Curriculum Vitae: pdf
Email: alison.haupt@umb.edu

I am interested in answering applied ecological questions that promote improved marine management and conservation by focusing on species and ecosystems confronting anthropogenic stressors such as urbanization and fishing pressure. To address questions of applied ecology, I use and apply a wide variety of nontraditional tools outside of the typical ecologist’s toolkit ranging from field ecology to population genetics and modeling to engaging directly with policy makers.

Current Research Projects – Anthropogenic impacts on near-shore ecology

1) Effects of urbanization and coastal development on kelp forests

I am focusing on a case study using kelp forests on the east and west coasts of the United States and canopy forming kelps globally. Kelps, a globally important group of seaweeds, create a three-dimensional underwater habitat that supports many ecosystem functions and services.  Through this work I am elucidating the effect of urban stressors on kelp forest ecosystems and identifying thresholds in urban stressors or combinations of stressors that create tipping points in kelp ecosystems. On the west coast, I am using a 30-year dataset covering over 2000 km of coastline (Northern California to Baja California, Mexico) to evaluate changes in kelp biomass with changes in urbanization parameters.  On the east coast, I am undertaking a field-based study to measure kelp abundance, biodiversity measures of kelp communities, and mean trophic level of communities along a gradient of urbanization.  Globally, I will take advantage of a recent citizen science project though Zooniverse to quantify canopy-forming kelps worldwide through aerial photography.  Chena Farhat an undergraduate student at UMB is currently working with me on this project.

2) Are cumulative impact indices an appropriate proxy for ecosystem health?

As humans expand current and planned uses of the ocean, it is increasingly important to understand how these impacts affect coastal ecosystems.  A cumulative human impact score was created for the California Current by synthesizing fine-scale information on the distribution of multiple environmental stressors (Halpern et al. 2009).  The resulting cumulative impact score is potentially useful to managers and policy makers, because it narrows a complex interaction of factors into a single number that can directly contribute to environmental management decisions.  These scores take into account multiple aspects of human impacts; however, it remains unclear whether impact scores accurately reflect the ecological status of marine systems. I am leading an NCEAS working group to examine the relationship of the cumulative human impact score with ecosystem conditions in the Southern California Bight subtidal kelp forest ecosystems.  This work is conducted in close collaboration with partners at NCEAS, Center for Ocean Solutions at Stanford, and The Nature Conservancy.

PREVIOUS RESEARCH – Connectivity in marine systems

1) Evolutionary context matters when using genetics to inform fisheries management

My work with the wavy top snail – Megastraea undosa – demonstrated the necessity of considering the evolutionary context of genetic data. Genetic data carry artifacts of past evolutionary history, which may affect estimates of dispersal.  By combining genetic, ecological, and coalescent-based modeling data, I was able to infer very local levels of dispersal for this species (Haupt et al. 2013). This allowed me to explain not only contemporary patterns of larval connectivity, but also uncover a historical range expansion.  During the final year of my thesis, I gave presentations in Spanish to Mexican fishermen and fisheries managers on the results of my research and its potential applications to snail, sea cucumber, and abalone fisheries.

2) Oceanography can inhibit dispersal and create separate fisheries stocks

Management and conservation approaches often assume that marine species with long pelagic larval durations will have high levels of connectivity. But this is not always the case and oceanographic processes may create barriers to dispersal even in species with high potential for long-distance dispersal.  I used a case study of a commercially important sea cucumber – Parastichopus parvimensis – that has long pelagic larval duration.  I discovered subtle but significant genetic structure associated with a major headland: Punta Eugenia, Mexico.  Using coalescent-based modeling, I showed that larval exchange across this headland might be as low as 50 migrants per generation (Haupt et al. in review). Analysis of oceanographic frontal probabilities also provided a potential mechanistic explanation of why Punta Eugenia is a barrier to dispersal.

3) Effective marine reserve planning must consider biogeographic barriers to dispersal

If oceanographic processes at Punta Eugenia can serve as a barrier to larval exchange, other headlands may also affect larval dispersal. Oceanographic patterns and recent genetic work indicate that Cape Mendocino, a prominent headland in northern California, could be a potential barrier to dispersal.  Although Point Conception in southern California is often accepted as a barrier to dispersal, Cape Mendocino has largely been ignored by comprehensive studies and reviews. I conducted a review and analysis of the genetic literature and found that Cape Mendocino was an area of concordant genetic structure for over half of the species surveyed. This has important implications for management, especially considering that Cape Mendocino lies in the middle of the Northern California region designated by the CA Marine Life Protection Act.

4) Gaps in science needed for marine conservation, policy, and management

To generate science that can seamlessly inform management and policy of marine resources the scientific needs of policy makers and managers need to be identified. As a fellow working for the WCGA,  I identified research priorities for the west coast where there are gaps in scientific knowledge that prevent progress on regional management of coastal and marine resources.   My experience with the WCGA has given me enormous insight into the policy world and how science has the potential to interact with and inform ocean management.



  • Haupt, AJ, B. Woodson, SR Palumbi, and F Micheli. In Review. Ecological Applications.  Subtle genetic structure translates to limited ecological connectivity in a commercially fished invertebrate species.
  • Samhouri JF, AJ Haupt, PS Levin, JS Link, R Shuford. 2013. Lessons learned from developing integrated ecosystem assessments to inform marine ecosystem-based management in the USA. ICES Journal of Marine Science Advance Access.
  • Haupt, AJ, F Micheli, and SR Palumbi. 2013. Dispersal at a snail’s pace: historical processes affect contemporary genetic structure in an exploited marine snail.  Journal of Heredity 104:327-340.
  • Haupt, AJ. 2013. Ocean acidification as a West Coast Governors Alliance priority area.  WCGA Technical Memo.
  • Iles, AC, TC Gouhier, BA Menge, JS Stewart, AJ Haupt, MC Lynch. 2011. Climate-driven trends and ecological implications of event-scale upwelling in the California Current System.  Global Change Biology 18:783-796.
  • Woodson, B, JA Barth, OM Cheriton, MA McManus, JP Ryan, L Washburn, KN Carden, BS Cheng, J. Fernandez, LE Garske, TC Gouhier, AJ Haupt, KT Honey, MF Hubbard, A Illes, L. Kara, MC Lynch, B Mahoney, M. Pfaff, ML Pinsky, MJ Robert, JS Stewart, SJ Teck, A True.  Observations of internal wave packets propagating along-shelf in northern Monterey Bay. 2011. Geophysical Research Letters. 38.
  • O’Connell CS, Haupt AJ, Palumbi SR.  2008. Molecular and morphological characterization of two species of sea cucumber, Parastichopus parvimensis and Parastichopus Californicus, in Monterey, CA. Stanford Undergraduate Research Journal 7 36-40.
  • Logan, CA, SE Alter, AJ Haupt, K Tomalty and SR Palumbi. 2008. An impediment to consumer choice: overfished species are sold as Pacific red snapper. Biological Conservation. 141:1591-1599.
  • Micheli, F, AO Shelton, SM Bushinsky, AL Chiu, AJ Haupt, KW Heiman, CV Kappel, MC Lynch, RG Martone, and J Watanabe. 2008. Persistence and recovery of depleted marine invertebrates in marine reserves of Central California. Biological Conservation. 141:1078-1090.
  • Ruttenberg, BI, AJ Haupt, A Chiriboga, and RR Warner. 2005. Patterns, causes and consequences of regional variation in the ecology and life history of a reef fish. Oecologia. 145: 394-403.