Characterization of the definitive classical calpain family of vertebrates using phylogenetic, evolutionary and expression analyses

Peer reviewedPublisher PD

Decoupling of morphological disparity and taxic diversity during the adaptive radiation of anomodont therapsids

Adaptive radiations are central to macroevolutionary theory. Whether triggered by acquisition of new traits or ecological opportunities arising from mass extinctions, it is debated whether adaptive radiations are marked by initial expansion of taxic diversity or of morphological disparity (the range of anatomical form). If a group rediversifies following a mass extinction, it is said to have passed through a macroevolutionary bottleneck, and the loss of taxic or phylogenetic diversity may limit the amount of morphological novelty that it can subsequently generate. Anomodont therapsids, a diverse clade of Permian and Triassic herbivorous tetrapods, passed through a bottleneck during the end-Permian mass extinction. Their taxic diversity increased during the Permian, declined significantly at the Permo–Triassic boundary and rebounded during the Middle Triassic before the clade's final extinction at the end of the Triassic. By sharp contrast, disparity declined steadily during most of anomodont history. Our results highlight three main aspects of adaptive radiations: (i) diversity and disparity are generally decoupled; (ii) models of radiations following mass extinctions may differ from those triggered by other causes (e.g. trait acquisition); and (iii) the bottleneck caused by a mass extinction means that a clade can emerge lacking its original potential for generating morphological variety

The fossil record of ichthyosaurs, completeness metrics and sampling biases

Ichthyosaurs were highly successful marine reptiles with an abundant and well-studied fossil record. However, their occurrences through geological time and space are sporadic, and it is important to understand whether times of apparent species richness and rarity are real or the result of sampling bias. Here, we explore the skeletal completeness of 351 dated and identified ichthyosaur specimens, belonging to all 102 species, the first time that such a study has been carried out on vertebrates from the marine realm. No correlations were found between time series of different skeletal metrics and ichthyosaur diversity. There is a significant geographical variation in completeness, with the well-studied northern hemisphere producing fossils of much higher quality than the southern hemisphere. Medium-sized ichthyosaurs are significantly more complete than small or large taxa: the incompleteness of small specimens was expected, but it was a surprise that larger specimens were also relatively incomplete. Completeness varies greatly between facies, with fine-grained, siliciclastic sediments preserving the most complete specimens. These findings may explain why the ichthyosaur diversity record is low at times, corresponding to facies of poor preservation potential, such as in the Early Cretaceous. Unexpectedly, we find a strong negative correlation between skeletal completeness and sea level, meaning the most complete specimens occurred at times of global low sea level, and vice versa. Completeness metrics, however, do not replicate the sampling signal and have limited use as a global-scale sampling proxy

Survival and selection biases in early animal evolution and a source of systematic overestimation in molecular clocks

Important evolutionary events such as the Cambrian Explosion have inspired many attempts at explanation: why do they happen when they do? What shapes them, and why do they eventually come to an end? However, much less attention has been paid to the idea of a ‘null hypothesis’—that certain features of such diversifications arise simply through their statistical structure. Such statistical features also appear to influence our perception of the timing of these events. Here, we show in particular that study of unusually large clades leads to systematic overestimates of clade ages from some types of molecular clocks, and that the size of this effect may be enough to account for the puzzling mismatches seen between these molecular clocks and the fossil record. Our analysis of the fossil record of the late Ediacaran to Cambrian suggests that it is likely to be recording a true evolutionary radiation of the bilaterians at this time, and that explanations involving various sorts of cryptic origins for the bilaterians do not seem to be necessary

The radiation of cynodonts and the ground plan of mammalian morphological diversity

Cynodont therapsids diversified extensively after the Permo-Triassic mass extinction event, and gave rise to mammals in the Jurassic. We use an enlarged and revised dataset of discrete skeletal characters to build a new phylogeny for all main cynodont clades from the Late Permian to the Early Jurassic, and we analyse models of morphological diversification in the group. Basal taxa and epicynodonts are paraphyletic relative to eucynodonts, and the latter are divided into cynognathians and probainognathians, with tritylodonts and mammals forming sister groups. Disparity analyses reveal a heterogeneous distribution of cynodonts in a morphospace derived from cladistic characters. Pairwise morphological distances are weakly correlated with phylogenetic distances. Comparisons of disparity by groups and through time are non-significant, especially after the data are rarefied. A disparity peak occurs in the Early/Middle Triassic, after which period the mean disparity fluctuates little. Cynognathians were characterized by high evolutionary rates and high diversity early in their history, whereas probainognathian rates were low. Community structure may have been instrumental in imposing different rates on the two clades

Could a potential Anthropocene mass extinction define a new geological period?

A key aspect of the current debate about the Anthropocene focuses on defining a new geological epoch. Features of the Anthropocene include a biodiversity crisis with the potential to reach ‘mass extinction’ status alongside increasing global CO₂ and temperature. Previous geological boundaries associated with mass extinctions, rises in atmospheric CO₂ and rises in global temperature are more usually associated with transitions between geological periods. The current rapid increase in species extinctions suggest that a new mass extinction event is most likely imminent in the near-term future. Although CO₂ levels are currently low in comparison with the rest of the Phanerozoic, they are rising rapidly along with global temperatures. This suggests that defining the Anthropocene as a new geological period, rather than a new epoch, may be more consistent with previous geological boundaries in the Phanerozoic

A mindfulness-based intervention to increase resilience to stress in university students (the Mindful Student Study): a pragmatic randomised controlled trial

Background More young people are going to university, but there is concern about an increasing demand for student mental health services. We designed a pragmatic randomised controlled trial to test the hypothesis that providing mindfulness courses to university students would promote their resilience to stress. Methods University of Cambridge students without severe mental illness or crisis (self-assessed) were remotely randomised to join an 8-week mindfulness course adapted for university students (MSS), or to mental health support as usual (SAU). The primary outcome was self-reported psychological distress during the examination period measured using the Clinical Outcomes in Routine Evaluation Outcome Measure. Main outcome intention-to-treat analysis was masked to allocation. Trial registration: ACTRN12615001160527 (complete). Findings In total, 616 students were randomised (circa 3% of all students; 309 to MSS, 307 to SAU); 74% completed the primary outcome measure; 65% of the MSS arm participants completed at least half of the MSS course. MSS reduced distress scores during the exam period compared with SAU (β=-0.44, 95%CI -0.60 to -0.29; p < 0.0001); 57% of SAU participants had distress scores above an accepted clinical threshold level compared with 37% of MSS participants. On average, six students needed to be offered the MSS course to prevent one from experiencing clinical levels of distress (number needed to treat 6, 95%CI 4 to 10). SAU distress worsened over the year whereas MSS scores improved after the course and were maintained during exams. Active monitoring revealed no adverse reactions related to self-harm, suicidality or harm to others. Interpretation The main limitation of this trial is the lack of control for non-specific effects. However, the provision of mindfulness training appears an effective component of a wider student mental health strategy. Funding University of Cambridge and NIHR Collaboration for Leadership in Applied Health Research and Care East of England.University of Cambridge and National Institute for Health Research Collaboration for Leadership in Applied Health Research and Care East of England

A re-evaluation of goniopholidid crocodylomorph material from Central Asia: Biogeographic and phylogenetic implications

Central Asia is a key area for crocodylomorph evolution, lying midway between the highly documented deposits in Europe and North America, but crocodylomorph fossils from this part of the world are rare. Included among these are specimens collected in the 1970s and 1980s by the Soviet-Mongolian Expeditions in the Jurassic and Cretaceous of Mon-golia, Tajikistan, and Kazakhstan. Three species, “Sunosuchus” shartegensis, Kansajsuchus extensus, and Turanosuchus aralensis are redescribed and subjected to phylogenetic analysis for the first time. “Sunosuchus” shartegensis and Kansajsuchus are relatively derived goniopholidids, and part of a pan-east-Laurasian radiation of goniopholidids from which the European goniopholidids subsequently radiated. No characters can be used to distinguish “Sunosuchus” shartegensis from “S.” thailandicus; the two species are therefore synonymized. Turanosuchus aralensis is here considered a nomen dubium. Cladistic analysis suggests that Sunosuchus is polyphyletic, indicating a higher degree of diversification than was previously thought, but also pointing to the need for further systematic revision

Digit-only sauropod pes trackways from China – evidence of swimming or a preservational phenomenon?

For more than 70 years unusual sauropod trackways have played a pivotal role in debates about the swimming ability of sauropods. Most claims that sauropods could swim have been based on manusonly or manus-dominated trackways. However none of these incomplete trackways has been entirely convincing, and most have proved to be taphonomic artifacts, either undertracks or the result of differential depth of penetration of manus and pes tracks, but otherwise showed the typical pattern of normal walking trackways. Here we report an assemblage of unusual sauropod tracks from the Lower Cretaceous Hekou Group of Gansu Province, northern China, characterized by the preservation of only the pes claw traces, that we interpret as having been left by walking, not buoyant or swimming, individuals. They are interpreted as the result of animals moving on a soft mud-silt substrate, projecting their claws deeply to register their traces on an underlying sand layer where they gained more grip during progression. Other sauropod walking trackways on the same surface with both pes and manus traces preserved, were probably left earlier on relatively firm substrates that predated the deposition of soft mud and silt . Presently, there is no convincing evidence of swimming sauropods from their trackways, which is not to say that sauropods did not swim at all

Geographic range did not confer resilience to extinction in terrestrial vertebrates at the end-Triassic crisis

Rates of extinction vary greatly through geological time, with losses particularly concentrated in mass extinctions. Species duration at other times varies greatly, but the reasons for this are unclear. Geographical range correlates with lineage duration amongst marine invertebrates, but it is less clear how far this generality extends to other groups in other habitats. It is also unclear whether a wide geographical distribution makes groups more likely to survive mass extinctions. Here we test for extinction selectivity amongst terrestrial vertebrates across the end-Triassic event. We demonstrate that terrestrial vertebrate clades with larger geographical ranges were more resilient to extinction than those with smaller ranges throughout the Triassic and Jurassic. However, this relationship weakened with increasing proximity to the end-Triassic mass extinction, breaking down altogether across the event itself. We demonstrate that these findings are not a function of sampling biases; a perennial issue in studies of this kind