Taxonomy based on science is necessary for global conservation

Peer reviewe

The development and validation of a scoring tool to predict the operative duration of elective laparoscopic cholecystectomy

Background: The ability to accurately predict operative duration has the potential to optimise theatre efficiency and utilisation, thus reducing costs and increasing staff and patient satisfaction. With laparoscopic cholecystectomy being one of the most commonly performed procedures worldwide, a tool to predict operative duration could be extremely beneficial to healthcare organisations. Methods: Data collected from the CholeS study on patients undergoing cholecystectomy in UK and Irish hospitals between 04/2014 and 05/2014 were used to study operative duration. A multivariable binary logistic regression model was produced in order to identify significant independent predictors of long (> 90 min) operations. The resulting model was converted to a risk score, which was subsequently validated on second cohort of patients using ROC curves. Results: After exclusions, data were available for 7227 patients in the derivation (CholeS) cohort. The median operative duration was 60 min (interquartile range 45–85), with 17.7% of operations lasting longer than 90 min. Ten factors were found to be significant independent predictors of operative durations > 90 min, including ASA, age, previous surgical admissions, BMI, gallbladder wall thickness and CBD diameter. A risk score was then produced from these factors, and applied to a cohort of 2405 patients from a tertiary centre for external validation. This returned an area under the ROC curve of 0.708 (SE = 0.013, p  90 min increasing more than eightfold from 5.1 to 41.8% in the extremes of the score. Conclusion: The scoring tool produced in this study was found to be significantly predictive of long operative durations on validation in an external cohort. As such, the tool may have the potential to enable organisations to better organise theatre lists and deliver greater efficiencies in care

Mid-cautleyan (Ashgill Series) trilobites and facies in the English lake distinct

During Zones 2 and 3 of the Cautleyan Stage (Ashgill Series) a marine transgressive sequence of conglomerates, sandstones (Longsleddale Formation), calcareous siltstone (Stile End and High Pike Haw Formations), mudstone (Torver Formation) and interbedded argillaceous limestone and calcareous mudstone (Applethwaite Formation) was deposited in the southern Lake District. Three tribolite associations are recognized within these rocks: a Proetid Association, found in the sandstones and calcareous siltstone; an Illaenid Association in the mudstone of the Torver Formation and at local, restricted horizons within the Applethwaite Formation; a Calymenid Association, found in the interbedded mudstone and limestone. It is suggested that strong causal relationships, both positive and negative, existed between the trilobites and facies type. Absences of particular trilobite groups do not appear, in the main, to be artifacts of sampling and, along with presences and abundances, are considered important to the understanding of the distribution of trilobites and their relationships with the facies type. Antipathetic relationships are noted between Prionocheilus and other calymenids; and between Tretaspis and both proetids and encrinurids. Because the trilobite associations could be recognised in the field prior to statistical analysis, it is possible to compare and contrast quantitative measures which summarize the relationships among localities and taxa. The following measures are calculated from abundances: correspondence, covariance (taxa) or average Euclidean distance squared (localities), and correlation coefficient (taxa) or standardized average Euclidean distance squared (localities). Of these the principal axes of the correspondence matrix separate the three associations much further than the other two measures. Considered as comparisons of taxa, correspondence values may offer a compromise, desirable in quantitative ecology, between emphasis on common taxa (covariance) and on rare taxa (correlation coefficient). When only occurrences are used, the trilobite associations are scattered more broadly and taxa behave more independently. The greater degree of interdependence of taxa when abundances are used is considered helpful to characterization of association in this study

Integrated species-phenon trees: visualizing infraspecific diversity within lineages

The unprecedented detail with which contemporary molecular phylogenetics are visualizing infraspecifc relationships within living species and species complexes cannot as yet be reliably extended into deep time. Yet paleontological systematics has routinely dealt in (mainly) morphotaxa envisaged in various ways to have been components of past species lineages. Bridging these perspectives can only enrich both. We present a visualization tool that digitally depicts infraspecifc diversity within species through deep time. Our integrated species–phenon tree merges ancestor– descendant trees for fossil morphotaxa (phena) into reconstructed phylogenies of lineages (species) by expanding the latter into “species boxes” and placing the phenon trees inside. A key programming strategy to overcome the lack of a simple overall parent–child hierarchy in the integrated tree has been the progressive population of a species–phenon relationship map which then provides the graphical footprint for the overarching species boxes. Our initial case has been limited to planktonic foraminfera via Aze & others’ important macroevolutionary dataset. The tool could potentially be appropriated for other organisms, to detail other kinds of infraspecifc granularity within lineages, or more generally to visualize two nested but loosely coupled trees

Future-Proofing the Cenozoic Macroperforate Planktonic foraminifera Phylogeny of Aze & Others (2011)

The unique macroevolutionary dataset of Aze & others has been transferred onto the TimeScale Creator visualisation platform while, as much as practicable, preserving the original unrevised content of its morphospecies and lineage evolutionary trees. This is a “Corrected Version” (not a revision), which can serve as an on-going historical case example because it is now updatable with future time scales. Both macroevolutionary and biostratigraphic communities are now equipped with an enduring phylogenetic database of Cenozoic macroperforate planktonic foraminiferal morphospecies and lineages for which both graphics and content can be visualised together. Key to maintaining the currency of the trees has been specification of time scales for sources of stratigraphic ranges; these scales then locate the range dates within the calibration series. Some ranges or their sources have undergone mostly minor corrections or amendments. Links between lineage and morphospecies trees have been introduced to improve consistency and transparency in timing within the trees. Also, Aze & others’ dual employment of morphospecies and lineage concepts is further elaborated here, given misunderstandings that have ensued. Features displayed on the trees include options for line styles for additional categories for range extensions or degrees of support for ancestor–descendant proposals; these have been applied to a small number of instances as an encouragement to capture more nuanced data in the future. In addition to labeling of eco- and morpho-groups on both trees, genus labels can be attached to the morphospecies tree to warn of polyphyletic morphogenera, and the lineage codes have been decoded to ease their recognition. However, it is the mouse-over pop-ups that provide the greatest opportunity to embed supporting information in the trees. They include details for stratigraphic ranges and their recalibration steps, positions relative to the standard planktonic-foraminiferal zonation, and applications as datums, as well as mutual listings between morphospecies and lineages which ease the tracing of their interrelated contents. The elaboration of the original dataset has been captured in a relational database, which can be considered a resource in itself, and, through queries and programming, serves to generate the TimeScale Creator datapacks

Timing and severity of immunizing diseases in rabbits is controlled by seasonal matching of host and pathogen dynamics

Infectious diseases can exert a strong influence on the dynamics of host populations, but it remains unclear why such disease-mediated control only occurs under particular environmental conditions. We used 16 years of detailed field data on invasive European rabbits (Oryctolagus cuniculus) in Australia, linked to individual-based stochastic models and Bayesian approximations, to test whether (i) mortality associated with rabbit haemorrhagic disease (RHD) is driven primarily by seasonal matches/mismatches between demographic rates and epidemiological dynamics and (ii) delayed infection (arising from insusceptibility and maternal antibodies in juveniles) are important factors in determining disease severity and local population persistence of rabbits. We found that both the timing of reproduction and exposure to viruses drove recurrent seasonal epidemics of RHD. Protection conferred by insusceptibility and maternal antibodies controlled seasonal disease outbreaks by delaying infection; this could have also allowed escape from disease. The persistence of local populations was a stochastic outcome of recovery rates from both RHD and myxomatosis. If susceptibility to RHD is delayed, myxomatosis will have a pronounced effect on population extirpation when the two viruses coexist. This has important implications for wildlife management, because it is likely that such seasonal interplay and disease dynamics has a strong effect on long-term population viability for many species.Konstans Wells, Barry W. Brook, Robert C. Lacy, Greg J. Mutze, David E. Peacock, Ron G. Sinclair, Nina Schwensow, Phillip Cassey, Robert B. O'Hara, Damien A. Fordha