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At least 631 records · Page 35Linked to original sources
PubMed1988

The complete nucleotide sequence of the small-subunit ribosomal RNA coding region for the cycad Zamia pumila: phylogenetic implications.

The DNA sequence of the small-subunit ribosomal RNA coding region for the cycad Zamia pumila L. was determined. The Zamia small-subunit rRNA was found to be 1813 nucleotides in length and approximately 92% identical to published angiosperm small-subunit rRNA sequences. Conserved regions interspersed with variable regions are observed corresponding to those found in other eukaryotic small-subunit sequences. Using representatives from protist, fungal, plant, and animal groups, a distance matrix was constructed of average nucleotide substitution rates for pairs of organisms. Phylogenetic trees were inferred from similarities between sequences. The sequence of Zamia represents the earliest divergence from the higher plant lineage reported to date for small-subunit rRNA data. Inferred phylogenies also support a monophyletic origin for the angiosperms consistent with studies citing phenotypic characters.

Base Sequence↗
PubMed2001

Evolution of the angiosperms: calibrating the family tree.

Growing evidence of morphological diversity in angiosperm flowers, seeds and pollen from the mid Cretaceous and the presence of derived lineages from increasingly older geological deposits both imply that the timing of early angiosperm cladogenesis is older than fossil-based estimates have indicated. An alternative to fossils for calibrating the phylogeny comes from divergence in DNA sequence data. Here, angiosperm divergence times are estimated using non-parametric rate smoothing and a three-gene dataset covering ca. 75% of all angiosperm families recognized in recent classifications. The results provide an initial hypothesis of angiosperm diversification times. Using an internal calibration point, an independent evaluation of angiosperm and eudicot origins is performed. The origin of the crown group of extant angiosperms is indicated to be Early to Middle Jurassic (179-158 Myr), and the origin of eudicots is resolved as Late Jurassic to mid Cretaceous (147-131 Myr). Both estimates, despite a conservative calibration point, are older than current fossil-based estimates.

Calibration↗
PubMed1995

The evolution of protamine P1 genes in dasyurid marsupials.

We report the complete DNA sequences of the protamine P1 gene and flanking regions for 13 species of the marsupial family Dasyuridae. The structure of the protamine locus is conserved in dasyurids and consists of two exons (of lengths 142-151 and 47 bp) separated by an intron (208-240 bp). A key feature of the dasyurid intron is a 38-40 bp duplication found in all species examined to date. This duplication apparently predates the radiation of modern dasyurid lineages and may be homologous to a similar feature in the marsupial mole (Notoryctes). Sequences from a species of Planigale demonstrate that this genus is unique among marsupials in possessing cysteine residues in its protamine P1 molecules. Cysteines may provide enhanced chemical stability for condensed sperm nuclei, a physiological feature that would converge on the common eutherian pattern. Phylogenetic analysis of the protamine genes yields a tree that is largely congruent with previous molecular systematic studies in two areas: (1) There are three main dasyurid lineages corresponding to the Sminthopsinae. Dasyurinae, and Phascogalinae; (2) Dasyurinae and Phascogalinae are sister groups. This study is the first estimate of dasyurid relationships based on a nuclear DNA sequence.

Amino Acid Sequence↗
PubMed1997

Identification of three lineages of wild measles virus by nucleotide sequence analysis of N, P, M, F, and L genes in Japan.

The nucleotide sequences of nucleocapsid (N), phosphoprotein (P), matrix (M), fusion (F), and large protein (L) genes were partly determined for 19 wild strains of measles virus (MV) isolated over the past 10 years in Japan (nucleotide position N: 1301-1700, P: 1751-2190, M: 3571-4057, F: 6621-7210, L: 10381-11133) and also for a MV strain obtained from a patient with subacute sclerosing panencephalitis (SSPE) who had natural measles in 1980. The phylogenetic trees of these strains drawn for respective genes were very similar to each other and revealed that all the wild strains were classified chronologically into 3 subgroups, those isolated in 1984, 1984-1989, and 1990-1994. The SSPE strain was classified into the subgroup of 1984. Phylogenetic tree analyses including other strains in the world revealed that Japanese strains in 1984 were classified into a distinct lineage which might correlate with the European strains from late 1970s to mid 1980s. Japanese strains from 1984 to 1989 were almost identical to those of the United States isolated from 1989 to 1992, and Japanese strains in 1990s were related closely to some of the MV strains isolated in 1994 in the United States. Genetic recombination among the MV genes seemed not to have occurred.

Adolescent↗
PubMed1995

Two Japanese wildcats, the Tsushima cat and the Iriomote cat, show the same mitochondrial DNA lineage as the leopard cat Felis bengalensis.

We previously revealed, based on mitochondrial DNA sequence analysis, that the Iriomote cat is very closely related to the leopard cat Felis bengalensis, which is widespread in Asia [24]. In this study, in order to understand the phylogenetic status of the Tsushima cat which is the other wildcat in Japan, partial sequences (402 bases) of the mitochondrial cytochrome b region were determined and compared with those of the Iriomote cat and other feline species. The phylogenetic tree of the cytochrome b sequences indicated that the Tsushima cat and the Iriomote cat have the same mitochondrial DNA lineage as the leopard cat. One or two transitional substitutions were observed among the two Japanese wildcats and the leopard cat. The divergence time (approximately 100,000 years ago) of the Tsushima cat and the leopard cat, estimated by sequence data, was in concordance with the formation date of the Tsushima Island. These results suggest that genetic drift after geographic isolation has brought fixation of some genetic and morphological characters to the Tsushima cat and the Iriomote cat, while these two Japanese wildcats are still genetically close to the continental leopard cat. Considering morphological differences and molecular phylogeny, it is reasonable for the two Japanese wildcats to be classified as two subspecies of F. bengalensis.

Animals↗
PubMed2005

Estimating the tempo and mode of gene family evolution from comparative genomic data.

Comparison of whole genomes has revealed that changes in the size of gene families among organisms is quite common. However, there are as yet no models of gene family evolution that make it possible to estimate ancestral states or to infer upon which lineages gene families have contracted or expanded. In addition, large differences in family size have generally been attributed to the effects of natural selection, without a strong statistical basis for these conclusions. Here we use a model of stochastic birth and death for gene family evolution and show that it can be efficiently applied to multispecies genome comparisons. This model takes into account the lengths of branches on phylogenetic trees, as well as duplication and deletion rates, and hence provides expectations for divergence in gene family size among lineages. The model offers both the opportunity to identify large-scale patterns in genome evolution and the ability to make stronger inferences regarding the role of natural selection in gene family expansion or contraction. We apply our method to data from the genomes of five yeast species to show its applicability.

Evolution, Molecular↗
PubMed1991

Homeoboxes in cnidarians.

Homeoboxes have previously been documented from various phyla of triploblastic, coelomate and pseudocoelomate, animals. We report here the first homeoboxes from cnidarians, a phylum of diploblastic organisms thought to occupy a near-basal position in metazoan phylogeny. We have sequenced three partial (77 bp) fragments of Antennapedia (Antp) class homeoboxes from the hydroids Hydractinia symbiolongicarpus and Eleutheria dichotoma. A pair of fragments, Cnox-2-Hs and Cnox-2-Ed, from the two species differ in nucleotide sequences but have identical derived amino acid sequences. A gene tree produced by parsimony analysis shows that these two fragments cluster within the Antp homeobox lineage. The third fragment, Cnox-1, clusters as a sister group of the other Antp class homeoboxes.

Amino Acid Sequence↗
PubMed1998

Rapid speciation, morphological evolution, and adaptation to extreme environments in South African sand lizards (Meroles) as revealed by mitochondrial gene sequences.

Data derived from the morphology of the seven species of South African sand lizards, Meroles (Reptilia, Lacertidae), and their outgroups produce a robust estimate of phylogeny when a maximum parsimony approach is applied. The estimate is fully resolved with little character conflict and internal branches are relatively long. This analysis indicates that Meroles is a true clade that includes the aberrant lacertid long separated as Aporosaura anchietae. The tree is pectinate, its successive external branches representing species with increasing adaptation to desert conditions, especially aeolian sand habitats. This pattern, and the robustness of the tree, support a model of invasion of severe habitats in which successive rounds of speciation, displacement, and adaptation result in spread into extreme ecological situations. To test the robust morphological phylogeny and, indirectly, the model as well, DNA from mitochondrial 12S and 16S ribosomal genes was sequenced and analyzed by both maximum parsimony and maximum likelihood approaches. Trees produced were largely congruent with that derived from morphology, although different from ones resulting from protein electrophoresis. However, in contrast to the internal branches of the morphological tree, those of the DNA maximum likelihood tree are quite short. The DNA data provide some corroboration for the relationships within Meroles based on morphology and consequently for the model as well. The disparity in internal branch lengths between the maximum parsimony morphological and maximum likelihood DNA trees may well indicate that the multiple adaptations to desert conditions arising on the main lineage of Meroles evolved quite rapidly. In this study DNA thus not only corroborates the phylogeny but also provides evidence about another aspect of evolutionary history.

Adaptation, Physiological↗
PubMed1994

Phylogenetic affiliations of Rhodoferax fermentans and related species of phototrophic bacteria as determined by automated 16S rDNA sequencing.

16S rDNA sequences of strains of Rhodoferax fermentans were analyzed and compared with those of species of the genera Rubrivivax and Rhodocyclus. Approximately 1.5-kb fragments of 16S rDNA from crude cell lysates were amplified by the polymerase chain reaction (PCR) and sequenced directly by using Tth DNA polymerase with the linear PCR sequencing protocol, followed by on-line detection with an automated laser fluorescent DNA sequencer. Pairwise sequence comparisons and distance matrix tree analysis showed that Rhodoferax fermentans, Rubrivivax gelatinosus, and Rhodocyclus species belong to three separate lineages within the beta subclass of the Proteobacteria, thereby confirming the phylogenetic validity of the genus Rhodoferax, as well as of the genera Rubrivivax and Rhodocyclus.

Automation↗
PubMed2004

The Evolution of SINEs and LINEs in the genus Chironomus (Diptera).

Genomic DNA amplification from 51 species of the family Chironomidae shows that most contain relatives of NLRCth1 LINE and CTRT1 SINE retrotransposons first found in Chironomus thummi. More than 300 cloned PCR products were sequenced. The amplified region of the reverse transcriptase gene in the LINEs is intact and highly conserved, suggesting active elements. The SINEs are less conserved, consistent with minimal/no selection after transposition. A mitochondrial gene phylogeny resolves the Chironomus genus into six lineages (Guryev et al. 2001). LINE and SINE phylogenies resolve five of these lineages, indicating their monophyletic origin and vertical inheritance. However, both the LINE and the SINE tree topologies differ from the species phylogeny, resolving the elements into "clusters I-IV" and "cluster V" families. The data suggest a descent of all LINE and SINE subfamilies from two major families. Based on the species phylogeny, a few LINEs and a larger number of SINEs are cladisitically misplaced. Most misbranch with LINEs or SINEs from species with the same families of elements. From sequence comparisons, cladistically misplaced LINEs and several misplaced SINEs arose by convergent base substitutions. More diverged SINEs result from early transposition and some are derived from multiple source SINEs in the same species. SINEs from two species (C. dorsalis, C. pallidivittatus), expected to belong to the clusters I-IV family, branch instead with cluster V family SINEs; apparently both families predate separation of cluster V from clusters I-IV species. Correlation of the distribution of active SINEs and LINEs, as well as similar 3' sequence motifs in CTRT1 and NLRCth1, suggests coevolving retrotransposon pairs in which CTRT1 transposition depends on enzymes active during NLRCth1 LINE mobility.

Animals↗
PubMed2005

Triplicate genes for mitochondrial ADP/ATP carriers in the aerobic yeast Yarrowia lipolytica are regulated differentially in the absence of oxygen.

Yarrowia lipolytica is a strictly aerobic fungus, which differs from the extensively studied model yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe with respect to its physiology, genetics and dimorphic growth habit. We isolated and sequenced cDNA and genomic clones (YlAAC1) from Y. lipolytica that encode a mitochondrial ADP/ATP carrier. The YlAAC1 gene can complement the S. cerevisiae Deltaaac2 deletion mutant. Southern hybridization, analysis of Yarrowia clones obtained in the course of the Genolevures project, and further sequencing revealed the existence of two paralogs of the YlAAC1 gene, which were named YlAAC2 and YlAAC3, respectively. Phylogenetic analysis showed that YlAAC1 and YlAAC2 were more closely related to each other than to YlAAC3, and are likely to represent the products of a recent gene duplication. All three Y. lipolytica YlAAC genes group together on the phylogenetic tree, suggesting that YlAAC3 is derived from a more ancient duplication within the Y. lipolytica lineage. A similar branching pattern for the three ScAAC paralogs in the facultative anaerobe S. cerevisiae demonstrates that two rounds of duplication of AAC genes occurred independently at least twice in the evolution of hemiascomycetous yeasts. Surprisingly, in both the aerobic Y. lipolytica and the facultative anaerobe S. cerevisiae, the three paralogs are differentially regulated in the absence of oxygen. Apparently, Y. lipolytica can sense hypoxia and down-regulate target genes in response.

Amino Acid Sequence↗
PubMed1992

Detecting morphological convergence in true fungi, using 18S rRNA gene sequence data.

For the true fungi, phylogenetic relationships inferred from 18S ribosomal DNA sequence data agree with morphology when (1) the fungi exhibit diagnostic morphological characters, (2) the sequence-based phylogenetic groups are statistically supported, and (3) the ribosomal DNA evolves at roughly the same rate in the lineages being compared. 18S ribosomal RNA gene sequence data and biochemical data provide a congruent definition of true fungi. Sequence data support the traditional fungal subdivisions Ascomycotina and Basidiomycotina. In conflict with morphology, some zygomycetes group with chytrid water molds rather than with other terrestrial fungi, possibly owing to unequal rates of nucleotide substitutions among zygomycete lineages. Within the ascomycetes, the taxonomic consequence of simple or reduced morphology has been a proliferation of mutually incongruent classification systems. Sequence data provide plausible resolution of relationships for some cases where reduced morphology has created confusion. For example, phylogenetic trees from rDNA indicate that those morphologically simple ascomycetes classified as yeasts are polyphyletic and that forcible spore discharge was lost convergently from three lineages of ascomycetes producing flask-like fruiting bodies.

DNA, Fungal↗
PubMed2004

Phylogeny of the festucoid grasses of subtribe Loliinae and allies (Poeae, Pooideae) inferred from ITS and trnL-F sequences.

Analyses of ribosomal ITS and chloroplast trnL-F sequences provide phylogenetic reconstruction for the festucoids (Poeae: Loliinae), a group of temperate grasses with morphological and molecular affinities to the large genus Festuca. Parsimony and Bayesian analyses of the combined ITS/trnL-F dataset show Loliinae to be monophyletic but unresolved for a weakly supported clade of 'broad-leaved Festuca,' a well-supported clade of 'fine-leaved Festuca,' and Castellia. The first group includes subgenera Schenodorus, Drymanthele, Leucopoa, and Subulatae, and sections Subbulbosae, Scariosa, and Pseudoscariosa of Festuca, plus Lolium and Micropyropsis. The second group includes sections Festuca, Aulaxyper, Eskia, and Amphigenes of Festuca, plus Vulpia, Ctenopsis, Psilurus, Wangenheimia, Cutandia, Narduroides, and Micropyrum. Subtribes Dactylidinae and Cynosurinae/Parapholiinae are sister clades and are the closest relatives of Loliinae. Vulpia is polyphyletic within the 'fine-leaved' fescues as revealed by the two genome analyses. Lolium is resolved as monophyletic in the ITS and combined analyses, but unresolved in the trnL-F based tree. Conflict between the ITS and the trnL-F trees in the placement of several taxa suggests the possibility of past reticulation events, although lineage sorting and possible ITS paralogy cannot be ruled out.

Bayes Theorem↗
PubMed2003

Detecting excess radical replacements in phylogenetic trees.

There are a few instances in which positive Darwinian selection has been convincingly demonstrated at the molecular level. In this study, we present a novel test for detecting excess of radical amino-acid replacements. Such excess is usually indicative of positive Darwinian selection, but may also be due to relaxed functional constraints or model misspecification. In our test, each amino-acid replacement is characterized in terms of a physicochemical distance, i.e., the degree of dissimilarity between the exchanged amino-acid residues. By using phylogenetic trees based on protein sequences, our test identifies statistically significant deviations of the mean physicochemical distance from the random expectation, either along a taxonomic lineage or across a subtree. The mean inferred distance is calculated as the average physicochemical distance over all possible ancestral sequence reconstructions weighted by their likelihood. Our method substantially improves over previous approaches by taking into account the stochastic process, tree phylogeny, among-site rate variation, and alternative ancestral reconstructions. We provide a fast linear time algorithm for applying this test to all branches and all subtrees of a given phylogenetic tree. We validate this approach by applying it to two well-studied datasets: the MHC class I glycoproteins serving as a positive control, and the house-keeping gene carbonic anhydrase I serving as a negative control.

Algorithms↗
PubMed2002

Mitochondrial-type hsp70 genes of the amitochondriate protists, Giardia intestinalis, Entamoeba histolytica and two microsporidians.

Genes encoding putative mitochondrial-type heat shock protein 70 (mit-hsp70) were isolated and sequenced from amitochondriate protists, Giardia intestinalis, Entamoeba histolytica, and two microsporidians, Encephalitozoon hellem and Glugea plecoglossi. The deduced mit-hsp70 sequences were analyzed by sequence alignments and phylogenetic reconstructions. The mit-hsp70 sequence of these four amitochondriate protists were divergent from other mit-hsp70 sequences of mitochondriate eukaryotes. However, all of these sequences were clearly located within a eukaryotic mitochondrial clade in the tree including various type hsp70 sequences, supporting the emerging notion that none of these amitochondriate lineages are primitively amitochodrial, but lost their mitochondria secondarily in their evolutionary past.

Amino Acid Sequence↗
PubMed1981

Simple method for constructing phylogenetic trees from distance matrices.

A simple method is proposed for constructing phylogenetic trees from distance matrices. The procedure for constructing tree topologies is similar to that of the unweighted pair-group method (UPG method) but makes corrections for unequal rates of evolution among lineages. The procedure for estimating branch lengths is the same as that of the Fitch and Margoliash method (F-M method) except that it allows no negative branch lengths. The performance of the present procedure for the construction of tree topologies is compared with that of the UPG method, the F-M method, Farris' method, and the modified Farris method by using Tateno's simulation outputs for nucleotide sequence divergence and his results for the performances of the latter four methods [Tateno, Y. (1978) Dissertation (Univ. Texas, Houston, TX). In this limited comparison, the present method performs considerably better than the UPG method and the F-M method and about equally well as the last two methods. The present method appears to be preferable to the UPG method for analysis of data from populations that have not differentiated much. Indeed, an application of the present method to gene frequency data from some Amerindian populations gives a tree topology far more reasonable than that obtained by the UPG method.

Biological Evolution↗
PubMed1998

Full-length sequence analysis of the vacA gene from cytotoxic and noncytotoxic Helicobacter pylori.

Some clinical isolates of Helicobacter pylori fail to express vacuolating cytotoxin, despite possessing a copy of the vacA gene on the chromosome. To gain insight into the differences between vacA from cytotoxic and noncytotoxic strains, the vacA open-reading frames from 16 cytotoxic and 22 noncytotoxic strains were sequenced. Mutations that cause truncation of VacA in 11 of 22 noncytotoxic strains were identified, including internal duplication, large deletion, 1-bp insertion, and non-sense mutations. In contrast, none of the 16 cytotoxic strains had any truncation of VacA. Four cytotoxic strains had inserted sequences downstream of vacA. Three were mini-IS605, and the other was a putative rfaJ gene that encodes lipopolysaccharide glucosyltransferase. The rfaJ gene identified in this study had a poly(C) tract, resulting in premature termination of the gene product. The phylogenetic tree based on the vacA open-reading frame indicated that two different H. pylori lineages are circulating in Japan and the West.

Bacterial Proteins↗
PubMed1998

Clonal distribution of the three alleles of the Gal(alpha1-4)Gal-specific adhesin gene papG among Escherichia coli strains from patients with bacteremia.

The three alleles of papG, the Gal(alpha1-4)Gal-specific adhesin gene of Escherichia coli P fimbriae, were detected in 101 (54%) of 187 E. coli bacteremia isolates from Boston, Long Beach, California, and Nairobi, Kenya, by a polymerase chain reaction-based assay, and their distribution was compared with clonal structure and other bacterial and host characteristics. Allele II predominated overall (57% of papG+ strains, vs. 32% for III and 2% for I). Allele distribution differed significantly between centers. Alleles segregated according to enzyme electrophoretic lineage and O serogroup in patterns suggesting both vertical and horizontal transmission and emergence within E. coli in the temporal sequence II-->III-->I. Strains containing allele III preferentially agglutinated sheep erythrocytes, whereas strains containing allele II preferentially agglutinated human erythrocytes. Allele III was associated with hly, sfa, multiple copies of the pap operon, and cluster III of the phylogenetic tree. These findings indicate that among bacteremia isolates of E. coli, the three papG alleles exhibit distinctive associations with evolutionary lineages, hemagglutination phenotypes, and non-pap virulence properties.

Adhesins, Escherichia coli↗