Research
Epigenetic aging of endangered cetacean populations
Age is a critical parameter for determining population dynamics and ensuring effective conservation and management approaches are being employed for species. However, the established approaches to aging cetaceans require tissues that can only be obtained post-mortem. Epigenetic approaches to aging, which alter gene expression without changing the underlying DNA sequence, have been increasingly used for estimating age in organisms ranging from zebrafish to humans. DNA methylation, which adds a methyl group at cytosine-guanine dinucleotides (CpGs) in DNA, has been used to construct models known as "epigenetic clocks" to estimate age from commonly collected tissue types. As part of my current postdoctoral position at Oregon State University and in collaboration with partners at the New Zealand Department of Conservation, the University of Auckland, Massey University and UCLA, we are developing an epigenetic clock to estimate the age of Hector's and Māui dolphins (Cephalorhynchus hectori hectori and C. h. maui). We then plan to integrate these age estimates into a capture-recapture or population dynamics model to understand population trajectory or age structure.
Phenotypic drivers of lifetime reproductive success in northern elephant seals
Lifetime reproductive success is a metric that incorporates an individual's reproductive output and survival, and is known to be skewed. Recent work has demonstrated that a small fraction of northern elephant seal (Mirounga angustirostris) females disproportionately contribute to subsequent generations, though the mechanisms behind this success are not yet known. Using life history, diet and movement data, we investigated potential links between phenotypic aspects of foraging behavior and an individual's lifetime reproductive success and annual survival. This collaboration includes partners at Sonoma State University, the Biodiversity Research Institute (Maine) and the Field Museum of Natural History (Chicago, IL).
Isotopic approaches to studying the foraging behavior of a recolonizing predator, the gray seal
Gray seals (Halichoerus grypus) were nearly extirpated from the New England coastline due to perceived conflicts with fisheries but have subsequently recolonized the region following state and federal protections. The returning population has reignited multiple concerns about the effects of seals in the local area, however, there is a lack of understanding about seal ecology in this part of their range. For my dissertation research in the Polito Lab at Louisiana State University, I investigated aspects of gray seal foraging ecology from a stable isotope perspective. Stable isotopes of carbon and nitrogen analyzed in animal tissues are frequently used to provide information about where a predator forages and what its trophic level is, respectively. Using this method on a variety of tissues types and in conjunction with data from complementary approaches, we found that gray seal foraging behavior is more nuanced than was previously known based on limited work in the previous decades. This massive effort benefitted from collaborations centered around the Northwest Atlantic Seal Research Consortium, and included NOAA's Northeast Fisheries Science Center, the Center for Coastal Studies, Woods Hole Oceanographic Institution, the University of New England, Tufts University, the Atlantic Marine Conservation Society, Duke University and the Department of Fisheries and Oceans (Canada).
Credit: A. Bogomolni
Integrating molecular genetic approaches in determining California sea lion diets
Pinniped (seal and sea lion) diets are often inferred from hard prey remains in stomach or fecal samples, though this method is prone to several biases and oftentimes cannot be used to examine individual differences in diet trends. DNA recovered from fecal samples has been used by conservation biologists for decades to non-invasively determine species and sex of free-ranging animals. Metagenomic approaches, which sequence small, diagnostic "barcode" fragments of DNA from a community of organisms in an environmental sample, has been utilized to improve taxonomic identifications of prey communities and identify those which lack identifiable remains (such as soft-bodied prey). While these barcoding genes are useful, they have limited utility for diverging lineages, which necessitates the use of alternative gene regions to differentiate closely related species. For my master's thesis, I integrated molecular sex identification and metagenomic diet analysis with established prey remain identification to investigate diet trends in California sea lions in Monterey Bay, California. Specifically, we wanted to investigate sex-specific trends in diet composition, and to use microhaplotype markers (small stretches of nuclear DNA with single nucleotide polymorphisms) to distinguish between the speciose and commercially important rockfishes (Sebastes spp.). This work included collaborations with the Molecular Ecology and Genetic Analysis team at NOAA's Southwest Fisheries Science Center, the Farallon Institute and the Año Nuevo Reserve. As part of my previous postdoctoral work at UCSC, I investigated regional and annual differences in sea lion diet using samples from colonies in the Channel Islands in collaboration with SWFSC.
Credit: J. Lindsey
Acoustic ecology of Atlantic cod in a National Marine Sanctuary
While bioacoustic studies have primarily focused on birds and mammals, fishes are also capable of sound production. Passive acoustic monitoring provides a useful method for identifying the occurrence and distribution of marine organisms when routine visual observations are logistically prohibitive. As part of a pilot project between NOAA's passive acoustic team, the Massachusetts Division of Marine Fisheries, the Stellwagen Bank National Marine Sanctuary and Cornell University, a bottom-mounted recording unit was deployed in an area suspected of being a spawning ground for Atlantic cod (Gadus morhua). I analyzed the 3 months of recording for cod 'grunts' and characterized the sounds obtained from this recording. Cod grunts were found on most recording days, and we noted daily trends in sound production, possibly associated with movements in and out of recording range. Grunt characteristics were similar to those obtained from captive cod. Since this study, the passive acoustic team has continued to monitor cod occurrence in the Sanctuary.
Credit: E. Ganson