Table of Contents

• Dataset Description
  • Methods & Sampling
  • Data Processing Description
• Data Files
• Parameters
• Deployments
• Project Information
• Program Information
• Funding

Single Nucleotide Polymorphism for each of the Strongylocentrotus purpuratus genes from the GLEAN3 genome build.

Data structure: Fractions are allele frequency values. Location, Day samples (D1 or D7), and CO2 level (385 or 1000) are listed.

Data are for each of the S. purpuratus genes from the GLEAN3 genome build.

Parameter Names/Definitions:
GLEAN ID: ID code
POS: base position
Random trails larger than observed value (running record):  no units
Sample ID code format: State_Site_Tidal Height_:
	OR: Oregon
	FC: Fogarty Creek Site
	ST:  Strawberry Hill
	BD: Bodega Bay
	NC: Northern California
	VD: Van Damme
	CC: Central California
	SH:  Sand Hill Bluff
	TP: Terrace Point
	SB: Santa Barbara region
	AL: Alegria

Resulting Publications:
2013. Pespeni, M. E. Sanford, B. Gaylord, T. M. Hill, J. D. Hosfelt, H. Jaris, M. LaVigne, E. Lenz, A. D. Russell, M. K. Young, S. R. Palumbi^. Evolutionary change during experimental ocean acidification. Published online before print April 8, 2013, http://dx.doi.org/10.1073/pnas.1220673110

Pespeni MH, Barney BT, Palumbi SR (2012) Differences in the regulation of growth and biomineralization genes revealed through long-term common garden acclimation and experimental genomics in the purple sea urchin. Evolution 67(7): 1901–1914. doi:10.1111/evo.12036

See resulting publications and http://sfg.stanford.edu/

filtered by: minimum 10 reads, <.1 diff day 1- 7, >5% minor allele

See: resulting publications and http://sfg.stanford.edu/

BCO-DMO Processing Notes
Original file: "larval SNPs for NSF-palumbi.xlsx"  contributed by Kristen Milligan
- Approx Lat/Lon of Hopkins Marine Station/Palumbi Lab appended to enable data discovery in MapServer
- Parameter names edited to conform to BCO-DMO parameter naming conventions

In 2010-2012/13, the OMEGAS consortium is investigating the impact of ocean acidification (OA) on two ecologically important, calcification-dependent marine invertebrates (sea urchins Strongylocentrotus purpuratus and mussels Mytilus californianus) in relation to local-to-coastal variation in carbonate chemistry in the California Current Large Marine Ecosystem (CCLME).  An interdisciplinary team of investigators with expertise in physical and chemical oceanography, marine ecology, biochemistry, molecular physiology, and molecular genetics carry out integrated, lab and field, multi-site investigations of the ecological, physiological, and evolutionary responses of sea urchins and mussels to spatial and temporal variation in OA.

The research takes place in the context of a mosaic of variable oceanography, including recently documented latitudinal variation in carbonate chemistry along the upwelling-dominated US west coast.  Variation in upwelling regimes from Washington to southern California generates spatial and temporal gradients in concentration of CO2 that shoal to surface waters during upwelling events, extending shoreward into the inner shelf region.  Because calcifiers in the upwelling-dominated CCLME probably have historically experienced wide fluctuation in pH, many likely are adapted to a variable carbonate chemistry environment.  The new challenge to these organisms is that they may have limited ability to respond to additional increases in CO2.  It is this challenge, the mechanistic ability of calcifying invertebrates to acclimate or adapt to increasing CO2 and aragonite saturation states < 1.0,  that is addressed in this program.

Our research includes several integrated elements that span our three project areas (Moorings and sensors; Genomics, physiology, and larval rearing; and Field transplants and growth experiments):

(1) Document the oceanographic context in which the study organisms operate in four regions of the CCLME with contrasting upwelling regimes.

(2) Examine physiological, genomic, and genetic mechanisms underlying acclimatization and adaptation to OA conditions with coordinated and integrated studies of adults and larvae of sea urchins and mussels collected from each of two sites within each of the four regions.  In common-garden experiments culture sea urchins and mussels, respectively, under different CO2 and temperature regimes, and use genomics techniques to determine the tolerance of larvae to present and future OA conditions.  

(3) Determine evolutionary responses and adaptational potential to OA using genetic surveys of urchins and mussels across the 8 sites and relate detected variability to the oceanographic conditions.

(4) Examine ecological responses to OA with transplants of mussels and urchins in the field and monitor growth rates and shell accretion rates in relation to oceanographic and physical conditions.

The team will investigate the impact of ocean acidification (OA) on two ecological important, calcification-dependent marine invertebrates (sea urchins Strongylocentrotus purpuratus and mussels Mytilus californianus) in relation to local-to-coastal variation in carbonate chemistry in the California Current Large Marine Ecosystem (CCLME). An interdisciplinary team of investigators with expertise in physical and chemical oceanography, marine ecology, biochemistry, molecular physiology, and molecular genetics will carry out an integrated, lab and field, multi-site investigation of the ecological, physiological, and evolutionary responses of sea urchins and mussels to spatial and temporal variation in OA. The research will take place in the context of a mosaic of variable oceanography, including recently documented latitudinal variation in carbonate chemistry along the upwelling-dominated US west coast. Variation in upwelling regimes from Washington to southern California generates spatial and temporal gradients in concentration of CO2 that shoal to surface waters during upwelling events, extending shoreward into the inner shelf region. Because calcifiers in the upwelling-dominated CCLME probably have historically experienced wide fluctuation in pH, many likely are adapted to a variable carbonate chemistry environment. The new challenge to these organisms is that they may have limited ability to respond to additional increases in CO2. It is this challenge, the mechanistic ability of calcifying invertebrates to acclimate or adapt to increasing CO2 and decreasing carbonate mineral saturation state, that is addressed in this project.

The OMEGAS Moorings and Sensors team will document the oceanographic context in which the study organisms operate in four regions of the CCLME with contrasting upwelling regimesThis project also coordinates closely with other OMEGAS projects [(i) Genetics, physiology, larval rearing and (ii) Field transplants] to achieve goals of the project to determine acclimatization and adaptational capacity to present and future OA conditions .

PUBLICATIONS PRODUCED AS A RESULT OF THIS RESEARCH

Gaylord, B., T. M. Hill, E. Sanford, E. A. Lenz, L. A. Jacobs, K. N. Sato, A. D. Russell, and A. Hettinger. "Functional impacts of ocean acidification in an ecologically critical foundation species", Journal of Experimental Biology, v.214, 2011, p. 2586.

Howarth, R., F. Chan, D. J. Conley, S. C. Doney, R. Marino, and G. Billen. "Coupled biogeochemical cycles: eutrophication and hypoxia in temperate estuaries and coastal marine ecosystems", Frontiers in Ecology and the Environment, v.9, 2011, p. 18.

Yu, P. D., P. G. Matson, T. R. Martz, and G. E. Hofmann. "The ocean acidification seascape and its relationship to theperformance of calcifying marine invertebrates: laboratory experiments on the development of urchin larvae framed by environmentally-relevant pCO2/pH", Journal of Experimental Marine Biology and Ecology, v.400, 2011, p. 288.

The Partnership for Interdisciplinary Studies of Coastal Oceans is a long-term ecosystem research and monitoring program established with the goals of: 

• understanding dynamics of the coastal ocean ecosystem along the U.S. west coast
• sharing that knowledge so ocean managers and policy makers can make science based decisions regarding coastal and marine stewardship
• producing a new generation of scientists trained in interdisciplinary collaborative approaches

Over the last 10 years, PISCO has successfully built a unique research program that combines complementary disciplines to answer critical environmental questions and inform management and policy. Activities are conducted at the latitudinal scale of the California Current Large Marine Ecosystem along the west coast of North America, but anchored around the dynamics of coastal, hardbottom habitats and the oceanography of the nearshore ocean – among the most productive and diverse components of this ecosystem. The program integrates studies of changes in the ocean environment through ecological monitoring and experiments. Scientists examine the causes and consequences of ecosystem changes over spatial scales that are the most relevant to marine species and management, but largely unstudied elsewhere.

Findings are linked to solutions through a growing portfolio of tools for policy and management decisions. The time from scientific discovery to policy change is greatly reduced by coordinated, efficient links between scientists and key decision makers.

Core elements of PISCO are:

• Interdisciplinary ecosystem science
• Data archiving and sharing
• Outreach to public and decision-making user groups
• Interdisciplinary training
• Coordination of distributed research team

Established in 1999 with funding from The David and Lucile Packard Foundation, PISCO is led by scientists from core campuses Oregon State University (OSU); Stanford University’s Hopkins Marine Station; University of California, Santa Cruz (UCSC); and University of California, Santa Barbara (UCSB). Collaborators from other institutions also contribute to leadership and development of PISCO programs.  As of 2005, core PISCO activities are funded by collaborative grants from The David and Lucile Packard Foundation and the Gordon and Betty Moore Foundation. Core support, along with additional funding from diverse public and private sources, make this unique partnership possible.

NSF Climate Research Investment (CRI) activities that were initiated in 2010 are now included under Science, Engineering and Education for Sustainability NSF-Wide Investment (SEES). SEES is a portfolio of activities that highlights NSF's unique role in helping society address the challenge(s) of achieving sustainability. Detailed information about the SEES program is available from NSF (https://www.nsf.gov/funding/pgm_summ.jsp?pims_id=504707).

In recognition of the need for basic research concerning the nature, extent and impact of ocean acidification on oceanic environments in the past, present and future, the goal of the SEES: OA program is to understand (a) the chemistry and physical chemistry of ocean acidification; (b) how ocean acidification interacts with processes at the organismal level; and (c) how the earth system history informs our understanding of the effects of ocean acidification on the present day and future ocean.

Solicitations issued under this program:
NSF 10-530, FY 2010-FY2011
NSF 12-500, FY 2012
NSF 12-600, FY 2013
NSF 13-586, FY 2014
NSF 13-586 was the final solicitation that will be released for this program.

PI Meetings:
1st U.S. Ocean Acidification PI Meeting(March 22-24, 2011, Woods Hole, MA)
2nd U.S. Ocean Acidification PI Meeting(Sept. 18-20, 2013, Washington, DC)
3rd U.S. Ocean Acidification PI Meeting (June 9-11, 2015, Woods Hole, MA – Tentative)

NSF media releases for the Ocean Acidification Program:

Press Release 10-186 NSF Awards Grants to Study Effects of Ocean Acidification

Discovery Blue Mussels "Hang On" Along Rocky Shores: For How Long?

Discovery nsf.gov - National Science Foundation (NSF) Discoveries - Trouble in Paradise: Ocean Acidification This Way Comes - US National Science Foundation (NSF)

Press Release 12-179 nsf.gov - National Science Foundation (NSF) News - Ocean Acidification: Finding New Answers Through National Science Foundation Research Grants - US National Science Foundation (NSF)

Press Release 13-102 World Oceans Month Brings Mixed News for Oysters

Press Release 13-108 nsf.gov - National Science Foundation (NSF) News - Natural Underwater Springs Show How Coral Reefs Respond to Ocean Acidification - US National Science Foundation (NSF)

Press Release 13-148 Ocean acidification: Making new discoveries through National Science Foundation research grants

Press Release 13-148 - Video nsf.gov - News - Video - NSF Ocean Sciences Division Director David Conover answers questions about ocean acidification. - US National Science Foundation (NSF)

Press Release 14-010 nsf.gov - National Science Foundation (NSF) News - Palau's coral reefs surprisingly resistant to ocean acidification - US National Science Foundation (NSF)

Press Release 14-116 nsf.gov - National Science Foundation (NSF) News - Ocean Acidification: NSF awards $11.4 million in new grants to study effects on marine ecosystems - US National Science Foundation (NSF)