ecological adaptation

Animals can be shaped by their environments through natural selection, phenotypic plasticity as well as epigenetic mechanisms. Teasing apart the roles of these complex processes is key not only to understand how organisms are adapted to their ecosystems (i.e., both abiotic conditions and biotic interactions), but also to understand how resilient or sensitive they may be to environmental changes and human impacts. Additionally, identifying key genes underlying specific traits such as environmental tolerance or life history (e.g., homing & migration) can serve as diagnostic tools to promote resilient populations or assess risk. Our research group studies these questions by combining functional genomic tools (e.g., transcriptomics and whole genome sequencing) with collaborative, complementary approaches to assess organismal responses and traits, such as environmental tolerance, biochemical assays, metabolic rate, habitat utilization (via animal telemetry & stable isotopes), and body condition assessments.

using genomes to understand drivers of behavioral & physiological adaptations

Leatherback turtles descend from an ancient extant sea turtle lineage. They have a complex life history and unique set of physiological adaptations that allow them to dive to great depths, survive in cold waters (exploiting habitats far beyond many other ectotherms), navigate across entire ocean basins, and meet the energetic demands of their up to 1500lb bodies from a diet of almost solely jellyfish. Perhaps even more impressively, young turtles reach remote foraging grounds without any parental guidance, and then navigate back to natal rookeries after years to decades of absence. However, we currently know very little about the genomic drivers of these fascinating behavioral & physiological adaptations in this and other species of sea turtles because we have not had the resources available to conduct these studies. Recent advances in genomic technologies now make this possible. Additionally, continued declines in Pacific leatherback turtles despite intensive conservation efforts have brought our lack of understanding on some key aspects of their complex biology into focus and urgency. In collaboration with the Vertebrates Genomes Project (a project of the Genome 10K Consortium) & the NOAA Southwest Fisheries Science Center, we are constructing near error-free chromosomal level reference genomes for leatherback and green sea turtles and performing whole genome re-sequencing of individuals to understand the genomic (and epigenomic) architecture and other determinants of long-distance navigation and natal homing, breeding seasonality and reproductive strategies, and other key behavioral and physiological adaptations.

Pacific leatherback foraging off the California coast after making the long-distance migration from Western Pacific nesting grounds (this animal was previously tagged at an Indonesian nesting beach).

infectious disease ecology of restored watershed connectivity

Improving habitat connectivity in ecosystems fragmented by human activity is a central goal of many conservation plans, but the roles of host-pathogen dynamics and genomic diversity in the recovery of populations of concern in restored systems are often not well understood. In aquatic ecosystems dams have been one of the largest causes of habitat fragmentation over the past century, such that dam removal has been a significant and increasing focus of watershed restoration efforts in North America. While dam removal allows animals to move more freely in freshwater systems with many associated benefits, there may be unintended disease consequences related to pathogen transmission and host immunity. This is of particular importance in the context of climate change because warm water can increase the disease susceptibility of fish. Many dams are decades old, meaning fish populations have been physically separated for generations. This isolation may result in: i) a loss of host genetic immune factors that help recognize pathogens through genetic drift in small sub-populations, ii) divergent pathogen species between isolated host populations, or iii) local immunological adaptation of hosts to resident pathogens. When a dam is removed, fish populations can mix freely, but so can their bacteria, viruses, and microparasites. Without an effective immune defense, disease processes could decrease host body size, survival, population productivity, and affect future disease resistance, especially in a warming climate.

Led by Dr. Amy Teffer as a Smith Conservation Fellow and in collaboration with Dr. Benjamin Letcher at the USGS Conte Anadromous Fish Laboratory, we are combining genomics, animal physiology and population forecast modeling to understand these dynamics and develop an interactive decision-making tool to aid the prioritization of New England dam removal projects. Using Brook Trout (Salvelinus fontinalis) in Massachusetts as a focal species, this project integrates data from i) field sampling to compare genetic immune factors (e.g., major histocompatibility complex diversity) and infectious agent community composition among brook trout subpopulations in a fragmented watershed, and ii) laboratory cohabitation experiments simulating dam removal to measure transmission within and among host subpopulations at current and projected temperatures under climate change.

Using transcriptomics to understand how marine turtles cope with environmental stress

Organisms can modulate physiological responses to environmental conditions in many ways, and transcriptomics can help identify key biological functions that may be altered under different environmental conditions or throughout development. Although there have been limited studies in sea turtles to date due to ethical and logistical challenges of obtaining high quality tissue samples, non-lethal blood samples can be used to understand the diversity of genes that are expressed differently among populations and species, and the biological functions that may be affected by different natural and anthropogenic conditions. Using RNA-Sequencing, we are coupling sampling with complementary approaches (whole organism physiological and health metrics, contaminant loads, and stable isotopes) to begin to understand these processes in marine turtles. This includes exploring the

baseline diversity of genes expressed and the allelic variation present among individuals and species and biomarkers associated with pollutant exposure (led by Shreya Banerjeee), and investigating transcriptomic profiles associated with disease, such as fibropapillomatosis, and sex determination (led by ECo MS student Jamie Stoll). These studies are being conducted in collaboration with Drs. Jennifer Lynch (National Institute of Standards & Technologies), Camryn Allen (NOAA PIFSC), Heather Harris (Cal Poly), Eugenia Naro-Maciel (New York U.), and Eleanor Sterling (American Museum of Natural History).