Complexity of avian evolution revealed by family-level genomes.

Despite tremendous efforts in the past decades, relationships among main avian lineages remain heavily debated without a clear resolution. Discrepancies have been attributed to diversity of species sampled, phylogenetic method and the choice of genomic regions1-3. Here we address these issues by analysing the genomes of 363 bird species4 (218 taxonomic families, 92% of total). Using intergenic regions and coalescent methods, we present a well-supported tree but also a marked degree of discordance. The tree confirms that Neoaves experienced rapid radiation at or near the Cretaceous-Palaeogene boundary. Sufficient loci rather than extensive taxon sampling were more effective in resolving difficult nodes. Remaining recalcitrant nodes involve species that are a challenge to model due to either extreme DNA composition, variable substitution rates, incomplete lineage sorting or complex evolutionary events such as ancient hybridization. Assessment of the effects of different genomic partitions showed high heterogeneity across the genome. We discovered sharp increases in effective population size, substitution rates and relative brain size following the Cretaceous-Palaeogene extinction event, supporting the hypothesis that emerging ecological opportunities catalysed the diversification of modern birds. The resulting phylogenetic estimate offers fresh insights into the rapid radiation of modern birds and provides a taxon-rich backbone tree for future comparative studies.

Polypharmacy during pregnancy and associated risk factors: a retrospective analysis of 577 medication exposures among 1.5 million pregnancies in the UK, 2000-2019.

BACKGROUND: The number of medications prescribed during pregnancy has increased over the past few decades. Few studies have described the prevalence of multiple medication use among pregnant women. This study aims to describe the overall prevalence over the last two decades among all pregnant women and those with multimorbidity and to identify risk factors for polypharmacy in pregnancy. METHODS: A retrospective cohort study was conducted between 2000 and 2019 using the Clinical Practice Research Datalink (CPRD) pregnancy register. Prescription records for 577 medication categories were obtained. Prevalence estimates for polypharmacy (ranging from 2+ to 11+ medications) were presented along with the medications commonly prescribed individually and in pairs during the first trimester and the entire pregnancy period. Logistic regression models were performed to identify risk factors for polypharmacy. RESULTS: During the first trimester (812,354 pregnancies), the prevalence of polypharmacy ranged from 24.6% (2+ medications) to 0.1% (11+ medications). During the entire pregnancy period (774,247 pregnancies), the prevalence ranged from 58.7 to 1.4%. Broad-spectrum penicillin (6.6%), compound analgesics (4.5%) and treatment of candidiasis (4.3%) were commonly prescribed. Pairs of medication prescribed to manage different long-term conditions commonly included selective beta 2 agonists or selective serotonin re-uptake inhibitors (SSRIs). Risk factors for being prescribed 2+ medications during the first trimester of pregnancy include being overweight or obese [aOR: 1.16 (1.14-1.18) and 1.55 (1.53-1.57)], belonging to an ethnic minority group [aOR: 2.40 (2.33-2.47), 1.71 (1.65-1.76), 1.41 (1.35-1.47) and 1.39 (1.30-1.49) among women from South Asian, Black, other and mixed ethnicities compared to white women] and smoking or previously smoking [aOR: 1.19 (1.18-1.20) and 1.05 (1.03-1.06)]. Higher and lower age, higher gravidity, increasing number of comorbidities and increasing level of deprivation were also associated with increased odds of polypharmacy. CONCLUSIONS: The prevalence of polypharmacy during pregnancy has increased over the past two decades and is particularly high in younger and older women; women with high BMI, smokers and ex-smokers; and women with multimorbidity, higher gravidity and higher levels of deprivation. Well-conducted pharmaco-epidemiological research is needed to understand the effects of multiple medication use on the developing foetus.

COVID-19 vaccination in pregnancy: the impact of multimorbidity and smoking status on vaccine hesitancy, a cohort study of 25,111 women in Wales, UK.

BACKGROUND: Multimorbidity, smoking status, and pregnancy are identified as three risk factors associated with more severe outcomes following a SARS-CoV-2 infection, thus vaccination uptake is crucial for pregnant women living with multimorbidity and a history of smoking. This study aimed to examine the impact of multimorbidity, smoking status, and demographics (age, ethnic group, area of deprivation) on vaccine hesitancy among pregnant women in Wales using electronic health records (EHR) linkage. METHODS: This cohort study utilised routinely collected, individual-level, anonymised population-scale linked data within the Secure Anonymised Information Linkage (SAIL) Databank. Pregnant women were identified from 13th April 2021 to 31st December 2021. Survival analysis was employed to examine and compare the length of time to vaccination uptake in pregnancy by considering multimorbidity, smoking status, as well as depression, diabetes, asthma, and cardiovascular conditions independently. The study also assessed the variation in uptake by multimorbidity, smoking status, and demographics, both jointly and separately for the independent conditions, using hazard ratios (HR) derived from the Cox regression model. RESULTS: Within the population cohort, 8,203 (32.7%) received at least one dose of the COVID-19 vaccine during pregnancy, with 8,572 (34.1%) remaining unvaccinated throughout the follow-up period, and 8,336 (33.2%) receiving the vaccine postpartum. Women aged 30 years or older were more likely to have the vaccine in pregnancy. Those who had depression were slightly but significantly more likely to have the vaccine compared to those without depression (HR = 1.08, 95% CI 1.03 to 1.14, p = 0.002). Women living with multimorbidity were 1.12 times more likely to have the vaccine compared to those living without multimorbidity (HR = 1.12, 95% CI 1.04 to 1.19, p = 0.001). Vaccine uptakes were significantly lower among both current smokers and former smokers compared to never smokers (HR = 0.87, 95% CI 0.81 to 0.94, p < 0.001 and HR = 0.92, 95% CI 0.85 to 0.98, p = 0.015 respectively). Uptake was also lower among those living in the most deprived areas compared to those living in the most affluent areas (HR = 0.89, 95% CI 0.83 to 0.96, p = 0.002). CONCLUSION: Younger women, living without multimorbidity, current and former smokers, and those living in the more deprived areas are less likely to have the vaccine, thus, a targeted approach to vaccinations may be required for these groups. Pregnant individuals living with multimorbidity exhibit a slight but statistically significant reduction in vaccine hesitancy towards COVID-19 during pregnancy.

Biodiversity cradles and museums segregating within hotspots of endemism.

The immense concentrations of vertebrate species in tropical mountains remain a prominent but unexplained pattern in biogeography. A long-standing hypothesis suggests that montane biodiversity hotspots result from endemic species aggregating within ecologically stable localities. Here, the persistence of ancient lineages coincides with frequent speciation events, making such areas both 'cradles' (where new species arise) and 'museums' (where old species survive). Although this hypothesis refers to processes operating at the scale of valleys, it remains supported primarily by patterns generated from coarse-scale distribution data. Using high-resolution occurrence and phylogenetic data on Andean hummingbirds, we find that old and young endemic species are not spatially aggregated. The young endemic species tend to have non-overlapping distributions scattered along the Andean treeline, a long and narrow habitat where populations easily become fragmented. By contrast, the old endemic species have more aggregated distributions, but mainly within pockets of cloud forests at lower elevations than the young endemic species. These findings contradict the premise that biogeographical cradles and museums should overlap in valley systems where pockets of stable climate persist through periods of climate change. Instead, Andean biodiversity hotspots may derive from large-scale fluctuating climate complexity in conjunction with local-scale variability in available area and habitat connectivity.

Shielding reduced incidence of COVID-19 in patients with inflammatory arthritis but vulnerability is associated with increased mortality.

OBJECTIVES: Investigate whether individuals with inflammatory arthritis (IA), their treatments and shielding status affect the risk of adverse outcomes from COVID-19 for the entire population of Wales, UK. METHODS: Retrospective, population-based cohort study using linked, anonymized electronic health data from SAIL Databank, including primary/secondary care, rheumatology, Office for National Statistics Mortality and COVID-19 laboratory data. Individuals aged 18 years and over testing positive for COVID-19 between March 2020 and May 2021 with READ Codes present for rheumatoid arthritis, psoriatic arthritis and ankylosing spondylitis formed the study cases. RESULTS: A total of 1966 people with IA and 166 602 without tested positive for COVID-19. The incidence rate was 3.5% (1966/56 914) in IA, vs 6% in the general population (166 602/2 760 442), (difference: 2.5%, 95% CI: 2.4%, 2.7%, P ≤0.001). In an adjusted Cox proportional hazard model, IA was not associated with higher mortality (HR: 0.56, 95% CI: 0.18, 1.64, P=0.286). Significant risk factors included shielding (HR: 1.52, 95% CI: 1.40, 1.64, P ≤0.001), hospitalization for previous infections (HR: 1.20, 95% CI: 1.12, 1.28, P ≤0.001), hospitalizations one year pre-pandemic (HR: 1.34, 95% CI: 1.25, 1.44, P ≤0.001) and glucocorticoid use (HR: 1.17, 95% CI: 1.09, 1.25, P ≤0.001). CONCLUSIONS: Individuals with IA had a lower incidence of COVID-19, probably due to shielding. IA was not associated with increased mortality following COVID-19 infection; being vulnerable (shielded), comorbidities and other factors were associated with increased risk. These key risk factors can identify individuals with IA at greater risk from COVID-19 and advised to shield during high community prevalence.

COVID-19 vaccination in pregnancy: views and vaccination uptake rates in pregnancy, a mixed methods analysis from SAIL and the Born-In-Wales Birth Cohort.

BACKGROUND: Vaccine hesitancy amongst pregnant women has been found to be a concern during past epidemics. This study aimed to (1) estimate COVID-19 vaccination rates among pregnant women in Wales and their association with age, ethnicity, and area of deprivation, using electronic health record (EHR) data linkage, and (2) explore pregnant women's views on receiving the COVID-19 vaccine during pregnancy using data from a survey recruiting via social media (Facebook, Twitter), through midwives, and posters in hospitals (Born-In-Wales Cohort). METHODS: This was a mixed-methods study utilising routinely collected linked data from the Secure Anonymised Information Linkage (SAIL) Databank (Objective 1) and the Born-In-Wales Birth Cohort participants (Objective 2). Pregnant women were identified from 13th April 2021 to 31st December 2021. Survival analysis was utilised to examine and compare the length of time to vaccination uptake in pregnancy, and variation in uptake by; age, ethnic group, and deprivation area was examined using hazard ratios (HR) from Cox regression. Survey respondents were women who had a baby during the COVID-19 pandemic or were pregnant between 1st November 2021 and 24th March 2022 and participating in Born-In-Wales. Codebook thematic analysis was used to generate themes from an open-ended question on the survey. RESULTS: Population-level data linkage (objective 1): Within the population cohort, 8203 (32.7%) received at least one dose of the COVID-19 vaccine during pregnancy, 8572 (34.1%) remained unvaccinated throughout the follow-up period, and 8336 (33.2%) received the vaccine postpartum. Younger women (< 30 years) were less likely to have the vaccine, and those living in areas of high deprivation were also less likely to have the vaccine (HR = 0.88, 95% CI 0.82 to 0.95). Asian and Other ethnic groups were 1.12 and 1.18 times more likely to have the vaccine in pregnancy compared with White women (HR = 1.12, 95% CI 1.00 to 1.25) and (HR = 1.18, 95% CI 1.03 to 1.37) respectively. Survey responses (objective 2): 207 (69%) of participants stated that they would be happy to have the vaccine during pregnancy. The remaining 94 (31%) indicated they would not have the vaccine during pregnancy. Reasons for having the vaccine included protecting self and baby, perceived risk level, and receipt of sufficient evidence and advice. Reasons for vaccine refusal included lack of research about long-term outcomes for the baby, anxiety about vaccines, inconsistent advice/information, and preference to wait until after the pregnancy. CONCLUSION: Potentially only 1 in 3 pregnant women would have the COVID-19 vaccine during pregnancy, even though 2 in 3 reported they would have the vaccination, thus it is critical to develop tailored strategies to increase its acceptance rate and decrease vaccine hesitancy. A targeted approach to vaccinations may be required for groups such as younger people and those living in higher deprivation areas.

Epidemiology of pre-existing multimorbidity in pregnant women in the UK in 2018: a population-based cross-sectional study.

BACKGROUND: Although maternal death is rare in the United Kingdom, 90% of these women had multiple health/social problems. This study aims to estimate the prevalence of pre-existing multimorbidity (two or more long-term physical or mental health conditions) in pregnant women in the United Kingdom (England, Northern Ireland, Wales and Scotland). STUDY DESIGN: Pregnant women aged 15-49 years with a conception date 1/1/2018 to 31/12/2018 were included in this population-based cross-sectional study, using routine healthcare datasets from primary care: Clinical Practice Research Datalink (CPRD, United Kingdom, n = 37,641) and Secure Anonymized Information Linkage databank (SAIL, Wales, n = 27,782), and secondary care: Scottish Morbidity Records with linked community prescribing data (SMR, Tayside and Fife, n = 6099). Pre-existing multimorbidity preconception was defined from 79 long-term health conditions prioritised through a workshop with patient representatives and clinicians. RESULTS: The prevalence of multimorbidity was 44.2% (95% CI 43.7-44.7%), 46.2% (45.6-46.8%) and 19.8% (18.8-20.8%) in CPRD, SAIL and SMR respectively. When limited to health conditions that were active in the year before pregnancy, the prevalence of multimorbidity was still high (24.2% [23.8-24.6%], 23.5% [23.0-24.0%] and 17.0% [16.0 to 17.9%] in the respective datasets). Mental health conditions were highly prevalent and involved 70% of multimorbidity CPRD: multimorbidity with ≥one mental health condition/s 31.3% [30.8-31.8%]). After adjusting for age, ethnicity, gravidity, index of multiple deprivation, body mass index and smoking, logistic regression showed that pregnant women with multimorbidity were more likely to be older (CPRD England, adjusted OR 1.81 [95% CI 1.04-3.17] 45-49 years vs 15-19 years), multigravid (1.68 [1.50-1.89] gravidity ≥ five vs one), have raised body mass index (1.59 [1.44-1.76], body mass index 30+ vs body mass index 18.5-24.9) and smoked preconception (1.61 [1.46-1.77) vs non-smoker). CONCLUSION: Multimorbidity is prevalent in pregnant women in the United Kingdom, they are more likely to be older, multigravid, have raised body mass index and smoked preconception. Secondary care and community prescribing dataset may only capture the severe spectrum of health conditions. Research is needed urgently to quantify the consequences of maternal multimorbidity for both mothers and children.

A qualitative evaluation of Southwark Council's public health response to mitigating the mental health impact of the 2017 London bridge and borough market terror attack.

BACKGROUND: Over recent years there have been several major terror attacks in cities across Europe. These attacks result in deaths, physical injuries, and pose long-term threats to mental health and wellbeing of large populations. Although psychologists have completed important work on mental health responses to disaster exposure including terrorist attacks, the mental health impacts of such attacks have been comparatively less examined in academic literature than the acute health response to physical injuries. This paper reflects on Southwark Council's pioneering public mental health response to the June 2017 terror attack at London Bridge and Borough Market. It aims to explore perceptions of the mental health impact of the incident by those living and working in the borough. METHODS: A rapid qualitative evaluation informed by the logic underpinning Southwark Council's response was conducted. Seven formative interviews were undertaken with individuals involved in the response planning and/or delivery, enabling the evaluation team to establish the response's theoretical basis. Subsequently, nineteen semi-structured interviews with consenting Council employees, residents, business owners, and workers from the Borough were conducted to understand perceived mental health impacts of the attack and the success of the Council response. Thematic analysis of transcribed interviews was undertaken to evaluate the extent to which the response was implemented successfully. RESULTS: Participants reported feeling the attack had a wide-reaching negative impact on the mental health of residents, those working in the borough and visitors who witnessed the attack. Delivering the response was a challenge and response visibility within the community was limited. Participants suggested a comprehensive systematic approach to health needs assessment informed by knowledge and relationships of key Council workers and community stakeholders is imperative when responding to terrorist incidents. Improved communication and working relationships between statutory organisations and community stakeholders would ensure community groups are better supported. Prioritising mental health needs of terror attack responders to mitigate persisting negative impacts was highlighted. CONCLUSIONS: This article highlights a potential public health approach and need for developing robust practical guidance in the aftermath of terror attacks. This approach has already influenced the response to the Christchurch mosque shooting in 2019.

E-prescribing and access to prescription medicines during lockdown: experience of patients in Aotearoa/New Zealand.

BACKGROUND: Health services internationally have been compelled to change their methods of service delivery in response to the global COVID-19 pandemic, to mitigate the spread of infection amongst health professionals and patients. In Aotearoa/New Zealand, widespread electronic delivery of prescriptions (e-prescribing) was enabled. The aim of the research was to explore patients' experiences of how lockdown, changes to prescribing and the interface between general practices and community pharmacy affected access to prescription medications. METHOD: The research employed a mixed-method approach. This included an online survey (n = 1,010) and in-depth interviews with a subset of survey respondents (n = 38) during the first COVID-19 lockdown (March-May 2020). Respondents were recruited through a snowballing approach, starting with social media and email list contacts of the research team. In keeping with the approach, descriptive statistics of survey data and thematic analysis of qualitative interview and open-ended questions in survey data were combined. RESULTS: For most respondents who received a prescription during lockdown, this was sent directly to the pharmacy. Most people picked up their medication from the pharmacy; home delivery of medication was rare (4%). Survey and interview respondents wanted e-prescribing to continue post-lockdown and described where things worked well and where they encountered delays in the process of acquiring prescription medication. CONCLUSIONS: E-prescribing has the potential to improve access to prescription medication and is convenient for patients. The increase in e-prescribing during lockdown highlighted how the system could be improved, through better feedback about errors, more consistency across practices and pharmacies, more proactive communication with patients, and equitable prescribing costs.

The association between morphological and ecological characters across a global passerine radiation.

Strong relationships between morphological and ecological characters are commonly predicted to reflect the association between form and function, with this hypothesis being well supported in restricted taxonomic and geographical contexts. Conversely, among broader sets of species, ecological variables have been shown to have limited power to explain morphological variation. To understand these apparent discrepancies, for a large and globally distributed passerine radiation, we test whether (a) the character states of four ecological variables (foraging mode, diet, strata and habitat) have different morphological optima, (b) ecological variables explain substantial variance in morphology and (c) ecological character states can be accurately predicted from morphology. We collected 10 linear morphological measurements for 782 species of corvoid passerines, and assessed (a) the fit of models of continuous trait evolution with different morphological optima for each ecological character state, (b) variation in morphological traits among ecological character states using phylogenetically corrected regressions and (c) the accuracy of morphological traits in predicting species-level membership of ecological character states using linear discriminant analysis (LDA). Models of morphological evolution with different ecological optima were well supported across numerous morphological axes, corresponding with significant differences in trait distributions among ecological character states. LDA also showed that membership of the ecological categories can be predicted with relatively high accuracy by morphology. In contrast to these findings, ecological variables explain limited amounts of variation in morphological traits. For a global radiation of passerine birds, we confirm that the generation of morphological variation is generally consistent with ecological selection pressures, but that ecological characters are of limited utility in explaining morphological differences among species. Although selection towards different optima means that membership of ecological character states tend to be well predicted by morphology, the overall morphospace of individual ecological character states tend to be broad, implying that morphology can evolve in multiple ways in response to similar selection pressures. Extensive variation in morphological adaptations among similar ecological strategies is likely to be a widespread phenomenon across the tree of life.

Telehealth consultations in general practice during a pandemic lockdown: survey and interviews on patient experiences and preferences.

BACKGROUND: During the first COVID-19 pandemic 'lockdown' in Aotearoa/New Zealand (March-May 2020, in which strict 'stay at home' measures were introduced), general practices were advised to use telephone and video consultations (telehealth) wherever possible instead of the usual in-person visits. This was a sudden change for most practices and patients. This research aimed to explore how patients accessed general practice during lockdown and evaluate their experiences with telehealth, to inform how telehealth could be most effectively used in the future. METHODS: Using a mixed-method approach, we undertook an online survey and in-depth interviews with adults (> 18 years) who had contact with practices during lockdown, recruited through social media and email lists. We present descriptive statistics from the survey data (n = 1010) and qualitative analysis of interview data (n = 38) and open-ended survey questions, using a framework of access to health care, from the patient's perspective. RESULTS: In general, patients reported high satisfaction with telehealth in general practice during lockdown. Telehealth was convenient and allowed patients to safely access health care without having to weigh-up the fear of COVID-19 infection against the need to be seen. Telehealth worked best for routine and familiar health issues and when rapport was established between patients and clinicians. This was easier with a pre-existing clinical relationship, but not impossible without one. Telehealth was less suitable when a physical examination was needed, when the diagnosis was unknown or for patients who had a strong preference to be seen in-person. CONCLUSIONS: Even in this disruptive lockdown period, that prompted an unexpected and rapid implementation of telehealth services in general practices, most patients had positive experiences with telehealth. In the future, patients want the choice of consultation type to match their needs, circumstances, and preferences. Technological issues and funding barriers may need to be addressed, and clear communication for both patients and clinicians is needed about key aspects of telehealth (e.g. cost, appropriateness, privacy). Maintaining telehealth as an option post-lockdown has the potential to increase timely and safe access to primary health care for many patients.

Near-complete phylogeny and taxonomic revision of the world's babblers (Aves: Passeriformes).

The babblers are a diverse group of passerine birds comprising 452 species. The group was long regarded as a "scrap basket" in taxonomic classification schemes. Although several studies have assessed the phylogenetic relationships for subsets of babblers during the past two decades, a comprehensive phylogeny of this group has been lacking. In this study, we used five mitochondrial and seven nuclear loci to generate a dated phylogeny for babblers. This phylogeny includes 402 species (ca. 89% of the overall clade) from 75 genera (97%) and all five currently recognized families, providing a robust basis for taxonomic revision. Our phylogeny supports seven major clades and reveals several non-monophyletic genera. Divergence time estimates indicate that the seven major clades diverged around the same time (18-20 million years ago, Ma) in the early Miocene. We use the phylogeny in a consistent way to propose a new taxonomy, with seven families and 64 genera of babblers, and a new linear sequence of names.

Populist politics and vaccine hesitancy in Western Europe: an analysis of national-level data.

BACKGROUND: Parents' reluctance to vaccinate their children undermines the effectiveness of vaccination programmes in Western Europe. There is anecdotal evidence suggesting a connection between the rise of political populism and vaccine hesitancy. METHODS: This paper analyses national-level data to examine the link between political populism and vaccine hesitancy in Western Europe. Political populism is operationalised as the percentage of people in a country who voted for populist parties in the 2014 European Parliament elections. Vaccine hesitancy is operationalised as the percentage of people in a country who believe that vaccines are not important, safe and effective according to data from the Vaccine Confidence Project (2015). RESULTS: There is a highly significant positive association between the percentage of people in a country who voted for populist parties and who believe that vaccines are not important (R = 0.7923, P = 0.007) and effective (R = 0.7222, P = 0.0035). The percentage of people who think vaccines are unsafe just misses being significant at the 5% level (R = 0.5027, P = 0.0669). CONCLUSIONS: Vaccine hesitancy and political populism are driven by similar dynamics: a profound distrust in elites and experts. It is necessary for public health scholars and actors to work to build trust with parents that are reluctant to vaccinate their children, but there are limits to this strategy. The more general popular distrust of elites and experts which informs vaccine hesitancy will be difficult to resolve unless its underlying causes-the political disenfranchisement and economic marginalisation of large parts of the Western European population-are also addressed.

Expansion in geographical and morphological space drives continued lineage diversification in a global passerine radiation.

Why diversification rates vary so extensively across the tree of life remains an important yet unresolved issue in biology. Two prominent and potentially independent factors proposed to explain these trends reflect the capacity of lineages to expand into new areas of (i) geographical or (ii) ecological space. Here, we present the first global assessment of how diversification rates vary as a consequence of geographical and ecological expansion, studying these trends among 15 speciose passerine families (together approximately 750 species) using phylogenetic path analysis. We find that relative slowdowns in diversification rates characterize families that have accumulated large numbers of co-occurring species (at the 1° scale) within restricted geographical areas. Conversely, more constant diversification through time is prevalent among families in which species show limited range overlap. Relative co-occurrence is itself also a strong predictor of ecological divergence (here approximated by morphological divergence among species); however, once the relationship between co-occurrence and diversification rates have been accounted for, increased ecological divergence is an additional explanatory factor accounting for why some lineages continue to diversify towards the present. We conclude that opportunities for prolonged diversification are predominantly determined by continued geographical range expansion and to a lesser degree by ecological divergence among lineages.

Trait evolution, resource specialization and vulnerability to plant extinctions among Antillean hummingbirds.

Species traits are thought to predict feeding specialization and the vulnerability of a species to extinctions of interaction partners, but the context in which a species evolved and currently inhabits may also matter. Notably, the predictive power of traits may require that traits evolved to fit interaction partners. Furthermore, local abiotic and biotic conditions may be important. On islands, for instance, specialized and vulnerable species are predicted to be found mainly in mountains, whereas species in lowlands should be generalized and less vulnerable. We evaluated these predictions for hummingbirds and their nectar-food plants on Antillean islands. Our results suggest that the rates of hummingbird trait divergence were higher among ancestral mainland forms before the colonization of the Antilles. In correspondence with the limited trait evolution that occurred within the Antilles, local abiotic and biotic conditions-not species traits-correlate with hummingbird resource specialization and the vulnerability of hummingbirds to extinctions of their floral resources. Specifically, hummingbirds were more specialized and vulnerable in conditions with high topographical complexity, high rainfall, low temperatures and high floral resource richness, which characterize the Antillean Mountains. These findings show that resource specialization and species vulnerability to extinctions of interaction partners are highly context-dependent.

School achievement as a predictor of depression and self-harm in adolescence: linked education and health record study.

BACKGROUND: Mental disorders in children and adolescents have an impact on educational attainment. Aims To examine the temporal association between attainment in education and subsequent diagnosis of depression or self-harm in the teenage years. METHOD: General practitioner, hospital and education records of young people in Wales between 1999 and 2014 were linked and analysed using Cox regression. RESULTS: Linked records were available for 652 903 young people and of these 33 498 (5.1%) developed depression and 15 946 (2.4%) self-harmed after the age of 12 but before the age of 20. Young people who developed depression over the study period were more likely to have achieved key stage 1 (age 7 years) but not key stage 2 (age 11) (hazard ratio (HR) = 0.79, 95% CI 0.74-0.84) milestones, indicating that they were declining in academic attainment during primary school. Conversely, those who self-harmed were achieving as well as those who did not self-harm in primary school, but showed a severe decline in their attainment during secondary school (HR = 0.72, 95% CI 0.68-0.78). CONCLUSIONS: Long-term declining educational attainment in primary and secondary school was associated with development of depression in the teenage years. Self-harm was associated with declining educational attainment during secondary school only. Incorporating information on academic decline with other known risk factors for depression/self-harm (for example stressful life events, parental mental health problems) may improve risk profiling methods. Declaration of interest None.

Diverse and Abundant Secondary Metabolism Biosynthetic Gene Clusters in the Genomes of Marine Sponge Derived Streptomyces spp. Isolates.

The genus Streptomyces produces secondary metabolic compounds that are rich in biological activity. Many of these compounds are genetically encoded by large secondary metabolism biosynthetic gene clusters (smBGCs) such as polyketide synthases (PKS) and non-ribosomal peptide synthetases (NRPS) which are modular and can be highly repetitive. Due to the repeats, these gene clusters can be difficult to resolve using short read next generation datasets and are often quite poorly predicted using standard approaches. We have sequenced the genomes of 13 Streptomyces spp. strains isolated from shallow water and deep-sea sponges that display antimicrobial activities against a number of clinically relevant bacterial and yeast species. Draft genomes have been assembled and smBGCs have been identified using the antiSMASH (antibiotics and Secondary Metabolite Analysis Shell) web platform. We have compared the smBGCs amongst strains in the search for novel sequences conferring the potential to produce novel bioactive secondary metabolites. The strains in this study recruit to four distinct clades within the genus Streptomyces. The marine strains host abundant smBGCs which encode polyketides, NRPS, siderophores, bacteriocins and lantipeptides. The deep-sea strains appear to be enriched with gene clusters encoding NRPS. Marine adaptations are evident in the sponge-derived strains which are enriched for genes involved in the biosynthesis and transport of compatible solutes and for heat-shock proteins. Streptomyces spp. from marine environments are a promising source of novel bioactive secondary metabolites as the abundance and diversity of smBGCs show high degrees of novelty. Sponge derived Streptomyces spp. isolates appear to display genomic adaptations to marine living when compared to terrestrial strains.

Development of an algorithm for determining smoking status and behaviour over the life course from UK electronic primary care records.

BACKGROUND: Patients' smoking status is routinely collected by General Practitioners (GP) in UK primary health care. There is an abundance of Read codes pertaining to smoking, including those relating to smoking cessation therapy, prescription, and administration codes, in addition to the more regularly employed smoking status codes. Large databases of primary care data are increasingly used for epidemiological analysis; smoking status is an important covariate in many such analyses. However, the variable definition is rarely documented in the literature. METHODS: The Secure Anonymised Information Linkage (SAIL) databank is a repository for a national collection of person-based anonymised health and socio-economic administrative data in Wales, UK. An exploration of GP smoking status data from the SAIL databank was carried out to explore the range of codes available and how they could be used in the identification of different categories of smokers, ex-smokers and never smokers. An algorithm was developed which addresses inconsistencies and changes in smoking status recording across the life course and compared with recorded smoking status as recorded in the Welsh Health Survey (WHS), 2013 and 2014 at individual level. However, the WHS could not be regarded as a "gold standard" for validation. RESULTS: There were 6836 individuals in the linked dataset. Missing data were more common in GP records (6%) than in WHS (1.1%). Our algorithm assigns ex-smoker status to 34% of never-smokers, and detects 30% more smokers than are declared in the WHS data. When distinguishing between current smokers and non-smokers, the similarity between the WHS and GP data using the nearest date of comparison was κ = 0.78. When temporal conflicts had been accounted for, the similarity was κ = 0.64, showing the importance of addressing conflicts. CONCLUSIONS: We present an algorithm for the identification of a patient's smoking status using GP self-reported data. We have included sufficient details to allow others to replicate this work, thus increasing the standards of documentation within this research area and assessment of smoking status in routine data.