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opencc-zeroDec 2015View details →

Data from: A Bayesian approach for detecting the impact of mass-extinction events on molecular phylogenies when rates of lineage diversification may vary

The paleontological record chronicles numerous episodes of mass extinction that severely culled the Tree of Life. Biologists have long sought to assess the extent to which these events may have impacted particular groups. We present a novel method for detecting the impact of mass-extinction events on molecular phylogenies, even in the presence of tree-wide diversification-rate variation and in the absence of additional information from the fossil record. Our approach is based on an episodic stochastic-branching process model in which rates of speciation and extinction are constant between events. We model three types of events: (i) instantaneous tree-wide shifts in speciation rate; (ii) instantaneous tree-wide shifts in extinction rate and (iii) instantaneous tree-wide mass-extinction events. Each type of event is modelled as an independent compound Poisson process (CPP), where the waiting times between events are exponentially distributed with event-specific rate parameters. The magnitude of each event is drawn from an event-specific prior distribution. Parameters of the model are then estimated in a Bayesian statistical framework using a reversible-jump Markov chain Monte Carlo algorithm. This Bayesian approach enables us to distinguish between tree-wide diversification-rate variation and mass-extinction events by specifying a biologically informed prior on the magnitude of mass-extinction events and empirical hyperpriors on the diversification-rate parameters. We demonstrate via simulation that this method has substantial power to detect the number of mass-extinction events and provides unbiased estimates of the timing of mass-extinction events, while exhibiting an appropriate (i.e. <5%) false-discovery rate, even when background diversification rates vary. Finally, we provide an empirical demonstration of this approach, which reveals that conifers experienced a major episode of mass extinction ≈23 Ma. This new approach – the CPP on Mass-Extinction Times (CoMET) model – provides an effective tool for detecting the impact of mass-extinction events on molecular phylogenies, even when the history of those groups includes temporal variation in diversification rates and when the fossil history of those groups is poorly known.

Data from: Body length of bony fishes was not a selective factor during the biggest mass extinction of all time

The Permo-Triassic mass extinction devastated life on land and in the sea, but it is not clear why some species survived and others went extinct. One explanation is that lineage loss during mass extinctions is a random process in which luck determines which species survive. Alternatively, a phylogenetic signal in extinction may indicate a selection process operating on phenotypic traits. Large body size has often emerged as an extinction risk factor in studies of modern extinction risk, but this is not so commonly the case for mass extinctions in deep time. Here, we explore the evolution of non-teleostean Actinopterygii (bony fishes) from the Devonian to the present day, and we concentrate on the Permo-Triassic mass extinction. We apply a variety of time-scaling metrics to date the phylogeny, and show that diversity peaked in the latest Permian and declined severely during the Early Triassic. In line with previous evidence, we find the phylogenetic signal of extinction increases across the mass extinction boundary: extinction of species in the earliest Triassic is more clustered across phylogeny compared to the more randomly distributed extinction signal in the late Permian. However, body length plays no role in differential survival or extinction of taxa across the boundary. In the case of fishes, size did not determine which species survived and which went extinct, but phylogenetic signal indicates that the mass extinction was not a random field of bullets.

opencc-zeroDec 2017View details →

Data from: Multifaceted disparity approach reveals dinosaur herbivory flourished before the end-Cretaceous mass extinction

Understanding temporal patterns in biodiversity is an enduring question in paleontology. Compared to studies of taxonomic diversity, long-term perspectives on ecological diversity are rare, particularly in terrestrial systems. Yet ecological diversity is critical for the maintenance of biodiversity, particularly during times of major perturbations. Here, we explore the ecological diversity of Cretaceous herbivorous dinosaurs leading up to the K-Pg extinction, using dental and jaw morphological disparity as a proxy. We test the hypothesis that a decline in ecological diversity could have facilitated their rapid extinction 66 mya. We apply three disparity metrics that together capture different aspects of morphospace occupation, and show how this approach is key to understanding patterns of morphological evolution. We find no evidence of declining disparity in herbivorous dinosaurs as a whole – suggesting that dinosaur ecological diversity remained high during the last 10 million years of their existence. Clades show different disparity trends through the Cretaceous, but none except sauropods exhibits a long-term decline. Herbivorous dinosaurs show two disparity peaks characterised by different processes; in the Early Cretaceous by expansion in morphospace and in the Campanian by morphospace packing. These trends were only revealed by using a combination of disparity metrics, demonstrating how this approach can offer novel insights into macroevolutionary processes underlying patterns of disparity and ecological diversity.

opencc-zeroDec 2015View details →

Data from: Quantitative analysis of the ecological dominance of benthic disaster taxa in the aftermath of the end-Permian mass extinction

The end-Permian mass extinction, the largest extinction of the Phanerozoic, led to a severe reduction in both taxonomic richness and ecological complexity of marine communities in its aftermath, eventually culminating in a dramatic ecological restructuring of communities. During the Early Triassic recovery interval, disaster taxa proliferated and numerically dominated many marine benthic invertebrate assemblages. These disaster taxa include the bivalve genera Claraia, Unionites, Eumorphotis and Promyalina, and the inarticulate brachiopod Lingularia. The exact nature and extent of their dominance remains uncertain. Here, a quantitative analysis of the dominance of these taxa within the fossil communities of Panthalassa and Tethys benthic realms is undertaken for the stages of the Early Triassic to examine temporal and regional changes in disaster taxon dominance as recovery progresses. Community dominance and disaster taxon abundance is markedly different between Panthalassic and Tethyan communities. In Panthalassa, community evenness is low in the Induan stage, but increases significantly in the Smithian and Spathian. This is coincident with a significant decrease in the relative abundance and occurrence frequency of the disaster taxa, most notably of low-oxygen affinity taxa Claraia and Lingularia. While the disaster taxa are present in post-Induan assemblages, other taxa, including two articulate brachiopod genera, outrank the disaster taxa in relative abundance. In the Tethys, assemblages are generally more even than contemporaneous Panthalassic assemblages. We observe an averaged trend towards more even communities with fewer disaster taxa in both Panthalassic and Tethyan assemblages over time.

opencc-zeroDec 2014View details →

Data from: The stratigraphy of mass extinction

Patterns of last occurrences of fossil species are often used to infer the tempo and timing of mass extinction, even though last occurrences generally precede the time of extinction. Numerical simulations with constant extinction demonstrate that last occurrences are not randomly distributed, but tend to cluster at subaerial unconformities, surfaces of forced regression, flooding surfaces and intervals of stratigraphical condensation, all of which occur in predictable stratigraphical positions. This clustering arises not only from hiatuses and non-deposition, but also from changes in water depth. Simulations with intervals of elevated extinction cause such clusters of last occurrences to be enhanced within and below the interval of extinction, suggesting that the timing and magnitude of extinctions in these instances could be misinterpreted. With the possible exception of the end-Cretaceous, mass extinctions in the fossil record are characterized by clusters of last occurrences at these sequence stratigraphical horizons. Although these clusters of last occurrences may represent brief pulses of elevated extinction, they are equally likely to form by stratigraphical processes during a protracted period (more than several hundred thousand years) of elevated extinction rate. Geochemical proxies of extinction causes are also affected similarly, suggesting that many local expressions of mass extinction should be re-evaluated for the timing of extinction and its relation to environmental change. We propose three tests for distinguishing pulses of extinction from clusters of last occurrences produced by stratigraphical processes.

Data from: The tree balance signature of mass extinction is erased by continued evolution in clades of constrained size with trait-dependent speciation

The kind and duration of phylogenetic topological "signatures" left in the wake of macroevolutionary events remain poorly understood. To this end, we examined a broad range of simulated phylogenies generated using trait-biased, heritable speciation probabilities and mass extinction that could be either random or selective on trait value, but also using background extinction and diversity-dependence to constrain clade sizes. In keeping with prior results, random mass extinction increased imbalance of clades that recovered to pre-extinction size, but was a relatively weak effect. Mass extinction that was selective on trait values tended to produce clades of similar or greater balance compared to random extinction or controls. Allowing evolution to continue past the point of clade-size recovery resulted in erosion and eventual erasure of this signal, with all treatments converging on similar values of imbalance, except for very intense extinction regimes targeted at taxa with high speciation rates. Return to a more balanced state with extended post-extinction evolution was also associated with loss of the previous phylogenetic root in most treatments. These results further demonstrate that while a mass extinction event can produce a recognizable phylogenetic signal, its effects become increasingly obscured the further an evolving clade gets from that event, with any sharp imbalance due to unrelated evolutionary factors.

Data from: Completeness of the eutherian mammal fossil record and implications for reconstructing mammal evolution through the Cretaceous/Paleogene mass extinction

There is a well-established discrepancy between paleontological and molecular data regarding the timing of the origin and diversification of placental mammals. Molecular estimates place interordinal diversification dates in the Cretaceous, whilst no unambiguous crown placental fossils have been found prior to the end-Cretaceous mass extinction. Here, the completeness of the eutherian fossil record through geological time is evaluated in order to assess the suggestion that a poor fossil record is largely responsible for the difference in estimates of placental origins. The completeness of fossil specimens was measured using the Character Completeness Metric, a metric that quantifies the completeness of fossil taxa as the percentage of phylogenetic characters that are available to be scored for any given taxon. Our dataset was comprised of 33 published cladistic matrices representing 445 genera, of which 333 were coded at the species-level. There was no significant difference in eutherian completeness across the Cretaceous/Palaeogene boundary. This suggests that the lack of placental mammal fossils in the Cretaceous is not due to a poor fossil record, but more likely represents a genuine absence of placental mammals in the Cretaceous. This result supports the 'explosive model' of early placental evolution, whereby placental mammals originated around the time of the Cretaceous/Palaeogene boundary and diversified soon after the event. No correlation was found between the completeness pattern observed in this study and those of previous completeness studies on birds and sauropodomorph dinosaurs, suggesting that different factors affect the preservation of these groups. No correlations were found with various isotope proxy measures, but Akaike Information Criterion analysis found that eutherian Character Completeness Metric scores were best explained by models involving the marine carbonate strontium isotope ratios (87Sr/86Sr), suggesting that the tectonic activity might play a role in controlling the completeness of the eutherian fossil record.

opencc-by-4.0Jul 2024View details →

Supporting Information for: Re-evaluating Water Column Reoxygenation in the Aftermath of the End Permian Mass Extinction

Open the record for dataset details and reuse information.

opencc-zeroDec 2010View details →

Data from: A geographic test of species selection using planktonic foraminifera during the Cretaceous/Paleogene mass extinction

Species selection has received a great deal of theoretical attention but it has rarely been empirically tested. It is important to determine the level of selection that operated during a particular extinction event because it can help distinguish between traits that were actually responsible for extinction and those that were merely correlated with it. Here, we present a test that can help distinguish between organismal and species-level selection, which we demonstrate using the high-resolution fossil record of planktonic foraminifera species recorded in deep-sea sediment cores. Our test examines the fate of survivors and victims during the Cretaceous/Paleogene (K/Pg) mass extinction within single geographic regions, where all individuals experience the same selection pressures. Selection at the organismal level implies that individual members of surviving species are more fit than those of victimized species, and therefore should be more likely to survive in affected areas; conversely, selection at the species level implies individuals will suffer equally within an affected area. We find that survivors of the mass extinction suffered very high extirpation rates in cores where the overall extinction rate was high, indicating that individual members of the surviving species were generally no more fit than individual members of extinct species. Rather, these species were able to survive because they possessed advantageous species-level traits, such as larger geographic ranges and greater abundances than victimized species. This geographic pattern of extirpation suggests that selection operated at the species, rather than organismal, level during the K/Pg mass extinction of planktonic foraminifera.

Data from: 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.

opencc-zeroDec 2017View details →

Data from: Evolutionary and biogeographical shifts in response to the Late Ordovician mass extinction

The Late Ordovician mass extinction was an interval of high extinction with inferred low ecological selectivity, resulting in little change in community structure after the event. In contrast, the mass extinction may have fundamentally changed evolutionary dynamics in the surviving groups. We investigated the phylogenetic relationships among strophomenoid brachiopods, a diverse brachiopod superfamily that was a primary component of Ordovician ecosystems. Four Ordovician families/subfamilies sampled in the analysis (Rafinesquinidae, Strophomeninae, Glyptomenidae and Furcitellinae) were reconstructed as monophyletic groups, and the base of the strophomenoid clade that dominated the Silurian recovery was reconstructed as diversifying alongside these families during the Middle Ordovician. We time‐calibrated the phylogeny and used geographical occurrences to investigate biogeographical changes in the strophomenoids through time with the R package BiogeoBEARS. Our results indicate that extinction was higher in taxa whose ranges were constrained to tropical or subtropical regions. Furthermore, our results suggest important shifts in the diversification patterns of these brachiopods after the mass extinction. While most of the strophomenoid families survived the Late Ordovician event, ecologically abundant taxonomic groups during the Ordovician were either driven to extinction, reduced in diversity, or slowly died off during the Silurian. The new abundant strophomenoid taxa derived from one clade (consisting of Silurian–Devonian groups such as Douvillinidae, Strophodontidae and Amphistrophiidae) that diversified during the post‐extinction radiation. Our results suggest the selective diversification during the Silurian radiation, rather than selective extinction in the Late Ordovician, had a greater impact on the evolutionary history of strophomenoid brachiopods.

opencc-zeroJun 2019View details →

Data from: Exploring the power of Bayesian birth-death skyline models to detect mass extinction events from phylogenies with only extant taxa

Mass extinction events (MEEs), defined as significant losses of species diversity in significantly short time periods, have attracted the attention of biologists because of their link to major environmental change. MEEs have traditionally been studied through the fossil record, but the development of birth-death models has made it possible to detect their signature based on extant-taxa phylogenies. Most birth-death models consider MEEs as instantaneous events where a high proportion of species are simultaneously removed from the tree ("single pulse" approach), in contrast to the paleontological record, where MEEs have a time-duration. Here, we explore the power of a Bayesian Birth-Death Skyline (BDSKY) model to detect the signature of MEEs through changes in extinction rates under a "time-slice" approach. In this approach, MEEs are time intervals where the extinction rate is greater than the speciation rate. Results showed BDSKY can detect and locate MEEs but that precision and accuracy depend on phylogenies size and MEE intensity. Comparisons of BDSKY with the single-pulse Bayesian model, CoMET, showed a similar frequency of Type II error and neither model exhibited Type I error. However, while CoMET performed better in detecting and locating MEEs for smaller phylogenies, BDSKY showed higher accuracy in estimating extinction and speciation rates.

opencc-zeroDec 2018View details →

Data from: Examining community stability in the face of mass extinction in communities of digital organisms

Digital evolution is a computer-based instantiation of Darwinian evolution in which short self-replicating computer programs compete, mutate, and evolve. It is an excellent platform for addressing topics in long-term evolution and paleobiology, such as mass extinction and recovery, with experimental evolutionary approaches. We evolved model communities with ecological interdependence among community members, which were subjected to two principal types of mass extinction: a pulse extinction that killed randomly, and a selective press extinction involving an alteration of the abiotic environment to which the communities had to adapt. These treatments were applied at two different strengths, along with unperturbed control experiments. We examined how stability in the digital communities was affected from the perspectives of division of labor, relative shift in rank abundance, and genealogical connectedness of the community's component ecotypes. Mass extinction that was due to a Strong Press treatment was most effective in producing reshaped communities that differed from the pre-treatment ones in all of the measured perspectives; weaker versions of the treatments did not generally produce significant departures from a Control treatment; and results for the Strong Pulse treatment generally fell between those extremes. The Strong Pulse treatment differed from others in that it produced a slight but detectable shift towards more generalized communities. Compared to Press treatments, Pulse treatments also showed a greater contribution from re-evolved ecological doppelgangers rather than new ecotypes. However, relatively few Control communities showed stability in any of these metrics over the whole course of the experiment, and most did not represent stable states (by some measure of stability) that were disrupted by the extinction treatments. Our results have interesting, broad qualitative parallels with findings from the paleontological record, and show the potential of digital evolution studies to illuminate many aspects of mass extinction and recovery by addressing them in a truly experimental manner.

opencc-zeroSep 2021View details →

A new faunistic component of the Lower Triassic Panchet Formation of India increases the continental non-archosauromorph neodiapsid record in the aftermath of the end-Permian mass extinction

<p>The fossil record of Early Triassic diapsids is very important to understand how the end-Permian mass extinction affected ecosystems and the patterns and processes involved in the subsequent biotic recovery. Vertebrate fossil assemblages of continental deposits in current-day South Africa, China and Russia are the best source of information of this clade during the aftermath of the extinction event. Although considerably less sampled, the Induan continental rocks of the Panchet Formation of the Damodar Basin (eastern India) have also yielded a relatively diverse vertebrate assemblage composed of fishes, temnospondyls, synapsids, and a single proterosuchid taxon. Here, we report on a small isolated diapsid partial ilium (ISIR 1132) from the upper Panchet Formation. This specimen has a distinct morphology to that present in other tetrapods that we are aware of, including a shallow emargination on the dorsal margin of the anterior portion of the iliac blade, and ratio between height of iliac blade versus maximum height of iliac acetabulum at level of the dorsalmost extension of supraacetabular crest ≤0.45. Comparisons and a quantitative phylogenetic analysis found ISIR 1132 as a non-archosauromorph neodiapsid. This new specimen expands the reptile diversity in the Panchet Formation as well as for the rest of Gondwana, where Early Triassic non-archosauromorph neodiapsid species are extremely scarce.</p>

opencc-by-4.0Dec 2004View details →

Fig. 5 in Diversity dynamics of Early-Middle Jurassic brachiopods of Caucasus, and the Pliensbachian-Toarcian mass extinction

Fig. 5. Brachiopods diversity changes in Lias of Bakony Mts (after Vörös 1993, 1995) and Swiss Alps and Jura Mts. (after Sulser 1999).

opencc-by-4.0Dec 2004View details →

Fig. 1 in Diversity dynamics of Early-Middle Jurassic brachiopods of Caucasus, and the Pliensbachian-Toarcian mass extinction

Fig. 1. Geographic location of studied area (A) and paleogeographic situation of areas discussed in the text (B; studied area indicated by 1). Paleogeographic base map is modified from Owen 1983 and Dommergues et al. 2001.

opencc-by-4.0Dec 2004View details →

Fig. 2 in Diversity dynamics of Early-Middle Jurassic brachiopods of Caucasus, and the Pliensbachian-Toarcian mass extinction

Fig. 2. Liassic composite lithological section of NW Caucasus and comparison of regional and global (simplified from Hallam and Wignall 1999) sea−level changes.