Simple repetitive DNA sequences are a widespread and abundant feature of genomic DNA. The following several features characterize such sequences: (1) they typically consist of a variety of repeated motifs of 1-10 bases--but may include much larger repeats as well; (2) larger repeat units often include shorter ones within them; (3) long polypyrimidine and poly-CA tracts are often found; and (4) tandem arrangements of closely related motifs are often found. We propose that slipped-strand mispairing events, in concert with unequal crossing-over, can readily account for all of these features. The frequent occurrence of long tandem repeats of particular motifs (polypyrimidine and poly-CA tracts) appears to result from nonrandom patterns of nucleotide substitution. We argue that the intrahelical process of slipped-strand mispairing is much more likely to be the major factor in the initial expansion of short repeated motifs and that, after initial expansion, simple tandem repeats may be predisposed to further expansion by unequal crossing-over or other interhelical events because of their propensity to mispair. Evidence is presented that single-base repeats (the shortest possible motifs) are represented by longer runs in mammalian introns than would be expected on a random basis, supporting the idea that SSM may be a ubiquitous force in the evolution of the eukaryotic genome. Simple repetitive sequences may therefore represent a natural ground state of DNA unselected for coding functions.

Slipped-strand mispairing: a major mechanism for DNA sequence evolution.

The structure and evolution of the human β-globin gene family

Argiris Efstratiadis Department of Biological Chemistry Harvard Medical School Boston, Massachusetts 02115 James W. Posakony, Tom Maniatis, Richard M. Lawn* and Catherine O’Connell+ Division of Biology California Institute of Technology Pasadena, California 91125 Richard A. Spritz, Jon K. DeRiel,# Bernard G. Forget and Sherman M. Weissman Departments of Genetics and Internal Medicine Yale University School of Medicine New Haven, Connecticut 06510 Jerry L. Slightom, Ann E. Blechl and Oliver Smithies Laboratory of Genetics University of Wisconsin Madison, Wisconsin 53706 Francisco E. Baralle, Carol C. Shoulders and Nicholas J. ProudfootQ MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 2QH, England Summary We present the results of a detailed comparison of the primary structure of human p-like globin genes and their flanking sequences. Among the se- quences located 5’ to these genes are two highly conserved regions which include the sequences ATA and CCAAT located 31 2 1 and 77 + 10 bp, respectively, 5’ to the mRNA capping site. Similar sequences are found in the corresponding locations in most other eucaryotic structural genes. Calcula- tion of the divergence times of individual @like globin gene pairs provides the first description of the evolutionary relationships within a gene family based entirely on direct nucleotide sequence com- parisons. In addition, the evolutionary relationship of the embryonic e-globin gene to the other human P-like globin genes is defined for the first time. Finally, we describe a model for the involvement of short direct repeat sequences in the generation of deletions in the noncoding and coding regions of B-like globin genes during evolution.

https://www.cell.com/cell/pdf/0092-8674(80)90429-8.pdf

The Structure and Evolution of the Human /?-Globin Gene Family

activating regulator mutations Analysis of amino acid sequence data from the alpha and beta hemoglobins and myoglobins suggests that the gene lineages deviate relatively little from established species relationships, and that most contemporary gene pairs in this phylogenetic system may be regarded as orthologous (split at the time of speciation) rather than paralogous (split prior to speciation) It also appears that as the statistical sample of orthologous sequence sites becomes greatly enlarged by tandem alignment of enough different types of protein chains, the parsimony reconstruction based strictly on minimal nucleotide replacement length will itself reveal the correct cladogram for the set of contemporary species [Phylogeny reconstruction; parsimony methods; globin sequences; gene phylogeny; species phylogeny]

https://www.jstor.org/stable/pdfplus/2412519.pdf

Fitting the Gene Lineage into its Species Lineage, a Parsimony Strategy Illustrated by Cladograms Constructed from Globin Sequences

We have determined the sequences of three recombinant cDNAs complementary to different mouse actin mRNAs that contain more than 90% of the coding sequences and complete or partial 3′ untranslated regions (3′UTRs): pAM 91, complementary to the actin mRNA expressed in adult skeletal muscle (αsk actin); pAF 81, complementary to an actin mRNA that is accumulated in fetal skeletal muscle and is the major transcript in adult cardiac muscle (αc actin); and pAL 41, identified as complementary to a β nonmuscle actin mRNA on the basis of its 3′UTR sequence. As in other species, the protein sequences of these isoforms are highly (>93%) conserved, but the three mRNAs show significant divergence (13.8–16.5%) at silent nucleotide positions in their coding regions. A nucleotide region located toward the 5′ end shows significantly less divergence (5.6–8.7%) among the three mouse actin mRNAs; a second region, near the 3′ end, also shows less divergence (6.9%), in this case between the mouse β and αsk actin mRNAs. We propose that recombinational events between actin sequences may have homogenized these regions. Such events distort the calculated evolutionary distances between sequences within a species. Codon usage in the three actin mRNAs is clearly different, and indicates that there is no strict relation between the tissue type, and hence the tRNA precursor pool, and codon usage in these and other muscle mRNAs examined. Analysis of codon usage in these coding sequences in different vertebrate species indicates two tendencies: increases in bias toward the use of G and C in the third codon position in paralogous comparisons (in the order αc), and in orthologous comparisons (in the order chicken < rodent < man). Comparison of actin-coding sequences between species was carried out using the Perler method of analysis. As one moves backward in time, changes at silent sites first accumulate rapidly, then begin to saturate after −(30–40) million years (MY), and actually decrease between −400 and −500 MY. Replacements or silent substitutions therefore cannot be used as evolutionary clocks for these sequences over long periods. Other phenomena, such as gene conversion or isochore compartmentalization, probably distort the estimated divergence time.

Comparison of three actin-coding sequences in the mouse; Evolutionary relationships between the actin genes of warm-blooded vertebrates

An ancestral myoglobin chain has been deduced by comparing the differences in the amino acid sequences of eighteen living species and assessing from the fossil evidence the probable times of divergence of their ancestors.

Molecular Evolution of Myoglobin and the Fossil Record: a Phylogenetic Synthesis

In previous studies, particularly of primates, a high degree of concordance was obtained between an evolutionary pattern based on comparative anatomy and another based on a reconstruction of the possible pathway of evolution of the myoglobin molecule. Accordingly, in extending our studies, we included species of uncertain evolutionary kinship, such as the tree shrew, and also increased the representation of species within the mammalian orders already studied, in the hope that it would be possible to resolve some contended issues and to establish the sequence of branching and pattern of relationship between those orders. As a first step, the phylogenetic pattern within each of the mammalian orders was constrained on zoological grounds according to generally accepted kinship based on the evidence of comparative anatomy and the fossil record. Eight phylogenetic patterns reflecting different possible kinship between the orders were chosen for detailed investigation and for each of these the most economical (parsimonious) pathway which could be obtained for the evolution of myoglobin was reconstructed. The uncertainties which are inherent in such reconstruction were increased by a high incidence of parallel substitutions. Although the eight phylogenetic patterns were widely different from one another it was found that none of the solutions had a An amino acid difference matrix is of special interest because it carries information which is more comparable with that obtained by immunological methods, where access to sequence information has not usually been available. Several different clustering procedures were applied to the amino acid difference matrix for myoglobin. As would be expected from the different assumptions on which each is based, the procedures resulted in different branching patterns which varied in their degree of zoological acceptability. Clustering of the harbour seal with the Cetacea suggested that there might be functional reasons, perhaps associated with diving, for several substitutions acquired in parallel by the myoglobins of these mammals. Repeated clustering of the horse with the sportive lemur, and a tendency for the opossum to join the primates, is associated with a high proportion of parallel substitutions. This tends to undermine confidence in phylogenetic inferences which might be drawn from the repeated clustering of the tree shrew (and often the hedgehog) among the primates. If we assume that there is an overall resemblance of the three-dimensional structure of all myoglobins, and use the crystallographic model of sperm whale myoglobin as a basis, the availability of over 30 vertebrate myoglobin sequences (and that of the mollusc Aplysia ) has provided an opportunity to consider the functional relevance of certain positions at which the nature of the amino acid residue appears to have remained unchanged, or to have changed only conservatively, during several hundred million years of evolution. Part of this conservation is attributable to the maintenance of the monomeric nature of the molecule, and it seems likely that much of the conservatism can be attributed to functional needs in initiating the folding of the molecule and in the maintenance of its tertiary structure. Concomitantly, consideration is given to the likely functional consequence of some of the substitutions which have been accepted. Atassi and his co-workers have carried out extensive immunological studies on myoglobin using antisera prepared in rabbit and goat. The availability of the amino acid sequences of rabbit and sheep (in lieu of goat) has made it possible to investigate the relation between amino acid sequence difference and the distance as measured by immunological criteria. It has not been possible to confirm Reichlin’s hypothesis that the myoglobin antigenic reactive regions of Atassi are particularly variable compared with the rest of the molecule; on the contrary it appears that differences in the immunological reactive regions occur approximately in proportion to those occurring in the molecule as a whole. Estimates of the rate of molecular evolution are of interest because its supposed constancy has been a major argument in favour of the hypothesis that a high proportion of fixed mutations are neutral, or nearly so, as far as selection is concerned. F urthermore, a near constant rate of molecular evolution holds promise for a molecular clock which might be used for dating evolutionary events. However, there is considerable variation in the rate of molecular evolution as evidenced by differences in the number of nucleotide substitutions (‘hits’) in lineages arising from the same phylogenetic branching point or by the examination of the changes at the amino acid level. In order to investigate absolute rates of evolution we sought to establish the best estimate of the date of divergence between the ancestors of the living species included in this study. These dates are based on direct fossil evidence and must be regarded as minimum dates because we have not indulged in open-ended speculations about fossils which have not yet been found. The combination of these dates with the evidence of our cladograms leads us to reaffirm our earlier finding that there are considerable differences in the amount of change in different lineages. For example, whereas one lineage (to gibbon) appears to have accepted no mutations during the past 20 Ma, another lineage (to ox) seems to have fixed seven mutations during the last 18 Ma. Goodman and others have drawn attention to the apparently low rate of molecular evolution among higher primates; a similar observation applies to the myoglobin of the Old World monkeys so far studied, but neither the myoglobins of New World monkeys nor the prosimian myoglobins share this feature. After their divergence from one another the two bird lineages included in this study appear to have fixed mutations at rates comparable with those found among mammals during the past 79 Ma. However, the number of differences between the bird and mammal ancestral stems appears to be remarkably low bearing in mind the date of divergence of their ancestors, about 293 Ma ago. Recognizing that this could be an artefact resulting from multiple changes at the same site, from undetectable back mutations and from isosemantic mutations accumulating during a long period of evolution, various procedures were adopted to transform the data in order to estimate the number of such events. None of these procedures, however, eliminated the phenomenon that during the first 214 Ma since their separation the ancestral stems leading eventually to birds and mammals seem to have fixed mutations in their myoglobin at a lower rate than the average rate prevailing during the past 79 Ma, the latter being approximately one mutation in 4 Ma. It is to be expected that sampling error will produce some fluctuations in rate, but even over the relatively long period of 79 Ma the fastest rate of fixation of mutations is about three times the slowest rate and so we are inclined to discard the molecular clock as unreliable for dating divergences, at least within this span of time. On integrating the various sections of this study we see that the changes in myoglobin have not been at random throughout the molecule. Given the constraints demanded by the functional morphology of the molecule itself and the constraints of the genetic code, it is to be expected that both will contribute to parallel change in different lineages. In the reconstructed pathways of evolution of myoglobin about 50 % of the changes were found in parallel in other lineages. There is an indication, provided by the larger number of arginine residues present in aquatic forms, that some of these parallel changes may be correlated with mode of life. The adaptive significance of the several parallel changes between the cetaceans and the pinnipeds certainly deserves physiological investigation. Regardless of the causes of parallel evolution at the molecular level this phenomenon has contributed to unexpected similarities between myoglobins and has led to difficulties in phylogenetic reconstruction of a nature already familiar to comparative anatomists.

On the evolution of myoglobin.

Rapid estimation (2 1/2 hours) of glycosylated hæmoglobin for routine purposes

The recent determination of the entire antigenic structure of sperm-whale myoglobin with rabbit and goat antisera has permitted the examination of whether the antigenic structure recognized by antibodies depends on the species in which the antisera are raised. Also, by knowledge of the antigenic structure, the molecular factors that determine and influence antigenicity can be better understood in terms of the effects of amino acid substitutions occurring in the antigenic sites and in the environmental residues of the sites. In the present work, the myoglobins from finback whale, killer whale, horse, chimpanzee, sheep, goat, bovine, echidna, viscacha, rabbit, dog, cape fox, mouse and chicken were examined for their ability to cross-react with antisera to sperm-whale myoglobin. By immunoadsorbent titration studies with radioiodinated antibodies, each of these myoglobins was able to bind antibodies to sperm-whale myoglobin raised in goat, rabbit, chicken, cat, pig and outbred mouse. It was found that the extent of cross-reaction of a given myoglobin was not dependent on the species in which the antisera were raised. This indicated that the antibody response to sperm-whale myoglobin (i.e. its antigenic structure) is independent of the species in which the antisera are raised and is not directed to regions of sequence differences between the injected myoglobin and the myoglobin of the immunized host. Indeed, in each antiserum from a given species examined, that antiserum reacted with the myoglobin of that species. The extent of this auto-reactivity for a given myoglobin was comparable with the general extent of cross-reactivity shown by that myoglobin with antisera raised in other species. The cross-reactivities and auto-reactivities (both of which are of similar extents for a given myoglobin) can be reasonably rationalized in terms of the effects of amino acid substitutions within the antigenic sites and within the residues close to these sites. These findings confirm that the antigenicity of the sites is inherent in their three-dimensional locations.

/pdf/the-antibody-response-to-myoglobin-is-independent-of-the-1mqssig8sf.pdf

The antibody response to myoglobin is independent of the immunized species. Analysis in terms of replacements in the antigenic sites and in environmental residues of the cross-reactions of fifteen myoglobins with sperm-whale myoglobin antisera raised in different species.

The primary sequences of the myoglobins of two rodents (the South American viscacha and the Mediterranean mole rat) have been determined. Both myoglobins exhibit one polymorphism. The two rodent sequences have been compared with each other and with other known myoglobins. The myoglobin of the viscacha is similar to those of the diving mammals and penguin in having a high arginine content. Among mammalian sequences, the arginines at positions 77 (in one of the viscacha myoglobins) and 79 have been found only in the myoglobin from viscacha. Mole rat myoglobin has a lysine at position 31, where arginine or serine is found in all other known vertebrate myoglobins.

H. Lehmann

Papers

Molecular Evolution of Myoglobin and the Fossil Record: a Phylogenetic Synthesis

On the evolution of myoglobin.

Rapid estimation (2 1/2 hours) of glycosylated hæmoglobin for routine purposes

The antibody response to myoglobin is independent of the immunized species. Analysis in terms of replacements in the antigenic sites and in environmental residues of the cross-reactions of fifteen myoglobins with sperm-whale myoglobin antisera raised in different species.

The myoglobin of rodents: Lagostomus maximus (viscacha) and Spalax ehrenbergi (mole rat)