Digging for gold nuggets : uncovering novel candidate genes for variation in gastrointestinal nematode burden in a wild bird species

Acknowledgements This study was funded by a BBSRC studentship (MAWenzel) and NERC grants NE/H00775X/1 and NE/D000602/1 (SB Piertney). The authors are grateful to Marianne James, Mario Roder and Keliya Bai for field-work assistance, Lucy M.I. Webster and Steve Paterson for help during prior development of genetic markers,Heather Ritchie for helpful comments on manuscript drafts and all estate owners, factors and keepers for access to field sites, most particularly MJ Taylor and Mike Nisbet (Airlie), Neil Brown (Allargue), RR Gledson and David Scrimgeour (Delnadamph), Andrew Salvesen and John Hay (Dinnet), Stuart Young and Derek Calder (Edinglassie), Kirsty Donald and DavidBusfield (Glen Dye), Neil Hogbin and Ab Taylor (Glen Muick), Alistair Mitchell (Glenlivet), Simon Blackett, Jim Davidson and Liam Donald (Invercauld), Richard Cooke and Fred Taylor (Invermark), Shaila Rao and Christopher Murphy (Mar Lodge), and Ralph Peters and Philip Astor (Tillypronie)Peer reviewedPostprin

Phylogenetic relationships among hadal amphipods of the Superfamily Lysianassoidea : Implications for taxonomy and biogeography

Date of Acceptance: 30/8/15 Acknowledgements We thank the chief scientists, crew and company of the Japanese RV Hakuho-Maru (KH0703 and KH0803), the RV Tansei-Maru (KT-09-03), the RV Kairei (KR0716), the German FS Sonne (SO197 and SO 209) and the New Zealand RV Kaharoa (KAH0190, KAH1109, KAH1202, KAH1301 and KAH1310). This work was supported by the HADEEP projects, funded by the Nippon Foundation, Japan (2009765188), the Natural Environmental Research Council, UK (NE/E007171/1) and the Total Foundation, France. We acknowledge additional support from the Marine Alliance for Science and Technology for Scotland (MASTS) funded by the Scottish Funding Council (Ref: HR09011) and contributing institutions. We also acknowledge support from the Leverhulme Research Fellowship granted to SBP. Additional sea time was supported by NIWA’s ‘Impact of Resource Use on Vulnerable Deep-Sea Communities’ project (CO1_0906). From NIWA we thank Malcolm Clark, Ashley Rowden, Kareen Schnabel, Sadie Mills for logistical support at the NIWA Invertebrate Collection. We also thank Fredrik Søreide from Promare, USA, for supply of the Puerto-Rico samples, Marius Wenzel for helpful comments on manuscript drafts, and Dr. Tammy Horton (NOCS, UK) for identifying some of the earlier amphipod samplesPeer reviewedPostprintPostprin

Heat-shock protein adaptation in abyssal and hadal amphipods

We thank the chief scientists, crew and company of the Japanese RV Hakuho-Maru (KH0703 and KH0803), the RV Tansei-Maru (KT-09-03), the RV Kairei (KR0716), the German FS Sonne (SO197 and SO 209) and the New Zealand RV Kaharoa (KAH0190, KAH1109, KAH1202, KAH1301 and KAH1310). This work was supported by the HADEEP projects, funded by the Nippon Foundation, Japan (2009765188), the Natural Environmental Research Council, UK (NE/E007171/1) and the Total Foundation, France. We acknowledge additional support from the Marine Alliance for Science and Technology for Scotland (MASTS) funded by the Scottish Funding Council (Refs: HR09011 and DSSG14), the Natural Environment Research Council (NE/N01149X/1), the Leverhulme Trust, and contributing institutions. Additional sea time was supported by NIWA's ‘Impact of Resource Use on Vulnerable Deep-Sea Communities’ project (CO1_0906). From NIWA we thank Malcolm Clark, Ashley Rowden, Kareen Schnabel, and Sadie Mills for logistical support at the NIWA Invertebrate Collection. We also thank Dr. Niamh Kilgallen for identifying the majority of the amphipod samples and Dr. Tammy Horton (NOCS, UK) for identifying some of the earlier amphipod samples.Peer reviewedPostprin

Isolation and characterisation of 17 microsatellite loci for the red-billed chough (Pyrrhocorax pyrrhocorax)

Peer reviewedPostprin

Eco-evolutionary dynamics. Experiments in a model system

Understanding the consequences of environmental change on both long- and short-term ecological and evolutionary dynamics is a basic pre-requisite for any effective conservation or management programme but inherently problematic because of the complex interplay between ecological and evolutionary processes. Components of such complexity have been described in isolation or within conceptual models on numerous occasions. What remains lacking are studies that characterise effectively the coupled ecological and evolutionary dynamics, to demonstrate feedback mechanisms that influence both phenotypic change, and its effects on population demography, in organisms with complex life histories. We present a systems-based approach that brings together multiple effects that 'shape' an organism's life history (e.g. direct and delayed life-history consequences of environmental variation) and the resulting eco-evolutionary population dynamics. Using soil mites in microcosms, we characterise ecological, phenotypic and evolutionary dynamics in replicated populations in response to experimental manipulations of environment (e.g. the competitive environment, female age, male quality). Our results demonstrate that population dynamics are complex and are affected by both plastic and evolved responses to past and present environments, and that the emergent population dynamic itself shaped the landscape for natural selection to act on in subsequent generations. Evolutionary and ecological effects on dynamics can therefore be almost impossible to partition, which needs to be considered and appreciated in research, management and conservation. © 2014 Elsevier Ltd

Microplastics and synthetic particles ingested by deep-sea amphipods in six of the deepest marine ecosystems on Earth

Funding Funding for the laboratory work and analysis was from Newcastle University internal support. This work was supported by the 2007–2010 HADEEP project, funded by the Nippon Foundation (2009765188) and the Natural Environmental Research Council (NE/E007171/1). The 2011–2013 Kermadec Trench sampling was supported by the TOTAL Foundation (France) through the projects ‘Multi-disciplinary investigations of the deepest scavengers on Earth’ (2010–2012) and ‘Trench Connection’ (2013–2015). The Mariana samples were derived from the ‘FISH2017’ expedition (RV Shinyo-Maru SY1615) supported by the Tokyo University for Marine Science and Technology. Acknowledgements We thank the captain, crew and company of the research expeditions who assisted in the collection of the amphipods between 2008 and 2017, namely the Japanese Hakuho-Maru, Tansei Maru and Shinyo-Maru, the German Sonne and the RV Kaharoa in New Zealand. The assistance of David Whitaker and Peter McParlin from The School of Marine Science and Technology at Newcastle University are much appreciated. We are extremely grateful to Bob Keighley and Dan Parnaby at Shimadzu UK Limited for facilitating the FTIR analysis and access to their material database. We also thank Heather Stewart from the British Geological Survey for calculating the distances between trenches.Peer reviewedPublisher PD

Honest sexual signalling mediated by parasite and testosterone effects on oxidative balance

Extravagant ornaments evolved to advertise their bearers' quality, the honesty of the signal being ensured by the cost paid to produce or maintain it. The oxidation handicap hypothesis (OHH) proposes that a main cost of testosterone-dependent ornamentation is oxidative stress, a condition whereby the production of reactive oxygen and nitrogen species (ROS/RNS) overwhelms the capacity of antioxidant defences. ROS/RNS are unstable, very reactive by-products of normal metabolic processes that can cause extensive damage to key biomolecules (cellular proteins, lipids and DNA). Oxidative stress has been implicated in the aetiology of many diseases and could link ornamentation and genetic variation in fitness-related traits. We tested the OHH in a free-living bird, the red grouse. We show that elevated testosterone enhanced ornamentation and increased circulating antioxidant levels, but caused oxidative damage. Males with smaller ornaments suffered more oxidative damage than those with larger ornaments when forced to increase testosterone levels, consistent with a handicap mechanism. Parasites depleted antioxidant defences, caused oxidative damage and reduced ornament expression. Oxidative damage extent and the ability of males to increase antioxidant defences also explained the impacts of testosterone and parasites on ornamentation within treatment groups. Because oxidative stress is intimately linked to immune function, parasite resistance and fitness, it provides a reliable currency in the trade-off between individual health and ornamentation. The costs induced by oxidative stress can apply to a wide range of signals, which are testosterone-dependent or coloured by pigments with antioxidant properties

A systematic review of phenotypic responses to between-population outbreeding

This work was supported by the UK Population Biology Network, through funding from the Natural Environment Research Council and Natural England. We thank Jack Brodie, Helen Hipperson, Marie Chadburn and Sophie Allen for assistance with literature searching, article assessment and data extraction. We also thank our review group for constructive criticism on the scope, development and structure of this review, and two peer reviewers for useful feedback on the review protocol. Finally we thank three peer reviewers who each provided constructive comments on this systematic review report.Peer reviewedPublisher PD

Evidence for directional selection at a novel major histocompatibility class I marker in wild common frogs (Rana temporaria) exposed to a viral pathogen (Ranavirus).

(c) 2009 Teacher et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.Whilst the Major Histocompatibility Complex (MHC) is well characterized in the anuran Xenopus, this region has not previously been studied in another popular model species, the common frog (Rana temporaria). Nor, to date, have there been any studies of MHC in wild amphibian host-pathogen systems. We characterise an MHC class I locus in the common frog, and present primers to amplify both the whole region, and specifically the antigen binding region. As no more than two expressed haplotypes were found in over 400 clones from 66 individuals, it is likely that there is a single class I locus in this species. This finding is consistent with the single class I locus in Xenopus, but contrasts with the multiple loci identified in axolotls, providing evidence that the diversification of MHC class I into multiple loci likely occurred after the Caudata/Anura divergence (approximately 350 million years ago) but before the Ranidae/Pipidae divergence (approximately 230 mya). We use this locus to compare wild populations of common frogs that have been infected with a viral pathogen (Ranavirus) with those that have no history of infection. We demonstrate that certain MHC supertypes are associated with infection status (even after accounting for shared ancestry), and that the diseased populations have more similar supertype frequencies (lower F(ST)) than the uninfected. These patterns were not seen in a suite of putatively neutral microsatellite loci. We interpret this pattern at the MHC locus to indicate that the disease has imposed selection for particular haplotypes, and hence that common frogs may be adapting to the presence of Ranavirus, which currently kills tens of thousands of amphibians in the UK each year