Pattern of marine mass extinction near the Permian-Triassic boundary in South China

The stability and collapse of marine ecosystems during the Permian-Triassic mass extinction

The history of Earth's biodiversity is punctuated episodically by mass extinctions. These are characterized by major declines of taxon richness, but the accompanying ecological collapse has rarely been evaluated quantitatively. The Permian-Triassic mass extinction (PTME; ∼252 mya), as the greatest known extinction, permanently altered marine ecosystems and paved the way for the transition from Paleozoic to Mesozoic evolutionary faunas. Thus, the PTME offers a window into the relationship between taxon richness and ecological dynamics of ecosystems during a severe extinction. However, the accompanying ecological collapse through the PTME has not been evaluated in detail. Here, using food-web models and a marine paleocommunity dataset spanning the PTME, we show that after the first extinction phase, community stability decreased only slightly despite the loss of more than half of taxonomic diversity, while community stability significantly decreased in the second phase. Thus, taxonomic and ecological changes were unequivocally decoupled, with species richness declining severely ∼61 ka earlier than the collapse of marine ecosystem stability, implying that in major catastrophes, a biodiversity crash may be the harbinger of a more devastating ecosystem collapse.

A diverse diapsid tooth assemblage from the Early Triassic (Driefontein locality, South Africa) records the recovery of diapsids following the end-Permian mass extinction

Mass extinctions change the trajectory of evolution and restructure ecosystems. The largest mass extinction, the end-Permian, is a particularly interesting case due to the hypothesized delay in the recovery of global ecosystems, where total trophic level recovery is not thought to have occurred until 5-9 million years after the extinction event. Diapsids, especially archosauromorphs, play an important role in this recovery, filling niches left vacant by therapsids and anapsids. However, the nature of lineage and ecological diversification of diapsids is obscured by the limited number of continuous, well-dated stratigraphic sections at the Permian-Triassic boundary and continuing through the first half of the Triassic. The Karoo Basin of South Africa is one such record, and particularly the late Early Triassic (Olenekian) Driefontein locality fills this gap in the diapsid fossil record. We collected a total of 102 teeth of which 81 are identified as diapsids and the remaining 21 as identified as temnospondyls. From the sample, seven distinct tooth morphotypes of diapsids are recognized, six of which are new to the locality. We used a combination of linear measurements, 3D geomorphometrics, and nMDS ordination to compare these morphotypes and made inferences about their possible diets. Although the morphotypes are readily differentiated in nMDS, the overall morphological disparity is low, and we infer five morphotypes are faunivorous with the other two potentially omnivorous or piscivorous based on their morphological similarities with dentitions from extant diapsids, demonstrating an unsampled taxonomic and ecological diversity of diapsids in the Early Triassic based on teeth. Although ecological specialization at Driefontein may be low, it records a diversity of diapsid taxa, specifically of archosauromorph lineages.

Maleimide index: a paleo-redox index based on fragmented fossil-chlorophylls obtained by chromic acid oxidation

The composition of past photosynthetic organisms provides information about the paleo-environment based on the habitat characteristics of photosynthetic organisms. Therefore, analysis of chlorophyll-derived materials from photosynthetic organisms in sedimentary rocks is important for understanding paleo-environmental changes. Fossilized chlorophylls present in sedimentary rocks can be detected by their conversion into maleimides and phthalimides. This can be achieved through the chromic acid oxidation of sedimentary rocks. Since the maleimides and phthalimides are derived from the pyrrole skeleton of fossil chlorophylls, their composition reflects the composition of paleo-photosynthetic organisms. We herein propose an indicator for detecting anoxic-sulfidic conditions in the paleo oceanic photic zone, which is based on the composition ratio of the maleimides produced during the oxidation process. The maleimide index in this study would be a useful analytical method to indicate that anoxic-sulfidic conditions in the paleo oceanic photic zone, which is associated with mass extinction events, have occurred.

The Evolution of Calcification in Reef-Building Corals

Corals build the structural foundation of coral reefs, one of the most diverse and productive ecosystems on our planet. Although the process of coral calcification that allows corals to build these immense structures has been extensively investigated, we still know little about the evolutionary processes that allowed the soft-bodied ancestor of corals to become the ecosystem builders they are today. Using a combination of phylogenomics, proteomics, and immunohistochemistry, we show that scleractinian corals likely acquired the ability to calcify sometime between ∼308 and ∼265 Ma through a combination of lineage-specific gene duplications and the co-option of existing genes to the calcification process. Our results suggest that coral calcification did not require extensive evolutionary changes, but rather few coral-specific gene duplications and a series of small, gradual optimizations of ancestral proteins and their co-option to the calcification process.

Different triggers for the two pulses of mass extinction across the Permian and Triassic boundary

Widespread ocean anoxia has been proposed to cause biotic mass extinction across the Permian-Triassic (P-Tr) boundary. However, its temporal dynamics during this crisis period are unclear. The Liangfengya section in the South China Block contains continuous marine sedimentary and fossil records. Two pulses of biotic extinction and two mass extinction horizons (MEH 1 & 2) near the P-Tr boundary were identified and defined based on lithology and fossils from the section. The data showed that the two pulses of extinction have different environmental triggers. The first pulse occurred during the latest Permian, characterized by disappearance of algae, large foraminifers, and fusulinids. Approaching the MEH 1, multiple layers of volcanic clay and yellowish micritic limestone occurred, suggesting intense volcanic eruptions and terrigenous influx. The second pulse occurred in the earliest Triassic, characterized by opportunist-dominated communities of low diversity and high abundance, and resulted in a structural marine ecosystem change. The oxygen deficiency inferred by pyrite framboid data is associated with biotic declines above the MEH 2, suggesting that the anoxia plays an important role.

The Growth and Sporulation of Bacillus subtilis in Nanotesla Magnetic Fields

The order of magnitude of increased growth, multiplication rate, and decreased sporulation of Bacillus subtilis after exposure to nanotesla magnetic fields (MFs) relative to control samples were observed experimentally. Earth's total magnetic field intensity was reduced from 47.9 ± 0.4 μT to cover the range from 97.5 ± 1.7 nT to 1115 ± 158 nT in eight subsequent experiments by using three pairs of Helmholtz coils combined with Mu-metal shielding. The growth, multiplication rate, sporulation, and potassium content were measured in the probe and control containing B. subtilis cultures after 24 h of exposure to nanotesla and Earth's magnetic fields, respectively. The observed effect is discussed with regard to its possible repercussions on Earth's living species during geomagnetic reversals that occurred when the magnetic field was much weaker than the field that exists today. In addition, effects on future manned voyages into deep space, an environment with reduced magnetic field intensity, are considered.

Using the Fossil Record to Evaluate Timetree Timescales

The fossil and geologic records provide the primary data used to established absolute timescales for timetrees. For the paleontological evaluation of proposed timetree timescales, and for node-based methods for constructing timetrees, the fossil record is used to bracket divergence times. Minimum brackets (minimum ages) can be established robustly using well-dated fossils that can be reliably assigned to lineages based on positive morphological evidence. Maximum brackets are much harder to establish, largely because it is difficult to establish definitive evidence that the absence of a taxon in the fossil record is real and not just due to the incompleteness of the fossil and rock records. Five primary methods have been developed to estimate maximum age brackets, each of which is discussed. The fact that the fossilization potential of a group typically decreases the closer one approaches its time of origin increases the challenge of estimating maximum age brackets. Additional complications arise: 1) because fossil data actually bracket the time of origin of the first relevant fossilizable morphology (apomorphy), not the divergence time itself; 2) due to the phylogenetic uncertainty in the placement of fossils; 3) because of idiosyncratic temporal and geographic gaps in the rock and fossil records; and 4) if the preservation potential of a group changed significantly during its history. In contrast, uncertainties in the absolute ages of fossils are typically relatively unimportant, even though the vast majority of fossil cannot be dated directly. These issues and relevant quantitative methods are reviewed, and their relative magnitudes assessed, which typically correlate with the age of the group, its geographic range, and species richness.

Evidence for a prolonged Permian-Triassic extinction interval from global marine mercury records

The latest Permian mass extinction, the most devastating biocrisis of the Phanerozoic, has been widely attributed to eruptions of the Siberian Traps Large Igneous Province, although evidence of a direct link has been scant to date. Here, we measure mercury (Hg), assumed to reflect shifts in volcanic activity, across the Permian-Triassic boundary in ten marine sections across the Northern Hemisphere. Hg concentration peaks close to the Permian-Triassic boundary suggest coupling of biotic extinction and increased volcanic activity. Additionally, Hg isotopic data for a subset of these sections provide evidence for largely atmospheric rather than terrestrial Hg sources, further linking Hg enrichment to increased volcanic activity. Hg peaks in shallow-water sections were nearly synchronous with the end-Permian extinction horizon, while those in deep-water sections occurred tens of thousands of years before the main extinction, possibly supporting a globally diachronous biotic turnover and protracted mass extinction event.

Phanerozoic survivors: Actinopterygian evolution through the Permo-Triassic and Triassic-Jurassic mass extinction events

Actinopterygians (ray‐finned fishes) successfully passed through four of the big five mass extinction events of the Phanerozoic, but the effects of these crises on the group are poorly understood. Many researchers have assumed that the Permo‐Triassic mass extinction (PTME) and end‐Triassic extinction (ETE) had little impact on actinopterygians, despite devastating many other groups. Here, two morphometric techniques, geometric (body shape) and functional (jaw morphology), are used to assess the effects of these two extinction events on the group. The PTME elicits no significant shifts in functional disparity while body shape disparity increases. An expansion of body shape and functional disparity coincides with the neopterygian radiation and evolution of novel feeding adaptations in the Middle‐Late Triassic. Through the ETE, small decreases are seen in shape and functional disparity, but are unlikely to represent major changes brought about by the extinction event. In the Early Jurassic, further expansions into novel areas of ecospace indicative of durophagy occur, potentially linked to losses in the ETE. As no evidence is found for major perturbations in actinopterygian evolution through either extinction event, the group appears to have been immune to two major environmental crises that were disastrous to most other organisms.

Stratigraphic signatures of mass extinctions: ecological and sedimentary determinants

Stratigraphic patterns of last occurrences (LOs) of fossil taxa potentially fingerprint mass extinctions and delineate rates and geometries of those events. Although empirical studies of mass extinctions recognize that random sampling causes LOs to occur earlier than the time of extinction (Signor–Lipps effect), sequence stratigraphic controls on the position of LOs are rarely considered. By tracing stratigraphic ranges of extant mollusc species preserved in the Holocene succession of the Po coastal plain (Italy), we demonstrated that, if mass extinction took place today, complex but entirely false extinction patterns would be recorded regionally due to shifts in local community composition and non-random variation in the abundance of skeletal remains, both controlled by relative sea-level changes. Consequently, rather than following an apparent gradual pattern expected from the Signor–Lipps effect, LOs concentrated within intervals of stratigraphic condensation and strong facies shifts mimicking sudden extinction pulses. Methods assuming uniform recovery potential of fossils falsely supported stepwise extinction patterns among studied species and systematically underestimated their stratigraphic ranges. Such effects of stratigraphic architecture, co-produced by ecological, sedimentary and taphonomic processes, can easily confound interpretations of the timing, duration and selectivity of mass extinction events. Our results highlight the necessity of accounting for palaeoenvironmental and sequence stratigraphic context when inferring extinction dynamics from the fossil record.

Rapid enhancement of chemical weathering recorded by extremely light seawater lithium isotopes at the Permian-Triassic boundary

Estimates of seawater Li isotopic composition at the Permian–Triassic boundary (PTB) reveal extremely light seawater Li isotopic signatures accompanying the most severe mass extinction in the history of animal life. Theoretical modeling indicates a rapid enhancement of continental weathering during this time, which was likely triggered by the eruption of the Siberian Traps, rapid global warming, and acid rains. Our results provide independent geochemical evidence for an enhanced continental chemical weathering at the PTB, illustrating that continental weathering may provide a key link between terrestrial and marine ecological crises.

Lithium (Li) isotope analyses of sedimentary rocks from the Meishan section in South China reveal extremely light seawater Li isotopic signatures at the Permian–Triassic boundary (PTB), which coincide with the most severe mass extinction in the history of animal life. Using a dynamic seawater lithium box model, we show that the light seawater Li isotopic signatures can be best explained by a significant influx of riverine [Li] with light δ⁷Li to the ocean realm. The seawater Li isotope excursion started ≥300 Ky before and persisted up to the main extinction event, which is consistent with the eruption time of the Siberian Traps. The eruption of the Siberian Traps exposed an enormous amount of fresh basalt and triggered CO₂ release, rapid global warming, and acid rains, which in turn led to a rapid enhancement of continental weathering. The enhanced continental weathering delivered excessive nutrients to the oceans that could lead to marine eutrophication, anoxia, acidification, and ecological perturbation, ultimately resulting in the end-Permian mass extinction.

Beyond the Big Five: Extinctions as Experiments in the History of Life

The past century has witnessed a number of significant breakthroughs in the study of extinction in the fossil record, from the discovery of a bolide impact as the probable cause of the end-Cretaceous (K/T) mass extinction to the designation of the “Big 5” mass extinction events. Here, I summarize the major themes that have emerged from the past thirty years of extinction research and highlight a number of promising directions for future research. These directions explore a central theme—the evolutionary consequences of extinction— and focus on three broad research areas: the effects of selectivity, the importance of recovery intervals, and the influence of spatial patterns. Examples of topics explored include the role that trait variation plays in survivorship, the comparative effects of extinctions of varying magnitudes on evolutionary patterns, the re-establishment of macroevolutionary patterns in the aftermath of extinction, and the extent to which spatial autocorrelation affects extinction patterns. These topics can be approached by viewing extinctions as repeated natural experiments in the history of life and developing hypotheses to explicitly test across multiple events. Exploring the effects of extinction also requires an interdisciplinary approach, applying evolutionary, ecological, geochronological, geochemical, tectonic, and paleoclimatic tools to both extinction and recovery intervals.

Estimates of the magnitudes of major marine mass extinctions in earth history

Procedures introduced here make it possible, first, to show that background (piecemeal) extinction is recorded throughout geologic stages and substages (not all extinction has occurred suddenly at the ends of such intervals); second, to separate out background extinction from mass extinction for a major crisis in earth history; and third, to correct for clustering of extinctions when using the rarefaction method to estimate the percentage of species lost in a mass extinction. Also presented here is a method for estimating the magnitude of the Signor-Lipps effect, which is the incorrect assignment of extinctions that occurred during a crisis to an interval preceding the crisis because of the incompleteness of the fossil record. Estimates for the magnitudes of mass extinctions presented here are in most cases lower than those previously published. They indicate that only ∼81% of marine species died out in the great terminal Permian crisis, whereas levels of 90-96% have frequently been quoted in the literature. Calculations of the latter numbers were incorrectly based on combined data for the Middle and Late Permian mass extinctions. About 90 orders and more than 220 families of marine animals survived the terminal Permian crisis, and they embodied an enormous amount of morphological, physiological, and ecological diversity. Life did not nearly disappear at the end of the Permian, as has often been claimed.

Effects of soil erosion and anoxic-euxinic ocean in the Permian-Triassic marine crisis

The largest mass extinction of biota in the Earth’s history occurred during the Permian–Triassic transition and included two extinctions, one each at the latest Permian (first phase) and earliest Triassic (second phase). High seawater temperature in the surface water accompanied by euxinic deep-intermediate water, intrusion of the euxinic water to the surface water, a decrease in pH, and hypercapnia have been proposed as direct causes of the marine crisis. For the first-phase extinction, we here add a causal mechanism beginning from massive soil and rock erosion and leading to algal blooms, release of toxic components, asphyxiation, and oxygen-depleted nearshore bottom water that created environmental stress for nearshore marine animals. For the second-phase extinction, we show that a soil and rock erosion/algal bloom event did not occur, but culmination of anoxia–euxinia in intermediate waters did occur, spanning the second-phase extinction. We investigated sedimentary organic molecules, and the results indicated a peak of a massive soil erosion proxy followed by peaks of marine productivity proxy. Anoxic proxies of surface sediments and water occurred in the shallow nearshore sea at the eastern and western margins of the Paleotethys at the first-phase extinction horizon, but not at the second-phase extinction horizon. Our reconstruction of ocean redox structure at low latitudes indicates that a gradual increase in temperature spanning the two extinctions could have induced a gradual change from a well-mixed oxic to a stratified euxinic ocean beginning immediately prior to the first-phase extinction, followed by culmination of anoxia in nearshore surface waters and of anoxia and euxinia in the shallow-intermediate waters at the second-phase extinction over a period of approximately one million years or more. Enhanced global warming, ocean acidification, and hypercapnia could have caused the second-phase extinction approximately 60 kyr after the first-phase extinction. The causes of the first-phase extinction were not only those environmental stresses but also environmental stresses caused by the soil and rock erosion/algal bloom event.

Genome Studies on Nematophagous and Entomogenous Fungi in China

The nematophagous and entomogenous fungi are natural enemies of nematodes and insects and have been utilized by humans to control agricultural and forestry pests. Some of these fungi have been or are being developed as biological control agents in China and worldwide. Several important nematophagous and entomogenous fungi, including nematode-trapping fungi (Arthrobotrys oligospora and Drechslerella stenobrocha), nematode endoparasite (Hirsutella minnesotensis), insect pathogens (Beauveria bassiana and Metarhizium spp.) and Chinese medicinal fungi (Ophiocordyceps sinensis and Cordyceps militaris), have been genome sequenced and extensively analyzed in China. The biology, evolution, and pharmaceutical application of these fungi and their interacting with host nematodes and insects revealed by genomes, comparing genomes coupled with transcriptomes are summarized and reviewed in this paper.

Thecamoebians (Testate Amoebae) Straddling the Permian-Triassic Boundary in the Guryul Ravine Section, India: Evolutionary and Palaeoecological Implications

Exceptionally well-preserved organic remains of thecamoebians (testate amoebae) were preserved in marine sediments that straddle the greatest extinction event in the Phanerozoic: the Permian-Triassic Boundary. Outcrops from the Late Permian Zewan Formation and the Early Triassic Khunamuh Formation are represented by a complete sedimentary sequence at the Guryul Ravine Section in Kashmir, India, which is an archetypal Permian-Triassic boundary sequence. Previous biostratigraphic analysis provides chronological control for the section, and a perspective of faunal turnover in the brachiopods, ammonoids, bivalves, conodonts, gastropods and foraminifera. Thecamoebians were concentrated from bulk sediments using palynological procedures, which isolated the organic constituents of preserved thecamoebian tests. The recovered individuals demonstrate exceptional similarity to the modern thecamoebian families Centropyxidae, Arcellidae, Hyalospheniidae and Trigonopyxidae, however, the vast majority belong to the Centropyxidae. This study further confirms the morphologic stability of the thecamoebian lineages through the Phanerozoic, and most importantly, their apparent little response to an infamous biological crisis in Earth's history.

Late Permian marine ecosystem collapse began in deeper waters: evidence from brachiopod diversity and body size changes

Analysis of Permian-Triassic brachiopod diversity and body size changes from different water depths spanning the continental shelf to basinal facies in South China provides insights into the process of environmental deterioration. Comparison of the temporal changes of brachiopod diversity between deepwater and shallow-water facies demonstrates that deepwater brachiopods disappeared earlier than shallow-water brachiopods. This indicates that high environmental stress commenced first in deepwater settings and later extended to shallow waters. This environmental stress is attributed to major volcanic eruptions, which first led to formation of a stratified ocean and a chemocline in the outer shelf and deeper water environments, causing the disappearance of deep marine benthos including brachiopods. The chemocline then rapidly migrated upward and extended to shallow waters, causing widespread mass extinction of shallow marine benthos. We predict that the spatial and temporal patterns of earlier onset of disappearance/extinction and ecological crisis in deeper water ecosystems will be recorded during other episodes of rapid global warming.

Time-calibrated Milankovitch cycles for the late Permian

An important innovation in the geosciences is the astronomical time scale. The astronomical time scale is based on the Milankovitch-forced stratigraphy that has been calibrated to astronomical models of paleoclimate forcing; it is defined for much of Cenozoic-Mesozoic. For the Palaeozoic era, however, astronomical forcing has not been widely explored because of lack of high-precision geochronology or astronomical modelling. Here we report Milankovitch cycles from late Permian (Lopingian) strata at Meishan and Shangsi, South China, time calibrated by recent high-precision U-Pb dating. The evidence extends empirical knowledge of Earth's astronomical parameters before 250 million years ago. Observed obliquity and precession terms support a 22-h length-of-day. The reconstructed astronomical time scale indicates a 7.793-million year duration for the Lopingian epoch, when strong 405-kyr cycles constrain astronomical modelling. This is the first significant advance in defining the Palaeozoic astronomical time scale, anchored to absolute time, bridging the Palaeozoic-Mesozoic transition.

High-precision timeline for Earth's most severe extinction

The end-Permian mass extinction was the most severe loss of marine and terrestrial biota in the last 542 My. Understanding its cause and the controls on extinction/recovery dynamics depends on an accurate and precise age model. U-Pb zircon dates for five volcanic ash beds from the Global Stratotype Section and Point for the Permian-Triassic boundary at Meishan, China, define an age model for the extinction and allow exploration of the links between global environmental perturbation, carbon cycle disruption, mass extinction, and recovery at millennial timescales. The extinction occurred between 251.941 ± 0.037 and 251.880 ± 0.031 Mya, an interval of 60 ± 48 ka. Onset of a major reorganization of the carbon cycle immediately precedes the initiation of extinction and is punctuated by a sharp (3‰), short-lived negative spike in the isotopic composition of carbonate carbon. Carbon cycle volatility persists for ∼500 ka before a return to near preextinction values. Decamillenial to millennial level resolution of the mass extinction and its aftermath will permit a refined evaluation of the relative roles of rate-dependent processes contributing to the extinction, allowing insight into postextinction ecosystem expansion, and establish an accurate time point for evaluating the plausibility of trigger and kill mechanisms.

Extinction space--a method for the quantification and classification of changes in morphospace across extinction boundaries

Three main modes of extinction are responsible for reductions in morphological disparity: (1) random (caused by a nonselective extinction event); (2) marginal (a symmetric, selective extinction event trimming the margin of morphospace); and (3) lateral (an asymmetric, selective extinction event eliminating one side of the morphospace). These three types of extinction event can be distinguished from one another by comparing changes in three measures of morphospace occupation: (1) the sum of range along the main axes; (2) the sum of variance; and (3) the position of the centroid. Computer simulations of various extinction events demonstrate that the pre-extinction distribution of taxa (random or normal) in the morphospace has little influence on the quantification of disparity changes, whereas the modes of the extinction events play the major role. Together, the three disparity metrics define an "extinction-space" in which different extinction events can be directly compared with one another. Application of this method to selected extinction events (Frasnian-Famennian, Devonian-Carboniferous, and Permian-Triassic) of the Ammonoidea demonstrate the similarity of the Devonian events (selective extinctions) but the striking difference from the end-Permian event (nonselective extinction). These events differ in their mode of extinction despite decreases in taxonomic diversity of similar magnitude.

Provincialization of terrestrial faunas following the end-Permian mass extinction

In addition to their devastating effects on global biodiversity, mass extinctions have had a long-term influence on the history of life by eliminating dominant lineages that suppressed ecological change. Here, we test whether the end-Permian mass extinction (252.3 Ma) affected the distribution of tetrapod faunas within the southern hemisphere and apply quantitative methods to analyze four components of biogeographic structure: connectedness, clustering, range size, and endemism. For all four components, we detected increased provincialism between our Permian and Triassic datasets. In southern Pangea, a more homogeneous and broadly distributed fauna in the Late Permian (Wuchiapingian, ∼257 Ma) was replaced by a provincial and biogeographically fragmented fauna by Middle Triassic times (Anisian, ∼242 Ma). Importantly in the Triassic, lower latitude basins in Tanzania and Zambia included dinosaur predecessors and other archosaurs unknown elsewhere. The recognition of heterogeneous tetrapod communities in the Triassic implies that the end-Permian mass extinction afforded ecologically marginalized lineages the ecospace to diversify, and that biotic controls (i.e., evolutionary incumbency) were fundamentally reset. Archosaurs, which began diversifying in the Early Triassic, were likely beneficiaries of this ecological release and remained dominant for much of the later Mesozoic.

Origin and evolution of carnivorism in the Ascomycota (fungi)

Carnivorism is one of the basic life strategies of fungi. Carnivorous fungi possess the ability to trap and digest their preys by sophisticated trapping devices. However, the origin and development of fungal carnivorism remains a gap in evolution biology. In this study, five protein-encoding genes were used to construct the phylogeny of the carnivorous fungi in the phylum Ascomycota; these fungi prey on nematodes by means of specialized trapping structures such as constricting rings and adhesive traps. Our analysis revealed a definitive pattern of evolutionary development for these trapping structures. Molecular clock calibration based on two fossil records revealed that fungal carnivorism diverged from saprophytism about 419 Mya, which was after the origin of nematodes about 550-600 Mya. Active carnivorism (fungi with constricting rings) and passive carnivorism (fungi with adhesive traps) diverged from each other around 246 Mya, shortly after the occurrence of the Permian-Triassic extinction event about 251.4 Mya. The major adhesive traps evolved around 198-208 Mya, which was within the time frame of the Triassic-Jurassic extinction event about 201.4 Mya. However, no major carnivorous ascomycetes divergence was correlated to the Cretaceous-Tertiary extinction event, which occurred more recently (about 65.5 Mya). Therefore, a causal relationship between mass extinction events and fungal carnivorism evolution is not validated in this study. More evidence including additional fossil records is needed to establish if fungal carnivorism evolution was a response to mass extinction events.

The earliest post-paleozoic freshwater bivalves preserved in coprolites from the karoo basin, South Africa

BACKGROUND

Several clades of bivalve molluscs have invaded freshwaters at various times throughout Phanerozoic history. The most successful freshwater clade in the modern world is the Unionoida. Unionoids arose in the Triassic Period, sometime after the major extinction event at the End-Permian boundary and are now widely distributed across all continents except Antarctica. Until now, no freshwater bivalves of any kind were known to exist in the Early Triassic.

PRINCIPAL FINDINGS

Here we report on a faunule of two small freshwater bivalve species preserved in vertebrate coprolites from the Olenekian (Lower Triassic) of the Burgersdorp Formation of the Karoo Basin, South Africa. Positive identification of these bivalves is not possible due to the limited material. Nevertheless they do show similarities with Unionoida although they fall below the size range of extant unionoids. Phylogenetic analysis is not possible with such limited material and consequently the assignment remains somewhat speculative.

CONCLUSIONS

Bivalve molluscs re-invaded freshwaters soon after the End-Permian extinction event, during the earliest part of the recovery phase during the Olenekian Stage of the Early Triassic. If the specimens do represent unionoids then these Early Triassic examples may be an example of the Lilliput effect. Since the oldest incontrovertible freshwater unionoids are also from sub-Saharan Africa, it is possible that this subcontinent hosted the initial freshwater radiation of the Unionoida. This find also demonstrates the importance of coprolites as microenvironments of exceptional preservation that contain fossils of organisms that would otherwise have left no trace.

Microbial response to limited nutrients in shallow water immediately after the end-Permian mass extinction

Previous work indicates that a variety of microbes bloomed in the oceans after the end-Permian faunal mass extinction, but evidence is sporadically documented. Thus, the nature and geographic distribution of such microbes and their associations are unclear, addressed in this study using a series of biomarker groups. On the basis of microbial biomarker records of the 2-methylhopane index, evidence is presented for cyanobacterial blooms in both the western and eastern Tethys Sea and in both shallow and deep waters, after the mass extinction. The enhanced relative abundance of C(28) (expressed by the C(28) /C(29) ratio of) regular steranes suggests a bloom of prasinophyte algae occurred immediately after the end-Permian faunal extinction, comparable with those observed in some other mass extinctions in Phanerozoic. Significantly, cyanobacteria and prasinophyte algae show a synchronized onset of bloom in the shallow water Bulla section, north Italy, inferring for the first time their coupled response to the biotic crisis and the associated environmental conditions. However, in Meishan of Zhejiang Province in south China, the bloom declined earlier than in Bulla. The association of increased 2-methylhopane index with a negative shift in the nitrogen isotope composition infers a scenario of enhanced nitrogen fixation by cyanobacteria immediately after the faunal mass extinction. N(2) fixation by cyanobacteria is here interpreted to have provided prasinophyte algae with ammonium in nutrient-limited shallow waters, and thus caused their associated blooms.

Volcanic perturbations of the marine environment in South China preceding the latest Permian mass extinction and their biotic effects

The Dongpan section in southern Guangxi Province records the influence of local volcanic activity on marine sedimentation at intermediate water depths (~200-500 m) in the Nanpanjiang Basin (South China) during the late Permian crisis. We analyzed ~100 samples over a 12-m-thick interval, generating palynological, paleobiological, and geochemical datasets to investigate the nature and causes of environmental changes. The section records at least two major volcanic episodes that culminated in deposition of approximately 25- to 35-cm-thick ash layers (bentonites) and that had profound effects on conditions in both the Dongpan marine environment and adjacent land areas. Intensification of eruptive activity during each volcanic cycle resulted in a shift toward conifer forests, increased wildfire intensity, and elevated subaerial weathering fluxes. The resulting increase in nutrient fluxes stimulated marine productivity in the short term but led to a negative feedback on productivity in the longer term as the OMZ of the Nanpanjiang Basin expanded, putting both phytoplankton and zooplankton communities under severe stress. Radiolarians exhibit large declines in diversity and abundance well before the global mass extinction horizon, demonstrating the diachroneity of the marine biotic crisis. The latest Permian crisis, which was probably triggered by the Siberian Traps flood basalts, intensified the destructive effects of the earlier local eruptions on terrestrial and marine ecosystems of the South China craton.

Calibrating the end-Permian mass extinction

The end-Permian mass extinction was the most severe biodiversity crisis in Earth history. To better constrain the timing, and ultimately the causes of this event, we collected a suite of geochronologic, isotopic, and biostratigraphic data on several well-preserved sedimentary sections in South China. High-precision U-Pb dating reveals that the extinction peak occurred just before 252.28 ± 0.08 million years ago, after a decline of 2 per mil (‰) in δ(13)C over 90,000 years, and coincided with a δ(13)C excursion of -5‰ that is estimated to have lasted ≤20,000 years. The extinction interval was less than 200,000 years and synchronous in marine and terrestrial realms; associated charcoal-rich and soot-bearing layers indicate widespread wildfires on land. A massive release of thermogenic carbon dioxide and/or methane may have caused the catastrophic extinction.

Evolutionary history of Otophysi (Teleostei), a major clade of the modern freshwater fishes: Pangaean origin and Mesozoic radiation

BACKGROUND

Freshwater harbors approximately 12,000 fish species accounting for 43% of the diversity of all modern fish. A single ancestral lineage evolved into about two-thirds of this enormous biodiversity (≈ 7900 spp.) and is currently distributed throughout the world's continents except Antarctica. Despite such remarkable species diversity and ubiquity, the evolutionary history of this major freshwater fish clade, Otophysi, remains largely unexplored. To gain insight into the history of otophysan diversification, we constructed a timetree based on whole mitogenome sequences across 110 species representing 55 of the 64 families.

RESULTS

Partitioned maximum likelihood analysis based on unambiguously aligned sequences (9923 bp) confidently recovered the monophyly of Otophysi and the two constituent subgroups (Cypriniformes and Characiphysi). The latter clade comprised three orders (Gymnotiformes, Characiformes, Siluriformes), and Gymnotiformes was sister to the latter two groups. One of the two suborders in Characiformes (Characoidei) was more closely related to Siluriformes than to its own suborder (Citharinoidei), rendering the characiforms paraphyletic. Although this novel relationship did not receive strong statistical support, it was supported by analyzing independent nuclear markers. A relaxed molecular clock Bayesian analysis of the divergence times and reconstruction of ancestral habitats on the timetree suggest a Pangaean origin and Mesozoic radiation of otophysans.

CONCLUSIONS

The present timetree demonstrates that survival of the ancestral lineages through the two consecutive mass extinctions on Pangaea, and subsequent radiations during the Jurassic through early Cretaceous shaped the modern familial diversity of otophysans. This evolutionary scenario is consistent with recent arguments based on biogeographic inferences and molecular divergence time estimates. No fossil otophysan, however, has been recorded before the Albian, the early Cretaceous 100-112 Ma, creating an over 100 million year time span without fossil evidence. This formidable ghost range partially reflects a genuine difference between the estimated ages of stem group origin (molecular divergence time) and crown group morphological diversification (fossil divergence time); the ghost range, however, would be filled with discoveries of older fossils that can be used as more reasonable time constraints as well as with developments of more realistic models that capture the rates of molecular sequences accurately.

Multiple S-isotopic evidence for episodic shoaling of anoxic water during Late Permian mass extinction

Global fossil data show that profound biodiversity loss preceded the final catastrophe that killed nearly 90% marine species on a global scale at the end of the Permian. Many hypotheses have been proposed to explain this extinction and yet still remain greatly debated. Here, we report analyses of all four sulphur isotopes (³²S, ³³S, ³⁴S and ³⁶S) for pyrites in sedimentary rocks from the Meishan section in South China. We observe a sulphur isotope signal (negative δ³⁴S with negative Δ³³S) that may have resulted from limitation of sulphate supply, which may be linked to a near shutdown of bioturbation during shoaling of anoxic water. These results indicate that episodic shoaling of anoxic water may have contributed to the profound biodiversity crisis before the final catastrophe. Our data suggest a prolonged deterioration of oceanic environments during the Late Permian mass extinction.

A final catastrophe killed 90% of marine species at the end of the Permian period, but significant biodiversity loss preceded this event. In this study, sulphur isotope evidence suggests that incursion of anoxic water into shallow regions may have contributed to biodiversity loss.

The Luoping biota: exceptional preservation, and new evidence on the Triassic recovery from end-Permian mass extinction

The timing and nature of biotic recovery from the devastating end-Permian mass extinction (252 Ma) are much debated. New studies in South China suggest that complex marine ecosystems did not become re-established until the middle-late Anisian (Middle Triassic), much later than had been proposed by some. The recently discovered exceptionally preserved Luoping biota from the Anisian Stage of the Middle Triassic, Yunnan Province and southwest China shows this final stage of community assembly on the continental shelf. The fossil assemblage is a mixture of marine animals, including abundant lightly sclerotized arthropods, associated with fishes, marine reptiles, bivalves, gastropods, belemnoids, ammonoids, echinoderms, brachiopods, conodonts and foraminifers, as well as plants and rare arthropods from nearby land. In some ways, the Luoping biota rebuilt the framework of the pre-extinction latest Permian marine ecosystem, but it differed too in profound ways. New trophic levels were introduced, most notably among top predators in the form of the diverse marine reptiles that had no evident analogues in the Late Permian. The Luoping biota is one of the most diverse Triassic marine fossil Lagerstätten in the world, providing a new and early window on recovery and radiation of Triassic marine ecosystems some 10 Myr after the end-Permian mass extinction.

The Triassic dicynodont Kombuisia (Synapsida, Anomodontia) from Antarctica, a refuge from the terrestrial Permian-Triassic mass extinction

Fossils from the central Transantarctic Mountains in Antarctica are referred to a new species of the Triassic genus Kombuisia, one of four dicynodont lineages known to survive the end-Permian mass extinction. The specimens show a unique combination of characters only present in this genus, but the new species can be distinguished from the type species of the genus, Kombuisia frerensis, by the presence of a reduced but slit-like pineal foramen and the lack of contact between the postorbitals. Although incomplete, the Antarctic specimens are significant because Kombuisia was previously known only from the South African Karoo Basin and the new specimens extend the taxon's biogeographic range to a wider portion of southern Pangaea. In addition, the new finds extend the known stratigraphic range of Kombuisia from the Middle Triassic subzone B of the Cynognathus Assemblage Zone into rocks that are equivalent in age to the Lower Triassic Lystrosaurus Assemblage Zone, shortening the proposed ghost lineage of this taxon. Most importantly, the occurrence of Kombuisia and Lystrosaurus mccaigi in the Lower Triassic of Antarctica suggests that this area served as a refuge from some of the effects of the end-Permian extinction. The composition of the lower Fremouw Formation fauna implies a community structure similar to that of the ecologically anomalous Lystrosaurus Assemblage Zone of South Africa, providing additional evidence for widespread ecological disturbance in the extinction's aftermath.

Recent advances in Chinese palaeontology

Discoveries are a driving force for progress in palaeontology. Palaeontology as a discipline of scientific inquiry has gained many fresh insights into the history of life, from the discoveries of many new fossils in China in the last 20 years, and from the new ideas derived from these fossils. This special issue of Proceedings of Royal Society B entitled Recent Advances in Chinese Palaeontology selects some of the very latest studies aimed at resolving the current problems of palaeontology and evolutionary biology based on new fossils from China. These fossils and their studies help to clarify some historical debates about a particular fossil group, or to raise new questions about history of life, or to pose a new challenge in our pursuit of science. These works on new Chinese fossils have covered the whole range of the diversity through the entire Phanerozoic fossil record.

Selective press extinctions, but not random pulse extinctions, cause delayed ecological recovery in communities of digital organisms

A key issue concerning recovery from mass extinctions is how extinction and diversification mechanisms affect the recovery process. We evolved communities of digital organisms, subjecting them to instantaneous "pulse" extinctions, choosing survivors at random, or to prolonged "pulse" extinctions involving a period of low resource availability. Functional activity at low trophic levels recovered faster than at higher levels, with the most extensive delays seen at the top level. Postpress communities generally did not fully recover functional activity in the allotted time, which equaled that of their original diversification. We measured recovery of phenotypic diversity, observing considerable variation in outcomes. Communities subjected to pulse extinctions recovered functional activity and phenotypic diversity substantially faster than when subjected to press extinctions. Follow-up experiments tested whether organisms with shorter generation times and low functional activity contributed to delayed recovery after press extinctions. The results indicate that adaptation during the press episode degraded the organisms' ability to re-evolve preextinction functionality. There are interesting parallels with patterns from the paleontological record. We suggest that some delayed recoveries from mass extinction may reflect the need to both re-evolve biological functions and reconstruct ecological interactions lost during the extinction. Adaptation to conditions during an extended disturbance may hinder subsequent recovery.

Colloquium paper: extinction as the loss of evolutionary history

Current plant and animal diversity preserves at most 1-2% of the species that have existed over the past 600 million years. But understanding the evolutionary impact of these extinctions requires a variety of metrics. The traditional measurement is loss of taxa (species or a higher category) but in the absence of phylogenetic information it is difficult to distinguish the evolutionary depth of different patterns of extinction: the same species loss can encompass very different losses of evolutionary history. Furthermore, both taxic and phylogenetic measures are poor metrics of morphologic disparity. Other measures of lost diversity include: functional diversity, architectural components, behavioral and social repertoires, and developmental strategies. The canonical five mass extinctions of the Phanerozoic reveals the loss of different, albeit sometimes overlapping, aspects of loss of evolutionary history. The end-Permian mass extinction (252 Ma) reduced all measures of diversity. The same was not true of other episodes, differences that may reflect their duration and structure. The construction of biodiversity reflects similarly uneven contributions to each of these metrics. Unraveling these contributions requires greater attention to feedbacks on biodiversity and the temporal variability in their contribution to evolutionary history. Taxic diversity increases after mass extinctions, but the response by other aspects of evolutionary history is less well studied. Earlier views of postextinction biotic recovery as the refilling of empty ecospace fail to capture the dynamics of this diversity increase.

Global warming and cyanobacterial harmful algal blooms

The Earth and the oceans have warmed significantly over the past four decades, providing evidence that the Earth is undergoing long-term climate change. Increasing temperatures and changing rainfall patterns have been documented. Cyanobacteria have a long evolutionary history, with their first occurrence dating back at least 2.7 billion years ago. Cyanobacteria often dominated the oceans after past mass extinction events. They evolved under anoxic conditions and are well adapted to environmental stress including exposure to UV, high solar radiation and temperatures, scarce and abundant nutrients. These environmental conditions favor the dominance of cyanobacteria in many aquatic habitats, from freshwater to marine ecosystems. A few studies have examined the ecological consequences of global warming on cyanobacteria and other phytoplankton over the past decades in freshwater, estuarine, and marine environments, with varying results. The responses of cyanobacteria to changing environmental patterns associated with global climate change are important subjects for future research. Results of this research will have ecological and biogeochemical significance as well as management implications.

Prolonged Permian Triassic ecological crisis recorded by molluscan dominance in Late Permian offshore assemblages

The end-Permian mass extinction was the largest biotic crisis in the history of animal life, eliminating as many as 95% of all species and dramatically altering the ecological structure of marine communities. Although the causes of this pronounced ecosystem shift have been widely debated, the broad consensus based on inferences from global taxonomic diversity patterns suggests that the shift from abundant brachiopods to dominant molluscs was abrupt and largely driven by the catastrophic effects of the end-Permian mass extinction. Here we analyze relative abundance counts of >33,000 fossil individuals from 24 silicified Middle and Late Permian paleocommunities, documenting a substantial ecological shift to numerical dominance by molluscs in the Late Permian, before the major taxonomic shift at the end-Permian mass extinction. This ecological change was coincident with the development of fluctuating anoxic conditions in deep marine basins, suggesting that numerical dominance by more tolerant molluscs may have been driven by variably stressful environmental conditions. Recognition of substantial ecological deterioration in the Late Permian also implies that the end-Permian extinction was the climax of a protracted environmental crisis. Although the Late Permian shift to molluscan dominance was a pronounced ecological change, quantitative counts of 847 Carboniferous-Cretaceous collections from the Paleobiology Database indicate that it was only the first stage in a stepwise transition that culminated with the final shift to molluscan dominance in the Late Jurassic. Therefore, the ecological transition from brachiopods to bivalves was more protracted and complex than their simple Permian-Triassic switch in diversity.

The effect of geographic range on extinction risk during background and mass extinction

Wide geographic range is generally thought to buffer taxa against extinction, but the strength of this effect has not been investigated for the great majority of the fossil record. Although the majority of genus extinctions have occurred between major mass extinctions, little is known about extinction selectivity regimes during these "background" intervals. Consequently, the question of whether selectivity regimes differ between background and mass extinctions is largely unresolved. Using logistic regression, we evaluated the selectivity of genus survivorship with respect to geographic range by using a global database of fossil benthic marine invertebrates spanning the Cambrian through the Neogene periods, an interval of approximately 500 My. Our results show that wide geographic range has been significantly and positively associated with survivorship for the great majority of Phanerozoic time. Moreover, the significant association between geographic range and survivorship remains after controlling for differences in species richness and abundance among genera. However, mass extinctions and several second-order extinction events exhibit less geographic range selectivity than predicted by range alone. Widespread environmental disturbance can explain the reduced association between geographic range and extinction risk by simultaneously affecting genera with similar ecological and physiological characteristics on global scales. Although factors other than geographic range have certainly affected extinction risk during many intervals, geographic range is likely the most consistently significant predictor of extinction risk in the marine fossil record.