Showing papers on "Phylogenetic tree published in 1989"

Dynamics of mitochondrial DNA evolution in animals: Amplification and sequencing with conserved primers (cytochrome b/12S ribosomal DNA/control region/evolutionary genetics/molecular phylogenies)

Abstract: With a standard set of primers directed toward conserved regions, we have used the polymerase chain reaction to amplify homologous segments ofmtDNA from more than 100 animal species, including mammals, birds, amphib- ians, fishes, and some invertebrates. Amplification and direct sequencing were possible using unpurified mtDNA from nano- gram samples of fresh specimens and microgram amounts of tissues preserved for months in alcohol or decades in the dry state. The bird and fish sequences evolve with the same strong bias toward transitions that holds for mammals. However, because the light strand of birds is deficient in thymine, thymine to cytosine transitions are less common than in other taxa. Amino acid replacement in a segment of the cytochrome b gene is faster in mammals and birds than in fishes and the pattern of replacements fits the structural hypothesis for cytochrome b. The unexpectedly wide taxonomic utility ofthese primers offers opportunities for phylogenetic and population research.

Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in hominoidea

Abstract: A maximum likelihood method for inferring evolutionary trees from DNA sequence data was developed by Felsenstein (1981). In evaluating the extent to which the maximum likelihood tree is a significantly better representation of the true tree, it is important to estimate the variance of the difference between log likelihood of different tree topologies. Bootstrap resampling can be used for this purpose (Hasegawa et al. 1988; Hasegawa and Kishino 1989), but it imposes a great computation burden. To overcome this difficulty, we developed a new method for estimating the variance by expressing it explicitly. The method was applied to DNA sequence data from primates in order to evaluate the maximum likelihood branching order among Hominoidea. It was shown that, although the orangutan is convincingly placed as an outgroup of a human and African apes clade, the branching order among human, chimpanzee, and gorilla cannot be determined confidently from the DNA sequence data presently available when the evolutionary rate constancy is not assumed.

The Phylogenetic Regression

Abstract: A new statistical method called the phylogenetic regression is proposed that applies multiple regression techniques to cross-species data. It allows continuous and categorical variables to be tested for and controlled for. The new method is valid despite the problem that phylogenetically close species tend to be similar, and is designed to be used when information about the phylogeny is incomplete. Information about the phylogeny of the species is assumed to be available in the form of a working phylogeny, which contains multiple nodes representing ignorance about the order of splitting of taxa. The non-independence between species is divided into that due to recognized phylogeny, that is, to phylogenetic associations represented in the working phylogeny; and that due to unrecognized phylogeny. The new method uses one linear contrast for each higher node in the working phylogeny, thus applying the ‘radiation principle’. For binary phylogenies the method is similar to an existing method. A criterion is suggested in the form of a simulation test for deciding on the acceptability of proposed statistical methods for analysing cross-species data with a continuous y-variable. This criterion is applied to the phylogenetic regression and to some other methods. The phylogenetic regression passes this test; the other methods tested fail it. Arbitrary choices have to be made about the covariance structure of the error in order to implement the method. It is argued that error results from omitted but relevant variables, and the implications for those arbitrary choices are discussed. One conclusion is that the dates of splits between taxa, even supplemented by rates of neutral gene evolution, do not provide the ‘ true ’ covariance structure. A pragmatic approach is adopted. Several analytical results about the phylogenetic regression are given, without proof, in a mathematical appendix. A computer program has been written in GLIM to implement the phylogenetic regression, and readers are informed how to obtain a copy.

Evolutionary relationship of archaebacteria, eubacteria, and eukaryotes inferred from phylogenetic trees of duplicated genes

Abstract: All extant organisms are though to be classified into three primary kingdoms, eubacteria, eukaryotes, and archaebacteria. The molecular evolutionary studies on the origin and evolution of archaebacteria to date have been carried out by inferring a molecular phylogenetic tree of the primary kingdoms based on comparison of a single molecule from a variety of extant species. From such comparison, it was not possible to derive the exact evolutionary relationship among the primary kingdoms, because the root of the tree could not be determined uniquely. To overcome this difficulty, we compared a pair of duplicated genes, elongation factors Tu and G, and the alpha and beta subunits of ATPase, which are thought to have diverged by gene duplication before divergence of the primary kingdoms. Using each protein pair, we inferred a composite phylogenetic tree with two clusters corresponding to different proteins, from which the evolutionary relationship of the primary kingdoms is determined uniquely. The inferred composite trees reveal that archaebacteria are more closely related to eukaryotes than to eubacteria for all the cases. By bootstrap resamplings, this relationship is reproduced with probabilities of 0.96, 0.79, 1.0, and 1.0 for elongation factors Tu and G and for ATPase subunits alpha and beta, respectively. There are also several lines of evidence for the close sequence similarity between archaebacteria and eukaryotes. Thus we propose that this tree topology represents the general evolutionary relationship among the three primary kingdoms.

Avian-to-human transmission of the PB1 gene of influenza A viruses in the 1957 and 1968 pandemics.

Abstract: We determined the origin and evolutionary pathways of the PB1 genes of influenza A viruses responsible for the 1957 and 1968 human pandemics and obtained information on the variable or conserved region of the PB1 protein. The evolutionary tree constructed from nucleotide sequences suggested the following: (i) the PB1 gene of the 1957 human pandemic strain, A/Singapore/1/57 (H2N2), was probably introduced from avian species and was maintained in humans until 1968; (ii) in the 1968 pandemic strain, A/NT/60/68 (H3N2), the PB1 gene was not derived from the previously circulating virus in humans but probably from another avian virus; and (iii) a current human H3N2 virus inherited the PB1 gene from an A/NT/60/68-like virus. Nucleotide sequence analysis also showed that the avian PB1 gene was introduced into pigs. Hence, transmission of the PB1 gene from avian to mammalian species is a relatively frequent event. Comparative analysis of deduced amino acid sequences disclosed highly conserved regions in PB1 proteins, which may be key structures required for PB1 activities.

Phylogenetic meaning of the kingdom concept: an unusual ribosomal RNA from Giardia lamblia

Abstract: An analysis of the small subunit ribosomal RNA (16S-like rRNA) from the protozoan Giardia lamblia provided a new perspective on the evolution of nucleated cells. Evolutionary distances estimated from sequence comparisons between the 16S-like rRNAs of Giardia lamblia and other eukaryotes exceed similar estimates of evolutionary diversity between archaebacteria and eubacteria and challenge the phylogenetic significance of multiple eukaryotic kingdoms. The Giardia lamblia 16S-like rRNA has retained many of the features that may have been present in the common ancestor of eukaryotes and prokaryotes.

Gene trees and organismal histories: a phylogenetic approach to population biology.

Abstract: A "gene tree" is the phylogeny of alleles or haplotypes for any specified stretch of DNA. Gene trees are components of population trees or species trees; their analysis entails a shift in perspective from many of the familiar models and concepts of population genetics, which typically deal with frequencies of phylogenetically unordered alleles. Molecular surveys of haplotype diversity in mitochondrial DNA (mtDNA) have provided the first extensive empirical data suitable for estimation of gene trees on a microevolutionary (intraspecific) scale. The relationship between phylogeny and geographic distribution constitutes the phylogeographic pattern for any species. Observed phylogeographic trees can be interpreted in terms of historical demography by comparison to predictions derived from models of gene lineage sorting, such as inbreeding theory and branching-process theory. Results of such analyses for more than 20 vertebrate species strongly suggest that the demographies of populations have been remarkably dynamic and unsettled over space and recent evolutionary time. This conclusion is consistent with ecological observations documenting dramatic population-size fluctuations and range shifts in many contemporary species. By adding an historical perspective to population biology, the gene-lineage approach can help forge links between the disciplines of phylogenetic systematics (and macroevolutionary study) and population genetics (microevolution). Preliminary extensions of the "gene tree" methodology to haplotypes of nuclear genes (such as Adh in Drosophila melanogaster) demonstrate that the phylogenetic perspective can also help to illuminate molecular-genetic processes (such as recombination or gene conversion), as well as contribute to knowledge of the origin, age, and molecular basis of particular adaptations.

Relative Efficiencies of the Fitch-Margoliash, Maximum-Parsimony, Maximum-Likelihood, Minimum-Evolution, and Neighbor-joining Methods of Phylogenetic Tree Construction in Obtaining the Correct Tree

Abstract: The relative efficiencies of several tree-making methods for obtaining the correct phylogenetic tree were studied by using computer simulation. The methods examined were the Fitch-Margoliash (FM), maximum-parsimony (MP), maximumlikelihood (ML), minimum-evolution (ME), and neighbor-joining (NJ) methods. We simulated the evolutionary changes of six DNA sequences each with a length of either 300 or 600 nucleotides. Both constant and varying rates of nucleotide substitution were considered. The DNA sequences generated were used to reconstruct phylogenetic trees by applying the five tree-making methods, and the trees obtained were compared with the model (correct) tree. This process was repeated 50 times for each case, and the following results were obtained: ( 1) The efficiency of obtaining the correct tree for the FM method was considerably lower than those for the other methods. (2) The NJ and ME methods showed a high performance in obtaining the correct tree, and their relative efficiencies were similar to each other. ( 3) For distance methods (NJ, FM, and ME), the results obtained by using corrected nucleotide substitutions were much better than those obtained by using nucleotide differences when the rate of substitution varied greatly among different branches. (4) The ML method was slightly inferior to the NJ and ME methods when a constant rate of nucleotide substitution was assumed, but it was slightly better than the latter two methods when the evolutionary rate varied drastically among branches. If one considers the computational time involved, the NJ method seems to be a method of choice.

Gene Genealogy in Three Related Populations: Consistency Probability between Gene and Population Trees

Abstract: A genealogical relationship among genes at a locus (gene tree) sampled from three related populations was examined with special reference to population relatedness (population tree). A phylogenetically informative event in a gene tree constructed from nucleotide differences consists of interspecific coalescences of genes in each of which two genes sampled from different populations are descended from a common ancestor. The consistency probability between gene and population trees in which they are topologically identical was formulated in terms of interspecific coalescences. It was found that the consistency probability thus derived substantially increases as the sample size of genes increases, unless the divergence time of populations is very long compared to population sizes. Hence, there are cases where large samples at a locus are very useful in inferring a population tree.

Phylogeny of some Fusarium species, as determined by large-subunit rRNA sequence comparison.

Abstract: Fifty-two strains from eight species of Fusarium were analyzed by rapid rRNA sequencing Two highly variable stretches (138 and 214 nucleotides) of the 5' end of the 28S-like rRNA molecule were sequenced Such stretches permit evaluation of the divergence between closely related species and even between varieties within a species The phylogenetic tree computed from the number of nucleotide differences shows seven Fusarium species to be more closely related to one another than the eighth species, F nivale, is to them On the basis of these data, we discuss both the phylogenetic value of taxonomical criteria and the impact of our findings on the demarcation of the genus Fusarium We conclude that this method is suitable for establishing a precise phylogeny between closely related species within a genus

Dinoflagellates in evolution. A molecular phylogenetic analysis of large subunit ribosomal RNA.

Abstract: The sequence of the large subunit ribosomal RNA (LsuRNA) gene of the dinoflagellateProrocentrum micans has been determined. The inferred rRNA sequence [3408 nucleotides (nt)] is presented in its most probable secondary structure based on compensatory mutations, energy, and conservation criteria. No introns have been found but a hidden break is present in the second variable domain, 690 nt from the 5′ end, as judged by agarose gel electrophoresis and primer extension experiments.Prorocentrum micans LsuRNA length and G+C content are close to those of ciliates and yeast. The conserved portions of the molecule (1900 nt) have been aligned with corresponding sequences from various eukaryotes, including five protista, one metaphyta, and three metazoa. An extensive phylogenetic study was performed, comparing two phenetic methods (neighbor joining on difference matrix, and Fitch and Margoliash on Knuc values matrix) and one cladistic (parsimony). The three methods led to similar tree topologies, except for the emergence of yeast that groups with ciliates and dinoflagellates when phenetic methods are used, but emerges later in the most parsimonious tree. This discrepancy was checked by statistical analyses on reduced trees (limited to four species) inferred using parsimony and evolutionary parsimony methods. The data support the phenetic tree topologies and a close relationship between dinoflagellates, ciliates, and yeast.

Host-independent evolution and a genetic classification of the hepadnavirus family based on nucleotide sequences.

Abstract: An analysis of molecular phylogeny was undertaken to examine whether the evolution of the hepadnavirus family is host-dependent. Using the nucleotide sequences of 18 strains, we constructed phylogenetic trees. The trees obtained show that all 12 strains of hepatitis B virus can be classified into four subgroups that are not compatible with conventional subtypes. We estimated the rate of synonymous (silent) substitution for hepatitis B virus to be 4.57 x 10(-5) per site per year. Applying this rate to the phylogenetic tree, we estimated that duck hepatitis B virus diverged from a common ancestor about 30,000 years ago at the earliest, that woodchuck hepatitis virus and ground squirrel hepatitis virus diverged about 10,000 years ago, and that hepatitis B virus diverged within the last 3000 years. Because these divergence times of the viruses are much more recent than those of the host species, it suggests that the hepadnavirus family evolved independently of host-species divergence.

Testing the Stochasticity of Patterns of Organismal Diversity: An Improved Null Model

Abstract: Evolutionary biologists, systematists, and paleontologists commonly have invoked deterministic explanations for certain patterns of diversity. However, few authors have considered the null model th...

Evolution of Eukaryotic Microorganisms and Their Small Subunit Ribosomal RNAs

Abstract: Traditional views about the origin of eukaryotes and relationships between major “kingdoms” reflect interpretations of the fossil record and comparisons of phenotypic characters. This perspective is challenged by phylogenetic frameworks inferred from comparisons of macromolecular sequences which share a common ancestry. Similarities between ribosomal RNA genes demonstrate that instead of being relatively recent biological inventions, eukaryotes represent a discrete lineage that may be as old as the archaebacterial and eubacterial lines of descent. The diversity of protistan small subunit rRNA sequences exceeds that seen within the entire prokaryotic world. The earliest branching lineages include diplomonads, microsporidians, and tritrichomonads. Yet, other major protistan groups diverged relatively late in the evolutionary history of nucleated cells. Rather than being a concise evolutionary assemblage, the Protista should be regarded as a collection of paraphyletic lineages. In contrast, the Fungi, Plantae, and Animalia are independent monophyletic groupings. They originated nearly simultaneously during a relatively recent period characterized by a massive diversification of forms. This novel view of eukaryotic evolution suggests that a reliance upon large phenotypic differences in delineating kingdoms can obscure true genealogical relationships. Instead of dividing eukaryotes into four or more major divisions, they should be considered as a single kingdom that encompasses a progression of independently diverging lineages.

Ribosomal-dna variation and distribution in rudbeckia missouriensis.

Abstract: Ribosomal DNA (rDNA) has been used to describe both the genetic structure within plant populations and the phylogenetic relationships among species of plants

Phylogenetic relationships of the green alga Volvox carteri deduced from small-subunit ribosomal RNA comparisons.

Abstract: The 1788-nucleotide sequence of the small-subunit ribosomal RNA (srRNA) coding region from the chlorophyteVolvox carteri was determined. The secondary structure bears features typical of the universal model of srRNA, including about 40 helices and a division into four domains. Phylogenetic relationships to 17 other eukaryotes, including two other chlorophytes, were explored by comparing srRNA sequences. Similarity values and the inspection of phylogenetic trees derived by distance matrix methods revealed a close relationship betweenV. carteri andChlamydomonas reinhardtii. The results are consistent with the view that these Volvocales, and the third green alga,Nanochlorum eucaryotum, are more closely related to higher plants than to any other major eukaryotic group, but constitute a distinct lineage that has long been separated from the line leading to the higher plants.

On the evolutionary origin of the plant mitochondrion and its genome

Abstract: Higher plants occupy very different positions in the mitochondrial and nuclear lineages of global phylogenetic trees based on conserved regions of small subunit (SSU) and large subunit (LSU) rRNA sequences. In the nuclear subtree, plants branch off late, at a position reflecting a massive radiation of the major multicellular (and some unicellular) groups; in the mitochondrial subtree, in contrast, plants branch off early, near the point of connection between the mitochondrial and eubacterial lineages. Moreover, in the nuclear lineage, plants branch together with the unicellular green alga Chlamydomonas reinhardtii, whereas in the mitochondrial lineage (in both SSU and LSU trees), metaphytes and chlorophyte branch separately. Statistical evaluation indicates that the anomalous branching position of higher plants in the mitochondrial lineage is not a treeing artifact attributable to the relatively rapid rate of sequence divergence of non-plant mitochondrial rRNA sequences. In considering alternative biological explanations for these results, we are led to propose that the rRNA genes in plant mitochondria may be of more recent evolutionary origin than the rRNA genes in other mitochondria. This proposal has implications for monophyletic vs. polyphyletic scenarios of mitochondrial origin and is consistent with other evidence indicating that plant mtDNA is an evolutionary mosaic.

Molecular evolution of human visual pigment genes.

Abstract: By comparing the published DNA sequences for (a) the genes encoding the human visual color pigments (red, green, and blue) with (b) the genes encoding human, bovine, and Drosophila rhodopsins, a phylogenetic tree for the mammalian pigment genes has been constructed. This evolutionary tree shows that the common ancestor of the visual color pigment genes diverged first from that of the rhodopsin genes; then the common ancestor of the red and green pigment genes and the ancestor of the blue pigment gene diverged; and finally the red and green pigment genes diverged from each other much more recently. Nucleotide substitutions in the rhodopsin genes are best explained by the neutral theory of molecular evolution. However, important functional adaptations seem to have occurred twice during the evolution of the color pigment genes in humans: first, to the common ancestor of the three color pigment genes after its divergence from the ancestor of the rhodopsin gene and, second, to the ancestor of the red pigment gene after its divergence from that of the green pigment gene.

Patterns of ribosomal RNA evolution in salamanders.

Abstract: Sequence comparisons are presented for four segments of the large subunit of ribosomal RNA, including divergent domains D7a and D7b, portions of the large divergent domains D2, D3, and D8, and evolutionarily conservative sequences flanking divergent domains. These results resolve phylogenetic relationships among exemplars of seven families of salamanders and the three amphibian orders. Phylogenetic analysis confirms the prediction that divergent domains feature the highest relative rates of base substitution and length variation within the ribosome, but the divergent domains evolve more slowly than nuclear noncoding DNA and the silent sites of structural genes. Base substitutions demonstrate approximately twice as many transitions as transversions and an uneven distribution among sites within the divergent domains but no apparent bias in base composition. Length mutations are primarily small insertions and deletions, with deletions predominating. The divergent domains appear to be a good source of phylogenetic information for evolutionary events occurring approximately 100-200 million years ago.

Phylogenetic analysis based on rRNA sequences supports the archaebacterial rather than the eocyte tree.

Abstract: HOW many primary lineages of life exist and what are their evolutionary relationships? These are fundamental but highly controversial issues1. Woese and co-workers2–4 propose that archaebacteria, eubacteria and eukaryotes are the three primary lines of descent and their relationships can be represented by Fig. 1a (the 'archaebacterial tree') if one neglects the root of the tree. In contrast, Lake5,6 claims that archaebacteria are paraphyletic, and he groups eocytes (extremely thermophilic, sulphur-dependent bacteria) with eukaryotes, and halobacteria with eubacteria (the 'eocyte tree', Fig. 1b). Lake's view has gained considerable support as a result of an analysis6 of small subunit ribosomal RNA sequence data by a new approach, the evolutionary parsimony method7. Here we report that analysis of small subunit data by the neighbour-joining and maximum parasimony methods8,9 favours the archaebacterial tree and that computer simulations using either the archaebacterial or the eocyte tree as a model tree show that the probability of recovering the model tree is very high (>90 per cent) for both the neighbour-joining and maximum parsimony methods but is relatively low for the evolutionary parsimony method. Moreover, analysis of large subunit rRNA sequences by all three methods strongly favours the archaebacterial tree.