Killifish Genomics

Our lab has worked towards establishing Fundulus killifish as genome-enabled model species for research in ecological physiology and evolutionary biology. Collaborators include Joe Shaw at Indiana University, John Colbourne at the University of Birmingham UK, Wes Warren at the University of Missouri, Doug Crawford and Margie Oleksiak at the University of Miami, Diane Nacci at the US EPA, Mark Hahn at Woods Hole Oceanographic Institution, and Cole Matson at Baylor University. We initially sequenced and assembled a reference genome for F. heteroclitus that is now available at NCBI. We also re-sequenced ~400 additional whole genomes from multiple populations of F. heteroclitus to discover the genomic basis of recently and repeatedly evolved extreme pollution tolerance (data available at NCBI). We have expanded this work to examine the genomic basis of adaptation to extreme pollution in the Gulf killifish (Fundulus grandis) in collaboration with Cole Matson‘s group. We have also recently released assembled genomes for several additional Fundulus species including euryhaline (estuarine) and freshwater species. Whitehead lab personnel involvement includes Noah Reid, Elias Oziolor, Jeff Miller, and Lisa Johnson.

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. Whitehead lab personnel involvement includes Jane Park, Nicole McNabb, and Whitney Pilcher.

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. Whitehead lab personnel involvement includes Reid Brennan, Lisa Johnson, and Joe McGirr

Genomics of adaptation to polluted environments

Some populations of Atlantic killifish (Fundulus heteroclitus) and Gulf killifish (Fundulus grandis) have evolved resistance to extraordinarily high concentrations of PCB/dioxin/PAH contaminants in urban estuaries along the east coast of North America and the northern Gulf of Mexico. Resistance is heritable (so it has a genetic basis) and has evolved over a very short time period. In collaboration with Diane Nacci (US EPA) and Cole Matson (Baylor University) we are exploring the genomic basis of these extraordinary adaptations. Whitehead lab personnel involvement includes Noah Reid, Jeff Miller, and Elias Oziolor.

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 sequenced a reference transcriptome for red abalone (Haliotis rufescens). This effort is in partnership with Andrew Severin (Iowa State U.) where we sequenced and assembled 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). We have are also examining red abalone landscape genomics, including populations sampled from across the mosaic of habitats that spans their range from Mexico through California to Oregon. Here is a video clip of the Al Jazeera reporting on our red abalone work. Whitehead lab personnel involvement includes Sara Boles, and Joanna Griffiths.

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 was a visiting scholar from China who spent 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 studying 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 involves laboratory challenge experiments, using comparative physiology, immunology, and transcriptomics, to discover causes and consequences of oil + pathogen interactions. We are also sequencing/assembling/annotating a reference genome for Pacific herring, and tracking 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 other Alaska populations that were not exposed to oil and did not collapse. In this survey of genome-wide genetic variation, we are also including populations from across their latitudinal range from Alaska to California. The exposure/pathogen work is in collaboration with Paul Hershberger (USGS) and Nat Scholz and John Incardona (NOAA). The study is funded by the Exxon Valdez Oil Spill Trustees Council. Whitehead lab personnel involvement includes Tony Gill, Elias Oziolor, and Joe McGirr.

Genetics of climate change resilience in Delta smelt: quantitative genetics of thermal resilience, and genomic imprinting from temperature and domestication

We are studying whether the critically endangered delta smelt, which is endemic to the San Francisco Bay-Delta estuary, may be resilient to climate change. We are examining whether the species harbors additive genetic variation for thermal resilience that may enable evolutionary adaptation to climate change. We are also testing whether thermal resilience varies between wild fish and hatchery-reared fish, and whether rearing temperature and hatchery rearing cause epigenetic modifications that may affect physiology. This work is a collaboration with Nann Fangue and Tien Hung, including interactions with Mandi Finger at the GVL and Britt Davis and Melinda Baerwald at DFW. Whitehead lab personnel involvement includes Joanna Griffiths.

Trans-generational impacts of flame retardants

Flame retardants are ubiquitous in the environment, yet little is known about their potential for toxicity. We are using a multi-omics approach, integrated with physiology and toxicology, to examine their role in causing impacts on bioenergetics, behavior, reproduction, and development. We are also testing whether exposure to adult or early life stage killifish has negative effects that propagate across one or more generations (trans-generational and multi-generational impacts). This work includes collaboration with Diane Nacci and Bryan Clark‘s group at the US EPA. Whitehead lab personnel involvement includes Nicole McNabb.

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