14. Role of Genetics in Conservation Biology
239
and thus recognize hybrids in captive populations and identify the origin of
illegally traded animals.
Mitochondrial Protein Coding Genes
DNA coding for proteins is based on a triplet code for amino acids. Several triplets
code for the same amino acids. The first and second codon positions are highly
conserved, whereas the third position is less constrained in terms of nucleotide
changes due to the degenerate nature of the amino acid code. Consequently, most
base pair substitutions in the third position do not change amino acid transcription
and are considered “silent.” Base pair substitutions that result in amino acid
replacements generally occur at a lower rate than silent substitutions due to
structural and functional constraints. Cytochrome b and ATPase 6 have been used
extensively in vertebrate studies to resolve relationships at close and intermediate
taxonomic levels (Kocher et al. 1989; Meyer et al. 1990). For example, Bowen
and colleagues (1992, 1993) have used cytochrome b sequence data to determine
the phylogeny of all known marine turtles, essential information in choosing
which taxonomic groups to conserve and in designing recovery plans.
Mitochondrial transfer RNA genes (tRNA) and mitochondrial ribosomal RNA
(rRNA) evolve more slowly than protein coding genes (Wolstenholme and Clary
1985), indicating greater structural and functional constraints (Simon et al. 1994).
Although their slow evolutionary rates render them generally unsuitable to answer
typical conservation genetics questions by themselves, they are occasionally combined with other molecular markers to resolve phylogenies (Mindell and Honeycutt 1990; Hillis and Dixon 1991; Hoelzel et al. 1993; Kretzmann et al. 1997).
Nuclear DNA Introns (Palumbi and Baker 1994)
Nuclear introns have been introduced as a suitable template for DNA sequencing
analysis to complement mtDNA data. Universal PCR primers that anneal to exons
of highly conserved nuclear genes are used to amplify across nuclear introns.
Noncoding introns generally exhibit high rates of evolutionary change, and sequence analysis can reveal high levels of diversity at these nuclear DNA sites.
Unlike mtDNA, nuclear DNA reflects the biparental contribution to population
structure at several independently segregating sites, and like mtDNA sequencing,
the resolution power of nuclear introns sequences is high. Consequently, nuclear
introns are expected to find their greatest application in resolving genetic population structure and taxonomic relationships. Using actin intron alleles, Palumbi and
Baker (1994) corroborated large-scale movements of Humpback Whales based on
mtDNA analysis. They revealed that sequence analysis of mtDNA and nuclear
introns predicted different amounts of gene flow between Hawaiian and Californian Humpback Whales, a result consistent with female philopatry and malebiased migration between populations.
In general, nuclear and mtDNA evolve and are transmitted differently, and
because mtDNA is haploid and maternally inherited, its effective population size
239
and thus recognize hybrids in captive populations and identify the origin of
illegally traded animals.
Mitochondrial Protein Coding Genes
DNA coding for proteins is based on a triplet code for amino acids. Several triplets
code for the same amino acids. The first and second codon positions are highly
conserved, whereas the third position is less constrained in terms of nucleotide
changes due to the degenerate nature of the amino acid code. Consequently, most
base pair substitutions in the third position do not change amino acid transcription
and are considered “silent.” Base pair substitutions that result in amino acid
replacements generally occur at a lower rate than silent substitutions due to
structural and functional constraints. Cytochrome b and ATPase 6 have been used
extensively in vertebrate studies to resolve relationships at close and intermediate
taxonomic levels (Kocher et al. 1989; Meyer et al. 1990). For example, Bowen
and colleagues (1992, 1993) have used cytochrome b sequence data to determine
the phylogeny of all known marine turtles, essential information in choosing
which taxonomic groups to conserve and in designing recovery plans.
Mitochondrial transfer RNA genes (tRNA) and mitochondrial ribosomal RNA
(rRNA) evolve more slowly than protein coding genes (Wolstenholme and Clary
1985), indicating greater structural and functional constraints (Simon et al. 1994).
Although their slow evolutionary rates render them generally unsuitable to answer
typical conservation genetics questions by themselves, they are occasionally combined with other molecular markers to resolve phylogenies (Mindell and Honeycutt 1990; Hillis and Dixon 1991; Hoelzel et al. 1993; Kretzmann et al. 1997).
Nuclear DNA Introns (Palumbi and Baker 1994)
Nuclear introns have been introduced as a suitable template for DNA sequencing
analysis to complement mtDNA data. Universal PCR primers that anneal to exons
of highly conserved nuclear genes are used to amplify across nuclear introns.
Noncoding introns generally exhibit high rates of evolutionary change, and sequence analysis can reveal high levels of diversity at these nuclear DNA sites.
Unlike mtDNA, nuclear DNA reflects the biparental contribution to population
structure at several independently segregating sites, and like mtDNA sequencing,
the resolution power of nuclear introns sequences is high. Consequently, nuclear
introns are expected to find their greatest application in resolving genetic population structure and taxonomic relationships. Using actin intron alleles, Palumbi and
Baker (1994) corroborated large-scale movements of Humpback Whales based on
mtDNA analysis. They revealed that sequence analysis of mtDNA and nuclear
introns predicted different amounts of gene flow between Hawaiian and Californian Humpback Whales, a result consistent with female philopatry and malebiased migration between populations.
In general, nuclear and mtDNA evolve and are transmitted differently, and
because mtDNA is haploid and maternally inherited, its effective population size