Archival mitogenomes identify invasion by the Batrachochytrium dendrobatidis CAPE lineage caused an African amphibian extinction in the wild.

Outbreaks of emerging infectious diseases are influenced by local biotic and abiotic factors, with host declines occurring when conditions favour the pathogen. Deterioration in the population of the micro-endemic Tanzanian Kihansi spray toad (Nectophrynoides asperginis) occurred after the construction of a hydropower dam, implicating habitat modification in this species decline. Population recovery followed habitat augmentation; however, a subsequent outbreak of chytridiomycosis caused by Batrachochytrium dendrobatidis (Bd) led to the spray toad's extinction in the wild. We show using spatiotemporal surveillance and mitogenome assembly of Bd from archived toad mortalities that the outbreak was caused by invasion of the BdCAPE lineage and not the panzootic lineage BdGPL. Molecular dating reveals an emergence of BdCAPE across southern Africa overlapping with the timing of the spray toad's extinction. That our post-outbreak surveillance of co-occurring amphibian species in the Udzungwa Mountains shows widespread infection by BdCAPE yet no signs of ill-health or decline suggests these other species can tolerate Bd when environments are stable. We conclude that, despite transient success in mitigating the impact caused by dams' construction, invasion by BdCAPE caused the ultimate die-off that led to the extinction of the Kihansi spray toad.

Avian diversity and function across the world's most populous cities.

Understanding the composition of urban wildlife communities is crucial to promote biodiversity, ecosystem function and links between nature and people. Using crowdsourced data from over five million eBird checklists, we examined the influence of urban characteristics on avian richness and function at 8443 sites within and across 137 global cities. Under half of the species from regional pools were recorded in cities, and we found a significant phylogenetic signal for urban tolerance. Site-level avian richness was positively influenced by the extent of open forest, cultivation and wetlands and avian functional diversity by wetlands. Functional diversity co-declined with richness, but groups including granivores and aquatic birds occurred even at species-poor sites. Cities in arid areas held a higher percentage of regional species richness. Our results indicate commonalities in the influence of habitat on richness and function, as well as lower niche availability, and phylogenetic diversity across the world's cities.

Real-time symptom reporting during elective intracranial pressure monitoring using an interactive handset.

BACKGROUND: Determining whether symptoms are related to abnormal intracranial pressure (ICP) may prove challenging in some cases. We evaluated the utility of an in-house designed interactive handset which allows the real-time recording of symptoms during ICP monitoring. METHODS: Adult patients undergoing elective continuous ICP monitoring using the device to investigate symptoms between November 2013 and June 2015 were included in this retrospective observational cohort study. The device allowed the following symptoms to be recorded: mild, moderate and severe headache, visual disturbance and nausea. The corresponding ICP and ICP trend were also recorded. RESULTS: Twenty seven patients underwent 29 episodes of ICP monitoring, reporting 383 symptoms (mild 18%, moderate 39%, severe 20% headaches, visual disturbance 15% and nausea 8%) over a median period of 48 hours (IQR 12). The median number of symptoms reported during each episode was 11 (IQR 11). The mean ICP associated with a symptom episode was 7mmHg (Range -10 to 45). Mild, moderate and severe headache complaints were associated with mean ICPs of 5 (-9 to 26), 6 (-10 to 35) and 14 (-10 to 45) mmHg respectively. The majority of complaints (68%) were reported during instances of normal ICP. Following monitoring, non-operative management was employed on 21 occasions (72%) including valve pressure adjustment on two occasions whilst surgical intervention was required on eight occasions (28%; two surgeries for under-drainage and six for over-drainage). CONCLUSIONS: The device allows the clinician to accurately match a patient's symptoms with ICP to facilitate management decisions. In most instances, symptoms did not closely correlate with an abnormal ICP. By automating and standardising the collection of symptom data, this device may serve as an efficient adjunct when investigating patients with complex hydrocephalus.

Science-driven management of protected areas: a Philippine case study.

The lack of scientific baseline information hinders appropriate design and management of protected areas. To illustrate the value of science to management, we consider five scenarios for the 202.0 km² Puerto Princesa Subterranean River National Park, Philippines: (1) closure to human activities, (2) and (3) two levels of increase in unplanned human activities, (4) creation of a forest corridor and (5) additional allocation of land for permanent or shifting agriculture. We then use habitat-specific bird density estimates to simulate the net effect of each scenario on 18 focal bird populations. Closure has significant benefits-populations of five species are predicted to increase by >50 % and nine by >25 %, but two secondary forest flycatchers, including the endemic and 'Vulnerable' Palawan flycatcher, decline dramatically, while the creation of a 4.0 km² forest corridor yields average increases across species of 2 ± 4 % (SD). In contrast, heavier unplanned park usage produces declines in all but a few species, while the negative effects of an extra 2.0 km² of shifting cultivation are 3-5 times higher than for a similar area of permanent agriculture and affect species whose densities are highest in primary habitats. Relatively small changes within the park, especially those associated with agricultural expansion, has serious predicted implications for local bird populations. Our models do not take into account the full complexities of bird ecology at a site, but they do provide park managers with an evidence base from which to make better decisions relating to biodiversity conservation obligations which their parks are intended to meet.

The anatomy of population change in a black grouse population 1992-2008.

We interrogate an 18-year-long dataset containing counts of displaying male black grouse Tetrao tetrix and incidental counts of females within an 800-km(2) region of Perthshire, Scotland. We examine the trends in the population and investigate how different components of the population might act as signposts of different stages of overall population change. We found statistical evidence for a decline in black grouse numbers between 1992 and 2000, and then a recovery from 2002 to 2008, but little evidence for a link between population change and weather during the decline phase. There was some evidence for a positive relationship between male and female counts. The two main components of male population size, lek size and lek frequency followed the overall population trend while it was increasing, but during the earlier decline, the two became uncoupled, to expose a complex structure within the data. During the decline, when black grouse numbers were approaching their minimum, mean lek size was actually increasing. Small leks lost proportionally more birds than did large leks, and lek longevity was positively correlated with lek size, indicating that maintenance of large leks is crucial in buffering the population against serious declines. During the decline, the spatial arrangement of leks changed, with remnant leks showing tight clustering at larger spatial scales, before expanding out to fill the large areas of unoccupied landscape during the population increase. We discuss these findings in terms of species monitoring and suggest that counts of young males may add much useful demographic information with little extra effort.

Taxonomic and Geographic Bias in Conservation Biology Research: A Systematic Review of Wildfowl Demography Studies.

Demographic data are important to wildlife managers to gauge population health, to allow populations to be utilised sustainably, and to inform conservation efforts. We analysed published demographic data on the world's wildfowl to examine taxonomic and geographic biases in study, and to identify gaps in knowledge. Wildfowl (order: Anseriformes) are a comparatively well studied bird group which includes 169 species of duck, goose and swan. In all, 1,586 wildfowl research papers published between 1911 and 2010 were found using Web of Knowledge (WoK) and Google Scholar. Over half of the research output involved just 15 species from seven genera. Research output was strongly biased towards 'high income' countries, common wildfowl species, and measures of productivity, rather than survival and movement patterns. There were significantly fewer demographic data for the world's 31 threatened wildfowl species than for non-threatened species. Since 1994, the volume of demographic work on threatened species has increased more than for non-threatened species, but still makes up only 2.7% of total research output. As an aid to research prioritisation, a metric was created to reflect demographic knowledge gaps for each species related to research output for the species, its threat status, and availability of potentially useful surrogate data from congeneric species. According to the metric, the 25 highest priority species include thirteen threatened taxa and nine species each from Asia and South America, and six from Africa.

Philippine protected areas are not meeting the biodiversity coverage and management effectiveness requirements of Aichi Target 11.

Aichi Target 11 of the Convention on Biological Diversity urges, inter alia, that nations protect at least 17 % of their land, and that protection is effective and targets areas of importance for biodiversity. Five years before reporting on Aichi targets is due, we assessed the Philippines' current protected area system for biodiversity coverage, appropriateness of management regimes and capacity to deliver protection. Although protected estate already covers 11 % of the Philippines' land area, 64 % of its key biodiversity areas (KBAs) remain unprotected. Few protected areas have appropriate management and governance infrastructures, funding streams, management plans and capacity, and a serious mismatch exists between protected area land zonation regimes and conservation needs of key species. For the Philippines to meet the biodiversity coverage and management effectiveness elements of Aichi Target 11, protected area and KBA boundaries should be aligned, management systems reformed to pursue biodiversity-led targets and effective management capacity created.

Scenario-Led Habitat Modelling of Land Use Change Impacts on Key Species.

Accurate predictions of the impacts of future land use change on species of conservation concern can help to inform policy-makers and improve conservation measures. If predictions are spatially explicit, predicted consequences of likely land use changes could be accessible to land managers at a scale relevant to their working landscape. We introduce a method, based on open source software, which integrates habitat suitability modelling with scenario-building, and illustrate its use by investigating the effects of alternative land use change scenarios on landscape suitability for black grouse Tetrao tetrix. Expert opinion was used to construct five near-future (twenty years) scenarios for the 800 km2 study site in upland Scotland. For each scenario, the cover of different land use types was altered by 5-30% from 20 random starting locations and changes in habitat suitability assessed by projecting a MaxEnt suitability model onto each simulated landscape. A scenario converting grazed land to moorland and open forestry was the most beneficial for black grouse, and 'increased grazing' (the opposite conversion) the most detrimental. Positioning of new landscape blocks was shown to be important in some situations. Increasing the area of open-canopy forestry caused a proportional decrease in suitability, but suitability gains for the 'reduced grazing' scenario were nonlinear. 'Scenario-led' landscape simulation models can be applied in assessments of the impacts of land use change both on individual species and also on diversity and community measures, or ecosystem services. A next step would be to include landscape configuration more explicitly in the simulation models, both to make them more realistic, and to examine the effects of habitat placement more thoroughly. In this example, the recommended policy would be incentives on grazing reduction to benefit black grouse.