3 Populations and Pathways
77
2007, Weiss et al. 2007) or marine plants (e.g. eelgrass Zostera marina; Oetjen
and Reusch 2007b). A tremendous number of EST-SSRs were also found in the
3 UTR regions of cDNAs in a collection of 100,000 sequence reads from the
deep-sea vent polychaete Alvinella pompejana (Daguin and Jollivet, unpublished
data). Microsatellites derived from genomic DNA have different properties to those
derived from expressed sequences (ESTs), Oetjen and Reusch (2007b) has indicated
that microsatellites derived from ESTs should be used with caution for population
genetics analyses as they are likely to be in strong linkage with selected genes.
However as these markers are found in known genes, they present a viable alternative to those methods that utilize anonymous genetic markers and there are several
other advantages:
• They can specifically be used for studying selection processes. For example,
based on the analysis of 58,146 Atlantic salmon EST sequences available in the
GenBank database, 75 EST-linked microsatellites were used by Vasemägi et al.
(2005) to examine the signature of selection in the Atlantic salmon Salmo salar.
• EST-derived markers are often conserved across species enabling comparative
studies across a wide range of non-model species. There is no comprehensive
review of such a transferability among aquatic organisms, but in plants, such an
approach has been very effective (Ellis and Burke 2007). A potential pitfall of
cross-amplification of markers across species is the increased occurrence of null
alleles which will bias estimations of allele frequencies, reduce any observed
heterozygosity, and increase the apparent levels of inbreeding (DeWoody et al.
2006). However, as primers flanking EST-SSRs are generally identified in more
conserved sequences than those of anonymous microsatellites, null alleles will be
less of a problem. Again, we are not aware of any comparative data on the relative
occurrence of null alleles among sets of markers in aquatic organisms, but this
has been documented in other organisms (plants: Rungis et al. 2004; beetle: Kim
et al. 2008).
• Contrasting the diversity and levels of population differentiation of microsatellite loci spread throughout non-coding DNA (i.e. “traditional” anonymous
microsatellites) against produced those from coding regions (e.g. EST-SSRs;
UTRs, introns) potentially allows us to gain a better estimation of population
genetics parameters and of the relative strength of selective pressures acting on
each type of marker (e.g. Luikart et al. 2003, Oetjen and Reusch 2007b).
3.1.3 DNA Studies: Single Nucleotide Polymorphisms (SNPs)
SNPs are considered to be the most abundant type of genetic variation (polymorphism). In coding regions, they can be used to compute the ratio of synonymous
to non-synonymous substitution that is of prime interest in evolutionary studies of selection (reviewed in Ford 2002, Vasemägi and Primmer 2005). Similar
77
2007, Weiss et al. 2007) or marine plants (e.g. eelgrass Zostera marina; Oetjen
and Reusch 2007b). A tremendous number of EST-SSRs were also found in the
3 UTR regions of cDNAs in a collection of 100,000 sequence reads from the
deep-sea vent polychaete Alvinella pompejana (Daguin and Jollivet, unpublished
data). Microsatellites derived from genomic DNA have different properties to those
derived from expressed sequences (ESTs), Oetjen and Reusch (2007b) has indicated
that microsatellites derived from ESTs should be used with caution for population
genetics analyses as they are likely to be in strong linkage with selected genes.
However as these markers are found in known genes, they present a viable alternative to those methods that utilize anonymous genetic markers and there are several
other advantages:
• They can specifically be used for studying selection processes. For example,
based on the analysis of 58,146 Atlantic salmon EST sequences available in the
GenBank database, 75 EST-linked microsatellites were used by Vasemägi et al.
(2005) to examine the signature of selection in the Atlantic salmon Salmo salar.
• EST-derived markers are often conserved across species enabling comparative
studies across a wide range of non-model species. There is no comprehensive
review of such a transferability among aquatic organisms, but in plants, such an
approach has been very effective (Ellis and Burke 2007). A potential pitfall of
cross-amplification of markers across species is the increased occurrence of null
alleles which will bias estimations of allele frequencies, reduce any observed
heterozygosity, and increase the apparent levels of inbreeding (DeWoody et al.
2006). However, as primers flanking EST-SSRs are generally identified in more
conserved sequences than those of anonymous microsatellites, null alleles will be
less of a problem. Again, we are not aware of any comparative data on the relative
occurrence of null alleles among sets of markers in aquatic organisms, but this
has been documented in other organisms (plants: Rungis et al. 2004; beetle: Kim
et al. 2008).
• Contrasting the diversity and levels of population differentiation of microsatellite loci spread throughout non-coding DNA (i.e. “traditional” anonymous
microsatellites) against produced those from coding regions (e.g. EST-SSRs;
UTRs, introns) potentially allows us to gain a better estimation of population
genetics parameters and of the relative strength of selective pressures acting on
each type of marker (e.g. Luikart et al. 2003, Oetjen and Reusch 2007b).
3.1.3 DNA Studies: Single Nucleotide Polymorphisms (SNPs)
SNPs are considered to be the most abundant type of genetic variation (polymorphism). In coding regions, they can be used to compute the ratio of synonymous
to non-synonymous substitution that is of prime interest in evolutionary studies of selection (reviewed in Ford 2002, Vasemägi and Primmer 2005). Similar