Publications by: Stephen Palumbi

Limnology and Oceanography
March, 2012

C. B. Woodson, M. A. McManus, J. A. Tyburczy, J. A. Barth, L. Washburn, J. E. Caselle, M. H. Carr, D. P. Malone, P. T. Raimondi, B. A. Menge, and S. R. Palumbi

We show that ocean fronts set recruitment patterns among both community-building invertebrates and commercially important fishes in nearshore intertidal and rocky reef habitats. Chlorophyll concentration and recruitment of several species of intertidal invertebrates (Balanus spp., Chthamalus spp., Mytilus spp.) and rockfishes (Sebastes spp.) are positively correlated with front probability along the coast of the California Current Large Marine Ecosystem. Abundances of recent settlers and adults for nearshore rockfish species are also positively correlated with front probability. The interaction of coastal topography and bathymetry sets spatial scales of fronts and consequently recruitment at approximately 50 km during active upwelling, compared to 200 km or greater during non-upwelling periods. Such relationships between fronts and recruitment are likely to be consistent across other marine ecosystems—from coastal waters to the open ocean—and provide a critical link between adults and widely dispersing young. Ocean fronts, already known as features with high biodiversity and resilience in pelagic habitats, also set recruitment and connectivity patterns across multiple taxa for intertidal and rocky reef communities, thus linking biodiversity and resilience in coastal and benthic habitats as well.

November, 2011

Author Team: Margaret R. Caldwell, Xavier Basurto, Alice Chiu, Larry Crowder, Rod Fujita, Peter Kareiva, Stephen Palumbi, Whitney Smith, Mike Weber, Thomas Hayden
Packard Foundation Staff Advisors: Walt Reid, Kai Lee, Lisa Monzon, Richard Cudney, Bernd Cordes, Heather Ludemann
Research Assistance: Blue Earth Consultants, LLC; Eric Hartge; George Leonard  

In 2010, the David and Lucile Packard Foundation (“Foundation”) Staff and Board of Trustees initiated a process to look beyond their ongoing ocean conservation efforts and gain a sense of the greater context of needs and opportunities in ocean philanthropy.  The Trustees gathered at a meeting in early June 2010 to review and discuss these opportunities.  In preparation for the meeting, Foundation staff commissioned a discussion paper that presents trends and future issues, surveys various ocean conservation strategies, and provides a qualitative analysis of opportunities, barriers to implementation, and potential for conservation results. This paper was first prepared to help inform and stimulate discussion among the Trustees at the June 2010 meeting. This final version has since been updated and expanded, and is meant to fuel lively discussion into the future.

Marine Policy
September, 2010

Melissa M. Foley, Benjamin S. Halpern, Fiorenza Micheli, Matthew H. Armsby, Margaret R. Caldwell, Caitlin M. Crain, Erin Prahler, Nicole Rohr, Deborah Sivas, Michael W. Beck, Mark H. Carr, Larry B. Crowder, J. Emmett Duffy, Sally D. Hacker, Karen L. McLeod, Stephen R. Palumbi, Charles H. Peterson, Helen M. Regan, Mary H. Ruckelshaus, Paul A. Sandifer, Robert S. Steneck

The declining health of marine ecosystems around the world is evidence that current piecemeal governance is inadequate to successfully support healthy coastal and ocean ecosystems and sustain human uses of the ocean. One proposed solution to this problem is ecosystem-based marine spatial planning (MSP), which is a process that informs the spatial distribution of activities in the ocean so that existing and emerging uses can be maintained, use conflicts reduced, and ecosystem health and services protected and sustained for future generations. Because a key goal of ecosystem-based MSP is to maintain the delivery of ecosystem services that humans want and need, it must be based on ecological principles that articulate the scientifically recognized attributes of healthy, functioning ecosystems. These principles should be incorporated into a decision-making framework with clearly defined targets for these ecological attributes. This paper identifies ecological principles for MSP based on a synthesis of previously suggested and/or operationalized principles, along with recommendations generated by a group of twenty ecologists and marine scientists with diverse backgrounds and perspectives on MSP. The proposed four main ecological principles to guide MSP—maintaining or restoring: native species diversity, habitat diversity and heterogeneity, key species, and connectivity—and two additional guidelines, the need to account for context and uncertainty, must be explicitly taken into account in the planning process. When applied in concert with social, economic, and governance principles, these ecological principles can inform the designation and siting of ocean uses and the management of activities in the ocean to maintain or restore healthy ecosystems, allow delivery of marine ecosystem services, and ensure sustainable economic and social benefits.

Journal of Heredity
March, 2010

Ryan P. Kelly, Thomas A. Oliver, Arjun Sivasundar, Stephen R. Palumbi

Detecting small amounts of genetic subdivision across geographic space remains a persistent challenge. Often a failure to detect genetic structure is mistaken for evidence of panmixia, when more powerful statistical tests may uncover evidence for subtle geographic differentiation. Such slight subdivision can be demographically and evolutionarily important as well as being critical for management decisions. We introduce here a method, called spatial analysis of shared alleles (SAShA), that detects geographically restricted alleles by comparing the spatial arrangement of allelic co-occurrences with the expectation under panmixia. The approach is allele-based and spatially explicit, eliminating the loss of statistical power that can occur with user-defined populations and statistical averaging within populations. Using simulated data sets generated under a stepping-stone model of gene flow, we show that this method outperforms spatial autocorrelation (SA) and ΦST under common real-world conditions: at relatively high migration rates when diversity is moderate or high, especially when sampling is poor. We then use this method to show clear differences in the genetic patterns of 2 nearshore Pacific mollusks, Tegula funebralis (= Chlorostoma funebralis) and Katharina tunicata, whose overall patterns of within-species differentiation are similar according to traditional population genetics analyses. SAShA meaningfully complements ΦST/FST, SA, and other existing geographic genetic analyses and is especially appropriate for evaluating species with high gene flow and subtle genetic differentiation.

January, 2010

Comparing many species' population genetic patterns across the same seascape can identify species with different levels of structure, and suggest hypotheses about the processes that cause such variation for species in the same ecosystem. This comparative approach helps focus on geographic barriers and selective or demographic processes that define genetic connectivity on an ecosystem scale, the understanding of which is particularly important for large-scale management efforts. Moreover, a multispecies dataset has great statistical advantages over single-species studies, lending explanatory power in an effort to uncover the mechanisms driving population structure. Here, we analyze a 50-species dataset of Pacific nearshore invertebrates with the aim of discovering the most influential structuring factors along the Pacific coast of North America. We collected cytochrome c oxidase I (COI) mtDNA data from populations of 34 species of marine invertebrates sampled coarsely at four coastal locations in California, Oregon, and Alaska, and added published data from 16 additional species. All nine species with non-pelagic development have strong genetic structure. For the 41 species with pelagic development, 13 show significant genetic differentiation, nine of which show striking FST levels of 0.1–0.6. Finer scale geographic investigations show unexpected regional patterns of genetic change near Cape Mendocino in northern California for five of the six species tested. The region between Oregon and Alaska is a second focus of intraspecific genetic change, showing differentiation in half the species tested. Across regions, strong genetic subdivision occurs more often than expected in mid-to-high intertidal species, a result that may reflect reduced gene flow due to natural selection along coastal environmental gradients. Finally, the results highlight the importance of making primary research accessible to policymakers, as unexpected barriers to marine dispersal break the coast into separate demographic zones that may require their own management plans.

Molecular Ecology Resources
January, 2009


In contrast to mitochondrial DNA, remarkably few general-use primer sets are available for single-copy nuclear genes across animal phyla. Here, we present a primer set that yields a c. 364-bp coding fragment of the metabolic gene enolase, which includes an intron in some taxa. In species where introns are absent or have few insertions/deletions, the amplified fragment can be sequenced directly for phylogenetic or population analysis. Between species variation in the coding region occurs widely at third codon positions, even between closely related taxa, making the fragment useful for species-level systematics. In low gene-flow species, the primers may also be of use for population genetics, as intraspecific polymorphisms occur at several silent positions in the taxa examined.
COS Publication
January, 2009

Meg Caldwell, Arlo Hemphill, Tegan C. Hoffmann, Stephen Palumbi, Jessica Teisch, Chelsea Tu

In August 2008, a group of over 30 natural, physical, and social scientists from around the Pacific convened in Honolulu, Hawaii to review a synthesis of more than 3,400 scientific articles and reports regarding the threats, impacts, and solutions to negative trends facing the Pacific Ocean. The meeting, convened by the Center for Ocean Solutions (COS) in collaboration with the World Conservation Union (IUCN) and Ocean Conservancy resulted in a consensus statement signed by more than 400 scientists. This document, entitled “Ecosystems and People of the Pacific Ocean—Threats and Opportunities for Action,” identifies four major threats to the health and productivity of the Pacific Ocean. Now, we present the entire synthesis of this Pacific Ocean research—a comprehensive and systematic survey of published scientific literature, government publications, and other peerreviewed reports from throughout the Pacific. Identified within are both regional, and Pacific basin-wide threats, as well as their environmental and socioeconomic impacts. Solutions, drawn from existing published literature, provide an initial “road map” and are presented here as a hopeful indication of humankind’s resolve to address these pressing issues. This Executive Summary is a distillation of our key findings.

COS Publication
January, 2009

The objective of this Pacific Ocean synthesis is to comprehensively and systematically survey the published scientific literature, government publications and other peer-reviewed reports to identify Pacific Ocean and regional threats as well as the environmental and socioeconomic impacts of those threats. In addition, the report highlights select regional and Pacific Ocean solutions presented by the literature. 

January, 2008

Stephen R. Palumbi, Karen L. McLeod, Daniel Grunbaum

The study of ecosystems in action, by measuring ecosystem recovery from disturbance, resistance to alterations, and the reversibility of ecosystem changes, highlights features of natural communities that contribute to resilience. Examples from marine intertidal and subtidal communities document the importance of species redundancy and complementarity in resistance and recovery, and they also show why recovery potential and resistance can differ from place to place within the same ecosystem. Whether a change is considered reversible may depend on the timescale of interest, and on whether fundamental new ecological processes have taken hold after a disturbance. By focusing on recovery, resistance, and reversibility as key components of resilience, marine ecologists have provided a much-needed empirical database about the response of the living world to human-mediated change.

Proceedings of the National Academy of Sciences
September, 2007

S. Elizabeth Alter, Eric Rynes, Stephen R. Palumbi

Ecosystem restoration may require returning threatened populations of ecologically pivotal species to near their former abundances, but it is often difficult to estimate historic population size of species that have been heavily exploited. Eastern Pacific gray whales play a key ecological role in their Arctic feeding grounds and are widely thought to have returned to their prewhaling abundance. Recent mortality spikes might signal that the population has reached long-term carrying capacity, but an alternative is that this decline was due to shifting climatic conditions on Arctic feeding grounds. We used a genetic approach to estimate prewhaling abundance of gray whales and report DNA variability at 10 loci that is typical of a population of ≈76,000–118,000 individuals, approximately three to five times more numerous than today's average census size of 22,000. Coalescent simulations indicate these estimates may include the entire Pacific metapopulation, suggesting that our average measurement of ≈96,000 individuals was probably distributed between the eastern and currently endangered western Pacific populations. These levels of genetic variation suggest the eastern population is at most at 28–56% of its historical abundance and should be considered depleted. If used to inform management, this would halve acceptable human-caused mortality for this population from 417 to 208 per year. Potentially profound ecosystem impacts may have resulted from a decline from 96,000 gray whales to the current population. At previous levels, gray whales may have seasonally resuspended 700 million cubic meters of sediment, as much as 12 Yukon Rivers, and provided food to a million sea birds.