522
When translating laboratory studies to the wild, it is imperative to consider that
while some observed phenotypes in the laboratory would be fatal in the natural
environment because of decreased performance, alterations to epigenomes are not
likely to be lethal and therefore could serve as biomarkers of past oil exposure. For
instance, Corrales et al. (2014) exposed zebrafish to varying levels of BaP, a known
PAH contaminant, but did not observe altered phenotypes in the exposed generation
(F 0 ); however, the F 1 and F 2 generations experienced increased mortality and higher
incidence of deformities. Follow-up studies found that larvae exposed to BaP had
neural degeneration (Gao et al. 2017; Knecht et al. 2017) and DNA methylation differences between the control and exposed zebrafish were found in several promoter
regions of genes involved in neural development in adult brain tissue (Gao et al.
2017). Studies in human epigenetics indicate that some neural development genes
are not reset during the demethylation of primordial germ cells (Tang et al. 2015),
suggesting that there could be transgenerational BaP effects in wild fishes.
Epigenetic biomarkers of exposure, discovered in controlled laboratory experiments, would be useful for monitoring wild populations for contaminant exposure
and potential population effects. With chronic oil exposure in the Gulf of Mexico
due to human and natural inputs (Murawski et al. 2014), it is very likely that some
epigenetic marker diagnostic of exposure may already be present in Gulf of Mexico
organisms. Further experimentation will be required to understand differences in
biological response to acute exposures and long-term exposures of both naturally
occurring and human-introduced hydrocarbons.
30.4 Population Genomics
Genomics in the context of this discussion refers to studies focused on characterizing the content of entire genomes (or reduced-representation genomes). In the past,
such studies were cost prohibitive because of the inefficiency of Sanger sequencing,
which relies on chain-terminating dideoxynucleotides. Massively parallel sequencing technologies (next-generation sequencing) have increased efficiency by allowing the simultaneous sequencing of millions of small fragments (Behjati and Tarpey
2013). The relative affordability and accessibility of these technologies has made
genomics approaches practical for a variety of researchers investigating both model
and non-model organisms alike.
At the most basic level, genomic studies focus on sequencing entire genomes
from individual organisms and annotating functional portions of those genomes.
Comparative genomic studies involve comparisons of genomic content across taxa
to look for common aspects of genomic architecture evolution and function and to
identify important differences (ICGSC et al. 2004; Lindblad-Toh et al. 2005).
Both basic and comparative genomics studies are useful for understanding organismal responses to oil exposure at the subcellular level (e.g., Wirgin and Waldman
D. S. Portnoy et al.
When translating laboratory studies to the wild, it is imperative to consider that
while some observed phenotypes in the laboratory would be fatal in the natural
environment because of decreased performance, alterations to epigenomes are not
likely to be lethal and therefore could serve as biomarkers of past oil exposure. For
instance, Corrales et al. (2014) exposed zebrafish to varying levels of BaP, a known
PAH contaminant, but did not observe altered phenotypes in the exposed generation
(F 0 ); however, the F 1 and F 2 generations experienced increased mortality and higher
incidence of deformities. Follow-up studies found that larvae exposed to BaP had
neural degeneration (Gao et al. 2017; Knecht et al. 2017) and DNA methylation differences between the control and exposed zebrafish were found in several promoter
regions of genes involved in neural development in adult brain tissue (Gao et al.
2017). Studies in human epigenetics indicate that some neural development genes
are not reset during the demethylation of primordial germ cells (Tang et al. 2015),
suggesting that there could be transgenerational BaP effects in wild fishes.
Epigenetic biomarkers of exposure, discovered in controlled laboratory experiments, would be useful for monitoring wild populations for contaminant exposure
and potential population effects. With chronic oil exposure in the Gulf of Mexico
due to human and natural inputs (Murawski et al. 2014), it is very likely that some
epigenetic marker diagnostic of exposure may already be present in Gulf of Mexico
organisms. Further experimentation will be required to understand differences in
biological response to acute exposures and long-term exposures of both naturally
occurring and human-introduced hydrocarbons.
30.4 Population Genomics
Genomics in the context of this discussion refers to studies focused on characterizing the content of entire genomes (or reduced-representation genomes). In the past,
such studies were cost prohibitive because of the inefficiency of Sanger sequencing,
which relies on chain-terminating dideoxynucleotides. Massively parallel sequencing technologies (next-generation sequencing) have increased efficiency by allowing the simultaneous sequencing of millions of small fragments (Behjati and Tarpey
2013). The relative affordability and accessibility of these technologies has made
genomics approaches practical for a variety of researchers investigating both model
and non-model organisms alike.
At the most basic level, genomic studies focus on sequencing entire genomes
from individual organisms and annotating functional portions of those genomes.
Comparative genomic studies involve comparisons of genomic content across taxa
to look for common aspects of genomic architecture evolution and function and to
identify important differences (ICGSC et al. 2004; Lindblad-Toh et al. 2005).
Both basic and comparative genomics studies are useful for understanding organismal responses to oil exposure at the subcellular level (e.g., Wirgin and Waldman
D. S. Portnoy et al.