Epicosm-a framework for linking online social media in epidemiological cohorts.

MOTIVATION: Social media represent an unrivalled opportunity for epidemiological cohorts to collect large amounts of high-resolution time course data on mental health. Equally, the high-quality data held by epidemiological cohorts could greatly benefit social media research as a source of ground truth for validating digital phenotyping algorithms. However, there is currently a lack of software for doing this in a secure and acceptable manner. We worked with cohort leaders and participants to co-design an open-source, robust and expandable software framework for gathering social media data in epidemiological cohorts. IMPLEMENTATION: Epicosm is implemented as a Python framework that is straightforward to deploy and run inside a cohort's data safe haven. GENERAL FEATURES: The software regularly gathers Tweets from a list of accounts and stores them in a database for linking to existing cohort data. AVAILABILITY: This open-source software is freely available at [https://dynamicgenetics.github.io/Epicosm/].

Mapping population vulnerability and community support during COVID-19: a case study from Wales.

BACKGROUND: Disasters such as the COVID-19 pandemic pose an overwhelming demand on resources that cannot always be met by official organisations. Limited resources and human response to crises can lead members of local communities to turn to one another to fulfil immediate needs. This spontaneous citizen-led response can be crucial to a community's ability to cope in a crisis. It is thus essential to understand the scope of such initiatives so that support can be provided where it is most needed. Nevertheless, quickly developing situations and varying definitions can make the community response challenging to measure. AIM: To create an accessible interactive map of the citizen-led community response to need during the COVID-19 pandemic in Wales, UK that combines information gathered from multiple data providers to reflect different interpretations of need and support. APPROACH: We gathered data from a combination of official data providers and community-generated sources to create 14 variables representative of need and support. These variables are derived by a reproducible data pipeline that enables flexible integration of new data. The interactive tool is available online (www.covidresponsemap.wales) and can map available data at two geographic resolutions. Users choose their variables of interest, and interpretation of the map is aided by a linked bee-swarm plot. DISCUSSION: The novel approach we developed enables people at all levels of community response to explore and analyse the distribution of need and support across Wales. While there can be limitations to the accuracy of community-generated data, we demonstrate that they can be effectively used alongside traditional data sources to maximise the understanding of community action. This adds to our overall aim to measure community response and resilience, as well as to make complex population health data accessible to a range of audiences. Future developments include the integration of other factors such as well-being.

Views on social media and its linkage to longitudinal data from two generations of a UK cohort study.

Background: Cohort studies gather huge volumes of information about a range of phenotypes but new sources of information such as social media data are yet to be integrated. Participant's long-term engagement with cohort studies, as well as the potential for their social media data to be linked to other longitudinal data, could provide novel advances but may also give participants a unique perspective on the acceptability of this growing research area. Methods: Two focus groups explored participant views towards the acceptability and best practice for the collection of social media data for research purposes. Participants were drawn from the Avon Longitudinal Study of Parents and Children cohort; individuals from the index cohort of young people (N=9) and from the parent generation (N=5) took part in two separate 90-minute focus groups. The discussions were audio recorded and subjected to qualitative analysis. Results: Participants were generally supportive of the collection of social media data to facilitate health and social research. They felt that their trust in the cohort study would encourage them to do so. Concern was expressed about the collection of data from friends or connections who had not consented. In terms of best practice for collecting the data, participants generally preferred the use of anonymous data derived from social media to be shared with researchers. Conclusion: Cohort studies have trusting relationships with their participants; for this relationship to extend to linking their social media data with longitudinal information, procedural safeguards are needed. Participants understand the goals and potential of research integrating social media data into cohort studies, but further research is required on the acquisition of their friend's data. The views gathered from participants provide important guidance for future work seeking to integrate social media in cohort studies.

A Cambrian-Ordovician Terrestrialization of Arachnids.

Understanding the temporal context of terrestrialization in chelicerates depends on whether terrestrial groups, the traditional Arachnida, have a single origin and whether or not horseshoe crabs are primitively or secondarily marine. Molecular dating on a phylogenomic tree that recovers arachnid monophyly, constrained by 27 rigorously vetted fossil calibrations, estimates that Arachnida originated during the Cambrian or Ordovician. After the common ancestor colonized the land, the main lineages appear to have rapidly radiated in the Cambrian-Ordovician boundary interval, coinciding with high rates of molecular evolution. The highest rates of arachnid diversification are detected between the Permian and Early Cretaceous. A pattern of ancient divergence estimates for terrestrial arthropod groups in the Cambrian while the oldest fossils are Silurian (seen in both myriapods and arachnids) is mirrored in the molecular and fossil records of land plants. We suggest the discrepancy between molecular and fossil evidence for terrestrialization is likely driven by the extreme sparseness of terrestrial sediments in the rock record before the late Silurian.

Participant acceptability of digital footprint data collection strategies: an exemplar approach to participant engagement and involvement in the ALSPAC birth cohort study.

Introduction: Digital footprint records - the tracks and traces amassed by individuals as a result of their interactions with the internet, digital devices and services - can provide ecologically valid data on individual behaviours. These could enhance longitudinal population study databanks; but few UK longitudinal studies are attempting this. When using novel sources of data, study managers must engage with participants in order to develop ethical data processing frameworks that facilitate data sharing whilst safeguarding participant interests. Objectives: This paper aims to summarise the participant involvement approach used by the ALSPAC birth cohort study to inform the development of a framework for using linked participant digital footprint data, and provide an exemplar for other data linkage infrastructures. Methods: The paper synthesises five qualitative forms of inquiry. Thematic analysis was used to code transcripts for common themes in relation to conditions associated with the acceptability of sharing digital footprint data for longitudinal research. Results: We identified six themes: participant understanding; sensitivity of location data; concerns for third parties; clarity on data granularity; mechanisms of data sharing and consent; and trustworthiness of the organisation. For cohort members to consider the sharing of digital footprint data acceptable, they require information about the value, validity and risks; control over sharing elements of the data they consider sensitive; appropriate mechanisms to authorise or object to their records being used; and trust in the organisation. Conclusion: Realising the potential for using digital footprint records within longitudinal research will be subject to ensuring that this use of personal data is acceptable; and that rigorously controlled population data science benefiting the public good is distinguishable from the misuse and lack of personal control of similar data within other settings. Participant co-development informs the ethical-governance framework for these novel linkages in a manner which is acceptable and does not undermine the role of the trusted data custodian.

Author Correction: Increasing species sampling in chelicerate genomic-scale datasets provides support for monophyly of Acari and Arachnida.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Increasing species sampling in chelicerate genomic-scale datasets provides support for monophyly of Acari and Arachnida.

Chelicerates are a diverse group of arthropods, represented by such forms as predatory spiders and scorpions, parasitic ticks, humic detritivores, and marine sea spiders (pycnogonids) and horseshoe crabs. Conflicting phylogenetic relationships have been proposed for chelicerates based on both morphological and molecular data, the latter usually not recovering arachnids as a clade and instead finding horseshoe crabs nested inside terrestrial Arachnida. Here, using genomic-scale datasets and analyses optimised for countering systematic error, we find strong support for monophyletic Acari (ticks and mites), which when considered as a single group represent the most biodiverse chelicerate lineage. In addition, our analysis recovers marine forms (sea spiders and horseshoe crabs) as the successive sister groups of a monophyletic lineage of terrestrial arachnids, suggesting a single colonisation of land within Chelicerata and the absence of wholly secondarily marine arachnid orders.

Soft-Bodied Fossils Are Not Simply Rotten Carcasses - Toward a Holistic Understanding of Exceptional Fossil Preservation: Exceptional Fossil Preservation Is Complex and Involves the Interplay of Numerous Biological and Geological Processes.

Exceptionally preserved fossils are the product of complex interplays of biological and geological processes including burial, autolysis and microbial decay, authigenic mineralization, diagenesis, metamorphism, and finally weathering and exhumation. Determining which tissues are preserved and how biases affect their preservation pathways is important for interpreting fossils in phylogenetic, ecological, and evolutionary frameworks. Although laboratory decay experiments reveal important aspects of fossilization, applying the results directly to the interpretation of exceptionally preserved fossils may overlook the impact of other key processes that remove or preserve morphological information. Investigations of fossils preserving non-biomineralized tissues suggest that certain structures that are decay resistant (e.g., the notochord) are rarely preserved (even where carbonaceous components survive), and decay-prone structures (e.g., nervous systems) can fossilize, albeit rarely. As we review here, decay resistance is an imperfect indicator of fossilization potential, and a suite of biological and geological processes account for the features preserved in exceptional fossils.

Molecular clocks indicate turnover and diversification of modern coleoid cephalopods during the Mesozoic Marine Revolution.

Coleoid cephalopod molluscs comprise squid, cuttlefish and octopuses, and represent nearly the entire diversity of modern cephalopods. Sophisticated adaptations such as the use of colour for camouflage and communication, jet propulsion and the ink sac highlight the unique nature of the group. Despite these striking adaptations, there are clear parallels in ecology between coleoids and bony fishes. The coleoid fossil record is limited, however, hindering confident analysis of the tempo and pattern of their evolution. Here we use a molecular dataset (180 genes, approx. 36 000 amino acids) of 26 cephalopod species to explore the phylogeny and timing of cephalopod evolution. We show that crown cephalopods diverged in the Silurian-Devonian, while crown coleoids had origins in the latest Palaeozoic. While the deep-sea vampire squid and dumbo octopuses have ancient origins extending to the Early Mesozoic Era, 242 ± 38 Ma, incirrate octopuses and the decabrachian coleoids (10-armed squid) diversified in the Jurassic Period. These divergence estimates highlight the modern diversity of coleoid cephalopods emerging in the Mesozoic Marine Revolution, a period that also witnessed the radiation of most ray-finned fish groups in addition to several other marine vertebrates. This suggests that that the origin of modern cephalopod biodiversity was contingent on ecological competition with marine vertebrates.

Uncertain-tree: discriminating among competing approaches to the phylogenetic analysis of phenotype data.

Morphological data provide the only means of classifying the majority of life's history, but the choice between competing phylogenetic methods for the analysis of morphology is unclear. Traditionally, parsimony methods have been favoured but recent studies have shown that these approaches are less accurate than the Bayesian implementation of the Mk model. Here we expand on these findings in several ways: we assess the impact of tree shape and maximum-likelihood estimation using the Mk model, as well as analysing data composed of both binary and multistate characters. We find that all methods struggle to correctly resolve deep clades within asymmetric trees, and when analysing small character matrices. The Bayesian Mk model is the most accurate method for estimating topology, but with lower resolution than other methods. Equal weights parsimony is more accurate than implied weights parsimony, and maximum-likelihood estimation using the Mk model is the least accurate method. We conclude that the Bayesian implementation of the Mk model should be the default method for phylogenetic estimation from phenotype datasets, and we explore the implications of our simulations in reanalysing several empirical morphological character matrices. A consequence of our finding is that high levels of resolution or the ability to classify species or groups with much confidence should not be expected when using small datasets. It is now necessary to depart from the traditional parsimony paradigms of constructing character matrices, towards datasets constructed explicitly for Bayesian methods.

A molecular palaeobiological exploration of arthropod terrestrialization.

Understanding animal terrestrialization, the process through which animals colonized the land, is crucial to clarify extant biodiversity and biological adaptation. Arthropoda (insects, spiders, centipedes and their allies) represent the largest majority of terrestrial biodiversity. Here we implemented a molecular palaeobiological approach, merging molecular and fossil evidence, to elucidate the deepest history of the terrestrial arthropods. We focused on the three independent, Palaeozoic arthropod terrestrialization events (those of Myriapoda, Hexapoda and Arachnida) and showed that a marine route to the colonization of land is the most likely scenario. Molecular clock analyses confirmed an origin for the three terrestrial lineages bracketed between the Cambrian and the Silurian. While molecular divergence times for Arachnida are consistent with the fossil record, Myriapoda are inferred to have colonized land earlier, substantially predating trace or body fossil evidence. An estimated origin of myriapods by the Early Cambrian precedes the appearance of embryophytes and perhaps even terrestrial fungi, raising the possibility that terrestrialization had independent origins in crown-group myriapod lineages, consistent with morphological arguments for convergence in tracheal systems.This article is part of the themed issue 'Dating species divergences using rocks and clocks'.

Bayesian methods outperform parsimony but at the expense of precision in the estimation of phylogeny from discrete morphological data.

Different analytical methods can yield competing interpretations of evolutionary history and, currently, there is no definitive method for phylogenetic reconstruction using morphological data. Parsimony has been the primary method for analysing morphological data, but there has been a resurgence of interest in the likelihood-based Mk-model. Here, we test the performance of the Bayesian implementation of the Mk-model relative to both equal and implied-weight implementations of parsimony. Using simulated morphological data, we demonstrate that the Mk-model outperforms equal-weights parsimony in terms of topological accuracy, and implied-weights performs the most poorly. However, the Mk-model produces phylogenies that have less resolution than parsimony methods. This difference in the accuracy and precision of parsimony and Bayesian approaches to topology estimation needs to be considered when selecting a method for phylogeny reconstruction.