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Publications 2011

Authors in bold are/were staff or students of the Institute for Ocean Conservation Science and its founding organization, the Pew Institute for Ocean Science

Kittinger, J. N., Pandolfi, J. M., Blodgett, J. H., Hunt, T. L., Jiang, H., Maly, K., McClenachan, L., Schultz, J.K., Wilcox, B. A. 2011. Historical reconstruction reveals recovery in Hawaiian coral reefs. PLoS ONE, 6(10).

Coral reef ecosystems are declining worldwide, yet regional differences in the trajectories, timing and extent of degradation highlight the need for in-depth regional case studies to understand the factors that contribute to either ecosystem sustainability or decline. We reconstructed social-ecological interactions in Hawaiian coral reef environments over 700 years using detailed datasets on ecological conditions, proximate anthropogenic stressor regimes and social change. Here we report previously undetected recovery periods in Hawaiian coral reefs, including a historical recovery in the MHI (~AD 1400–1820) and an ongoing recovery in the NWHI (~AD 1950–2009+). These recovery periods appear to be attributed to a complex set of changes in underlying social systems, which served to release reefs from direct anthropogenic stressor regimes. Recovery at the ecosystem level is associated with reductions in stressors over long time periods (decades+) and large spatial scales (>103 km2). Our results challenge conventional assumptions and reported findings that human impacts to ecosystems are cumulative and lead only to long-term trajectories of environmental decline. In contrast, recovery periods reveal that human societies have interacted sustainably with coral reef environments over long time periods, and that degraded ecosystems may still retain the adaptive capacity and resilience to recover from human impacts.

Article (pdf)
News Release

Fitzpatrick, S., Shivji, M.S., Chapman, D.D., Prodõhl, P.A. 2011. Development and characterization of 10 polymorphic microsatellite loci for the blue shark, Prionace glauca, and their cross shark-species amplification. Conservation Genetics Resources, 3(3): 523-527.

Ten polymorphic nuclear microsatellite loci were developed from a microsatellite enriched genomic library of the blue shark, Prionace glauca. The utility of these markers for genetic studies of this globally distributed, heavily exploited, oceanic predator was assessed by screening 120 specimens sampled from six locations throughout the species’ range. Both moderately and highly polymorphic marker loci were identified. Three to 35 alleles were found to be segregating per locus (mean 10.1) with observed heterozygosities ranging from 24 to 91%. Evaluation of the cross-species amplification of these markers across 18 additional shark species indicates that these microsatellites are potentially useful for genetic studies of other species of conservation concern.


Benavides, M.T., Feldheim, K.A., Duffy, C.A., Wintner, S., Braccini, J.M., Boomer, J., Huveneers, C., Rogers, P., Mangel, J.C., Alfaro-Shigueto, J., Cartamil, D.P., Chapman D.D. 2011. Phylogeography of the copper shark (Carcharhinus brachyurus) in the southern hemisphere: implications for the conservation of a coastal apex predator. Marine and Freshwater Research, 6(7): 861-869.

The copper or bronze whaler shark (Carcharhinus brachyurus) is a large, coastal top predator that is vulnerable to overexploitation. We test the null hypothesis that copper sharks are panmictic throughout the southern hemisphere. We analysed part of the mitochondrial control region (mtCR) in 120 individuals from eight sampling areas, defining 20 mtCR haplotypes (h¼0.76_0.06,p¼0.016_0.0007). Significant genetic structure was detected among the following three major coastal regions separated by oceanic habitat: Australia–New Zealand, South Africa–Namibia and Peru´ (AMOVA FST¼0.95, P,0.000001). A major phylogeographic discontinuity exists across the Indian Ocean, indicating an absence of at least female-mediated gene flow for,3 million years. We propose that this species originated in the Atlantic, experienced vicariant isolation of Pacific and Atlantic lineages by the rise of the Isthmus of Panama and, subsequently, dispersed across the Pacific to colonise Australasia. Oceanic expanses appear to be traversed over evolutionary but not ecological timescales, which means that regional copper-shark populations should be assessed and managed independently.

Paper | News release

Estes, J.A., Terborgh, J., Brashares, J.S., Power, M.E., Berger J., Bond, W.J., Carpenter, S.R., Essington, T., Holt, R.D., Jackson, J.B.C., Marquis, R.J., Oksanen, L., Oksanen, T., Paine, R.T., Pikitch, E.K., Ripple, W.J., Sandin, S.A., Scheffer, M., Schoener, T.W., Shurin, J.B., Sinclair, A.R.E., Soulé, M.E., Virtanen, R., Wardle, D.A. 2011. Trophic Downgrading of Planet Earth. Science, 33(640): 301-306.

Until recently, large apex consumers were ubiquitous across the globe and had been for millions of years. The loss of these animals may be humankind’s most pervasive influence on nature. While such losses are widely viewed as an ethical and aesthetic problem, recent research reveals extensive cascading effects of their disappearance in marine, terrestrial, and freshwater ecosystems worldwide. This empirical work supports long-standing theory about the role of topdown forcing in ecosystems, but also highlights the unanticipated impacts of trophic cascades on processes as diverse as the dynamics of disease, wildfire, carbon sequestration, invasive species and biogeochemical cycles. These findings emphasize the urgent need for interdisciplinary research to forecast the effects of trophic downgrading on process, function, and resilience in global ecosystems.

Abstract | News release

Erickson, D.L., A. Kahnle, M. J. Millard, E.A. Mora, G. Bryja, A. Higgs, J. Mohler, M. DuFour, G. Kenney, J. Sweka, and E.K. Pikitch. 2011. Use of pop-off satellite archival tags to identify oceanic-migratory patterns for adult Atlantic Sturgeon Ascipenser oxyrinchus oxyrinchus Mitchell, 1815. Journal of Applied Ichthyology, 27(2): 356–365.

Oceanic-migratory behavior of adult Atlantic Sturgeon, Acipenser oxyrinchus oxyrinchus, was examined using pop-up satellite archival tags (PSAT). Twenty-three Atlantic Sturgeons were caught and tagged with PSATs in the Hudson River, New York during 2006 and 2007. Fifteen of those fish returned to the ocean (with PSATs attached) 6 to 132 days after tagging. These PSATs remained attached to fish for a period of 108 to 360 days archiving light, temperature, and depth, before releasing from fish, ascending to the surface, and transmitting data to satellites. The location of PSATs was measured to within + 150 m by satellites using Doppler shift of radio transmissions within hours after tags reached the surface. Positions prior to pop up were initially estimated using only archived-light data and the tag manufacturers’ proprietary software. Positional error associated with light-based estimates is high, especially with regard to latitude. This error was reduced by applying depth, distance, and temperature filters. Thirteen of the 15 Atlantic Sturgeons that left the Hudson River with PSATs attached remained within the Mid-Atlantic Bight for up to one year after tagging. Their geographic distributions generally extended from Long Island, New York to Chesapeake Bay at depths between 5 and 40 m. Aggregation ar eas were identified off southwest Long Island, along the New Jersey coast, off Delaware Bay, and off Chesapeake Bay. Depth distribution was seasonal; fish inhabited deepest waters during winter and shallowest waters during summer and early fall. Two Atlantic Sturgeons traveled outside of the Mid-Atlantic Bight. One migrated north to Cobequid Bay (terminal end of the Bay of Fundy, Nova Scotia), whereas the other traveled south to the coast of Georgia.

Journal article | News release

Benavides, M.T., Horn, R.L., Feldheim, K.A., Shivji, M.S., Clarke, S.C., Wintner, S., Natanson, L., Braccini, M., Boomer, J., Gulak, S.J.B. , Chapman, D.D. 2011. Global phylogeography of the dusky shark, Carcharhinus obscurus: implications for fisheries management and monitoring the shark fin trade. Endangered Species Research, 14(1): 13-22.

Genetic stock structure information is needed to delineate management units and monitor trade in sharks, many of which are heavily exploited and declining. The dusky shark, Carcharhinus obscurus, is a large apex predator that is sought after for its fins and is considered highly susceptible to overexploitation. The International Union for the Conservation of Nature (IUCN) classifies this species as "Vulnerable" globally and "Endangered" in the Northwest Atlantic. We make the first assessment of global stock structure of C. obscurus by analyzing part of the mitochondrial control region (mtCR) in 255 individuals sampled from 8 geographically dispersed locations. We found 25 mtCR haplotypes and rejected a null hypothesis of panmixia (AMOVA, ΦST ≅ 0.55, p < 0.000001), detecting significant differentiation between three "management units": "U.S. Atlantic (USATL)", "South Africa (SAF)" and "Australia (AUS)". We also found preliminary evidence of population structure between the USATL and Southwest Atlantic (Brazil). There were no shared haplotypes between the Western Atlantic and Indo-Pacific. These analyses suggest that replenishment of the collapsed USATL management unit via immigration of females from elsewhere is unlikely. Mixed stock analysis (MSA) simulations show that reconstruction of the relative contributions of USATL, SAF and AUS management units to the Asian fin trade is possible using these mtCR sequences. We suggest avenues for obtaining samples to conduct MSA of the shark fin trade, which could enhance management of dusky sharks and other species that are exploited for their fins.

Read more (pdf) | News Release

Doukakis, P., Hanner, R., Shivji, M., Bartholomew, C., Chapman, D., Wong, E., Amato, G. 2011. Applying Genetic Techniques to Study Remote Shark Fisheries in Northeastern Madagascar. Mitochondrial DNA, 22(Suppl. 1): 15-20.

The shark fisheries of Madagascar remain largely unstudied. Remoteness makes fisheries monitoring challenging while the high value of shark fins combined with the extreme poverty in Madagascar creates intensive pressure on shark resources. We use DNA barcoding and species-specific PCR assays to characterize shark fisheries in Antongil Bay in northeastern Madagascar. The 239 samples taken from individuals collected in 2001 and 2002 correspond to 19 species. The four most common species were Sphyrna lewini, Rhizoprionodon acutus, Carcharhinus brevipinna and C. sorrah. Antongil Bay may be a breeding area for C. brevipinna, C. leucas, and S. lewini. Local names are generally not a useful proxy for monitoring the species harvested in the fishery. Conservation efforts should characterize species exploitation at present, create spatial and temporal fishing restrictions to protect endangered species, and restrict large mesh gillnets. Read more

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