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University of Auckland Institute of Marine Science Publications List maintained by Richard Taylor. Last updated: 31 July 2019. This map shows the relative frequencies of words in the publication titles listed below (1966-Nov. 2017), with “New Zealand” removed (otherwise it dominates), and variants of stem words and taxonomic synonyms amalgamated (e.g., ecology/ecological, Chrysophrys/Pagrus). It was created using Jonathan Feinberg’s utility at www.wordle.net. In press Markic, A., Gaertner, J.-C., Gaertner-Mazouni, N., Koelmans, A.A. Plastic ingestion by marine fish in the wild. Critical Reviews in Environmental Science and Technology. McArley, T.J., Hickey, A.J.R., Wallace, L., Kunzmann, A., Herbert, N.A. Intertidal triplefin fishes have a lower critical oxygen tension (Pcrit), higher maximal aerobic capacity, and higher tissue glycogen stores than their subtidal counterparts. Journal of Comparative Physiology B: Biochemical, Systemic, and Environmental Physiology. O'Rorke, R., Lavery, S.D., Wang, M., Gallego, R., Waite, A.M., Beckley, L.E., Thompson, P.A., Jeffs, A.G. Phyllosomata associated with large gelatinous zooplankton: hitching rides and stealing bites. ICES Journal of Marine Science. Sayre, R., Noble, S., Hamann, S., Smith, R., Wright, D., Breyer, S., Butler, K., Van Graafeiland, K., Frye, C., Karagulle, D., Hopkins, D., Stephens, D., Kelly, K., Basher, Z., Burton, D., Cress, J., Atkins, K., Van Sistine, D.P., Friesen, B., Allee, R., Allen, T., Aniello, P., Asaad, I., Costello, M.J., Goodin, K., Harris, P., Kavanaugh, M., Lillis, H., Manca, E., Muller-Karger, F., Nyberg, B., Parsons, R., Saarinen, J., Steiner, J., Reed, A. A new 30 meter resolution global shoreline vector and associated global islands database for the development of standardized ecological coastal units. Journal of Operational Oceanography. Taylor, R.B. Phylum Priapulida. In: New Zealand coastal marine invertebrates, vol. 2. Cook, S. de C. (ed.). Canterbury University Press. 2019 Asaad, I., Lundquist, C.J., Erdmann, M.V., Costello, M.J. 2019. An interactive atlas for marine biodiversity conservation in the Coral Triangle. Earth System Science Data 11: 163-174. Bates, A.E., Cooke, R.S.C., Duncan, M.I., Edgar, G.J., Bruno, J.F., Benedetti-Cecchi, L., Côté, I.M., Lefcheck, J.S., Costello, M.J., Barrett, N., Bird, T.J., Fenberg, P.B., Stuart-Smith, R.D. 2019. Climate resilience in marine protected areas and the ‘Protection Paradox’. Biological Conservation 236: 305-314. Blain, C.O., Shears, N.T. 2019. Seasonal and spatial variation in photosynthetic response of the kelp Ecklonia radiata across a turbidity gradient. Photosynthesis Research 140: 21-38. Cetina-Heredia, P., Roughan, M., Liggins, G., Coleman, M.A., Jeffs, A. 2019. Mesoscale circulation determines broad spatio-temporal settlement patterns of lobster. PLoS ONE 14 (2): e0211722. Charry, M.P., Northcott, G.L., Gaw, S., Keesing, V., Costello, M.J., Tremblay, L.A. 2019. Development of acute and chronic toxicity bioassays using the pelagic copepod Gladioferens pectinatus. Ecotoxicology and Environmental Safety 174: 611-617. Costello, M.J., Beard, K.H., Primack, R.B., Devictor, V., Bates, A.E. 2019. Are killer bees good for coffee? The contribution of a paper's title and other factors to its future citations. Biological Conservation 229: A1-A5. Davie, P.S., Walker, S.P., Perrott, M.R., Symonds, J.E., Preece, M., Lovett, B.A., Munday, J.S. 2019. Vertebral fusions in farmed Chinook salmon (Oncorhynchus tshawytscha) in New Zealand. Journal of Fish Diseases 42: 965-974. Dayton, P.K., Jarrell, S.C., Kim, S., Parnell, E., P., Thrush, S.F., Hammerstrom, K., Leichter, J.J. 2019. Benthic responses to an Antarctic regime shift: food particle size and recruitment biology. Ecological Applications 29: e01823. Dayton, P.K., Oliver, J.S., Thrush, S.F., Hammerstrom, K. 2019. Bacteria defend carrion from scavengers. Antarctic Science 31: 13-15. De La Fuente, G., Asnaghi, V., Chiantore, M., Thrush, S., Povero, P., Vassallo, P., Petrillo, M., Paoli, C. 2019. The effect of Cystoseira canopy on the value of midlittoral habitats in NW Mediterranean, an emergy assessment. Ecological Modelling 404: 1-11. Devaux, J.B.L., Hedges, C.P., Birch, N., Herbert, N., Renshaw, G.M.C., Hickey, A.J.R. 2019. Acidosis maintains the function of brain mitochondria in hypoxia-tolerant triplefin fish: a strategy to survive acute hypoxic exposure? Frontiers in Physiology 9: 1941. Hartebrodt, L. 2019. The biology, ecology, and societal importance of marine isopods. In: Encyclopedia of the world's biomes. https://doi.org/10.1016/B978-0-12-409548-9.11682-3 Heasman, K.G., Jeffs, A.G. 2019. Fecundity and potential juvenile production for aquaculture of the New Zealand Scampi, Metanephrops challengeri (Balss, 1914) (Decapoda: Nephropidae). Aquaculture 511: 634184. Jetz, W., McGeoch, M.A., Guralnick, R., Ferrier, S., Beck, J., Costello, M.J., Fernandez, M., Geller, G.N., Keil, P., Merow, C., Meyer, C., Muller-Karger, F.E., Pereira, H.M., Regan, E.C., Schmeller, D.S., Turak, E. 2019. Essential biodiversity variables for mapping and monitoring species populations. Nature Ecology and Evolution 3: 539-551. Jones, A.T., Lavery, S.D., Le Port, A., Wang, Y.-G., Blower, D., Ovenden, J. 2019. Sweepstakes reproductive success is absent in a New Zealand snapper (Chrysophrus auratus) population protected from fishing despite “tiny” Ne/N ratios elsewhere. Molecular Ecology, 28: 2986-2995. Junge, C., Donnellan, S.C., Huveneers, C., Bradshaw, C.J.A., Simon, A., Drew, M., Duffy, C., Johnson, G., Cliff, G., Braccini, M., Cutmore, S.C., Butcher, P., McAuley, R., Peddemors, V., Rogers, P., Gillanders, B.M. 2019. Comparative population genomics confirms little population structure in two commercially targeted carcharhinid sharks. Marine Biology 166: 16. Kroh, A., Costello, M.J., Horton, T. 2019. Biodiversity databases in the future: reply to Cene Fišer. Trends in Ecology and Evolution 34: 185-186. Lovett, B.A., Firth, E.C., Plank, L.D., Symonds, J.E., Preece, M.A., Herbert, N.A. 2019. Investigating a relationship between body composition and spinal curvature in farmed adult New Zealand king salmon (Oncorhynchus tshawytscha): a novel application of dual-energy X-ray absorptiometry. Aquaculture 502: 48-55. Montgomery, J., Perks, K. 2019. Understanding cerebellum in vertebrate neuroethology: from sensing in sharks and electric fish to motor sequences in movement and birdsong. Behavioral Neuroscience 133: 267-281. Nahmad-Rohen, L., Vorobyev, M. 2019. Contrast sensitivity and behavioural evidence for lateral inhibition in octopus. Biology Letters 15: 134. Norrie, C.R., Dunphy, B.J., Ragg, N.L.C., Lundquist, C.J. 2019. Comparative influence of genetics, ontogeny and the environment on elemental fingerprints in the shell of Perna canaliculus. Scientific Reports 9: 8533. Pamungkas, J., Glasby, C.J., Read, G.B., Wilson, S.P., Costello, M.J. 2019. Progress and perspectives in the discovery of polychaete worms (Annelida) of the world. Helgoland Marine Research 73: 4. Putland, R.L., Montgomery, J.C., Radford, C.A. 2019. Ecology of fish hearing. Journal of Fish Biology 95: 39-52. Radford, C., Slater, M. 2019. Soundscapes in aquaculture systems. Aquaculture Environment Interactions 11: 53-62. Roycroft, E.J., Le Port, A., Lavery, S.D. 2019. Population structure and male-biased dispersal in the short-tail stingray Bathytoshia brevicaudata (Myliobatoidei: Dasyatidae). Conservation Genetics 20: 717-728. Saeedi, H., Costello, M.J. 2019. The biology, ecology, and societal importance of razor clams. In: Encyclopedia of the world's biomes. https://doi.org/10.1016/B978-0-12-409548-9.11681-1 Saeedi, H., Costello, M.J., Warren, D., Brandt, A. 2019. Latitudinal and bathymetrical species richness patterns in the NW Pacific and adjacent Arctic Ocean. Scientific Reports 9: 9303. South, P.M., Floerl, O., Jeffs, A.G. 2019. The role of biofouling development in the loss of seed mussels in aquaculture. Biofouling 35: 259-272. Suong, N.T., Banks, J.C., Fidler, A., Jeffs, A., Wakeman, K.C., Webb, S. 2019. PCR and histology identify new bivalve hosts of Apicomplexan-X (APX), a common parasite of the New Zealand flat oyster Ostrea chilensis. Diseases of Aquatic Organisms 132: 181-189. Taylor, R.B. 2019. Epifauna and epiflora. In: Encyclopedia of ecology, 2nd ed., Vol. 3. Fath, B.D. (ed.). Elsevier, Oxford. pp. 375-380. Wilcox, M., Jeffs, A. 2019. Impacts of sea star predation on mussel bed restoration. Restoration Ecology 27: 189-197. Woodings, L.N., Murphy, N.P., Jeffs, A., Suthers, I.M., Liggins, G.W., Strugnell, J.M. 2019. Distribution of Palinuridae and Scyllaridae phyllosoma larvae within the East Australian Current: a climate change hot spot. Marine and Freshwater Research 70: 1020-1033. Yorke, C.E., Hanns, B., Shears, N., Page, H.M., Miller, R.J. 2019. Living kelp versus plankton as food sources for suspension feeders. Marine Ecology Progress Series 614: 21-23. Zha, H., Lewis, G., Waite, D.W., Wu, J., Chang, K., Dong, Y., Jeffs, A. 2019. Bacterial communities associated with tail fan necrosis in spiny lobster, Jasus edwardsii. FEMS Microbiology Ecology 95: fiz070 Zhao, Q., Costello, M.J. 2019. Marine ecosystems of the world. In: Encyclopedia of the world's biomes. https://doi.org/10.1016/B978-0-12-409548-9.11688-4 Zhao, Q., Costello, M.J. 2019. Summer and winter ecosystems of the world ocean photic zone. Ecological Research 34: 457-471. 2018 Allison, A.E.F., Dickson, M.E., Fisher, K.T., Thrush, S.F. 2018. Dilemmas of modelling and decision-making in environmental research. Environmental Modelling and Software 99: 147-155. Arfianti, T., Wilson, S., Costello, M.J. 2018. Progress in the discovery of amphipod crustaceans. PeerJ 2018 (7): e5187. Asaad, I., Lundquist, C.J., Erdmann, M.V., Costello, M.J. 2018. Delineating priority areas for marine biodiversity conservation in the Coral Triangle. Biological Conservation 222: 198- 211. Asaad, I., Lundquist, C.J., Erdmann, M.V., Van Hooidonk, R., Costello, M.J.
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  • An Accuracy Assessment of Ultrasonic Transmitter Locations Determined by Mobile Telemetry in Aquatic Systems

    An Accuracy Assessment of Ultrasonic Transmitter Locations Determined by Mobile Telemetry in Aquatic Systems

    Fisheries Management and Ecology Fisheries Management and Ecology, 2014 Management and Ecological Note An accuracy assessment of ultrasonic transmitter locations determined by mobile telemetry in aquatic systems D.A.JAMES,J.L.FISCHER,J.D.LAUBE&M.E.SPINDLER U.S. Fish and Wildlife Service, Great Plains Fish and Wildlife Conservation Office, Pierre, SD, USA Underwater telemetry is a common and effective method This study was conducted at two sites, Hipple Lake and to evaluate gear efficiency and the behaviour, physiology the upstream, riverine section of Lake Sharpe approxi- and mortality of free-ranging fish (Winter 1996; Lucas mately 13 km downstream from Oahe Dam, both within & Baras 2001; Wanner et al. 2007; Guy et al. 2009; the Missouri River, South Dakota, USA. Hipple Lake is a Cooke et al. 2013; Friedl et al. 2013). A telemetry sys- 178 ha backwater of upper Lake Sharpe near Pierre, South tem basically consists of a transmitter that emits radio Dakota. Average depth in Hipple Lake was about 2.0 m (27–300 MHz) or ultrasonic signals (27–300 kHz), an (D. A. James, personal observation). Lake Sharpe is a antenna or hydrophone that detects the signal (passively 128-km long, flow-through reservoir that extends from or actively) and a receiver that decodes signals into audi- Oahe Dam near Pierre, South Dakota, downstream to Big ble sounds (Winter 1996). Each type of telemetry system Bend Dam near Chamberlain, South Dakota. The com- has a set of advantages and disadvantages (Cooke et al. bined riverine and lacustrine areas of Lake Sharpe have a 2013).
  • [I]Metanephrops Challengeri[I]

    [I]Metanephrops Challengeri[I]

    A peer-reviewed version of this preprint was published in PeerJ on 20 September 2018. View the peer-reviewed version (peerj.com/articles/5641), which is the preferred citable publication unless you specifically need to cite this preprint. van der Reis AL, Laroche O, Jeffs AG, Lavery SD. 2018. Preliminary analysis of New Zealand scampi (Metanephrops challengeri) diet using metabarcoding. PeerJ 6:e5641 https://doi.org/10.7717/peerj.5641 Preliminary analysis of New Zealand scampi (Metanephrops challengeri) diet using metabarcoding Aimee L van der Reis Corresp., 1 , Olivier Laroche 2 , Andrew G Jeffs 1, 2 , Shane D Lavery 1, 2 1 Institute of Marine Science, University of Auckland, Auckland, New Zealand 2 School of Biological Sciences, University of Auckland, Auckland, New Zealand Corresponding Author: Aimee L van der Reis Email address: [email protected] Deep sea lobsters are highly valued for seafood and provide the basis of important commercial fisheries in many parts of the world. Despite their economic significance, relatively little is known about their natural diets. Microscopic analyses of foregut content in some species have suffered from low taxonomic resolution, with many of the dietary items difficult to reliably identify as their tissue is easily digested. DNA metabarcoding has the potential to provide greater taxonomic resolution of the diet of the New Zealand scampi (Metanephrops challengeri) through the identification of gut contents, but a number of methodological concerns need to be overcome first to ensure optimum DNA metabarcoding results. In this study, a range of methodological parameters were tested to determine the optimum protocols for DNA metabarcoding, and provide a first view of M.