Showing papers on "Phylogenetic tree published in 1992"

Signal, Noise, and Reliability in Molecular Phylogenetic Analyses

Abstract: DNA sequences and other molecular data compared among organisms may contain phylogenetic signal, or they may be randomized with respect to phylogenetic history. Some method is needed to distinguish phylogenetic signal from random noise to avoid analysis of data that have been randomized with respect to the historical relationships of the taxa being compared. We analyzed 8,000 random data matrices consisting of 10-500 binary or four-state characters and 5-25 taxa to study several options for detecting signal in systematic data bases. Analysis of random data often yields a single most-parsimonious tree, especially if the number of characters examined is large and the number of taxa examined is small (both often true in molecular studies). The most-parsimonious tree inferred from random data may also be considerably shorter than the second-best alternative. The distribution of tree lengths of all tree topologies (or a random sample thereof) provides a sensitive measure of phylogenetic signal: data matrices with phylogenetic signal produce tree-length distributions that are strongly skewed to the left, whereas those composed of random noise are closer to symmetrical. In simulations of phylogeny with varying rates of mutation (up to levels that produce random variation among taxa), the skewness of tree-length distributions is closely related to the success of parsimony in finding the true phylogeny. Tables of critical values of a skewness test statistic, g1, are provided for binary and four-state characters for 10-500 characters and 5-25 taxa. These tables can be used in a rapid and efficient test for significant structure in data matrices for phylogenetic analysis.

Gene trees and species trees: Molecular systematics as one-character taxonomy

Abstract: Reconstruction of phylogenies from molecular data has become an important and increasingly common approach in systematics. The product of such studies is a gene tree, hypoth- esizing relationships among genes or genomes. This gene tree may be fundamentally incongruent with the true species phylogeny, due to various biological phenomena such as introgression, lineage sorting, or mistaken orthology. In such circumstances all of the gene tree characters defining the relationships of molecular taxa (haplotypes) may be necessarily correlated, and the gene or genome may behave as a single species tree character. In these circumstances robustness of the gene hypoth- esis is meaningless as a measure of confidence in the species phylogenetic hypothesis. Incongruence between a phylogenetic hypothesis based on numerous, presumably independent, non-molecular characters and a single gene tree should not be assumed to be due to noise in non-molecular data. As with other characters, a character phylogeny, in this case a gene tree, can be tested best by a parsimony analysis in which other characters are included. If independence of molecular characters is assumed, then each is an equivalent phylogenetic hypothesis, as is each non-molecular character, leading to the suggestion that direct combination is appropriate. Swamping becomes an issue when a large molecular data set may be behaving as a single character. To alleviate this problem, a gene tree may be treated as a single multistate character, either ordered or unordered, and included with non-molecular data to obtain a globally parsimonious result. An example is given using published molecular and non-molecular data from the Asteraceae.

Populations, Genetic Variation, and the Delimitation of Phylogenetic Species

Abstract: Systematists should distinguish between cladistic analysis, i.e., a numerical procedure, and phylogenetic analysis, i.e., the reconstruction of hierarchic descent relationships. Modern cladistic analysis uses parsimony to construct hierarchic arrangements (trees) of terminal units (terminals) that have been scored for a series of attributes. The interpretation of cladistic relationships as representative of phylogenetic relationships requires two conditions, both of which were identified by Hennig (1966, Phylogenetic systematics, Univ. Illinois Press, Urbana). First, descent relationships among the terminals must be hierarchic; that is, all terminals must have been generated by the subdivision or replication of previously existing ancestors

The endosymbiont hypothesis revisited.

Abstract: Publisher Summary This chapter highlights endosymbiont hypothesis. All contemporary genomes (including those of plastids and mitochondria) ultimately derive from a single genome—the genome of a single, presumably cellular, entity which was the ancestor of all surviving forms of live. The construction and interpretation of phylogenetic trees based on small subunit (SSU, or 16S-like) and large subunit (LSU, or 23S-like) rRNA sequences have proven especially informative in instances where morphological diversity tends to confound traditional methods of phylogenetic analysis. In addition to ribosomal RNA (rRNA) sequence, there are a number of traits that characterize the archaebacteria as a distinct group of organisms, separate from all other prokaryotes. These include (1) cell walls that, when present, lack peptidoglycan and muramic acid; (2) the presence of lipids containing phytanyl side groups in ether linkage; and (3) the presence of RNA polymerases that are distinct from those of eubacteria in subunit composition, response to RNA synthesis inhibitors or stimulators, immunological reactivity, and gene sequence. Two major divisions of archaebacteria include (1) sulfur-dependent, extreme thermophiles; and (2) methane-producers (methanogens) and their relatives, including the extreme halophiles.

DNA sequence variation of the mitochondrial control region among geographically and morphologically remote European brown trout Saltno trutta populations

Abstract: Summary Throughout its natural range, the brown trout Salmo trutta L. exhibits a complex pattern of morphological and life-history variation. This has led to considerable taxonomic confusion, hampering the understanding of the evolutionary history of the species. To document the phylogenetic relationships among morphologically and geographically remote brown trout populations across western Europe, we determined the DNA sequence variation in segments of the mitochondrial control region for 151 individuals representing 24 populations. DNA was prepared for double-stranded sequencing by the polymerase chain reaction (PCR). Twenty-one variable nucleotide positions within a 640-bp fragment surveyed defined 12 genotypes differing by a mean of 7 nucleotide substitutions (range 1–12). Five major phylogenetic assemblages differing by mean sequence divergence estimates of 0.96 to 1.44% were identified. These groupings exhibited a strong spatial partitioning but lacked congruence with either ecological or morphological differentiation. Complete mitochondrial DNA (mtDNA) monomorphism across all Atlantic basin populations contrasted with the high interdrainage genetic diversity observed in more southerly populations. This study exemplified the usefulness of mitochondrial DNA sequence analysis for estimating phylogenetic relationships within S. trutta populations.

Analysis of a new hepatitis C virus type and its phylogenetic relationship to existing variants.

Abstract: Sequences obtained in the 5' non-coding region (5'NCR) of hepatitis C virus (HCV) were obtained from Scottish blood donors and compared with previously published HCV sequences. Phylogenetic analysis revealed the existence of three distinct groups of sequences; two of these corresponded to the recently described HCV types 1 and 2 variants, while viral sequences detected in around a third of the blood donors formed a separate phylogenetic group that probably represents infection with a novel virus species. Nucleotide sequences of this latter group differed from all previously published 5'NCR sequence variants by at least 9%. This new virus type also differed considerably from previously published variants in other regions of the viral genome (core, NS-3 and NS-5), with corrected nucleotide distances of 15, 43 and 49% respectively from the prototype HCV-1 sequence. Formal phylogenetic analysis of each of the coding regions confirmed that HCV type 1 variants could be clearly differentiated into regional variants (Far East and U.S.A./European), in contrast to the clearly overlapping geographical distributions of the main HCV types in U.K. blood donors. We discuss the evidence for and against the hypothesis that the three main phylogenetic groups identified in this study represent separate species of HCV.

Phylogeny of five fungus-like protoctistan Phytophthora species, inferred from the internal transcribed spacers of ribosomal DNA.

Abstract: Ribosomal DNA variation was used to study evolutionary relationships among five fungal-like protoctistan Phytophthora species. On the basis of morphological and ecological characteristics, four of these species--P. palmivora, P. megakarya, P. capsici, and P. citrophthora--were once thought to be related. Variation within a species was extensively studied in a fifth, outgroup species--P. cinnamomi--known, on the basis of ecological, isozyme, and mitochondrial DNA studies, to be variable. Internal transcribed spacer regions (ITS I, between the 18S and 5.8S rDNAs; and ITS II, between the 5.8S and 25S rDNAs) from 27 isolates of these five species were analyzed by polymerase chain reaction amplification and direct sequencing. Intraspecific variability was undetected or low. Interspecific nucleotide difference was 0.3%-14.6%, and comparisons of variable regions permitted the evaluation of phylogenetic relationships among species. Both neighbor-joining and parsimony analysis of ITS variability support a close relationship between cacao isolates of P. capsici and P. citrophthora and a common lineage for P. palmivora and P. megakarya. Large distance values were estimated between P. cinnamomi and the other species. Inferred relationships based on ITS variability were compared with those based on other characters. The catalog of sequences provides the information necessary to design taxon-specific probes potentially useful in taxonomic, ecological, and population-level studies.

Ty1-copia group retrotransposons are ubiquitous and heterogeneous in higher plants.

Abstract: We have used the polymerase chain reaction to isolate fragments of Ty1-copia group retrotransposons from a wide variety of members of the higher plant kingdom 56 out of 57 species tested generate an amplified fragment of the size expected for reverse transcriptase fragments of Ty1-copia group retrotransposons Sequence analysis of subclones shows that the PCR fragments display varying degrees of sequence heterogeneity Sequence heterogeneity therefore seems a general property of Ty1-copia group retrotransposons of higher plants, in contrast to the limited diversity seen in retrotransposons of Saccharomyces cerevisiae and Drosophila melanogaster Phylogenetic analysis of all these sequences shows, with some significant exceptions, that the degree of sequence divergence in the retrotransposon populations between any pair of species is proportional to the evolutionary distance between those species This implies that sequence divergence during vertical transmission of Ty1-copia group retrotransposons within plant lineages has been a major factor in the evolution of Ty1-copia group retrotransposons in higher plants Additionally, we suggest that horizontal transmission of this transposon group between different species has also played a role in this process

Ribosomal RNA as a Phylogenetic Tool in Plant Systematics

Abstract: The traditional classification of plants into respective classes, orders, families, genera, and species has until recently been based on shared morphologic, cytologic, biochemical, and ecologic traits. The development of techniques in molecular biology including those for molecular hybridization, cloning, restriction endo-nuclease digestions, and protein and nucleic acid sequencing have provided many new tools for the investigation of phylogenetic relationships. At the molecular level, the most fundamental comparison possible is of the primary nucleotide sequences of homologous genes in different populations or species.

Phylogenetics of the Cotton Genus (Gossypium): Character-State Weighted Parsimony Analysis of Chloroplast-DNA Restriction Site Data and Its Systematic and Biogeographic Implications

Abstract: ABsTRAcr. Total genomic DNAs from 61 accessions of 40 species of Gossypium were surveyed for restriction site variation in the maternally inherited plastid genome using 25 endonucleases. One hundred thirty-five of the 202 restriction site variants detected were potentially synapomorphous and served as binary characters for phylogeny estimation. Two cladistic methods were employed: Wagner parsimony analysis, which resulted in four equally most-parsimonious topologies requiring 161 steps (CI = 0.84), and a novel character-state weighting approach that models the relative probabilities of restriction site losses versus gains. This latter technique, which is theoretically preferable to both Dollo and Wagner parsimony analysis in that it optimizes against parallel site gains, resulted in two optimal phylogenetic estimates (a subset of the Wagner topologies) that differ only in the placement of G. longicalyx. In general, maternal cladistic relationships are congruent with both cytogenetic groupings and geographic clustering. Three major monophyletic clades among diploid species correspond to three continents: Australia (C-, G-genome), the Americas (D-genome), and Africa (A-, E-, and F-genome). African B-genome diploids are placed as sister to the New World D-genome species, albeit by a single homoplasious character state. Substantial agreement is also evident between the cpDNA phylogeny and traditional taxonomic treatments, although there is considerable disagreement at lower infrageneric ranks, particularly among the American and Australian cottons. These discrepancies are discussed, as is the possibility that inconsistency may reflect, at least in part, reticulation events among diploids, which may have occurred in at least three cases. An area cladogram suggests that Gossypium originated in either Africa or Australia. Because paleocontinental reconstructions, palynological evidence and cpDNA sequence divergence estimates concur in suggesting that the two primary clades diverged during the mid to upper Oligocene, the initial cladogenetic event most likely involved long-distance, intercontinental dispersal. Two colonizations of the New World are indicated, a relatively early long-distance dispersal from Africa leading to the evolution of the D-genome diploids, and a second, later dispersal of the maternal, A-genome ancestor of the allopolyploids. American diploid species are hypothesized to have originated in northwestern Mexico, with later radiations into other regions. The radiation of Gossypium in Australia is suggested to have proceeded from the westernmost portion of the continent. The maternal phylogenetic hypothesis and area cladogram suggest the possibility that New World allopolyploids originated following a trans-Pacific transfer of an ancestral A-genome taxon to the Pacific coast of Mesoamerica or South America.

Use of Chloroplast DNA Rearrangements in Reconstructing Plant Phylogeny

Abstract: Reconstructing phytogenies among genera and at higher taxonomic levels always has been fraught with difficulties. Conventional plant classifications employ a diverse array of approaches (phytochemical, anatomic, morphologic, etc.) and often offer a synthesis of these data sets. Many of these traditional characters are susceptible to convergent evolution by natural selection; the ensuing homoplasy largely precludes robust phytogenies. Only recently have we been able to examine the genetic material itself to investigate phylogenetic relationships. Chloroplast DNA (cpDNA) variation has proven to be immensely valuable in reconstructing phytogenies at the species level, and the application of cpDNA comparisons at higher taxonomic levels is now being pursued actively.

Experimental phylogenetics: generation of a known phylogeny.

Abstract: Although methods of phylogenetic estimation are used routinely in comparative biology, direct tests of these methods are hampered by the lack of known phylogenies. Here a system based on serial propagation of bacteriophage T7 in the presence of a mutagen was used to create the first completely known phylogeny. Restriction-site maps of the terminal lineages were used to infer the evolutionary history of the experimental lines for comparison to the known history and actual ancestors. The five methods used to reconstruct branching pattern all predicted the correct topology but varied in their predictions of branch lengths; one method also predicts ancestral restriction maps and was found to be greater than 98 percent accurate.

Molecular phylogeny of northern hemisphere species of Armillaria

Abstract: This study used polymerase chain reaction amplification and direct sequencing of double-stranded DNA to compare the intergenic region between the 3' end of the 26S gene and the 5S gene of the nuclear, ribosomal DNA of several northern hemisphere species of Armillaria. The aligned sequences were scored for base substitutions and phylogenetic relationships among species were analyzed by parsimony. We concluded 1) that the intergenic region sequences of A. ostoyae, A. gemina, and A. borealis are more closely related to one another than to any other species; 2) that the intergenic region sequences of A. lutea, A. calvescens, A. cepistipes, A. sinapina, species IX and species X constitute a closely related group distinguishable from those of A. ostoyae, A. boralis, and A. gemina by a significant number of substitutions; and 3) that the morphological divergence in A. mellea and A. tabescens relative to the majority of northern hemisphere species and to each other has been roughly paralleled by divergence in the intergenic region, which aligned poorly in all interspecies comparisons including A. mellea and A. tabescens. A byproduct of this study was the identification of several substitutions in the intergenic region sequence that could potentially provide the basis for rapid species diagnosis.

Origins of genes: "big bang" or continuous creation?

Abstract: Many protein families are common to all cellular organisms, indicating that many genes have ancient origins. Genetic variation is mostly attributed to processes such as mutation, duplication, and rearrangement of ancient modules. Thus it is widely assumed that much of present-day genetic diversity can be traced by common ancestry to a molecular "big bang." A rarely considered alternative is that proteins may arise continuously de novo. One mechanism of generating different coding sequences is by "overprinting," in which an existing nucleotide sequence is translated de novo in a different reading frame or from noncoding open reading frames. The clearest evidence for overprinting is provided when the original gene function is retained, as in overlapping genes. Analysis of their phylogenies indicates which are the original genes and which are their informationally novel partners. We report here the phylogenetic relationships of overlapping coding sequences from steroid-related receptor genes and from tymovirus, luteovirus, and lentivirus genomes. For each pair of overlapping coding sequences, one is confined to a single lineage, whereas the other is more widespread. This suggests that the phylogenetically restricted coding sequence arose only in the progenitor of that lineage by translating an out-of-frame sequence to yield the new polypeptide. The production of novel exons by alternative splicing in thyroid receptor and lentivirus genes suggests that introns can be a valuable evolutionary source for overprinting. New genes and their products may drive major evolutionary changes.

Clonal analysis of methicillin-resistant Staphylococcus aureus strains from intercontinental sources: association of the mec gene with divergent phylogenetic lineages implies dissemination by horizontal transfer and recombination.

Abstract: Genetic relationships among 254 isolates of Staphylococcus aureus resistant to methicillin recovered between 1961 and 1992 from nine countries on four continents were determined by analyzing electrophoretically demonstrable allelic variation at 15 chromosomal enzyme loci. Fifteen distinctive electrophoretic types, marking clones, were identified. The mec gene is harbored by many divergent phylogenetic lineages representing a large portion of the breadth of chromosomal diversity in the species, a result that is interpreted as evidence that multiple episodes of horizontal transfer and recombination have contributed to the spread of this resistance determinant in natural populations. Isolates recovered in the United Kingdom, Denmark, Switzerland, Egypt, and Uganda in the 1960s are of a single multilocus enzyme genotype and probably are progeny of an ancestral methicillin-resistant clone. There is geographic variation in the frequency of recovery of the common methicillin-resistant clones, an observation that may in part explain reported regional differences in natural history correlates of resistant organisms.

Phylogenetic Classification of Human Papillomaviruses: Correlation With Clinical Manifestations

Abstract: Human papillomaviruses (HPVs) are a heterogeneous group of small dsDNA viruses which cause a variety of proliferative epithelial lesions at specific anatomical sites. Although more than 65 different virus types have been cloned and characterized, no uniform classification system exists. In order to classify HPV DNA types, phylogenetic trees were constructed based on nucleotide sequence alignments using parsimony and distance matrix algorithms. The resulting phylogenetic trees provide a classification of the HPVs into specific groups encompassing the known tissue tropism and oncogenic potential of each HPV type. The implications of a phylogenetic taxonomy on the diagnostic detection of HPVs and the concept of different HPV species are discussed.

The Role of Phylogenetic Analysis in the Inference of Unpreserved Attributes of Extinct Taxa

Abstract: A research programme is proposed for the inference of unpreserved attributes of fossil taxa. The programme includes: (i) phylogenetic inference of attributes based on the cladistic distribution of known features in related taxa; and (ii) extrapolatory analyses that infer unpreserved features from the known attributes of the fossil. Phylogenetic inferences regarding the fossil taxon are based on the attributes of both the sister group of the fossil taxon and more distantly related clades. Unlike phylogenetic inferences that are based on a single related taxon, this broader phylogenetic context avoids unjustified assumptions regarding the occurrence of unpreserved features in particular fossil taxa. Phylogenetic inference is conservative; only features in related taxa can be inferred in the fossil. Extrapolatory analyses, such as form-function correlation and biomechanical design analysis, provide a means for choosing among equivocal phylogenetic inferences, and, on occasion, can provide a basis for rejecting a phylogenetic inference. Extrapolatory approaches provide the only means of inferring or interpreting autapomorphies in fossils. The results of phylogenetic and extrapolatory approaches to the reconstruction of the shoulder musculature of the ornithomimid Struthiomimus are compared. Results are congruent in most instances; however, many of the extrapolatory inferences are implicitly phylogenetic. The phylogenetic inferences constitute a null hypothesis regarding fossil attributes, and place constraints on the inferences generated by extrapolatory analyses. The potential uncertainty and untestability of many extrapolatory analyses suggests that the phylogenetic inference should be overturned only when the functional or other extrapolatory evidence is compelling. This procedure should identify and reduce speculation in fossil reconstruction.

Patterns in tree balance among cladistic, phenetic, and randomly generated phylogenetic trees.

Abstract: I examine patterns in tree balance for a sample of 208 cladograms and phenograms from the recent literature. I provide an expression for expected imbalance under a simple, uniform-rate random speciation model, and I estimate variances by simulation for the same model. Imbalance decreases with tree size (number of included taxa) in both theoretical and literature trees. In contrast to previous suggestions, I find cladistic trees to be no more imbalanced than phenetic trees when confounding variables are appropriately controlled. The degree of imbalance found in literature trees is inconsistent with the uniform-rate speciation model; this is most likely a result of variability in speciation and extinction rates among real lineages. The existence of such variation is a necessary (but not sufficient) condition for the operation of the macroevolutionary processes of species sorting and species selection.

The use of rRNA sequences and fluorescent probes to investigate the phylogenetic positions of the anaerobic ciliate Metopus palaeformis and its archaeobacterial endosymbiont.

Abstract: The polymerase chain reaction (PCR) was used to amplify small-subunit ribosomal DNA from the anaerobic ciliated protozoon Metopus palaeformis, and from its uncultured endosymbiotic bacteria. This was accomplished directly from total DNA extracted from protozoa without prior isolation or enrichment for symbiont cells. The double-stranded amplification products were precipitated and directly sequenced using the linear PCR reaction. Fluorescent oligonucleotide probes were designed and used in whole-cell hybridizations to provide direct visual evidence that the sequences originated from the host ciliate and from the endosymbiont. Phylogenetic analysis of the Metopus palaeformis sequence consistently placed it as a deep-branching lineage near the root of the ciliate tree. However, the present data were insufficient to resolve the detailed relationship between Blepharisma and Metopus and thus to determine if the heterotrichs are mono- or paraphyletic. Phylogenetic analysis of the symbiont partial sequence clearly demonstrated that it is an archaeobacterium and that it is closely related to, but distinct from, Methanobacterium formicicum.

Evolution of the capsid protein genes of foot-and-mouth disease virus: antigenic variation without accumulation of amino acid substitutions over six decades.

Abstract: The genetic diversification of foot-and-mouth disease virus (FMDV) of serotype C over a 6-decade period was studied by comparing nucleotide sequences of the capsid protein-coding regions of viruses isolated in Europe, South America, and The Philippines. Phylogenetic trees were derived for VP1 and P1 (VP1, VP2, VP3, and VP4) RNAs by using the least-squares method. Confidence intervals of the derived phylogeny (significance levels of nodes and standard deviations of branch lengths) were placed by application of the bootstrap resampling method. These procedures defined six highly significant major evolutionary lineages and a complex network of sublines for the isolates from South America. In contrast, European isolates are considerably more homogeneous, probably because of the vaccine origin of several of them. The phylogenetic analysis suggests that FMDV CGC Ger/26 (one of the earliest FMDV isolates available) belonged to an evolutionary line which is now apparently extinct. Attempts to date the origin (ancestor) of the FMDVs analyzed met with considerable uncertainty, mainly owing to the stasis noted in European viruses. Remarkably, the evolution of the capsid genes of FMDV was essentially associated with linear accumulation of silent mutations but continuous accumulation of amino acid substitutions was not observed. Thus, the antigenic variation attained by FMDV type C over 6 decades was due to fluctuations among limited combinations of amino acid residues without net accumulation of amino acid replacements over time.

Heterogeneity in the substitution process of amino acid sites of proteins coded for by mitochondrial DNA.

Abstract: Several forms of maximum likelihood models are applied to aligned amino acid sequence data coded for in the mitochondrial DNA of six species (chicken, frog, human, bovine, mouse, and rat). These models range in form from relatively simple models of the type currently used for inferring phylogenetic tree structure to models more complex than those that have been used previously. No major discrepancies between the optimal trees inferred by any of these methods are found, but there are huge differences in adequacy of fit. A very significant finding is that the fit of any of these models is vastly improved by allowing a certain proportion of the amino acid sites to be invariant. An even more important, although disquieting, finding is that none of these models fits well, as judged by standard statistical criteria. The primary reason for this is that amino acid sites undergo substitution according to a process that is very heterogeneous. Because most phylogenetic inference is accomplished by choosing the optimal tree under the assumption that a homogeneous process is acting on the sites, the potential invalidity of some such conclusions is raised by this article's results. The seriousness of this problem depends upon the robustness of the phylogenetic inferential procedure to departures from the underlying model.