Academic Appointments

Current Research and Scholarly Interests

Stephen R. Palumbi received his Ph.D. from University of Washington in marine ecology. His research group studies the genetics, evolution, conservation, population biology and systematics of a diverse array of marine organisms.

Professor Palumbi's own research interests are similarly widespread, and he has published on the genetics and evolution of sea urchins, whales, cone snails, corals, sharks, spiders, shrimps, bryozoans, and butterflyfishes. A primary focus is the use of molecular genetic techniques in conservation, including the identification of whale and dolphin products available in commercial markets.

Current conservation work centers on the genetics of marine reserves designed for conservation and fisheries enhancement, with projects in the Philippines, Bahamas and western U.S. coast. In addition, basic work on the molecular evolution of reproductive isolation and its influence on patterns of speciation uses marine model systems such as sea urchins. This work is expanding our view of the evolution of gamete morphology and the genes involved. Steve's recent book, The Evolution Explosion: How Humans Cause Rapid Evolutionary Change, shows how rapid evolution is central to emerging problems in modern society. In January 2003, Steve appeared in the TV series, The Future is Wild, a computer-animated exploration of the possible courses of evolution in the next few hundred million years. His new book, published in November 2010, The Death and Life of Monterey Bay: A Story of Revival, is a good-news environmental story about the difference that ordinary citizens can make in creating diverse, sustainable ecosystems and diverse, sustainable economies.

In 2002, Professor Palumbi moved his laboratory from Harvard University to Stanford University's Hopkins Marine Station, where he is now the Director of the station. Steve is a Pew Fellow in Marine Conservation, senior fellow at the Woods Institute for the Environment, married to physician Mary Roberts, father of two grown children, and founding member of the band Sustainable Sole (sample a song).

2015-16 Courses

Stanford Advisees

All Publications

  • DNA evidence for historic population size and past ecosystem impacts of gray whales PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Alter, S. E., Rynes, E., Palumbi, S. R. 2007; 104 (38): 15162-15167


    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 approximately 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 approximately 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.

    View details for DOI 10.1073/pnas.0706056104

    View details for Web of Science ID 000249715100052

    View details for PubMedID 17848511

  • Restricted gene flow in the Caribbean staghorn coral Acropora cervicomis: Implications for the recovery of endangered reefs JOURNAL OF HEREDITY Vollmer, S. V., Palumbi, S. R. 2007; 98 (1): 40-50


    Coral reef conservation requires information about the distance over which healthy reefs can rescue damaged reefs through input of coral larvae. This information is desperately needed in the Caribbean where the 2 dominant shallow water corals Acropora cervicornis and Acropora palmata have suffered unprecedented declines. Here we compare the population genetic structure in the staghorn coral A. cervicornis across the greater Caribbean using DNA sequence data from 1 mitochondrial and 3 nuclear genes. Data from 160 individuals from 22 populations and 9 regions show that A. cervicornis exhibits significant population genetic structure across the greater Caribbean in both the mitochondrial (Phi(st) = 0.130) and nuclear data (Phi(st) = 0.067). The highest population structure was observed in the species' own, native mtDNA haplotypes (Phi(st) = 0.235). Introgressed alleles from A. palmata tempered higher population structure in A. cervicornis over regional scales but in some cases generated highly localized "introgression hot spots" and fine-scale genetic structure among reefs separated by as few as 2 km. These data show that larval dispersal over moderate or long distances (>500 km) is limited for this threatened species and in some cases locally limited as well. Thus, the endangered Caribbean staghorn corals require local source populations for their recovery and targeted conservation efforts over spatial scales much smaller than the hundreds to thousands of kilometers usually proposed for marine reserves.

    View details for DOI 10.1093/jhered/esl057

    View details for Web of Science ID 000243585900005

    View details for PubMedID 17158464

  • Seascape genetics: A coupled oceanographic-genetic model predicts population structure of Caribbean corals CURRENT BIOLOGY Galindo, H. M., Olson, D. B., Palumbi, S. R. 2006; 16 (16): 1622-1626


    Population genetics is a powerful tool for measuring important larval connections between marine populations [1-4]. Similarly, oceanographic models based on environmental data can simulate particle movements in ocean currents and make quantitative estimates of larval connections between populations possible [5-9]. However, these two powerful approaches have remained disconnected because no general models currently provide a means of directly comparing dispersal predictions with empirical genetic data (except, see [10]). In addition, previous genetic models have considered relatively simple dispersal scenarios that are often unrealistic for marine larvae [11-15], and recent landscape genetic models have yet to be applied in a marine context [16-20]. We have developed a genetic model that uses connectivity estimates from oceanographic models to predict genetic patterns resulting from larval dispersal in a Caribbean coral. We then compare the predictions to empirical data for threatened staghorn corals. Our coupled oceanographic-genetic model predicts many of the patterns observed in this and other empirical datasets; such patterns include the isolation of the Bahamas and an east-west divergence near Puerto Rico [3, 21-23]. This new approach provides both a valuable tool for predicting genetic structure in marine populations and a means of explicitly testing these predictions with empirical data.

    View details for DOI 10.1016/j.cub.2006.06.052

    View details for Web of Science ID 000240155400025

    View details for PubMedID 16920623

  • The use of genetic clines to estimate dispersal distances of marine larvae ECOLOGY Sotka, E. E., Palumbi, S. R. 2006; 87 (5): 1094-1103


    Many unresolved issues in the ecology and evolution of marine populations center on how far planktonic larvae disperse away from their parents. Genetic tools provide a promising way to define the spatial spread of larvae, yet their accurate interpretation depends on the extent to which genetic loci are under selection. Genetic clines, geographic zones in which genetically differentiated populations interbreed, provide opportunities to explicitly and simultaneously quantify the relative roles of selection and dispersal. Here, we review the theory and analysis of genetic clines and apply these techniques to published studies of multilocus clines in the sea. The geographic width of a stable genetic cline is determined by a balance between the homogenizing effects of dispersal and the diversifying effects of selection. For marine researchers, the power of genetic clines is that, if selection and clinal width are quantified, then the average geographic distances that larvae move can be inferred. Measuring selection or dispersal through laboratory or field-based experimentation is possible, though logistically difficult, for pelagically dispersed organisms. Instead, dispersal may be more robustly quantified from the degree of linkage disequilibrium between two or more loci, because linkage disequilibrium integrates selection across multiple life stages and generations. It is also relatively insensitive to whether exogenous or endogenous selection operates. Even without quantifying linkage disequilibrium, the theory of genetic clines indicates that the average dispersal distance of larvae is a fraction (i.e., generally <35%) of the clinal width. Because cline theory is based on several underlying assumptions, including near-equilibrium between selection and migration, the dispersal distances inferred from empirical data should be of the correct order but may not be precise. Even so, such estimates of larval dispersal are valuable, as they can be utilized to design appropriate scales for future investigations and provide some guidance to conservation efforts.

    View details for Web of Science ID 000237552400003

    View details for PubMedID 16761586

  • Coral gardens: Paternity and drug testing on the reef CURRENT BIOLOGY Palumbi, S. R. 2005; 15 (14): R544-R545


    An international team has used molecular genetics and chemical tagging to trace how baby clownfish travel from their mother's nest through the ocean to the anemone they will live on. More than one out of five juveniles came from nests that were only meters away, despite spending over a week drifting in ocean currents. Such surprising fidelity to a small area of the coral reef bodes well for efforts to preserve coral reef diversity with reserves.

    View details for Web of Science ID 000230903900011

    View details for PubMedID 16051159

  • Evolutionary animation: How do molecular phylogenies compare to Mayr"s reconstruction of speciation patterns in the sea? PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Palumbi, S. R., Lessios, H. A. 2005; 102: 6566-6572


    Ernst Mayr used the geography of closely related species in various stages of increasing divergence to "animate" the process of geographic, or allopatric, speciation. This approach was applied to a wide set of taxa, and a seminal paper by Mayr used it to explore speciation patterns in tropical sea urchins. Since then, taxonomic information in several of these genera has been augmented by detailed molecular phylogenies. We compare Mayr's animation with the phylogenies of eight sea urchin genera placed by Mayr into four speciation groups. True to Mayr's predictions, early-stage genera have on average lower species divergence and more polytypic species than genera in later stages. For six of these genera, we also have information about the evolution of the gamete recognition protein bindin, which is critical to reproductive isolation. These comparisons show that later-stage genera with many sympatric species tend to be those with rapid bindin evolution. By contrast, early-stage genera with few sympatric species are not necessarily earlier in the divergence process; they happen to be those with slow rates of bindin evolution. These results show that the rate of speciation in sea urchins does not only depend on the steady accumulation of genome divergence over time, but also on the rate of evolution of gamete recognition proteins. The animation method used by Mayr is generally supported by molecular phylogenies. However, the existence of multiple rates in the acquisition of reproductive isolation complicates placement of different genera in an evolutionary series.

    View details for DOI 10.1073/pnas.0501806102

    View details for Web of Science ID 000229023700009

    View details for PubMedID 15851681

  • Strong genetic clines and geographical variation in gene flow in the rocky intertidal barnacle Balanus glandula MOLECULAR ECOLOGY Sotka, E. E., Wares, J. P., Barth, J. A., Grosberg, R. K., Palumbi, S. R. 2004; 13 (8): 2143-2156


    A long-standing issue in marine biology is identifying spatial scales at which populations of sessile adults are connected by planktonic offspring. We examined the genetic continuity of the acorn barnacle Balanus glandula, an abundant member of rocky intertidal communities of the northeastern Pacific Ocean, and compared these genetic patterns to the nearshore oceanography described by trajectories of surface drifters. Consistent with its broad dispersal potential, barnacle populations are genetically similar at both mitochondrial (cytochrome oxidase I) and nuclear (elongation factor 1-alpha) loci across broad swaths of the species' range. In central California, however, there is a striking genetic cline across 475 km of coastline between northern and southern populations. These patterns indicate that gene flow within central California is far more restricted spatially than among other populations. Possible reasons for the steep cline include the slow secondary introgression of historically separated populations, a balance between diversifying selection and dispersal, or some mix of both. Geographic trajectories of oceanic drifters closely parallel geographical patterns of gene flow. Drifters placed to the north (Oregon; approximately 44 degrees N) and south (Santa Barbara, California; approximately 34 degrees N) of the cline disperse hundreds of kilometers within 40 days, yet over the long-term their trajectories never overlapped. The lack of communication between waters originating in Oregon and southern California probably helps to maintain strong genetic differentiation between these regions. More broadly, the geographical variation in gene flow implies that focusing on species-level averages of gene flow can mask biologically important variance within species which reflects local environmental conditions and historical events.

    View details for DOI 10.1111/j.1365-294X.2004.02225.x

    View details for Web of Science ID 000222521300004

    View details for PubMedID 15245390

  • Ecological subsidies alter the structure of marine communities PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Palumbi, S. R. 2003; 100 (21): 11927-11928

    View details for DOI 10.1073/pnas.2335832100

    View details for Web of Science ID 000186024300001

    View details for PubMedID 14530398

  • Why gobies are like hobbits SCIENCE Palumbi, S. R., Warner, R. R. 2003; 299 (5603): 51-52

    View details for Web of Science ID 000180165800022

    View details for PubMedID 12511632