Tempo and Mode in Evolution Genetics and Paleontology 50 Years After Simpson (1995) / Chapter Skim
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Rates and Patterns of Chloroplast DNA Evolution
Rates and Patterns of Chloroplast DNA Evolution
Pages 215-234
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From page 215... ...
Complete sequences of six chloroplast genomes are now available, and these represent virtually the full range of plant diversity [an alga, Euglena (Hallick et al., 1993~; a bryophyte, Marchantia (Ohyama et al., 1986~; a conifer, black pine (Wakasugi et al., 1993~; a dicot, tobacco (Shinozaki et al., 1986~; a monocot, rice (Hiratsuka et al., 1989~; and a parasitic dicot, Epifagus (Wolfe et al., 1992~. With the possible exception of Euglena and Epifagus, the picture that has emerged is one of a relatively stable genome with marked conservation of gene content and a substantial conservation of structural organization.
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From page 216... ...
Among land plants, gene content is almost perfectly conserved, although a few recent transfers of function from the chloroplast to the nuclear genome have been demonstrated (Downie and Palmer 1991; Gantt et al., 1991~. Conservation of gene content and a relatively slow rate of nucleotide substitution in protein-coding genes has made the chloroplast genome an ideal focus for studies of plant evolutionary history (reviewed in Clegg, 1993~.
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From page 217... ...
The methodological approach is that of comparative sequence analysis, where complete DNA sequences from phylogenetically structured samples are analyzed to reveal the pattern of mutational change in evolution. Evolution of Noncoding DNA Regions The chloroplast genome is highly condensed compared with eukaryotic genomes; for example, only 32% of the rice genome is noncoding.
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From page 218... ...
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From page 219... ...
A comparison of the insertion among members of the grass family revealed widespread diversity in terms of indel mutations as well as an increased rate of nucleotide substitution (Cummings et al., 1994~. The low noncoding content of the cpDNA generally and the high rate of large deletion events observed in the largest contiguous noncoding segment in the rice genome suggest that nonessential sequences are rapidly removed from the chloroplast genome as a result of both intraand intermolecular recombination.
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From page 220... ...
The codon utilization pattern of chloroplast genes of the green algae Chlamydomonas reinhardtii and Chlamydomonas moewasii appears to be closely adapted to the chloroplast tRNA population. In contrast, land plant chloroplast genes are dominated by a genomic bias towards a high A+T content, which is reflected in a high third-codon position A+T content.
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From page 221... ...
Relative rate tests may also fail to detect stochastic changes in rate within a lineage because the test compares average substitution rates. More importantly, relative rates contain less information on variation than do absolute rates, but absolute rates are difficult to estimate because of imperfect knowledge of the time dimension.
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From page 222... ...
Clearly a simple stochastically constant molecular clock does not hold for the rbcL locus; however, there may be a generation-time effect (Li, 1993~. While it is difficult to estimate generation times in most plant taxa, the monocot sequences show a clear negative correlation between the minimum generation time and substitution rates (Gaut et al., 1992~.
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From page 223... ...
. Comparison of sequence data from the maize and rice chloroplast genomes revealed little rate heterogeneity (using tobacco as an outgroup)
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From page 224... ...
was then used to locate amino acid replacement on branches of the tree and to count the total number of amino acid changes required through the phylogeny. Of the 1350 amino acid replacements, 762 could be unambiguously inferred; 568 and 182 were in a-helices and Strands, respectively.
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From page 226... ...
What conclusions may we draw from these analyses of the patterns of amino acid variation? The analyses suggest that in angiosperms, amino acid replacements among hydrophobic (nonpolar)
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From page 227... ...
bStates is the number of different kinds of amino acids found at the indicated site. Predominant replacement indicates the most frequent unambiguously inferred amino acid replacement in the character state reconstruction for the dendrogram at the indicated site; the number of unambiguously inferred independent occurrences is in parentheses.
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From page 228... ...
Although comparative sequence analyses of both group I and group III introns could provide information about rates and mechanisms of chloroplast DNA evolution, there are few comparative data, and consequently our discussion will be limited to group II introns. Group II introns form the most numerous and best characterized class of plastic intervening sequences.
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From page 229... ...
When land plant and algal genes are compared, it is evident that patterns of selection for codon utilization have changed over evolutionary time and that models that assume equilibrium nucleotide frequencies are likely to be violated. Patterns of amino acid replacement in the rbcL gene also reveal substantial variation in site-dependent probabilities of substitution.
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From page 230... ...
Comparative sequence analyses have utility beyond the study of phylogeny. The pattern of amino acid replacements observed over evolutionary time reflects the pattern of functional constraints that are imposed by natural selection on the protein molecule.
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From page 231... ...
(1991) Synonymous nucleotide substitution rates in mammalian genes: implication for the molecular clock and the relationship of mammalian orders.
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From page 232... ...
(1993) Relative rates of nucleotide substitution in the chloroplast genome.
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From page 233... ...
(1986) Chloroplast gene organization deduced from complete sequence of liverwort Marchantia polymorpha chloroplast DNA.
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From page 234... ...
(1986) The complete nucleotide sequence of the tobacco chloroplast genome: its gene organization and expression.
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