Biology Reference
In-Depth Information
techniques such as restriction fragment length polymorphism (RFLP), single strand con-
formation polymorphism, and denaturating gel gradient electrophoresis.
Recent advances in molecular technologies have made genome-wide sampling in popu-
lations feasible through genome typing (Luikart et al. 2003). Genome typing is the simul-
taneous genotyping of hundreds of loci from across the genome [microsatellites, amplified
fragment length polymorphism (AFLPs), or nucleotide polymorphisms], combining both
neutral markers and markers potentially under selection. The classical AFLP protocol uses
a polymerase chain reaction PCR-based DNA fingerprinting technique to produce doz-
ens of polymorphic markers (presence or absence of a restriction enzyme site) that cover
the entire genome. AFLPs are increasingly used to identify markers associated with traits
under selection in nonmodel organisms (Skøt et al. 2002; Wang et al. 2003); these markers
were successfully used to detect signatures of selection in natural populations adapted to
chronic pollution (Williams and Oleksiak 2008).
The Diversity Array technology (DArt) approach uses a microarray, in which each spot
contains a DNA fragment that has been amplified from a library of polymorphic markers
that were identified during an initial screening phase (Jaccoud et al. 2001). DArt is attractive
because a single PCR can amplify hundreds of polymorphic markers and because automa-
tion is easier using images rather than gel electrophoresis. However, this technique can only
be used on species for which large data sets and effective genomic tools have been developed.
Single nucleotide polymorphisms (SNPs) have recently attracted the interest of geneti-
cists and ecotoxicologists; they require species-specific marker development but they
have potential for automation and high throughput (Bozinovic and Oleksiak 2011). The
rapid development of numerous SNPs (including nonsynonymous and functional SNPs)
is becoming feasible in some nonmodel species, owing to the rapid growth of expressed
sequence tag (EST) databases, data-mining software, and primer-design strategies such as
Comparative Anchor-Tag Sequences and Exon-Primed Intron-Crossing PCR (Luikart et al.
2003; Moen et al. 2008a, 2008b).
14.4 Links between Chemical Stress, Genetic
Diversity, and Phenotypic Responses
14.4.1 Chemical Contamination and Impact on Genetic Diversity
Interest in evolutionary ecotoxicology (i.e., the study of effects of chemical pollutants on
the genetics of natural populations) is rapidly growing among ecotoxicologists; the major
population genetic impacts in the context of contamination studies include (1) changes
in allelic or genotypic frequencies caused by increased mutation rates, (2) genome-wide
changes in genetic diversity linked to demographic bottlenecks, (3) changes in allelic or
genotypic frequencies caused by contaminant-induced selection, and (4) changes in disper-
sal patterns of gene flow that alter the genetic relationship among populations (Bickham
2011). In this part 14.4.1, we will focus mainly on the points (1) to (3).
14.4.1.1 Direct Interactions between Pollutants and DNA through Mutations
Evidence of direct effects of pollution on genomes has been highlighted in terrestrial
organisms and especially in the case of radionuclide contamination. For example, Dubrova
Search WWH ::
Custom Search