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D Graur

Publications and source records attributed to D Graur.

36 records · Page 2Linked to original sources
PubMed1993

Towards a molecular resolution of the ordinal phylogeny of the eutherian mammals.

Reconstructing the evolutionary relationships among the orders of eutherian mammals entails the identification of a single true phylogenetic tree out of approximately 10(19) possible ones. The morphological and paleontological legacy to the field consists of numerous contradictory trees that are mostly devoid of binary resolution. With the introduction of molecular methodologies, several superordinal relationships have been identified, and in several instances a complete taxonomic revision was indicated. In this review, I present a summary of the phylogenetic affinities of the eutherian orders as revealed by molecular studies, and outline the differences between the molecular phylogenetic schemes and the phylogenetic trees produced through the use of morphological data. Questions of monophyly or paraphyly of the eutherian orders are also discussed. It is estimated that all but 10(9) of the 10(19) possible phylogenetic trees have been ruled out by molecular analysis, and that DNA and protein sequences with their potential to supply millions of phylogenetically useful characters will resolve the phylogeny of the orders of mammals into a consistently bifurcating tree in the not-so-distant future.

Animals↗
PubMed1993

Structure and evolution of opossum, guinea pig, and porcupine cytochrome b genes.

We have sequenced the mitochondrial cytochrome b gene from the guinea pig, the African porcupine, and a South American opossum. A phylogenetic analysis, which includes 22 eutherian and four other vertebrate cytochrome b sequences, indicates that the guinea pig and the porcupine constitute a natural clade (Hystricomorpha) that is not a sister group to the clade of mice and rats (Myomorpha). Therefore, the hypothesis that the Rodentia is paraphyletic receives additional support. The artiodactyls, the perissodactyls, and the cetaceans form a group that is separated from the primates and the rodents. The 26 sequences are used to study the structure/function relationships in cytochrome b, whose function is electron transport. Most of the amino acid residues involved in the two reaction centers are well conserved in evolution. The four histidines that are believed to ligate the two hemes are invariant among the 26 sequences, but their nearby residues are not well conserved in evolution. The eight transmembrane domains represent some of the most divergent regions in the cytochrome b sequence. The rate of nonsynonymous substitution is considerably faster in the human and elephant lineages than in other eutherian lineages; the faster rate might be due to coevolution between cytochrome b and cytochrome c.

Amino Acid Sequence↗
PubMed1992

The biochemical phylogeny of guinea-pigs and gundis, and the paraphyly of the order rodentia.

1. Molecular data indicate that caviomorphs (guinea-pig-like rodents) and myomorphs (rat-like rodents) are not monophyletic. 2. Rather, the evolutionary lineage leading to the guinea-pig may have branched off prior to the divergence among myomorphs, lagomorphs, primates, chiropterans, artiodactyls, and carnivores. 3. Thus, the guinea-pig lineage probably represents an ancient eutherian lineage, and should be conferred an independent ordinal status. 4. The gundis (Ctenodactylidae) also seem to have branched off before the divergence among myomorphs, primates, and artiodactyls, but after the divergence of the guinea-pig. 5. Therefore, the order Rodentia as defined at the present time is in all probability a paraphyletic group devoid of taxonomic validity. 6. Previous claims pertaining to large differences in the rate of molecular evolution between guinea-pigs and myomorphs may have been exaggerated in many cases as a result of the erroneous phylogenetic position attributed to the guinea-pig. 7. The average rate of amino acid replacement in the guinea-pig is comparable to that in the rat and the mouse. 8. Protein-coding genes of myomorphs and caviomorphs evole, on average, about two times faster than their counterparts in gundis and humans.

Amino Acid Sequence↗
PubMed1991

Is the guinea-pig a rodent?

The guinea-pig (Cavia porcellus), traditionally classified as a New World hystricomorph rodent, often shows anomalous morphological and molecular features in comparison with other eutherian mammals. For example, its insulin differs from that of other mammals in anabolic and growth-promoting activities and in its capability to form hexamers. Indeed, the literature about the molecular evolution of guinea-pigs abounds in references to 'convergent evolution', 'extremely rapid rates of substitution', and 'unique evolutionary mechanisms'. These claims are based on the assumption that the guinea-pig is a rodent. Our phylogenetic analyses of amino-acid sequence data, however, imply that the guinea-pig diverged before the separation of the primates and the artiodactyls from the myomorph rodents (rats and mice). If true, then the myomorphs and the caviomorphs do not constitute a natural clade, and the Caviomorpha (or the Histricomorpha) should be elevated in taxonomical rank and regarded as a separate mammalian order distinct from the Rodentia. If, as suggested by recent data, the myomorphs branched off before the divergence among the carnivores, lagomorphs, artiodactyls and primates, then the new order would represent an early divergence in eutherian radiation.

Animals↗
PubMed1991

Evolution of the sarafotoxin/endothelin superfamily of proteins.

Sixteen protein and nucleic acid sequences from the vasoconstrictor sarafotoxin/endothelin/endothelin-like superfamily of peptides were studied, and the evolutionary relationships between the sarafotoxin and endothelin gene families as well as the phylogenetic topology within each gene family and the three endothelin subfamilies was reconstructed. The endothelin gene family has diverged from an ancestral gene that has experienced an exon duplication event followed by two gene duplication events. The sarafotoxins' lineage diverged from the ancestral gene prior to the first endothelin gene duplication event. Analysis of the resulting phylogenetic trees revealed that in several lineages, the peptides have independently accumulated identical replacements in position 2, therefore supporting the hypothesis that residue 2 is crucial to their activity.

Amino Acid Sequence↗
PubMed1991

The evolutionary history of the sarafotoxin/endothelin/endothelin-like superfamily.

The evolutionary relationships among 17 protein and nucleic acid sequences from the sarafotoxin/endothelin/endothelin-like superfamily of peptides were studied. The endothelin/endothelin-like gene family has diverged from an ancestral gene that has experienced an exon duplication event followed by two complete gene duplications. The sarafotoxin lineage diverged from the ancestral gene prior to the first gene duplication event. In several lineages, the peptides have independently accumulated identical amino acid replacements in position 2. This finding supports the hypothesis that residue 2 is crucial to biological activity.

Amino Acid Sequence↗
PubMed1990

Evolution of isopenicillin N synthase genes may have involved horizontal gene transfer.

The isopenicillin N synthase genes from three fungal species, three Gram-positive species, and one Gram-negative bacterial species share an unusually high sequence similarity. A phylogenetic analysis was carried out to determine which type of evolutionary scenario best accounts for this similarity. The most plausible scenario is one in which a horizontal gene-transfer event, from the prokaryotes to the eukaryotes, occurred at a time close to the divergence between the Gram-positive and the Gram-negative bacteria.

Amino Acid Sequence↗
PubMed1989

Deletions in processed pseudogenes accumulate faster in rodents than in humans.

The relative rates of point nucleotide substitution and accumulation of gap events (deletions and insertions) were calculated for 22 human and 30 rodent processed pseudogenes. Deletion events not only outnumbered insertions (the ratio being 7:1 and 3:1 for human and rodent pseudogenes, respectively), but also the total length of deletions was greater than that of insertions. Compared with their functional homologs, human processed pseudogenes were found to be shorter by about 1.2%, and rodent pseudogenes by about 2.3%. DNA loss from processed pseudogenes through deletion is estimated to be at least seven times faster in rodents than in humans. In comparison with the rate of point substitutions, the abridgment of pseudogenes during evolutionary times is a slow process that probably does not retard the rate of growth of the genome due to the proliferation of processed pseudogenes.

Animals↗
PubMed1989

Nucleic acid composition, codon usage, and the rate of synonymous substitution in protein-coding genes.

Based on the rates of synonymous substitution in 42 protein-coding gene pairs from rat and human, a correlation is shown to exist between the frequency of the nucleotides in all positions of the codon and the synonymous substitution rate. The correlation coefficients were positive for A and T and negative for C and G. This means that AT-rich genes accumulate more synonymous substitutions than GC-rich genes. Biased patterns of mutation could not account for this phenomenon. Thus, the variation in synonymous substitution rates and the resulting unequal codon usage must be the consequence of selection against A and T in synonymous positions. Most of the variation in rates of synonymous substitution can be explained by the nucleotide composition in synonymous positions. Codon-anticodon interactions, dinucleotide frequencies, and contextual factors influence neither the rates of synonymous substitution nor codon usage. Interestingly, the nucleotide in the second position of codons (always a nonsynonymous position) was found to affect the rate of synonymous substitution. This finding links the rate of nonsynonymous substitution with the synonymous rate. Consequently, highly conservative proteins are expected to be encoded by genes that evolve slowly in terms of synonymous substitutions, and are consequently highly biased in their codon usage.

Animals↗
PubMed1986

The evolution of electrophoretic mobility of proteins.

A model was constructed that predicts the electric charge of a protein and its isoelectric point from its primary and quaternary structures. By using two different patterns of mutation and purifying selection, four schemes of nucleotide substitution were simulated. In the absence of selection for a specific value of pI, proteins are expected to evolve toward a mildly basic pI. Thus, the selection for maintaining extreme values of pI must be stringent, and proteins with extreme pI's will evolve very slowly. This prediction is consistent with observations on the evolution of histones and ubiquitin. The mean charge change is expected to be about 0.005 units pI per nucleotide substitution. The amount of electrophoretically hidden variation is expected to be considerable even for large degrees of divergence at the nucleotide and amino acid levels. Electrophoretic detectability depends on the size of the protein. The longer the protein the larger the amount of variation at the amino acid level that is undetectable by isoelectric focusing. This property may be partially responsible for the imperfect correlation between molecular weight and gene diversity observed for electrophoretic data. Very basic and very acidic proteins are expected to generate less electrophoretic variability than proteins with intermediate pI's. Unequal rates of mutation between nucleotides and asymmetrical patterns of purifying selection have almost no effect on the equilibrium pI of proteins, but affect the rates of change in pI, and increase the amount of electrophoretically hidden variation in comparison to the expectations derived from random patterns of mutation and constant selection. Comparison of detectability of protein differences among four electrophoretical techniques suggests that the best performance is obtained by the sequential electrophoresis method.

Amino Acid Sequence↗
PubMed1985

Amino acid composition and the evolutionary rates of protein-coding genes.

Based on the rates of amino acid substitution for 60 mammalian genes of 50 codons or more, it is shown that the rate of amino acid substitution of a protein is correlated with its amino acid composition. In particular, the content of glycine residues is negatively correlated with the rate of amino acid substitution, and this content alone explains about 38% of the total variation in amino acid substitution rates among different protein families. The propensity of a polypeptide to evolve fast or slowly may be predicted from an index or indices of protein mutability directly derivable from the amino acid composition. The propensity of an amino acid to remain conserved during evolutionary times depends not so much on its being featured prominently in active sites, but on its stability index, defined as the mean chemical distance [R. Grantham (1974) Science 185:862-864] between the amino acid and its mutational derivatives produced by single-nucleotide substitutions. Functional constraints related to active and binding sites of proteins play only a minor role in determining the overall rate of amino acid substitution. The importance of amino acid composition in determining rates of substitution is illustrated with examples involving cytochrome c, cytochrome b5, ras-related genes, the calmodulin protein family, and fibrinopeptides.

Amino Acids↗
PubMedDate not supplied

Pattern of nucleotide substitution and the extent of purifying selection in retroviruses.

The patterns of point mutation and nucleotide substitution are inferred from nucleotide differences in three coding and two noncoding regions of retroviral genomes. Evidence is presented in favor of the view that the majority of mutations accumulate at the reverse transcription stage. Purifying selection is apparently very weak at the amino acid level, and almost nonexistent between synonymous codons. The pattern of purifying selection obeys the rules previously established in vertebrates [Gojobori T, Li W-H, Graur D (1982) J Mol Evol 18:360-369]; i.e., the magnitude of purifying selection at the amino acid level is negatively correlated with Grantham's [Grantham R (1974) Science 185: 862-864] chemical distances between the amino acids interchanged. We refute Modiano et al.'s [Modiano G, Battistuzzi G, Motulsky AG (1981) Proc Natl Acad Sci USA 78:1110-1114] hypothesis, according to which the pattern of mutation is preadapted to buffer against deleterious mutations. On the contrary, the pattern of mutation reduces the level of conservativeness from that imposed on the amino acid substitution pattern by the structure of the genetic code. The extraordinarily high rate of nucleotide substitution in retroviruses in comparison with that in other organisms is apparently caused by an extremely high rate of mutation coupled with a lack of stringent purifying selection at both the codon and the amino acid levels.

Animals↗
PubMedDate not supplied

Evolution of protein inhibitors of serine proteinases: positive Darwinian selection or compositional effects?

In at least two instances involving serine proteinase inhibitors it has been shown that functionally important sites evolve faster and exhibit more interspecific variability than functionally neutral sites. Because these phenomena are difficult to reconcile with the neutral theory of molecular evolution, it has been suggested that the accelerated rate of amino acid substitution at the reactive sites is brought about by positive Darwinian selection. We show that differences in the amino acid composition in the different regions of proteinase inhibitors can account for the differences in the rates of amino acid substitution. By using an index of protein mutability [D. Graur (1985) J Mol Evol 22:53-62], we show that the amino acid composition of the reactive center in the ovomucoids and Spi-2 gene products is such that, regardless of function, they are expected to evolve more rapidly than any other polypeptide for which the rate of substitution is known. In addition, the reactive region in the Spi-2 proteins is shown to be free of compositional constraint. Positive Darwinian selection need not be invoked at the present time in these cases.

Amino Acid Sequence↗
PubMedDate not supplied

The molecular taxonomy and evolution of the guinea pig.

On the basis of 18 protein sequences totaling 2,413 aligned amino acid sites, it is suggested that the guinea pigs and the myomorphs (rat-like rodents) are not monophyletic. Rather, the evolutionary lineage leading to the guinea pig seems to have branched off prior to the divergence among myomorphs, lagomorphs, primates, chiropterans, artiodactyls, and carnivores. It is suggested therefore that the Caviomorpha (guinea pig-like rodents) and possibly the Hystricomorpha (porcupine-like rodents) should be elevated in taxonomic rank and conferred an ordinal status distinct from the Rodentia. This suggestion calls for a reevaluation of the morphological evolution of guinea pigs and further molecular studies on the possibility of paraphyly of the order Rodentia. If the monophyly of rodents holds, it must be concluded that the pattern of molecular evolution in many guinea pig genes has been extremely unusual and that the causes for this pattern should be sought. It is also suggested that claims of large differences in the rate of molecular evolution between guinea pigs and myomorphs may have been exaggerated in many cases as a result of an erroneous phylogenetic position for the guinea pig. The average rate of amino acid replacement in the guinea pig seems to be comparable to that in the rat and the mouse. However, the data indicate that myomorph and caviomorph genes evolve, on average, about two times faster than their human counterparts. Finally, our analysis provides evidence against the hypothesis that the gundi (an African rodent) represents the most ancient rodent lineage.

Amino Acid Sequence↗