Environmentally mediated trends in otolith composition of juvenile Atlantic cod (Gadus morhua)

Author Posting. © The Author(s), 2015. This is the author's version of the work. It is posted here by permission of Oxford University Press for personal use, not for redistribution. The definitive version was published in ICES Journal of Marine Science 72 (2015): 2350-2363, doi: 10.1093/icesjms/fsv070.We evaluated the influence of environmental exposure of juvenile Atlantic cod (Gadus morua) to inform interpretations of natal origins and movement patterns using otolith geochemistry. Laboratory rearing experiments were conducted with a variety of temperature (~ 5, 8.5 and 12 °C) and salinity (~ 25, 28.5 and 32 PSU) combinations. We measured magnesium (Mg), manganese (Mn), strontium (Sr) and barium (Ba), expressed as a ratio to calcium (Ca), using laser ablation inductively coupled plasma mass spectrometry (ICP-MS), and stable carbon (δ13C) and oxygen (δ18O) isotopes using isotope ratio monitoring mass spectrometry. Temperature and salinity significantly affected all elements and isotopes measured, with the exception of salinity on Mg:Ca. We detected significant interactions among temperature and salinity for Mn:Ca and Ba:Ca partition coefficients (ratio of otolith chemistry to water chemistry), with significant temperature effects only detected in the 32 and 28.5 PSU salinity treatments. Similarly, we detected a significant interaction between temperature and salinity in incorporation of δ13C, with a significant temperature effect except at intermediate salinity. These results support the contention that environmental mediation of otolith composition varies among species, thus limiting the ability of generalized models to infer life history patterns from chemistry. Our results provide essential baseline information detailing environmental influence on juvenile Atlantic cod otolith composition, punctuating the importance of laboratory validations to translate species-specific otolith composition when inferring in situ life histories and movements.Research funding and support was provided by a Natural Sciences and Engineering Research Council of Canada (NSERC) Strategic Grant on Connectivity in Marine Fishes. R. Stanley was supported by an NSERC Postgraduate Scholarship and a Research and Development Corporation of Newfoundland (RDC) student fellowship.2016-04-2

Using movement, diet, and genetic analyses to understand Arctic charr responses to ecosystem change

ACKNOWLEDGEMENTS The extensive datasets used in this study were reliant on the dedication and innovation of many residents of Nunatsiavut (Food Skills and Environmental Research Program), technicians and biologists from DFO (J. Seiden, D. Lancaster, M. Shears, M. Bloom, S. Duffy), the Nunatsiavut Government (P. McCarney, C. Andersen, L. Pijogge), Oceans North (S. Pain), and of the captains and crew of the What’s Happening and the Safe Passage. Suggestions by three anonymous reviewers also greatly improved the manuscript. Funding for this research was provided in part by ArcticNet and DFO Oceans.Peer reviewedPublisher PD

MEGASAT: automated inference of microsatellite genotypes from sequence data

MEGASAT is software that enables genotyping of microsatellite loci using next-generation sequencing data. Microsatellites are amplified in large multiplexes, and then sequenced in pooled amplicons. MEGASAT reads sequence files and automatically scores microsatellite genotypes. It uses fuzzy matches to allow for sequencing errors and applies decision rules to account for amplification artefacts, including nontarget amplification products, replication slippage during PCR (amplification stutter) and differential amplification of alleles. An important fea- ture of MEGASAT is the generation of histograms of the length–frequency distributions of amplification products for each locus and each individual. These histograms, analogous to electropherograms traditionally used to score microsatellite genotypes, enable rapid evaluation and editing of automatically scored genotypes. MEGASAT is written in Perl, runs on Windows, Mac OS X and Linux systems, and includes a simple graphical user interface. We demon- strate MEGASAT using data from guppy, Poecilia reticulata. We genotype 1024 guppies at 43 microsatellites per run on an Illumina MiSeq sequencer. We evaluated the accuracy of automatically called genotypes using two methods, based on pedigree and repeat genotyping data, and obtained estimates of mean genotyping error rates of 0.021 and 0.012. In both estimates, three loci accounted for a disproportionate fraction of genotyping errors; conversely, 26 loci were scored with 0–1 detected error (error rate ≤0.007). Our results show that with appropriate selection of loci, automated genotyping of microsatellite loci can be achieved with very high throughput, low genotyping error and very low genotyping costs

Geography, environment, and colonization history interact with morph type to shape genomic variation in an Arctic fish

Funding Information: Thanks go to our editor and three anonymous reviewers whose suggestions greatly improved this study. We thank S. Avery, J. Callahan, S. Duffy, S. Hann, L. Pike, R. Solomon, A. Walsh, for assistance with sample collection and fieldwork. We are grateful to X. Dallaire and J.S. Moore for providing samples from Ungava, Bay (HAB) and to L. Bernatchez for his valuable comments on an earlier version of this manuscript. Thanks to Parks Canada for allowing us access to the Torngat Mountains National Park and the Nunatsiavut government for allowing us to collect samples from their lands. Thanks to A. Belay at Mount Sinai Hospital for her help with sequencing, A. Mesmer for help with genotyping, and S. Lehnert for insightful data analysis suggestions. We also thank the Institute for Biodiversity, Ecosystem Science, and Sustainability of the Department of Environment and Conservation of the Government of Labrador and Newfoundland for funding for this project; NSERC for the Strategic Grant STPGP 430198 and Discovery Grant awarded to DER, for the CGS‐D awarded to SJS; the Killam Trust for the Level 2 Izaak awarded to SJS; and the Government of Nova Scotia for the Graduate Scholarship awarded to SJS. Publisher Copyright: © 2023 The Authors. Molecular Ecology published by John Wiley & Sons Ltd.Peer reviewedPublisher PD

Model-based evaluation of the genetic impacts of farm-escaped Atlantic salmon on wild populations

Acknowledgements. The authors thank R. Gregory and T. Kess for comments on this manuscript. Funding was provided through the Fisheries and Oceans Program for Aquaculture Regulatory Research. This work has benefited greatly from a 3 year Canada-EU Galway Statement for the Transatlantic Ocean Research Alliance Working Group on modelling genetic interactions among wild and farm escaped Atlantic Salmon in the North Atlantic, involving participants from 7 countries. The models applied here were evaluated and discussed as part of this working group.Peer reviewedPublisher PD

Environmentally associated chromosomal structural variation influences fine-scale population structure of Atlantic Salmon (Salmo salar)

acceptedVersio

Evaporation, seepage and water quality management in storage dams: a review of research methods

One of the most significant sources of water wastage in Australia is loss from small storage dams, either by seepage or evaporation. Over much of Australia, evaporative demand routinely exceeds precipitation. This paper outlines first, methodologies and measurement techniques to quantify the rate of evaporative loss from fresh water storages. These encompass high-accuracy water balance monitoring; determination of the validity of alternative estimation equations, in particular the FAO56 Penman- Monteith ETo methodology; and the commencement of CFD modeling to determine a 'dam factor' in relation to practical atmospheric measurement techniques. Second, because the application of chemical monolayers is the only feasible alternative to the high cost of physically covering the storages to retard evaporation, the use of cetyl alcohol-based monolayers is reviewed, and preliminary research on their degradation by photolytic action, by wind break-up and by microbial degradation reported. Similarly, preliminary research on monolayer visualisation techniques for field application is reported; and potential enhancement of monolayers by other chemicals and attendant water quality issues are considered

Genomic evidence of recent European introgression into North American farmed and wild Atlantic salmon

publishedVersio

Quality control for multiple breath washout tests in multicentre bronchiectasis studies:Experiences from the BRONCH-UK clinimetrics study

Multiple Breath Washout (MBW) to measure Lung Clearance Index (LCI) is increasingly being used as a secondary endpoint in multicentre bronchiectasis studies. LCI data quality control or “over-reading” is resource intensive and the impact is unclear. Objectives: To assess the proportion of MBW tests deemed unacceptable with over-reading, and to assess the change in LCI (number of turnovers), LCI coefficient of variation (CV%) and tidal volume (VT) CV% results after over-reading. Methods: Data were analysed from 250 MBW tests (from 98 adult bronchiectasis patients) collected as part of the Bronch-UK Clinimetrics study in 5 UK centres. Each MBW test was over-read centrally using pre-defined criteria. MBW tests with <2 technically valid and repeatable trials were deemed unacceptable to include in analysis. In accepted tests, values for LCI, LCI CV% and VT CV% before and after over-reading, were compared. Results: Insufficient data was collected in 10/250 tests. With over-reading, 30/240 (12%) were deemed unacceptable to include in analysis. In those accepted tests, overall the change in LCI, LCI CV% and VT CV% with over-reading was not statistically significant. When MBW new sites were compared to MBW expert sites, the change in LCI with over-reading was significantly greater in MBW new sites (p = 0.047). Data suggests that over-reading could be important up to at least 12 months post initiation of MBW activity. Conclusion: MBW over-reading was important in this study as 12% of tests were considered unacceptable. Over-reading improved test result accuracy in sites new to MBW