Biology Reference
In-Depth Information
and commercial resources conduct automated Sanger sequencing so that few
laboratories need to carry out their own sequencing reactions. Now that Next-
Generation sequencing methods are available, sequencing of entire genomes
can provide multiple DNA sequences and even allow comparisons of entire
genomes of related species (comparative genomics).
DNA sequence data can be used to 1) construct molecular phylogenies to eval-
uate the evolution of particular genes or gene families, 2) evaluate evolutionary
changes within species, and 3) construct phylogenies of different species. DNA
sequences can be obtained for single-copy genes, mtDNA, ribosomal DNA, and
entire genomes. Sequences can be used to study most systematics problems from
intraspecific variability to phylogeny of all organisms ( Table 12.3 ). Sequence data
are appropriate for analysis of intraspecific variation, cryptic species, geographic
variation, reproductive behavior, and heterozygosity estimates. However, DNA
sequencing can be relatively expensive and time-consuming if multiple genes
from very large numbers of individuals must be analyzed. Sequence analysis of
nuclear or mtDNA sequences provides very large amounts of detailed data. The
number of potential characters that can be examined theoretically is limited only
by the number of nucleotides in the DNA of the organism.
12.4.5 Fragment Analyses of Genomic DNA
Fragment analyses, which include RAPD-PCR, single-locus microsatellites or
multilocus DNA fingerprinting, can be used for some systematics problems
( Table 12.3 ). The Random Amplified Polymorphic DNA (RAPD) method of the
PCR (described in Chapter 8) has been used to discriminate between cryptic spe-
cies. Multiple RAPD markers may have to be used to produce a banding pattern
that can be analyzed by discriminant analysis, although the need to conduct
multiple RAPD reactions would make RAPD-PCR more expensive and time-
consuming. RAPD-PCR may be useful for examining hybridization and species
boundaries, as well as clonal variation.
Single-locus microsatellites are potentially useful for analysis of population
structure, mating systems, clonal boundaries, heterozygosity, paternity testing,
relatedness, and geographic variation ( Table 12.3 ). Multilocus DNA fingerprint-
ing can be used for clonal detection, species delimitation, and paternity testing
( Lunt et al. 1998, 1999 ).
12.5 Targets of DNA Analysis
Sequence analyses of nuclear, mitochondrial, and ribosomal DNA have been
used in systematics studies, as have microsatellites and introns ( Caterino et  al.
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