Hare Jonathan A.

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Jonathan A.

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  • Article
    Transgenerational marking of embryonic otoliths in marine fishes using barium stable isotopes
    (NRC Research Press, 2006-04-13) Thorrold, Simon R. ; Jones, Geoffrey P. ; Planes, Serge ; Hare, Jonathan A.
    We describe a new technique for transgenerational marking of embryonic otoliths that promises significant advancements in the study of larval dispersal and population connectivity in marine fishes. The approach is based on maternal transmission of 137Ba from spawning females to egg material that is ultimately incorporated into the otoliths of embryos produced by an individual after exposure to the isotope. We injected females of a benthic-spawning clownfish (Amphiprion melanopus) and a pelagic-spawning serranid (Centropristis striata) with enriched 137BaCl2 and then reared the resulting progeny through to settlement. Barium isotope ratios in the cores of larval otoliths were quantified using laser ablation inductively coupled plasma mass spectrometry. Larval otoliths from both species contained unequivocal Ba isotope signatures over a wide range of doses (0.8–23 μg 137Ba·g female–1). Female A. melanopus continued to produce marked larvae over multiple clutches and for at least 90 days after a single injection. The ability to administer different combinations of stable Ba isotopes provides a new means of mass-marking larvae of benthic- and pelagic-spawning fishes from multiple populations over extended spawning periods.
  • Article
    Larval transport and dispersal in the coastal ocean and consequences for population connectivity
    (Oceanography Society, 2007-09) Pineda, Jesus ; Hare, Jonathan A. ; Sponaugle, Su
    Many marine species have small, pelagic early life stages. For those species, knowledge of population connectivity requires understanding the origin and trajectories of dispersing eggs and larvae among subpopulations. Researchers have used various terms to describe the movement of eggs and larvae in the marine environment, including larval dispersal, dispersion, drift, export, retention, and larval transport. Though these terms are intuitive and relevant for understanding the spatial dynamics of populations, some may be nonoperational (i.e., not measurable), and the variety of descriptors and approaches used makes studies difficult to compare. Furthermore, the assumptions that underlie some of these concepts are rarely identified and tested. Here, we describe two phenomenologically relevant concepts, larval transport and larval dispersal. These concepts have corresponding operational definitions, are relevant to understanding population connectivity, and have a long history in the literature, although they are sometimes confused and used interchangeably. After defining and discussing larval transport and dispersal, we consider the relative importance of planktonic processes to the overall understanding and measurement of population connectivity. The ideas considered in this contribution are applicable to most benthic and pelagic species that undergo transformations among life stages. In this review, however, we focus on coastal and nearshore benthic invertebrates and fishes.
  • Article
    Wind-induced interannual variability of sea level slope, along-shelf flow, and surface salinity on the Northwest Atlantic shelf
    (John Wiley & Sons, 2014-04-16) Li, Yun ; Ji, Rubao ; Fratantoni, Paula S. ; Chen, Changsheng ; Hare, Jonathan A. ; Davis, Cabell S. ; Beardsley, Robert C.
    In this study, we examine the importance of regional wind forcing in modulating advective processes and hydrographic properties along the Northwest Atlantic shelf, with a focus on the Nova Scotian Shelf (NSS)-Gulf of Maine (GoM) region. Long-term observational data of alongshore wind stress, sea level slope, and along-shelf flow are analyzed to quantify the relationship between wind forcing and hydrodynamic responses on interannual time scales. Additionally, a simplified momentum balance model is used to examine the underlying mechanisms. Our results show significant correlation among the observed interannual variability of sea level slope, along-shelf flow, and alongshore wind stress in the NSS-GoM region. A mechanism is suggested to elucidate the role of wind in modulating the sea level slope and along-shelf flow: stronger southwesterly (northeastward) winds tend to weaken the prevailing southwestward flow over the shelf, building sea level in the upstream Newfoundland Shelf region, whereas weaker southwesterly winds allow stronger southwestward flow to develop, raising sea level in the GoM region. The wind-induced flow variability can influence the transport of low-salinity water from the Gulf of St. Lawrence to the GoM, explaining interannual variations in surface salinity distributions within the region. Hence, our results offer a viable mechanism, besides the freshening of remote upstream sources, to explain interannual patterns of freshening in the GoM.
  • Article
    Biophysical mechanisms of larval fish ingress into Chesapeake Bay
    (Inter-Research, 2005-11-21) Hare, Jonathan A. ; Thorrold, Simon R. ; Walsh, Harvey J. ; Reiss, Christian S. ; Valle-Levinson, Arnoldo ; Jones, Cynthia M.
    Selective tidal stream transport is hypothesized as a dominant mechanism by which larvae of marine animals move through estuarine openings. For larvae moving from the shelf to estuarine habitats, selective tidal stream transport proposes that larvae are higher in the water column during flood tide and lower in the water column during ebb tide. Although a number of studies conclude that selective tidal stream transport is the mechanism responsible for larval ingress, few studies consider alternative mechanisms or consider passive explanations for tidal patterns in larval distributions. We examined the biophysical mechanisms responsible for larval ingress into Chesapeake Bay using an Eulerian approach. We made flux calculations for 3 species and partitioned flux estimates among 3 different ingress mechanisms (wind forcing, residual bottom inflow and tidal). For the Atlantic croaker Micropogonias undulatus (Sciaenidae), all 3 mechanisms of ingress contributed to the net up-estuary flux of larvae, but tidal mechanisms become more important for larger sizes. Net up-estuary flux of the Atlantic menhaden Brevoortia tyrannus (Clupeidae) was dominated by residual bottom inflow and wind forcing. Ingress of the summer flounder Paralichthys dentatus (Paralichthyidae) was dominated by tidal mechanisms, and the importance of tides increased with developmental stage. We found little evidence for the hypothesis that tidal patterns in larval distributions resulted from passive processes (water mass-specific distributions, buoyancy, vertical mixing), thereby supporting the hypothesis that tidal patterns resulted from active behaviors. However, our estimates of vertical mixing were not direct and additional work is needed to examine the role of vertical mixing in influencing vertical distributions in areas with strong tides. We conclude that a combination of wind forcing, residual bottom inflow, and selective tidal stream transport are responsible for the ingress of larval fishes into Chesapeake Bay, and that the relative importance of the 3 mechanisms differs among species and changes with larval development.
  • Article
    Identification of larval sea basses (Centropristis spp.) using ribosomal DNA-specific molecular assays
    (U.S. Dept. of Commerce, NOAA, 2008) Vandersea, Mark W. ; Litaker, R. Wayne ; Marancik, Katrin E. ; Hare, Jonathan A. ; Walsh, Harvey J. ; Lem, Siya ; West, Melissa A. ; Wyanski, David M. ; Laban, Elisabeth H. ; Tester, Patricia A.
    The identification of sea bass (Centropristis) larvae to species is difficult because of similar morphological characters, spawning times, and overlapping species ranges. Black sea bass (Centropristis striata) is an important fishery species and is currently considered to be overfished south of Cape Hatteras, North Carolina. We describe methods for identifying three species of sea bass larvae using polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) assays based on species-specific amplification of rDNA internal transcribed spacer reg ions. The assays were tested against DNA of ten other cooccurring reef fish species to ensure the assay’s specificity. Centropristis larvae were collected on three cruises during cross-shelf transects and were used to validate the assays. Seventysix Centropristis larvae were assayed and 69 (91%) were identified successfully. DNA was not amplified from 5% of the larvae and identification was inconclusive for 3% of the larvae. These assays can be used to identify sea bass eggs and larvae and will help to assess spawning locations, spawning times, and larval dispersal.
  • Preprint
    Re-evaluating the effect of wind on recruitment in Gulf of Maine Atlantic Cod (Gadus morhua) using an environmentally-explicit stock recruitment model
    ( 2013-10) Hare, Jonathan A. ; Brooks, Elizabeth N. ; Palmer, Michael C. ; Churchill, James H.
    A previous study documented a correlation between Atlantic Cod (Gadus morhua) recruitment in the Gulf of Maine and an annual index of the north component of May winds. This correlation was supported by modeling studies that indicated unusually strong recruitment of Gulf of Maine Atlantic Cod results from high retention of spring-spawned larvae in years when winds were predominately out of the north, which favor downwelling. We re-evaluated this relationship using updated recruitment estimates and found that the correlation decreased between recruitment and wind. The original relationship was largely driven by two recruitment estimates, one of which (2005 year class) was highly uncertain because it was near the terminal year of the assessment. With additional data, the updated assessment estimated lower recruitment for the 2005 year class, which consequently lowered the correlation between recruitment and wind. We then investigated whether an environmentally-explicit stock recruit function that incorporated an annual wind index was supported by either the original or updated assessment output. Although incorporation of the annual wind index produced a better fitting model, the uncertainty in the estimated parameters and the implied unexploited conditions were not appropriate for providing management advice. These results suggest the need for caution in the development of environmentally-explicit stock recruitment relationships, in particular when basing relationships and hypotheses on recruitment estimates from the terminal years of stock assessment models. More broadly, this study highlights a number of sources of uncertainty that should be considered when analyses are performed on the output of stock assessment models.
  • Preprint
    Toward cyberinfrastructure to facilitate collaboration and reproducibility for marine integrated ecosystem assessments
    ( 2016-10-20) Beaulieu, Stace E. ; Fox, Peter A. ; Di Stefano, Massimo ; Maffei, Andrew R. ; West, Patrick ; Hare, Jonathan A. ; Fogarty, Michael J.
    There is a growing need for cyberinfrastructure to support science-based decision making in management of natural resources. In particular, our motivation was to aid the development of cyberinfrastructure for Integrated Ecosystem Assessments (IEAs) for marine ecosystems. The IEA process involves analysis of natural and socio-economic information based on diverse and disparate sources of data, requiring collaboration among scientists of many disciplines and communication with other stakeholders. Here we describe our bottom-up approach to developing cyberinfrastructure through a collaborative process engaging a small group of domain and computer scientists and software engineers. We report on a use case evaluated for an Ecosystem Status Report, a multi-disciplinary report inclusive of Earth, life, and social sciences, for the Northeast U.S. Continental Shelf Large Marine Ecosystem. Ultimately, we focused on sharing workflows as a component of the cyberinfrastructure to facilitate collaboration and reproducibility. We developed and deployed a software environment to generate a portion of the Report, retaining traceability of derived datasets including indicators of climate forcing, physical pressures, and ecosystem states. Our solution for sharing workflows and delivering reproducible documents includes IPython (now Jupyter) Notebooks. We describe technical and social challenges that we encountered in the use case and the importance of training to aid the adoption of best practices and new technologies by domain scientists. We consider the larger challenges for developing end-to-end cyberinfrastructure that engages other participants and stakeholders in the IEA process.
  • Article
    Juvenile fish assemblages collected on unconsolidated sediments of the southeast United States continental shelf
    (U.S. Department of Commerce, NOAA, 2006) Walsh, Harvey J. ; Marancik, Katrin E. ; Hare, Jonathan A.
    Patterns were investigated in juvenile fish use of unconsolidated sediments on the southeast United States continental shelf off Georgia. Juvenile fish and environmental data were sampled at ten stations along a 110-km cross-shelf transect, including four stations surrounding Gray’s Reef National Marine Sanctuary (Gray’s Reef NMFS). Cross-shelf stations were sampled approximately quarterly from spring 2000 to winter 2002. Additional stations were sampled on three transects inshore of Gray’s Reef NMS and four transects offshore of the Sanctuary during three cruises to investigate along-shelf patterns in the juvenile fish assemblages. Samples were collected in beam trawls, and 121 juvenile taxa, of which 33 were reef-associated species, were identif ied. Correspondence analysis on untransformed juvenile fish abundance indicated a cross-shelf gradient in assemblages, and the station groupings and assemblages varied seasonally. During the spring, fall, and winter, three cross-shelf regions were identified: inner-shelf, mid-shelf, and outer-shelf regions. In the summer, the shelf consisted of a single juvenile fish assemblage. Water depth was the primary environmental variable correlated with cross-shelf assemblages. However, salinity, density, and water column stratification also correlated with the distribution of assemblages during the spring, fall, and winter, and along with temperature likely inf luenced the distribution of juvenile fish. No along-shelf spatial patterns were found in the juvenile fish assemblages, but the along-shelf dimension sampled was small (~60 km). Our results revealed that a number of commercially and recreationally important species used unconsolidated sediments on the shelf off Georgia as juvenile habitat. We conclude that management efforts would be improved through a greater recognition of the importance of these habitats to fish production and the interconnectedness of multiple habitats in the southeast U.S. continental shelf ecosystem.
  • Article
    Decadal changes in zooplankton of the Northeast U.S. continental shelf
    (Public Library of Science, 2014-01-31) Bi, Hongsheng ; Ji, Rubao ; Liu, Hui ; Jo, Young-Heon ; Hare, Jonathan A.
    The abundance of the subarctic copepod, Calanus finmarchicus, and temperate, shelf copepod, Centropages typicus, was estimated from samples collected bi-monthly over the Northeast U.S. continental shelf (NEUS) from 1977–2010. Latitudinal variation in long term trends and seasonal patterns for the two copepod species were examined for four sub-regions: the Gulf of Maine (GOM), Georges Bank (GB), Southern New England (SNE), and Mid-Atlantic Bight (MAB). Results suggested that there was significant difference in long term variation between northern region (GOM and GB), and the MAB for both species. C. finmarchicus generally peaked in May – June throughout the entire study region and Cen. typicus had a more complex seasonal pattern. Time series analysis revealed that the peak time for Cen. typicus switched from November – December to January - March after 1985 in the MAB. The long term abundance of C. finmarchicus showed more fluctuation in the MAB than the GOM and GB, whereas the long term abundance of Cen. typicus was more variable in the GB than other sub-regions. Alongshore transport was significantly correlated with the abundance of C. finmarchicus, i.e., more water from north, higher abundance for C. finmarchicus. The abundance of Cen. typicus showed positive relationship with the Gulf Stream north wall index (GSNWI) in the GOM and GB, but the GSNWI only explained 12–15% of variation in Cen. typicus abundance. In general, the alongshore current was negatively correlated with the GSNWI, suggesting that Cen. typicus is more abundant when advection from the north is less. However, the relationship between Cen. typicus and alongshore transport was not significant. The present study highlights the importance of spatial scales in the study of marine populations: observed long term changes in the northern region were different from the south for both species.
  • Article
    An integrated assessment model for helping the United States sea scallop (Placopecten magellanicus) fishery plan ahead for ocean acidification and warming
    (Public Library of Science, 2015-05-06) Cooley, Sarah R. ; Rheuban, Jennie E. ; Hart, Deborah R. ; Luu, Victoria ; Glover, David M. ; Hare, Jonathan A. ; Doney, Scott C.
    Ocean acidification, the progressive change in ocean chemistry caused by uptake of atmospheric CO2, is likely to affect some marine resources negatively, including shellfish. The Atlantic sea scallop (Placopecten magellanicus) supports one of the most economically important single-species commercial fisheries in the United States. Careful management appears to be the most powerful short-term factor affecting scallop populations, but in the coming decades scallops will be increasingly influenced by global environmental changes such as ocean warming and ocean acidification. In this paper, we describe an integrated assessment model (IAM) that numerically simulates oceanographic, population dynamic, and socioeconomic relationships for the U.S. commercial sea scallop fishery. Our primary goal is to enrich resource management deliberations by offering both short- and long-term insight into the system and generating detailed policy-relevant information about the relative effects of ocean acidification, temperature rise, fishing pressure, and socioeconomic factors on the fishery using a simplified model system. Starting with relationships and data used now for sea scallop fishery management, the model adds socioeconomic decision making based on static economic theory and includes ocean biogeochemical change resulting from CO2 emissions. The model skillfully reproduces scallop population dynamics, market dynamics, and seawater carbonate chemistry since 2000. It indicates sea scallop harvests could decline substantially by 2050 under RCP 8.5 CO2 emissions and current harvest rules, assuming that ocean acidification affects P. magellanicus by decreasing recruitment and slowing growth, and that ocean warming increases growth. Future work will explore different economic and management scenarios and test how potential impacts of ocean acidification on other scallop biological parameters may influence the social-ecological system. Future empirical work on the effect of ocean acidification on sea scallops is also needed.