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Introduction
Publications
Reports
Abstracts

Northeast Fisheries Science Center Reference Document 14-12

Northeast Fisheries Science Center Publications, Reports, and Abstracts for Calendar Year 2013

compiled by Laura Garner and Anne O'Brien
NOAA Fisheries, Northeast Fisheries Science Center, 166 Water Street, Woods Hole MA 02543

Web version posted October 30, 2014

Citation: Garner L, O'Brien A. 2014. Northeast Fisheries Science Center Publications, Reports, and Abstracts for Calendar Year 2013. NEFSC Ref Doc 14-12; 22 p. Available from: National Marine Fisheries Service, 166 Water Street, Woods Hole, MA 02543-1026, or online at 10.7289/V5KW5D1N

Information Quality Act Compliance: In accordance with section 515 of Public Law 106-554, the Northeast Fisheries Science Center completed both technical and policy reviews for this report. These predissemination reviews are on file at the NEFSC Editorial Office.

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Introduction

The following bibliography consists of three sections: (1) anonymously peer-reviewed publications ("publications"); (2) transparently peer-reviewed and non-peer reviewed publications ("reports"); and (3) abstracts for oral presentations and poster displays. The bibliography covers works with a 2013 publication or presentation date, prepared by Northeast Fisheries Science Center (NEFSC) employees. (Publications appearing “online first” in 2013 but with a 2014 publication date are not included in this list.) Bibliographies of publications, reports, and abstracts for earlier years are available online at: http://nefsc.noaa.gov/publications/lists/.

Availability varies for each work. Web links to online publications and Digital Object Identifiers (DOI) are provided when possible.

Editorial treatment of bibliographic entries is based on the Council of Science Editors style manual, seventh edition[1].

Publications

Able KW, Wuenschel M, Grothues TM, Vasslides JM, Rowe P. 2013. Do surf zones in New Jersey provide "nursery" habitat for southern fishes? Environ Biol Fishes. 96: 661-675. DOI: 10.1007/s10641-012-0056-8

Appeltans W, et al (including Collins AG). 2013. The magnitude of global marine biodiversity. Curr Biol. 22(23):2189–2202. DOI: 10.1016/j.cub.2012.09.036

Arendt MD, Schwenter JA, Witherington BE, Meylan AB, Saba VS. 2013. Historical versus contemporary climate forcing on the annual nesting variability of loggerhead sea turtles in the Northwest Atlantic Ocean. PLoS ONE. 8(12):e81097. DOI: 10.1371/journal.pone.0081097

Auster PJ, Kilgour M, Packer D, Waller R, Auscavitch S, Watling L. 2013. Octocoral gardens in the Gulf of Maine (NW Atlantic). Biodiversity. 14(4):193-194. DOI: 10.1080/14888386.2013.850446

Auster PJ, Packer DB, Kilgour M, Watling L. 2013. Supplementary comment: conservation of deep-sea corals off the northeast United States. Biodiversity. 14(4):195. DOI 10.1080/14888386. 2013. 850885

Backus EH, Collette BB. 2013. Obituary: Richard Haven Backus (1922-2012). Copeia. 2013(1):173-176. DOI: 10.1643/OT-12-141

Basilone G, Bonanno A, Patti B, Mazzola S, Barra M, Cuttitta A, McBride R. 2013. Spawning site selection by European anchovy (Engraulis encrasicolus) in relation to oceanographic conditions in the Strait of Sicily. Fish Oceanogr. 22(4):309-323. DOI: 10.1111/fog.12024

Baumann H, Sutherland SJ, McBride RS. 2013. Longitudinal length back-calculations from otoliths and scales differ systematically in haddock. Trans Am Fish Soc. 142(1):184-192. DOI: 10.1080/00028487.2012.728168

Baumgartner MF, Fratantoni DM, Hurst T, Brown MW, Cole TVN, Van Parijs SM, Johnson MP. 2013. Real-time reporting of baleen whale passive acoustic detections from ocean gliders. J Acoust Soc Am. 134(3):1814-1823. DOI: 10.1121/1.4816406

Bernaldo de Quirós Y, Seewald J, Sylva S, Greer B, Niemeyer M, Bogomolni A. 2013. Compositional discrimination of decompression and decomposition gas bubbles in bycaught seals and dolphins. PLoS ONE. 8:12; e83994. DOI: 10.1371/journal.pone.0083994

Betancur-R R, Li CH, Munroe TA, Ballesteros J, Orti G. 2013. Addressing gene tree discordance and non-stationarity to resolve a multi-locus phylogeny of the flatfishes (Teleostei: Pleuronectiformes). System Zool. 62(5)763-785. DOI: 10.1093/sysbio/syt039

Brooks EN. 2013. Effects of variable reproductive potential on reference points. Fish Res. 138:152-158. DOI: 10.1016/j.fishres.2012.06.003

Capossela KM, Fabrizio MC, Brill RW. 2013. Migratory and within-estuary behaviors of adult summer flounder (Paralichthys dentatus) in a lagoon system of the southern mid-Atlantic Bight. Fish Bull. 111:189-201. DOI: 10.7755/FB.111.2.6

Cholewiak D, Baumann-Pickering S, Van Parijs S. 2013. Description of sounds associated with Sowerby's beaked whales (Mesoplodon bidens) in the western North Atlantic Ocean. J Acoust Soc Am. 134(5):3905-12. DOI: 10.1121/1.4823843

Cole TVN, Hamilton P, Henry AG, Duley P, Pace RM III, White BN, Frasier T. 2013. Evidence of a North Atlantic right whale Eubalaena glacialis mating ground. Endang Species Res. 21: 55-64. DOI: 10.3354/esr00507

Collette BB. 2013. Obituary: Nikolai Vasil'evich Parin (1932-2012). Copeia. 2013(4):768-780. DOI: 10.1643/OT-13-102

Collette BB, Polidoro B, Carpenter K. 2013. Corrected numbers for fish on Red List. Nature. 495(7439):47. DOI: 10.1038/495047a

Cowen RK, Greer A, Guigand CM, Hare JA, Richardson DE, Walsh HJ. 2013. Evaluation of the In Situ Ichthyoplankton Imaging System (ISIIS): comparison with the traditional (bongo net) sampler. Fish Bull. 111(1):1-12. DOI: 10.7755/FB.111.1.1

Curti KL, Collie JS, Legault CM, Link JS. 2013. Evaluating the performance of a multispecies statistical catch-at-age model. Can J Fish Aquat Sci. 70(3): 470-484. DOI: 10.1139/cjfas-2012-0229

DePiper G, Higgins N, Lipton D, Stocking A.  2013. Auction design, incentives, and buying back Maryland and Virginia crab licenses. Can J Agric Econ. 61(2):353-370. DOI: 10.1111/cjag.12005

Deroba JJ, Schueller AM. 2013. Performance of stock assessments with misspecified age- and time-varying natural mortality. Fish Res. 146:27-40. DOI: 10.1016/j.fishres.2013.03.015

Diaz MC, Thacker RW, Redmond NE, Matterson KO, Collins AG. 2013. Phylogenetic novelties and geographic anomalies among tropical Verongida. Integr Comp Biol. 53 (3):482-494. DOI:10.1093/icb/ict033

Dohrmann M, Vargas S, Janussen D, Collins AG, Wörheide G. 2013. Molecular paleobiology of early-branching animals: integrating DNA and fossils elucidates the evolutionary history of hexactinellid sponges. Paleobiology. 39(1): 95-108. DOI: 10.1666/0094-8373-39.1.95

Fay G, Large SI, Link JS, Gamble RJ. 2013. Testing systemic fishing responses with ecosystem indicators. Ecol Model. 265(10): 45-55. DOI: 10.1016/j.ecolmodel.2013.05.016

Friedland KD, Kane J, Hare JA, Lough G, Fratantoni PS, Fogarty MJ, Nye JA. 2013. Thermal habitat constraints on zooplankton species associated with Atlantic cod (Gadus morhua) on the US Northeast Continental Shelf. Prog Oceanogr. 116:1-13. DOI: 10.1016/j.pocean.2013.05.011

Fuentes S, Wikfors GH, Meseck SL. 2013. Silicon deficiency induces alkaline phosphatase enzyme activity in cultures of four marine diatoms. Estuar Coasts. 37:312-324. DOI: 10.1007/s12237-013-9695-z

Galimany E, Dixon MS, Rose JM, Wikfors GH. 2013. Quantifying feeding behavior of ribbed mussels (Geukensia demissa) in two urban sites (Long Island Sound, USA) with different seston characteristics. Estuar Coasts. 36:1265-1273. DOI: 10.1007/s12237-013-9633-0

Gervelis BJ, Natanson LJ. 2013. Age and growth of the thresher shark, Alopias vulpinus, in the western North Atlantic Ocean. Trans Am Fish Soc. 142(6)1535-1545. DOI: 10.1080/00028487.2013.815658

Glaser SM, Fogarty MJ, Liu H, Altman I, Hsieh C, Kaufman L, MacCall AD, Rosenberg AA, Ye H, Sugihara G. 2013. Complex dynamics may limit prediction in marine fisheries. Fish Fish. DOI: 10.1111/faf.12037

Grossmann MM, Lindsay DJ, Collins AG. 2013. The end of an enigmatic taxon: Eudoxia macra is the eudoxid stage of Lensia cossack (Siphonophora, Cnidaria). Syst Biodivers. 11(3):381-387. DOI: 10.1080/14772000. 2013. 825658

Gurshin C, Howell H, Jech M. 2013. Synoptic acoustic and trawl surveys of pre-spawning Atlantic cod in the Gulf of Maine cod spawning protection area. Fish Res. 141:44-61. DOI: 10.1016/j.fishres.2012.09.018

Hajdu E, de Paula T, Redmond NE, Gomes B, Collins AG, Lobo-Hajdu G. 2013. Mycalina: another crack in the Poecilosclerida framework. Integr Comp Biol. 53 (3): 462-472.DOI: 10.1093/icb/ict074

Hare J, Richardson D. 2013. The use of early life stages in stock identification studies. In: Cadrin SX, Kerr LA, Mariani S, eds. Stock Identification Methods. Second Edition. London (UK): Academic Press; p 329-364.

Harrison GF, Kim K, Collins AG. 2013. Low genetic diversity of the putatively introduced, brackish water hydrozoan, Blackfordia virginica (Leptothecata: Blackfordiidae), throughout the United States, with a new record for Lake Pontchartrain, Louisiana. Proc Biol Soc Wash. 126: 91-102. DOI: 10.2988/0006-324X-126.2.91

Hart DR. 2013. Quantifying the tradeoff between precaution and yield in fishery reference points. ICES J Mar Sci. 70: 591-603. DOI: 10.1093/icesjms/fss204

Hart DR, Jacobson L, Tang J. 2013. To split or not to split: Assessment of Georges Bank sea scallops in the presence of marine protected areas. Fish Res. 144:74-83. DOI: 10.1016/j.fishres.2012.11.004

Hawkes JP, Saunders R, Vashon A, Cooperman MS. 2013. Assessing efficacy of non-lethal harassment of double-crested cormorants to improve Atlantic salmon smolt survival. Northeast Nat. 20(1):1-18. DOI: 10.1656/045.020.0101

Hernandez KM, Risch D, Cholewiak DM, Dean MJ, Hatch LT, Hoffman WS, Rice AN, Zemeckis D, Van Parijs SM. 2013. Acoustic monitoring of Atlantic cod (Gadus morhua) in Massachusetts Bay: implications for management and conservation. ICES J Mar Sci. 70 (3): 628-635. DOI: 10.1093/icesjms/fst003

Hill MS, Hill AL, Lopez J, Peterson KJ, Pomponi S, Diaz MC, Thacker RW, Adamska M, Boury-Esnault N, Cárdenas P, Chaves-Fonnegra A, Danka E, De Laine B-O, Formica D, Hajdu E. 2013. Reconstruction of family-level phylogenetic relationships within demospongiae (Porifera) using nuclear encoded housekeeping genes. PLoS ONE. 8(1): e50437. DOI:10.1371/journal.pone.0050437

Himes-Cornell A, Orbach M (lead authors); Allen S, Auad G, Boatman M, Clay PM, Dalton M, Herrick S, Kotowicz D, Little P, Lopez C, Loring P, Niemeier P, Norman K, Pfeiffer L, Plummer M, Rust M, Singer M, Speirs. 2013. Impacts of climate change on human uses of the ocean and ocean services. In: Griffis R, Howard J, eds. Oceans and Marine Resources in a Changing Climate: Technical Input to the 2013 National Climate Assessment. Washington (DC): Island Press; p 64-118.

Holland DS, Kitts A, Pinto da Silva P, Wiersma J. 2013. Social capital and the success of harvest cooperatives in the New England groundfish fishery. Mar Resour Econ. 28: 133-153. DOI: 10.5950/0738-1360-28.2.133

Howard J, Babij E, Griffis R, Helmuth B, Himes-Cornell A, Niemier P, Orbach M, Petes L, Allen S, Auad G, Auer C, Beard R, Boatman M, Bond N, Boyer T, Brown D, Clay P, et al. 2013. Oceans and marine resources in a changing climate. In: Hughes RN, Hughes DJ, Smith IP, eds. Oceanography and Marine Biology: An Annual Review, Vol 51. Boca Raton (FL): CRC Press; p 71-192.

Jacobson LD, McClatchie S. 2013. Comment on temperature-dependent stock–recruit modeling for Pacific sardine (Sardinops sagax) in Jacobson and MacCall (1995), McClatchie et al. (2010), and Lindegren and Checkley (2013).  Can J Fish Aquat Sci. 70: 1566-1569. DOI: 10.1139/cjfas-2013-0128

Johnson DL, Fogarty MJ. 2013. Intercalibration of MOCNESS and bongo nets: Assessing relative efficiency for ichthyoplankton. Prog Oceanogr. 108:43-71. DOI: 10.1016/j.pocean.2012.10.007

Kane J. 2013. Long-term abundance and distribution trends of the cladoceran Penilia avirostris in the US Northeast Shelf Ecosystem. J Northwest Atl Fish Sci. 45: 1-10. DOI: 10.2960/J.v45.m682

Kayal E, Roure B, Philippe H, Collins AG, Lavrov DV. 2013. Cnidarian phylogenetic relationships as revealed by mitogenomics. BMC Evol Biol. 13:5. DOI: 10.1186/1471-2148-13-5

Klautau, Michelle, Rapp, Hans, Collins, Allen, Russo Claudia. 2013. A molecular phylogeny of the order Clathrinida rekindles and refines Haeckel’s taxonomic proposal for calcareous sponges. Integr Comp Biol. 53 (3): 447-461. DOI: 10.1093/icb/ict039

Large SI, Fay G, Friedland KD, Link JS. 2013. Defining trends and thresholds in responses of ecological indicators to fishing and environmental pressures. ICES J Mar Sci. 70:755-767. DOI: 10.1093/icesjms/fst067

Lee MY, Munroe TA, Shao KT. 2013. Symphurus orientalis (Bleeker) redefined based on morphological and molecular characters (Pleuronectiformes: Cynoglossidae). Zootaxa. 3620(3):379-403. DOI: 10.11646/zootaxa.3620.3.3

Lee M, Thunberg EM. 2013. An inverse demand system for New England groundfish: welfare analysis of the transition to catch share management. Am J Agric Econ. 95(5): 1178-1195.  DOI: 10.1093/ajae/aat061

Legault CM, Brooks EN. 2013. Can stock-recruitment points determine which spawning potential ratio is the best proxy for maximum sustainable yield reference points? ICES J Mar Sci. 70(6):1075-1080. DOI: 10.1093/icesjms/fst105

Lewis C, Bentlage B, Yanagihara A, Gillan W, Van Blerk J, Keil D, Bely AE, Collins AG. 2013. Redescription of Alatina alata (Reynaud 1830) (Cnidaria: Cubozoa) from Bonaire, Dutch Caribbean. Zootaxa. 3737 (4):473–487. DOI: 10.11646/zootaxa.3737.4.8

Lucey SM, Duffy WJ, Adams E, Marshall H, Nichols O, Thompson K. 2013. A review of scientific communication for natural resource professionals. Trans Am Fish Soc. 142(4):1154-1155. DOI: 10.1080/00028487.2013.810015

Lucey SM, Fogarty MJ. 2013. Operational fisheries in New England: Linking current fishing patterns to proposed ecological production units. Fish Res. 141:3-12. DOI: 10.1016/j.fishres.2012.05.002

Marques AC, Maronna MM, Collins AG. 2013. Putting GenBank data on the map. Science. 341:1341-1341. DOI: 10.1126/science.341.6152.1341-a

McBride RS, Somarakis S, Fitzhugh GR, Albert A, Yaragina NA, Wuenschel MJ, Alonso-Fernández A, Basilone G. 2013. Energy acquisition and allocation to egg production in relation to fish reproductive strategies. Fish Fish. DOI: 10.1111/faf.12043

McBride RS, Vidal TE, Cadrin SX. 2013. Changes in size and age at maturity of the northern stock of tilefish (Lopholatilus chamaeleonticeps) after a period of overfishing. Fish Bull. 111(2):161-174. DOI: 10.7755/FB.111.2.4

McBride RS, Wuenschel MJ, Nitschke P, Thornton G, King JR. 2013. Latitudinal and stock-specific variation in size- and age-at-maturity of female winter flounder, Pseudopleuronectes americanus, as determined with gonad histology. J Sea Res. 75:41-51. DOI: 10.1016/j.seares.2012.04.005

McCormick SD, Sheehan T, Björnsson BT, Lipsky C, Kocik J, Regish AM, O’Dea MF. 2013. Physiological and endocrine changes in Atlantic salmon smolts during hatchery rearing, downstream migration, and ocean entry. Can J Fish Aquat Sci. 70:105-118. DOI: 10.1139/cjfas-2012-0151

McElroy WD, Press YK, Towle EK, Wuenschel MJ, McBride RS. 2013. Differences in female individual reproductive potential among three stocks of winter flounder, Pseudopleuronectes americanus. J Sea Res. 75:52-61. DOI: 10.1016/j.seares.2012.05.018

McLellan WA, Berman M, Cole T, Costidis AM, Knowlton A, Neilson J, Pabst DA, Raverty S. 2013. Blunt force trauma induced by vessel collisions with large whales. In: Moore MJ, van der Hoop J, Barco SG, Costidis AM, Gulland FM, Jepson PD, Moore KT, Raverty S, McLellan WA, eds. Criteria and case definitions for serious injury and death of pinnipeds and cetaceans caused by anthropogenic trauma. Dis Aquat Org. 103:245-251. DOI: 10.3354/dao02566

Miller AS, Cadrin SX, Stevens BG. 2013. Effects of epizootic shell disease on egg quality of the American lobster. J Crustac Biol. 33(4):461-469. DOI: 10.2307/23446215

Miller TJ. 2013. A comparison of hierarchical models for relative catch efficiency based on paired-gear data for U.S. northwest Atlantic fish stocks. Can J Fish Aquat Sci. 70(9): 1306-1316. DOI: 10.1139/cjfas-2013-0136

Miranda LS, Collins AG, Marques AC. 2013. Internal anatomy of Haliclystus antarcticus (Cnidaria, Staurozoa) with a discussion on histological features used in staurozoan taxonomy. J Morphol. 274(12):1365-1383. DOI: 10.1080/14772000.2013.825658

Moore MJ, Garron M, Hall L, Henry A, Landry S, Pettis H, Robbins J, Rotstein D, van der Hoop J, Mattila D. 2013. Chronic entanglement trauma of pininipeds and cetaceans. In: Moore MJ, van der Hoop J, Barco SG, Costidis AM, Gulland FM, Jepson PD, Moore KT, Raverty S, McLellan WA, eds. Theme Section: Criteria and case definitions for serious injury and death of pinnipeds and cetaceans caused by anthropogenic trauma. Dis Aquat Org. 103:240-245. DOI: 10.3354/dao02566

Morrow CC, Redmond NE, Picton BE, Thacker RW, Collins AG, Maggs CA, Sigwart JD, Allcock AL. 2013. Molecular phylogenies support homoplasy of multiple morphological characters used in the taxonomy of Heteroscleromorpha (Porifera: Demospongiae). Integr Comp Biol. 53 (3): 428-446. DOI: 10.1093/icb/ict065

Murray K, Orphanides C. 2013. Estimating risk of loggerhead turtle Caretta caretta bycatch in the US mid-Atlantic using fishery independent and dependent data. Mar Ecol Prog Ser. 47:259-270. DOI: 10.3354/meps10173

Natanson LJ, Gervelis B. 2013. The reproductive biology of the common thresher shark in the western North Atlantic Ocean. Trans Am Fish Soc. 142(6):1546-1562. DOI: 10.1080/00028487.2013.811099

Natanson LJ, Gervelis BJ, Winton MV, Hamady LL, Gulak SJB, Carlson JK. 2013. Pre- and post management growth comparisons for Carcharhinus obscurus in the northwestern Atlantic Ocean,with age validation. Environ Biol Fishes.  DOI 10.1007/s10641-01300189-4

Nawrocki AM, Collins, AG, Hirano YM, Schuchert P, Cartwright P. 2013. Phylogenetic placement of Hydra and relationships within Aplanulata (Cnidaria: Hydrozoa). Molec Phylogen Evol. 67:60-71. DOI: 10.1016/j.ympev.2012.12.016

Nye JA, Gamble RJ, Link JS. 2013. The relative impact of warming and removing top predators on the Northeast US large marine biotic community. Ecol Model. 264: 157-168. DOI: 10.1016/j.ecolmodel.2012.08.019

Orphanides CD, Palka DL. 2013. Analysis of harbor porpoise gillnet bycatch, compliance, and enforcement trends in the US northwestern Atlantic, January 1999 to May 2010. Endang Species Res. 20:251-269. DOI: 10.3354/esr00499

Perry DM, Redman DH, Mercaldo-Allen R, Kuropat CA, Widman Jr. JC. 2013. Growth of juvenile scup fed two commercial diets. N Am J Aqua. 75(3):352-355. DOI: 10.1080/15222055.2013.786007

Perry MC, Olsen GH, Richards RA, Osenton PC. 2013. Predation on dovekies by goosefish over deep water in the Northwest Atlantic Ocean. Northeast Nat. 20(1):148-154. DOI: 10.1656/045.020.0112

Persson A, Smith BC. 2013. Cell density-dependent swimming patterns of Alexandrium fundyense early stationary phase cells. Aquat Microb Ecol. 68:251-258. DOI: 10.3354/ame01617

Persson A, Smith BC, Morton S, Shuler A, Wikfors GH. 2013. Sexual life stages and temperature dependent morphological changes allow cryptic occurrence of the Florida red tide dinoflagellate Karenia brevis. Harmful Algae. 30:1-9. DOI: 10.1016/j.hal.2013.08.004

Persson A, Smith BC, Wikfors GH, Alix J. 2013. Differences in swimming pattern between life cycle stages of the toxic dinoflagellate Alexandrium fundyense. Harmful Algae. 21:36-43. DOI: 10.1016/j.hal.2012.11.005

Redmond NE, Morrow CC, Thacker RW, Diaz MC, Boury-Esnault N, Cárdenas P, Hajdu E, Hill AL, Hill MS, Lôbo-Hajdu G, Picton BE, Pomponi SA, Alvarez B, Hubert R, Collins AG. 2013. Phylogeny and systematics of demospongiae in light of new small subunit ribosomal DNA sequences. Integ Comp Biol. 53 (3): 388-415. DOI: 10.1093/icb/ict078

Reynaud Y, Pitchford S, De Decker S, Wikfors GH, Brown CL. 2013. Molecular typing of environmental and clinical strains of Vibrio vulnificus Isolated in the northeastern USA. PloS ONE. 8(12):e83357. DOI: 10.1371/journal.pone.0083357

Risch D, Clark CW, Dugan PJ, Popescu M, Siebert U, Van Parijs SM. 2013. Minke whale acoustic behavior and multi-year seasonal and diel vocalization patterns in Massachusetts Bay, USA. Mar Ecol Prog Ser. 489:279-295. DOI: 10.3354/meps10426

Rosa M, Holohan BA, Shumway SE, Bullard SG, Wikfors G, H, Morton S, Getchis T. 2013. Biofouling ascidians on aquaculture gear as potential vectors of harmful algal introductions. Harmful Algae. 23:1-7. DOI: 10.1016/j.hal.2012.11.008

Rosa M, Ward JE, Shumway SE, Wikfors GH, Pales-Espinosa E, Allam B. 2013. Effects of particle surface properties on feeding selectivity in the eastern oyster Crassostrea virginica and the blue mussel Mytilus edulis. J Exp Mar Biol Ecol. 446:320-327. DOI: 10.1016/j.jembe.2013.05.011

Ruzicka JJ, Steele JH, Ballerini T, Gaichas S, Ainley D. 2013. Dividing up the pie: whales, fish, and man as competitors. Prog Oceanogr. 116: 207-219. DOI: 10.1016/j.pocean.2013.07.009

Ruzicka J, Steele J, Gaichas S, Ballerini T, Gifford D, Brodeur R, Hofmann E. 2013. Analysis of energy flow in US GLOBEC ecosystems using end-to-end models. Oceanography. 26(4): 82-97. DOI: 10.5670/oceanog.2013.77

Saba VS. 2013. Oceanic habits and habitats: Dermochelys coriacea. In: Wyneken J, Musick J, Lohmann K, eds. The Biology of Sea Turtles, Volume III. Boca Raton (FL): CRC Press; p 163-188.

Sant'Anna VB, Collette BB, Godfrey SJ. 2013. †Belone countermani, a new Miocene needlefish (Belonidae) from the St. Marys Formation of Calvert Cliffs, Maryland. Proc Biol Soc Wash. 126(2): 137-150. DOI: 10.2988/0006-324X-126.2.137

Sherman K, Belkin I, Friedland KD, O'Reilly J. 2013. Changing states of North Atlantic large marine ecosystems. Environ Devel. 7: 46-58. DOI: 10.1016/j.envdev.2013.05.004

Smith BE, Collie JS, Lengyel NL. 2013. Effects of chronic bottom fishing on the benthic epifauna and diets of demersal fishes on northern Georges Bank. Mar Ecol Prog Ser. 472:199-217. DOI: 10.3354/meps10031

Smith-Vaniz WF, Collette BB. 2013. Fishes of Bermuda. aqua Int J Ichthyol. 19(4):165-186.

Stanistreet JE, Risch D, Van Parijs SM. 2013. Passive acoustic tracking of singing humpback whales (Megaptera novaeangliae) on a Northwest Atlantic feeding ground. PLoS ONE. 8(4): e61263. DOI: 10.1371/journal.pone.0061263

Stockwell JD, Weber TC, Baukus AJ, Jech JM. 2013. On the use of omnidirectional sonars and downwards-looking echosounders to assess pelagic fish distributions during and after midwater trawling. ICES J Mar Sci. 70(1):196-203. DOI: 10.1093/icesjms/fss139

Thacker R, Hill A, Hill M, Redmond N, Collins A Morrow C, Spicer L, Carmack C, Zappe M, Pohlmann D, Hall C, Diaz M C, Bangalore P. 2013. Nearly complete 28S rRNA gene sequences confirm new hypotheses of sponge evolution. Integr Comp Biol. 53(3):373-387. DOI: 10.1093/icb/ict071

Tyler JC, Collette BB, Broughton EA. 2013. Northern range extension to Georges Bank for Hollardia hollardi (reticulate spikefish) (Triacanthodidae). Northeast Nat. 20(4):N33-N36. DOI: 10.1656/045.020.0421

Valtierra RD, Holt RG, Cholewiak D, Van Parijs SM. 2013. Calling depths of baleen whales from single sensor data: Development of an autocorrelation method using multipath localization. J Acoust Soc Am. 134(3):2571-2581. DOI: 10.1121/1.4816582

Van Der Hoop JM, Moore MJ, Barco SG, Cole TVN, Daoust PY, Henry AG, Mcalpine DF, Mclellan WA, Wimmer T, Solow AR. 2013. Assessment of management to mitigate anthropogenic effects on large whales. Conserv Biol. 27(1):121-133. DOI: 10.1111/j.1523-1739.2012.01934.x

Van Opzeeland IC, Van Parijs S, Kindermann L, Burkhardt E, Boebel O. 2013. Calling in the cold: Pervasive acoustic presence of humpback whales (Megaptera novaeangliae) in Antarctic coastal waters. PLoS ONE. 8(9):e73007; DOI: 10.1371/journal.pone.0073007

Vitaliano J, Packer DB, Reid R, Guida VG. 2013. Broad-scale, dense amphipod tube aggregations on the sea bed: implications for resource species that utilize benthic habitats. Fish Oceanogr. 22(1):61-67. DOI: 10.1111/fog.1200

Walden JB. 2013. Economic health of the northeast (U.S.) multispecies trawl fleet 1996–2010. Fish Res. 139:98-104. DOI: 10.1016/j.fishres.2012.10.002

Weitkamp L, Goulette G, Hawkes J, O'Malley M, Lipsky C. 2013. Juvenile salmon in estuaries: comparisons between Atlantic and Pacific salmon. Rev Fish Biol Fish. DOI: 10.1007/s11160-014-9345-y.

Wenzel FW, Polloni PT, Craddock JE, Gannon D, Nicolas J, Read A, Rosel P. 2013. Food habits of Sowerby’s beaked whales, Mesoplodon bidens, taken in the western North Atlantic pelagic drift gillnet fishery. Fish Bull. 111(4):381-389. DOI: 10.7755/FB.111.4.7

Wikfors GH, Fernandez E. 2013. Induced bacteriovory in a declining culture of the mixotrophic dinoflagellate Prorocentrum minimum (Pavillard) Schiller. Int J Ecol. 2013:234372; DOI: 10.1155/2013/234372

Wood AD, Cadrin SX. 2013. Mortality and movement of yellowtail flounder (Limanda Ferruginea) tagged off New England.  Fish Bull. 111:279-287. DOI: 10.7755/FB.111.3.6

Wuenschel MJ, Able KW, Vasslides JM, Byrne D. 2013. Habitat and diet overlap of 4 piscivorous fishes: variation on the inner continental shelf off New Jersey. Fish Bull. 111:352-369.

Wuenschel MJ, McBride RS, Fitzhugh GR. 2013. Relations between total gonad energy and physiological measures of condition in the period leading up to spawning: Results of a laboratory experiment on black sea bass (Centropristis striata). Fish Res. 138:110-119. DOI: 10.1016/j.fishres.2012.05.012

Reports

Alix RJ, Schreiner W, Meseck SL. 2013. Construction of an inexpensive gravity sediment corer for micro-profiling O2 and pH in marine sediments. NOAA Tech Memo NMFS NE 224; 13 p.

Blaylock J, Wigley SE, Rago PJ, Mood M, Palmer MC. 2013. A brief description of Northeast region fish and invertebrate discard estimation for the 2013 update to the National Bycatch Report. NEFSC Ref Doc. 13-05; 38 p

Cholewiak D, Risch D, Valtierra R, Van Parijs SM. 2013. Methods for passive acoustic tracking of marine mammals: estimating calling rates, depths and detection probability for density estimation. In: Adam, O, Samaran F, directors. Detection, Classification and Localization of Marine Mammals Using Passive Acoustics. 2003-2013: 10 years of International Research; p 107-145.

Chute A, Hennen D, Russell R, Jacobson L. 2013. Stock assessment update for ocean quahogs (Arctica islandica) through 2011. NEFSC Ref Doc. 13-17; 156 p

Chute A, Jacobson L, Redding B. 2013. Clarification of methods used to determine deep sea red crab (Chaceon quinquedens) abundance from data collected during the 1974 photographic survey. NEFSC Ref Doc. 13-22; 19 p

Cole TVN, Henry AG. 2013. Serious injury determinations for baleen whale stocks along the Gulf of Mexico, United States East Coast and Atlantic Canadian Provinces, 2007-2011. NEFSC Ref Doc. 13-24; 14 p.

Fratantoni PS, Holzwarth-Davis T, Bascuñán C, Taylor MH. 2013. Description of the 2012 oceanographic conditions on the Northeast U.S. Continental Shelf. NEFSC Ref Doc. 13-26; 40 p.

Frazier BS, McCandless CT. 2013. Standardized catch rates of bonnethead (Sphyrna tiburo) from the South Carolina Department of Natural Resources trammel net survey. Southeast Data Assessment and Review 34 Data Workshop for Atlantic sharpnose and bonnethead sharks, SEDAR34-WP-32.

Garner L. 2013. Northeast Fisheries Science Center publications, reports, and abstracts for calendar year 2012. NEFSC Ref Doc. 13-25: 26 p.

Gatzke J, Khan C, Henry A, Duley P, Cole T. 2013. North Atlantic Right Whale Sighting Survey (NARWSS) and Right Whale Sighting Advisory System (RWSAS) 2012 results summary. NEFSC Ref Doc. 13-08; 7 p.

Hendrickson LC, Showell MA. 2013. Assessment of Northern shortfin squid (Illex illecebrosus) in Subareas 3+4 for 2012. NAFO Sci Counc Res Doc. 13/31, Ser No. 6185 25 p.

Henry AG, Cole TVN, Hall L, Ledwell W, Morin D, Reid A. 2013. Mortality determinations for baleen whale stocks along the Gulf of Mexico, United States East Coast, and Atlantic Canadian Provinces, 2007-2011. NEFSC Ref Doc. 13-18; 15 p

Jech JM, Price V. 2013. Comparisons of acoustic and trawl-based Atlantic herring population estimates in the Gulf of Maine. ICES WGFAST Report 2013: SciCom Steering Group on Ecosystem Surveys, Science, and Technology. ICES CM. 2013/SSGESST:09; p 25-26.

Jepson M, Colburn LL. 2013. Development of social indicators of fishing community vulnerability and resilience in the U.S. Southeast and Northeast regions. NOAA Tech Memo NMFS F/SPO 129; 64 p.

Jossi J, Kane K. 2013. An atlas of the dominant zooplankton collected along a Continuous Plankton Recorder transect between Massachusetts USA and Cape Sable NS, 1961-2008. NEFSC Ref Doc. 13-12; 104 p

Kitts A, Demarest C. 2013. Impact of quota trading on net revenues in the Northeast U.S. groundfish fishery. NEFSC Ref Doc. 13-19; 24 p

Kocik J, Lipsky C, Miller T, Rago P, Shepherd G. 2013. An Atlantic sturgeon population index for ESA management analysis. NEFSC Ref Doc. 13-06; 36 p

Kohler NE, Bailey D, Turner PA, McCandless CT. 2013. Mark/Recapture data for the Atlantic sharpnose shark (Rhizoprionodon terranovae) in the Western North Atlantic from the NEFSC Cooperative Shark Tagging Program.  Southeast Data Assessment and Review 34 Data Workshop for Atlantic sharpnose and bonnethead sharks, SEDAR34-WP-25.

Kohler NE, Sawicki L, Turner PA, McCandless CT. 2013. Mark/Recapture data for the bonnethead (Sphyrna tiburo), in the Western North Atlantic from the NEFSC Cooperative Shark Tagging Program.  Southeast Data Assessment and Review 34 Data Workshop for Atlantic sharpnose and bonnethead sharks, SEDAR34-WP-26.

McCandless CT, Belcher CN. 2013. Standardized indices of abundance for Atlantic sharpnose sharks from the Georgia Department of Natural Resources red drum longline survey. Southeast Data Assessment and Review 34 Data Workshop for Atlantic sharpnose and bonnethead sharks, SEDAR34-WP-34.

McCandless CT, Belcher CN, Frazier BS, McCallister M, Ford R, Gelsleichter J. 2013. Standardized indices of abundance for bonnethead and Atlantic sharpnose sharks caught during the Cooperative Atlantic States Shark Pupping and Nursery longline surveys from South Carolina to northern Florida.  Southeast Data Assessment and Review 34 Data Workshop for Atlantic sharpnose and bonnethead sharks, SEDAR34-WP-37.

McCandless, C.T. and B.S. Frazier. 2013. Standardized indices of abundance for bonnethead and Atlantic sharpnose sharks caught during the South Carolina Department of Natural Resources red drum longline and Cooperative Atlantic States Shark Pupping and Nursery gillnet surveys.  Southeast Data Assessment and Review 34 Data Workshop for Atlantic sharpnose and bonnethead sharks, SEDAR34-WP-36.

McCandless CT, Page J, Belcher CN. 2013. Standardized catch rates for bonnetheads and Atlantic sharpnose sharks from the Georgia Department of Natural Resources ecological monitoring trawl survey. Southeast Data Assessment and Review 34 Data Workshop for Atlantic sharpnose and bonnethead sharks, SEDAR34-WP-35.

Murray KT. 2013. Estimated loggerhead and unidentified hard-shelled turtle interactions in mid-Atlantic gillnet gear, 2007-2011. NOAA Tech Memo NMFS NE-225; 20 p.

NEFSC, NERO. 2013. Proposed 2013 observer sea day allocation. Informal report; 15 p. Available at: http://nefsc.noaa.gov/fsb/SBRM/

Nieland JL, Sheehan TF, Saunders R, Murphy JS, Trinko Lake TR, Stevens JR. 2013. Dam impact analysis model for Atlantic salmon in the Penobscot River, Maine. NEFSC Ref Doc. 13-09; 524 p.

Northeast Fisheries Science Center. 2013. 55th Northeast Regional Stock Assessment Workshop (55th SAW) Assessment Report. NEFSC Ref Doc. 13-11; 845 p

Northeast Fisheries Science Center. 2013. 55th Northeast Regional Stock Assessment Workshop (55th SAW) Assessment Summary Report. NEFSC Ref Doc. 13-01; 41 p

Northeast Fisheries Science Center. 2013. 56th Northeast Regional Stock Assessment Workshop (56th SAW) Assessment Report. NEFSC Ref Doc. 13-10; 868 p

Northeast Fisheries Science Center. 2013. 56th Northeast Regional Stock Assessment Workshop (56th SAW) Assessment Summary Report. NEFSC Ref Doc. 13-04; 42 p

Northeast Fisheries Science Center. 2013. 57th Northeast Regional Stock Assessment Workshop (57th SAW) Assessment Report. NEFSC Ref Doc. 13-16; 967 p

Northeast Fisheries Science Center. 2013. 57th Northeast Regional Stock Assessment Workshop (57th SAW) Assessment Summary Report. NEFSC Ref Doc. 13-14; 39 p.

Northeast Fisheries Science Center. 2013. NEFSC policy and guidelines for using social media. NEFSC Ref Doc. 13-02; 6 p

Northeast Fisheries Science Center. 2013. 2013 Monkfish operational assessment. NEFSC Ref Doc. 13-23; 116 p

Orphanides CD. 2013. Estimates of cetacean and pinniped bycatch during 2010 and 2011 in the New England sink gillnet fishery, mid-Atlantic gillnet fishery, and two NMFS gillnet experiments, 2nd Edition. NEFSC Ref Doc. 13-13; 37 p

Palmer MC, Hersey P, Marotta H, Shield GR, Cierpich SB. 2013. The design, implementation and performance of an observer pre-trip notification system (PTNS) for the northeast United States groundfish fishery. NEFSC Ref Doc. 13-21; 82 p

Schwartz FJ, McCandless CT, Hoey JJ. 2013. Standardized indices of abundance for Atlantic sharpnose sharks from the University of North Carolina bottom longline survey.  Southeast Data Assessment and Review 34 Data Workshop for Atlantic sharpnose and bonnethead sharks, SEDAR34-WP-38.

Sheehan TF, Assunção MGL, Deschamps D, Laughton B, Ó Cuaig M, Nygaard R, King TL, Robertson MJ, Ó Maoiléidigh N. 2013. The International Sampling Program: Continent of origin and biological characteristics of Atlantic salmon collected at West Greenland in 2012. NEFSC Ref Doc. 13-20; 25 p

Shepherd G, Shertzer K, Coakley J, Caldwell M, editors. 2013. Proceedings from a Workshop on Modeling Protogynous Hermaphrodite Fishes, Raleigh NC. Available from: Mid-Atlantic Fishery Management Council, 800 North State Street, Suite 201, Dover, DE 19901, or online at www.mafmc.org. 33 p.

Steinback SR, Brinson AA. 2013. The economics of the recreational for-hire fishing industry in the northeast United States. NEFSC Ref Doc. 13-03; 49 p

Upite C, Murray K, Stacy B, Weeks S, Williams, R. 2013. Serious injury and mortality determinations for sea turtles in U.S. Northeast and Mid-Atlantic fishing gear. NOAA Tech Memo NMFS NMFS-NE 222; 18 p.

Waring GT, Josephson E, Maze-Foley K, Rosel, PE, editors. 2013. U.S. Atlantic and Gulf of Mexico Marine Mammal Stock Assessments -- 2012. NOAA Tech Memo NMFS NE 223; 419 p.

Wigley SE, Blaylock J, Rago PJ, Shield G. 2013. 2013 discard estimation, precision, and sample size analyses for 14 federally managed species groups in the Northeast region. NEFSC Ref Doc. 13-15; 150 p

Wood A. 2013. Bluefish 2012 stock assessment update. NEFSC Ref Doc. 13-07; 32 p.

Abstracts

Bérubé M, Ryan C, Berrow SD, Lopez-Suárez P, Monteiro V, Wenzel F, Robbins J, Mattila DK, Vikingsson G, Øien N, Palsbøll PJ. 2013. The Cape Verde Islands are home to a small and genetically distinct humpback whale breeding population [abstract]. Presented at: 27th Annual Conference of the European Cetacean Society; 8-10 Apr 2013; Setubal, Portugal; np.

Blogoslawski W, Davis C, Leonard D, Milke L. 2013. Overview of the joint meeting of the Northeast Aquaculture Conference and Exposition, Milford Aquaculture Seminar, and the International Conference on Shellfish Restoration. In: Abstracts of shellfish technical papers presented at the Joint Meeting of the Northeast Aquaculture Conference and Exposition Milford Aquaculture Seminar and the International Conference on Shellfish Restoration Groton, Connecticut, December 12-15, 2012. J Shellfish Res. 32(2):571-612.

Bochenek E, Morson J, Robillard E, Powell EN, Hasbrouck E Jr, Gerbino K. 2013. Spatial and temporal variability in sex-at-age of summer flounder landed in the commercial and recreational fisheries from Massachusetts to Virginia [abstract]. Presented at: American Fisheries Society 143rd Annual Meeting; 8-12 Sep 2013; Little Rock AR; np.

Bricker SB, Ferreira JG, Zhu C, Rose JM, Galimany E, Wikfors GH, Miller RL, Wands J, Wellman K, Rheault RB, Trowbridge P, Grizzle R. 2013. How important is nutrient removal through shellfish harvest in Long Island Sound and Great Bay Piscataqua Estuaries? [abstract]. Presented at: CERF 2013, Toward Resilient Coasts and Estuaries, Science for Sustainable Solutions; 3-7 Nov 2013; San Diego CA; p 25.

Bricker S, Getchis T, Chadwick C, Rose J, Rose C. 2013. Merging modeling and mapping: The integration of ecosystem-based models and interactive web-based visualization tools for improved aquaculture decision making  [abstract]. In: Abstracts of shellfish technical papers presented at the Joint Meeting of the Northeast Aquaculture Conference and Exposition Milford Aquaculture Seminar and the International Conference on Shellfish Restoration Groton, Connecticut, December 12-15, 2012. J Shellfish Res. 32(2):571-612.

Candelmo AC, Chambers RC, Habeck EA, Poach ME, Wieczorek D, Phelan BA, Caldarone EM, Greenfield C, Cooper KR. 2013. The effects of ocean acidification on the early life stages of winter flounder, Pseudopleuronectes americanus [abstract]. Presented at: 37th Annual Larval Fish Conference; 2-6 Jun 2013; Miami FL; p 22.

Chambers RC. 2013. Time and timing in the ecology of marine fish early life stages [abstract]. Presented at: 37th Annual Larval Fish Conference; 2-6 Jun 2013; Miami FL; p 21.

Chelikowsky D, Kapareiko D, Jeffress D, Wikfors G, Cuomo C. 2013. The microalga Pavlova contains an analog for the hormone ecdysone that promotes metamorphosis of larval bay scallops (Argopecten irradians irradians) [abstract]. In: Abstracts of shellfish technical papers presented at the Joint Meeting of the Northeast Aquaculture Conference and Exposition Milford Aquaculture Seminar and the International Conference on Shellfish Restoration Groton, Connecticut, December 12-15, 2012. J Shellfish Res. 32(2):571-612.

Choromanski J, Stiles S, Jeffress D, Ladeau H. 2013. Evaluation of bay scallops from genetic lines of two geographic populations for growth and survival in the Niantic River, Connecticut [abstract]. In: Abstracts of shellfish technical papers presented at the Joint Meeting of the Northeast Aquaculture Conference and Exposition Milford Aquaculture Seminar and the International Conference on Shellfish Restoration Groton, Connecticut, December 12-15, 2012. J Shellfish Res. 32(2):571-612.

Colburn LL, Clay PM. 2013. Understanding impacts on fishermen and their families from New England catch shares [abstract]. Presented at: National Working Waterfronts and Waterways Symposium; 25-28 Mar 2013; Tacoma WA; np.

Colburn LL, Jepson M, Pollnac RB. 2013. Healthy oceans, healthy communities: Indicators of coastal vulnerability and resilience [abstract]. Presented at: The Society for Applied Anthropology 73rd Annual Meeting; 19-23 Mar 2013; Denver CO; p 80.

Croxton A, Wikfors G. 2013. Apoptosis measurements in several bivalve species during a seasonal cycle [abstract]. In: Abstracts of shellfish technical papers presented at the Joint Meeting of the Northeast Aquaculture Conference and Exposition Milford Aquaculture Seminar and the International Conference on Shellfish Restoration Groton, Connecticut, December 12-15, 2012. J Shellfish Res. 32(2):571-612.

Deshpande A, Dockum B, Farrington C, Kohler N, Natanson L. 2013. A pilot survey of polychlorinated biphenyls and chlorinated pesticides in the muscle, stomach content, and liver samples of shortfin mako, Isurus oxyrinchus, caught in the waters offshore of Long Island, New York [abstract]. Presented at: Mid-Atlantic Chapter of American Fisheries Society 2013 Annual Meeting; 14-15 Nov 2013; Tuckerton NJ; p 10-11.

Dixon MS, Bernatchez G, Boeff K, Galimany E, Li Y, Lok A, Meseck SL, Petit M. 2013. The Atlantic ribbed mussel (Geukensia demissa), grown using standard aquaculture methods, has potential for use in nutrient bioextraction [abstract]. In: Abstracts of shellfish technical papers presented at the Joint Meeting of the Northeast Aquaculture Conference and Exposition Milford Aquaculture Seminar and the International Conference on Shellfish Restoration Groton, Connecticut, December 12-15, 2012. J Shellfish Res. 32(2):571-612.

Färe R, Grosskopf S, Walden JB. 2013. Industry restructuring and productivity change in an individual transferable quota fishery [abstract]. Presented at: 13th European Workshop on Efficiency and Productivity Analysis; 17-20 Jun 2013; Helsinki, Finland; np.

Farrow K, Brinson A, Thunberg E. 2013. Evaluating the economic performance of U.S. catch share programs [abstract]. Presented at: North American Association of Fisheries Economists (NAAFE) 2013; 21-24 May 2013; St. Petersburg FL; p 64.

Fay G, Large SI, Link JS, Gamble RJ. 2013. Comparing single-species and ecological indicator-based assessments: practical approaches for implementing ecosystem-based fisheries management [abstract]. Presented at: ICES WCSAM 2013 (World Conference on Stock Assessment Methods); 17-19 Jul 2013; Boston MA; p 29-30.

Fay G, Link JS, Large SI, Gamble RJ, Gaichas S, Gorton R, Fulton EA, Nye J, Hare J. 2013. Incorporating climate change scenarios into models for Ecosystem-Based Management [abstract]. Presented at: International Congress for Conservation Biology; 21-25 Jul 2013 Baltimore MD; np.

Fay G, Link JS, Large SI, Gamble RJ, Gorton R, Fulton EA. 2013. Performance of foodweb indicator-based control rules for Ecosystem-Based Fisheries Management [abstract]. Presented at: ICES Annual Science Conference; 23-27 Sep 2013; Reykjavik, Iceland; np.

Fox DA, Brown LM, Armstrong JL, Milliken HO, Wark K. 2013. Cooperative development and testing of sink gillnet modifications for reducing Atlantic sturgeon bycatch in the monkfish fishery [abstract]. Presented at: American Fisheries Society 143rd Annual Meeting; 8-12 Sep 2013; Little Rock AR; np.

Galbraith J, Johnston R. 2013. Potential gains in operational efficiency during multi-species bottom trawl surveys through the use of real-time multibeam sonar [abstract]. Presented at: American Fisheries Society 143rd Annual Meeting; 8-12 Sep 2013; Little Rock AR; np.

Gamble R, Gaichas S, Fogarty M, Smith L, Lucey S, Miller T, Fay G, DePiper G, Curti K. 2013. Multispecies modeling for fisheries management advice: a pilot project for Georges Bank, USA [abstract]. Presented at: ICES WCSAM 2013 (World Conference on Stock Assessment Methods); 17-19 Jul 2013; Boston MA; p 33-34.

Getchis T, Visel T, Blogoslawski W. 2013. A history of the shellfishing industry in Connecticut [abstract]. In: Abstracts of shellfish technical papers presented at the Joint Meeting of the Northeast Aquaculture Conference and Exposition Milford Aquaculture Seminar and the International Conference on Shellfish Restoration Groton, Connecticut, December 12-15, 2012. J Shellfish Res. 32(2):571-612.

Goethel DR, Legault CM, Cadrin SX. 2013. Application of a tag-integrated stock assessment model to three interconnected stocks of yellowtail flounder stocks off New England [abstract]. Presented at: ICES WCSAM 2013 (World Conference on Stock Assessment Methods); 17-19 Jul 2013; Boston MA; p 40.

Goldberg R, Sennefelder G. 2013. Culture of bivalve molluscs – a Milford Laboratory perspective, 1920s-1960s [abstract]. In: Abstracts of shellfish technical papers presented at the Joint Meeting of the Northeast Aquaculture Conference and Exposition Milford Aquaculture Seminar and the International Conference on Shellfish Restoration Groton, Connecticut, December 12-15, 2012. J Shellfish Res. 32(2):571-612.

Goulette GS, Hawkes JP, O’Malley MB, Kocik JF, Music PA, Stevens JR,  Lipsky CA. 2013. Could predator satiation through a greater abundance of buffer species increase Atlantic salmon smolt survival in the Penobscot Estuary, Maine? [abstract]. Presented at: 69th Annual Meeting of the Northeast Association of Fish and Wildlife Agencies; 7-9 Apr 2013; Saratoga Springs NY; np.

Hawkes J, Sheehan T. 2013. Evaluation of river specific Age-1 hatchery reared Atlantic salmon smolts using acoustic telemetry [abstract]. Presented at: 39th Annual Meeting of the Atlantic International Chapter of the American Fisheries Society; 22-24 Sep 2013; Winter Harbor ME; np.

Hyde K, Fogarty M, Selig E, Kristiansen T, Longo C, Kleisner K, Dickey-Collas M, Fulton E, Minto C. 2013. How phytoplankton size influences fisheries management [abstract]. Presented at: ICES Annual Science Conference; 23-27 Sep 2013; Reykjavik, Iceland; np.

Ji R, Li Y, Chen C, Fratantoni P, Hare J. 2013. Stratification indices for stock and ecosystem assessments from a data assimilative circulation model [abstract]. Presented at: 37th Annual Larval Fish Conference; 2-6 Jun 2013; Miami FL; p 32-33.

Ji R, Li Y, Fratantoni P, Chen C, Hare J, Sun Y, Hyde K, Davis C. 2013. Stratification on the Northwest Atlantic shelf: Patterns, drivers and implications for plankton production [abstract]. Presented at: ICES Annual Science Conference; 23-27 Sep 2013; Reykjavik, Iceland; np.

Kapareiko D, Alix J, Jeffress D, Wikfors G. 2013. A look at species-specific and seasonal effects of two probiotic bacteria up on hemocytes of the eastern oyster (Crassostrea virginica) and the northern bay scallop (Argopecten irradians irradians) [abstract]. In: Abstracts of shellfish technical papers presented at the Joint Meeting of the Northeast Aquaculture Conference and Exposition Milford Aquaculture Seminar and the International Conference on Shellfish Restoration Groton, Connecticut, December 12-15, 2012. J Shellfish Res. 32(2):571-612.

Keppel AG, Breitburg D, Burrell R, Wikfors GH, Steppe C. 2013. Breathless nights on acid: the effects of co-varying diel-cycling hypoxia and pH on Crassostrea virginica [abstract]. Presented at: CERF 2013, Toward Resilient Coasts and Estuaries, Science for Sustainable Solutions; 3-7 Nov 2013; San Diego CA; p 118.

Krumholz J, Burg R, Rose J, Tedesco M. 2013. Developing a sound criterion: The past, present, and future of the LISS Environmental Indicators Program [abstract]. Presented at: 11th Biennial Long Island Sound Research Conference; 19 Apr 2013; Port Jefferson NY; np.

Krumholz J, Rose J, Deonarine S, Parker M, Barrett J, Pagach J, Tedesco M. 2013. Developing a program for sentinel monitoring of climate change in an urban estuary [abstract]. Presented at: CERF 2013, Toward Resilient Coasts and Estuaries, Science for Sustainable Solutions; 3-7 Nov 2013; San Diego CA; p 126.

Large SI, Fay G, Friedland KD, Link JS. 2013. Quantifying critical points in ecological indicators' response to the combined effects of fishing and the environment [abstract]. Presented at: ICES Annual Science Conference; 23-27 Sep 2013; Reykjavik, Iceland; np.

Large SI, Fay G, Friedland KD, Link JS. 2013. Quantifying trends and thresholds in responses of ecological indicators to the combined effects of fishing and environmental pressure [abstract]. Presented at: 37th Annual Larval Fish Conference; 2-6 Jun 2013; Miami FL; p 40.

Lawson GL, Lavery AC, Wiebe PH, Jech J, Copley NJ. 2013. Multi-sensor studies of euphausiid-fish interactions in the Gulf of Maine [poster]. Presented at: ICES Annual Science Conference; Reykjavik, Iceland; 23-27 Sep 2013; np.

Li Y, Meseck SL, Dixon MS, Wikfors GH. 2013. Light limitation of primary productivity in the high-nutrient, low-chlorophyll a East River tidal strait, New York City, New York [abstract]. Presented at: CERF 2013, Toward Resilient Coasts and Estuaries, Science for Sustainable Solutions; 3-7 Nov 2013; San Diego CA; p 136.

Limburg, KE, Wuenschel MJ. 2013. Phylogenetic constraints on elemental uptake in flounder otoliths: aid to interpreting migration and other life history events [poster]. Presented at: 22nd Biennial Coastal and Estuarine Research Federation conference; 3-7 Nov 2013; San Diego, CA; np.

Link JS, Legault C, Essington T, Punt A, Cadrin S, Methot R. 2013. Ecosystem data for use in stock assessment models [abstract]. Presented at: ICES WCSAM 2013 (World Conference on Stock Assessment Methods); 17-19 Jul 2013; Boston MA; p 31.

Lipsky C, O'Farrell H. 2013. A novel biotic integrity index for the Penobscot Estuary [abstract]. Presented at: 39th Annual Meeting of the Atlantic International Chapter of the American Fisheries Society; 22-24 Sep 2013; Winter Harbor ME; np.

Lipsky C, Saunders R. 2013. Evidence of successful spawning of American shad in the Penobscot River, Maine [abstract]. Presented at: DSRRN 2013 Science Meeting, Diadromous Species Restoration Science 2013: Migration, Habitat, Species Interactions, and Management; 10-11 Jan 2013; Orono ME; p 30.

Lipton DW, DePiper G. 2013. Using markets to achieve large scale ecosystem restoration: oysters and nutrient trading in the Chesapeake Bay [abstract]. Presented at: 2013 AAEA & CAES Joint Annual Meeting; 4-6 Aug 2013; Washington DC; np.

Lovell S, Steinback S. 2013. Marine angler expenditures and economic impacts in the Gulf of Mexico in 2011 [abstract]. Presented at: North American Association of Fisheries Economists (NAAFE) 2013; 21-24 May 2013; St. Petersburg FL; p 7.

Lowder K, Goulette GS, Kocik JF. 2013. Coming to life: animated visualizations of Atlantic salmon smolt tracks [abstract]. Presented at: 39th Annual Meeting of the Atlantic International Chapter of the American Fisheries Society; 22-24 Sep 2013; Winter Harbor ME; np.

MacKenzie CL, Boyce P. 2013. Large increases in cormorants and the red alga (Gracilaria spp.) coincide with reduced abundances of key species in Massachusetts bays [abstract]. Presented at: Mid-Atlantic Chapter of American Fisheries Society 2013 Annual Meeting; 14-15 Nov 2013; Tuckerton NJ; p 7.

Matzen E, Milliken H. 2013. Development and testing of a tow time data logger to monitor and enforce tow time restrictions in trawl fisheries [abstract]. In: Tucker T, Belskis L, Panagopoulou A, Rees A, Frick M, Williams K, LeRoux R, Stewart K, compilers. Proceedings of the Thirty-Third Annual Symposium on Sea Turtle Biology and Conservation. NOAA Tech Memo NOAA NMFS-SEFSC-645; p 107.

McCorkle D, Widman J, Cohen A, Milke L, Ramon B. 2013. Impacts of ocean acidification on survival and growth of larval surfclams (Spisula solidissima) – environmental conditions (Waquoit Bay, MA) and culture studies [abstract]. In: Abstracts of shellfish technical papers presented at the Joint Meeting of the Northeast Aquaculture Conference and Exposition Milford Aquaculture Seminar and the International Conference on Shellfish Restoration Groton, Connecticut, December 12-15, 2012. J Shellfish Res. 32(2):571-612.

McManus MC, Smith LM, Krumholz JS, Oviatt CA. 2013. Using in situ metabolism estimates to identify ecosystem responses to environmental change in Narragansett Bay, RI [abstract]. Presented at: ASLO 2013 Aquatic Sciences Meeting;17-23 Feb 2013; New Orleans LA; np.

Meseck S, Clark P, Mercaldo-Allen R, Rose J, Goldberg R. 2013.  Does the frequency of hydraulic dredging on cultivated shellfish beds influence the sediment chemistry and is there a relationship between benthic organisms present? [abstract]. In: Abstracts of shellfish technical papers presented at the Joint Meeting of the Northeast Aquaculture Conference and Exposition Milford Aquaculture Seminar and the International Conference on Shellfish Restoration Groton, Connecticut, December 12-15, 2012. J Shellfish Res. 32(2):571-612.

Milke LM, Widman J, Cohen A, McCorkle D. 2013. Physiological effects of elevated CO2 on Atlantic surfclams [abstract]. Presented at: U.S. Ocean Acidification Principal Investigators' Meeting; 28-30 Sep 2013; Washington DC; np.

Milliken HO, DeAlteris J, Parkins C, Matzen E, Ruhle J, Gahm M, O’Rourke M, Knight J. 2013. Reducing sea turtle mortality in the mid-Atlantic and southern New England summer flounder trawl fishery [abstract]. Presented at: American Fisheries Society 143rd Annual Meeting; 8-12 Sep 2013; Little Rock AR; np.

Neville KM, Mello JJ. 2013. Summary of incidental takes of Atlantic swordfish (Xiphias gladius) in squid bottom trawl trips sampled in waters off the east coast of the United States by the Northeast Fisheries Observer Program [poster]. Presented at: 7th International Fisheries Observer and Monitoring Conference; 8-12 Apr 2013; Vina del Mar, Chile; p 116.

Newell CR, Wikfors G, Galimany E, Rose J, Green A. 2013. The use of mussels for bioremediation efforts in the Bronx River, New York Harbor: a feasibility study [abstract]. Presented at: Aquaculture 2013 Conference; 3-7 Nov 2013; Grand Canaria; np.

Nieland JL, Sheehan TF, Saunders R. 2013. Dam impact analysis on the Penobscot River  [abstract]. Presented at: International Conference on Engineering & Ecohydrology for Fish Passage; 25-27 Jun 2013; Corvallis OR; np.

Nieland JL, Sheehan TF, Saunders R. 2013. Using the Dam Impact Analysis Model to Assess the Recovery Potential of Atlantic Salmon [abstract]. Presented at: What Works? A Workshop on Wild Atlantic Salmon Recovery Programs; 18-19 Sep 2013; Chamcook NB; np.

Palamara L, Manderson J, Kohut J, DiDomenico G, Curchitser E, Kang D, Oliver MJ, Dobson C, Snow A. 2013. Putting the dynamics of the ocean into marine spatial planning: Temporal variation in butterfish habitat [abstract]. Presented at: ASLO 2013 Aquatic Sciences Meeting; 17-23 Feb 2013; New Orleans LA; np.

Perry DM, Redman DH. 2013. Flow-through seawater experimental ocean acidification system and experimental results from studying the effects of elevated levels of carbon dioxide on otolith condition and growth of juvenile scup, Stenotomus chrysops [poster]. Presented at: U.S. Ocean Acidification Principal Investigators' Meeting; 28-30 Sep 2013; Washington DC; np.

Pollnac RB, Colburn LL. 2013. Fisheries resource governance, equity and social justice [abstract]. Presented at: The Society for Applied Anthropology 73rd Annual Meeting; 19-23 Mar 2013; Denver CO; p 63.

Price V, Liu H, Jech M. 2013. Integrating acoustic, midwater and bottom trawl data to assess sampling strategies and abundance trends of spawning stock of Atlantic herring (Clupea harengus) in the Georges Bank-Gulf of Maine region [abstract]. Presented at: American Fisheries Society 143rd Annual Meeting; 8-12 Sep 2013; Little Rock AR; np.

Rosa M, Holohan B, Bullard S, Wikfors G, Getchis T, Shumway S. 2013. Biofouling ascidians on aquaculture gear as potential vectors of harmful algal introductions [abstract]. In: Abstracts of shellfish technical papers presented at the Joint Meeting of the Northeast Aquaculture Conference and Exposition Milford Aquaculture Seminar and the International Conference on Shellfish Restoration Groton, Connecticut, December 12-15, 2012. J Shellfish Res. 32(2):571-612.

Rose JM, Bricker SB, Wikfors GH, Dwyer L, Tedesco MA. 2013. Shellfish aquaculture in the coastal environment: potential for nutrient management and challenges to implementation [abstract]. Presented at: CERF 2013, Toward Resilient Coasts and Estuaries, Science for Sustainable Solutions; 3-7 Nov 2013; San Diego CA; p 193.

Rowe S, Smith B. 2013. Predation of Atlantic sea scallops on the Northeast United States Continental Shelf -- Are commercial scallop discards contributing to groundfish diets? [abstract]. Presented at: American Fisheries Society 143rd Annual Meeting; 8-12 Sep 2013; Little Rock AR; np.

Roy K, Kellogg L, Neville K, Mello J. 2013. Summary of the Northeast Fisheries Observer Program’s Species Verification Program [poster]. Presented at: 7th International Fisheries Observer and Monitoring Conference; 8-12 Apr 2013; Vina del Mar, Chile; p 90.

Sagarese SR , Frisk MG, Cerrato RM, Sosebee KA, Musick JA, Rago PJ. 2013. Application of generalized additive models to examine ontogenetic and seasonal distributions of spiny dogfish (Squalus acanthias) in the Northeast (US) Shelf Large Marine Ecosystem [abstract]. Presented at: American Fisheries Society 143rd Annual Meeting; 8-12 Sep 2013; Little Rock AR; np.

Schott E, Mensinger M, McIntosh D, Perry D, Goldberg R, Hanif A. 2013. Will climate change alter the prevalence of pathogens of the blue crab (Callinectes sapidus) in the northeast USA? [abstract]. In: Abstracts of shellfish technical papers presented at the Joint Meeting of the Northeast Aquaculture Conference and Exposition Milford Aquaculture Seminar and the International Conference on Shellfish Restoration Groton, Connecticut, December 12-15, 2012. J Shellfish Res. 32(2):571-612.

Smith BE, Rowe S. 2013. Temporal trends in pelagic communities and forage fish removals: Connections between zooplankton, Atlantic herring (Clupea harengus), and herring consumption across the northeast U.S. continental shelf [abstract]. Presented at: ICES Annual Science Conference 2013; 23-27 Sep 2013; Reykjavik, Iceland; np.

Smith LM, McManus C, Stoffel H, Krumholz J, Oviatt C. 2013. Hypoxia, nutrients, and climate change in Narragansett Bay [abstract]. Presented at: NEERS (New England Estuarine Research Society) Meeting; 11-13 Apr 2013; Portland ME; np.

Stevens J, Dill R, Borsky A, Duffy W. 2013. Evidence of the Penobscot River Estuary providing prolonged river herring nursery habitat [abstract]. Presented at: 39th Annual Meeting of the Atlantic International Chapter of the American Fisheries Society; 22-24 Sep 2013; Winter Harbor ME; np.

Stiles S, Choromanski J, Jeffress D. 2013. Genetic applications for shellfish restoration [abstract]. In: Abstracts of shellfish technical papers presented at the Joint Meeting of the Northeast Aquaculture Conference and Exposition Milford Aquaculture Seminar and the International Conference on Shellfish Restoration Groton, Connecticut, December 12-15, 2012. J Shellfish Res. 32(2):571-612.

Van Atten A, Rossi N, Neville K, Chamberlain G. 2013. Electronic monitoring project in the Northeastern United States [abstract]. Presented at: 7th International Fisheries Observer and Monitoring Conference; 8-12 Apr 2013; Vina del Mar, Chile; p 42.

Widman JC Jr. 2013. Is it time to expand bay scallop, Argopecten irradians irradians, culture in the USA? [abstract]. In: Abstracts of shellfish technical papers presented at the Joint Meeting of the Northeast Aquaculture Conference and Exposition Milford Aquaculture Seminar and the International Conference on Shellfish Restoration Groton, Connecticut, December 12-15, 2012. J Shellfish Res. 32(2):571-612.

Wikfors GH. 2013. Pollutant nitrogen <=> nutritional protein: the symmetrical, alliterative poetry of bioextraction [abstract]. In: Abstracts of shellfish technical papers presented at the Joint Meeting of the Northeast Aquaculture Conference and Exposition Milford Aquaculture Seminar and the International Conference on Shellfish Restoration Groton, Connecticut, December 12-15, 2012. J Shellfish Res. 32(2):571-612.

Wiley D, Arsenault R, Clark CW, Cole T, DeCola P, Hadden D, Josephson B, Khan C, Levenson J, Ramage P, Schwehr K, Thompson M, Wellock B, Winney B. 2013. WhaleAlert: A mobile app for transmitting right whale conservation and management information to the maritime industry [abstract]. Presented at: 20th Biennial Conference on the Biology of Marine Mammals; 9-13 Dec 2013; Dunedin, New Zealand; np.

Endnote

[1] Council of Science Editors, Style Manual Committee. 2006. Scientific style and format: the CSE manual for authors, editors, and publishers. 7th ed. Reston, VA: The Council; 658 p.

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