I am a postdoctoral researcher at Hopkins Marine Station of Stanford University working on the trophic and spatial ecology of marine and estuarine fishes, in particular elasmobranchs (sharks, skates and rays). My research interests are broadly focused on how the abiotic and biotic environment and organismal biology interact to influence the behavior, distribution, and ecology of species, and how these interactions impact their population dynamics, life history strategies and ecosystem roles. I believe that it is important to not only address fundamental questions in biology and ecology, but to also conduct applied research that can be used to help manage and conserve species and ecosystems in an ocean that is rapidly changing due to human activity and climate change.

Professional Education

  • Doctor of Philosophy, Stanford University, BIOL-PHD (2012)
  • Bachelor of Arts, Princeton University, Ecology and Evolutionary Bio. (1999)
  • Master of Science, San Jose State University, Marine Science (2006)

Stanford Advisors

Lab Affiliations

All Publications

  • The complete mitochondrial genome of the salmon shark, Lamna ditropis (Chondrichthyes, Lamnidae) MITOCHONDRIAL DNA Chang, C., Jang-Liaw, N., Lin, Y., Carlisle, A., Hsu, H. H., Liao, Y., Shao, K. 2016; 27 (1): 316-317

    View details for DOI 10.3109/19401736.2014.892095

    View details for Web of Science ID 000366388100138

    View details for PubMedID 24660916

  • Assessing niche width of endothermic fish from genes to ecosystem. Proceedings of the National Academy of Sciences of the United States of America Madigan, D. J., Carlisle, A. B., Gardner, L. D., Jayasundara, N., Micheli, F., Schaefer, K. M., Fuller, D. W., Block, B. A. 2015; 112 (27): 8350-8355


    Endothermy in vertebrates has been postulated to confer physiological and ecological advantages. In endothermic fish, niche expansion into cooler waters is correlated with specific physiological traits and is hypothesized to lead to greater foraging success and increased fitness. Using the seasonal co-occurrence of three tuna species in the eastern Pacific Ocean as a model system, we used cardiac gene expression data (as a proxy for thermal tolerance to low temperatures), archival tag data, and diet analyses to examine the vertical niche expansion hypothesis for endothermy in situ. Yellowfin, albacore, and Pacific bluefin tuna (PBFT) in the California Current system used more surface, mesopelagic, and deep waters, respectively. Expression of cardiac genes for calcium cycling increased in PBFT and coincided with broader vertical and thermal niche utilization. However, the PBFT diet was less diverse and focused on energy-rich forage fishes but did not show the greatest energy gains. Ecosystem-based management strategies for tunas should thus consider species-specific differences in physiology and foraging specialization.

    View details for DOI 10.1073/pnas.1500524112

    View details for PubMedID 26100889

  • Climate mediates hypoxic stress on fish diversity and nursery function at the land-sea interface PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Hughes, B. B., Levey, M. D., Fountain, M. C., Carlisle, A. B., Chavez, F. P., Gleason, M. G. 2015; 112 (26): 8025-8030


    Coastal ecosystems provide numerous important ecological services, including maintenance of biodiversity and nursery grounds for many fish species of ecological and economic importance. However, human population growth has led to increased pollution, ocean warming, hypoxia, and habitat alteration that threaten ecosystem services. In this study, we used long-term datasets of fish abundance, water quality, and climatic factors to assess the threat of hypoxia and the regulating effects of climate on fish diversity and nursery conditions in Elkhorn Slough, a highly eutrophic estuary in central California (United States), which also serves as a biodiversity hot spot and critical nursery grounds for offshore fisheries in a broader region. We found that hypoxic conditions had strong negative effects on extent of suitable fish habitat, fish species richness, and abundance of the two most common flatfish species, English sole (Parophrys vetulus) and speckled sanddab (Citharichthys stigmaeus). The estuary serves as an important nursery ground for English sole, making this species vulnerable to anthropogenic threats. We determined that estuarine hypoxia was associated with significant declines in English sole nursery habitat, with cascading effects on recruitment to the offshore adult population and fishery, indicating that human land use activities can indirectly affect offshore fisheries. Estuarine hypoxic conditions varied spatially and temporally and were alleviated by strengthening of El Niño conditions through indirect pathways, a consistent result in most estuaries across the northeast Pacific. These results demonstrate that changes to coastal land use and climate can fundamentally alter the diversity and functioning of coastal nurseries and their adjacent ocean ecosystems.

    View details for DOI 10.1073/pnas.1505815112

    View details for Web of Science ID 000357079400049

    View details for PubMedID 26056293

  • Reconstructing habitat use by juvenile salmon sharks links upwelling to strandings in the California Current MARINE ECOLOGY PROGRESS SERIES Carlisle, A. B., Litvin, S. Y., Hazen, E. L., Madigan, D. J., Goldman, K. J., Lea, R. N., Block, B. A. 2015; 525: 217-228

    View details for DOI 10.3354/meps11183

    View details for Web of Science ID 000354393700017

  • Stable isotope analysis of vertebrae reveals ontogenetic changes in habitat in an endothermic pelagic shark PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES Carlisle, A. B., Goldman, K. J., Litvin, S. Y., Madigan, D. J., Bigman, J. S., Swithenbank, A. M., Kline, T. C., Block, B. A. 2015; 282 (1799)


    Ontogenetic changes in habitat are driven by shifting life-history requirements and play an important role in population dynamics. However, large portions of the life history of many pelagic species are still poorly understood or unknown. We used a novel combination of stable isotope analysis of vertebral annuli, Bayesian mixing models, isoscapes and electronic tag data to reconstruct ontogenetic patterns of habitat and resource use in a pelagic apex predator, the salmon shark (Lamna ditropis). Results identified the North Pacific Transition Zone as the major nursery area for salmon sharks and revealed an ontogenetic shift around the age of maturity from oceanic to increased use of neritic habitats. The nursery habitat may reflect trade-offs between prey availability, predation pressure and thermal constraints on juvenile endothermic sharks. The ontogenetic shift in habitat coincided with a reduction of isotopic niche, possibly reflecting specialization upon particular prey or habitats. Using tagging data to inform Bayesian isotopic mixing models revealed that adult sharks primarily use neritic habitats of Alaska yet receive a trophic subsidy from oceanic habitats. Integrating the multiple methods used here provides a powerful approach to retrospectively study the ecology and life history of migratory species throughout their ontogeny.

    View details for DOI 10.1098/rspb.2014.1446

    View details for Web of Science ID 000354866500003

    View details for PubMedID 25621332

  • Reconstructing transoceanic migration patterns of Pacific bluefin tuna using a chemical tracer toolbox ECOLOGY Madigan, D. J., Baumann, Z., Carlisle, A. B., Hoen, D. K., Popp, B. N., Dewar, H., Snodgrass, O. E., Block, B. A., Fisher, N. S. 2014; 95 (6): 1674-1683
  • Stable isotope analysis of Humboldt squid prey: Comment on Miller et al. (2013) MARINE ECOLOGY PROGRESS SERIES Field, J. C., Litvin, S. Y., Carlisle, A., Stewart, J. S., Gilly, W. F., Ruiz-Cooley, R. I. 2014; 500: 281-285

    View details for DOI 10.3354/meps10533

    View details for Web of Science ID 000332900300020

  • Effects of trophic ecology and habitat use on maternal transfer of contaminants in four species of young of the year lamniform sharks MARINE ENVIRONMENTAL RESEARCH Lyons, K., Carlisle, A., Preti, A., Mull, C., Blasius, M., O'Sullivan, J., Winkler, C., Lowe, C. G. 2013; 90: 27-38


    Organic contaminant and total mercury concentrations were compared in four species of lamniform sharks over several age classes to examine bioaccumulation patterns and gain insights into trophic ecology. Contaminants found in young of the year (YOY) sharks were assumed to be derived from maternal sources and used as a proxy to investigate factors that influence maternal offloading processes. YOY white (Carcharodon carcharias) and mako (Isurus oxyrinchus) sharks had comparable and significantly higher concentrations of PCBs, DDTs, pesticides, and mercury than YOY thresher (Alopias vulpinus) or salmon (Lamna ditropis) sharks. A significant positive relationship was found between YOY contaminant loads and maternal trophic position, suggesting that trophic ecology is one factor that plays an important role in maternal offloading. Differences in organic contaminant signatures and contaminant concentration magnitudes among species corroborated what is known about species habitat use and may be used to provide insights into the feeding ecology of these animals.

    View details for DOI 10.1016/j.marenvres.2013.05.009

    View details for Web of Science ID 000324610200004

    View details for PubMedID 23773783

  • Tissue Turnover Rates and Isotopic Trophic Discrimination Factors in the Endothermic Teleost, Pacific Bluefin Tuna (Thunnus orientalis) PLOS ONE Madigan, D. J., Litvin, S. Y., Popp, B. N., Carlisle, A. B., Farwell, C. J., Block, B. A. 2012; 7 (11)


    Stable isotope analysis (SIA) of highly migratory marine pelagic animals can improve understanding of their migratory patterns and trophic ecology. However, accurate interpretation of isotopic analyses relies on knowledge of isotope turnover rates and tissue-diet isotope discrimination factors. Laboratory-derived turnover rates and discrimination factors have been difficult to obtain due to the challenges of maintaining these species in captivity. We conducted a study to determine tissue- (white muscle and liver) and isotope- (nitrogen and carbon) specific turnover rates and trophic discrimination factors (TDFs) using archived tissues from captive Pacific bluefin tuna (PBFT), Thunnus orientalis, 1-2914 days after a diet shift in captivity. Half-life values for (15)N turnover in white muscle and liver were 167 and 86 days, and for (13)C were 255 and 162 days, respectively. TDFs for white muscle and liver were 1.9 and 1.1‰ for δ(15)N and 1.8 and 1.2‰ for δ(13)C, respectively. Our results demonstrate that turnover of (15)N and (13)C in bluefin tuna tissues is well described by a single compartment first-order kinetics model. We report variability in turnover rates between tissue types and their isotope dynamics, and hypothesize that metabolic processes play a large role in turnover of nitrogen and carbon in PBFT white muscle and liver tissues. (15)N in white muscle tissue showed the most predictable change with diet over time, suggesting that white muscle δ(15)N data may provide the most reliable inferences for diet and migration studies using stable isotopes in wild fish. These results allow more accurate interpretation of field data and dramatically improve our ability to use stable isotope data from wild tunas to better understand their migration patterns and trophic ecology.

    View details for DOI 10.1371/journal.pone.0049220

    View details for Web of Science ID 000311935800234

    View details for PubMedID 23145128

  • Stable Isotope Analysis Challenges Wasp-Waist Food Web Assumptions in an Upwelling Pelagic Ecosystem SCIENTIFIC REPORTS Madigan, D. J., Carlisle, A. B., Dewar, H., Snodgrass, O. E., Litvin, S. Y., Micheli, F., Block, B. A. 2012; 2


    Eastern boundary currents are often described as 'wasp-waist' ecosystems in which one or few mid-level forage species support a high diversity of larger predators that are highly susceptible to fluctuations in prey biomass. The assumption of wasp-waist control has not been empirically tested in all such ecosystems. This study used stable isotope analysis to test the hypothesis of wasp-waist control in the southern California Current large marine ecosystem (CCLME). We analyzed prey and predator tissue for δ¹³C and δ¹⁵N and used Bayesian mixing models to provide estimates of CCLME trophic dynamics from 2007-2010. Our results show high omnivory, planktivory by some predators, and a higher degree of trophic connectivity than that suggested by the wasp-waist model. Based on this study period, wasp-waist models oversimplify trophic dynamics within the CCLME and potentially other upwelling, pelagic ecosystems. Higher trophic connectivity in the CCLME likely increases ecosystem stability and resilience to perturbations.

    View details for DOI 10.1038/srep00654

    View details for Web of Science ID 000308807000002

    View details for PubMedID 22977729

  • Using Stable Isotope Analysis to Understand the Migration and Trophic Ecology of Northeastern Pacific White Sharks (Carcharodon carcharias) PLOS ONE Carlisle, A. B., Kim, S. L., Semmens, B. X., Madigan, D. J., Jorgensen, S. J., Perle, C. R., Anderson, S. D., Chapple, T. K., Kanive, P. E., Block, B. A. 2012; 7 (2)


    The white shark (Carcharodon carcharias) is a wide-ranging apex predator in the northeastern Pacific (NEP). Electronic tagging has demonstrated that white sharks exhibit a regular migratory pattern, occurring at coastal sites during the late summer, autumn and early winter and moving offshore to oceanic habitats during the remainder of the year, although the purpose of these migrations remains unclear. The purpose of this study was to use stable isotope analysis (SIA) to provide insight into the trophic ecology and migratory behaviors of white sharks in the NEP. Between 2006 and 2009, 53 white sharks were biopsied in central California to obtain dermal and muscle tissues, which were analyzed for stable isotope values of carbon (δ(13)C) and nitrogen (δ(15)N). We developed a mixing model that directly incorporates movement data and tissue incorporation (turnover) rates to better estimate the relative importance of different focal areas to white shark diet and elucidate their migratory behavior. Mixing model results for muscle showed a relatively equal dietary contribution from coastal and offshore regions, indicating that white sharks forage in both areas. However, model results indicated that sharks foraged at a higher relative rate in coastal habitats. There was a negative relationship between shark length and muscle δ(13)C and δ(15)N values, which may indicate ontogenetic changes in habitat use related to onset of maturity. The isotopic composition of dermal tissue was consistent with a more rapid incorporation rate than muscle and may represent more recent foraging. Low offshore consumption rates suggest that it is unlikely that foraging is the primary purpose of the offshore migrations. These results demonstrate how SIA can provide insight into the trophic ecology and migratory behavior of marine predators, especially when coupled with electronic tagging data.

    View details for DOI 10.1371/journal.pone.0030492

    View details for Web of Science ID 000302741300013

    View details for PubMedID 22355313

    View details for PubMedCentralID PMC3280240

  • Seasonal changes in depth distribution of salmon sharks (Lamna ditropis) in Alaskan waters: implications for foraging ecology CANADIAN JOURNAL OF FISHERIES AND AQUATIC SCIENCES Carlisle, A. B., Perle, C. R., Goldman, K. J., Block, B. A. 2011; 68 (11): 1905-1921

    View details for DOI 10.1139/F2011-105

    View details for Web of Science ID 000298441500004

  • Tidal movements of female leopard sharks (Triakis semifasciata) in Elkhorn Slough, California ENVIRONMENTAL BIOLOGY OF FISHES Carlisle, A. B., Starr, R. M. 2010; 89 (1): 31-45
  • Habitat use, residency, and seasonal distribution of female leopard sharks Triakis semifasciata in Elkhorn Slough, California MARINE ECOLOGY PROGRESS SERIES Carlisle, A. B., Starr, R. M. 2009; 380: 213-228

    View details for DOI 10.3354/meps07907

    View details for Web of Science ID 000265907000018