Theoretical foundations for quantitative paleogenetics

Holmquist, Richard; Pearl, Dennis K.

doi:10.1007/bf01804977

Cited by 32 publications

(4 citation statements)

References 33 publications

(25 reference statements)

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“…To calculate the approximate total mutation rates, the observed percent divergence can be corrected for multiple substitutions (Salser, 1977;Perler et al, 1980; and Materials and methods). The corrections do not exceed a factor of 2 (Table I) and are slightly too low since the incidence of base substitutions does not follow an exact Poisson distribution as assumed in these calculations (Holmquist and Pearl, 1980;Holmquist et al, 1981). From the corrected percent divergence (Table I) and the times of speciation suggested by the paleontological record, the bases in the silent sites of the sea urchin histone genes are seen to evolve at 0.2-0.9q% base changes/Myr.…”

Section: Resultsmentioning

confidence: 92%

“…Strong evidence suggests that a percentage of base changes resulting in synonymous codons are selected against (Fitch, 1980;Miyata and Hayashida, 1981;Holmquist and Pearl, 1980). But comparison of the DNA sequences of a great many different protein-coding genes shows that the overall rate of synonymous substitutions even over a large timespan has proceeded at a remarkably even rate of ".s0.5% base changes/Myr (Miyata et al, 1981), i.e., the evolutionary clock of nucleic acid sequences (in their silent sites) seems to run at a similar rate in all structural genes analyzed to date.…”

Section: Introductionmentioning

confidence: 99%

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An unusual evolutionary behaviour of a sea urchin histone gene cluster

1982

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DNA sequences of cloned histone coding sequences and spacers of sea urchin species that diverged long ago in evolution were compared. The highly repeated H4 and H3 genes active during early embryogenesis had evolved (in their silent sites) at a rate (0.5‐0.6% base changes/Myr) similar to single‐copy protein‐coding genes and nearly as fast as spacer DNA (0.7% base changes/Myr) and unique DNA. Thus, evolution in the major histone genes conforms to a universal evolutionary clock based on the rate of base sequence change. By contrast, the H4 and H3 coding sequences and a non‐transcribed spacer of the DNA clone h19 of Psammechinus miliaris show an exceptionally low rate of sequence evolution only 1/100 to 1/200 that predicted from the clock hypothesis. According to the classical model of gene inheritance, the h19 DNA sequences in the Psammechinus genome require unusual conservation mechanisms by selection at the level of the gene and spacer sequences. An alternative explanation could be recent horizontal gene transfer of a histone gene cluster from the very distantly related Strongylocentrotus dröbachiensis to the P. miliaris genome.

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Section: Resultsmentioning

confidence: 92%

Section: Introductionmentioning

confidence: 99%

An unusual evolutionary behaviour of a sea urchin histone gene cluster

1982

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“…The multiple changes predicted by these mechanisms will alter the apparent rates of evolution. In general, the rate at which evolution (35). The presence of nearby repeats might also explain repeated, convergent substitutions as have, for example, been noted by Aquadro and Greenberg (36) in human mitochondrial sequences and by Fitch (37) in human globin sequences.…”

Section: Discussionmentioning

confidence: 90%

Sequence-directed mutagenesis: evidence from a phylogenetic history of human alpha-interferon genes.

Golding¹,

Glickman²

1985

Proc. Natl. Acad. Sci. U.S.A.

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We have studied the potential contribution of template-dependent events to genetic variation in mammals by examining the sequence alterations that have occurred in the recent evolution of human interferon genes. Fifteen members of the human a-interferon gene family were aligned, and a phylogenetic history was inferred. Many multiple events are inferred to have occurred in the evolution of the interferon genes and for the majority of these local DNA sequences were present that were capable of serving as templates for their occurrence. We conclude that the DNA sequence has the potential to explain many of the inferred spontaneous events and to explain complex alterations to sequences-i.e., the joint occurrence of base substitutions and insertions/deletions. Thus, such a mechanism would often cause multiple sequence changes as a result of a single mutational event and would provide additional genetic variation for evolution. Sequencedirected mutations would depend upon the local DNA sequences and, hence, would not be random at the DNA level.Inherent in the reproduction of all organisms is the potential for mutation. Such errors, though rare, provide the ultimate driving force behind evolution. It is through the genetic variation provided by mutation that natural selection and random drift can alter the genetic composition ofpopulations. The rate of mutation has been estimated to be on the order of 10-8-10-10 errors per base pair (bp) copied in a wide range of organisms (1). This high level of fidelity is astonishing considering the properties of the DNA bases, the complexity of the processes of DNA replication and repair, and the environmental threats to the integrity of the DNA.The number of potential DNA sequence changes as well as the mechanisms behind them are extensive, but they all provide opportunity for genetic variation. The relative contribution of each kind of mutational event to spontaneous mutation is not known. Such information is particularly sparse in mammals, but an analysis of 176 spontaneous lacI mutations isolated by Schaaper et al. (2) reveals that only 11% were base substitutions and just 4% involved insertion elements. The majority of events were frameshifts, deletions, and duplications. Similarly, within the flanking and intron sequences of globin it has been suggested that deletion/ insertion events and "block mutations" are prevalent compared to single-base substitutions (3,4).Mechanisms proposed to account for frameshift, deletion, and insertion events are diverse, but they share a commonality such that in the proposed mutational intermediates the bases are correctly paired in the Watson and Crick (5) sense but are misaligned because they are out of register. Misalignment mutational intermediates were first proposed by Streisinger et al. (6) to explain frameshift mutations at sites of repetitive sequences. This model was later supported by the data of Okada et al. (7) and Pribnow et al. (8) who showed that frameshift hotspots in bacteriophage T4 occur in sequences ofthe same nucl...

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“…All variable nucleotide sites were assumed equally mutable and equally likely to mutate to each of the other three nucleotides. This has been shown not to be the case (see, e.g., Fitch, 1980;Holmquist and Pearl, 1980). Relaxing this assumption would result in higher probabilities of multiple mutations at the same site.…”

Section: Resultsmentioning

confidence: 98%

Testing the Constant-Rate Neutral Allele Model With Protein Sequence Data

1983

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ue of X 2 LF' With Omin determined, it is possible to test the constant-rate neutral allele model by checking the compatibility of observed levels of heterozygosity in extant populations with the levels expected with oequal to Omln. Omln for a-and ,B-hemoglobin are shown to be inconsistent with observed levels of heterozygosities at these loci in humans. There is apparently no value of 0 which is compatible with both the observed value of X 2 LF and the observed levels of heterozygosity at the aand ,B-hemoglobin loci of humans. It is concluded that the simple constant-rate neutral model can be regarded as highly improbable in the light of available data.To determine the distribution of X 2 LF under the neutral model, Monte Carlo simulations were used to produce sequences analogous to those analyzed by Langley and Fitch. These simulation-produced sequences were then analyzed in the same way that Langley and Fitch analyzed the actual sequence data. Their analysis is described in the next section. Following that section, the results of Gillespie and Langley are reviewed and extended approximately. Also discussed are the difficulties with applying these analytic results to estimate 0 or to test the neutral model directly. Next, the simulation algorithm is described and the results are presented and discussed. Langley-Fitch AnalysisThe analysis of Langley and Fitch consisted of three main steps. 1.) Inferring the numbers of substitutions occurring on each branch of the phylogenetic tree, for each protein, using a maximum parsimony procedure (Fitch, 1971;Fitch and Farris, 1974).2.) Finding maximum likelihood estimates of the substitution rate of each protein and of the times of each of the nodes of the phylogenetic tree. 3.) Calcu-203 ! Present address: Department of Genetics, University of California, Davis, California 95616. Fitch (1973, 1974) and Fitch and Langley (1976) statistically analyzed the pattern of nucleotide substitutions in seven proteins and 17 taxa and rejected the null hypothesis of a constantrate Poisson model of protein evolution, Their rejection of the constant-rate model was based on the extremely large observed value of a statistic (henceforth referred to as X 2 LF) , which has a standard Chi-squared distribution under their null hypothesis. Gillespie and Langley (1979) showed that under a constant-rate neutral allele model, X 2 L F is not Chi-squared distributed. Though they did not obtain the exact distribution of X 2 LF ' they were able to show that the expectation of X 2 LF is an increasing function of 0 = 4Nu, where N is the population size and u is the neutral mutation rate. Thus, the Langley and Fitch analysis does not constitute a test of the constant-rate neutral model. Evidently no test of the neutral model is possible using only the statistic X 2 LF ' since no matter how large the observed value of X 2 L F ' a sufficiently large value of 0 could account for the observation.If one knew the distribution of X 2 LF as a function of 0, one could use the observed value of X\F to estimate O....

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Theoretical foundations for quantitative paleogenetics

Abstract: greater than earlier estimates. The replacements are distributed over approximately 114 codon sites that were free to accept base mutations during the divergence of these two genes. 1

Cited by 32 publications

References 33 publications

An unusual evolutionary behaviour of a sea urchin histone gene cluster

An unusual evolutionary behaviour of a sea urchin histone gene cluster

Sequence-directed mutagenesis: evidence from a phylogenetic history of human alpha-interferon genes.

Testing the Constant-Rate Neutral Allele Model With Protein Sequence Data

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