Abrupt and gradual extinction among Late Permian land vertebrates in the Karoo basin, South Africa

Testing extinction events and temporal shifts in diversification and fossilization rates through the skyline Fossilized Birth-Death (FBD) model: The example of some mid-Permian synapsid extinctions

In the last decade, the Fossilized Birth-Death (FBD) process has yielded interesting clues about the evolution of biodiversity through time. To facilitate such studies, we extend our method to compute the probability density of phylogenetic trees of extant and extinct taxa in which the only temporal information is provided by the fossil ages (i.e. without the divergence times) in order to deal with the piecewise constant FBD process, known as the "skyline FBD", which allows rates to change between pre-defined time intervals, as well as modelling extinction events at the bounds of these intervals. We develop approaches based on this method to assess hypotheses about the diversification process and to answer questions such as "Does a mass extinction occur at this time?" or "Is there a change in the fossilization rate between two given periods?". Our software can also yield Bayesian and maximum-likelihood estimates of the parameters of the skyline FBD model under various constraints. These approaches are applied to a simulated dataset in order to test their ability to answer the questions above. Finally, we study an updated dataset of Permo-Carboniferous synapsids to get additional insights into the dynamics of biodiversity change in three clades (Ophiacodontidae, Edaphosauridae and Sphenacodontidae) in the Pennsylvanian (Late Carboniferous) and Cisuralian (Early Permian), and to assess support for end-Sakmarian (or Artinskian) and end-Cisuralian mass extinction events discussed in previous studies.

Rapid turnover of top predators in African terrestrial faunas around the Permian-Triassic mass extinction

Catastrophic ecosystem disruption in the late Permian period resulted in the greatest loss of biodiversity in Earth's history, the Permian-Triassic mass extinction (PTME).¹ The dominant terrestrial vertebrates of the Permian (synapsids) suffered major losses at this time, leading to their replacement by reptiles in the Triassic.² The dominant late Permian predatory synapsids, gorgonopsians, were completely extirpated by the PTME. The largest African gorgonopsians, the Rubidgeinae, have traditionally been assumed to go extinct at the Permo-Triassic boundary (PTB).^3,4,5 However, this apparent persistence through the sustained extinction interval characterizing the continental PTME⁶ is at odds with ecological theory indicating that top predators have high extinction risk.⁷ Here, we report the youngest known large-bodied gorgonopsians, gigantic specimens from the PTB site of Nooitgedacht 68 in South Africa. These specimens are not rubidgeine, and instead are referable to Inostrancevia, a taxon previously thought to be a Russian endemic.⁸ Based on comprehensive review of the South African gorgonopsian record, we show that rubidgeines were early victims of ecosystem disruption preceding the PTME and were replaced as top predators by Laurasian immigrant inostranceviines. The reign of this latter group was short-lived, however; by the PTB, gorgonopsians were extinct, and a different group (therocephalians) became the largest synapsid predators, before themselves going extinct. The extinction and replacement of top predators in rapid succession at the clade level underlines the extreme degree of ecosystem instability in the latest Permian and earliest Triassic, a phenomenon that was likely global in extent.

Mercury evidence from southern Pangea terrestrial sections for end-Permian global volcanic effects

The latest Permian mass extinction (LPME) was triggered by magmatism of the Siberian Traps Large Igneous Province (STLIP), which left an extensive record of sedimentary Hg anomalies at Northern Hemisphere and tropical sites. Here, we present Hg records from terrestrial sites in southern Pangea, nearly antipodal to contemporaneous STLIP activity, providing insights into the global distribution of volcanogenic Hg during this event and its environmental processing. These profiles (two from Karoo Basin, South Africa; two from Sydney Basin, Australia) exhibit significant Hg enrichments within the uppermost Permian extinction interval as well as positive Δ¹⁹⁹Hg excursions (to ~0.3‰), providing evidence of long-distance atmospheric transfer of volcanogenic Hg. These results demonstrate the far-reaching effects of the Siberian Traps as well as refine stratigraphic placement of the LPME interval in the Karoo Basin at a temporal resolution of ~10⁵ years based on global isochronism of volcanogenic Hg anomalies.

The numbers of fungi: contributions from traditional taxonomic studies and challenges of metabarcoding

The global diversity of fungi has been estimated using several different approaches. There is somewhere between 2–11 million estimated species, but the number of formally described taxa is around 150,000, a tiny fraction of the total. In this paper, we examine 12 ascomycete genera as case studies to establish trends in fungal species descriptions, and introduce new species in each genus. To highlight the importance of traditional morpho-molecular methods in publishing new species, we introduce novel taxa in 12 genera that are considered to have low species discovery. We discuss whether the species are likely to be rare or due to a lack of extensive sampling and classification. The genera are Apiospora, Bambusicola, Beltrania, Capronia, Distoseptispora, Endocalyx, Neocatenulostroma, Neodeightonia, Paraconiothyrium, Peroneutypa, Phaeoacremonium and Vanakripa. We discuss host-specificity in selected genera and compare the number of species epithets in each genus with the number of ITS (barcode) sequences deposited in GenBank and UNITE. We furthermore discuss the relationship between the divergence times of these genera with those of their hosts. We hypothesize whether there might be more species in these genera and discuss hosts and habitats that should be investigated for novel species discovery.

Distributions of extinction times from fossil ages and tree topologies: the example of mid-Permian synapsid extinctions

Given a phylogenetic tree that includes only extinct, or a mix of extinct and extant taxa, where at least some fossil data are available, we present a method to compute the distribution of the extinction time of a given set of taxa under the Fossilized-Birth-Death model. Our approach differs from the previous ones in that it takes into account (i) the possibility that the taxa or the clade considered may diversify before going extinct and (ii) the whole phylogenetic tree to estimate extinction times, whilst previous methods do not consider the diversification process and deal with each branch independently. Because of this, our method can estimate extinction times of lineages represented by a single fossil, provided that they belong to a clade that includes other fossil occurrences. We assess and compare our new approach with a standard previous one using simulated data. Results show that our method provides more accurate confidence intervals. This new approach is applied to the study of the extinction time of three Permo-Carboniferous synapsid taxa (Ophiacodontidae, Edaphosauridae, and Sphenacodontidae) that are thought to have disappeared toward the end of the Cisuralian (early Permian), or possibly shortly thereafter. The timing of extinctions of these three taxa and of their component lineages supports the idea that the biological crisis in the late Kungurian/early Roadian consisted of a progressive decline in biodiversity throughout the Kungurian.

Felsic volcanism as a factor driving the end-Permian mass extinction

The Siberian Traps large igneous province (STLIP) is commonly invoked as the primary driver of global environmental changes that triggered the end-Permian mass extinction (EPME). Here, we explore the contributions of coeval felsic volcanism to end-Permian environmental changes. We report evidence of extreme Cu enrichment in the EPME interval in South China. The enrichment is associated with an increase in the light Cu isotope, melt inclusions rich in copper and sulfides, and Hg concentration spikes. The Cu and Hg elemental and isotopic signatures can be linked to S-rich vapor produced by felsic volcanism. We use these previously unknown geochemical data to estimate volcanic SO₂ injections and argue that this volcanism would have produced several degrees of rapid cooling before or coincident with the more protracted global warming. Large-scale eruptions near the South China block synchronous with the EPME strengthen the case that the STLIP may not have been the sole trigger.

Evidence from South Africa for a protracted end-Permian extinction on land

Earth's largest biotic crisis occurred during the Permo-Triassic Transition (PTT). On land, this event witnessed a turnover from synapsid- to archosauromorph-dominated assemblages and a restructuring of terrestrial ecosystems. However, understanding extinction patterns has been limited by a lack of high-precision fossil occurrence data to resolve events on submillion-year timescales. We analyzed a unique database of 588 fossil tetrapod specimens from South Africa's Karoo Basin, spanning ∼4 My, and 13 stratigraphic bin intervals averaging 300,000 y each. Using sample-standardized methods, we characterized faunal assemblage dynamics during the PTT. High regional extinction rates occurred through a protracted interval of ∼1 Ma, initially co-occurring with low origination rates. This resulted in declining diversity up to the acme of extinction near the Daptocephalus-Lystrosaurus declivis Assemblage Zone boundary. Regional origination rates increased abruptly above this boundary, co-occurring with high extinction rates to drive rapid turnover and an assemblage of short-lived species symptomatic of ecosystem instability. The "disaster taxon" Lystrosaurus shows a long-term trend of increasing abundance initiated in the latest Permian. Lystrosaurus comprised 54% of all specimens by the onset of mass extinction and 70% in the extinction aftermath. This early Lystrosaurus abundance suggests its expansion was facilitated by environmental changes rather than by ecological opportunity following the extinctions of other species as commonly assumed for disaster taxa. Our findings conservatively place the Karoo extinction interval closer in time, but not coeval with, the more rapid marine event and reveal key differences between the PTT extinctions on land and in the oceans.

Trends in Stable Isotopes and Climate Proxies From Late Changhsingian Ghost Landscapes of the Karoo Basin, South Africa

The stable carbon- and oxygen-isotope values derived from in situ pedogenic carbonate-cemented nodules and vertebrate apatite in the Daptocephalus and overlying Lystrosaurus Assemblage Zones of the Balfour Formation, Karoo Basin, South Africa, have formed the basis for previous interpretations of a unidirectional climate trend toward hyper-aridity across the biozone boundary. This assemblage-zone boundary has been considered by many authors to be equivalent to the Permian–Triassic boundary in the basin. To better understand the climate under which these vertebrate assemblages existed, we have analyzed the carbon- and oxygen-stable isotopes of pedogenic carbonate nodules sampled from fourteen horizons of intraformational pedogenic nodular conglomerate (PNC) at Old Lootsberg Pass, a classic locality at which the Permian–Triassic boundary is reported. Analysis of these refractory soil constituents provides insight into the climate under which these “ghost” soils formed, where no other physical record of their existence is found in the stratigraphy. A positive correlation between δ13CVPDB and δ18OVSMOW values of micrite cements is defined by analyses of carbonate nodules taken from a measured stratigraphic thickness of ∼200 m, which spans the biozone boundary as currently defined. For samples taken from the same lag deposit, similar and relatively narrow ranges of isotope values are encountered. Samples cluster into two isotopic groups. The values in the first group cluster more tightly in all sampled nodules (δ13CVPDB −2.3 to −6.5‰; δ18OVSMOW 13.8–15.1‰), and are interpreted to indicate that these originated from paleosols that formed under similar climate controls. Values from the second sample group display a wider variance between analyses (δ13CVPDB −5.2 to 14.0‰; δ18OVSMOW 8.8–15.5‰). These nodules are interpreted to indicate that they originated under polygenetic soil-forming conditions representing the reworking of either: (1) more than one paleosol, the calcite-cemented nodules of which represent precipitation under both closed and open-system controls; or (2) one or more compound-composite paleosols. Stable-isotope trends based on PNCs analyzed, thus far, demonstrate an overall shift over time in the ghost landscapes. More seasonally dry soils formed under a climate that can be characterized as warm/dry accompanied by lower precipitation in the lower part of the section. In contrast, soils in the upper part of the section formed under cool and moist conditions, with increased precipitation near the biozone boundary. Hence, latest Permian climate associated with the more seasonally dry landscapes demonstrate a trend toward cooler and wetter conditions, which is opposite to the trend widely held in the literature.

The paleobiology and paleoecology of South African Lystrosaurus

Lystrosaurus was one of the few tetrapods to survive the end-Permian mass extinction (EPME), the most catastrophic biotic crisis in Phanerozoic history. The significant increased abundance of this genus during the post-extinction Early Triassic recovery period has made Lystrosaurus an iconic survivor taxon globally and ideal for studying changes in growth dynamics during a mass extinction. There is potential evidence of a Lilliput effect in Lystrosaurus in South Africa as the two Triassic species that became highly abundant after the EPME are relatively smaller than the two Permian species. In order to test this hypothesis a detailed examination of the body size and life history of Permo-Triassic Lystrosaurus is required. In this study, the basal skull length and growth patterns of the four South African Lystrosaurus species from the Karoo Basin, L. maccaigi, L. curvatus, L. murrayi and L. declivis, were examined using cranial measurements and bone histology. The basal skull length measurements show that the Triassic species are smaller than the Permian species and supports previous studies. The osteohistology examination of all four species reveal rapidly forming fibrolamellar bone tissues during early to mid-ontogeny. Growth marks are common in L. maccaigi and L. curvatus, but rare and inconsistent in the purely Triassic L. murrayi and L. declivis. The inconsistency of the growth marks in these latter two taxa suggests the presence of developmental plasticity. This feature may have been advantageous in allowing these species to alter their growth patterns in response to environmental cues in the post-extinction Early Triassic climate. An overall transition to slower forming parallel-fibered bone is observed in the largest individuals of L. maccaigi, but absent from the limb bones of the other species. The absence of such bone tissue or outer circumferential lamellae in L. curvatus, L. murrayi and L. declivis indicates that even the largest collected specimens do not represent fully grown individuals. Although L. murrayi and L. declivis are smaller in size, the lack of a growth asymptote in the largest specimens indicates that adult individuals would have been notably larger and may have been similar in size to large L. maccaigi and L. curvatus when fully grown. Thus, the previously described Lilliput effect, recognized by some authors in the Karoo fossil record (such as the therocephalian Moschorhinus kitchingi), may be a product of high juvenile excess mortality in the Triassic rather than a strict "dwarfing" of Lystrosaurus species. The lifestyle of Lystrosaurus was also re-examined. Although previous studies have proposed an aquatic lifestyle for the genus, the similar morphology and bone microanatomy to several other large terrestrial Permo-Triassic dicynodonts supports a fully terrestrial mode of life.

Effects of taphonomic deformation on geometric morphometric analysis of fossils: a study using the dicynodont Diictodon feliceps (Therapsida, Anomodontia)

Taphonomic deformation, the distortion of fossils as a result of geological processes, poses problems for the use of geometric morphometrics in addressing paleobiological questions. Signal from biological variation, such as ontogenetic trends and sexual dimorphism, may be lost if variation from deformation is too high. Here, we investigate the effects of taphonomic deformation on geometric morphometric analyses of the abundant, well known Permian therapsid Diictodon feliceps. Distorted Diictodon crania can be categorized into seven typical styles of deformation: lateral compression, dorsoventral compression, anteroposterior compression, “saddle-shape” deformation (localized collapse at cranial mid-length), anterodorsal shear, anteroventral shear, and right/left shear. In simulated morphometric datasets incorporating known “biological” signals and subjected to uniform shear, deformation was typically the main source of variance but accurate “biological” information could be recovered in most cases. However, in empirical datasets, not only was deformation the dominant source of variance, but little structure associated with allometry and sexual dimorphism was apparent, suggesting that the more varied deformation styles suffered by actual fossils overprint biological variation. In a principal component analysis of all anomodont therapsids, deformed Diictodon specimens exhibit significant dispersion around the “true” position of this taxon in morphospace based on undistorted specimens. The overall variance associated with deformation for Anomodontia as a whole is minor, and the major axes of variation in the study sample show a strong phylogenetic signal instead. Although extremely problematic for studying variation in fossil taxa at lower taxonomic levels, the cumulative effects of deformation in this study are shown to be random, and inclusion of deformed specimens in higher-level analyses of morphological disparity are warranted. Mean morphologies of distorted specimens are found to approximate the morphology of undistorted specimens, so we recommend use of species-level means in higher-level analyses when possible.

The base of the Lystrosaurus Assemblage Zone, Karoo Basin, predates the end-Permian marine extinction

The current model for the end-Permian terrestrial ecosystem crisis holds that systematic loss exhibited by an abrupt turnover from the Daptocephalus to the Lystrosaurus Assemblage Zone (AZ; Karoo Basin, South Africa) is time equivalent with the marine Permian–Triassic boundary (PTB). The marine event began at 251.941 ± 0.037 Ma, with the PTB placed at 251.902 ± 0.024 Ma (2σ). Radio-isotopic dates over this interval in the Karoo Basin were limited to one high resolution ash-fall deposit in the upper Daptocephalus AZ (253.48 ± 0.15 (2σ) Ma) with no similar age constraints for the overlying biozone. Here, we present the first U-Pb CA-ID-TIMS zircon age (252.24 ± 0.11 (2σ) Ma) from a pristine ash-fall deposit in the Karoo Lystrosaurus AZ. This date confirms that the lower exposures of the Lystrosaurus AZ are of latest Permian age and that the purported turnover in the basin preceded the end-Permian marine event by over 300 ka, thus refuting the previously used stratigraphic marker for terrestrial end-Permian extinction.

The end-Permian is associated with major changes in both marine and terrestrial biodiversity. Here, Gastaldo et al. present high resolution dating of the Lystrosaurus Assemblage Zone in the Karoo Basin, South Africa, demonstrating that the marine crisis did not mirror a coeval event on land.

Altered fluvial patterns in North China indicate rapid climate change linked to the Permian-Triassic mass extinction

The causes of the severest crisis in the history of life around the Permian-Triassic boundary (PTB) remain controversial. Here we report that the latest Permian alluvial plains in Shanxi, North China, went through a rapid transition from meandering rivers to braided rivers and aeolian systems. Soil carbonate carbon isotope (δ¹³C), oxygen isotope (δ¹⁸O), and geochemical signatures of weathering intensity reveal a consistent pattern of deteriorating environments (cool, arid, and anoxic conditions) and climate fluctuations across the PTB. The synchronous ecological collapse is confirmed by a dramatic reduction or disappearance of dominant plants, tetrapods and invertebrates and a bloom of microbially-induced sedimentary structures. A similar rapid switch in fluvial style is seen worldwide (e.g. Karoo Basin, Russia, Australia) in terrestrial boundary sequences, all of which may be considered against a background of global marine regression. The synchronous global expansion of alluvial fans and high-energy braided streams is a response to abrupt climate change associated with aridity, hypoxia, acid rain, and mass wasting. Where neighbouring uplands were not uplifting or basins subsiding, alluvial fans are absent, but in these areas the climate change is evidenced by the disruption of pedogenesis.

Effect of climate change on distribution of species of common horned frogs in South America

Our main objectives were to verify the effect of climate change on distribution of frogs of the family Ceratophryidae and if the legal protection areas in South America will be effective or ineffective in ensuring the preservation of the toads this family in coming decades. The results showed that in the last 140,000 years, species of the family Ceratophryidae expanded and contracted their distribution areas, which naturally reflected the climate and vegetation changes in the Quaternary of South America. The maps of projections showed that changes in temperature determined the area of habitat suitability of 63.7% of the species of ceratophrids both during the last interglacial period and nowadays, and it seems that this will also be the case for the next 62 years. Given the current concerns about future extinctions in the tropics, it is prudent to examine, with special attention, the effects of climate fluctuations on the diversity and distribution of species, because the current estimates of reduction in biodiversity caused by habitat destruction and emission of greenhouse gases are comparable to estimated reductions during glacial intervals.

A geochemical view into continental palaeotemperatures of the end-Permian using oxygen and hydrogen isotope composition of secondary silica in chert rubble breccia: Kaibab Formation, Grand Canyon (USA)

The upper carbonate member of the Kaibab Formation in northern Arizona (USA) was subaerially exposed during the end Permian and contains fractured and zoned chert rubble lag deposits typical of karst topography. The karst chert rubble has secondary (authigenic) silica precipitates suitable for estimating continental weathering temperatures during the end Permian karst event. New oxygen and hydrogen isotope ratios of secondary silica precipitates in the residual rubble breccia: (1) yield continental palaeotemperature estimates between 17 and 22 °C; and, (2) indicate that meteoric water played a role in the crystallization history of the secondary silica. The continental palaeotemperatures presented herein are broadly consistent with a global mean temperature estimate of 18.2 °C for the latest Permian derived from published climate system models. Few data sets are presently available that allow even approximate quantitative estimates of regional continental palaeotemperatures. These data provide a basis for better understanding the end Permian palaeoclimate at a seasonally-tropical latitude along the western shoreline of Pangaea.

Using Confidence Intervals to Quantify the Uncertainty in the End-Points of Stratigraphic Ranges

One of the many contributions paleontology makes to our understanding of the biosphere and its evolution is a direct temporal record of biotic events. However, assuming fossils have been correctly identified and accurately dated, stratigraphic ranges underestimate true temporal ranges: observed first occurrences are too young, and observed last occurrences are too old. Here I introduce the techniques developed for placing confidence intervals on the end-points of stratigraphic ranges. I begin with the analysis of single taxa in local sections – with the simplest of assumptions – random fossilization. This is followed by a discussion of the methods developed to handle the fact that the recovery of fossils is often non-random in space and time. After discussion of how confidence intervals can be used to test for simultaneous origination and extinctions, I conclude with an example application of confidence intervals to unravel the relative importance of background extinction, environmental change and mass extinction of ammonite species at the end of the Cretaceous in western Tethys.

An early geikiid dicynodont from the Tropidostoma Assemblage Zone (late Permian) of South Africa

Based on specimens previously identified as Tropidostoma, a new taxon of dicynodont (Bulbasaurus phylloxyron gen. et sp. nov.) from the Karoo Basin of South Africa is described. Bulbasaurus is a medium-sized dicynodont (maximum dorsal skull length 16.0 cm) restricted to the Tropidostoma Assemblage Zone (early Lopingian) of the Beaufort Group. Bulbasaurus can be distinguished from Tropidostoma by an array of characters including the presence of a tall, sharp premaxillary ridge, large, rugose, nearly-confluent nasal bosses, a nasofrontal ridge, massive tusks, robust pterygoids, prominently twisted subtemporal bar, and absence of a distinct postfrontal. Inclusion of Bulbasaurus in a phylogenetic analysis of anomodont therapsids recovers it as a member of Geikiidae, a clade of otherwise later Permian dicynodonts such as Aulacephalodon and Pelanomodon. Bulbasaurus exhibits many of the characters typical of adult Aulacephalodon, but at substantially smaller skull size (these characters are absent in comparably-sized Aulacephalodon juveniles), suggesting that the evolution of typical geikiid morphology preceded gigantism in the clade. Bulbasaurus is the earliest known geikiid and the only member of the group known from the Tropidostoma Assemblage Zone; discovery of this taxon shortens a perplexing ghost lineage and indicates that abundant clades from the later Permian of South Africa (e.g., Geikiidae, Dicynodontoidea) may have originated as rare components of earlier Karoo assemblage zones.

Boreal earliest Triassic biotas elucidate globally depauperate hard substrate communities after the end-Permian mass extinction

The end-Permian mass extinction constituted the most devastating biotic crisis of the Phanerozoic. Its aftermath was characterized by harsh marine conditions incorporating volcanically induced oceanic warming, widespread anoxia and acidification. Bio-productivity accordingly experienced marked fluctuations. In particular, low palaeolatitude hard substrate communities from shallow seas fringing Western Pangaea and the Tethyan Realm were extremely impoverished, being dominated by monogeneric colonies of filter-feeding microconchid tubeworms. Here we present the first equivalent field data for Boreal hard substrate assemblages from the earliest Triassic (Induan) of East Greenland. This region bordered a discrete bio-realm situated at mid-high palaeolatitude (>30°N). Nevertheless, hard substrate biotas were compositionally identical to those from elsewhere, with microconchids encrusting Claraia bivalves and algal buildups on the sea floor. Biostratigraphical correlation further shows that Boreal microconchids underwent progressive tube modification and unique taxic diversification concordant with changing habitats over time. We interpret this as a post-extinction recovery and adaptive radiation sequence that mirrored coeval subequatorial faunas, and thus confirms hard substrate ecosystem depletion as a hallmark of the earliest Triassic interval globally.

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.

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.

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.

Delayed recovery of non-marine tetrapods after the end-Permian mass extinction tracks global carbon cycle

During the end-Permian mass extinction, marine ecosystems suffered a major drop in diversity, which was maintained throughout the Early Triassic until delayed recovery during the Middle Triassic. This depressed diversity in the Early Triassic correlates with multiple major perturbations to the global carbon cycle, interpreted as either intrinsic ecosystem or external palaeoenvironmental effects. In contrast, the terrestrial record of extinction and recovery is less clear; the effects and magnitude of the end-Permian extinction on non-marine vertebrates are particularly controversial. We use specimen-level data from southern Africa and Russia to investigate the palaeodiversity dynamics of non-marine tetrapods across the Permo-Triassic boundary by analysing sample-standardized generic richness, evenness and relative abundance. In addition, we investigate the potential effects of sampling, geological and taxonomic biases on these data. Our analyses demonstrate that non-marine tetrapods were severely affected by the end-Permian mass extinction, and that these assemblages did not begin to recover until the Middle Triassic. These data are congruent with those from land plants and marine invertebrates. Furthermore, they are consistent with the idea that unstable low-diversity post-extinction ecosystems were subject to boom-bust cycles, reflected in multiple Early Triassic perturbations of the carbon cycle.

The Triassic timescale based on nonmarine tetrapod biostratigraphy and biochronology

The Triassic timescale based on nonmarine tetrapod biostratigraphy and biochronology divides Triassic time into eight land-vertebrate faunachrons (LVFs) with boundaries defined by the first appearance datums (FADs) of tetrapod genera or, in two cases, the FADs of a tetrapod species. Definition and characterization of these LVFs is updated here as follows: the beginning of the Lootsbergian LVF=FAD of Lystrosaurus; the beginning of the Nonesian=FAD Cynognathus; the beginning of the Perovkan LVF=FAD Eocyclotosaurus; the beginning of the Berdyankian LVF=FAD Mastodonsaurus giganteus; the beginning of the Otischalkian LVF=FAD Parasuchus; the beginning of the Adamanian LVF=FAD Rutiodon; the beginning of the Revueltian LVF=FAD Typothorax coccinarum; and the beginning of the Apachean LVF=FAD Redondasaurus. The end of the Apachean (= beginning of the Wasonian LVF, near the beginning of the Jurassic) is the FAD of the crocodylomorph Protosuchus. The Early Triassic tetrapod LVFs, Lootsbergian and Nonesian, have characteristic tetrapod assemblages in the Karoo basin of South Africa, the Lystrosaurus assemblage zone and the lower two-thirds of the Cynognathus assemblage zone, respectively. The Middle Triassic LVFs, Perovkan and Berdyankian, have characteristic assemblages from the Russian Ural foreland basin, the tetrapod assemblages of the Donguz and the Bukobay svitas, respectively. The Late Triassic LVFs, Otischalkian, Adamanian, Revueltian and Apachean, have characteristic assemblages in the Chinle basin of the western USA, the tetrapod assemblages of the Colorado City Formation of Texas, Blue Mesa Member of the Petrified Forest Formation in Arizona, and Bull Canyon and Redonda formations in New Mexico. Since the Triassic LVFs were introduced, several subdivisions have been proposed: Lootsbergian can be divided into three sub-LVFs, Nonesian into two, Adamanian into two and Revueltian into three. However, successful inter-regional correlation of most of these sub-LVFs remains to be demonstrated. Occasional records of nonmarine Triassic tetrapods in marine strata, palynostratigraphy, conchostracan biostratigraphy, magnetostratigraphy and radioisotopic ages provide some basis for correlation of the LVFs to the standard global chronostratigraphic scale. These data indicate that Lootsbergian=uppermost Changshingian, Induan and possibly earliest Olenekian; Nonesian=much of the Olenekian; Perovkan=most of the Anisian; Berdyankian=latest Anisian? and Ladinian; Otischalkian=early to late Carnian; Adamanian=most of the late Carnian; Revueltian=early–middle Norian; and Apachean=late Norian–Rhaetian. The Triassic timescale based on tetrapod biostratigraphy and biochronology remains a robust tool for the correlation of nonmarine Triassic tetrapod assemblages independent of the marine timescale.

The biostratigraphic importance of conchostracans in the continental Triassic of the northern hemisphere

Conchostracans or clam shrimp (order Conchostraca Sars) are arthropods with a carapace consisting of two chitinous lateral valves. Triassic conchostracans range in size from 2 to 12.5 mm long and are common in deposits that formed in fresh water lakes, isolated ponds and brackish areas. Their dessication- and freeze-resistant eggs can be dispersed by wind over long distances. Therefore many conchostracan species are distributed throughout the entire northern hemisphere. In the Late Permian to Middle Triassic interval, several of these forms are also found in Gondwana. Many wide-ranging conchostracan species have short stratigraphic ranges, making them excellent guide forms for subdivision of Triassic time and for long-range correlations. The stratigraphic resolution that can be achieved with conchostracan zones is often as high as for ammonoid and conodont zones found in pelagic marine deposits. This makes conchostracans the most useful group available for biostratigraphic subdivision and correlation in continental lake deposits. Upper Triassic Gondwanan conchostracan faunas are different from conchostracan faunas of the northern hemisphere. In the Norian, some slight provincialism can be observed even within the northern hemisphere. For example, the Sevatian Redondestheria seems to be restricted to North America and Acadiestheriella n. gen. so far has been found only in the Sevatian deposits from the Fundy Basin of southeastern Canada. Here we establish a conchostracan zonation for the Changhsingian (Late Permian) to Hettangian (Early Jurassic) of the northern hemisphere that, for the most part, is very well correlated with the marine scale. This zonation is especially robust for the Changhsingian to early Anisian, late Ladinian to Cordevolian and Rhaetian to Hettangian intervals. For most of the Middle and Upper Triassic, this zonation is still preliminary. Five new genera, six new species and a new subspecies of conchostracans are described that are stratigraphically important.

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.

Global taxonomic diversity of anomodonts (tetrapoda, therapsida) and the terrestrial rock record across the Permian-Triassic boundary

The end-Permian biotic crisis (~252.5 Ma) represents the most severe extinction event in Earth's history. This paper investigates diversity patterns in Anomodontia, an extinct group of therapsid synapsids ('mammal-like reptiles'), through time and in particular across this event. As herbivores and the dominant terrestrial tetrapods of their time, anomodonts play a central role in assessing the impact of the end-Permian extinction on terrestrial ecosystems. Taxonomic diversity analysis reveals that anomodonts experienced three distinct phases of diversification interrupted by the same number of extinctions, i.e. an end-Guadalupian, an end-Permian, and a mid-Triassic extinction. A positive correlation between the number of taxa and the number of formations per time interval shows that anomodont diversity is biased by the Permian-Triassic terrestrial rock record. Normalized diversity curves indicate that anomodont richness continuously declines from the Middle Permian to the Late Triassic, but also reveals all three extinction events. Taxonomic rates (origination and extinction) indicate that the end-Guadalupian and end-Permian extinctions were driven by increased rates of extinction as well as low origination rates. However, this pattern is not evident at the final decline of anomodont diversity during the Middle Triassic. Therefore, it remains unclear whether the Middle Triassic extinction represents a gradual or abrupt event that is unique to anomodonts or more common among terrestrial tetrapods. The end-Permian extinction represents the most distinct event in terms of decline in anomodont richness and turnover rates.

Trophic network models explain instability of Early Triassic terrestrial communities

Studies of the end-Permian mass extinction have emphasized potential abiotic causes and their direct biotic effects. Less attention has been devoted to secondary extinctions resulting from ecological crises and the effect of community structure on such extinctions. Here we use a trophic network model that combines topological and dynamic approaches to simulate disruptions of primary productivity in palaeocommunities. We apply the model to Permian and Triassic communities of the Karoo Basin, South Africa, and show that while Permian communities bear no evidence of being especially susceptible to extinction, Early Triassic communities appear to have been inherently less stable. Much of the instability results from the faster post-extinction diversification of amphibian guilds relative to amniotes. The resulting communities differed fundamentally in structure from their Permian predecessors. Additionally, our results imply that changing community structures over time may explain long-term trends like declining rates of Phanerozoic background extinction.

Early Penguin Fossils, Plus Mitochondrial Genomes, Calibrate Avian Evolution

Testing models of macroevolution, and especially the sufficiency of microevolutionary processes, requires good collaboration between molecular biologists and paleontologists. We report such a test for events around the Late Cretaceous by describing the earliest penguin fossils, analyzing complete mitochondrial genomes from an albatross, a petrel, and a loon, and describe the gradual decline of pterosaurs at the same time modern birds radiate. The penguin fossils comprise four naturally associated skeletons from the New Zealand Waipara Greensand, a Paleocene (early Tertiary) formation just above a well-known Cretaceous/Tertiary boundary site. The fossils, in a new genus (Waimanu), provide a lower estimate of 61-62 Ma for the divergence between penguins and other birds and thus establish a reliable calibration point for avian evolution. Combining fossil calibration points, DNA sequences, maximum likelihood, and Bayesian analysis, the penguin calibrations imply a radiation of modern (crown group) birds in the Late Cretaceous. This includes a conservative estimate that modern sea and shorebird lineages diverged at least by the Late Cretaceous about 74 +/- 3 Ma (Campanian). It is clear that modern birds from at least the latest Cretaceous lived at the same time as archaic birds including Hesperornis, Ichthyornis, and the diverse Enantiornithiformes. Pterosaurs, which also coexisted with early crown birds, show notable changes through the Late Cretaceous. There was a decrease in taxonomic diversity, and small- to medium-sized species disappeared well before the end of the Cretaceous. A simple reading of the fossil record might suggest competitive interactions with birds, but much more needs to be understood about pterosaur life histories. Additional fossils and molecular data are still required to help understand the role of biotic interactions in the evolution of Late Cretaceous birds and thus to test that the mechanisms of microevolution are sufficient to explain macroevolution.

Hypoxia, global warming, and terrestrial late Permian extinctions

A catastrophic extinction occurred at the end of the Permian Period. However, baseline extinction rates appear to have been elevated even before the final catastrophe, suggesting sustained environmental degradation. For terrestrial vertebrates during the Late Permian, the combination of a drop in atmospheric oxygen plus climate warming would have induced hypoxic stress and consequently compressed altitudinal ranges to near sea level. Our simulations suggest that the magnitude of altitudinal compression would have forced extinctions by reducing habitat diversity, fragmenting and isolating populations, and inducing a species-area effect. It also might have delayed ecosystem recovery after the mass extinction.