2BAD: an application to estimate the parental contributions during two independent admixture events

Several approaches have been developed to calculate the relative contributions of parental populations in single admixture event scenarios, including Bayesian methods. In many breeds and populations, it may be more realistic to consider multiple admixture events. However, no approach has been developed to date to estimate admixture in such cases. This report describes a program application, 2BAD (for 2-event Bayesian ADmixture), which allows the consideration of up to two independent admixture events involving two or three parental populations and a single admixed population, depending on the number of populations sampled. For each of these models, it is possible to estimate several parameters (admixture, effective sizes, etc.) using an approximate Bayesian computation approach. In addition, the program allows comparing pairs of admixture models, determining which is the most likely given data. The application was tested through simulations and was found to provide good estimates for the contribution of the populations at the two admixture events. We were also able to determine whether an admixture model was more likely than a simple split model

European wildcat populations are subdivided into five main biogeographic groups: consequences of Pleistocene climate changes or recent anthropogenic fragmentation?

Extant populations of the European wildcat are fragmented across the continent, the likely consequence of recent extirpations due to habitat loss and over-hunting. However, their underlying phylogeographic history has never been reconstructed. For testing the hypothesis that the European wildcat survived the Ice Age fragmented in Mediterranean refuges, we assayed the genetic variation at 31 microsatellites in 668 presumptive European wildcats sampled in 15 European countries. Moreover, to evaluate the extent of subspecies/population divergence and identify eventual wild × domestic cat hybrids, we genotyped 26 African wildcats from Sardinia and North Africa and 294 random-bred domestic cats. Results of multivariate analyses and Bayesian clustering confirmed that the European wild and the domestic cats (plus the African wildcats) belong to two well-differentiated clusters (average Ф ST = 0.159, r st = 0.392, P > 0.001; Analysis of molecular variance [AMOVA]). We identified from c. 5% to 10% cryptic hybrids in southern and central European populations. In contrast, wild-living cats in Hungary and Scotland showed deep signatures of genetic admixture and introgression with domestic cats. The European wildcats are subdivided into five main genetic clusters (average Ф ST = 0.103, r st = 0.143, P > 0.001; AMOVA) corresponding to five biogeographic groups, respectively, distributed in the Iberian Peninsula, central Europe, central Germany, Italian Peninsula and the island of Sicily, and in north-eastern Italy and northern Balkan regions (Dinaric Alps). Approximate Bayesian Computation simulations supported late Pleistocene-early Holocene population splittings (from c. 60 k to 10 k years ago), contemporary to the last Ice Age climatic changes. These results provide evidences for wildcat Mediterranean refuges in southwestern Europe, but the evolution history of eastern wildcat populations remains to be clarified. Historical genetic subdivisions suggest conservation strategies aimed at enhancing gene flow through the restoration of ecological corridors within each biogeographic units. Concomitantly, the risk of hybridization with free-ranging domestic cats along corridor edges should be carefully monitored

Potential impacts of climate change on habitat suitability for the Queensland fruit fly

Anthropogenic climate change is a major factor driving shifts in the distributions of pests and invasive species. The Queensland fruit fly, Bactrocera tryoni Froggatt (Qfly), is the most economically damaging insect pest of Australia's horticultural industry, and its management is a key priority for plant protection and biosecurity. Identifying the extent to which climate change may alter the distribution of suitable habitat for Qfly is important for the development and continuation of effective monitoring programs, phytosanitary measures, and management strategies. We used Maxent, a species distribution model, to map suitable habitat for Qfly under current climate, and six climate scenarios for 2030, 2050 and 2070. Our results highlight that south-western Australia, northern regions of the Northern Territory, eastern Queensland, and much of south-eastern Australia are currently suitable for Qfly. This includes southern Victoria and eastern Tasmania, which are currently free of breeding populations. There is substantial agreement across future climate scenarios that most areas currently suitable will remain so until at least 2070. Our projections provide an initial estimate of the potential exposure of Australia's horticultural industry to Qfly as climate changes, highlighting the need for long-term vigilance across southern Australia to prevent further range expansion of this species

Increase of dissolved inorganic carbon and decrease in pH in near-surface waters in the Mediterranean Sea during the past two decades

Two 3-year time series of hourly measurements of the fugacity of CO2 (fCO2) in the upper 10 m of the surface layer of the northwestern Mediterranean Sea have been recorded by CARIOCA sensors almost two decades apart, in 1995–1997 and 2013–2015. By combining them with the alkalinity derived from measured temperature and salinity, we calculate changes in pH and dissolved inorganic carbon (DIC). DIC increased in surface seawater by ∼25 µmol kg−1 and fCO2 by 40 µatm, whereas seawater pH decreased by ∼0.04 (0.0022 yr−1). The DIC increase is about 15 % larger than expected from the equilibrium with atmospheric CO2. This could result from natural variability, e.g. the increase between the two periods in the frequency and intensity of winter convection events. Likewise, it could be the signature of the contribution of the Atlantic Ocean as a source of anthropogenic carbon to the Mediterranean Sea through the Strait of Gibraltar. We then estimate that the part of DIC accumulated over the last 18 years represents ∼30 % of the total inventory of anthropogenic carbon in the Mediterranean Sea

Quality check of cardiac MRI exams for Fallot patients: Interest of a simple formula to detect invalid exams

PurposeCardiac MRI (CMR) is the key exam for Fallot patients but remains tricky. The CMR report should at least mention left and right ventricle end-diastole volumes (Vl and Vr), ejection fraction (EFl and EFr) and pulmonary regurgitation (PR). Obviously, these variables are linked together by basic physiology rules and indeed Vl×EFl=Vr×EFr×(1-PR). We investigated the interest of using such formula as quality check during Fallot CMR exams in our center.Methods98 consecutive CMR examinations for Fallot (or Fallot-like) cardiopathy between 2010 and 2014 were retrospectively included. The exams failing to pass the formula (with a 10% tolerance) constituted the Invalid-group and a control group of the same size was also constituted. CMR of both groups were randomly submitted to a blinded senior observer. The inter-observer limits of agreements were compared for the different variables within both groups.Results(Fig. 1) 12 CMR (12%) failed to pass the validation formula. From the 24 reanalyzed CMR, only 4 failed to pass the formula (all from the Invalid-group). Two had persistent defect (VSD or ASD) which were not mentioned to the radiologist and not detected during the CMR. Two had significant artefacts in the aorta or pulmonary trunk due to sterna wires. The inter-observer disagreements for the 8 other CMR of the Invalid-group concerned the Right ventricle end-diastole volume (P<0.05).ConclusionThe use of a simple formula as quality check of CMR examinations for Fallot patients was useful to detect a total of 12% of CMR with issues. 8% of the CMR corresponded to uncertain right ventricle contours, 2% to persistent septal defects that should have been noticed during the examination and 2% to unreliable aortic or pulmonary flow due to artifacts. The formula could have permitted either to detect the anomalies or at least to conclude that the quality of the exams was impaired

Biopython: freely available Python tools for computational molecular biology and bioinformatics

Summary: The Biopython project is a mature open source international collaboration of volunteer developers, providing Python libraries for a wide range of bioinformatics problems. Biopython includes modules for reading and writing different sequence file formats and multiple sequence alignments, dealing with 3D macro molecular structures, interacting with common tools such as BLAST, ClustalW and EMBOSS, accessing key online databases, as well as providing numerical methods for statistical learning. Availability: Biopython is freely available, with documentation and source code at www.biopython.org under the Biopython license. Contact: All queries should be directed to the Biopython mailing lists, see www.biopython.org/wiki/[email protected]

A new method for tracking of motor skill learning through practical application of Fitts’ law

This article is made available through the Brunel Open Access Publishing Fund.A novel upper limb motor skill measure, task productivity rate (TPR) was developed integrating speed and spatial error, delivered by a practical motor skill rehabilitation task (MSRT). This prototype task involved placement of 5 short pegs horizontally on a spatially configured rail array. The stability of TPR was tested on 18 healthy right-handed adults (10 women, 8 men, median age 29 years) in a prospective single-session quantitative within-subjects study design. Manipulations of movement rate 10% faster and slower relative to normative states did not significantly affect TPR, F(1.387, 25.009) = 2.465, p = .121. A significant linear association between completion time and error was highest during the normative state condition (Pearson's r = .455, p < .05). Findings provided evidence that improvements in TPR over time reflected motor learning with possible changes in coregulation behavior underlying practice under different conditions. These findings extend Fitts’ law theory to tracking of practical motor skill using a dexterity task, which could have potential clinical applications in rehabilitation

Psychotherapeutic benefits of compassion-focused therapy: an early systematic review

Background. Compassion-focused therapy (CFT) is a relatively novel form of psychotherapy that was developed for people who have mental health problems primarily linked to high shame and self-criticism. The aim of this early systematic review was to draw together the current research evidence of the effectiveness of CFT as a psychotherapeutic intervention, and to provide recommendations that may inform the development of further trials. Method. A comprehensive search of electronic databases was undertaken to systematically identify literature relating to the effectiveness of CFT as a psychotherapeutic intervention. Reference lists of key journals were hand searched and contact with experts in the field was made to identify unpublished data. Results. Fourteen studies were included in the review, including three randomized controlled studies. The findings from the included studies were, in the most part, favourable to CFT, and in particular seemed to be effective for people who were high in self-criticism. Conclusions. CFT shows promise as an intervention for mood disorders, particularly those high in self-criticism. However, more large-scale, high-quality trials are needed before it can be considered evidence-based practice. The review highlights issues from the current evidence that may be used to inform such trials