523
2004; Hahn et al. 2006; Oleksiak et al. 2011), contributing important background
information for the types of transcriptomic and epigenetic studies discussed previously. Population genomic studies, the focus of this section, compare genomic
content among individuals within the same species to understand how microevolutionary processes (drift, migration, selection, and mutation) interact to produce
observed patterns of contemporary genomic variation and consider variants like
single nucleotide polymorphisms (SNPs), insertions and deletions (indels), and
larger chromosomal changes (e.g., inversions, recombination, duplications, etc.).
Population genomics is an important field of study for understanding organismal
response to oil spills, because exposure to toxins can lead to direct changes at the
nucleotide level via mutation and changes in the frequency of alleles at the population level due to increased drift, changing levels and/or patterns of migration (population connectivity), and selection for resistant genotypes. These changes can
affect individual organismal functioning, while having population-level effects
(Belfiore and Anderson 2001; van Straalen and Timmermans 2002). Changes
resulting from microevolutionary processes can be broadly divided into those that
are manifest throughout the genome and those that influence only certain areas in
the genome.
Chromosomal aberrations and point mutations associated with mutagenic properties of the components of crude oil (Pashin and Bakhitova 1979; Al-Sabti 1985)
are changes at the sequence level that are specific to individuals and occur at specific sites or regions of chromosomes, which if replicated can become permanent.
When affected sites/regions impact coding regions or regulatory elements, basic
organismal functioning may be impaired, and negative health outcomes may result
(Haensly et al. 1982; Wirgin and Waldman 1998). If mutations occur in germline
cells or during early development, progeny may perform poorly or fail to develop
properly (Frank 2010), and this can lead to population-level effects by decreasing
the reproductive output of populations (Carls et al. 1999). While individual chromosomal aberrations are site specific, populations exposed to toxins, including oil,
have been shown in some cases to present increased variation associated with accelerated mutation rates (e.g., oil, Klekowski et al. 1994; heavy metals and radiation,
Eeva et al. 2006; radiation, Volkova et al. 2018). Alternatively, populations may lose
genetic variation after exposure as deleterious and lethal mutations accumulate and
interact with other microevolutionary processes (Bickham et al. 2000).
When populations of organisms experience mass-mortality events, the number
of reproductive individuals decreases, and this can lead to reductions in effective
size (N E ) that may persist across generations, a phenomenon often referred to as a
bottleneck. Because the rate by which drift changes allele frequencies is inversely
proportional to N E , bottlenecks can lead to decreases in genetic diversity (Nei et al.
1975). Drift impacts the entire genome, so reductions in genetic diversity associated with bottlenecks are genome-wide phenomena, affecting neutral (non-coding)
markers and coding regions as well. The latter is of concern because decreased
variation at coding regions may equate to decreased adaptive variation (genetic
30 Genetics and Oil: Transcriptomics, Epigenetics, and Population Genomics as Tools…
2004; Hahn et al. 2006; Oleksiak et al. 2011), contributing important background
information for the types of transcriptomic and epigenetic studies discussed previously. Population genomic studies, the focus of this section, compare genomic
content among individuals within the same species to understand how microevolutionary processes (drift, migration, selection, and mutation) interact to produce
observed patterns of contemporary genomic variation and consider variants like
single nucleotide polymorphisms (SNPs), insertions and deletions (indels), and
larger chromosomal changes (e.g., inversions, recombination, duplications, etc.).
Population genomics is an important field of study for understanding organismal
response to oil spills, because exposure to toxins can lead to direct changes at the
nucleotide level via mutation and changes in the frequency of alleles at the population level due to increased drift, changing levels and/or patterns of migration (population connectivity), and selection for resistant genotypes. These changes can
affect individual organismal functioning, while having population-level effects
(Belfiore and Anderson 2001; van Straalen and Timmermans 2002). Changes
resulting from microevolutionary processes can be broadly divided into those that
are manifest throughout the genome and those that influence only certain areas in
the genome.
Chromosomal aberrations and point mutations associated with mutagenic properties of the components of crude oil (Pashin and Bakhitova 1979; Al-Sabti 1985)
are changes at the sequence level that are specific to individuals and occur at specific sites or regions of chromosomes, which if replicated can become permanent.
When affected sites/regions impact coding regions or regulatory elements, basic
organismal functioning may be impaired, and negative health outcomes may result
(Haensly et al. 1982; Wirgin and Waldman 1998). If mutations occur in germline
cells or during early development, progeny may perform poorly or fail to develop
properly (Frank 2010), and this can lead to population-level effects by decreasing
the reproductive output of populations (Carls et al. 1999). While individual chromosomal aberrations are site specific, populations exposed to toxins, including oil,
have been shown in some cases to present increased variation associated with accelerated mutation rates (e.g., oil, Klekowski et al. 1994; heavy metals and radiation,
Eeva et al. 2006; radiation, Volkova et al. 2018). Alternatively, populations may lose
genetic variation after exposure as deleterious and lethal mutations accumulate and
interact with other microevolutionary processes (Bickham et al. 2000).
When populations of organisms experience mass-mortality events, the number
of reproductive individuals decreases, and this can lead to reductions in effective
size (N E ) that may persist across generations, a phenomenon often referred to as a
bottleneck. Because the rate by which drift changes allele frequencies is inversely
proportional to N E , bottlenecks can lead to decreases in genetic diversity (Nei et al.
1975). Drift impacts the entire genome, so reductions in genetic diversity associated with bottlenecks are genome-wide phenomena, affecting neutral (non-coding)
markers and coding regions as well. The latter is of concern because decreased
variation at coding regions may equate to decreased adaptive variation (genetic
30 Genetics and Oil: Transcriptomics, Epigenetics, and Population Genomics as Tools…