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Showing papers in "Molecular Biology and Evolution in 1983"


Journal ArticleDOI
TL;DR: The results indicate that the tertiary and quaternary structures of deoxy- and oxyhemoglobin have remained almost invariant during vertebrate evolution and that most of the amino acid replacements between species are functionally neutral.
Abstract: The allosteric properties of hemoglobins, especially their responses to ligands other than oxygen, vary widely in different classes of vertebrates. Knowing the stereochemistry of the cooperative effects in human hemoglobin, one can infer the stereochemical basis of these variations from the changes in amino acid sequence. The results indicate that the tertiary and quaternary structures of deoxy- and oxyhemoglobin have remained almost invariant during vertebrate evolution and that most of the amino acid replacements between species are functionally neutral. Adaptations leading to responses to new chemical stimuli have evolved by only a few (one to five) amino acid substitutions in key positions. Once such a response has become superfluous, it may be inactivated, not necessarily by a reversal of one of the original substitutions but by any other that happens to inhibit it.

365 citations


Journal ArticleDOI
TL;DR: The theoretical and empirical results for mtDNA in maniculatus and polionotus appear to conform closely to case III, and it is suggested that the distribution patterns of mtDNA sequence variation within and among extant species should be of considerable relevance to the particular demographies of speciation.
Abstract: We address the problem of the possible significance of biological speciation to the magnitude and pattern of divergence of asexually transmitted characters in bisexual species. The empirical data for this report consist of restriction endonuclease site variability in maternally transmitted mitochondrial DNA (mtDNA) isolated from 82 samples of Peromyscus polionotus and P. leucopus collected from major portions of the respective species' ranges. Data are analyzed together with previously published information on P. maniculatus, a sibling species to polionotus. Maps of restriction sites indicate that all of the variation observed can be reasonably attributed to base substitutions leading to loss or gain of particular recognition sites. Magnitude of mtDNA sequence divergence within polionotus (maximum approximately equal to 2%) is roughly comparable to that observed within any of five previously identified mtDNA assemblages in maniculatus. Sequence divergence within leucopus (maximum approximately equal to 4%) is somewhat greater than that within polionotus. Consideration of probable evolutionary links among mtDNA restriction site maps allowed estimation of matriarchal phylogenies within polionotus and leucopus. Clustering algorithms and qualitative Wagner procedures were used to generate phenograms and parsimony networks, respectively, for the between-species comparisons. Three simple graphical models are presented to illustrate some conceivable relationships of mtDNA differentiation to speciation. In theoretical case I, each of two reproductively defined species (A and B) is monophyletic in matriarchal genealogy; the common female ancestor of either species can either predate or postdate the speciation. In case II, neither species is monophyletic in matriarchal genotype. In case III, species B is monophyletic but forms a subclade within A which is thus paraphyletic with respect to B. The empirical results for mtDNA in maniculatus and polionotus appear to conform closely to case III. These theoretical and empirical considerations raise a number of questions about the general relationship of the speciation process to the evolution of uniparentally transmitted traits. Some of these considerations are presented, and it is suggested that the distribution patterns of mtDNA sequence variation within and among extant species should be of considerable relevance to the particular demographies of speciation.

244 citations


Journal ArticleDOI
TL;DR: The kanamycin resistance gene from Staphylococcus aureus has been sequenced and its structure compared with similar genes isolated from Streptomyces fradiae and from two transposons, originally isolated from Klebsiella pneumoniae and Salmonella typhimurium, respectively, suggest that homologous genes of this type be called xenologous.
Abstract: The kanamycin resistance gene from Staphylococcus aureus has been sequenced and its structure compared with similar genes isolated from Streptomyces fradiae and from two transposons, Tn5 and Tn903, originally isolated from Klebsiella pneumoniae and Salmonella typhimurium, respectively. The genes are all homologous but, since their common ancestor, have undergone extensive divergence, with more than 43% divergence between the closest pair. The phylogeny of the genes cannot be made congruent to the phylogeny of the taxa from which they were isolated without requiring rather improbable differences in rates. One is therefore led to conclude that there have been multiple occurrences of gene transfer between these species. Thus, although they are homologous, they are neither orthologous nor paralogous. It is suggested that homologous genes of this type be called xenologous.

161 citations


Journal ArticleDOI
TL;DR: It is proposed that cryptic genes persist as a vital element of the genetic repertoire, ready for recall by mutational activation in future generations, indicating that powerful and biologically important mechanisms exist to prevent the loss of cryptic genes.
Abstract: Cryptic genes are phenotypically silent DNA sequences, not normally expressed during the life cycle of an individual. They may, however, be activated in a few individuals of a large population by mutation, recombination, insertion elements, or other genetic mechanisms. A consideration of the microbial literature concerning biochemical evolution, physiology, and taxonomy provides the basis for a hypothesis of microbial adaptation and evolution by mutational activation of cryptic genes. Evidence is presented, and a mathematical model is derived, indicating that powerful and biologically important mechanisms exist to prevent the loss of cryptic genes. We propose that cryptic genes persist as a vital element of the genetic repertoire, ready for recall by mutational activation in future generations. Cryptic genes provide a versatile endogenous genetic reservoir that enhances the adaptive potential of a species by a mechanism that is independent of genetic exchange.

158 citations


Journal ArticleDOI
TL;DR: Statistical analyses of DNA sequences of globin genes (beta A, beta C, and gamma) from goat and sheep indicate that the rates of nonsynonymous substitution in these genes have been greatly accelerated following the gene duplication separating gamma and the ancestor of beta A and beta C.
Abstract: Statistical analyses of DNA sequences of globin genes (beta A, beta C, and gamma) from goat and sheep (including new sequence information for the second intron of sheep beta A and gamma, kindly provided by A. Davis and A. W. Nienhuis) indicate that the rates of nonsynonymous substitution in these genes have been greatly accelerated following the gene duplication separating gamma and the ancestor of beta A and beta C and the gene duplication separating beta A and beta C. In both cases the acceleration was apparently due to relaxation of purifying selection (functional constraints) rather than advantageous mutations because acceleration occurred only in less important parts of the beta globin chain. The rates of nonsynonymous substitution in these genes are estimated to be about 2.3 x 10(-9) per site per year, which is three times higher than that for the divergence between human beta and mouse beta major globin genes. Our analyses further suggest that the rate of synonymous substitution in functional genes and the rate of substitution in pseudogenes are approximately equal and are between 2.8 x 10(-9) and 5.0 x 10(-9) and that the rate of substitution in introns is about 3.0 x 10(-9). The divergence time between beta A and beta C and that between gamma and the beta A-beta C pair are about 12 and 30 million years, respectively. The proportion of transition mutations is estimated to be 64%, two times higher than expected under random mutation but considerably lower than the 96% estimated for animal mitochondrial DNA.

117 citations


Journal ArticleDOI
TL;DR: A method is proposed which enables us to estimate the fraction of selectively neutral alleles (denoted by Pneut) among newly arisen mutations, which makes use of data on the distribution of rare variant alleles in large samples together with information on the average heterozygosity.
Abstract: Based on the neutral theory of molecular evolution and polymorphism, and particularly assuming "the model of infinite alleles," a method is proposed which enables us to estimate the fraction of selectively neutral alleles (denoted by Pneut) among newly arisen mutations. It makes use of data on the distribution of rare variant alleles in large samples together with information on the average heterozygosity. The formula proposed is Pneut = [He/(1-He)] [loge(2nq)/n alpha (x less than q)], where n alpha(x less than q) is the average number of rare alleles per locus whose frequency, x, is less than q; n is the average sample size used to count rare alleles; He is the average heterozygosity per locus; and q is a small preassigned number such as q = 0.01. The method was applied to observations on enzyme and other protein loci in plaice, humans (European and Amerindian), Japanese monkeys, and fruit flies. Estimates obtained for them range from 0.064 to 0.21 with the mean and standard error Pneut = 0.14 +/- 0.06. It was pointed out that these estimates are consistent with the corresponding estimate Pneut(Hb) = 0.14 obtained independently based on the neutral theory and using data on the evolutionary rate of nucleotide substitutions in globin pseudogenes together with those in the normal globins.

112 citations


Journal ArticleDOI
TL;DR: Evidence indicates that substitutive recombination rates in natural populations are sufficiently low to permit indirect periodic selection to play a prominent role in generating multilocus genetic structure.
Abstract: Geographic variation in the genetic structure of natural enteric populations of Escherichia coli was assessed at both the single-locus and dilocus levels from allozyme genotypes at 12 enzyme loci in 178 cell lines isolated from human hosts in Sweden, Iowa, and Tonga. Although there was significant heterogeneity in allele frequencies at six of the 12 loci, geographic variation accounted for only 2.0% of the total genetic diversity (HT = 0.518). Ohta's D-statistics were used to partition the total variance of dilocus linkage disequilibrium into within-population and between-population components. The observed total variance in disequilibrium (0.0339), averaged over 66 locus-pairs, was significantly greater than would be expected (0.0103) if alleles were randomly associated in an unstructured total population; and both within-locality and between-locality components made substantial contributions to the total variance. Half the locus-pairs exhibited the specific dual relationship among components expected when random factors are generating disequilibrium, but 20% of the locus-pairs showed the opposite relationship, reflecting systematic allele associations. The magnitude of dilocus disequilibrium apparently is unrelated to the chromosomal distance between loci. This and other evidence indicates that substitutive recombination rates in natural populations are sufficiently low to permit indirect periodic selection to play a prominent role in generating multilocus genetic structure.

98 citations


Journal ArticleDOI
TL;DR: Some of the assumptions underlying estimates of DNA and protein sequence divergence are examined and it is shown that these conditions do not strongly affect estimates of divergence, and the binomial variance that is usually assumed for these estimates is safely conservative.
Abstract: Some of the assumptions underlying estimates of DNA and protein sequence divergence are examined. A solution for the variance of these estimates that allows for different mutation rates and different population sizes in each species and for an arbitrary structure in the initial population is obtained. It is shown that these conditions do not strongly affect estimates of divergence. In general, they cause the variance of divergence to be smaller than a binomial variance. Thus, the binomial variance that is usually assumed for these estimates is safely conservative. It is shown that variability in the mutation rate among sites can have an effect as large as or larger than variability in the mutation rate among bases. Variability in the mutation rate among bases and among sites causes the number of substitutions between two sequences to be underestimated. Protein and DNA sequences from several species are collected to estimate the variability in mutation rates among sites. When many homologous sequences are known, standard methods to estimate this variability can be used. The estimates of this variability show that this factor is important when considering the spectrum of spontaneous mutations and is strongly reflected in the divergence of sequences. Smaller variability is found for the third position of codons than for the first and second codon positions. This may be because of less selective constraints on this position or because the third position has been saturated with mutations for the sequences examined.

93 citations


Journal ArticleDOI
TL;DR: Aspects of their structure and phylogenetic distribution suggest that the 18S pseudogenes no longer interact genetically with normal ribosomal genes and therefore may not be linked to nucleolus organizer regions.
Abstract: We discuss the evolutionary significance of four aberrant 18S rDNA clones that were obtained from human, chimpanzee, and gorilla DNA libraries. We show that these clones carry representatives of a small 18S rDNA pseudogene family that arose in a common ancestor of these species. Aspects of their structure and phylogenetic distribution suggest that the 18S pseudogenes no longer interact genetically with normal ribosomal genes and therefore may not be linked to nucleolus organizer regions.

22 citations