Recognizing pulses of extinction from clusters of last occurrences

The distribution of last occurrences of fossil taxa in a stratigraphic column are used to infer the pattern, timing and tempo of extinction from the fossil record. Clusters of last occurrences are commonly interpreted as an abrupt pulse of extinction. However, stratigraphic architecture alone can produce clusters of last occurrences that can be misinterpreted as an extinction pulse. These clusters will typically occur in strata that immediately underlie facies changes and sequence‐stratigraphic surfaces. It has been proposed that a basin‐wide analysis of the fossil record within a sequence‐stratigraphic framework can be used to distinguish between clusters of last occurrences caused solely by extinction pulses from those generated by sequence‐stratigraphic architecture. A basin‐wide approach makes it possible to observe lateral facies shifts in response to sea‐level change, mitigating the effects of stratigraphic architecture. Using computer simulations of plausible Late Ordovician mass‐extinction scenarios tuned to an inferred Late Ordovician sea‐level curve, we show that stratigraphically‐generated clusters of last occurrences are observed even in basin‐wide analyses of the simulated fossil records due to the basin‐wide loss of preferred facies for many taxa. Nonetheless, we demonstrate that by coarsening the stratigraphic resolution to the systems‐tract level and identifying facies preferences of simulated taxa, we can filter out taxa whose last occurrences coincide with the basin‐wide loss of their preferred facies. This enables consistent identification of the underlying extinction pattern for a wide variety of extinction scenarios. Applying this approach to empirical field data can help to constrain underlying extinction patterns from the fossil record.     

The case for extraterrestrial causes of extinction

The dramatic increase in our knowledge of large-body impacts that have occurred in Earth's history has led to strong arguments for the plausibility of meteorite impact as a cause of extinction. Proof of causation is often hampered, however, by our inability to demonstrate the synchronism of specific impacts and extinctions. A central problem is range truncation: the last reported occurrences of fossil taxa generally underestimate the true times of extinction. Range truncation, because of gaps in sedimentation, lack of preservation, or lack of discovery, can make sudden extinctions appear gradual and gradual extinctions appear sudden. Also, stepwise extinction may appear as an artefact of range truncation. These effects are demonstrated by experiments performed on data from field collections of Cretaceous ammonities from Zumaya (Spain). The challenge for future research is to develop a new calculus for treating biostratigraphic data so that fossils can provide more accurate assessments of the timing of extinctions.     

Reductions in connectivity and habitat quality drive local extinctions in a plant diversity hotspot

It is well documented that habitat loss is a major cause of biodiversity decline. However, the roles of the different aspects of habitat loss in local extinctions are less understood. Anthropogenic destruction of an area of habitat causes immediate local extinction but subsequently three additional gradual drivers influence the likelihood of delayed extinction: decreased habitat patch size, lower connectivity and habitat deterioration. We investigated the role of these drivers in local extinctions of 82 declining species in a UK biodiversity hotspot. We combined a unique set of ≈ 7000 vegetation surveys and habitat maps from the 1930s with contemporary species’ occurrences. We extrapolated from these surveys to the whole 2500‐km² study area using habitat suitability surfaces. The strengths of drivers in explaining local extinctions over this 70 yr period were determined by contrasting connectivity, patch size and habitat quality loss for locations at which a species went extinct and those with persisting occurrences. Species’ occurrences declined on average by 60%, with half of local extinctions attributable to immediate habitat loss and half to the gradual processes causing delayed extinctions. On average, locations where a species persisted had a 73% higher contemporary connectivity than those suffering extinctions, but showed no differences in historical connectivity. Furthermore, locations with extinctions experienced a 37% greater decline in suitability associated with changes in habitat type. The strength of the drivers and the proportion of extinctions depended on the species’ habitat specialism, but were affected only minimally by life‐history characteristics. In conclusion, we identified a hierarchy of drivers influencing local extinction: with connectivity loss being the strongest, suitability change being moderately important, but changes in habitat patch size having only weak effects. We suggest conservation efforts could be most effective by strengthening connectivity along with reducing habitat deterioration, which would benefit a wide range of species.     

The evolutionary significance of mass extinctions

Local extinctions of populations, species or groups of species in a particular area are commonly observed by biologists. There are also historical records of the total extinction of single species such as the Dodo, the Great Auk and the Tasmanian Wolf. Mass extinctions are on a much larger scale, and their study is based on the fossil record. The aims of this review are to explore the nature of mass extinctions and their evolutionary significance. The key questions are: what is mass extinction, what are the causes of mass extinctions, do mass extinctions follow a regular pattern, and how do mass extinctions affect our understanding of evolutionary processes?     

Some remarks on the structure and function of refugia in ecology and palaeoecology

Studies of processes connected with various Phanerozoic mass extinctions suggest that although these events differ in details from each other, they manifest certain global mutual similarities. There is a number of detailed data on the mass extinction phases but only scarce information on the survival and recovery intervals directly following the crises. In connection with the biota crises studies also the problem of refugia started to be discussed very intensively, because namely fossil refugia can contain fossils representing important connecting links getting over boundaries of mass extinctions. The aim of this article is to join some general considerations of possible refugia structures, functions and spatial and temporal changes to the discussion being in progress.     

The ghosts of mammals past: biological and geographical patterns of global mammalian extinction across the Holocene

Although the recent historical period is usually treated as a temporal base-line for understanding patterns of mammal extinction, mammalian biodiversity loss has also taken place throughout the Late Quaternary. We explore the spatial, taxonomic and phylogenetic patterns of 241 mammal species extinctions known to have occurred during the Holocene up to the present day. To assess whether our understanding of mammalian threat processes has been affected by excluding these taxa, we incorporate extinct species data into analyses of the impact of body mass on extinction risk. We find that Holocene extinctions have been phylogenetically and spatially concentrated in specific taxa and geographical regions, which are often not congruent with those disproportionately at risk today. Large-bodied mammals have also been more extinction-prone in most geographical regions across the Holocene. Our data support the extinction filter hypothesis, whereby regional faunas from which susceptible species have already become extinct now appear less threatened; they may also suggest that different processes are responsible for driving past and present extinctions. We also find overall incompleteness and inter-regional biases in extinction data from the recent fossil record. Although direct use of fossil data in future projections of extinction risk is therefore not straightforward, insights into extinction processes from the Holocene record are still useful in understanding mammalian threat.     

The end and the beginning: recoveries from mass extinctions

The evolutionary consequences of mass extinctions depend as much on the processes of survival and recovery following these biotic crises as on the patterns of extinction themselves. Paleontologists are currently documenting biotic recoveries from six major mass extinctions and several smaller biotic crises. Although the immediate responses are remarkably similar after each event, with low-diversity assemblages dominated by widespread, eurytopic species, the recovery response in the long-term is more varied. Lineages that survive the extinction can lack the resilience for recovery, whereas others vanish from the fossil record seemingly to return from the dead after several million years.     

浙江长兴煤山二叠纪末大灭绝化石记录的置信区间分析

化石的保存与采集普遍具有随机性,以至直接观察结果往往不能反映真实的生物分类单元延限以及生物事件,而必须对化石记录进行统计分析,从定量的角度发掘其可信内涵,。浙江长兴煤山财区二叠系－三叠系剖面的化石资料经过数十年采集研究,已提出多期生物群灭绝模式,文中运用置信区间作了分析,。说明了长兴期末生物大灭绝为突发性,灾难性事件。     

Organism activity levels predict marine invertebrate survival during ancient global change extinctions

Multistressor global change, the combined influence of ocean warming, acidification, and deoxygenation, poses a serious threat to marine organisms. Experimental studies imply that organisms with higher levels of activity should be more resilient, but testing this prediction and understanding organism vulnerability at a global scale, over evolutionary timescales, and in natural ecosystems remain challenging. The fossil record, which contains multiple extinctions triggered by multistressor global change, is ideally suited for testing hypotheses at broad geographic, taxonomic, and temporal scales. Here, I assess the importance of activity level for survival of well‐skeletonized benthic marine invertebrates over a 100‐million‐year‐long interval (Permian to Jurassic periods) containing four global change extinctions, including the end‐Permian and end‐Triassic mass extinctions. More active organisms, based on a semiquantitative score incorporating feeding and motility, were significantly more likely to survive during three of the four extinction events (Guadalupian, end‐Permian, and end‐Triassic). In contrast, activity was not an important control on survival during nonextinction intervals. Both the end‐Permian and end‐Triassic mass extinctions also triggered abrupt shifts to increased dominance by more active organisms. Although mean activity gradually returned toward pre‐extinction values, the net result was a permanent ratcheting of ecosystem‐wide activity to higher levels. Selectivity patterns during ancient global change extinctions confirm the hypothesis that higher activity, a proxy for respiratory physiology, is a fundamental control on survival, although the roles of specific physiological traits (such as extracellular pCO₂ or aerobic scope) cannot be distinguished. Modern marine ecosystems are dominated by more active organisms, in part because of selectivity ratcheting during these ancient extinctions, so on average may be less vulnerable to global change stressors than ancient counterparts. However, ancient extinctions demonstrate that even active organisms can suffer major extinction when the intensity of environmental disruption is intense.     

Extinction patterns in the avifauna of the Hawaiian islands

Through the continuing accumulation of fossil evidence, it is clear that the avifauna of the Hawaiian Islands underwent a large‐scale extinction event around the time of Polynesian arrival. A second wave of extinctions since European colonization has further altered this unique avifauna. Here I present the first systematic analysis of the factors characterizing the species that went extinct in each time period and those that survived in order to provide a clearer picture of the possible causal mechanisms. These analyses were based on mean body size, dietary and ecological information and phylogenetic lineage of all known indigenous, non‐migratory land and freshwater bird species of the five largest Hawaiian Islands. Extinct species were divided into ‘prehistoric’ and ‘historic’ extinction categories based on the timing of their last occurrence. A model of fossil preservation bias was also incorporated. I used regression trees to predict probability of prehistoric and historic extinction based on ecological variables. Prehistoric extinctions showed a strong bias toward larger body sizes and flightless, ground‐nesting species, even after accounting for preservation bias. Many small, specialized species, mostly granivores and frugivores, also disappeared, implicating a wide suite of human impacts including destruction of dry forest habitat. In contrast, the highest extinction rates in the historic period were in medium‐sized nectarivorous and insectivorous species. These differences result from different causal mechanisms underlying the two waves of extinction.     

The best sections method of studying mass extinctions

Phanerozoic mass extinctions have been studied primarily by analysing global diversity patterns compiled from the published literature. However, such compilations are beset by problems of incorrect correlation, imprecise age assignments and changing taxonomy. An alternative approach is to analyse mass extinctions by the ‘best sections’ method. This method identifies abundantly fossiliferous, well‐studied, stratigraphically dense and temporally extensive fossil records in strata that contain geochemical and other relevant non‐palaeontological data from a single depositional basin or geographically restricted outcrop area as the ‘best sections’ by which to analyse extinctions. A strength of the best sections method is that it allows the extinctions identified to be compared directly to changes in facies and other factors recorded in the best section. And, the hypothesis of a widespread extinction based on an extinction seen in a best section can be tested by its presence or absence in temporally equivalent sections. What we need are more field‐based studies of the best sections that encompass mass extinctions (real and hypothetical) and less of a reliance on literature‐based diversity compilations to produce a more reliable and comprehensive understanding of the history of extinctions.     

Trends and patterns in the evolution of vascular plants: macroevolutionary implications of a multilevel taxonomic analysis

Cascales‐Miñana, B., Muñoz‐Bertomeu, J., Ros, R., Segura, J. 2010: Trends and patterns in the evolution of vascular plants: macroevolutionary implications of a multilevel taxonomic analysis. Lethaia, 10.1111/j.1502‐3931.2009.00212.x Studying the macroevolutionary patterns of vascular plants from the Silurian to the present‐day provides a global record of plant life history. Evolutionary rates (origination, extinction and diversification) for families, orders, classes and divisions were analysed, as was abundance and richness for 21 time intervals. An accumulative analysis, based on the total plant fossil record, the accumulated extinctions and relative diversity, was also carried out. The diversification rate shows a uniquely constant and progressive reduction from the end of the Carboniferous to the Permian when the lowest values are registered. Very small peaks seem to reflect Cretaceous extinction for families. At family level, only two time intervals present higher extinctions, than originations. Richness and accumulative analyses reveal that only 32% of the families analysed became extinct, and that approximately 90% of them disappeared at the end of the Palaeozoic. Our results indicate that plants did not undergo mass extinction events in the ‘big five’ sense, but rather, mass ecological reorganization the absence of important extinction events or evolutionary innovations producing diversification patterns without abrupt changes. □Diversification, evolutionary, extinction, fossil record, innovations, radiation, vascular plants.     

The late Devonian trilobite crises

Mid‐Devonian to end‐Late Devonian trilobites of different taxonomic categories are updated as to their actual stratigraphical range with respect to the internationally defined stage boundaries. The main palaeogeographical and ecological occurrences are summarized. Numerical analyses emphasize the clear relationship between fluctuations in diversity and global eustatic events. Already declining in diversity from the early mid‐Devonian, shallow‐water communities became most restricted during the mid‐Givetian Taghanic transgression. After a phase of adaptive radiation, off‐shore trilobite communities were severely affected during the mid‐ and end‐Late Devonian crises. From an initial 5 orders 3 were lost at the end‐Frasnian Kellwasser crisis while only 1 from the remaining 2 orders survived the Devonian‐Carboniferous boundary Hangenberg event. In both cases extinction was preceded by a unidirectional evolutionary trend in eye reduction accompanied by impoverishment of lower rank taxa. This phenomenon is obviously a result of selective adaptation under constant long‐lasting environmental influences. Specialization to obligate epi‐ or even endo‐benthic life habit, however, led fatally to extinction when stable conditions became substantially perturbed. Sudden sea‐level changes with subsequent break in the REDOX‐equilibrium took place at the Kellwasser and Hangenberg events, which were most probably responsible for trilobite mass extinctions.     

Large-scale heterogeneity of the fossil record: implications for Phanerozoic biodiversity studies

Patterns of origination, extinction and standing diversity through time have been inferred from tallies of taxa preserved in the fossil record. This approach assumes that sampling of the fossil record is effectively uniform over time. Although recent evidence suggests that our sampling of the available rock record has indeed been very thorough and effective, there is also overwhelming evidence that the rock record available for sampling is itself distorted by major systematic biases. Data on rock outcrop area compiled for post-Palaeozoic sediments from Western Europe at stage level are presented. These show a strongly cyclical pattern corresponding to first- and second-order sequence stratigraphical depositional cycles. Standing diversity increases over time and, at the coarsest scale, is decoupled from surface outcrop area. This increasing trend can therefore be considered a real pattern. Changes in standing diversity and origination rates over time-scales measured in tens of millions of years, however, are strongly correlated with surface outcrop area. Extinction peaks conform to a random-walk model, but larger peaks occur at just two positions with respect to second-order stratigraphical sequences, towards the culmination of stacked transgressive system tracts and close to system bases, precisely the positions where taxonomic last occurrences are predicted to cluster under a random distribution model. Many of the taxonomic patterns that have been described from the fossil record conform to a species-area effect. Whether this arises primarily from sampling bias, or from changing surface area of marine shelf seas through time and its effect on biodiversity, remains problematic.     

A dynamic global equilibrium in carnivoran diversification over 20 million years

The ecological and evolutionary processes leading to present-day biological diversity can be inferred by reconstructing the phylogeny of living organisms, and then modelling potential processes that could have produced this genealogy. A more direct approach is to estimate past processes from the fossil record. The Carnivora (Mammalia) has both substantial extant species richness and a rich fossil record. We compiled species-level data for over 10 000 fossil occurrences of nearly 1400 carnivoran species. Using this compilation, we estimated extinction, speciation and net diversification for carnivorans through the Neogene (22–2 Ma), while simultaneously modelling sampling probability. Our analyses show that caniforms (dogs, bears and relatives) have higher speciation and extinction rates than feliforms (cats, hyenas and relatives), but lower rates of net diversification. We also find that despite continual species turnover, net carnivoran diversification through the Neogene is surprisingly stable, suggesting a saturated adaptive zone, despite restructuring of the physical environment. This result is strikingly different from analyses of carnivoran diversification estimated from extant species alone. Two intervals show elevated diversification rates (13–12 Ma and 4–3 Ma), although the precise causal factors behind the two peaks in carnivoran diversification remain open questions.     

On the potential for ocean acidification to be a general cause of ancient reef crises

Anthropogenic rise in the carbon dioxide concentration in the atmosphere leads to global warming and acidification of the oceans. Ocean acidification (OA) is harmful to many organisms but especially to those that build massive skeletons of calcium carbonate, such as reef corals. Here, we test the recent suggestion that OA leads not only to declining calcification of reef corals and reduced growth rates of reefs but may also have been a trigger of ancient reef crises and mass extinctions in the sea. We analyse the fossil record of biogenic reefs and marine organisms to (1) assess the timing and intensity of ancient reef crises, (2) check which reef crises were concurrent with inferred pulses of carbon dioxide concentrations and (3) evaluate the correlation between reef crises and mass extinctions and their selectivity in terms of inferred physiological buffering. We conclude that four of five global metazoan reef crises in the last 500 Myr were probably at least partially governed by OA and rapid global warming. However, only two of the big five mass extinctions show geological evidence of OA.     

Fossil and phylogenetic analyses reveal recurrent periods of diversification and extinction in dictyopteran insects

Variations of speciation and extinction rates determine the fate of clades through time. Periods of high diversification and extinction (possibly mass-extinction events) can punctuate the evolutionary history of various clades, but they remain loosely defined for many biological groups, especially nonmarine invertebrates like insects. Here, we examine whether the cockroaches, mantises and termites (altogether included in Dictyoptera) have experienced episodic pulses of speciation or extinction and how these pulses may be associated with environmental fluctuations or mass extinctions. We relied on molecular phylogeny and fossil data to shed light on the times and rates at which dictyopterans diversified. The diversification of Dictyoptera has alternated between (i) periods of high diversification in the late Carboniferous, Early–Middle Triassic, Early Cretaceous and middle Palaeogene, and (ii) periods of high extinction rates particularly at the Permian-Triassic boundary, but not necessarily correlated with the major global biodiversity crises as in the mid-Cretaceous. This study advocates the importance of analyzing, when possible, both molecular phylogeny and fossil data to unveil diversification and extinction periods for a given group. The causes and consequences of extinction must be studied beyond mass-extinction events alone to gain a broader understanding of how clades wax and wane.     

Was the Late Ordovician mass extinction truly exceptional?

The Late Ordovician mass extinction event is the oldest of the five great extinction events in the fossil record. It has long been regarded as an outlier among mass extinctions, primarily due to its association with a cooling climate. However, recent temporally better resolved fossil biodiversity estimates complicate this view, providing growing evidence for a prolonged but punctuated biodiversity decline modulated by changes in atmospheric composition, ocean chemistry, and viable habitat area. This evolving view invokes extinction drivers similar to those that occurred during other major extinctions; some are even factors in the current human-induced biodiversity crisis. Even this very ancient and, at first glance, exceptional event conveys important lessons about the intensifying ‘sixth mass extinction’.     

Resistance of spiders to Cretaceous-Tertiary extinction events

Throughout Earth history a small number of global catastrophic events leading to biotic crises have caused mass extinctions. Here, using a technique that combines taxonomic and numerical data, we consider the effects of the Cenomanian-Turonian and Cretaceous-Tertiary mass extinctions on the terrestrial spider fauna in the light of new fossil data. We provide the first evidence that spiders suffered no decline at the family level during these mass extinction events. On the contrary, we show that they increased in relative numbers through the Cretaceous and beyond the Cretaceous-Tertiary extinction event.     

Discriminating signal from noise in the fossil record of early vertebrates reveals cryptic evolutionary history

The fossil record of early vertebrates has been influential in elucidating the evolutionary assembly of the gnathostome bodyplan. Understanding of the timing and tempo of vertebrate innovations remains, however, mired in a literal reading of the fossil record. Early jawless vertebrates (ostracoderms) exhibit restriction to shallow-water environments. The distribution of their stratigraphic occurrences therefore reflects not only flux in diversity, but also secular variation in facies representation of the rock record. Using stratigraphic, phylogenetic and palaeoenvironmental data, we assessed the veracity of the fossil records of the jawless relatives of jawed vertebrates (Osteostraci, Galeaspida, Thelodonti, Heterostraci). Non-random models of fossil recovery potential using Palaeozoic sea-level changes were used to calculate confidence intervals of clade origins. These intervals extend the timescale for possible origins into the Upper Ordovician; these estimates ameliorate the long ghost lineages inferred for Osteostraci, Galeaspida and Heterostraci, given their known stratigraphic occurrences and stem–gnathostome phylogeny. Diversity changes through the Silurian and Devonian were found to lie within the expected limits predicted from estimates of fossil record quality indicating that it is geological, rather than biological factors, that are responsible for shifts in diversity. Environmental restriction also appears to belie ostracoderm extinction and demise rather than competition with jawed vertebrates.