240
(Sambrook et al., 1989; Lane et aI., 1985; Medlin et al., 1988) sequence data bases are
expanding rapidly.
Molecular phylogenetic studies also have application for ecology and oceanography, largely
because they provide a means to identify and quantify species in environmental samples. The
methods are particularly useful for studying those species which may be difficult or impossible
to cultivate in the laboratory. In one application, phylogenetically informative genes are
clonally isolated from heterogeneous natural populations, and their sequences determined and
compared to homologous genes of known, well-characterized organisms (Pace et al., 1986a).
Ideally, these comparative sequence analyses indicate the phylogenetic affiliations of individual
population members, and provide a snapshot of overall community structure. The same
sequence data is also useful for designing taxa-specific nucleic acid hybridization probes, to
monitor the spatial and temporal distributions of particular groups (Pace et al., 1986a; Stahl
et al., 1988; Giovanonni et al., 1990a). Thus, molecular techniques can provide a means for
assessing overall community diversity, and simultaneously provide data useful for studying
the temporal and spatial variability of individual species. Nucleic acid probes that bind target
molecules with high intracellular concentration (e.g. rRNA) can also be used to determine the
phylogenetic affiliations of individual cells (Giovanonni et al., 1988; DeLong et al., 1989a;
DeLong and Shah, 1990; Amman et al., 1990a; Tsien et al., 1990).
FROM MOLECULAR SEQUENCE DATA TO ORGANISMAL PHYLOGENY
Molecular phylogenetic analyses use a known quantity, sequence similarity, to estimate an
unknown quantity, evolutionary divergence. The inference of organismal phylogenies from
molecular sequence comparisons depends partly on a model of the evolutionary process which
assumes a random accumulation of mutational change, occurring at a stochastically constant
rate (Wilson et al., 1977; Felsenstein, 1988). The random, stochastically constant
accumulation of mutations can be viewed as a molecular clock. Comparative sequence
analyses use these accumulated mutations to estimate the relative divergence of organisms
from their most recent common ancestor. These quantitative estimates of evolutionary
divergence form the basis of molecular phylogenetic analysis. Molecular clocks tick at
different rates, so molecular phylogenies based on different macromolecules are not
(Sambrook et al., 1989; Lane et aI., 1985; Medlin et al., 1988) sequence data bases are
expanding rapidly.
Molecular phylogenetic studies also have application for ecology and oceanography, largely
because they provide a means to identify and quantify species in environmental samples. The
methods are particularly useful for studying those species which may be difficult or impossible
to cultivate in the laboratory. In one application, phylogenetically informative genes are
clonally isolated from heterogeneous natural populations, and their sequences determined and
compared to homologous genes of known, well-characterized organisms (Pace et al., 1986a).
Ideally, these comparative sequence analyses indicate the phylogenetic affiliations of individual
population members, and provide a snapshot of overall community structure. The same
sequence data is also useful for designing taxa-specific nucleic acid hybridization probes, to
monitor the spatial and temporal distributions of particular groups (Pace et al., 1986a; Stahl
et al., 1988; Giovanonni et al., 1990a). Thus, molecular techniques can provide a means for
assessing overall community diversity, and simultaneously provide data useful for studying
the temporal and spatial variability of individual species. Nucleic acid probes that bind target
molecules with high intracellular concentration (e.g. rRNA) can also be used to determine the
phylogenetic affiliations of individual cells (Giovanonni et al., 1988; DeLong et al., 1989a;
DeLong and Shah, 1990; Amman et al., 1990a; Tsien et al., 1990).
FROM MOLECULAR SEQUENCE DATA TO ORGANISMAL PHYLOGENY
Molecular phylogenetic analyses use a known quantity, sequence similarity, to estimate an
unknown quantity, evolutionary divergence. The inference of organismal phylogenies from
molecular sequence comparisons depends partly on a model of the evolutionary process which
assumes a random accumulation of mutational change, occurring at a stochastically constant
rate (Wilson et al., 1977; Felsenstein, 1988). The random, stochastically constant
accumulation of mutations can be viewed as a molecular clock. Comparative sequence
analyses use these accumulated mutations to estimate the relative divergence of organisms
from their most recent common ancestor. These quantitative estimates of evolutionary
divergence form the basis of molecular phylogenetic analysis. Molecular clocks tick at
different rates, so molecular phylogenies based on different macromolecules are not