal–extinction–sampling (DES) model, which estimates biogeographic parameters using fossil occurrences instead of phylogenetic trees. The model estimates dispersal and extinction rates while explicitly accounting for the incompleteness of the fossil record. Rates can vary between areas and through time, thus providing the opportunity to assess complex scenarios of biogeographic evolution. We implement the DES model in a Bayesian framework and demonstrate through simulations that it can accurately infer all the relevant parameters. We demonstrate the use of our model by analysing the Cenozoic fossil record of land plants and inferring dispersal and extinction rates across Eurasia and North America. Our results show that biogeographic range evolution is not a time-homogeneous process, as assumed in most phylogenetic analyses, but varies through time and between areas. In our empirical assessment, this is shown by the striking predominance of plant dispersals from Eurasia into North America during the Eocene climatic cooling, followed by a shift in the opposite direction, and finally, a balance in biotic interchange since the middle Miocene. We conclude by discussing the potential of fossil-based analyses to test biogeographic hypotheses and improve phylogenetic methods in historical biogeography.     

How many dinosaur species were there? Fossil bias and true richness estimated using a Poisson sampling model

The fossil record is a rich source of information about biological diversity in the past. However, the fossil record is not only incomplete but has also inherent biases due to geological, physical, chemical and biological factors. Our knowledge of past life is also biased because of differences in academic and amateur interests and sampling efforts. As a result, not all individuals or species that lived in the past are equally likely to be discovered at any point in time or space. To reconstruct temporal dynamics of diversity using the fossil record, biased sampling must be explicitly taken into account. Here, we introduce an approach that uses the variation in the number of times each species is observed in the fossil record to estimate both sampling bias and true richness. We term our technique TRiPS (True Richness estimated using a Poisson Sampling model) and explore its robustness to violation of its assumptions via simulations. We then venture to estimate sampling bias and absolute species richness of dinosaurs in the geological stages of the Mesozoic. Using TRiPS, we estimate that 1936 (1543–2468) species of dinosaurs roamed the Earth during the Mesozoic. We also present improved estimates of species richness trajectories of the three major dinosaur clades: the sauropodomorphs, ornithischians and theropods, casting doubt on the Jurassic–Cretaceous extinction event and demonstrating that all dinosaur groups are subject to considerable sampling bias throughout the Mesozoic.     

Dinosaurs and fluctuating sea levels during the mesozoic

The very different frequency of dinosaurs during the Mesozoic can be allied to the correlation between global sea level cyclicity and fossilization. This is based upon the sedimentary situation in the inner shelf, the area of predominant fossil record of dinosaurs, and sea level fluctuations. A rich fossil record is found in times of high sea level, and vice versa. Due to natural laws acting on sea level stands, the fossil record of dinosaurs and other terrestrial tetrapods is incomplete. This is causally explainable in the sequence stratigraphy. Among causes of global sea level fluctuations, the change from warm to cold times has been accorded greatest probability even in the Mesozoic. Consequently, the problem of dinosaur evolution and distribution should not be confused with the pattern of their fossil record. The latter, however, is so far nearly always used for all interpretations. The context presented here results in basic modifications.

During the phases of reduced to missing fossil record (low sea level, cold times), dinosaurs existed at least in circumequatorial regions in high diversity. Highly diverse faunas recorded exceptionally in the Upper Jurassic, Middle and Late Cretaceous, were each time the result of a long previous evolution and not the result of short term radiations at these times. Phases of sea level highstand and warm times caused an increased fossil record and poleward distribution. Cretaceous dinosaurs in paleolatitudes of 70° to 80° N and S are no proof for endothermy, but are only the effect of favorable climatic conditions at limited times. Any endothermy of the dinosaurs is not coincident with the supposedly uniformly warm equable climate of the Mesozoic, but with the opposite. Cold times did not hamper the existence of dinosaurs, but led in extreme cases (Aalenian and Valanginian) to the global lack of their fossil record. The situation at the Cretaceous‐Tertiary boundary is also explainable in this context. According to the sea level cyclicity, no extreme sea level fall and no globablly cold time were present in the critical time segment. The regression in the late Maastrichtian is found to belong to a sequence of third‐order cycles beginning in the Campanian. Every one of the cycle boundaries with regression and transgression produced apparent extinction effects which in reality are only gaps in the fossil record. After the late Maastrichtian regression the dinosaurs persisted with six lineages. The so far youngest dinosaur fauna in the Puercan (basal Paleocene) lies in a phase of sea level highstand of minor amplitude and duration with comparatively minor chances for a fossil record. The occurrences in the Puercan are governed by natural law, and, thus, dinosaurs are untied from the short term problems of the Cretaceous‐Tertiary boundary. Why dinosaurs are then missing at the next highstand, remains an open question. Anyhow, mechanisms which control fossil record, diversification and distribution, including global cold periods, do not belong to the direct causes of extinction, because identical occurrences happened many times during the Mesozoic without inducing extinction.     

Extinction and diversification in the Devonian Brachiopoda of New York state: No correlation with sea level?

Sea level highstand is generally considered to promote high species diversities among marine organisms through habitat expansion and global climatic amelioration, and marine regression to trigger elevated extinction rates among marine benthic organisms by habitat reduction (the species‐area effect), and among both marine and terrestrial organisms by global climatic deterioration. The Devonian is unusual in that the Late Devonian mass extinction occurs during an interval of global sea level highstand. To further explore this anomaly, the potential relationship between relative sea level and evolutionary biology is analyzed here for the Brachiopoda of the Devonian Period. Successive linear modeling reveals a total lack of correlation between relative sea level and either origination rates, extinction rates, or standing diversity among the Devonian brachiopods.     

A long-term association between global temperature and biodiversity, origination and extinction in the fossil record

The past relationship between global temperature and levels of biological diversity is of increasing concern due to anthropogenic climate warming. However, no consistent link between these variables has yet been demonstrated. We analysed the fossil record for the last 520 Myr against estimates of low latitude sea surface temperature for the same period. We found that global biodiversity (the richness of families and genera) is related to temperature and has been relatively low during warm 'greenhouse' phases, while during the same phases extinction and origination rates of taxonomic lineages have been relatively high. These findings are consistent for terrestrial and marine environments and are robust to a number of alternative assumptions and potential biases. Our results provide the first clear evidence that global climate may explain substantial variation in the fossil record in a simple and consistent manner. Our findings may have implications for extinction and biodiversity change under future climate warming.     

Overcoming the issue of small sample sizes in fragmentation genetics

Nazareno & Jump (2012) highlight potential issues with using small sample sizes in population genetic studies. By reanalysing allelic richness data from our recent publication on habitat fragmentation (Struebig et al. 2011), they assert that the observed relationship has been driven by three sites with the lowest number of individuals sampled. While sample size issues have been raised before in the genetic literature, Nazareno & Jump’s (2012) comment serves as a useful reminder to us all. Nevertheless, we disagree that our findings were significantly biased by sampling limitations. Here, we demonstrate by jackknifing that, contrary to the claims of Nazareno & Jump (2012), our correlations of allelic richness and fragment area are not driven solely by sites with low sample sizes. We maintain that small sample sizes can be accounted for in fragmentation studies and that sampling limitations should not detract from undertaking conservation genetic research.