Identification and characterisation of 17 polymorphic candidate genes for response to parasitic nematode (Trichostrongylus tenuis) infection in red grouse (Lagopus lagopus scotica)

Acknowledgements This study was funded by a BBSRC studentship (MA Wenzel) and NERC Grants NE/H00775X/1 and NE/D000602/1 (SB Piertney). We are grateful to Jacob Hoglund for providing willow grouse samples, Mario Roder, Keliya Bai, Marianne James, Matt Oliver, Gill Murray-Dickson, Francois Mougeot and Jesus Martınez-Padilla for help with fieldwork, and all grouse estate factors, owners and keepers, most particularly Alistair Mitchell, Shaila Rao, Christopher Murphy, Richard Cooke and Fred Taylor, for providing access to estate game larders.Peer reviewedPostprin

A transcriptomic investigation of handicap models in sexual selection

We are grateful to D. Calder and T. Helps for access to study sites, and G. Murray-Dickson and M. Oliver for help with fieldwork and comments on manuscript drafts. This work was funded by NERC grant NE/D000602/1 (SBP), a NERC advanced fellowship (FM) and a BBSRC studentship (MAW)Peer reviewedPostprin

Pronounced genetic structure and low genetic diversity in European red-billed chough (Pyrrhocorax pyrrhocorax) populations

Conservation Genetics August 2015, Volume 16, Issue 4, pp 1011–1012 Erratum to: Pronounced genetic structure and low genetic diversity in European red-billed chough (Pyrrhocorax pyrrhocorax) populations Erratum to: Conserv Genet (2012) 13:1213–1230 DOI 10.1007/s10592-012-0366-6 In the original publication, Tables 3 and 6 were published with incorrect estimates of population heterozygosities. All other diversity statistics were correct as originally presented. Updated versions of Tables 3 and 6 with corrected heterozygosity estimates confirmed using Arlequin 3.5 (Excoffier and Lischer 2010) as in Dávila et al. (2014) are provided in this erratum. Discrepancies were minor for populations on the British Isles. The correct estimates for Spain are slightly larger than those reported for La Palma by Dávila et al. (2014), but this does not necessarily affect their interpretation that choughs on La Palma may have originated from multiple migration events. The original conclusion that chough populations on the British Isles have low genetic diversity compared to continental European populations remains and is now, in fact, strengthened.Peer reviewedPostprin

Investigating the origins of ivory recovered in the United Kingdom

Over recent years, mounting pressure has been placed on countries to assess their role in the ivory trade, with a view to tackling the rapidly declining numbers of elephants, due to poaching. The United Kingdom has been identified as a large re-exporter of ivory. Despite much of this trade being reported as legal or antique ivory, such provision of ivory to meet demand is known to fuel illegal markets and provide trade routes for modern ivory sales. Aside from ivory species and age, further analysis to evaluate geographic provenance, can inform where an elephant had lived, and so identify a source region or population where poaching occurred. The purpose of this study was to determine the age and species of ivory objects surrendered or seized in the UK and assess their likely geographic provenance through comparison of results from mitochondrial DNA and stable isotope analysis to publicly accessible georeferenced African elephant databases. The results demonstrated that the objects tested from an airport seizure were modern and matched existing haplotypes allowing for regional geographic inferences (supported by both techniques) to be obtained for most of these objects. In contrast, antique and modern ivory was detected amongst the amnesty objects, and several new mtDNA haplotypes were identified. Regional geographic inferences were achieved for some but not all of the objects tested. Our findings show this combination of methods provides a wealth of information which, could provide insight into targeted elephant populations and assist in disrupting international wildlife trade networks

Assessment of the incorporation of CNV surveillance into gene panel next-generation sequencing testing for inherited retinal diseases.

BACKGROUND: Diagnostic use of gene panel next-generation sequencing (NGS) techniques is commonplace for individuals with inherited retinal dystrophies (IRDs), a highly genetically heterogeneous group of disorders. However, these techniques have often failed to capture the complete spectrum of genomic variation causing IRD, including CNVs. This study assessed the applicability of introducing CNV surveillance into first-tier diagnostic gene panel NGS services for IRD. METHODS: Three read-depth algorithms were applied to gene panel NGS data sets for 550 referred individuals, and informatics strategies used for quality assurance and CNV filtering. CNV events were confirmed and reported to referring clinicians through an accredited diagnostic laboratory. RESULTS: We confirmed the presence of 33 deletions and 11 duplications, determining these findings to contribute to the confirmed or provisional molecular diagnosis of IRD for 25 individuals. We show that at least 7% of individuals referred for diagnostic testing for IRD have a CNV within genes relevant to their clinical diagnosis, and determined a positive predictive value of 79% for the employed CNV filtering techniques. CONCLUSION: Incorporation of CNV analysis increases diagnostic yield of gene panel NGS diagnostic tests for IRD, increases clarity in diagnostic reporting and expands the spectrum of known disease-causing mutations

An internationally standardized species identification test for use on suspected seized rhinoceros horn in the illegal wildlife trade

Published by Elsevier Ireland Ltd. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/BY-NC-ND/4.0/).Rhinoceros (rhino) numbers have dwindled substantially over the past century. As a result, three of the five species are now considered to be critically endangered, one species is vulnerable and one species is near-threatened. Poaching has increased dramatically over the past decade due to a growing demand for rhino horn products, primarily in Asia. Improved wildlife forensic techniques, such as validated tests for species identification of seized horns, are critical to aid current enforcement and prosecution efforts and provide a deterrent to future rhino horn trafficking. Here, we present an internationally standardized species identification test based on a 230 base pair cytochrome-b region. This test improves on previous nested PCR protocols and can be used for the discrimination of samples with <20 pg of template DNA, thus suitable for DNA extracted from horn products. The assay was designed to amplify water buffalo samples, a common ‘rhino horn’ substitute, but to exclude human DNA, a common contaminant. Phylogenetic analyses using this partial cytochrome-b region resolved the five extant rhino species. Testing successfully returned a sequence and correct identification for all of the known rhino horn samples and vouchered rhino samples from museum and zoo collections, and provided species level identification for 47 out of 52 unknown samples from seizures. Validation and standardization was carried out across five different laboratories, in four different countries, demonstrating it to be an effective and reproducible test, robust to inter laboratory variation in equipment and consumables (such as PCR reagents). This is one of the first species identification tests to be internationally standardized to produce data for evidential proceedings and the first published validated test for rhinos, one of the flagship species groups of the illegal wildlife trade and for which forensic tools are urgently required. This study serves as a model for how species identification tests should be standardized and disseminated for wildlife forensic testing

Taking stock: provider prescribing practices in the presence and absence of ACT stock

BACKGROUND: Globally, the monitoring of prompt and effective treatment for malaria with artemisinin combination therapy (ACT) is conducted largely through household surveys. This measure; however, provides no information on case management processes at the health facility level. The aim of this review was to assess evidence from health facility surveys on malaria prescribing practices using ACT, in the presence and absence of ACT stock, at time and place where treatment was sought. METHODS: A systematic search of published literature was conducted. Findings were collated and data extracted on proportion of patients prescribed ACT and alternative anti-malarials in the presence and absence of ACT stock. RESULTS: Of the 14 studies identified in which ACT prescription for uncomplicated malaria in the public sector was evaluated, just six, from three countries (Kenya, Uganda and Zambia), reported this in the context of ACT stock. Comparing facilities with ACT stock to facilities without stock (i) ACT prescribing was significantly higher in all six studies, increasing by a range of 21.3% in children < 5 yrs weighing ≥ 5 kg (p < 0.001; Kenya 2006) to 51.7% in children ≥ 10 kg (p < 0.001; Zambia 2006); (ii) SP prescribing decreased significantly in five studies, by a range of 14.4% (p < 0.001; Kenya 2006), to 46.3% (p < 0.001; Zambia 2006); (iii) Where quinine was a reported alternative, prescriptions decreased in five of the six studies by 0.1% (p = 1.0, Kenya 2010) to 10.2% (p < 0.001; Zambia 2006). At facilities with no ACT stock on the survey day, the proportion of febrile patients prescribed ACT was < 10% in five of the nine target groups included in the six studies, with the proportion prescribed ACT ranging from 0 to 28.4% (Uganda 2007). CONCLUSIONS: Prescriber practices vary based on ACT availability. Although ACT prescriptions increased and alternative anti-malarials prescriptions decreased in the presence of ACT stock, ACT was prescribed in the absence, and alternative anti-malarials were prescribed in the presence of, ACT. Presence of stock alone does not ensure that treatment guidelines are followed. More health facility surveys, together with qualitative research, are needed to understand the role of ACT stock-outs on provider prescribing behaviours and preferences

Physiological Stress Mediates the Honesty of Social Signals

Peer reviewedPublisher PD

A clinical and molecular characterisation of CRB1-associated maculopathy

To date, over 150 disease-associated variants in CRB1 have been described, resulting in a range of retinal disease phenotypes including Leber congenital amaurosis and retinitis pigmentosa. Despite this, no genotype–phenotype correlations are currently recognised. We performed a retrospective review of electronic patient records to identify patients with macular dystrophy due to bi-allelic variants in CRB1. In total, seven unrelated individuals were identified. The median age at presentation was 21 years, with a median acuity of 0.55 decimalised Snellen units (IQR = 0.43). The follow-up period ranged from 0 to 19 years (median = 2.0 years), with a median final decimalised Snellen acuity of 0.65 (IQR = 0.70). Fundoscopy revealed only a subtly altered foveal reflex, which evolved into a bull’s-eye pattern of outer retinal atrophy. Optical coherence tomography identified structural changes—intraretinal cysts in the early stages of disease, and later outer retinal atrophy. Genetic testing revealed that one rare allele (c.498_506del, p.(Ile167_Gly169del)) was present in all patients, with one patient being homozygous for the variant and six being heterozygous. In trans with this, one variant recurred twice (p.(Cys896Ter)), while the four remaining alleles were each observed once (p.(Pro1381Thr), p.(Ser478ProfsTer24), p.(Cys195Phe) and p.(Arg764Cys)). These findings show that the rare CRB1 variant, c.498_506del, is strongly associated with localised retinal dysfunction. The clinical findings are much milder than those observed with bi-allelic, loss-of-function variants in CRB1, suggesting this in-frame deletion acts as a hypomorphic allele. This is the most prevalent disease-causing CRB1 variant identified in the non-Asian population to date

A microsatellite baseline for genetic stock identification of European Atlantic salmon (Salmo salar L.)

Atlantic salmon (Salmo salar L.) populations from different river origins mix in the North Atlantic during the marine life stage. To facilitate marine stock identification, we developed a genetic baseline covering the European component of the species’ range excluding the Baltic Sea, from the Russian River Megra in the north-east, the Icelandic Ellidaar in the west, and the Spanish Ulla in the south, spanning 3737 km North to South and 2717 km East to West. The baseline encompasses data for 14 microsatellites for 26 822 individual fish from 13 countries, 282 rivers, and 467 sampling sites. A hierarchy of regional genetic assignment units was defined using a combination of distance-based and Bayesian clustering. At the top level, three assignment units were identified comprising northern, southern, and Icelandic regions. A second assignment level was also defined, comprising eighteen and twenty-nine regional units for accurate individual assignment and mixed stock estimates respectively. The baseline provides the most comprehensive geographical coverage for an Atlantic salmon genetic data-set, and a unique resource for the conservation and management of the species in Europe. It is freely available to researchers to facilitate identification of the natal origin of European salmon