Showing papers on "Phylogenetic tree published in 1985"

The quantitative assessment of phylogenetic constraints in comparative analyses: sexual dimorphism in body weight among primates.

Abstract: We have presented a formal model for the quantitative analysis of phylogenetic and specific effects on the distribution of trait values among species. Total trait values are divided into phylogenetic values, inherited from an ancestral species, and specific values, the result of independent evolution. This allows a quantitative assessment of the strength of the phylogenetic inertia, or burden, displayed by a character in a lineage, so that questions concerning the relative importance of phylogenetic constraints in evolution can be answered. The separation of phylogenetic from specific effects proposed here also allows phylogenetic factors to be explicitly included in cross-species comparative analyses of adaptation. This solves a long-standing problem in evolutionary comparative studies. Only species' specific values can provide information concerning the independent evolution of characters in a set of related species. Therefore, only correlations among specific values for traits may be used as evidence for adaptation in cross-species comparative analyses. The phylogenetic autocorrelation model was applied to a comparative analysis of the determinants of sexual dimorphism in weight among 44 primate species. In addition to sexual dimorphism in weight, mating system, habitat, diet, and size (weight itself) were included in the analysis. All of the traits, except diet, were substantially influenced by phylogenetic inertia. The comparative analysis of the determinants of sexual dimorphism in weight indicates that 50% of the variation among primate species is due to phylogeny. Size, or scaling, could account for a total of 36% of the variance, making it almost as important as phylogeny in determining the level of dimorphism displayed by a species. Habitat, mating system, and diet follow, accounting for minor amounts of variation. Thus, in attempting to explain why a particular modern primate species is very dimorphic compared to other primates, we would say first because its ancestor was more dimorphic than average, second because it is a relatively large species, and third because it is terrestrial, polygynous, and folivorous.

Methods for computing the standard errors of branching points in an evolutionary tree and their application to molecular data from humans and apes.

Abstract: Statistical methods for computing the standard errors of the branching points of an evolutionary tree are developed. These methods are for the unweighted pair-group method-determined (UPGMA) trees reconstructed from molecular data such as amino acid sequences, nucleotide sequences, restriction-sites data, and electrophoretic distances. They were applied to data for the human, chimpanzee, gorilla, orangutan, and gibbon species. Among the four different sets of data used, DNA sequences for an 895-nucleotide segment of mitochondrial DNA (Brown et al. 1982) gave the most reliable tree, whereas electrophoretic data (Bruce and Ayala 1979) gave the least reliable one. The DNA sequence data suggested that the chimpanzee is the closest and that the gorilla is the next closest to the human species. The orangutan and gibbon are more distantly related to man than is the gorilla. This topology of the tree is in agreement with that for the tree obtained from chromosomal studies and DNA-hybridization experiments. However, the difference between the branching point for the human and the chimpanzee species and that for the gorilla species and the human-chimpanzee group is not statistically significant. In addition to this analysis, various factors that affect the accuracy of an estimated tree are discussed.

Comparison of undirected phylogenetic trees based on subtrees of four evolutionary units

Abstract: A method to measure how similar are two phylogenetic trees for the same collection of evolutionary units (EUs) is described. The measure does not change with changes in the direction of evolution in either of the two trees being compared, and thus it depends only on the convexity and proximity of the groups of EUs within the collection under study. It can also be used with only partially resolved phylogenetic trees. The measure is based on the idea that a group of four EUs is the smallest group for which there is more than one possible distinct undirected phylogenetic tree. For a given phylogenetic tree, the undirected subtree inherited by a group of four EUs is the tree that results when all the branches containing only EUs not in this group of four are removed. Every group of four EUs either inherits one of three distinct types of undirected phylogenetic trees, or is unresolved. Two phylogenetic trees can be com- pared on the basis of which groups of four EUs inherit the same type of undirected phylogenetic tree. The ideas can be extended to comparisons of three or more trees. (Phylogenetic trees; compatibility; subtree.)

Trichostrongyloid nematodes and their vertebrate hosts: reconstruction of the phylogeny of a parasitic group.

Abstract: Publisher Summary This chapter introduces trichostrongyloid nematodes as a model for discussing the reconstruction of the phylogeny of a parasitic group. Morphological and biological characters are studied and assessed for their relative phylogenetic importance. On the basis of morphological characters and their presumed evolution, trichostrongyloids are divided into 14 families and 24 subfamilies. The evolutionary trends of each character are analyzed and used to construct a classification that recognizes different phylogenetic lines. A parasitic line may become isolated from its ancestral forms by passing from one host group to another; the isolation may be followed by the evolutionary radiations of variable importance. In the Trichostrongyloidea, the most important characters from a phylogenetic point of view are those of the caudal bursa and synlophe. Using these characters, a number of different evolutionary lines become evident and the degree of evolution of the different genera composing each of those lines can be assessed. The chapter also presents a phylogenetic tree of the Trichostrongyloidea.

Evolutionary relationships among rodents : a multidisciplinary analysis

Abstract: Origin and Eutherian Affinities of Rodentia.- The Order Rodentia: Major Questions on Their Evolutionary Origin, Relationships and Suprafamilial Systematics.- Possible Phylogenetic Relationship of Asiatic Eurymylids and Rodents, with Comments on Mimotonids.- Cranial Evidence for Rodent Affinities.- Rodent and Lagomorph Morphotype Adaptations, Origins, and Relationships: Some Postcranial Attributes Analyzed.- Enamel Structure of Early Mammals and Its Role in Evaluating Relationships among Rodents.- Reconstruction of Ancestral Cranioskeletal Features in the Order Lagomorpha.- A Phylogeny of Rodentia and Other Eutherian Orders: Parsimony Analysis Utilizing Amino Acid Sequences of Alpha and Beta Hemoglobin Chains.- Superordinal Affinities of Rodentia Studied by Sequence Analysis of Eye Lens Protein.- Superordinal and Intraordinal Affinities of Rodents: Developmental Evidence from the Dentition and Placentation.- Phyletic Relationships Among Rodent Higher Categories.- Possible Evolutionary Relationships among Eocene and Lower Oligocene Rodents of Asia, Europe and North America.- Cranial Foramina of Rodents.- Phylogenetic Analysis of Middle Ear Features in Fossil and Living Rodents.- Systematic Value of the Carotid Arterial Pattern in Rodents.- Homologies of Molar Cusps and Crests, and Their Bearing on Assessments of Rodent Phylogeny.- Evolutionary Trends in the Enamel of Rodent Incisors.- Rodent Macromolecular Systematics.- Specific Problems of Intraordinal Relationships.- Reproductive and Chromosomal Characters of Ctenodactylids as a Key to Their Evolutionary Relationships.- The Relationships, Origin and Dispersal of the Hystricognathous Rodents.- Myology of Hystricognath Rodents: An Analysis of Form, Function, and Phylogeny.- Amino Acid Sequence Data and Evolutionary Relationships among Hystricognaths and Other Rodents.- New Phiomorpha and Anomaluridae from the Late Eocene of North-West Africa: Phylogenetic Implications.- Problems in Muroid Phylogeny: Relationship to Other Rodents and Origin of Major Groups.- Origin and Evolutionary Relationships among Geomyoids.- Evolutionary Data on Steppe Lemmings (Arvicolidae, Rodentia).- Karyotype Variability and Chromosome Transilience in Rodents: The Case of the Genus Mus.- Electromorphs and Phylogeny in Muroid Rodents.- Concluding Remarks.- Evolutionary Relationships among Rodents: Comments and Conclusions.- Contributors.

Statistical methods of DNA sequence analysis: detection of intragenic recombination or gene conversion.

Abstract: Simple but exact statistical tests for detecting a cluster of associated nucleotide changes in DNA are presented. The tests are based on the linear distribution of a set of s sites among a total of n sites, where the s sites may be the variable sites, sites of insertion/deletion, or categorized in some other way. These tests are especially useful for detecting gene conversion and intragenic recombination in a sample of DNA sequences. In this case, the sites of interest are those that correspond to particular ways of splitting the sequences into two groups (e.g., sequences A and D vs. sequences B, C, and E-J). Each such split is termed a phylogenetic partition. Application of these methods to a well-documented case of gene conversion in human gamma-globin genes shows that sites corresponding to two of the three observed partitions are significantly clustered, whereas application to hominoid mitochondrial DNA sequences--among which no recombination is expected to occur--shows no evidence of such clustering. This indicates that clustering of partition-specific sites is largely due to intragenic recombination or gene conversion. Alternative hypotheses explaining the observed clustering of sites, such as biased selection or mutation, are discussed.

Construction of the mycoplasma evolutionary tree from 5S rRNA sequence data

Abstract: The 5S rRNA sequences of eubacteria and mycoplasmas have been analyzed and a phylogenetic tree constructed. We determined the sequences of 5S rRNA from Clostridium innocuum, Acholeplasma laidlawii, Acholeplasma modicum, Anaeroplasma bactoclasticum, Anaeroplasma abactoclasticum, Ureaplasma urealyticum, Mycoplasma mycoides mycoides, Mycoplasma pneumoniae, and Mycoplasma gallisepticum. Analysis of these and published sequences shows that mycoplasmas form a coherent phylogenetic group that, with C. innocuum, arose as a branch of the low G+C Gram-positive tree, near the lactobacilli and streptococci. The initial event in mycoplasma phylogeny was formation of the Acholeplasma branch; hence, loss of cell wall probably occurred at the time of genome reduction to approximately to 1000 MDa. A subsequent branch produced the Spiroplasma. This branch appears to have been the origin of sterol-requiring mycoplasmas. During development of the Spiroplasma branch there were several independent genome reductions, each to approximately 500 MDa, resulting in Mycoplasma and Ureaplasma species. Mycoplasmas, particularly species with the smallest genomes, have high mutation rates, suggesting that they are in a state of rapid evolution.

Phylogenetic analysis of the Digenea (Platyhelminthes: Cercomeria) with comments on their adaptive radiation

Abstract: Phylogenetic analysis of 63 digenean family groups, based on 113 adult characters and 90 larval characters, produced a phylogenetic tree comprising nine orders. Adult characters alone resolved 76% of the phylogenetic tree, whereas larval characters alone resolved 74%. There was no disagreement in phylogenetic inferences drawn from only larval or only adult characters, and yet the larval forms of digeneans do not seem to be recapitulations of ancestral adult forms. The consistency index for the tree is 74%, indicating a low degree of parallel evolution in digenean morphology. Diversification in six sets of ecological characteristics combined resolves 26% of the phylogenetic tree. The combination of (i) larval and adult congruence in the absence of recapitulation, (ii) low levels of parallel evolution in morphology, and (iii) ecological diversification lagging far behind morphological change discounts traditional notions of adaptive radiations. Digeneans have experienced great morphological diversification ...

Phylogenetic relationships among eukaryotic kingdoms inferred from ribosomal RNA sequences.

Abstract: Phylogenetic trees among eukaryotic kingdoms were inferred for large- and small-subunit rRNAs by using a maximum-likelihood method developed by Felsenstein. Although Felsenstein's method assumes equal evolutionary rates for transitions and transversions, this is apparently not the case for these data. Therefore, only transversiontype substitutions were taken into account. The molecules used were large-subunit rRNAs fromXenopus laevis (Animalia), rice (Plantae),Saccharomyces cerevisiae (Fungi),Dictyostelium discoideum (Protista), andPhysarum polycephalum (Protista); and small-subunit rRNAs from maize (Plantae),S. cerevisiae, X. laevis, rat (Animalia), andD. discoideum. Only conservative regions of the nucleotide sequences were considered for this study. In the maximum-likelihood trees for both large- and small-subunit rRNAs, Animalia and Fungi were the most closely related eukaryotic kingdoms, and Plantae is the next most closely related kingdom, although other branching orders among Plantae, Animalia, and Fungi were not excluded by this work. These three eukaryotic kingdoms apparently shared a common ancestor after the divergence of the two species of Protista,D. discoideum andP. polycephalum. These two species of Protista do not form a clade, andP. polycephalum diverged first andD. discoideum second from the line leading to the common ancestor of Plantae, Animalia, and Fungi. The sequence data indicate that a drastic change occurred in the nucleotide sequences of rRNAs during the evolutionary separation between prokaryote and eukaryote.

Factors determining the accuracy of cladogram estimation: evaluation using computer simulation.

Abstract: We developed a simulation model of phylogenesis with which we generated a large number of phylogenies and associated data matrices We examined the characteristics of these and evaluated the success of three taxonomic methods (Wagner parsimony, character compatibility, and UPGMA clustering) as estimators of phylogeny, paying particular attention to the consequences of changes in certain evolutionary assumptions: relative rate of evolution in three different evolutionary contexts (phyletic, parent lineage, and daughter lineage); relative rate of evolution in different directions (novel forward, convergent forward, or reverse); variation of evolutionary rates; and topology of the phylogenetic tree Except for variation of evolutionary rates, all the evolutionary parameters that we controlled had significant effects on accuracy of phylogenetic reconstructions Unexpectedly, the topology of the phylogeny was the most important single factor affecting accuracy; some phylogenies are more readily estimated than others for simply historical reasons We conclude that none of the three estimation methods is very accurate, that the differences in accuracy among them are rather small, and that historical effects (the branching pattern of a phylogeny) may outweigh biological effects in determining the accuracy with which a phylogeny can be reconstructed

Molecular perspective on higher-level relationships in the tyrannoidea (aves)

Abstract: Allelic frequency data were used to identify familial limits within the avian su- perfamily Tyrannoidea. Several hypotheses were generated from this data set using distance- Wagner, Fitch-Margoliash, and cladistic analyses. In addition, a jackknifing procedure was em- ployed to identify those portions of the phylogenetic hypotheses that were robust to such factors as the choice of taxa analyzed. The genus Sapayoa, previously considered to be a manakin (Pipridae), was found to be distant from all other taxa considered. The true affinities of this taxon, therefore, may lie outside of the Tyrannoidea. The electrophoretic data also indicated that the 12 cotinga species (Cotingidae) analyzed belong to five distinct lineages, each of un- known affinity within the superfamily. Finally, sister taxa were identified for the monogeneric families Oxyruncidae and Phytotomidae. The former was found to be closely related to tityras, becards, and flycatchers (as indicated by Myiarchus), while the latter family is closely related to the cotinga genera Ampelion, Doliornis, and Zaratornis. The improved ability to determine higher- level relationships within this assemblage was tonsidered a consequence of the use of biochem- ical characters, the interpretation of which is greatly simplified because of the stochastic nature of molecular evolution. However, conflicts between this and a recent DNA-DNA hybridization study indicate that the extraction of phylogenetic information from biochemical data may not be as free from assumptions as we would like. Several explanations for this lack of concordance are discussed. (Electrophoresis; phylogeny reconstruction; tyrannoids; biochemical evolution; distance analysis; jackknifing; flycatchers; cotingas; manakins.)

Biochemical pathways in prokaryotes can be traced backward through evolutionary time.

Abstract: For the first time, a credible prokaryotic phylogenetic tree is being assembled by Woese and others using quantitative sequence analysis of oligonucleotides in the highly conservative rRNA. This provides an evolutionary scale against which the evolutionary steps that led to the arrangement and regulation of contemporary biochemical pathways can be measured. This paper presents an emerging evolutionary picture of aromatic amino acid biosynthesis within a large superfamily assemblage of prokaryotes that is sufficiently developed to illustrate a new perspective that will be applicable to many other biochemical pathways.

Genetic and evolutionary relationships among Asian Macaques

Abstract: Published gene frequency data, checked for consistency of allele definitions across laboratories and for comparability of geographically identical samples, were pooled into a data set containing frequencies at nine loci for each of 20 populations that encompassed 10 macaque species Genetic distances were calculated by the methods of Kidd and Cavalli-Sforza (1974) These distances were used to construct phylogenetic trees and to evaluate the relationships between divergence times and effective population sizes Inter-and intraspecific genetic distances and the groupings defined by phenetic tree analyses support Fooden’s (1976) classification of the genus Macacainto four species groups A paleozoogeographical model of Asia including the known times of major sea-level changes allows us to explain Macacainto four species groups A paleozoogeographical model of Asia including the known times of major sea-level changes allows us to explain qualitatively the inferred evolutionary relationships among macaque species Many assumptions are required in order to estimate the variables necessary in the quantitative prediction of genetic differences for a comparison between any two populations Examination of those assumptions demonstrates the need for more accurate genetic as well as paleozoogeographic information

Phylogenetic pathways in the Chilopoda

Abstract: The phylogenetic relationships of the chilopod orders are discussed on the basis of cladistic principles. The autapomorphies of the five orders (Scutigeromorpha, Lithobiomorpha, Craterostigmomorpha, Scolopendromorpha, and Geophilomorpha) are summarized. The monophyly of the Epimorpha is established. Craterostigmus is tentatively regarded as belonging to the epimorph branch. The Lithobiomorpha are united with the Epimorpha on the ground of a great number of common characters which must be classified as synapomorphies. A detailed phylogenetic tree is proposed. The probable characteristics of the chilopod ancestor are worked out.

The Cucumis plastome: physical map, intrageneric variation and phylogenetic relationships

Abstract: A restriction map of the Cucumis melo L. (melon) plastome was constructed by using several mapping approaches: single and double digestions of the chloroplast DNA (chlDNA) with endonucleases (XhoI, SmaI, SacI and PvuII) and hybridization to heterologous chlDNA probes and to isolated melon chlDNA fragments. Four plastome-coded genes were located using heterologous probes. The overall organization and gene position of the melon plastome was found to be similar to that of tobacco and other angiosperm species. Restriction patterns based on digestion of the chlDNA with nine endonucleases were obtained in over 20 wild species and cultivated varieties of Cucumis. These led to mutational analysis of the restiction sites yielding the most parsimonious phylogenetic tree of the Cucumis plastome. Most African species from a compact group (“Anguria group”) which is distant from the melon, the cucumber and a few other species (C. sagittatus, C. metuliferus and C. humifructus). All of these are also far apart from each other. The distribution of polymorphic restriction sites along the Cucumis plastome is described and conservative regions as well as “hot spots” are suggested.

Phylogenetic analysis of polymorphic DNA sequences at the Adh locus in Drosophila melanogaster and its sibling species.

Abstract: Recent sequencing of over 2300 nucleotides containing the alcohol dehydrogenase (Adh) locus in each of 11 Drosophila melanogaster lines makes it possible to estimate the approximate age of the electrophoretic "fast-slow" polymorphism. Our estimates, based on various possible patterns of evolution, range from 610,000 to 3,500,000 years, with 1,000,000 years as a reasonable point estimate. Furthermore, comparison of these sequences with those of the homologous region of D. simulans and D. mauritiana allows us to infer the pattern of evolutionary change of the D. melanogaster sequences. The integrity of the Adh-f electrophoretic alleles as a single lineage is supported by both unweighted pair-group method (UPGMA) and parsimony analyses. However, considerable divergence among the Adh-s lines seems to have preceded the origin of the Adh-f allele. Comparisons of the sequences of D. melanogaster genes with those of D. simulans and D. mauritiana genes suggest that the split between the latter two species occurred more recently than the divergence of some of the present-day Adh-s genes in D. melanogaster. The phylogenetic analyses of the D. melanogaster sequences show that the fast-slow distinction is not perfect, and suggest that intragenic recombination or gene conversion occurred in the evolution of this locus. We extended conventional phylogenetic analyses by using a statistical technique for detecting and characterizing recombination events. We show that the pattern of differentiation of DNA sequences in D. melanogaster is roughly compatible with the neutral theory of molecular evolution.

Mys, a family of mammalian transposable elements isolated by phylogenetic screening.

Abstract: It has recently been demonstrated both emperically1–3 and mathematically4 that transposable elements may spread rapidly throughout a population once introduced even when they dramatically reduce the fitness of individuals that carry them. Such events result in pronounced differences in the phylogenetic distribution of genetic elements capable of rapid genome invasion. Using a simple and general procedure to screen the genome of the white footed mouse Peromyscus leucopus, we have isolated a family of retrovirus-like elements which is apparently absent from the genome of the house mouse Mus domesticus. Here, we report this procedure and an analysis of the organization, phylogenetic distribution and sequence of this family of transposable elements.

Evolutionary Genetics of the Andean Lizard Genus Pholidobolus (Sauria: Gymnophthalmidae): Phylogeny, Biogeography, and a Comparison of Tree Construction Techniques

Abstract: Electrophoretic examination of the products of 29 gene loci in the five species of Pholidobolus and three species of Proctoporus largely substantiates the taxonomic arrangement that was based on earlier morphological work. The electrophoretic data are used to construct a phylogeny of the species and the morphological data are reanalyzed for comparison; these data sets are largely consistent. The hypothesized phylogeny places Ph. affinis as the sister species to the other Pholidobolus, Ph. macbrydei as the sister species to the remaining taxa, and the two populations referred to Ph. prefrontalis as the sister species to Ph. montium plus Ph. annectens. Because of the small size of the genus Pholidobolus and the concomitant small number of possible phylogenetic hypotheses, comparisons among various methods of constructing phylogenetic trees from electrophoretic data are facilitated. All 105 possible bifurcating unrooted trees were examined for each of 13 goodness-of-fit statistics; three similar trees were consistently favored by all criteria. If outgroup rooting is used, the most favored of these trees is identical to the most parsimonious cladogram. However, with midpoint rooting, almost all phylogenetic infor- mation is lost and the resulting tree is identical to the UPGMA phenogram. The midpoint- rooting option of distance trees reinvokes an assumption (equal rates of change) that the distance methods are supposed to avoid. This assumption is clearly not met for the genus Pholidobolus. Biogeographic analysis of the species of Pholidobolus with respect to the hypothesized phylog- eny of the genus reveals that no contact zones of this parapatric complex involve two sister species. This emphasizes the need for phylogenetic reconstruction as the first step in the ex- amination of speciation mechanisms. This finding also suggests that competing species, rather than geographic barriers, may at times serve to isolate differentiating populations. (Evolutionary genetics; phylogeny; biogeography; speciation; genetic distances; network rooting; Pholidobolus; Proctoporus.)

Evolutionary Trees from Nucleic Acid and Protein Sequences

Abstract: The problem addressed is that of estimating evolutionary relationship by the comparative study of the nucleic acid or protein sequences of living organisms. The most important point made in this account is that estimation of evolutionary relationship should be based on clearly defined models the assumptions of which are open to test. The models should as far as possible conform to what is known about the processes of evolutionary change in the organisms concerned. Prevailing approaches, grouped here as divergence models, are stated below in such a way that it is clear that they involve unrealistic assumptions about the nature of evolutionary change. Emphasis is placed on the use of probabilistic models of evolutionary change. The historical development of these models has proceeded in parallel with the more commonly used `parsimony' methods. The problem of reconstructing phylogenies is simplified by assuming that the pathways of genetic transmission conform to a tree structure. The tree model is justified on the grounds that such pathways may be traced in a genealogy, however, the tree model ignores hybridization and horizontal transmission of the genetic material. The other essential component is a probabilistic formulation of the processes of genetic change. Consideration of genetic reliability (a view of mutation as failure correctly to copy information) leads to such a probabilistic description. Several proposed schemes which make numerical assessment of the relative frequencies of base substitution in DNA are considered. We next examine methods for the estimation of phylogenetic trees on the basis of probabilistic models. Pairwise estimates of divergence times lead rapidly to hypotheses of evolutionary relationship, but it is stressed that joint estimation procedures, which simultaneously take account of all the data, lead to more complete estimates of relationship. The various methods are illustrated as applied to the analysis of nucleic acid sequence data from the mammalian mitochondrial genome. Finally, we discuss weaknesses of the current stochastic models and point out ways in which accumulating experimental information may lead to their refinement or refutation.

Evolutionary change of restriction cleavage sites and phylogenetic inference for man and apes.

Abstract: A mathematical theory for the evolutionary change of restriction endonuclease cleavage sites is developed, and the probabilities of various types of restriction-site changes are evaluated. A computer simulation is also conducted to study properties of the evolutionary change of restriction sites. These studies indicate that parsimony methods of constructing phylogenetic trees often make erroneous inferences about evolutionary changes of restriction sites unless the number of nucleotide substitutions per site is less than 0.01 for all branches of the tree. This introduces a systematic error in estimating the number of mutational changes for each branch and, consequently, in constructing phylogenetic trees. Therefore, parsimony methods should be used only in cases where nucleotide sequences are closely related. Reexamination of Ferris et al.'s data on restriction-site differences of mitochondrial DNAs does not support Templeton's conclusions regarding the phylogenetic tree for man and apes and the molecular clock hypothesis. Templeton's claim that Nei and Li's method of estimating the number of nucleotide substitutions per site is seriously affected by parallel losses and loss-gains of restriction sites is also unsupported.

Molecular organization of dinoflagellate ribosomal DNA: evolutionary implications of the deduced 5.8 S rRNA secondary structure.

Abstract: The 5.8 S rRNA gene of Prorocentrum micans, a primitive dinoflagellate, has been cloned and its 159 base pairs (bp) have been sequenced along with the two flanking internal transcribed spacers (ITS 1 and 2), respectively, 212 and 195 bp long. Nucleotide sequence homologies between several previously published 5.8 S rRNA sequences including those from another dinoflagellate, an ascomycetous yeast, protozoans, a higher plant and a mammal have been determined by sequence alignment. Two procaryotic 5′-ends of the 23 S rRNA gene have been compared owing to their probable common origin with eucaryotic 5.8 S rRNA genes. Several nucleotides are distinctive for dinoflagellates when compared with either typical eucaryotes or procaryotes. This is consistent with an early divergence of the dinoflagellate lineage from the typical eucaryotes. The secondary structure of dinoflagellate 5.8 S rRNA molecules fits the model of Walker et al. (1983). Conserved nucleotides which distinguish dinoflagellate 5.8 S rRNA from that of other eucaryotes are located in specific loops which are assumed to play a structural role in the ribosome. A 5.8 S rRNA phylogenetic tree which is proposed, based on sequence data, supports our initial assumption of an early divergence of the dinoflagellates.

Complete nucleotide sequences of three VH genes in Caiman, a phylogenetically ancient reptile: evolutionary diversification in coding segments and variation in the structure and organization of recombination elements

Abstract: Complete nucleotide sequences are described for three caiman (Caiman crocodylus crocodylus) immunoglobulin VH genes (C3, E1, and G4) that hybridize with a murine VH probe. The E1 and G4 genes are physically linked (intergenic distance, approximately equal to 6.5 kilobases) in the same transcriptional orientation but are not directly contiguous with the C3 gene. When the coding segments, including both framework and complementarity-determining regions, of these genes and the murine probe sequences are compared by metric analysis, it is apparent that the caiman genes are only slightly more related to each other than to the mammalian sequence, consistent with significant preservation of nucleotide sequence over an extended period of phylogenetic time. Based on the presence of transcriptionally critical 5' sequences and the absence of terminator codons, frameshift mutations, or other recognizable alterations, the genes do not appear to be pseudogenes. The E1 gene, however, is distinguished from other VH genes because (i) the spacer region within the 3' recombination signal sequence is 12 base pairs, typical of VK genes but not of VH genes, which possess 22- to 23-base-pair spacers and (ii) a near-perfect VH recombination signal sequence is present within the intervening sequence that splits the segment encoding the leader. These studies establish VH gene multiplicity in a species that arose prior to mammalian radiation and provide a description of differences in the configuration and location of recombination elements associated with an otherwise potentially functional gene.

Electromorphs and Phylogeny in Muroid Rodents

Abstract: How do we infer phylogenetic relationships from electrophoretic studies? What is the value of such phylogenies? What can we infer from these phylogenies about the processes of divergence? These are the questions that we have tried to answer empirically by analyzing genetic variability in 76 taxa of rodents, most of them being muroids. Our approach is comparable to that of Patton and Avise (1983), and is aimed at comparing the values of quantitative and qualitative analyses of electrophoretic data. However, their material and ours differ in evolutionary patterns, and the results differ accordingly in some respects.

Chloroplast DNA and molecular phylogeny

Abstract: The small, relatively constant size and conservative evolution of chloroplast DNA (cpDNA) make it an ideal molecule for tracing the evolutionary history of plant species. At lower taxonomic levels, cpDNA variation is easily and conveniently assayed by comparing restriction patterns and maps, while at higher taxonomic levels, DNA sequencing and inversion analysis are the methods of choice for comparing chloroplast genomes. The study of cpDNA variation has already yielded important new insights into the origin and evolution of many agriculturally important crop plants, and promises to significantly enhance our phylogenetic understanding of the major lines of descent among land plants and algae.

Sequence-directed mutagenesis: evidence from a phylogenetic history of human alpha-interferon genes.

Abstract: We have studied the potential contribution of template-dependent events to genetic variation in mammals by examining the sequence alterations that have occurred in the recent evolution of human interferon genes. Fifteen members of the human alpha-interferon gene family were aligned, and a phylogenetic history was inferred. Many multiple events are inferred to have occurred in the evolution of the interferon genes and for the majority of these local DNA sequences were present that were capable of serving as templates for their occurrence. We conclude that the DNA sequence has the potential to explain many of the inferred spontaneous events and to explain complex alterations to sequences--i.e., the joint occurrence of base substitutions and insertions/deletions. Thus, such a mechanism would often cause multiple sequence changes as a result of a single mutational event and would provide additional genetic variation for evolution. Sequence-directed mutations would depend upon the local DNA sequences and, hence, would not be random at the DNA level.