14. Role of Genetics in Conservation Biology
235
Random Amplified Polymorphic DNA (RAPD) (Williams
et al. 1990; Welsh and McClelland 1990)
Random amplified polymorphic DNA (RAPD) analysis uses primers of a randomized oligonucleotide sequence to amplify DNA from various anonymous
sites. The detected polymorphism can be applied to estimate genetic distances
among closely related species or recent hybrids and in some cases to perform
paternity exclusions (Lewis and Snow 1992; Levitan and Grosberg 1993; Milligan and McMurray 1993; Avise 1994). However, RAPD fragments do not always
amplify reliably or show Mendelian inheritance, which renders some polymorphisms unsuitable for population genetics and parentage analyses (Riedy et al.
1992).
Ribosomal RNA Genes (rRNA)
Ribosomal RNA (rRNA) plays a crucial role in protein assembly, and therefore
most regions of the molecule are structurally and functionally highly constrained
(Mindell and Honeycutt 1990; Hillis and Dixon 1991). Nuclear rRNA is considered middle-repetitive DNA and generally consists of repeat units that contain
highly conserved coding regions and less-conserved noncoding spacer regions
(Avise 1994). Probes for rRNA genes are readily available and can detect intraand interspecific restriction fragment length differences, which are either the
consequence of heterogeneity in the length of noncoding DNA regions or the
position of restriction sites. Several studies have found the hypervariability of the
noncoded part of the nuclear rRNA gene families useful to differentiate populations and closely related species (Williams et al. 1985; Davis et al. 1990).
Major Histocompatability Complex (MHC) Genes
(Klein 1986)
MHC genes code for cell surface proteins crucial to the immune response of
animals as discussed above. The MHC is a family of tightly linked loci, many with
scores of alleles, making it one of the most variable regions in the genome. Allelic
variation associated with those regions can be detected through RFLP analysis
using DNA probes (Klein 1986; Nei and Hughes 1991). MHC variability has been
used to study inbreeding and fitness, genealogies, and population histories. Specific MHC haplotypes are thought to be associated with kin recognition and mate
choice in mice and humans and disease resistance in birds and humans (Briles et
al. 1977; Tiwari and Terasaki 1985; Hedrick et al. 1991; Howard 1991; Hughes
1991; Potts et al. 1991; Vrijenhoek and Leberg 1991; Hedrick 1992a; Ellegren et
al. 1993; Klein et al. 1993; Brown and Eklund 1994; Wedekind et al. 1995).
235
Random Amplified Polymorphic DNA (RAPD) (Williams
et al. 1990; Welsh and McClelland 1990)
Random amplified polymorphic DNA (RAPD) analysis uses primers of a randomized oligonucleotide sequence to amplify DNA from various anonymous
sites. The detected polymorphism can be applied to estimate genetic distances
among closely related species or recent hybrids and in some cases to perform
paternity exclusions (Lewis and Snow 1992; Levitan and Grosberg 1993; Milligan and McMurray 1993; Avise 1994). However, RAPD fragments do not always
amplify reliably or show Mendelian inheritance, which renders some polymorphisms unsuitable for population genetics and parentage analyses (Riedy et al.
1992).
Ribosomal RNA Genes (rRNA)
Ribosomal RNA (rRNA) plays a crucial role in protein assembly, and therefore
most regions of the molecule are structurally and functionally highly constrained
(Mindell and Honeycutt 1990; Hillis and Dixon 1991). Nuclear rRNA is considered middle-repetitive DNA and generally consists of repeat units that contain
highly conserved coding regions and less-conserved noncoding spacer regions
(Avise 1994). Probes for rRNA genes are readily available and can detect intraand interspecific restriction fragment length differences, which are either the
consequence of heterogeneity in the length of noncoding DNA regions or the
position of restriction sites. Several studies have found the hypervariability of the
noncoded part of the nuclear rRNA gene families useful to differentiate populations and closely related species (Williams et al. 1985; Davis et al. 1990).
Major Histocompatability Complex (MHC) Genes
(Klein 1986)
MHC genes code for cell surface proteins crucial to the immune response of
animals as discussed above. The MHC is a family of tightly linked loci, many with
scores of alleles, making it one of the most variable regions in the genome. Allelic
variation associated with those regions can be detected through RFLP analysis
using DNA probes (Klein 1986; Nei and Hughes 1991). MHC variability has been
used to study inbreeding and fitness, genealogies, and population histories. Specific MHC haplotypes are thought to be associated with kin recognition and mate
choice in mice and humans and disease resistance in birds and humans (Briles et
al. 1977; Tiwari and Terasaki 1985; Hedrick et al. 1991; Howard 1991; Hughes
1991; Potts et al. 1991; Vrijenhoek and Leberg 1991; Hedrick 1992a; Ellegren et
al. 1993; Klein et al. 1993; Brown and Eklund 1994; Wedekind et al. 1995).