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

Universities futureproofing youth mental health: research confirms that offering mindfulness courses to students increases their wellbeing and resilience to stress

ABSTRACT Introduction Worldwide, increasing numbers of young people go to university, but there is concern about students’ rising need for mental health services. Young people’s journey through university provides a golden yet under-used opportunity for prevention. Mindfulness meditation training is popular amongst young people, but its effectiveness to increase wellbeing and resilience to stress in university students needs confirmation. Objective To address these issues the University of Cambridge has funded an implementation and evaluation project co-produced between the University Counselling Service, the Academic Division and the Department of Psychiatry. We designed a pragmatic, randomised controlled trial assessing the impact of providing mindfulness teaching before examinations to test the main hypothesis that it reduces students’ distress. Methods University of Cambridge students without severe mental illness or related crisis were randomly allocated to join an 8-week mindfulness course adapted for university students, or to just continue accessing to mental health support as usual (SAU). The main outcome was self-reported psychological distress during the examination period measured with the CORE Outcome Measure. Other results included the Warwick-Edinburgh Mental Wellbeing Scale, and adverse events. Main outcome analysis was masked to random allocation. An Advisory Reference Group involved students and other stakeholders. An independent committee provided oversight. Results A sample of 616 students took part (median age 22 years, 63% women); 309 were allocated to mindfulness, and 307 to SAU. Participants’ initial distress was higher than the general student population, but lower than students attending counselling; 74% completed the main outcome questionnaire. During the exam season mindfulness participants’ distress score was on average 0.25 CORE-OM points lower (95% confidence interval (CI) 0.16 to 0.34) than SAU participants’ distress. This difference bridges the gap between participants’ initial distress (0.99) and the general student population mean (0.76). Mindfulness participants were one third less likely to be in the clinical range of distress than SAU participants (risk ratio 0.65, 95%CI 0.53 to 0.80). SAU participants’ distress increased over the academic year whereas mindfulness group distress decreased after the course and was maintained during the exam period. Mindfulness also increased wellbeing. Effects were extremely unlikely to be due to chance (p<0.001). Mindfulness did not cause any significant adverse events. Conclusion Findings confirm that the provision of an 8-week mindfulness course effectively reduces distress and enhances wellbeing in university students. We hope that these results will impact significantly on student welfare policy, with mindfulness being implemented at universities more widely

Variable ranking and selection with random forest for unbalanced data

When one or several classes are much less prevalent than another class (unbalanced data), class error rates and variable importances of the machine learning algorithm random forest can be biased, particularly when sample sizes are smaller, imbalance levels higher, and effect sizes of important variables smaller. Using simulated data varying in size, imbalance level, number of true variables, their effect sizes, and the strength of multicollinearity between covariates, we evaluated how eight versions of random forest ranked and selected true variables out of a large number of covariates despite class imbalance. The version that calculated variable importance based on the area under the curve (AUC) was least adversely affected by class imbalance. For the same number of true variables, effect sizes, and multicollinearity between covariates, the AUC variable importance ranked true variables still highly at the lower sample sizes and higher imbalance levels at which the other seven versions no longer achieved high ranks for true variables. Conversely, using the Hellinger distance to split trees or downsampling the majority class already ranked true variables lower and more variably at the larger sample sizes and lower imbalance levels at which the other algorithms still ranked true variables highly. In variable selection, a higher proportion of true variables were identified when covariates were ranked by AUC importances and the proportion increased further when the AUC was used as the criterion in forward variable selection. In three case studies, known species–habitat relationships and their spatial scales were identified despite unbalanced data

Multi-locus homozygosity promotes actuarial senescence in a wild mammal.

This is the final version. Available from Wiley via the DOI in this record. DATA AVAILABILITY STATEMENT: Data available from the Dryad Digital Repository https://doi. org/10.5061/dryad.bk3j9kdg6 (Hudson, 2023)Genome-wide homozygosity, caused for example by inbreeding, is expected to have deleterious effects on survival and/or reproduction. Evolutionary theory predicts that any fitness costs are likely to be detected in late life because natural selection will filter out negative impacts on younger individuals with greater reproductive value. Here we infer associations between multi-locus homozygosity (MLH), sex, disease and age-dependent mortality risks using Bayesian analysis of the life histories of wild European badgers Meles meles in a population naturally infected with Mycobacterium bovis (the causative agent of bovine tuberculosis [bTB]). We find important effects of MLH on all parameters of the Gompertz-Makeham mortality hazard function, but particularly in later life. Our findings confirm the predicted association between genomic homozygosity and actuarial senescence. Increased homozygosity is particularly associated with an earlier onset, and greater rates of actuarial senescence, regardless of sex. The association between homozygosity and actuarial senescence is further amplified among badgers putatively infected with bTB. These results recommend further investigation into the ecological and behavioural processes that result in genome-wide homozygosity, and focused work on whether homozygosity is harmful or beneficial during early life-stages.Natural Environment Research Council (NERC)Natural Environment Research Council (NERC)Animal and Plant Health AgencyExpanding Excellence in EnglandUniversity of Exete

Integrating evolution into ecological modelling: accommodating phenotypic changes in agent based models.

PMCID: PMC3733718This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.Evolutionary change is a characteristic of living organisms and forms one of the ways in which species adapt to changed conditions. However, most ecological models do not incorporate this ubiquitous phenomenon. We have developed a model that takes a 'phenotypic gambit' approach and focuses on changes in the frequency of phenotypes (which differ in timing of breeding and fecundity) within a population, using, as an example, seasonal breeding. Fitness per phenotype calculated as the individual's contribution to population growth on an annual basis coincide with the population dynamics per phenotype. Simplified model variants were explored to examine whether the complexity included in the model is justified. Outputs from the spatially implicit model underestimated the number of individuals across all phenotypes. When no phenotype transitions are included (i.e. offspring always inherit their parent's phenotype) numbers of all individuals are always underestimated. We conclude that by using a phenotypic gambit approach evolutionary dynamics can be incorporated into individual based models, and that all that is required is an understanding of the probability of offspring inheriting the parental phenotype

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

Risk-stratified faecal immunochemical testing (FIT) for urgent colonoscopy in Lynch syndrome during the COVID-19 pandemic

BACKGROUND: Lynch syndrome is a hereditary cancer disease resulting in an increased risk of colorectal cancer. Herein, findings are reported from an emergency clinical service implemented during the COVID-19 pandemic utilizing faecal immunochemical testing ('FIT') in Lynch syndrome patients to prioritize colonoscopy while endoscopy services were limited. METHODS: An emergency service protocol was designed to improve colonoscopic surveillance access throughout the COVID-19 pandemic in England for people with Lynch syndrome when services were extremely restricted (1 March 2020 to 31 March 2021) and promoted by the English National Health Service. Requests for faecal immunochemical testing from participating centres were sent to the National Health Service Bowel Cancer Screening South of England Hub and a faecal immunochemical testing kit, faecal immunochemical testing instructions, paper-based survey, and pre-paid return envelope were sent to patients. Reports with faecal haemoglobin results were returned electronically for clinical action. Risk stratification for colonoscopy was as follows: faecal haemoglobin less than 10 µg of haemoglobin/g of faeces (µg/g)-scheduled within 6-12 weeks; and faecal haemoglobin greater than or equal to 10 µg/g-triaged via an urgent suspected cancer clinical pathway. Primary outcomes of interest included the identification of highest-risk Lynch syndrome patients and determining the impact of faecal immunochemical testing in risk-stratified colonoscopic surveillance. RESULTS: Fifteen centres participated from June 2020 to March 2021. Uptake was 68.8 per cent amongst 558 patients invited. For 339 eligible participants analysed, 279 (82.3 per cent) had faecal haemoglobin less than 10 µg/g and 60 (17.7 per cent) had faecal haemoglobin greater than or equal to 10 µg/g. In the latter group, the diagnostic accuracy of faecal immunochemical testing was 65.9 per cent and escalation to colonoscopy was facilitated (median 49 versus 122 days, χ2 = 0.0003, P < 0.001). CONCLUSION: Faecal immunochemical testing demonstrated clinical value for Lynch syndrome patients requiring colorectal cancer surveillance during the pandemic in this descriptive report of an emergency COVID-19 response service. Further longitudinal investigation on faecal immunochemical testing efficacy in Lynch syndrome is warranted and will be examined under the 'FIT for Lynch' study (ISRCTN15740250)

A symmoriiform chondrichthyan braincase and the origin of chimaeroid fishes

Chimaeroid fishes (Holocephali) are one of the four principal divisions of modern gnathostomes (jawed vertebrates). Despite only 47 described living species1, chimaeroids are the focus of resurgent interest as potential archives of genomic data2 and for the unique perspective they provide on chondrichthyan and gnathostome ancestral conditions. Chimaeroids are also noteworthy for their highly derived body plan1,3,4. However, like other living groups with distinctive anatomies5, fossils have been of limited use in unravelling their evolutionary origin, as the earliest recognized examples already exhibit many of the specializations present in modern forms6,7. Here we report the results of a computed tomography analysis of Dwykaselachus, an enigmatic chondrichthyan braincase from the ~280 million year old Karoo sediments of South Africa8. Externally, the braincase is that of a symmoriid shark9,10,11,12,13and is by far the most complete uncrushed example yet discovered. Internally, the morphology exhibits otherwise characteristically chimaeroid specializations, including the otic labyrinth arrangement and the brain space configuration relative to exceptionally large orbits. These results have important implications for our view of modern chondrichthyan origins, add robust structure to the phylogeny of early crown group gnathostomes, reveal preconditions that suggest an initial morpho-functional basis for the derived chimaeroid cranium, and shed new light on the chondrichthyan response to the extinction at the end of the Devonian period

Vegetarian diets are associated with healthy mood states: a cross-sectional study in Seventh Day Adventist adults

<p>Abstract</p> <p>Background</p> <p>The physical health status of vegetarians has been extensively reported, but there is limited research regarding the mental health status of vegetarians, particularly with regard to mood. Vegetarian diets exclude fish, the major dietary source of eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), critical regulators of brain cell structure and function. Omnivorous diets low in EPA and DHA are linked to impaired mood states in observational and experimental studies.</p> <p>Methods</p> <p>We examined associations between mood state and polyunsaturated fatty acid intake as a result of adherence to a vegetarian or omnivorous diet in a cross-sectional study of 138 healthy Seventh Day Adventist men and women residing in the Southwest. Participants completed a quantitative food frequency questionnaire, Depression Anxiety Stress Scale (DASS), and Profile of Mood States (POMS) questionnaires.</p> <p>Results</p> <p>Vegetarians (VEG:n = 60) reported significantly less negative emotion than omnivores (OMN:n = 78) as measured by both mean total DASS and POMS scores (8.32 ± 0.88 vs 17.51 ± 1.88, <it>p </it>= .000 and 0.10 ± 1.99 vs 15.33 ± 3.10, <it>p </it>= .007, respectively). VEG reported significantly lower mean intakes of EPA (<it>p </it>< .001), DHA (<it>p </it>< .001), as well as the omega-6 fatty acid, arachidonic acid (AA; <it>p </it>< .001), and reported higher mean intakes of shorter-chain α-linolenic acid (<it>p </it>< .001) and linoleic acid (<it>p </it>< .001) than OMN. Mean total DASS and POMS scores were positively related to mean intakes of EPA (<it>p </it>< 0.05), DHA (<it>p </it>< 0.05), and AA (<it>p </it>< 0.05), and inversely related to intakes of ALA (<it>p </it>< 0.05), and LA (<it>p </it>< 0.05), indicating that participants with low intakes of EPA, DHA, and AA and high intakes of ALA and LA had better mood.</p> <p>Conclusions</p> <p>The vegetarian diet profile does not appear to adversely affect mood despite low intake of long-chain omega-3 fatty acids.</p