529
N, Camarata J, Cheshatsang Y, Chu J, Citroen M, Collymore A, Cooke P, Dawoe T, Daza R,
Decktor K, DeGray S, Dhargay N, Dooley K, Dooley K, Dorje P, Dorjee K, Dorris L, Duffey
N, Dupes A, Egbiremolen O, Elong R, Falk J, Farina A, Faro S, Ferguson D, Ferreira P, Fisher
S, FitzGerald M, Foley K, Foley C, Franke A, Friedrich D, Gage D, Garber M, Gearin G,
Giannoukos G, Goode T, Goyette A, Graham J, Grandbois E, Gyaltsen K, Hafez N, Hagopian
D, Hagos B, Hall J, Healy C, Hegarty R, Honan T, Horn A, Houde N, Hughes L, Hunnicutt L,
Husby M, Jester B, Jones C, Kamat A, Kanga B, Kells C, Khazanovich D, Kieu AC, Kisner
P, Kumar M, Lance K, Landers T, Lara M, Lee W, Leger J-P, Lennon N, Leuper L, LeVine S,
Liu J, Liu X, Lokyitsang Y, Lokyitsang T, Lui A, Macdonald J, Major J, Marabella R, Maru K,
Matthews C, McDonough S, Mehta T, Meldrim J, Melnikov A, Meneus L, Mihalev A, Mihova
T, Miller K, Mittelman R, Mlenga V, Mulrain L, Munson G, Navidi A, Naylor J, Nguyen T,
Nguyen N, Nguyen C, Nguyen T, Nicol R, Norbu N, Norbu C, Novod N, Nyima T, Olandt
P, O'Neill B, O'Neill K, Osman S, Oyono L, Patti C, Perrin D, Phunkhang P, Pierre F, Priest
M, Rachupka A, Raghuraman S, Rameau R, Ray V, Raymond C, Rege F, Rise C, Rogers J,
Rogov P, Sahalie J, Settipalli S, Sharpe T, Shea T, Sheehan M, Sherpa N, Shi J, Shih D, Sloan
J, Smith C, Sparrow T, Stalker J, Stange-Thomann N, Stavropoulos S, Stone C, Stone S, Sykes
S, Tchuinga P, Tenzing P, Tesfaye S, Thoulutsang D, Thoulutsang Y, Topham K, Topping I,
Tsamla T, Vassiliev H, Venkataraman V, Vo A, Wangchuk T, Wangdi T, Weiand M, Wilkinson J,
Wilson A, Yadav S, Yang S, Yang X, Young G, Yu Q, Zainoun J, Zembek L, Zimmer A, Lander
ES (2005) Genome sequence, comparative analysis and haplotype structure of the domestic
dog. Nature 438:803. https://doi.org/10.1038/nature04338
Ljungman M, Hanawalt PC (1992) Efficient protection against oxidative DNA damage in chromatin. Mol Carcinog 5(4):264–269. https://doi.org/10.1002/mc.2940050406
Love MI, Huber W, Anders S (2014) Moderated estimation of fold change and dispersion for
RNA-seq data with DESeq2. Genome Biol 15(12):550
McEachern KL (2014) Toxicity of oil from BP Deepwater Horizon blowout on the early life stage
of red drum, Sciaenops ocellatus. Faculty of the College of Arts and Sciences, Florida Gulf
Coast University
Metzger JM, Westfall MV (2004) Covalent and noncovalent modification of thin filament action:
the essential role of troponin in cardiac muscle regulation. Circ Res 94(2):146–158
Meyer JN, Di Giulio RT (2003) Heritable adaptation and fitness costs in killifish (Fundulus
heteroclitus) inhabiting a polluted estuary. Ecol Appl 13(2):490–503. https://doi.
org/10.1890/1051-0761(2003)013[0490:HAAFCI]2.0.CO;2
Murawski SA, Hogarth WT, Peebles EB, Barbeiri L (2014) Prevalence of external skin lesions
and polycyclic aromatic hydrocarbon concentrations in Gulf of Mexico fishes, post-Deepwater
Horizon. Trans Am Fish Soc 143(4):1084–1097. https://doi.org/10.1080/00028487.2014.911
205
Magnuson JT, Khursigara AJ, Allmon EB, Esbaugh AJ, Roberts AP (2018). Effects of Deepwater
Horizon crude oil on ocular development in two estuarine fish species, red drum (Sciaenops ocellatus) and sheepshead minnow (Cyprinodon variegatus). Ecotoxicol Environ Saf 166:186–191
Nacci D, Proestou D, Champlin D, Martinson J, Waits ER (2016) Genetic basis for rapidly evolved
tolerance in the wild: adaptation to toxic pollutants by an estuarine fish species. Mol Ecol
25(21):5467–5482. https://doi.org/10.1111/mec.13848
Nei M, Maruyama T, Chakraborty R (1975) The bottleneck effect and genetic variability in populations. Evolution 29(1):1–10. https://doi.org/10.2307/2407137
Nilsen BM, Berg K, GoksoØr A (1998) Induction of cytochrome P4501A (CYP1A) in fish: a biomarker for environmental pollution. In: Phillips IR, Shephard EA (eds) Cytochrome P450 protocols. Humana Press, Totowa, NJ, pp 423–438. https://doi.org/10.1385/0-89603-519-0:423
O’Leary SJ, Hollenbeck CM, Vega RR, Gold JR, Portnoy DS (2018) Genetic mapping and comparative genomics to inform restoration enhancement and culture of southern flounder, Paralichthys
lethostigma. BMC Genomics 19(1):163. https://doi.org/10.1186/s12864-018-4541-0
Oleksiak MF, Karchner SI, Jenny MJ, Franks DG, Welch DBM, Hahn ME (2011) Transcriptomic
assessment of resistance to effects of an aryl hydrocarbon receptor (AHR) agonist in embryos
30 Genetics and Oil: Transcriptomics, Epigenetics, and Population Genomics as Tools…
N, Camarata J, Cheshatsang Y, Chu J, Citroen M, Collymore A, Cooke P, Dawoe T, Daza R,
Decktor K, DeGray S, Dhargay N, Dooley K, Dooley K, Dorje P, Dorjee K, Dorris L, Duffey
N, Dupes A, Egbiremolen O, Elong R, Falk J, Farina A, Faro S, Ferguson D, Ferreira P, Fisher
S, FitzGerald M, Foley K, Foley C, Franke A, Friedrich D, Gage D, Garber M, Gearin G,
Giannoukos G, Goode T, Goyette A, Graham J, Grandbois E, Gyaltsen K, Hafez N, Hagopian
D, Hagos B, Hall J, Healy C, Hegarty R, Honan T, Horn A, Houde N, Hughes L, Hunnicutt L,
Husby M, Jester B, Jones C, Kamat A, Kanga B, Kells C, Khazanovich D, Kieu AC, Kisner
P, Kumar M, Lance K, Landers T, Lara M, Lee W, Leger J-P, Lennon N, Leuper L, LeVine S,
Liu J, Liu X, Lokyitsang Y, Lokyitsang T, Lui A, Macdonald J, Major J, Marabella R, Maru K,
Matthews C, McDonough S, Mehta T, Meldrim J, Melnikov A, Meneus L, Mihalev A, Mihova
T, Miller K, Mittelman R, Mlenga V, Mulrain L, Munson G, Navidi A, Naylor J, Nguyen T,
Nguyen N, Nguyen C, Nguyen T, Nicol R, Norbu N, Norbu C, Novod N, Nyima T, Olandt
P, O'Neill B, O'Neill K, Osman S, Oyono L, Patti C, Perrin D, Phunkhang P, Pierre F, Priest
M, Rachupka A, Raghuraman S, Rameau R, Ray V, Raymond C, Rege F, Rise C, Rogers J,
Rogov P, Sahalie J, Settipalli S, Sharpe T, Shea T, Sheehan M, Sherpa N, Shi J, Shih D, Sloan
J, Smith C, Sparrow T, Stalker J, Stange-Thomann N, Stavropoulos S, Stone C, Stone S, Sykes
S, Tchuinga P, Tenzing P, Tesfaye S, Thoulutsang D, Thoulutsang Y, Topham K, Topping I,
Tsamla T, Vassiliev H, Venkataraman V, Vo A, Wangchuk T, Wangdi T, Weiand M, Wilkinson J,
Wilson A, Yadav S, Yang S, Yang X, Young G, Yu Q, Zainoun J, Zembek L, Zimmer A, Lander
ES (2005) Genome sequence, comparative analysis and haplotype structure of the domestic
dog. Nature 438:803. https://doi.org/10.1038/nature04338
Ljungman M, Hanawalt PC (1992) Efficient protection against oxidative DNA damage in chromatin. Mol Carcinog 5(4):264–269. https://doi.org/10.1002/mc.2940050406
Love MI, Huber W, Anders S (2014) Moderated estimation of fold change and dispersion for
RNA-seq data with DESeq2. Genome Biol 15(12):550
McEachern KL (2014) Toxicity of oil from BP Deepwater Horizon blowout on the early life stage
of red drum, Sciaenops ocellatus. Faculty of the College of Arts and Sciences, Florida Gulf
Coast University
Metzger JM, Westfall MV (2004) Covalent and noncovalent modification of thin filament action:
the essential role of troponin in cardiac muscle regulation. Circ Res 94(2):146–158
Meyer JN, Di Giulio RT (2003) Heritable adaptation and fitness costs in killifish (Fundulus
heteroclitus) inhabiting a polluted estuary. Ecol Appl 13(2):490–503. https://doi.
org/10.1890/1051-0761(2003)013[0490:HAAFCI]2.0.CO;2
Murawski SA, Hogarth WT, Peebles EB, Barbeiri L (2014) Prevalence of external skin lesions
and polycyclic aromatic hydrocarbon concentrations in Gulf of Mexico fishes, post-Deepwater
Horizon. Trans Am Fish Soc 143(4):1084–1097. https://doi.org/10.1080/00028487.2014.911
205
Magnuson JT, Khursigara AJ, Allmon EB, Esbaugh AJ, Roberts AP (2018). Effects of Deepwater
Horizon crude oil on ocular development in two estuarine fish species, red drum (Sciaenops ocellatus) and sheepshead minnow (Cyprinodon variegatus). Ecotoxicol Environ Saf 166:186–191
Nacci D, Proestou D, Champlin D, Martinson J, Waits ER (2016) Genetic basis for rapidly evolved
tolerance in the wild: adaptation to toxic pollutants by an estuarine fish species. Mol Ecol
25(21):5467–5482. https://doi.org/10.1111/mec.13848
Nei M, Maruyama T, Chakraborty R (1975) The bottleneck effect and genetic variability in populations. Evolution 29(1):1–10. https://doi.org/10.2307/2407137
Nilsen BM, Berg K, GoksoØr A (1998) Induction of cytochrome P4501A (CYP1A) in fish: a biomarker for environmental pollution. In: Phillips IR, Shephard EA (eds) Cytochrome P450 protocols. Humana Press, Totowa, NJ, pp 423–438. https://doi.org/10.1385/0-89603-519-0:423
O’Leary SJ, Hollenbeck CM, Vega RR, Gold JR, Portnoy DS (2018) Genetic mapping and comparative genomics to inform restoration enhancement and culture of southern flounder, Paralichthys
lethostigma. BMC Genomics 19(1):163. https://doi.org/10.1186/s12864-018-4541-0
Oleksiak MF, Karchner SI, Jenny MJ, Franks DG, Welch DBM, Hahn ME (2011) Transcriptomic
assessment of resistance to effects of an aryl hydrocarbon receptor (AHR) agonist in embryos
30 Genetics and Oil: Transcriptomics, Epigenetics, and Population Genomics as Tools…