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Showing papers in "Molecular Biology and Evolution in 1988"


Journal ArticleDOI
TL;DR: It is well known that a phylogenetic tree (gene tree) constructed from DNA sequences for a genetic locus does not necessarily agree with the tree that represents the actual evolutionary pathway of the species involved (species tree).
Abstract: It is well known that a phylogenetic tree (gene tree) constructed from DNA sequences for a genetic locus does not necessarily agree with the tree that represents the actual evolutionary pathway of the species involved (species tree). One of the important factors that cause this difference is genetic polymorphism in the ancestral species. Under the assumption of neutral mutations, this problem can be studied by evaluating the probability (P) that a gene tree has the same topology as that of the species tree. When one gene (allele) is used from each of the species involved, the probability can be expressed as a simple function of Ti = ti/(2N), where ti is the evolutionary time measured in generations for the ith internodal branch of the species tree and N is the effective population size. When any of the Ti's is less than 1, the probability P becomes considerably less than 1.0. This probability cannot be substantially increased by increasing the number of alleles sampled from a locus. To increase the probability, one has to use DNA sequences from many different loci that have evolved independently of each other.

1,643 citations


Journal ArticleDOI
TL;DR: The patterns of synonymous codon usage in 91 Drosophila melanogaster genes have been examined, and data discussed are consistent with the effects of translational selection among synonymous codons, as seen in unicellular organisms.
Abstract: The patterns of synonymous codon usage in 91 Drosophila melanogaster genes have been examined. Codon usage varies strikingly among genes. This variation is associated with differences in G+C content at silent sites, but (unlike the situation in mammalian genes) these differences are not correlated with variation in intron base composition and so are not easily explicable in terms of mutational biases. Instead, those genes with high G+C content at silent sites, resulting from a strong "preference" for a particular subset of the codons that are mostly C-ending, appear to be the more highly expressed genes. This suggests that G+C content is reduced in sequences where selective constraints are weaker, as indeed seen in a pseudogene. These and other data discussed are consistent with the effects of translational selection among synonymous codons, as seen in unicellular organisms. The existence of selective constraints on silent substitutions, which may vary in strength among genes, has implications for the use of silent molecular clocks.

547 citations


Journal ArticleDOI
TL;DR: The proof given by Saitou and Nei that the correct tree is recovered if D is treelike is incorrect is supplied, and an alternative formulation that runs in time 0( N3), where N is the number of operational taxonomic units (OTUs) .

481 citations


Journal ArticleDOI
TL;DR: It is shown that unbiased estimates of relatedness cannot be obtained at the individual level without knowledge of the allelic distributions in both the individuals of interest and the base population unless the proportion of shared marker alleles between unrelated individuals is essentially zero.
Abstract: The recent discovery of hypervariable VNTR (variable number of tandem repeat) loci has led to much excitement among population biologists regarding the feasibility of deriving individual estimates of relatedness in field populations by DNA fingerprinting. It is shown that unbiased estimates of relatedness cannot be obtained at the individual level without knowledge of the allelic distributions in both the individuals of interest and the base population unless the proportion of shared marker alleles between unrelated individuals is essentially zero. Since the latter is usually on the order of 0.1-0.5 and since there are enormous practical difficulties in obtaining the former, only an approximate estimator for the relatedness can be given. The bias of this estimator is individual specific and inversely related to the number of marker loci and frequencies of marker alleles. Substantial sampling variance in estimates of relatedness arises from variation in identity by descent within and between loci and, with finite numbers of alleles, from variation in identity in state between genes that are not identical by descent. In the extreme case of 25 assayed loci, each with an effectively infinite number of alleles, the standard error of a relatedness estimate is no less than 14%, 20%, 35%, and 53% of the expectation for full sibs and second-, third-, and fourth-order relationships, respectively. Attempts to ascertain relatedness by means of DNA fingerprinting should proceed with caution.

437 citations


Journal ArticleDOI
Colin Patterson1
TL;DR: There are more kinds of homologous relation between molecular sequences than in morphology, and the terms paraxenology and plerology are proposed for two of these kinds--respectively, the consequence of multiple xenology and of gene conversion.
Abstract: Hypotheses of homology are the basis of comparative morphology and comparative molecular biology. The kinds of homologous and nonhomologous relations in classical and molecular biology are explored through the three tests that may be applied to a hypothesis of homology: congruence, conjunction, and similarity. The same three tests apply in molecular comparisons and in morphology, and in each field they differentiate eight kinds of relation. These various relations are discussed and compared. The unit or standard of comparison differs in morphology and in molecular biology; in morphology it is the adult or life cycle, but with molecules it is the haploid genome. In morphology the congruence test is decisive in separating homology and nonhomology, whereas with molecular sequence data similarity is the decisive test. Consequences of this difference are that the boundary between homology and nonhomology is not the same in molecular biology as in morphology, that homology and synapomorphy can be equated in morphology but not in all molecular comparisons, and that there is no detected molecular equivalent of convergence. Since molecular homology may reflect either species phylogeny or gene phylogeny, there are more kinds of homologous relation between molecular sequences than in morphology. The terms paraxenology and plerology are proposed for two of these kinds--respectively, the consequence of multiple xenology and of gene conversion.

399 citations


Journal ArticleDOI
TL;DR: Detailed analyses reveal, in addition to unequal crossing-over, the involvement of slippage and biased mutation in the evolution of the rDNA multigene family and the molecular coevolution of both expansion segments and the nucleotides involved with compensatory changes required to maintain secondary structures of RNA.
Abstract: In this, the first of three papers, we present the sequence of the ribosomal RNA (rRNA) genes of Drosophila melanogaster. The gene regions of D. melanogaster rDNA encode four individual rRNAs: 18S (1,995 nt), 5.8S (123 nt), 2S (30 nt), and 28S (3,945 nt). The ribosomal DNA (rDNA) repeat of D. melanogaster is AT rich (65.9% overall), with the spacers being particularly AT rich. Analysis of DNA simplicity reveals that, in contrast to the intergenic spacer (IGS) and the external transcribed spacer (ETS), most of the rRNA gene regions have been refractory to the action of slippage-like events, with the exception of the 28S rRNA gene expansion segments. It would seem that the 28S rRNA can accommodate the products of slippage-like events without loss of activity. In the following two papers we analyze the effects of sequence divergence on the evolution of (1) the 28S gene "expansion segments" and (2) the 28S and 18S rRNA secondary structures among eukaryotic species, respectively. Our detailed analyses reveal, in addition to unequal crossing-over, (1) the involvement of slippage and biased mutation in the evolution of the rDNA multigene family and (2) the molecular coevolution of both expansion segments and the nucleotides involved with compensatory changes required to maintain secondary structures of RNA.

338 citations


Journal ArticleDOI
TL;DR: The observed molecular distances among mtDNA lineages were two to three orders of magnitude lower than predicted from census sizes of breeding females, suggesting that rate of mtDNA evolution is decelerated in these species and/or that long-term effective population size is vastly smaller than present-day population size.
Abstract: Using inbreeding theory as applied to neutral alleles inherited maternally, we generate expected probability distributions of times to identity by descent for random pairs of mitochondrial genotypes within a population or within an entire species characterized by high gene flow. For comparisons with these expectations, empirical distributions of times to most recent common ancestry were calculated (by conventional mtDNA clock calibrations) from mtDNA haplotype distances observed within each of three vertebrate species--American eels, hardhead catfish, and redwinged blackbirds. These species were chosen for analysis because census population size in each is currently large and because both genetic and life-history data are consistent with the postulate that historical gene flow within these species has been high. The observed molecular distances among mtDNA lineages were two to three orders of magnitude lower than predicted from census sizes of breeding females, suggesting that rate of mtDNA evolution is decelerated in these species and/or that long-term effective population size is vastly smaller than present-day population size. Several considerations point to the latter possibility as most likely. The genetic structure of any species is greatly influenced by historical demography; even for species that are currently abundant, mtDNA gene lineages appear to have been channeled through fairly small numbers of ancestors.

281 citations


Journal ArticleDOI
TL;DR: The analysis suggests that the AIDS virus had existed in central Africa before 1960 and spread to North America before the mid 1970s, and the result is consistent with the view that AIDS spread from Haiti to the United States.
Abstract: The acquired immune deficiency syndrome (AIDS), caused by a retrovirus called human immunodeficiency virus (HIV), has become a pandemic. A knowledge of the rate of nucleotide substitution in HIV and of the history and pattern of spread of the virus is important for understanding the epidemiology and pathogenesis of AIDS and for developing therapies and vaccine strategies. A new model has been developed and used to estimate the substitution rates in various regions in the HIV genome. The rate of nonsynonymous (amino acid-changing) substitution is lowest in the regions coding for the capsid proteins and the reverse transcriptase, being - 1.7 X 1 OW3 nucleotide substitutions/site/year. The nonsynonymous rate is extremely high ( 14 X 1 Om3) in the hypervariable regions of the envelope gene, suggesting extremely rapid change in viral antigenicity. The nonsynonymous rates in the other coding regions are between 3 X 10m3 and 7 X 10e3. The average synonymous rate for the HIV genome is 10 X 10m3. These rates are lo6 times greater than the rates in DNA genomes and at least as high as the rates in other RNA viruses. Evidence is provided for a case of recombination between different HIV strains. Our analysis suggests that the AIDS virus had existed in central Africa before 1960 and spread to North America before the mid 1970s. The evolutionary relationships among HIV isolates are inferred from nucleotide sequence data, and the result is consistent with the view that AIDS spread from Haiti to the United States.

265 citations


Journal ArticleDOI
TL;DR: Through analysis of chordate, arthropod, and plant 5S ribosomal RNA sequences, it is shown that Darwinian selection operates on these nucleotide sequences to maintain functionally important secondary structure.
Abstract: Ribosomal RNAs have secondary structures that are maintained by internal Watson-Crick pairing. Through analysis of chordate, arthropod, and plant 5S ribosomal RNA sequences, we show that Darwinian selection operates on these nucleotide sequences to maintain functionally important secondary structure. Insect phylogenies based on nucleotide positions involved in pairing and the production of secondary structure are incongruent with those constructed on the basis of positions that are not. Furthermore, phylogeny reconstruction using these nonpairing bases is concordant with other, morphological data.

247 citations


Journal ArticleDOI
TL;DR: The available evidence is consistent with the hypothesis of a worldwide P-element invasion of D. melanogaster during the past 30 years and suggests that the putative invasion of the Americas possibly preceded by approximately a decade that in Europe, Africa, and the rest of the world.
Abstract: Approximately 100 strains derived from natural populations of Drosophila melanogaster were tested for the presence or absence of P-element sequences by using two molecular probes derived from internal regions of a full-sized P element. Strains that had been collected from several continents at varying times during the past 60 years were examined. The oldest available strains, representing most major geographical regions of the world, exhibited no detectable hybridization to the P-element probes. In contrast, all recently collected natural populations that were tested carried P-element sequences. The earliest appearance of P elements occurred in collections made during the 1950s and early 1960s in the Americas and during the late 1960s on other continents. The youngest strains that were completely devoid of P elements originated in populations sampled during the mid-1960s in America, but as late as 1974 in populations from the USSR. There are differences in the patterns of hybridization to the two P-element probes between populations from different geographical regions. These differences are consistent with the varying P-M phenotypic properties of these populations. Taken together with the results of phenotypic tests reported in earlier studies, the available evidence is consistent with the hypothesis of a worldwide P-element invasion of D. melanogaster during the past 30 years and suggests that the putative invasion of the Americas possibly preceded by approximately a decade that in Europe, Africa, and the rest of the world.

236 citations


Journal ArticleDOI
TL;DR: The processes by which compensatory pairs of mutations are generated and spread are discussed, and a model is suggested by which a second mutation is more likely to occur in a unit with a first mutation as such a unit begins to spread through the family and concomitantly through the population.
Abstract: This paper examines the effects of DNA sequence evolution on RNA secondary structures and compensatory mutations. Models of the secondary structures of Drosophila melanogaster 18S ribosomal RNA (rRNA) and of the complex between 2S, 5.8S, and 28S rRNAs have been drawn on the basis of comparative and energetic criteria. The overall AU richness of the D. melanogaster rRNAs allows the resolution of some ambiguities in the structures of both large rRNAs. Comparison of the sequence of expansion segment V2 in D. melanogaster 18S rRNA with the same region in three other Drosophila species and the tsetse fly (Glossina morsitans morsitans) allows us to distinguish between two models for the secondary structure of this region. The secondary structures of the expansion segments of D. melanogaster 28S rRNA conform to a general pattern for all eukaryotes, despite having highly divergent sequences between D. melanogaster and vertebrates. The 70 novel compensatory mutations identified in the 28S rRNA show a strong (70%) bias toward A-U base pairs, suggesting that a process of biased mutation and/or biased fixation of A and T point mutations or AT-rich slippage-generated motifs has occurred during the evolution of D. melanogaster rDNA. This process has not occurred throughout the D. melanogaster genome. The processes by which compensatory pairs of mutations are generated and spread are discussed, and a model is suggested by which a second mutation is more likely to occur in a unit with a first mutation as such a unit begins to spread through the family and concomitantly through the population. Alternatively, mechanisms of proofreading in stem-loop structures at the DNA level, or between RNA and DNA, might be involved. The apparent tolerance of noncompensatory mutations in some stems which are otherwise strongly supported by comparative criteria within D. melanogaster 28S rRNA must be borne in mind when compensatory mutations are used as a criterion in secondary-structure modeling. Noncompensatory mutation may extend to the production of unstable structures where a stem is stabilized by RNA-protein or additional RNA-RNA interactions in the mature ribosome. Of motifs suggested to be involved in rRNA processing, one (CGAAAG) is strongly overrepresented in the 28S rRNA sequence. The data are discussed both in the context of the forces involved with the evolution of multigene families and in the context of molecular coevolution in the rDNA family in particular.

Journal ArticleDOI
TL;DR: The transposable elements, copia and Ty, were found to be the most difficult to position on the phylogenetic tree, as a result of their higher rate of sequence divergence.
Abstract: Sequences similar to reverse transcriptase (RT) of retroviruses have been found in certain DNA viruses, mitochondrial intron sequences, and a wide variety of transposable elements. While total amino acid similarity between these diverse elements is quite low, we have identified seven regions, consisting of 182 amino acids, that are common to all elements. Highly conserved residues identified in each of these regions are diagnostic for the identification and alignment of these and for future RT-like sequences. Using both the neighbor-joining and the unweighted-pair-group methods, we have derived a probable phylogenetic tree for all RT-containing elements. These elements can be divided into two major groups. Retroviruses and DNA viruses whose propagation involves an RNA intermediate are grouped with a series of transposable elements containing long terminal repeats (LTRs). The second group is made up of RT-containing sequences of fungal mitochondrial introns and a series of transposable elements that lack LTRs. The transposable elements, copia and Ty, were found to be the most difficult to position on the phylogenetic tree, as a result of their higher rate of sequence divergence. The data are most consistent with their being distant members of the LTR group (retroviruses/LTR retrotransposons).

Journal ArticleDOI
TL;DR: The relative efficiencies of the maximum parsimony (MP) and distance-matrix methods in obtaining the correct tree (topology) were studied by using computer simulation, indicating that when the number of nucleotide substitutions per site is small and a relatively small number ofucleotides are used, the probability of obtaining thecorrect topology (P1) is generally lower in the MP method than in the distance-Matrix methods.
Abstract: The relative efficiencies of the maximum parsimony (MP) and distance-matrix methods in obtaining the correct tree (topology) were studied by using computer simulation. The distance-matrix methods examined are the neighbor-joining, distance-Wagner, Tateno et al. modified Farris, Faith, and Li methods. In the computer simulation, six or eight DNA sequences were assumed to evolve following a given model tree, and the evolutionary changes of the sequences were followed. Both constant and varying rates of nucleotide substitution were considered. From the sequences thus obtained, phylogenetic trees were constructed using the six tree-making methods and compared with the model (true) tree. This process was repeated 300 times for each different set of parameters. The results obtained indicate that when the number of nucleotide substitutions per site is small and a relatively small number of nucleotides are used, the probability of obtaining the correct topology (P1) is generally lower in the MP method than in the distance-matrix methods. The P1 value for the MP method increases with increasing number of nucleotides but is still generally lower than the value for the NJ or DW method. Essentially the same conclusion was obtained whether or not the rate of nucleotide substitution was constant or whether or not a transition bias in nucleotide substitution existed. The relatively poor performance of the MP method for these cases is due to the fact that information from singular sites is not used in this method. The MP method also showed a relatively low P1 value when the model of varying rate of nucleotide substitution was used and the number of substitutions per site was large. However, the MP method often produced cases in which the correct tree was one of several equally parsimonious trees. When these cases were included in the class of "success," the MP method performed better than the other methods, provided that the number of nucleotide substitutions per site was small.

Journal ArticleDOI
TL;DR: A phylogenetic tree for the four groups of primates is constructed and suggests that the rate of nucleotide substitution for mtDNAs in hominines (human, chimpanzee, and gorilla) may have slowed down compared with that for old-world monkeys.
Abstract: We determined nucleotide sequences of homologous 0.9-kb fragments of mitochondrial DNAs (mtDNAs) derived from four species of old-world monkeys, one species of new-world monkeys, and two species of prosimians. With these nucleotide sequences and homologous sequences for five species of hominoids, we constructed a phylogenetic tree for the four groups of primates. The phylogeny obtained is generally consistent with evolutionary trees constructed in previous studies. Our results also suggest that the rate of nucleotide substitution for mtDNAs in hominines (human, chimpanzee, and gorilla) may have slowed down compared with that for old-world monkeys. This evolutionary feature of mitochondrial genes is similar to one found in nuclear genes.

Journal ArticleDOI
TL;DR: A survey of restriction-site haplotypes of mitochondrial DNA showed that Japanese mice have two main maternal lineages, which suggest that M. molossinus is a hybrid between ancestral colonies of M. m.
Abstract: The Japanese mouse, A4us musculus molossinus, has long been considered an independent subspecies of the house mouse. A survey of restriction-site haplotypes of mitochondrial DNA (mtDNA) showed that Japanese mice have two main maternal lineages. The most common haplotype is closely related to the mtDNA of the European subspecies A4. m. musculus. The other common haplotype and two minor ones are closely related to each other and to the mtDNA of an Asiatic subspecies, M. m. castaneus. Two other rare variants are probably the result of recent contamination by European A4. m. domesticus. The musculus type of mtDNA is found in the southern two-thirds of Japan, whereas the common castaneus type is found in the northern third and the minor variants are found sporadically throughout Japan. The castaneus mtDNA lineage had a few minor variants, whereas the musculus lineage was completely monomorphic. By contrast, the native population of M. m. castaneus and the Chinese and Korean musculus populations were highly polymorphic. These results suggest that M. m. molossinus is a hybrid between ancestral colonies, possibly very small, of M. m. musculus and M. m. castaneus, rather than an independent subspecies.

Journal ArticleDOI
TL;DR: The molecular coevolution of expansion segments is discussed, which takes place against a background of slippage-like and unequal crossing-over mechanisms of turnover that are responsible for the accumulation of interspecific differences in rDNA sequences.
Abstract: The set of "expansion segments" of any eukaryotic 26S/28S ribosomal RNA (rRNA) gene is responsible for the bulk of the difference in length between the prokaryotic 23S rRNA gene and the eukaryotic 26S/28S rRNA gene. The expansion segments are also responsible for interspecific fluctuations in length during eukaryotic evolution. They show a consistent bias in base composition in any species; for example, they are AT rich in Drosophila melanogaster and GC rich in vertebrate species. Dot-matrix comparisons of sets of expansion segments reveal high similarities between members of a set within any 28S rRNA gene of a species, in contrast to the little or spurious similarity that exists between sets of expansion segments from distantly related species. Similarities among members of a set of expansion segments within any 28S rRNA gene cannot be accounted for by their base-compositional bias alone. In contrast, no significant similarity exists within a set of "core" segments (regions between expansion segments) of any 28S rRNA gene, although core segments are conserved between species. The set of expansion segments of a 26S/28S gene is coevolving as a unit in each species, at the same time as the family of 28S rRNA genes, as a whole, is undergoing continual homogenization, making all sets of expansion segments from all ribosomal DNA (rDNA) arrays in a species similar in sequence. Analysis of DNA simplicity of 26S/28S rRNA genes shows a direct correlation between significantly high relative simplicity factors (RSFs) and sequence similarity among a set of expansion segments. A similar correlation exists between RSF values, overall rDNA lengths, and the lengths of individual expansion segments. Such correlations suggest that most length fluctuations reflect the gain and loss of simple sequence motifs by slippage-like mechanisms. We discuss the molecular coevolution of expansion segments, which takes place against a background of slippage-like and unequal crossing-over mechanisms of turnover that are responsible for the accumulation of interspecific differences in rDNA sequences.

Journal ArticleDOI
TL;DR: The phylogenetic relationships of 21 relatively common and well-studied genera of camarodont echinoids were established using a numerical cladistic approach, and the results are wholly consistent with such a model.
Abstract: The phylogenetic relationships of 21 relatively common and well-studied genera of camarodont echinoids were established using a numerical cladistic approach. This combines data about test morphology, pedicellarial structure, tooth ultrastructure, and larval morphology. The fossil record of the group was reappraised in the light of this analysis, and times of divergence for taxa were estimated. Camarodont families are considered to have diverged much more recently than has previously been suggested, and all except the paraphyletic Temnopleuridae have originated between 65 and 35 Myr ago. Estimates of rates of molecular evolution established on the basis of both thermal stability of heterologous single-copy DNA duplexes and gene sequence data were recalculated using the revised divergence times. Rate of nucleotide divergence, as measured by thermal stability of single-copy DNA heteroduplexes, was calculated to be 0.65-0.85 degrees C/Myr, while sequence data on histone genes indicated a rate of silent substitution of 0.70%-0.85%/Myr. Times of divergence estimated from the fossil record remain too poorly constrained to prove whether molecular evolution proceeds at a stochastically constant rate, but the results are wholly consistent with such a model.

Journal ArticleDOI
TL;DR: The phylogenetic relationships of the sequences indicate that the human sequence shares a most recent coancestor with the chimpanzee sequence and that great apes have accumulated fewer mutations in this part of the genome than has the rhesus monkey.
Abstract: A 3.1-kb intergenic DNA fragment located between the VP-globin and 8-globin genes in the @globin gene cluster was cloned from gorilla, orangutan, rhesus monkey, and spider monkey, and the nucleotide sequence of each fragment was determined. The phylogeny of these four sequences, together with two previously published allelic sequences from humans and one from chimpanzee, was constructed, and the accumulation of mutations in the region was analyzed. The sites of base substitutions are not evenly distributed within the region: two Alu repeats have accumulated 0.2 1 + 0.02 substitutions/site with 0.15 + 0.008 substitutions/site in the remainder of the fragment. The occurrence of substitutions at neighboring sites is more frequent than would be expected if they were independent. The observed excesses disappear when ancestral -CC- dinucleotide sites are excluded. The phylogenetic relationships of the sequences indicate that the human sequence shares a most recent coancestor with the chimpanzee sequence. The data also show that great apes have accumulated fewer mutations in this part of the genome than has the rhesus monkey. The relative rates of accumulation of 12 kinds of nucleotide substitution in the region during primate evolution are asymmetric in the DNA strands. From these rates of accumulation, the origin of a simple stretch of sequence near the 3’ end of the 3. I-kb fragment was deduced to be a sequence comprising 50% T and 50% C on one strand. The two oppositely oriented Alu sequences in the 3.1-kb region were inserted at their present positions before the divergence of the New-World monkeys from other lineages. Our analysis shows that the nucleotide sequences of the two Alu repeats in spider monkey are unexpectedly similar both to each other and to the deduced ancestral sequence of Alu repeats. The data suggest that there has been some type of recombinational event between the spider monkey Alu repeats but that it was not a simple gene conversion.

Journal ArticleDOI
TL;DR: It is proposed that proteins of the Drosophila male reproductive tract may have diverged more extensively between species than have other types of proteins and that much of this divergence may involve large changes in levels of polypeptide expression.
Abstract: We compared male-reproductive-tract polypeptides of Drosophila melanogaster and D. simulans by using two-dimensional gel electrophoresis. Approximately 64% of male-reproductive-tract polypeptides were identical between two randomly chosen isofemale lines from these two species, compared with 83% identity for third-instar imaginal wing-disc polypeptides. Qualitatively similar differences were found between reproductive tracts and imaginal discs when D. sechellia was compared with D. melanogaster and with D. simulans. When genic polymorphism was taken into account, approximately 10% of male-reproductive-tract polypeptides were apparently fixed for different alleles between D. melanogaster and D. simulans; this proportion is the same as that found for soluble enzymes by one-dimensional gel electrophoresis. Strikingly, approximately 20% of male-reproductive-tract polypeptides of either D. melanogaster or D. simulans had no detectable homologue in the other species. We propose that proteins of the Drosophila male reproductive tract may have diverged more extensively between species than have other types of proteins and that much of this divergence may involve large changes in levels of polypeptide expression.

Journal ArticleDOI
TL;DR: The results suggest that MRS-A represents a stable, functional region of the maize genome, and it is speculated that a similar sequence was encompassed by Mu termini to generate a Mu transposable element.
Abstract: Mutator stocks of maize exhibit a high mutation rate correlated with the activity of a family of transposable elements. Mu1 and, to a lesser extent, the closely related Mu1.7 elements are responsible for most mutator-induced mutations that have been characterized. These elements are found in 10-60 copies in mutator stocks, and zero to a few intact elements exist in nonmutator maize stocks. Additionally, the component parts of Mu elements exist separately in the maize genome. The Mu terminal inverted repeats are found in multiple copies in all maize lines and related Zea species tested, and Mu internal sequences exist unassociated with Mu termini. In the present paper, we describe the structure and genomic distribution of one Mu-homologous sequence termed MRS-A (for Mu-related sequence). DNA sequencing shows that MRS-A is closely related to the internal region of Mu1 and Mu1.7 elements. However, it has no Mu termini and does not have the structure of a transposable element. This sequence is present in one or two copies in all maize lines and is highly conserved in the genus Zea. A similar sequence exists in a species within the genus most closely related to Zea, Tripsacum dactyloides, although the T. dactyloides genome does not contain any Mu termini or intact Mu elements. Furthermore, an RNA transcript homologous to MRS-A and its flanking DNA is found in both mutator and nonmutator maize plants. These results suggest that MRS-A represents a stable, functional region of the maize genome, and we speculate that a similar sequence was encompassed by Mu termini to generate a Mu transposable element.

Journal ArticleDOI
TL;DR: A phylogenetic tree is constructed that supports the suggested polyphyletic origin of amoebas and suggests a flagellate ancestry for Naegleria.
Abstract: We have sequenced the small-subunit ribosomal RNA gene of the amoebo-flagellate protozoan Naegleria gruberi. Comparison of this sequence with the rRNA sequences of other eukaryotes resulted in a phylogenetic tree that supports the suggested polyphyletic origin of amoebas and suggests a flagellate ancestry for Naegleria.

Journal ArticleDOI
TL;DR: It is proposed that four esterases form part of a multigene family essentially separate from the serine proteases, three of them cholinesterases, which share 27%-53% overall sequence similarity and evidence of a catalytic mechanism involving the same Arg-Asp-Ser or His-AsP-Ser charge relay.
Abstract: Comparisons among the primary sequences of five cloned eukaryotic esterases reveal two distinct lineages, neither bearing any significant overall sequence similarity to the functionally related serine protease multigene family. We have not eliminated the possibility that the esterases may have residual conformational similarities to the serine proteases. However, our profile analysis and analyses of the predicted conformations of the esterases reveal little similarity to the serine proteases. Four of the esterase proteins share 27%-53% overall sequence similarity and evidence of a catalytic mechanism involving the same Arg-Asp-Ser or His-Asp-Ser charge relay. We propose that these four esterases, three of them cholinesterases, form part of a multigene family essentially separate from the serine proteases.

Journal ArticleDOI
TL;DR: In this paper, the authors developed formulas for using these two methods in tandem and apply them to study transversion differences in (1) nuclear DNA for a 7-kb segment of the psi eta-globin locus and (2) mitochondrial DNA for the 896-bp fragment of Brown et al.
Abstract: In the companion paper (Holmquist et al 1988), we concluded that there is no agreement on either the correct branching order or differential rates of evolution among the higher primates, and we examined in depth why this uncertainty in the evolutionary understanding of our closest living relatives persists Recently, Lake developed two novel methods, based on group properties of transition and transversion operators, that (a) permit, in principle, objective resolution of problems of the above type and (b) attach a statistical significance level to the conclusions drawn In the present paper, we develop formulas for using these two methods in tandem and apply them to study transversion differences in (1) nuclear DNA for a 7-kb segment of the psi eta-globin locus and a 3-kb intergenic region between the psi beta- and delta-globin loci and (2) mitochondrial DNA for the 896-bp fragment of Brown et al Although each of these nucleotide sequence regions has its characteristic tempo and mode of evolution, the nuclear and mitochondrial data together, comprising a total of 10,939 base positions, support a Homo/Pan clade at the 97% confidence level If we calibrate the divergence point for humans and chimpanzees at 5 Myr, consideration of the transversion branch lengths for the combined nuclear data indicates that the gorilla lineage branched off 600,000-900,000 years prior to that, although the 2 sigma sampling errors do not preclude either a temporal trifurcation for the three species or a considerably more ancient branch point for the gorilla To resolve the length of this central branch to a relative accuracy of 25% and 30% will require a factor of 16 and nine times more data, respectively--ie, in excess of 100,000 homologous nucleotides for each of the four primates For the nuclear genes, heterogeneity in evolutionary rates between different parts of the genome is mostly restricted to the human lineage for these two segments The lineage leading to chimpanzees has evolved 04 (3-kb fragment) to 35 (7-kb segment) times as rapidly as the lineage leading to humans, and that leading to the gorilla has evolved approximately one-fifth to one-half as rapidly as that leading to chimpanzees Thus, even local molecular clocks can "tick" badly As significant is the fact that virtually contiguous parts of the genome tick at markedly different rates(ABSTRACT TRUNCATED AT 400 WORDS)

Journal ArticleDOI
TL;DR: This paper is a synthetic and critical review of the methodological literature and isolates some 20 specific reasons why uncertainty in the evolutionary understanding of the authors' closest living relatives persists, many of which are eliminated or ameliorated by Lake's new methods of phylogenetic invariants and operator metrics.
Abstract: At present, no definitive agreement on either the correct branching order or differential rates of evolution among the higher primates exists, despite the accumulated integration of decades of morphological, immunological, protein and nucleic acid sequence data, and numerous reasonable theoretical models for the analysis, interpretation, and understanding of those data. Of the three distinct unrooted phylogenetic trees, that joining human with chimpanzee and the gorilla with the orangutan is currently favored, but the two alternatives that group humans with either gorillas or the orangutan rather than with chimpanzees also have support. This paper is a synthetic and critical review of the methodological literature and isolates some 20 specific reasons why uncertainty in the evolutionary understanding of our closest living relatives persists. Many of the difficulties are eliminated or ameliorated by Lake’s new methods of phylogenetic invariants and operator metrics. In the companion paper these new methods are used to analyze both the nuclear and mitochondrial DNA of the higher primates.

Journal ArticleDOI
TL;DR: This study identified conserved flanking elements that, in conjunction with other studies, suggest regions that may be involved in the control of Adh expression that are not related to the structural gene and flanking sequence.
Abstract: The alcohol dehydrogenase (Adh) gene was isolated from Drosophila simulans and D. mauritiana, and the DNA sequence of a 4.6-kb region, containing the structural gene and flanking sequence, was determined for each. These sequences were compared with the Adh region of D. melanogaster to characterize changes that occur in the Drosophila genome during evolution and to identify conserved sequences of functional importance. Drosophila simulans and D. mauritiana Adh are organized in a manner similar to that of D. melanogaster Adh, including the presence of two promoters for the single Adh gene. This study identified conserved flanking elements that, in conjunction with other studies, suggest regions that may be involved in the control of Adh expression. Inter- and intraspecies comparisons revealed differences in the kinds of sequence changes that have accumulated. Sequence divergence in and around the Adh gene was used to assess inter- and intraspecies evolutionary relationships. Finally, there appears to be an unrelated structural gene located directly 3' of the Adh transcribed region.

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TL;DR: The genetic variation estimates in the Notch region were comparable with those of the alcohol dehydrogenase region in D. melanogaster, suggesting that molecular genetic variation on the X chromosome is not dramatically reduced by selection against slightly deleterious alleles.
Abstract: A worldwide sample of 37 X chromosomes of Drosophila melanogaster was analyzed with four restriction endonucleases for a 60-kb region of the Notch locus. Any two randomly chosen homologous chromosomes were heterozygous at one in 143 nucleotides (theta = 0.007). The chromosomes that were sampled contained no more than one insertion/deletion. The four insertions and one deletion observed in the 37 chromosomes sampled were located 3' to the Notch transcript; one insertion was represented twice in the sample. The amount of linkage disequilibrium in the Notch region appears to be lower than that of the alcohol dehydrogenase locus in D. melanogaster. The few instances of linkage disequilibrium observed could be due to geographic differentiation of African populations. The genetic variation estimates in the Notch region were comparable with those of the alcohol dehydrogenase region in D. melanogaster, suggesting that molecular genetic variation on the X chromosome is not dramatically reduced by selection against slightly deleterious alleles.

Journal ArticleDOI
TL;DR: The presence of the J-1 mtDNA genotype on Jamaica and on St. Vincent and Barbados demonstrates that maternal lineages in these bats are not necessarily confined to single islands or limited geographic regions.
Abstract: The Neotropical fruit bat, Artibeus jumaicensis, occurs throughout Latin America and on many islands in the Caribbean. Populations from Jamaica (in the Greater Antilles) to Barbados (in the Lesser Antilles) have been classified as a subspecies (A. j. jumaicensis) separate from that on the Lesser Antillean island of St. Vincent (A. j. schwartzi). Mitochondrial DNA (mtDNA) was isolated from 54 individuals collected on these islands, analyzed by digestion with restriction endonucleases, and the restriction sites were mapped. Three different mtDNA genotypes (16,000 + 200 bp) were identified: J-l (16 animals from Jamaica, one from St. Vincent, 15 from Barbados), J-2 (two animals from Jamaica), and SV-1 (18 animals from St. Vincent, two from Barbados). The J-l and J-2 genotypes were estimated to differ from each other by only 0.4%, but the SV-1 genotype differed from J-l and J-2 by 8.1%-10.5%. The estimated sequence divergence between SV-1 and J-l is unusually large for mammals that are regarded as conspecific. Restriction mapping showed that the differences among the genotypes (presence or absence of particular restriction sites) were located throughout the genome. The presence of the J- 1 mtDNA genotype on Jamaica and on St. Vincent and Barbados (1,400 km away) demonstrates that maternal lineages in these bats are not necessarily confined to single islands or limited geographic regions. The presence of the J-l mtDNA genotype within the A. j. schwartzi population on St. Vincent and the presence of the SV-1 genotype in two specimens of A. j. jumaicensis from Barbados document genetic exchange between subspecific populations on these islands, which are separated by 180 km of open water.

Journal ArticleDOI
TL;DR: Divergence between the HIV1 and HIV2 strains seems to have occurred greater than 200 years ago, implying that AIDS has existed for a long time but went unnoticed, whereas synonymous changes are more variable among different lineages.
Abstract: A phylogenetic tree for different human immunodeficiency viruses type 1 (HIV1) and type 2 (HIV2), lentiviruses, and oncoviruses has been constructed by comparing the nucleotide sequences of the two regions of their pol genes that encode the reverse transcriptase and endonuclease/integrase. The analysis indicates that (1) different HIV1 strains form one cluster and their common ancestor diverged from the ancestor of HIV2, (2) the common ancestor of the HIV1 and HIV2 strains diverged from that of the lentivirus, and (3) the common ancestor of the lentivirus group and that of the oncoviruses diverged earlier than that. Divergence between the HIV1 and HIV2 strains seems to have occurred greater than 200 years ago, implying that AIDS has existed for a long time but went undetected. Furthermore, nonsynonymous changes are occurring uniformly through time, whereas synonymous changes are more variable among different lineages.

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TL;DR: Findings suggest that the crab-eating monkey diverged from the other three monkeys approximately 1.5-3.0 Myr before the present (Mybp) and that the Japanese, rhesus, and Formosan monkeys diverged approximately 0.9-1.8 Mybp, although the branching order cannot be determined conclusively.
Abstract: Mitochondrial DNA (mtDNA) polymorphisms in four species of macaques, i.e., Japanese monkey (Macaca fuscata), rhesus monkey (M. mulatta), Formosan monkey (M. cyclopis), and crab-eating monkey (M. fascicularis), were analyzed to study phylogenetic relationships. When 17 restriction enzymes of 6-bp recognition were used, 42-49 sites were observed in the samples. The estimated number of nucleotide substitutions per site among Japanese, rhesus, and Formosan monkeys ranges from 0.0318 to 0.0396, and that between the crab-eating monkey and the other monkeys from 0.0577 to 0.0653. These findings suggest that the crab-eating monkey diverged from the other three approximately 1.5-3.0 Myr before the present (Mybp) and that the Japanese, rhesus, and Formosan monkeys diverged approximately 0.9-1.8 Mybp, although the branching order cannot be determined conclusively.

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TL;DR: Two genetic procedures were used to obtain amino acid replacements in the lacZ-encoded beta-galactosidase in Escherichia coli by selecting spontaneous mutations that relieved the strong polarity of six nonsense mutations.
Abstract: Two genetic procedures were used to obtain amino acid replacements in the lacZ-encoded beta-galactosidase in Escherichia coli. Amino acid replacements could be obtained without regard to their effects on lactase activity by selecting spontaneous mutations that relieved the strong polarity of six nonsense mutations. When streaked on MacConkey-lactose indicator plates, approximately 75% of these mutants gave strong red lactose-fermenting colonies, and 25% gave white nonfermenting colonies. Mutants from 11 other nonsense codons were isolated directly using MacConkey-lactose indicator plates, on which positive color indication requires only 0.5% of the wildtype lactase activity. Among the total of 17 codons, 25 variant beta-galactosidases were identified using electrophoresis and thermal denaturation studies. The fitness effects of these variant beta-galactosidases were determined using competition experiments conducted with lactose as the sole nutrient limiting the growth rate in chemostat cultures. Three of the replacements were deleterious, one was selectively advantageous, and the selective effects of the remaining 21 were undetectable under conditions in which the smallest detectable selection coefficient was approximately 0.4%/generation.