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Showing papers in "Molecular Biology and Evolution in 1987"


Journal ArticleDOI
TL;DR: The neighbor-joining method and Sattath and Tversky's method are shown to be generally better than the other methods for reconstructing phylogenetic trees from evolutionary distance data.
Abstract: A new method called the neighbor-joining method is proposed for reconstructing phylogenetic trees from evolutionary distance data. The principle of this method is to find pairs of operational taxonomic units (OTUs [= neighbors]) that minimize the total branch length at each stage of clustering of OTUs starting with a starlike tree. The branch lengths as well as the topology of a parsimonious tree can quickly be obtained by using this method. Using computer simulation, we studied the efficiency of this method in obtaining the correct unrooted tree in comparison with that of five other tree-making methods: the unweighted pair group method of analysis, Farris's method, Sattath and Tversky's method, Li's method, and Tateno et al.'s modified Farris method. The new, neighbor-joining method and Sattath and Tversky's method are shown to be generally better than the other methods.

57,055 citations


Journal ArticleDOI
TL;DR: 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.
Abstract: 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.

2,312 citations


Journal ArticleDOI
TL;DR: The method of evolutionary parsimony accurately predicts the tree, even when substitution rates differ greatly in neighboring peripheral branches (conditions under which parsimony will consistently fail), as the number of substitutions in peripheral branches becomes fewer, the parsimony and the evolutionary-parsimony solutions converge.
Abstract: The method of evolutionary parsimony-or operator invariants-is a technique of nucleic acid sequence analysis related to parsimony analysis and explicitly designed for determining evolutionary relationships among four distantly related taxa. The method is independent of substitution rates because it is derived from consideration of the group properties of substitution operators rather than from an analysis of the probabilities of substitution in branches of a tree. In both parsimony and evolutionary parsimony, three patterns of nucleotide substitution are associated one-to-one with the three topologically linked trees for four taxa. In evolutionary parsimony, the three quantities are operator invariants. These invariants are the remnants of substitutions that have occurred in the interior branch of the tree and are analogous to the substitutions assigned to the central branch by parsimony. The two invariants associated with the incorrect trees must equal zero (statistically), whereas only the correct tree can have a nonzero invariant. The x*-test is used to ascertain the nonzero invariant and the statist&thy favored tree. Examples, obtained using data calculated with evolutionary rates and branchings designed to camouflage the true tree, show that the method accurately predicts the tree, even when substitution rates differ greatly in neighboring peripheral branches (conditions under which parsimony will consistently fail). As the number of substitutions in peripheral branches becomes fewer, the parsimony and the evolutionary-parsimony solutions converge. The method is robust and easy to use.

403 citations


Journal ArticleDOI
TL;DR: It is concluded that both the rate of synonymous substitution and the degree of codon usage bias largely reflect the intensity of selection at the translational level.
Abstract: Genes sequences from Escherichia coli, Salmonella typhimurium, and other members of the Enterobacteriaceae show a negative correlation between the degree of synonymous-codon usage bias and the rate of nucleotide substitution at synonymous sites. In particular, very highly expressed genes have very biased codon usage and accumulate synonymous substitutions very slowly. In contrast, there is little correlation between the degree of codon bias and the rate of protein evolution. It is concluded that both the rate of synonymous substitution and the degree of codon usage bias largely reflect the intensity of selection at the translational level. Because of the high variability among genes in rates of synonymous substitution, separate molecular clocks of synonymous substitution might be required for different genes.

349 citations


Journal ArticleDOI
H Hori1, S Osawa
TL;DR: A phylogenetic tree of most of the major groups of organisms has been constructed from the 352 5S ribosomal RNA sequences now available, and suggests that there are several majorgroups of eubacteria that diverged during the early stages of their evolution.
Abstract: A phylogenetic tree of most of the major groups of organisms has been constructed from the 352 5S ribosomal RNA sequences now available. The tree suggests that there are several major groups of eubacteria that diverged during the early stages of their evolution. Metabacteria (= archaebacteria) and eukaryotes separated after the emergence of eubacteria. Among eukaryotes, red algae emerged first; and, later, thraustochytrids (a Proctista group), ascomycetes (yeast), green plants (green algae and land plants), "yellow algae" (brown algae, diatoms, and chrysophyte algae), basidiomycetes (mushrooms and rusts), slime- and water molds, various protozoans, and animals emerged, approximately in that order. Three major types of photosynthetic eukaryotes--i.e., red algae (= Chlorophyll a group), green plants (Chl. a + b group) and yellow algae (Chl. a + c)--are remotely related to one another. Other photosynthetic unicellular protozoans--such as Cyanophora (Chl. a), Euglenophyta (Chl. a + b), Cryptophyta (Chl. a + c), and Dinophyta (Chl. a + c)--seem to have separated shortly after the emergence of the yellow algae.

261 citations


Journal ArticleDOI
TL;DR: Thirty-four cytochrome P-450 sequences from one bacterial and six vertebrate species have been aligned with the aid of a computer alignment algorithm and it is noted that an apparent increase in the rate of cyto Chrome P- 450 evolution is noted between the bird-mammal divergence and the mammalian radiation.
Abstract: Thirty-four cytochrome P-450 sequences from one bacterial and six vertebrate species have been aligned with the aid of a computer alignment algorithm. Phylogenetic trees were constructed using the unweighted-pair-group and neighbor-joining methods. The two trees differed at only a single branch point near the base of the tree. The cytochrome P-450 superfamily of proteins clustered into eight families and contained 16 gene-duplication events. The first gene duplication occurred approximately 1,360 Myr before the present (Mybp) and gave rise to cytochrome P-450s found in two different cellular organelles, the mitochondria and the endoplasmic reticulum. Both groups utilize cholesterol or its metabolites as substrates, implying that cholesterol existed greater than 1,360 Mybp. The fourth gene duplication (approximately 900 Mybp) gave rise to the drug-metabolizing P-450s. These proteins aid in the detoxification of foreign chemicals, as opposed to the metabolism of endogenous compounds. The importance of the capacity to metabolize drugs is reflected in 11 further gene duplications occurring in this lineage. The first occurred approximately 800 Mybp and gave rise to the two major P-450 families, the phenobarbital and 3-methylcholanthrene families. An apparent increase in the rate of cytochrome P-450 evolution is noted between the bird-mammal divergence (300 Mybp) and the mammalian radiation (75 Mybp).

206 citations


Journal ArticleDOI
TL;DR: Analysis of mitochondrial DNA restriction-site variation within and between populations of fall-adult field crickets across a narrow hybrid zone in Connecticut reveals two distinct mtDNA lineages, each consisting of a single common genotype together with one or more rare genotypes.
Abstract: We have examined mitochondrial DNA (mtDNA) restriction-site variation within and between populations of fall-adult field crickets across a narrow hybrid zone in Connecticut. Our analysis reveals two distinct mtDNA lineages, each consisting of a single common genotype together with one or more rare genotypes. Outside the hybrid zone, the association between mtDNA genotype and species designation is nearly perfect. The A lineage corresponds to Gryllus pennsylvanicus and the B lineage to G. firmus. However, two G. firmus individuals from a coastal Connecticut population carry the A mtDNA genotype. Within the hybrid zone, the association between morphological characters, enzyme genotypes, and mtDNA genotypes breaks down to varying degrees. We compare patterns of introgression for these three types of markers. Previous authors have suggested that the behavior of mtDNA in hybrid zones may be different from that of nuclear-gene markers. We argue that differences in behavior are probably quantitative, not qualitative, and depend on the genetic architecture of speciation. We also document patterns of mtDNA length variation and associated heteroplasmy in both the A and B mtDNA lineages. The existence of identical size classes in both lineages suggests that the mutation rate for generating length variants is high. Therefore, genome size may not be a reliable marker of common ancestry.

153 citations


Journal ArticleDOI
TL;DR: Compared sequences of the Alu family of repeated DNA elements found within the human thymidine kinase and beta-tubulin genes were compared and confirmed the species-specific differences between human and the prosimian Galago crassicaudatus Alufamily members.
Abstract: Thirteen and 10 sequences of the Alu family of repeated DNA elements found within the human thymidine kinase and beta-tubulin genes, respectively, were compared. These genes have approximately five times the expected density of Alu family members. The consensus sequence that could be drawn from these 23 Alu family members would differ slightly from others drawn from random Alu family sequences but only at very heterogeneous positions. The different Alu family members do show different pairwise percentage identities, with approximately 15% (7 of 48 Alu family members analyzed) of them clearly representing a separate subfamily of sequences. This analysis also confirms the species-specific differences between human and the prosimian Galago crassicaudatus Alu family members. These data are consistent with both the origin of these sequences in primates less than 65-70 Myr ago and amplification since that time to their present 500,000 copies. The data do not show any special relationships among densely clustered Alu family members.

136 citations


Journal ArticleDOI
TL;DR: The results agree with previous reports of accelerated DNA evolution in muroid rodents and extend the DNA-DNA hybridization data set of Brownell.
Abstract: Single-copy nuclear DNAs (scnDNAs) of eight species of arvicoline and six species of murine rodents were compared using DNA-DNA hybridization. The branching pattern derived from the DNA comparisons is congruent with the fossil evidence and supported by comparative biochemical, chromosomal, and morphological studies. The recently improved fossil record for these lineages provides seven approximate divergence dates, which were used to calibrate the DNA-hybridization data. The average rate of scnDNA divergence was estimated as 2.5%/Myr. This is approximately 10 times the rate in the hominoid primates. These results agree with previous reports of accelerated DNA evolution in muroid rodents and extend the DNA-DNA hybridization data set of Brownell.

122 citations


Journal ArticleDOI
TL;DR: Comparison of the bovine and rat beta-casein coding sequences shows that their divergence has involved a high rate of nucleotide substitution but that no major insertions or deletions of sequence have occurred.
Abstract: The nucleotide sequences corresponding to bovine alpha S2- and beta-casein mRNAs have been determined by cDNA analysis. Both sequences appear to be complete at their 5' ends. The nucleotide sequence of alpha S2-casein, when compared with the corresponding cavine A sequence, helps to define the boundaries of a large amino acid repeat (approximately 80 residues) whereas comparisons with the nucleotide sequences of rat gamma- and mouse epsilon-casein mRNAs also reveal extensive sequence similarities. An alignment of these four sequences shows that the divergence of their translated regions has been characterized by the duplication and deletion of discrete segments of sequence that probably correspond to exons. A high degree of nucleotide substitution is also found when the four sequences are compared, except for well-conserved leader-peptide and phosphorylation-site sequences and, to a lesser extent, the 5'-untranslated regions. Similar comparison of the bovine and rat beta-caseins shows that their divergence has involved a high rate of nucleotide substitution but that no major insertions or deletions of sequence have occurred. The several splice sites that have veen defined in the rat beta-casein gene are likely to have been conserved in the bovine. The contrasting evolutionary histories of the alpha- and beta-casein coding sequences correlate with the distinctive functions of these proteins in the casein micelle system in milk.

103 citations


Journal ArticleDOI
TL;DR: The consistency index--the number of character states less the number of characters in a data set, divided by the total number of changes in the character states on a cladogram--was used to examine the relative resolving powers of recently published morphological and molecular-sequence data.
Abstract: To a large extent, the mutual affinities of the mammalian orders continue to puzzle systematists, even though comparative anatomy and amino acid sequencing offer a massive data base from which these relationships could potentially be adduced. In the present paper the consistency index--the number of character states less the number of characters in a data set, divided by the total number of changes in the character states on a cladogram--was used to examine the relative resolving powers of recently published morphological and molecular-sequence data. Consistency indices were calculated for previously published alpha crystallin A chain and myoglobin amino acid-sequence cladograms and for four original amino acid-sequence cladograms (alpha crystallin A, myoglobin, and alpha and beta hemoglobin); these were found to be comparable to the consistency indices of morphologically based cladograms. Qualitative comparisons between the morphologically based and molecularly based trees were also made; only moderate congruence between the two was observed. Moreover, there was a general lack of congruence between the cladograms specified by each of the four proteins. Amino acid-sequence and morphological data agreed on the placement of edentates as an early eutherian offshoot and on the grouping of hyracoids, proboscideans, and sirenians. Otherwise there was only limited congruence: morphology strongly supported the grouping of lagomorphs and rodents and the alliance of pholidotes and edentates, but sequence analyses did not. The placement of tubulidentates differed widely among proteins. Morphology indicated the close association of sirenians with proboscideans; proteins suggested a pairing of sirenians with hyracoids. Sequence data did not identify many (morphologically well-diagnosed) orders as monophyletic (e.g., Lagomorpha).(ABSTRACT TRUNCATED AT 250 WORDS)

Journal ArticleDOI
TL;DR: Thirty-one bacterial type ferredoxins were examined by means of the parsimony method for their phylogenetic implications, showing reasonable relationships in that photosynthetic, thermophilic, and desulfovibrio groups are identifiable; but a number of interesting anomalies occur.
Abstract: Thirty-one bacterial type ferredoxins were examined by means of the parsimony method for their phylogenetic implications. The results show reasonable relationships in that photosynthetic, thermophilic, and desulfovibrio groups are identifiable; but a number of interesting anomalies occur. These include a methanogen sequence that clusters among the desulfovibrios. There are several differences from the phylogeny of Woese. At least two duplications producing paralogous genes are demonstrated, plus the probable existence of two more. The partial internal gene duplication that doubled the length of ferredoxin is confirmed by showing that the probability of the two ancestrally reconstructed halves possessing that much similarity by chance is 10(-7). Howard and co-workers proposed that the two halves of the Azotobacter vinelandii are reversed relative to most other sequences. A phylogeny, drawn with the halves of the azotobacter sequence (and its relatives) reversed produced a tree that had only three less nucleotide substitutions than did the tree without their halves reversed. This plus other evidence suggests that the significantly greater similarity observed across rather than within the halves is more likely the result of convergence.

Journal ArticleDOI
TL;DR: Diversity values indicate either that the rate of rosella genome evolution is 2-3 orders of magnitude below the rate reported for primates or that the effective sizes of therosella populations are 2- 3 orders of orders below the sizes estimated on the basis of ecological methods.
Abstract: .We used six restriction endonucleases (D&I, HinfI, HpaII, MM, TagI, and Zmo37), each with a unique four-base recognition site, to digest 26 mitochondrial genomes from six Platycercus species in an investigation of the systematics of this speciose and variable Australian genus. The resulting fragments were end labeled and separated by means of polyacrylamide-gel electrophoresis. The number of substitutions per nucleotide site between each of the genomes was estimated on the basis of the distribution of fragments between samples by means of the method of Nei and Li. These pairwise distances were used to construct evolutionary trees either by assuming an evolutionary clock or by allowing the branch lengths to vary independently. The presence or absence of each restriction fragment was also scored and used as characters in Wagner parsimony analysis. In general, the phylogenies produced from mitochondrial genome diversity mirror the current classification of the genus, except for P. icterotis, which is not clustered with either of the superspecies of Platycercus and, as such, should probably be placed in a third group. To confirm that the family of parrots to which Platycercus belongs has a conservative nuclear genome, Nei’s genetic distance between and within Platycercus and other related species was estimated by means of cellogel electrophoresis of liver isozymes. Of the 26 Platycercus mitochondrial genomes studied, 23 different haplotypes were identified according to the limits of resolution of the technique. The mean interspecific mitochondrial genome diversity was 0.0457, and the intraspecific genome diversity varied between 0.003 1 (for P. caledonicus) and 0.0 142 (for P. eximius). These diversity values indicate either that the rate of rosella genome evolution is 2-3 orders of magnitude below the rate reported for primates or that the effective sizes of the rosella populations are 2-3 orders of magnitude below the sizes estimated on the basis of ecological methods.

Journal ArticleDOI
TL;DR: In this article, the relative merits of four different tree-making methods in obtaining the correct topology were studied by using computer simulation, including unweighted pair-group method with arithmetic mean (UPGMA), Fitch and Margoliash's (FM), thd distance Wagner (DW) method, and Tateno et al.'s modified Farris (MF) method.
Abstract: The relative merits of four different tree-making methods in obtaining the correct topology were studied by using computer simulation. The methods studied were the unweighted pair-group method with arithmetic mean (UPGMA), Fitch and Margoliash's (FM) method, thd distance Wagner (DW) method, and Tateno et al.'s modified Farris (MF) method. An ancestral DNA sequence was assumed to evolve into eight sequences following a given model tree. Both constant and varying rates of nucleotide substitution were considered. Once the DNA sequences for the eight extant species were obtained, phylogenetic trees were constructed by using corrected (d) and uncorrected (p) nucleotide substitutions per site. The topologies of the trees obtained were then compared with that of the model tree. The results obtained can be summarized as follows: (1) The probability of obtaining the correct rooted or unrooted tree is low unless a large number of nucleotide differences exists between different sequences. (2) When the number of nucleotide substitutions per sequence is small or moderately large, the FM, DW, and MF methods show a better performance than UPGMA in recovering the correct topology. The former group of methods is particularly good for obtaining the correct unrooted tree. (3) When the number of substitutions per sequence is large, UPGMA is at least as good as the other methods, particularly for obtaining the correct rooted tree. (4) When the rate of nucleotide substitution varies with evolutionary lineage, the FM, DW, and MF methods show a better performance in obtaining the correct topology than UPGMA, except when a rooted tree is to be produced from data with a large number of nucleotide substitutions per sequence.(ABSTRACT TRUNCATED AT 250 WORDS)

Journal ArticleDOI
TL;DR: DNA-DNA hybridization was used to discover the extent of single-copy DNA similarity among 13 species of herons and one ibis, and the existence of different rates of DNA evolution in different heron lineages was established.
Abstract: DNA-DNA hybridization was used to discover the extent of single-copy DNA similarity among 13 species of herons and one ibis. Genetic distances among taxa were summarized as Tm values in a folded matrix. From this matrix, trees with the same branching pattern were constructed by least squares under one of two assumptions: (1) that sister branches are equal in length and (2) that sister branches are not necessarily equal in length. The residual sums of squares of these trees were compared by F-test to see whether the branches of the tree built under assumption (2) fit the matrix data significantly better than those of the tree built under assumption (1). By this method the existence of different rates of DNA evolution in different heron lineages was established. Bittern single-copy DNA has evolved at a rate approximately 25% faster, and boat-billed heron (Cochearius) and rufescent tiger heron (Tigrisoma lineatum) DNA has evolved approximately 19% slower, than that of day and night herons. It appears that the differences in rates of DNA evolution may increase proportionally with genealogical distance.

Journal ArticleDOI
TL;DR: In two wild mice of the European subspecies Mus mus musculus the authors found a mitochondrial mutant with a very large deletion in a coding region, which represents 78%-79% of the mtDNA molecules in preparations from each animal.
Abstract: Polymorphism of animal mitochondrial DNA (mtDNA) has been shown to involve point mutations and limited length variations affecting essentially noncoding regions. In two wild mice of the European subspecies A4us mus musculus we found a mitochondrial mutant with a very large deletion in a coding region. The deletion is 5 kbp long (3 1% of the mitochondrial chromosome) and encompasses six tRNA genes and seven protein genes. The two mice were heteroplasmic: they contained a mixture of normal mtDNA and the deletion mutant. Although the latter is functionally defective, it represents 78%79% of the mtDNA molecules in our preparations from each animal.

Journal ArticleDOI
TL;DR: A genomic library of partially EcoRI-digested DNA from the lesser snow goose was constructed in the phage vector Charon 4 and RFLPs identified are valuable DNA markers that can be used for the examination of DNA variation, relatedness, and genetic distance and assessing paternity and maternity.
Abstract: A genomic library of partially EcoRI-digested DNA from the lesser snow goose, Anser caerulescens caerulescens, was constructed in the phage vector Charon 4. Phage containing only unique sequences were identified by screening plaques with 32P-labeled genomic DNA. Restriction-fragment-length polymorphisms (RFLPs) were identified by probing DNA from 11-13 male birds from the breeding colony at La Perouse Bay. Of the 17 probes examined, all detected RFLPs with at least one of EcoRi, HindIII, Msp1, and Taq1. Several of them identified highly variable regions with multiple alleles. These RFLPs are valuable DNA markers that can be used for (1) the examination of DNA variation, relatedness, and genetic distance and (2) assessing paternity and maternity. These data suggest that there are higher levels of variation of DNA sequence in birds than had previously been thought to exist.

Journal ArticleDOI
TL;DR: In this article, the authors cloned and sequenced a 975-bp segment of mtDNA from Drosophila melanogaster, D. simulans, and D. mauritiana containing the genes for three transfer RNAs and parts of two protein-coding genes.
Abstract: To study the rate and pattern of nucleotide substitution in mitochondrial DNA (mtDNA), we cloned and sequenced a 975-bp segment of mtDNA from Drosophila melanogaster, D. simulans, and D. mauritiana containing the genes for three transfer RNAs and parts of two protein-coding genes, ND2 and COI. Statistical analysis of synonymous substitutions revealed a predominance of transitions over transversions among the three species, a finding differing from previous results obtained from a comparison of D. melanogaster and D. yakuba. The number of transitions observed was nearly the same for each species comparison, including D. yakuba, despite the differences in divergence times. However, transversions seemed to increase steadily with increasing divergence time. By contrast, nonsynonymous substitutions in the ND2 gene showed a predominance of transversions over transitions. Most transversions were between A and T and seemed to be due to some kind of mutational bias to which the A+T-rich mtDNA of Drosophila species may be subject. The overall rate of nucleotide substitution in Drosophila mtDNA appears to be slightly faster (- 1.4 times) than that of the Adh gene. This contrasts with the result obtained for mammals, in which the mtDNA evolves - 10 times faster than single-copy nuclear DNA. We have also shown that the start codon of the CO1 gene is GTGA in D. simulans and GTAA in D. mauritiana. These codons are different from that of D. melanogaster (ATAA).

Journal ArticleDOI
TL;DR: The present results demonstrate that paternal leakage of mtDNA must be extremely low or absent in these fishes and provide a foundation for estimation of both origins and phylogeny of the unisexual forms.
Abstract: A genetic survey of mitochondrial DNA (mtDNA) in a hybridogenetic complex of fishes (genus Poeciliopsis) was conducted to assess the possibility of low-level paternal transmission of mtDNA to progeny. In this reproductive system, females of the unisexual hybrid biotype between P. monacha and P. lucida effectively participate in a perpetual backcross to males of a sexual species, P. lucida. As judged on the basis of numerous restriction digests, the mtDNAs of the bisexual parental species (P. monacha and P. lucida) were highly distinct, yet the mtDNA of the natural hybridogens was not different from that of P. monacha from the same river system. Since the hybridogens are probably thousands of generations old, the present results demonstrate that paternal leakage of mtDNA must be extremely low or absent in these fishes. MtDNA genotypic differences among hybridogenetic strains were also present and corresponded to geographic locale. These differences provide a foundation for estimation of both origins and phylogeny of the unisexual forms.

Journal ArticleDOI
TL;DR: A Wagner parsimony tree reveals that mutationally close variants show geographical clumping, suggesting local differentiation of mtDNA in populations, and suggest a common origin of D. melanogaster populations in North America.
Abstract: The understanding of the genetic structure of a species can be improved by considering together data from different types of genetic markers. In the past, a number of worldwide populations of Drosophila melanogaster have been extensively studied for several such markers, including allozymes, chromosomal inversions, and quantitative characters. Here we present results from a study of restriction-fragment-length polymorphisms of mitochondrial DNA (mtDNA) in 92 isofemale lines from many of the same geographic populations of D. melanogaster. Eleven restriction enzymes were used, of which four revealed restriction-site polymorphism. A total of 24 different haplotypes were observed, of which 18 were unique to single populations. In many populations, the unique haplotypes have reached high frequency without being observed in neighboring populations. A Wagner parsimony tree reveals that mutationally close variants show geographical clumping, suggesting local differentiation of mtDNA in populations. The Old-World and the New-World populations are differentiated, with the predominant Old-World haplotype being virtually absent from the New World. These results contrast with those for the nuclear genes, in which many loci show parallel clines in different continents, and suggest a common origin of D. melanogaster populations in North America.

Journal ArticleDOI
TL;DR: The extent to which highly expressed protein genes can modulate base usage at two successive codon positions III, given the constraints on codon usage and protein sequence that act on them, was quantified and demonstrates that the above-mentioned favored patterns are not a characteristic of weakly expressed genes but occur in all genes in which codon context can vary appreciably.
Abstract: This investigation of the codon context of enterobacteria, plasmid, and phage protein genes was based on a search for correlations between the presence of one base type at codon position III and the presence of another base type at some other position in adjacent codons. Enterobacterial genes were compared with eukaryotic sequences for codon context effects. In enterobacterial genes, base usage at codon position III is correlated with the third position of the upstream adjacent codon and with all three positions of the downstream codon. Plasmid genes are free of context biases. Phage genes are heterogeneous: MS2 codons have no biased context, whereas lambda genes partly follow the trends of the host bacterium, and T7 genes have biased codon contexts that differ from those of the host. It has been reported that two successive third-codon positions tend to be occupied by two purines or two pyrimidines in Escherichia coli genes of low expression level. Here, the extent to which highly expressed protein genes can modulate base usage at two successive codon positions III, given the constraints on codon usage and protein sequence that act on them, was quantified. This demonstrates that the above-mentioned favored patterns are not a characteristic of weakly expressed genes but occur in all genes in which codon context can vary appreciably. The correlation between successive third-codon positions is a distinct feature of enterobacteria and of some phages, one that may result from adaptation of gene structure to translational efficiency. Conversely, codon context in yeast and human genes is biased--but for reasons unrelated to translation.

Journal ArticleDOI
TL;DR: Variation of ribosomal DNA (rDNA) was analyzed within and among individuals, populations, and subspecies of Phlox divaricata, a widespread woodland perennial of the midwestern United States, and on the basis of morphological criteria, ssp.
Abstract: Variation of ribosomal DNA (rDNA) was analyzed within and among individuals, populations, and subspecies of Phlox divaricata. Phlox divaricata is a widespread woodland perennial of the midwestern United States. It consists of a large eastern subspecies, ssp. divaricata, and a more restricted western subspecies, ssp. Zaphami. As in other plant species, individual plants may contain as many as five types of rDNA length variants. rDNA repeat-type frequencies were determined within eight populations, four of each subspecies. There is clear differentiation among populations of a subspecies, and there also are differences between the two subspecies in both the number and types of rDNA repeats. Subspecies divaricata has more variation than does ssp. Zaphami, both in the number of rDNA repeat types (nine vs. eight, respectively) and in the average number of repeat types within an individual (2.47 vs. 1.52, respectively). rDNA diversity was analyzed using the Shannon diversity index. Of the total diversity in the species, 6 1% is found among individuals of a population, 2 1% is found within subspecies among populations, and 18% is found between the two subspecies. On the basis of morphological criteria, ssp. Zamphami is considered derived from ssp. divaricata. The rDNA data are not completely consistent with this interpretation. The diversity of rDNA found within ssp. Zaphami is less than that in ssp. divaricata, as would be expected for a derived taxon. On the other hand, laphami has three repeat types not present in divaricata.

Journal ArticleDOI
TL;DR: The capacity to form zinc-binding hexamers was lost once in the ancestor of the hystricomorph rodents, followed by moderately increased evolutionary rates in the lineages to African porcupine and chinchilla but highly increased rates in at least three independent lines to other taxa of this suborder.
Abstract: Several trees of amino acid sequences of rodent insulins were derived with the maximum-parsimony procedure. Possible orthologous and paralogous relationships were investigated. Except for a recent gene duplication in the ancestor of rat and mouse, there are no strong arguments for other paralogous relationships. Therefore, a tree in agreement with other biological data is the most reasonable one. According to this tree, the capacity to form zinc-binding hexamers was lost once in the ancestor of the hystricomorph rodents, followed by moderately increased evolutionary rates in the lineages to African porcupine and chinchilla but highly increased rates in at least three independent lines to other taxa of this suborder: guinea pig, cuis, and Octodontoidea (coypu and casiragua).

Journal ArticleDOI
TL;DR: Mouse t haplotypes were found to share restriction fragments and polypeptide spots that are absent in mice carrying wild-type forms of chromosome 17, providing the first direct evidence that all of the known t haplotype are descendents of a single ancestral chromosome.
Abstract: Mouse t haplotypes are variant forms of chromosome 17 that exist at high frequencies in worldwide populations of two species of commensal mice. To determine both the relationship of t haplotypes to each other and the species within which they exist, 35 representative t haplotypes were analyzed by means of 10 independent molecular probes, including five DNA clones and five polypeptide spots identified by means of two-dimensional gel electrophoresis. All of the tested haplotypes were found to share restriction fragments and polypeptide spots that are absent in mice carrying wild-type forms of chromosome 17. This observation provides the first direct evidence that all of the known t haplotypes are descendents of a single ancestral chromosome. The absence of variation among t haplotypes could mean that this ancestral chromosome existed relatively recently, in which case it would be necessary to postulate introgressions of t haplotypes across species lines to explain their presence in both Mus domesticus and M. musculus. Alternatively, it is possible that the ancestral chromosome existed prior to the split between M. domesticus and M. musculus and that, by chance, our probes fail to detect polymorphisms that exist among the t haplotypes. A further result of our analysis is the characterization of a partial t haplotype in a wild population of Israeli mice.

Journal ArticleDOI
TL;DR: High haplotype diversity and low linkage disequilibrium suggest that the polymorphic restriction sites around Adh have segregated almost randomly during the history of this D. pseudoobscura population and that the effects of inbreeding and periodic reduction of population size have been negligible.
Abstract: A 32-kb region including the Adh structural gene was analyzed with six restriction endonucleases in 20 lines of Drosophila pseudoobscura, one line of D. persimilis, and one line of D. miranda. Nineteen lines of D. pseudoobscura from a single population were estimated to be polymorphic at one in every 15 nucleotides (p = 0.066). Any two homologous chromosomes chosen at random were heterozygous at one in 48 (H = 0.021) nucleotides. Two small insertions of 50 and 200 bp were found approximately 7 kb upstream from the Adh transcript. High haplotype diversity and low linkage disequilibrium suggest that the polymorphic restriction sites around Adh have segregated almost randomly during the history of this D. pseudoobscura population and that the effects of inbreeding and periodic reduction of population size have been negligible. The restriction-endonuclease analysis for the Adh region of D. pseudoobscura stands in sharp contrast to the strong linkage disequilibrium, high levels of insertion/deletion polymorphism, and lower estimates of nucleotide polymorphism found for this same region in D. melanogaster. A phylogeny for the Adh haplotypes is consistent with an early divergence of D. miranda, while D. persimilis falls within the cluster of D. pseudoobscura haplotypes.

Journal ArticleDOI
TL;DR: Each member of the central population in the four chromosomal groups of mole rats has a characteristic combination of the NTS types, suggesting that the karyotype groups were genetically diverged.
Abstract: Genetic differentiation of ribosomal DNA (rDNA) nontranscribed-spacer (NTS) polymorphism was analyzed in 50 individuals from 13 populations among the four chromosomal species (2n = 52, 2n = 54, 2n = 58, and 2n = 60) of subterranean mole rats of the Spalax ehrenbergi complex in Israel. Southern blot analysis with a mouse rDNA probe and two restriction enzymes, EcoRI and BamHI, revealed various sizes of major restriction fragments. The assumption that this variation is due to length polymorphism of NTS DNA was supported by the construction of restriction-site maps. On the basis of the EcoRI and BamHi fragment lengths, we could characterize the major types of NTS rDNA repeating units in each individual. Each member of the central population in the four chromosomal groups of mole rats has a characteristic combination of the NTS types, suggesting that the karyotype groups were genetically diverged. Some near-hybrid-zone populations reflect similarities with the rDNA spectra of a neighbor chromosomal group. This might have resulted from gene flow across the hybrid zones.

Journal ArticleDOI
TL;DR: In contrast to earlier reports of the variation in other regions of the Drosophila melanogaster genome, there seemed to be less linkage disequilibrium and perhaps more nucleotide polymorphism.
Abstract: Restriction-map variation among 38 chromosomes collected from natural populations from around the world was surveyed using probes for a 45-kb region containing and surrounding the white locus. Insertion and deletion variation was more common in the regions flanking the white transcriptional unit, and restriction-site polymorphism appears to be most common 5' of the white locus. The frequencies of individual large insertions (suspected transposable elements) were low, although 37% of the chromosomes had at least one insertion in the white-locus region. The estimated level of nucleotide heterozygosity over the whole region was 0.012. There was little linkage disequilibrium among the polymorphic sites. In contrast to earlier reports of the variation in other regions of the Drosophila melanogaster genome, there seemed to be less linkage disequilibrium and perhaps more nucleotide polymorphism.

Journal ArticleDOI
TL;DR: Pseudogenes behave as if they are in a low -G+C, CG-deficient part of the genome, although the genes from which they arose are variable in these respects, and variation is evolutionarily conserved and correlated with the G+C content.
Abstract: DNA sequences of 56 human genes for which information on both exons and introns was available were examined. The variance in G+C content among genes is estimated and shown to be substantial. There is a high correlation in G+C content between exons and introns within the same gene. The dinucleotide frequencies of introns are similar to those of intergenic spacer regions and are in reasonable agreement with predictions from substitution rates estimated from pseudogenes, except that the observed deficiency of TA doublets is not predicted. Duplicated bases also show a frequency greater than the expectation under independence. There is marked variability among genes in the frequency of the doublet CG relative to its expectation under independence. This variation is evolutionarily conserved and is correlated with the G+C content. Pseudogenes behave as if they are in a low -G+C, CGdeficient part of the genome, although the genes from which they arose are variable in these respects.

Journal ArticleDOI
TL;DR: Overall intraspecific genetic variation among three independently derived strains that represent three independent genomes is higher than generally is thought to exist but is consistent with growing evidence of extensive DNA diversity within species of invertebrates.
Abstract: Drosophila mercatorurn is a species that can give rise to totally homozygous parthenogenetic strains. Using the technique of DNA-DNA hybridization, we have assessed the overall single-copy DNA differences among three independently derived strains that represent three independent genomes. Among strains, the average difference between homoduplex and heteroduplex median melting temperatures is 1.3 degrees C. This represents > 1.3% base-pair mismatch. Normalized percent of reassociation indicates further genetic differences, probably reflecting insertion/ deletion differences and/or regions of the genome that are highly variable. This overall intraspecific genetic variation is higher than generally is thought to exist but is consistent with growing evidence of extensive DNA diversity within species of invertebrates. High intraspecific DNA variation may be correlated with rapid phyletic rates of evolution. Because of this high level of variation, the technique of DNADNA hybridization may be used to study intraspecific variation in invertebrates but is limited in its usefulness for higher systematic studies.

Journal ArticleDOI
TL;DR: It is concluded that at fourfold-degenerate sites rodent genes have evolved two times faster than human genes, contradictory to the general belief that primates, artiodactyls, and carnivores have been distinct since late in the Mesozoic.
Abstract: In a comparative study of the DNA sequences of a variety of mammalian genes, we concluded that rodents (rat and mouse) have accumulated significantly more nucleotide substitutions than has man since the rodent-primate split (Wu and Li 1985). Easteal ( 1985) challenges our conclusion and maintains that our results are compatible with the rate-constancy hypothesis. We compared the rates of nucleotide substitution in rodents and man using the relative-rate test. For each of the 12 genes considered, we used cow, goat, pig, dog, or rabbit as a reference species. We obtained the results shown in table 1. We assumed that man and rodents are more closely related to each other than either is to the reference species (fig. 1 a). This phylogenetic scheme implies the following approximate numbers of substitutions per fourfold-degenerate site in the three branches of the phylogenetic tree: man, 0.2; rodents, 0.4; reference, 0.2. From these calculations, we concluded that at fourfold-degenerate sites rodent genes have evolved two times faster than human genes. Easteal contends that the alternative explanation shown in figure 1 b is equally plausible and can be taken as evidence that substitutions have occurred at a constant rate in all species. In our paper we stated that our results cannot be explained by this alternative evolutionary scheme. Our reason, not explicitly stated, was that this scheme assumes that the divergence time between man and the reference species is only two-thirds (27’/3) of the divergence time (T) between man and rodents. We point out below two serious difficulties with Easteal’s explanation. First, under Easteal’s evolutionary scheme (fig. 1 b), the rate-constancy hypothesis does not hold for nonsynonymous substitutions. For example, from table 1 we can show that at nondegenerate sites the numbers of substitutions per site are 0.075 for the human branch, 0.075 for the reference branch, and 0.095 for the rodent branch. Therefore, the rates of substitution per nondegenerate site per unit time are 0.0751 (27’/3) = O.l13/Tfor the human branch andO.O95/(T+ T/3) = O.O71/Tfor the rodent branch, the former rate being 1.6 times higher than the latter. Obviously, this is contradictory to Easteal’s contention that our results support the rate-constancy hypothesis. The only way to salvage the rate-constancy hypothesis is to assume that the divergence time between man and the reference species is somewhere between 2T/3 and T. The best choice seems to be 0.8T, under which the rate of substitution per nondegenerate site is 1.2 times higher in man than in rodents while the rate of substitution per fourfold-degenerate site is 1.3 times higher in rodents than in man. But this evolutionary scheme is not compatible with the mammalian fossil record (see below). Second, Easteal’s evolutionary scheme (fig. 1 b) is at variance with the mammalian fossil record. Primates and rodents are thought to have diverged -75 Myr ago. Thus, Easteal’s assumption would imply that primates and artiodactyls (or carnivores) diverged only 50 Myr ago. This is contradictory to the general belief that primates, artiodactyls, and carnivores have been distinct since late in the Mesozoic, i.e., at least