Oleksiak Marjorie F.

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Marjorie F.

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Now showing 1 - 6 of 6
  • Article
    The landscape of extreme genomic variation in the highly adaptable Atlantic killifish
    (Oxford University Press, 2017-03-01) Reid, Noah M. ; Jackson, Craig E. ; Gilbert, Don ; Minx, Patrick ; Montague, Michael J. ; Hampton, Thomas H. ; Helfrich, Lily W. ; King, Benjamin L. ; Nacci, Diane E. ; Aluru, Neelakanteswar ; Karchner, Sibel I. ; Colbourne, John K. ; Hahn, Mark E. ; Shaw, Joseph R. ; Oleksiak, Marjorie F. ; Crawford, Douglas L. ; Warren, Wesley C. ; Whitehead, Andrew
    Understanding and predicting the fate of populations in changing environments require knowledge about the mechanisms that support phenotypic plasticity and the adaptive value and evolutionary fate of genetic variation within populations. Atlantic killifish (Fundulus heteroclitus) exhibit extensive phenotypic plasticity that supports large population sizes in highly fluctuating estuarine environments. Populations have also evolved diverse local adaptations. To yield insights into the genomic variation that supports their adaptability, we sequenced a reference genome and 48 additional whole genomes from a wild population. Evolution of genes associated with cell cycle regulation and apoptosis is accelerated along the killifish lineage, which is likely tied to adaptations for life in highly variable estuarine environments. Genome-wide standing genetic variation, including nucleotide diversity and copy number variation, is extremely high. The highest diversity genes are those associated with immune function and olfaction, whereas genes under greatest evolutionary constraint are those associated with neurological, developmental, and cytoskeletal functions. Reduced genetic variation is detected for tight junction proteins, which in killifish regulate paracellular permeability that supports their extreme physiological flexibility. Low-diversity genes engage in more regulatory interactions than high-diversity genes, consistent with the influence of pleiotropic constraint on molecular evolution. High genetic variation is crucial for continued persistence of species given the pace of contemporary environmental change. Killifish populations harbor among the highest levels of nucleotide diversity yet reported for a vertebrate species, and thus may serve as a useful model system for studying evolutionary potential in variable and changing environments.
  • Article
    Can diversifying selection be distinguished from history in geographic clines? A population genomic study of killifish (Fundulus heteroclitus)
    (Public Library of Science, 2012-09-26) Strand, Allan E. ; Williams, Larissa M. ; Oleksiak, Marjorie F. ; Sotka, Erik E.
    A common geographical pattern of genetic variation is the one-dimensional cline. Clines may be maintained by diversifying selection across a geographical gradient but can also reflect historical processes such as allopatry followed by secondary contact. To identify loci that may be undergoing diversifying selection, we examined the distribution of geographical variation patterns across the range of the killifish (Fundulus heteroclitus) in 310 loci, including microsatellites, allozymes, and single nucleotide polymorphisms. We employed two approaches to detect loci under strong diversifying selection. First, we developed an automated method to identify clinal variation on a per-locus basis and examined the distribution of clines to detect those that exhibited signifcantly steeper slopes. Second, we employed a classic -outlier method as a complementary approach. We also assessed performance of these techniques using simulations. Overall, latitudinal clines were detected in nearly half of all loci genotyped (i.e., all eight microsatellite loci, 12 of 16 allozyme loci and 44% of the 285 SNPs). With the exception of few outlier loci (notably mtDNA and malate dehydrogenase), the positions and slopes of Fundulus clines were statistically indistinguishable. The high frequency of latitudinal clines across the genome indicates that secondary contact plays a central role in the historical demography of this species. Our simulation results indicate that accurately detecting diversifying selection using genome scans is extremely difficult in species with a strong signal of secondary contact; neutral evolution under this history produces clines as steep as those expected under selection. Based on these results, we propose that demographic history can explain all clinal patterns observed in F. heteroclitus without invoking natural selection to either establish or maintain the pattern we observe today.
  • Preprint
    Fundulus as the premier teleost model in environmental biology : opportunities for new insights using genomics
    ( 2007-09-01) Burnett, Karen G. ; Bain, Lisa J. ; Baldwin, William S. ; Callard, Gloria V. ; Cohen, Sarah ; Di Giulio, Richard T. ; Evans, David H. ; Gomez-Chiarri, Marta ; Hahn, Mark E. ; Hoover, Cindi A. ; Karchner, Sibel I. ; Katoh, Fumi ; MacLatchy, Deborah L. ; Marshall, William S. ; Meyer, Joel N. ; Nacci, Diane E. ; Oleksiak, Marjorie F. ; Rees, Bernard B. ; Singer, Thomas D. ; Stegeman, John J. ; Towle, David W. ; Van Veld, Peter A. ; Vogelbein, Wolfgang K. ; Whitehead, Andrew ; Winn, Richard N. ; Crawford, Douglas L.
    A strong foundation of basic and applied research documents that the estuarine fish Fundulus heteroclitus and related species are unique laboratory and field models for understanding how individuals and populations interact with their environment. In this paper we summarize an extensive body of work examining the adaptive responses of Fundulus species to environmental conditions, and describe how this research has contributed importantly to our understanding of physiology, gene regulation, toxicology, and ecological and evolutionary genetics of teleosts and other vertebrates. These explorations have reached a critical juncture at which advancement is hindered by the lack of genomic resources for these species. We suggest that a more complete genomics toolbox for F. heteroclitus and related species will permit researchers to exploit the power of this model organism to rapidly advance our understanding of fundamental biological and pathological mechanisms among vertebrates, as well as ecological strategies and evolutionary processes common to all living organisms.
  • Article
    Transcriptomic assessment of resistance to effects of an aryl hydrocarbon receptor (AHR) agonist in embryos of Atlantic killifish (Fundulus heteroclitus) from a marine Superfund site
    (BioMed Central, 2011-05-24) Oleksiak, Marjorie F. ; Karchner, Sibel I. ; Jenny, Matthew J. ; Franks, Diana G. ; Mark Welch, David B. ; Hahn, Mark E.
    Populations of Atlantic killifish (Fundulus heteroclitus) have evolved resistance to the embryotoxic effects of polychlorinated biphenyls (PCBs) and other halogenated and nonhalogenated aromatic hydrocarbons that act through an aryl hydrocarbon receptor (AHR)-dependent signaling pathway. The resistance is accompanied by reduced sensitivity to induction of cytochrome P450 1A (CYP1A), a widely used biomarker of aromatic hydrocarbon exposure and effect, but whether the reduced sensitivity is specific to CYP1A or reflects a genome-wide reduction in responsiveness to all AHR-mediated changes in gene expression is unknown. We compared gene expression profiles and the response to 3,3',4,4',5-pentachlorobiphenyl (PCB-126) exposure in embryos (5 and 10 dpf) and larvae (15 dpf) from F. heteroclitus populations inhabiting the New Bedford Harbor, Massachusetts (NBH) Superfund site (PCB-resistant) and a reference site, Scorton Creek, Massachusetts (SC; PCB-sensitive). Analysis using a 7,000-gene cDNA array revealed striking differences in responsiveness to PCB-126 between the populations; the differences occur at all three stages examined. There was a sizeable set of PCB-responsive genes in the sensitive SC population, a much smaller set of PCB-responsive genes in NBH fish, and few similarities in PCB-responsive genes between the two populations. Most of the array results were confirmed, and additional PCB-regulated genes identified, by RNA-Seq (deep pyrosequencing). The results suggest that NBH fish possess a gene regulatory defect that is not specific to one target gene such as CYP1A but rather lies in a regulatory pathway that controls the transcriptional response of multiple genes to PCB exposure. The results are consistent with genome-wide disruption of AHR-dependent signaling in NBH fish.
  • Preprint
    The genomic landscape of rapid repeated evolutionary adaptation to toxic pollution in wild fish
    ( 2016-10) Reid, Noah M. ; Proestou, Dina A. ; Clark, Bryan W. ; Warren, Wesley C. ; Colbourne, John K. ; Shaw, Joseph R. ; Karchner, Sibel I. ; Hahn, Mark E. ; Nacci, Diane E. ; Oleksiak, Marjorie F. ; Crawford, Douglas L. ; Whitehead, Andrew
    Atlantic killifish populations have rapidly adapted to normally lethal levels of pollution in four urban estuaries. Through analysis of 384 whole killifish genome sequences and comparative transcriptomics in four pairs of sensitive and tolerant populations, we identify the aryl hydrocarbon receptor-based signaling pathway as a shared target of selection. This suggests evolutionary constraint on adaptive solutions to complex toxicant mixtures at each site. However, distinct molecular variants apparently contribute to adaptive pathway modification among tolerant populations. Selection also targets other toxicity-mediating genes, and genes of connected signaling pathways, indicating complex tolerance phenotypes and potentially compensatory adaptations. Molecular changes are consistent with selection on standing genetic variation. In killifish high nucleotide diversity has likely been a crucial substrate for selective sweeps to propel rapid adaptation.
  • Thesis
    Diversity and characterization of novel Cytochrome P450 2 genes in the marine teleost Fundulus Heteroclitus
    (Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 1997-09) Oleksiak, Marjorie F.
    The multiplicity and roles of cytochrome P450 CYP genes in the 2 family are not well known in fish. Characterizations of CYP2 genes were done in the killifish, Fundulus heteroclitus. Multiple cDNAs from three CYP2 subfamilies were isolated from killifish cDNA libraries. Sequence analyses showed that one cloned from liver is related to trout CYP2K1. The other cDNAs were classified into two new subfamilies, CYP2N and CYP2P. CYP2N1, CYP2P2, and CYP2P3 were cloned from liver, and CYP2N2 was cloned from heart CYP2P1 was cloned from a killifish genomic DNA library. Northern analyses showed that CYP2P transcripts are expressed strongly in gut and liver. Likewise, CYP2N1 transcripts are expressed strongly in liver and gut and also in heart and brain while CYP2N2 transcripts are expressed strongly in heart and brain and also in liver, gut, eye, kidney, and gill. The CYP2Ns and CYP2Ps are phylogenetically most closely related to the mammalian CYP2Js, and their transcripts also have similar tissue specific sites of expression as the CYP2Js. These phylogenetic and expression site similarities suggest functional similarities as well. To evaluate the functions of the killifish CYP, full length CYP2N 1, CYP2N2, and CYP2P3 proteins were expressed in Sf9 insect cells using a baculovirus system, and their metabolism of arachidonic acid was examined. CYP2N 1, CYP2N2, and CYP2P3 metabolized arachidonic acid at respective rates of 435, 95, and 135 pmol/nmol CYP/min forming a variety of eicosanoids including epoxyeicosatrienoic acids 14,15-, 11,12-, and 8,9- and hydroxyeicosatrienoic acids 5-, 9-, 11-, 12-, 16-, 19-, and 20-. Eicosanoids, especially arachidonic acid metabolites, have been shown to modulate epithelial salt and water transport in a wide variety of organisms including mammals, frogs, toads, fishes, molluscs and insects. They also have been shown to act in various aspects of reproductive biology in sea stars, sea urchins, molluscs, insects, fishes, reptiles, and mammals. Arachidonic acid metabolites thus are involved in the regulation of cellular processes that are fundamental to organisms in general, and their synthesis is of primary interest. These results suggest that the CYP2Ns and CYP2Ps may be early vertebrate arachidonic acid catalysts.