Jonathan Carr

Bio: Jonathan Carr is an academic researcher from Atlantic Salmon Federation. The author has contributed to research in topics: Salmo & Population. The author has an hindex of 7, co-authored 10 publications receiving 135 citations.

Ocean migration of pop-up satellite archival tagged Atlantic salmon from the Miramichi River in Canada

Abstract: This is a pre-copyedited, author-produced version of an article accepted for publication in ICES Journal of Marine Science following peer review. The version of record Strom, J.F., Thorstad, E.B., Chafe, G., Sorbye, S.H., Righton, D., Rikardsen, A.H. & Carr, J. (2017). Ocean migration of pop-up satellite archival tagged Atlantic salmon from the Miramichi River in Canada. ICES Journal of Marine Science, 74(5), 1356-1370 is available online at: https://doi.org/10.1093/icesjms/fsw220 .

Atlantic salmon (Salmo salar) smolt and early post-smolt migration and survival inferred from multi-year and multi-stock acoustic telemetry studies in the Gulf of St. Lawrence, northwest Atlantic

Abstract: The migration dynamics and inter-annual variation in early at-sea survival of Atlantic salmon (Salmo salar) smolts over 14 years of study are reported for four river populations located in the Gulf of St. Lawrence (Canada). Acoustically tagged smolts were monitored at three points along their migration from freshwater to the Labrador Sea, a migration extending more than 800 km at sea and a period of 2 months. A hierarchical state-space version of the Cormack–Jolly–Seber model was used to estimate apparent survival rates from incomplete acoustic detections at key points. There was a positive size-dependent probability of survival through the freshwater and estuary areas; the odds of survival of a 16 cm smolt were 1.5–1.7 times higher than for a 13.5 cm smolt, length at tagging. Length adjusted (centred to the mean fork length of smolts during the study of 14.6 cm) survivals through the estuary and nearshore waters were estimated to range between 67 and 90% for the two river populations migrating through Chaleur Bay in contrast to lower survival estimates of 28–82% for the two populations from the neighbouring Miramichi Bay. Across the 14 years of study, survival estimates varied without trend for the populations of Chaleur Bay, but declined for the populations migrating through Miramichi Bay. Survival through the Gulf of St. Lawrence was variable but generally high among years and rivers, ranging from 96% day−1 to 99% day−1. Long term, replicated studies at multiple sites using acoustically tagged smolts can provide empirical data to examine hypotheses of the location and timing of factors contributing to smolt and post-smolt mortality of salmon at sea.

Ocean predation and mortality of adult Atlantic salmon.

Abstract: Acknowledgements We thank Alta Laksefiskeri Interessentskap, Atlantic Salmon Conservation Foundation, Danish Rod and Net License Fund, Inland Fisheries Ireland, Miramichi Salmon Association, Research Council of Norway project 280308 SeaSalar, Tromso Research Foundation, and Xunta de Galicia for supporting and funding this project. We also thank all staff, students, and volunteers who have contributed to the fieldwork, and Timothy F. Sheehan and Jaakko Erkinaro for insightful discussion on an earlier version of the manuscript.

Estimating consumption rate of Atlantic salmon smolts (Salmo salar) by striped bass (Morone saxatilis) in the Miramichi River estuary using acoustic telemetry

Abstract: Differentiating detections of a telemetered fish from those of predators that may have consumed that telemetered fish presents problems and opportunities. Previous efforts to classify predation eve...

Sea lice infestation rates on wild and escaped farmed Atlantic salmon (Salmo salar L.) entering the Magaguadavic River, New Brunswick

Abstract: A monitoring program for the prevalence and intensity of sea lice infestations of wild and escaped farmed salmon has been underway on the Magaguadavic River since 1992. Fish are screened in a fish ladder trap located in freshwater a short distance above the head of tide. No trends with time were evident in observed sea lice burdens, and in all years the majority of salmon, both wild and escapees, had no or low levels of infestation with sea lice. In the spring of 2002, 23 landlocked salmon moving to sea from the Magaguadavic River were acoustically tagged. Two fish returned to the river after a brief period of residence in Passamaquoddy Bay, with significant dermal damage from sea lice. These fish were tracked to areas close to commercial salmon farms.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

Abstract: The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

Atlantic Salmon, Salmo Salar

Abstract: Farming of Atlantic salmon (Salmo salar) began in Norway in the late 1960s. During the 1980s and 1990s the production spread, mainly to other northwestern European countries and to Chile. In 1980 annual world production was less than 10,000 t and this increased to 850,000 t whole fish produced in 2000. It is projected to approach 2 million t in 2010. The growth rate of the fish in the farms is continuously improving, due to genetic selection, improved diets and feeding and improved management. The improvement in growth ascribed to genetic selection can be as much as 15–20% per generation if the salmon are from a combined family–phenotype selection programme (Gjedrem, 1983). Recent Canadian results have shown that transgenic salmon, which express growth hormone receptor activity in muscle tissues, have a growth rate 2.6–2.9 times that of the control population, mainly because of increased feed intake (Cook et al., 2000a). Selection or transgenic techniques may also influence the composition of the growth, result in improved feed conversion (Thodesen et al., 1999; Cook et al., 2000a) and change the rate of metabolism (Thodesen et al., 1999; Cook et al., 2000b,c). Economical feed conversions in Norwegian salmon farming have changed from more than 2 kg feed dry matter (DM) kg−1 gain in 1980 to approximately 1.15 kg kg−1 at the end of the 1990s. In salmon the biological feed conversion can vary from less than 0.6 to more than 1.3 kg intake kg−1 gain, and the proportion of protein and energy in diet partitioned into gain can vary from 25 to 60%, depending on the formulation of the diet and the size of the fish. Thus, requirement figures must be based on the requirements of the animal, related to growth, nutrient partitioning and the specific physiological processes in which the nutrient is required. Requirements differ throughout the life cycle. This is especially important in salmon, which undergo physiological changes during smoltification and transfer from a life in fresh water to salt water. In addition to developing the ability to maintain the ion balance in the hyperosmotic salt water, the salmon also

Transmission dynamics of parasitic sea lice from farm to wild salmon

Abstract: Marine salmon farming has been correlated with parasitic sea lice infestations and concurrent declines of wild salmonids. Here, we report a quantitative analysis of how a single salmon farm altered the natural transmission dynamics of sea lice to juvenile Pacific salmon. We studied infections of sea lice (Lepeophtheirus salmonis and Caligus clemensi ) on juvenile pink salmon (Oncorhynchus gorbuscha) and chum salmon (Oncorhynchus keta) as they passed an isolated salmon farm during their seaward migration down two long and narrow corridors. Our calculations suggest the infection pressure imposed by the farm was four orders of magnitude greater than ambient levels, resulting in a maximum infection pressure near the farm that was 73 times greater than ambient levels and exceeded ambient levels for 30 km along the two wild salmon migration corridors. The farm-produced cohort of lice parasitizing the wild juvenile hosts reached reproductive maturity and produced a second generation of lice that re-infected the juvenile salmon. This raises the infection pressure from the farm by an additional order of magnitude, with a composite infection pressure that exceeds ambient levels for 75 km of the two migration routes. Amplified sea lice infestations due to salmon farms are a potential limiting factor to wild salmonid conservation.

A review of the biology and genetics of sea lice

Abstract: Studies of the biology of sea lice have been conducted from various perspectives for two decades. For Lepeophtheirus spp., most of the published literature has centred on the economically important Lepeophtheirus salmonis, while for Caligus spp., research has focused on a wider range of species. The most numerous species of Caligus in North Atlantic waters, however, is Caligus elongatus, which is also economically important to salmon farming. Since the last review by Pike, A. W., and Wadsworth, S. L. (1999. Sea lice on salmonids: their biology and control. Advances in Parasitology, 44: 234-337.), research on sea lice has developed considerably, including the application of genetic methods. This new research has focused on life history biology, studying developmental stages under different environmental conditions (e.g. temperature and salinity), behaviour, distribution and the dispersal of free-living stages, monitoring practices, population structure, and modelling. The results of this research have informed risk analyses and allowed the refinement of management strategies to reduce sea lice infestations in wild and farmed populations of anadromous salmonids. Molecular techniques have been used to describe population structure and identify differences in genetic characterization of geographically separate populations and population markers. Research has been initiated to understand the parasite-host relationship at a molecular level and to develop a vaccine against sea lice.