Showing papers in "Molecular Biology and Evolution in 1991"

Evolution of the cetacean mitochondrial D-loop region.

Abstract: We sequenced the mitochondrial DNA D-loop regions from two cetacean species and compared these with the published D-loop sequences of several other mammalian species, including one other cetacean. Nucleotide substitution rates, DNA sequence simplicity, possible open reading frames (ORFs), and potential RNA secondary structure were investigated. The substitution rate is an order of magnitude lower than would be expected on the basis of reports on human sequence variation in this region but are consistent with interspecific primate and rodent D-loop sequence variation and with estimates of substitution rates from whole mitochondrial genomes. Deletions/insertions are less common in the cetacean D-loop than in other vertebrate species. Areas of high sequence simplicity (clusters of short repetitive motifs) across the region correspond to areas of high sequence divergence. Three regions predicted to form secondary structures are homologous to such putative structures in other species; however, the presumptive structures most conserved in cetaceans are different from those reported for other taxa. While all three species have possible long ORFs, only a short sequence of seven amino acids is shared with other mammalian species, and those changes that had occurred within it are all nonsynonymous. We conclude that DNA slippage, in addition to point mutation, contributes to the evolution of the D-loop and that regions of conserved secondary structure in cetaceans and an ORF are unlikely to contribute significantly to the conservation of the central region.

Strong reproductive isolation between closely related tropical sea urchins (genus Echinometra).

Abstract: Morphological, mitochondrial DNA, and single-copy nuclear DNA differences show that the tropical sea urchin Echinometra mathaei is composed of at least four independent gene pools. Evolutionary distance between species measured with restriction-site changes (for mitochondrial DNA) and thermal renaturation (for single-copy nuclear DNA) is 1%-3% nucleotide divergence. Thus these are the most closely related sea urchin species known. Despite this genetic similarity, strong blocks to interspecific fertilization exist in this genus. Between two Hawaiian species, few eggs are fertilized in hybrid crosses, even in the presence of excess sperm. Microscopic examination of such crosses shows that sperm attachment to heterologous eggs is inhibited. Measures of genetic distance between species can help reveal the tempo of speciation and allow comparisons of morphological, biochemical, and ecological characteristics to be made in an evolutionary framework. Our results show that strong reproductive isolation can evolve by changes in egg-sperm recognition without extensive genetic divergence between species. Such mechanisms are most easily studied in free-spawning animals such as sea urchins but as well may represent an important aspect of speciation in species with internal fertilization.

Variation in mitochondrial cytochrome b sequence in natural populations of South American akodontine rodents (Muridae: Sigmodontinae).

Abstract: A 401-bp fragment of the mitochondrial cytochrome b gene was sequenced from polymerase chain reaction-amplified products for 20 natural populations representing 12 species of South American akodontine rodents (Muridae). Variation among these taxa increased with their hierarchical position, from comparisons within local populations to those among different genera. Two individuals from the same local population differed by less than 1% sequence divergence. Sequence divergence among geographic samples within a species was 0.25%-8%, while that among species was 3%-21%. Comparisons of the akodontine sequences with that for the house mouse show 21%-25% sequence difference. A parsimony-based phylogenetic analysis of the data supports the placement of the taxon Microxus within Akodon (sensu stricto), of Bolomys just outside the Akodon cluster, and of Chroeomys as a separate genus quite distinct from the other members of this group. This phylogenetic hypothesis is identical to that determined from electrophoretic data but is quite divergent from the present taxonomy of the group.

The phylogenetic status of arthropods, as inferred from 18S rRNA sequences.

Abstract: Partial 18S rRNA sequences of five chelicerate arthropods plus a crustacean, myriapod, insect, chordate, echinoderm, annelid, and platyhelminth were compared. The sequence data were used to infer phylogeny by using a maximum-parsimony method, an evolutionary-distance method, and the evolutionary-parsimony method. The phylogenetic inferences generated by maximum-parsimony and distance methods support both monophyly of the Arthropoda and monophyly of the Chelicerata within the Arthropoda. These results are congruent with phylogenies based on rigorous cladistic analyses of morphological characters. Results support the inclusion of the Arthropoda within a spiralian or protostome coelomate clade that is the sister group of a deuterostome clade, refuting the hypothesis that the arthropods represent the "primitive" sister group of a protostome coelomate clade. Bootstrap analyses and consideration of all trees within 1% of the length of the most parsimonious tree suggest that relationships between the nonchelicerate arthropods and relationships within the chelicerate clade cannot be reliably inferred with the partial 18S rRNA sequence data. With the evolutionary-parsimony method, support for monophyly of the Arthropoda is found in the majority of the combinations analyzed if the coelomates are used as "outgroups." Monophyly of the Chelicerata is supported in most combinations assessed. Our analyses also indicate that the evolutionary-parsimony method, like distance and parsimony, may be biased by taxa with long branches. We suggest that a previous study's inference of the Arthropoda as paraphyletic may be the result of (a) having two few arthropod taxa available for analysis and (b) including long-branched taxa.

The order of sequence alignment can bias the selection of tree topology.

Abstract: Sequential pairwise alignment of multiple sequences is a widely used procedure (Kruskal 1983 ). It is useful and generally successful when sequences within a set differ by relatively few substitutions. Although it is well known that differential substitution rates can artifactually bias the assessment of tree topology (Felsenstein 1978), it is not generally known that the order in which sequences are aligned can bias tree selection. To test the effect of alignment order, the classical four-taxon test has been applied to the “tree of life” (Lake et al. 1984; Woese and Olsen 1986) by using alternative alignments and three reconstruction algorithms [maximum parsimony (Fitch 197 1)) transversion parsimony (Brown et al. 1982), and evolutionary parsimony (Lake 1987)]. There is enormous interest in this tree because it relates all known organisms and because its topology is expected to provide insight into the evolution of modem organisms. Because the tree spans large evolutionary distances, its topology has been difficult to establish. By means of sequences from elongation factor Tu ( EF-Tu), the most conserved protein sequence known to span the tree of life, it is shown that specific alignment orders systematically favor alternative trees. In particular, if taxa A and B are pairwise aligned and if C and D are pairwise aligned, the resulting alignment of the EF-Tu sequences more often gives the tree that has A and B as topological neighbors and C and D as topological neighbors, regardless of the tree reconstruction algorithm used. Because all three reconstruction algorithms produced the same tree for any particular alignment, unequal rate effects appear to be secondary for EF-Tu sequences. This indicates that order-dependent alignment biases are distinct from unequal rate effects and that, for some data, they could be as important as unequal rate effects. Pairwise alignments of protein sequences were performed with the ALIGN program available in the Dayhoff package (Dayhoff et al. 1983 ). The penalty for a break was 6, and the mutation data matrix corresponded to 250 accepted point mutations with a bias of +2. These are reasonable values for the weights and correspond to those used in the examples in the description of the ALIGN program. [For an insightful discussion of alignment weights, see the paper by Fitch and Smith ( 1983); also see Waterman and Perlwitz ( 1984) .] EF-Tu sequences were aligned as protein sequences to obtain more robust alignments and were back-translated into nucleic acid sequences (e.g., phe was translated as UUY, leu as YUN, arg as NGN, and ser as NNN) so that the maximum-, transversion-, and evolutionary-parsimony methods could be compared by equivalent data. Only positions consisting of a single nucleotide (i.e., U, C, A, or G but not R, Y, or N) in each of the four sequences were scored. These uniquely defined replacement sites are presumed to correspond to the most conserved nucleotide positions. A multiple alignment of four sequences can be achieved by successively aligning

Molecular evolution of the psi eta-globin gene locus: gibbon phylogeny and the hominoid slowdown.

Abstract: An 8.4-kb genomic region spanning both the Wq-globin gene locus and flanking DNA was sequenced from the common gibbon (Hylobutes lur). In addition, sequencing of the entire orthologous region from galago (Galago crassicaudatus) was completed. The gibbon and galago sequences, along with published orthologous sequences from 10 other species, were aligned. These noncoding nucleotide sequences represented four human alleles, four apes (chimpanzee, gorilla, orangutan, and gibbon), an Old World monkey (rhesus monkey), two New World monkeys (spider and owl monkeys), tarsier, two strepsirhines (galago and lemur), and goat. Divergence and maximum parsimony analyses of the m genomic region frrst groups humans and chimpanzees and then, at progressively more ancient branch points, successively joins gorillas, orangutans, gibbons, Old World monkeys, New World monkeys, tarsiers, and strepsirhines (the lemuriform-lorisiform branch of primates). This cladistic pattern supports the taxonomic grouping of all extant hominoids into family Hominidae, the division of Hominidae into subfamilies Hylobatinae (gibbons) and Homininae, the division of Homininae into tribes Pongini (orangutans) and Hominini, and the division of Hominini into subtribes Gorillina (gorillas) and Hominina (chimpanzees and humans). The additional gibbon and galago sequence data provide further support for the occurrence of a graded evolutionaryrate slowdown in the descent of simian primates, with the slowing rate being more pronounced in the great-ape and human lineages than in the gibbon or monkey lineages. A comparison of global versus local molecular clocks reveals that local clock predictions, when focused on a specific number of species within a narrow time frame, provide a more accurate estimate of divergence dates than do those of global clocks.

Evolution of retroposons by acquisition or deletion of retrovirus-like genes.

Abstract: The retroid family consists of all genetic elements that encode a potential reverse transcriptase (RT). Members of this family include a diversity of eukaryotic genetic elements (viruses, transposable elements, organelle introns, and plasmids) and the retrons of prokaryotes. Some retroid elements have, in addition to the RT gene, other genes in common with the retroviruses. On the basis of RT sequence similarity, the retroposon group is defined as the eukaryotic long interspersed nuclear elements, the transposable elements of (1) Drosophila melanogaster (I and F factors), (2) Trypanosoma brucei (ingi element), (3) Zea mays (Cin4), (4) Bombyx mori (R2Bm), and members of the group II introns and plasmids of yeast mitochondria. The data presented here elucidate the extent of the relationships between the retroposons and other retroid-family members. Protein-sequence alignment data demonstrate that subsets of the retroposons contain different assortments of retroviral-like genes. Sequence similarities can be detected between the capsid, protease, ribonuclease H, and integrase proteins of retroviruses and several retroposon sequences. The relationships among the retroposon capsid-like sequences are congruent with the RT sequence phylogeny. In contrast, the similarity between ribonuclease H sequences varies in different subbranches of the retroposon lineage. These data suggest that xenologous recombination (i.e., the replacement of a homologous resident gene by a homologous foreign gene) and/or independent gene assortment have played a role in the evolution of the retroposons.

Molecular distance and divergence time in carnivores and primates.

Abstract: Numerous studies have used indices of genetic distance between species to reconstruct evolutionary relationships and to estimate divergence time. However, the empirical relationship between molecular-based indices of genetic divergence and divergence time based on the fossil record is poorly known. To date, the results of empirical studies conflict and are difficult to compare because they differ widely in their choice of taxa, genetic techniques, or methods for calibrating rates of molecular evolution. We use a single methodology to analyze the relationship of molecular distance and divergence time in 86 taxa (72 carnivores and 14 primates). These taxa have divergence times of 0.0 l-55 Myr and provide a graded series of phylogenetic divergences such that the shape of the curve relating genetic distance and divergence time is often well defined. The techniques used to obtain genetic distance estimates include one- and two-dimensional protein electrophoresis, DNA hybridization, and microcomplement fixation. Our results suggest that estimates of molecular distance and divergence time are highly correlated. However, rates of molecular evolution are not constant; rather, in general they decline with increasing divergence time in a linear fashion. The rate of decline may differ according to technique and taxa. Moreover, in some cases the variability in evolutionary rates changes with increasing divergence time such that the accuracy of nodes in a phylogenetic tree varies predictably with time.

Use of the Method of Generalized Least Squares in Reconstructing Phylogenies from Sequence Data

Abstract: The method of generalized least squares provides a flexible method of phylogenetic reconstruction from sequence data, after reducing them to pairwise distances between species, corrected for multiple and back mutation. It gives efficient estimates of the branch lengths of a given tree. It also provides a natural measure of the departure of the observed from the predicted set of distances which has a x2 distribution under the true topology; this fact is used to construct a significance test on the topology and so to determine a “confidence interval” for the set of trees which are compatible with the data. To use this method it is necessary to know the variances and covariances of the corrected pairwise distances. A new method of estimating these variances and covariances empirically is described. The methodology is illustrated using data on the phylogeny of four mammalian orders (with the conclusion that rodents and lagomorphs are not sister groups) and of six primates (with the conclusion that the human/chimp/gorilla trichotomy cannot be resolved with these data alone).

Phylogenetic relationships and biogeography of xantusiid lizards, inferred from mitochondrial DNA sequences.

Abstract: Portions of two mitochondrial genes (12S ribosomal RNA and cytochrome b) were sequenced in seven species to examine phylogenetic relationships within the lizard family Xantusiidae. Phylogenies derived from these sequences (709 total bp) are concordant and indicate that the Cuban species Cricosaura typica is the sister group to all other xantusiids. The Middle American genus Lepidophyma is the closest relative of Xantusia, and X. riversiana (California Islands) the closest relative of X. vigilis (mainland). These findings are not in agreement either with the results of a recent morphological analysis that united Cricosaura and Lepidophyma as closest relatives or with past studies that have recognized X. riversiana as a separate genus. Levels of sequence divergence, as well as the age and affinities of some mainland fossil taxa, suggest that the origin of Cricosaura was associated with the tectonic evolution of the Greater Antilles in the late Cretaceous. These results further demonstrate that significant resolution of phylogenies can be obtained with relatively short DNA sequences and that these mitochondrial genes are concordant in their estimation of phylogeny.

Phylogenetic relationships of neopterygian fishes, inferred from mitochondrial DNA sequences.

Abstract: To investigate the relationships among the three main groups of extant neopterygian fishes--Amiidae, Lepisosteidae, and Teleostei--we sequenced fragments of three mitochondrial genes from 12 different actinopterygian fishes and translated the nucleotide sequences into amino acid sequences. When all three regions are considered together, Amiidae clusters with Lepisosteidae in the most parsimonious cladograms, but other clades, such as Neopterygii and Teleostei, that are well supported by morphological evidence fail to emerge as monophyletic. When the cytochrome b sequences are analyzed together with previously published sequences for other taxa, the majority-rule consensus tree is consistent with the monophyly of Teleostei and Neopterygii and marginally supports the Amiidae + Lepisosteidae clade. In either analysis, when Neopterygii and Teleostei are constrained to monophyly, all the most-parsimonious cladograms support the Amiidae + Lepisosteidae topology. Where molecules and morphology disagree, provisional morphology-based constraints on the analysis of molecular data offer a practical means of integrating the two types of data.

Heteroplasmy and polymorphism in the major noncoding region of mitochondrial DNA in Japanese monkeys: association with tandemly repeated sequences.

Abstract: We have sequenced the major noncoding region of mitochondrial DNA (mtDNA) of four Japanese monkeys and have found length polymorphism in the sequenced region. The length polymorphism resulted from two tandem duplications of 160-bp sequences which contained the conserved sequence blocks 2 and 3 and the light-strand transcription-promoter region. We also found polymorphisms in this mtDNA region among 100 Japanese monkeys from 12 localities, 90 of which were analyzed using DNA amplified through the polymerase chain reaction. In two localities, we found individuals with heteroplasmic mtDNA which had different numbers of the 160-bp repeats mentioned above. The 100 samples were classified into six types in terms of length and presence/absence of the recognition site of two restriction enzymes in the major noncoding region.

Ribosomal DNA Variation in Daphnia pulex

Abstract: Variation in the ribosomal DNA (rDNA) gene family was surveyed in five cyclically parthenogenetic populations of Daphnia pulex from central Illinois and in obligately parthenogenetic clones from Illinois and Ontario. A total of 37 distinct rDNA repeat types were identified on the basis of restriction-site and repeat-length polymorphism in a sample of 90 isolates. Repeat-type diversity was high within cyclic populations; however, individuals possessed only a small subset of the repeat-type variation present in each population. The distribution of repeat types within and among individuals suggested that new variants spread within rDNA arrays much faster than arrays carrying the variants spread within populations. This observation is contrary to a model developed by Ohta and Dover for strictly sexual organisms. Previous surveys of isozyme and mitochondrial DNA variation in these populations showed that gene flow among them is limited. Hierarchical analysis of rDNA restriction-site variation was consistent with this observation and showed that genetic divergence accumulates between populations for rDNA almost as rapidly as it does for single-copy nuclear genes (isozymes). Analysis of rDNA variation in obligately parthenogenetic clones provided evidence that both intraand interchromosomal exchanges occur between rDNA arrays in the absence of meiosis. Moreover, individuals reproducing by obligate parthenogenesis possessed fewer rDNA repeat types, on average, than did individuals from cyclic populations, suggesting that there is a net loss of rDNA repeat-type variability within obligately clonal lineages over time. Preliminary analyses of two additional species, D. pulicaria and D. obtusa, revealed several restriction-site polymorphisms that were found in more than one of the three species. The existence of such shared polymorphisms advises caution in the use of multigene-family variation to infer phylogenies among species when levels of intraspecific variation have not been assessed.

Evolutionary relationships of avian Eimeria species among other Apicomplexan protozoa: monophyly of the apicomplexa is supported.

Abstract: Direct, reverse transcriptase-mediated, partial sequencing of the small-subunit (16S-like) ribosomal RNA (srRNA) of Eimeria tenella and E. acervulina was performed. Sequences were aligned by eye with six previously published, partial or complete srRNA sequences of apicomplexan protists (Plasmodium berghei, Theileria annulata, Cryptosporidium sp., Toxoplasma gondii, Sarcocystis muris, and S. gigantea). Six eukaryotic protists (a slime mold, a yeast, two dinoflagellates, and two ciliates) acted as an outgroup for a parsimony-based phylogenetic analysis (PAUP Ver. 3.0). The 188 phylogenetically informative sites (i.e., those positions that neither were unvaried nor had only autapomorphic substitutions) supported a single tree topology 481 steps in length with a consistency index of 0.65 in which the monophyly of the Apicomplexa was supported. The two Eimeria species and S. muris, S. gigantea, and T. gondii formed a pair of monophyletic groups that were sister groups. The two Sarcocystis species were not hypothesized to be sister taxa. The genera Plasmodium and Cryptosporidium were hypothesized to form the sister group to these five coccidia and T. annulata. A priori data-editing techniques that deleted "variable" positions prior to analysis failed to recognize the monophyly of the Apicomplexa when the same parsimony-based tree-building algorithm was used. Inability of the outgroup taxa to root the well-supported ingroup tree (Apicomplexa) at a unique site when these taxa were used individually for this purpose reinforces the need for an appropriate, multiple-taxon outgroup in such analyses.

Comparison of the bindin proteins of Strongylocentrotus franciscanus, S. purpuratus, and Lytechinus variegatus: sequences involved in the species specificity of fertilization.

Abstract: Bindin is the sea urchin sperm acrosomal protein that is responsible for the species-specific adhesion of the sperm to the egg. Two new bindin cDNA sequences that contain the entire open reading frame for the binding precursor are reported: one for Strongylocentrotus franciscanus and one for Lytechinus variegatus. Both contain inverted repetitive sequences in their 3' untranslated regions, and the S. franciscanus cDNA contains an inverted repetitive sequence match between the 5' untranslated region and the coding region. The middle third of the mature bindin sequence is highly conserved in all three species, and the flanking sequences share short repeated sequences that vary in number between the species. Cross-fertilization data are reported for the species S. purpuratus, S. franciscanus, L. variegatus, and L. pictus. A barrier to cross-fertilization exists between the sympatric Strongylocentrotus species, but there is no barrier between the allopatric Lytechinus species.

An extreme codon preference strategy: codon reassignment.

Abstract: We argue that in animal mitochondria codon reassignments, such as those for AGA and AGG from arginine to serine or of AUA from isoleucine to methionine, are the result of an interplay between biased mutational forces and selective ones. In particular, there is a marked tendency for animal mitochondria to have very small genomes and to minimize their investment in components required for gene expression. These tendencies are expressed as a reduction in the diversity of tRNA isoacceptor species. In our view, the pressure to simplify tRNA populations, together with mutational bias against certain codons, will account for the codon reassignments observed in animal mitochondria. A parallel to the major codon bias in microorganisms, which likewise tends to reduce the diversity of the tRNA isoacceptor populations under fast growth conditions, may be drawn. Therefore, we suggest that codon reassignments are usefully viewed as an extreme form of codon bias.

Assessing the Reliability of 5S rRNA Sequence Data for Phylogenetic Analysis in Green Plants

Abstract: Elimination of compensating substitutions in portions of 5S rRNA sequences that exhibit secondary structure and scoring of common gaps as homologous characters affects both the topology of phylogenetic estimates within green plants and measures of their reliability. Allowing for a transition / transversion bias, on the other hand, has little affect. Detailed analysis of these data results in phylogenetic estimates largely congruent with widely accepted hypotheses of relationships among green plants, but bootstrapping provides little statistical support for most of these groupings. The lack of statistical support is a direct result of both the small number of phylogenetically informative sites in the SS rRNA molecule and the high rate of change at those positions that are free to vary. When considered in conjunction with earlier distance-based analyses of phylogeny that use 5s rRNA, these results demonstrate that phylogenetic estimates based only on analyses of 5S rRNA sequences must be viewed with considerable caution.

Evolution of ribosomal RNA gene copy number on the sex chromosomes of Drosophila melanogaster.

Abstract: A diverse array of cellular and evolutionary forces-including unequal crossingover, magnification, compensation, and natural selection-is at play modulating the number of copies of ribosomal RNA (rRNA) genes on the X and Y chromosomes of Drosophila. Accurate estimates of naturally occurring distributions of copy numbers on both the X and Y chromosomes are needed in order to explore the evolutionary end result of these forces. Estimates of relative copy numbers of the ribosomal DNA repeat, as well as of the type I and type II inserts, were obtained for a series of 96 X chromosomes and 144 Y chromosomes by using densitometric measurements of slot blots of genomic DNA from adult D. melanogaster bearing appropriate deficiencies that reveal chromosome-specific copy numbers. Estimates of copy number were put on an absolute scale with slot blots having serial dilutions both of the repeat and of genomic DNA from nonpolytene larval brain and imaginal discs. The distributions of rRNA copy number are decidedly skewed, with a long tail toward higher copy numbers. These distributions were fitted by a population genetic model that posits three different types of exchange events-sister-chromatid exchange, intrachromatid exchange, and interchromosomal crossing-over. In addition, the model incorporates natural selection, because experimental evidence shows that there is a minimum number of fimctional elements necessary for survival. Adequate fits of the model were found, indicating that either natural selection also eliminates chromosomes with high copy number or that the rate of intrachromatid exchange exceeds the rate of interchromosomal exchange.

Rates of DNA change and phylogeny from the DNA sequences of the alcohol dehydrogenase gene for five closely related species of Hawaiian Drosophila.

Abstract: The sequence of 1.6 kb of DNA surrounding the alcohol dehydrogenase (Adh) gene from five species of the Planitibia subgroup of the Hawaiian picture-winged Drosophila, with estimated divergence times of 0.4-S. 1 Myr, has been determined. The gene trees which were found by using the sequence divergence from different regions of the sequences are generally in accord with the phylogeny proposed for these species when chromosomal inversions and island of origin are used. One of the species (D. picticornis) appears to be more distant from the other species in this group than they are from a member of the Grimshawi group (D. afinidisjwzcta) which is chromosomally more distant. Two of the species (D. dzjkens and D. planitibia) show heterogeneity in the nucleotide changes in the Adh coding region, heterogeneity which is interpreted to be due to a gene conversion or recombination after hybridization between the two species. The minimal rate of nucleotide substitution of synonymous nucleotides and of nontranscribed nucleotides downstream from the coding region is estimated as 1.5 X lo-* and 1.1 X lo-* substitutions/ nucleotide/year, respectively. This rate is two to three times the maximal rate estimated for mammalian synonymous substitutions.

Methods for inferring phylogenies from nucleic acid sequence data by using maximum likelihood and linear invariants.

Abstract: Likelihood methods and methods using invariants are procedures for inferring the evolutionary relationships among species through statistical analysis of nucleic acid sequences. A likelihood-ratio test may be used to determine the feasibility of any tree for which the maximum likelihood can be computed. The method of linear invariants described by Cavender, which includes Lake's method of evolutionary parsimony as a special case, is essentially a form of the likelihood-ratio method. In the case of a small number of species (four or five), these methods may be used to find a confidence set for the correct tree. An exact version of Lake's asymptotic chi 2 test has been mentioned by Holmquist et al. Under very general assumptions, a one-sided exact test is appropriate, which greatly increases power.

Distribution of hobo transposable elements in natural populations of Drosophila melanogaster.

Abstract: Forty-six strains derived from American and French natural populations of Drosophila melanogaster were tested for the presence and activity of hobo elements by using Southern blotting and a gonadal dysgenesis assay. The oldest available strains exhibited weak detectable hybridization to the hobo-element probe and revealed neither hobo-activity potential nor hobo-repression potential. In contrast, all recently collected strains harbored hobo sequences and revealed a strong hobo-repression potential but no strong hobo-activity potential. On the basis of restriction-enzyme analysis, old strains appear to have numerous fragments hybridizable to hobo sequences, several probably conserved at the same locations in the genome of the tested strain and others dispersed. In recently isolated strains, and unlike the situation in the published sequence of the cloned hobo108 element, a PvuII site is present in the great majority of full-sized hobo elements and their deletion derivatives. When the genetic and molecular characteristics are considered together, the available evidence is consistent with the hypothesis of a worldwide hobo-element invasion of D. melanogaster during the past 50 years. Comparison of data from the I-R and P-M systems suggests that the putative invasion followed the introduction of the I element but preceded that of the P element. This hypothesis poses the problem of the plausibility of three virtually simultaneous element invasions in this species. Such a possibility might be due to a modification of the genetic structure of American populations of D. melanogaster during the first part of the 20th century.

Evolution of higher-plant glutamine synthetase genes : tissue specificity as a criterion for predicting orthology

Abstract: Evolutionary relationships among members of the nuclear multigene family encoding isozymes of glutamine synthetase (GS) in flowering plants were studied by using parsimony and distance methods. Analyses using subsets of the data indicated that the consistency index is not a sufficient measure of phylogenetic data quality and that assumptions about the information content of third-codon positions and transitions may be misleading. Tissue-specific expression patterns of GS isozymes were not uniformly useful as predictors of orthology. Chloroplast and cytosolic genes were shown to form two groups of orthologous sequences. Within the cytosolic group, however, genes expressed in the nodule did not form a single orthologous group, suggesting that a regulatory shift has occurred in the pea-alfalfa lineage. Organismal relationships inferred from the limited sampling are generally in concert with current phylogenetic hypotheses.

Evidence for replication slippage in the evolution of Oenothera chloroplast DNA.

Abstract: Evolutionary relationships of four plastid genomes (plastomes) from different Oenothera species have been assessed by sequence comparisons of two intergenic regions that separate the ribosomal protein genes rpl16, rpl14, and rps8. Sequence changes include base substitutions, the occurrence of a 29-base tandem duplication, and variation in the length of two poly-A stretches. Additions/deletions in chloroplast DNA may not be useful for evolutionary comparisons more distant than these, particularly if the sequences undergo divergence after the initial event, but the length mutations reported here allow a finer resolution of the phylogeny of the closely related Oenothera plastomes than would have been possible if only base substitutions had been considered. Comparisons with the orthogous sequence from tobacco chloroplast DNA indicate the direction of change at most of the sites. The results suggest that plastomes I and II are closely related to each other, as are plastomes III and IV. Replication slippage is proposed as a mechanism to explain the length mutations.

The dipole moment of cytochrome c.

Abstract: Vertebrate cytochromes c and the cytochromes c of insects and plants have, on average, dipole moments of 320 and 340 debye, respectively. The direction of the dipole vector with respect to the haem plane, at the solvent-accessible edge of which electron transfer presumably takes place, is conserved in these two groups--at 32 degrees +/- 7 degrees and 22 degrees +/- 10 degrees, respectively. The variation of dipole orientations and magnitudes observed in these species is compared with the results of a model in which charge distributions occur randomly. Since this model does not generate the observed charge asymmetries of the various cytochromes c, it is concluded that the dipole moment of cytochrome c is a feature that is evolutionarily conserved, apparently because it has an important influence on the interaction of this mobile electron carrier with its physiological electron donors and acceptors in the intermembrane space of mitochondria.

Evolutionary origin and diversification of the mammalian CD1 antigen genes.

Abstract: CD1 antigens are cell-surface glycoproteins which have a molecular structure which is similar (consisting of extracellular domains alpha 1, alpha 2, and alpha 3, a transmembrane portion, and a cytoplasmic tail) to that of class I MHC molecules. Phylogenetic analysis of mammalian CD1 DNA sequences revealed that these genes are more closely related to the class I major histocompatibility complex (MHC) than to the class II MHC and that mammalian genes are more closely related to avian class I MHC genes than they are to mammalian class I MHC genes. The CD1 genes form a multigene family with different numbers of genes in different species (five in human, eight in rabbit, and two in mouse). Known CD1 genes are grouped into the following three families, on the basis of evolutionary relationship: (1) the human HCD1B gene and a partial sequence from the domestic rabbit, (2) the human HCD1A and HCD1C genes, and (3) the human HCD1D and HCD1E genes plus the two mouse genes and a sequence from the cottontail rabbit. The alpha 1 and alpha 2 domains of CD1 are much less conserved at the amino acid level than are the corresponding domains of class I MHC molecules, but the alpha 3 domain of CD1 seems to be still more conserved than the well-conserved alpha 3 domain of class I MHC molecules. Furthermore, in the human CD1 gene family, interlocus exon exchange has homogenized alpha 3 domains of all CD1 genes except HCD1C.

The molecular evolution of the alcohol dehydrogenase locus and the phylogeny of Hawaiian Drosophila.

Abstract: DNA sequences in the alcohol dehydrogenase genes of flies representing the major groups of Hawaiian Drosophila are used to clarify the relationships of these groups, among themselves and with mainland Drosophila. The topology of the tree derived from these sequences agrees with karyotypic and morphological data but disagrees, in part, with the results of an earlier study that used immunological comparisons between variants of a larval hemolymph protein. A time scale, derived from a comparison of closely related Hawaiian Drosophila species, provides divergence-time estimates that are substantially more recent than those obtained from the immunological studies, although they are still within the bounds set by fossil and biogeographical evidence. The two major lineages of Hawaiian Drosophila, the scaptomyzoids and the drosophiloids, are shown to be widely separated from one another. The scaptomyzoids appear to have diverged early in the history of the subgenus Drosophila, greater than 25 Mya. While hundreds of scaptomyzoid species are found in the Hawaiian archipelago, many fewer are found elsewhere around the world, suggesting that they could have originated outside Hawaii. The drosophiloid lineage is strictly endemic to Hawaii and originated little more than 10 Mya, according to the alcohol dehydrogenase molecular clock. Thus, Drosophila apparently inhabited the Hawaiian archipelago (greater than or equal to 5 Myr before the emergence of the oldest existing high island, Kauai, 5 Mya.

Identification of adaptive changes in an evolving population of Escherichia coli: the role of changes with regulatory and highly pleiotropic effects.

Abstract: A population of Escherichia coli initiated with a single clone developed extensive morphological and physiological polymorphism after being maintained for 773 generations in glucose-limited continuous culture. To understand the mechanisms of adaptation to this environment, total protein patterns of four adaptive clones and of the parent strains were examined by two-dimensional gel electrophoresis. Approximately 20% of the proteins (approximately 160 in absolute numbers) showed significantly different levels of expression in pairwise comparisons of parent and adapted clones. The extent of these changes points to the importance of mutations with regulatory and/or highly pleiotropic effects in the adaptive process. The four evolved clones all expressed fewer proteins than did the parent strain, supporting the hypothesis of energy conservation during evolutionary change. Forty-two proteins that could be assigned to known cellular functions were identified. The changes in some of them indicated that the evolved clones developed different adaptive mechanisms to glucose-limited environment. Changes were observed in the expression levels of proteins associated with translation, membrane composition, shock response, and active transport. A fraction of the changes could not be either explained or predicted from a consideration of the nature of the environment in which the clones evolved.

Relative efficiencies of the maximum-parsimony and distance-matrix methods of phylogeny construction for restriction data.

Abstract: The relative efficiencies of the maximum-parsimony (MP), UPGMA, and neighbor-joining (NJ) methods in obtaining the correct tree (topology) for restriction-site and restriction-fragment data were studied by computer simulation. In this simulation, six DNA sequences of 16,000 nucleotides were assumed to evolve following a given model tree. The recognition sequences of 20 different six-base restriction enzymes were used to identify the restriction sites of the DNA sequences generated. The restriction-site data and restriction-fragment data thus obtained were used to reconstruct a phylogenetic tree, and the tree obtained was compared with the model tree. This process was repeated 300 times. The results obtained indicate that when the rate of nucleotide substitution is constant the probability of obtaining the correct tree (Pc) is generally higher in the NJ method than in the MP method. However, if we use the average topological deviation from the model tree (dT) as the criterion of comparison, the NJ and MP methods are nearly equally efficient. When the rate of nucleotide substitution varies with evolutionary lineage, the NJ method is better than the MP method, whether Pc or dT is used as the criterion of comparison. With 500 nucleotides and when the number of nucleotide substitutions per site was very small, restriction-site data were, contrary to our expectation, more useful than sequence data. Restriction-fragment data were less useful than restriction-site data, except when the sequence divergence was very small. UPGMA seems to be useful only when the rate of nucleotide substitution is constant and sequence divergence is high.