Research

CURRENT RESEARCH PROJECTS:

  • Killifish genomics: developing genomics resources for the killifish community
  • Ecotoxicogenomics of the Deepwater Horizon Oil Spill
  • Comparative genomics of osmotic stress tolerance
  • Genomics of adaptation to polluted environments
  • Abalone genomics: comparing genomic responses to climate change
  • Mangrove killifish genomics: comparing genomic responses to life out of water
  • Pacific herring genomics: reference genome, population genomic change through time, and functional genomics of oil + pathogen challenge interaction

Killifish Genomics

Our lab is heading a 5-institution collaborative research program to sequence the genome of our model killifish Fundulus heteroclitus. Collaborators include Joe Shaw at Indiana University, John Colbourne at the University of Birmingham UK, Wes Warren at Washington University, Doug Crawford and Margie Oleksiak at the University of Miami, Diane Nacci at the US EPA, and Mark Hahn at Woods Hole Oceanographic Institution. This project involved sequencing and assembling a reference genome for F. heteroclitus that is now available at NCBI. We also re-sequenced ~400 additional whole genomes from multiple populations to discover the genomic basis of recently and repeatedly evolved extreme pollution tolerance (data available at NCBI).

Ecotoxicogenomics of the Deepwater Horizon Oil Spill

We are using the Gulf killifish Fundulus grandis as a model in field and lab studies to examine the sub-lethal consequences of exposure to contaminating oil from the DH spill, integrating biological measures from the molecular genome expression level to the physiological level, in collaboration with the labs of Fernando Galvez and Chris Green (LSU). We are particularly interested in how sensitivity to oil exposure can vary among individuals and populations, how effects from oil exposures may propagate across generations, and the molecular mechanisms that mediate developmental impacts of oil exposures. We are also collaborating with Rob Ricker (NOAA), Christoph Aeppli (Bigelow Lab), and Diane Nacci (US EPA) to understand the mechanisms whereby different oil fractions cause developmental toxicity. Press Release from our first set of studies.  Press Release from our second set of studies.

Comparative Genomics of osmotic stress tolerance

Salinity is arguably the single most important variable that defines the limits of aquatic species distributions in nature. We seek to understand the genetic and physiological mechanisms of acclimation and adaptation to osmotic stress. We compare fish taxa that vary in their ability to tolerate osmotic stress, and that correspondingly vary in their ecological distributions (freshwater, marine, or brackish habitats). We couple physiological characterization (in collaboration with Fernando Galvez, LSU) with functional genomics, population genomics, and comparative genomics. We are also exploring the role of gut and gill microbiome variation in contributing to fish adaptation to different osmotic environments (in collaboration with Greg Mayer, Texas Tech U).  Research Highlight

Genomics of adaptation to polluted environments

Some populations of Atlantic killifish (Fundulus heteroclitus) have evolved tolerance to extraordinarily high concentrations of PCB/dioxin/PAH contaminants in urban estuaries along the East Coast of North America. Tolerance is heritable (so it has a genetic basis) and has evolved over a very short time period. In collaboration with Diane Nacci (US EPA) we are exploring the genomic basis of these extraordinary adaptations. With a large collaborative group (Joe Shaw Indiana U., John Colbourne U. of Birmingham UK, Wes Warren  Washington U., Doug Crawford and Margie Oleksiak U. of Miami, Mark Hahn Woods Hole OI) we sequenced ~400  whole genomes from multiple populations to discover the genes and pathways under selection, and that contributed to this rapidly evolved extreme tolerance phenotype (data available at NCBI).  Research Highlight

Abalone genomics: comparing genomic responses to climate change

Abalone are sensitive to the negative developmental impacts of ocean acidification which is an important consequence of global climate change. We seek to discover the physiological mechanisms that mediate sensitivity to acidification. We also seek to discover genetic variation within and among populations that may contribute to variable tolerance to the impacts of acidification – this is important for evaluating their ability to evolve and adapt to climate change. We are developing genomics resources for research and conservation. We are sequencing a reference transcriptome for red abalone (Haliotis rufescens). This effort is in partnership with Andrew Severin (Iowa State U.) whose group is sequencing and assembling a reference genome for red abalone (as well as reference genomes for pink, green, black, and white abalone species). Experiments on the impacts of acidification and diet on growth and development are in collaboration with Laura Rogers-Bennett, Eric Sanford, Brian Gaylord, and Tessa Hill (UC Davis, Bodega Marine Laboratory), and Doug Bush and Dan Swezey (The Cultured Abalone Farm). Here is a video clip of the Al Jazeera reporting on our red abalone work.

Mangrove killifish genomics: comparing genomic responses to life out of water

Mangrove killifish (Kryptolebias marmoratus) are strange and cool animals: they are the only vertebrate species that is capable of simultaneous self-fertilization, AND they can survive up to 3 months out of water (they are amphibious)! However this ability to survive out of water varies quite a bit among genotypes. In collaboration with Patricia Wright’s group (University of Guelph) we are studying the physiological and gene regulatory mechanisms that enable this amazing ability to survive out of water, and we are comparing these responses across genotypes that vary in their ability to do this. The transcriptomics work is being led by Yunwei Dong (Xiamen University), who is a visiting scholar from China doing his sabbatical in the Whitehead lab.

Pacific herring genomics: reference genome, population genomic change through time, and functional genomics of oil + pathogen challenge interaction

We are starting to study how oil exposures and pathogen exposures may interact to affect fish health. This study may shed insights into the contributions of the Exxon Valdez oil spill and pathogen stress to the massive 1993 collapse of the herring fishery in Prince William Sound, Alaska. The project will involve laboratory challenge experiments, using comparative physiology, immunology, and transcriptomics, to discover causes and consequences of oil + pathogen interactions. We will also sequence/assemble/annotate a reference genome for Pacific herring, and track population genetic change through time, dating from the Exxon Valdez spill to current day, to illuminate how the spill and collapse affected genetic diversity within Prince William Sound compared to another Alaska population that was not exposed to oil and did not collapse. This work is in collaboration with Paul Hershberger (USGS). We will also partner with Nat Scholz and John Incardona (NOAA). The study is funded by the Exxon Valdez Oil Spill Trustees Council.

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