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At least 361 records · Page 20Linked to original sources
PubMed1995

Phylogenetic analysis of the ballistosporous anamorphic genera Udeniomyces and Bullera, and related basidiomycetous yeasts, based on 18S rDNA sequence.

The small subunit nuclear ribosomal DNA (18S rDNA) sequence was determined for twelve species of basidiomycetous anamorphic yeasts, i.e. three species of Udeniomyces, seven species of Bullera, Cryptococcus albidus and Phaffia rhodozyma. For phylogentic analysis, these sequences were aligned with published sequences for 36 other fungal species. Molecular phylogenetic analysis of maximum likelihood and parsimony showed that the 44 species of basidiomycetes analysed were divided into three major lineages. The ballistosporous yeast genera Udeniomyces and Bullera were clearly separated. On the phylogenetic tree, Udeniomyces megalosporus, U. puniceus and U. piricola showed a very close relationship with one another, and composed a lineage with Mrakia frigida, P. rhodozyma and Cystofilobasidium capitatum at high bootstrap confidence level. On the other hand, eight species of Bullera made lineages with selected species of Tremella (Tremellaceae), Filobasidium and Filobasidiella (Filobasidiaceae), Cryptococcus albidus and Trichosporon cutaneum. The molecular phylogeny deduced from the 18S rDNA sequence showed a possibility of heterogeneity among the species of Bullera at the generic level.

Base Sequence↗
PubMed2000

Testing hybridization hypotheses based on incongruent gene trees.

Hybridization is an important evolutionary mechanism in plants and has been increasingly documented in animals. Difficulty in reconstruction of reticulate evolution, however, has been a long-standing problem in phylogenetics. Consequently, hybrid speciation may play a major role in causing topological incongruence between gene trees. The incongruence, in turn, offers an opportunity to detect hybrid speciation. Here we characterized certain distinctions between hybridization and other biological processes, including lineage sorting, paralogy, and lateral gene transfer, that are responsible for topological incongruence between gene trees. Consider two incongruent gene trees with three taxa, A, B, and C, where B is a sister group of A on gene tree 1 but a sister group of C on gene tree 2. With a theoretical model based on the molecular clock, we demonstrate that time of divergence of each gene between taxa A and C is nearly equal in the case of hybridization (B is a hybrid) or lateral gene transfer, but differs significantly in the case of lineage sorting or paralogy. After developing a bootstrap test to test these alternative hypotheses, we extended the model and test to account for incongruent gene trees with numerous taxa. Computer simulation studies supported the validity of the theoretical model and bootstrap test when each gene evolved at a constant rate. The computer simulation also suggested that the model remained valid as long as the rate heterogeneity was occurring proportionally in the same taxa for both genes. Although the model could not test hypotheses of hybridization versus lateral gene transfer as the cause of incongruence, these two processes may be distinguished by comparing phylogenies of multiple unlinked genes.

Biological Evolution↗
PubMed2002

Early steps in the formation of neural tissue in ascidian embryos.

Ascidians are simple invertebrate chordates whose lineage diverged from that of vertebrates at the base of the chordate tree. Their larvae display a typical chordate body plan, but are composed of a remarkably small number of cells. Ascidians develop with an invariant cell lineage, and their embryos can be easily experimentally manipulated during the cleavage stages. Their larval nervous system is organised in a similar way as in vertebrates but is composed of less than 130 neurones and around 230 glial cells. This remarkable simplicity offers an opportunity to understand, at the cellular and molecular levels, the ontogeny and function of each neural cell. Here, we first review the organisation of the ascidian nervous system and its lineage. We then focus on the current understanding of the processes of neural specification and patterning before and during gastrulation. We discuss these advances in the context of what is currently known in vertebrates.

Animals↗
PubMed1999

Phylogenetic history of hominoid DRB loci and alleles inferred from intron sequences.

The evolutionary relationships among the MHC class II DRB4, DRB5 and DRB6 loci as well as the allelic lineages and alleles of the DRB1 locus were studied based on intron 1 and intron 2 sequences from humans, chimpanzee (Pan troglodytes), bonobo (Pan paniscus) and gorilla (Gorilla gorilla). The phylogenetic trees for these sequences indicate that most of the DRB1 allelic lineages predate the separation of the hominoid species studied, consistent with previous analysis of the coding sequences of these lineages. However, the intron sequence variation among alleles within DRB1 allelic lineages is very limited, consistent with the notion that the majority of the contemporary alleles have been generated within the last 250,000 years. The clustering of the DRB1 allelic lineages *08 and *12 with *03 supports a common ancestry for the DR8 and DR52 haplotypes. Similarly, the clustering of DRB1 allelic lineages *15 and *01 with the DRB3 locus is consistent with a common ancestry for the DR1 and DR51 haplotypes. Two cases of recombination around the second exon were observed: 1) the HLA-DRB6 locus appears to have been generated through a recombination between a DRB5 allele and an ancestral DRB6 allele, and 2) the gorilla sequence Gogo-DRB1 *03 appears to have been generated through a recombination between the DRB3 locus and an allele from the DRB1 *03 allelic lineage. The nucleotide substitution rate of DRB introns was estimated to 0.85-1.63 x 10(-9) per site per year, based on comparisons between the most closely related sequences from different hominoid species. This estimate is similar to the substitution rate for other intronic regions of the primate genome.

Alleles↗
PubMed2001

Complete mitochondrial DNA genome sequences of extinct birds: ratite phylogenetics and the vicariance biogeography hypothesis.

The ratites have stimulated much debate as to how such large flightless birds came to be distributed across the southern continents, and whether they are a monophyletic group or are composed of unrelated lineages that independently lost the power of flight. Hypotheses regarding the relationships among taxa differ for morphological and molecular data sets, thus hindering attempts to test whether plate tectonic events can explain ratite biogeography. Here, we present the complete mitochondrial DNA genomes of two extinct moas from New Zealand, along with those of five extant ratites (the lesser rhea, the ostrich, the great spotted kiwi, the emu and the southern cassowary and two tinamous from different genera. The non-stationary base composition in these sequences violates the assumptions of most tree-building methods. When this bias is corrected using neighbour-joining with log-determinant distances and non-homogeneous maximum likelihood, the ratites are found to be monophlyletic, with moas basal, as in morphological trees. The avian sequences also violate a molecular clock, so we applied a non-parametric rate smoothing algorithm, which minimizes ancestor-descendant local rate changes, to date nodes in the tree. Using this method, most of the major ratite lineages fit the vicariance biogeography hypothesis, the exceptions being the ostrich and the kiwi, which require dispersal to explain their present distribution.

Animals↗
PubMed2002

A molecular phylogeny of ichthyophiid caecilians (Amphibia: Gymnophiona: Ichthyophiidae): out of India or out of South East Asia?

Recent molecular phylogenetic studies indicate that the rafting Indian plate harboured several isolated vertebrate lineages between ca. 130 and 56 Myr ago that dispersed and diversified 'out of India' following accretion with Eurasia. A single family of the amphibian order Gymnophiona, the Ichthyophiidae, presently occurs on the Indian plate and across much of South East Asia. Ichthyophiid phylogeny is investigated in order to test competing out of India and out of South East Asia hypotheses for their distribution. Partial sequences of mitochondrial 12S and 16S rRNA and cytochrome b genes for 20 ichthyophiids and proximate outgroups were assembled. Parsimony, maximum-likelihood and distance analyses all recover optimum trees in which uraeotyphlids plus Ichthyophis cf. malabarensis are the sister taxa to all other Ichthyophis, among which the South East Asian taxa are monophyletic. Tree topology and branch lengths indicate that the Indian lineages are more basal and older, and thus are more consistent with the hypothesis that ichthyophiids dispersed from the Indian subcontinent into South East Asia. The estimated relationships also support monophyly of Sri Lankan Ichthyophis, and non-monophyly of striped and unstriped Ichthyophis species groups. Mitochondrial DNA sequences provide evidence that should assist current problematic areas of caecilian taxonomy.

Amphibians↗
PubMedDate not supplied

Phyletic patterns of early development in gastropod molluscs.

Cell lineage data for 30 exemplar gastropod taxa representing all major subclades and the outgroup Polyplacophora were examined for phylogenetic signal using cladistic analysis. Most cell lineages show phyletic trends of acceleration or retardation relative to the outgroup and more basal ingroup taxa, and when coded this variation is phylo-genetically informative. PAUP analyses of a cell lineage data set under three sets of character ordering assumptions produced similar tree topologies. The topologies of the strict consensus trees for both ordered and Dollo (near irreversibility of character transformations) character assumptions were similar, whereas the unordered character assumption recovers the least phyletic information. The cell lineage cladograms are also in agreement with the fossil record of the timing and sequence of gastropod subclade origination. A long branch lies between the Patellogastropoda+Vetigastropoda grade and the Neritopsina+Apogastropoda clade. The geological timing of this long branch is correlated with the first large-scale terrestrially derived eutrophication of the near-shore marine habitat, and one possible explanation for this branch may be a developmental shift associated with the evolution of feeding larvae in response to the more productive conditions in the near-shore water column. Although character transformations are highly ordered in this data set, developmental rate characters (like all other morphological and molecular characters) are also subject to homoplasy. Finally, this study further supports the hypothesis that early development of gastropod molluscs has conserved a strong phyletic signal for about half a billion years.

Animals↗
PubMed1998

Evolution of histone H4 and H3 genes in different ciliate lineages.

The histones H4 are known as highly conserved proteins. However, in ciliates a high degree of variation was found compared both to other eukaryotes and between the ciliate species. To date, only H4 histones of species belonging to two distantly related classes have been investigated. In order to obtain more detailed information on histone H4 variation in ciliates we undertook a comprehensive sequence analysis of PCR-amplified internal H4 fragments from 12 species belonging to seven out of the nine currently recognized ciliate classes. In addition, we used PCR primers to amplify longer fragments of H3 and H4 genes including the intergenic region. The encoded amino acid sequences reveal a high number of differences when compared with those of other eukaryotes and the ciliate species investigated. Furthermore, in some species H4 gene variants were detected, which result in amino acid differences. The greatest number of substitutions and insertions found was in the amino terminal region of the H4 histones. However, all sequences possess a conserved region corresponding to those of all other eukaryotic H4 histones. The histone gene variations were used to reconstruct phylogenetic relationships. The tree from our data matches perfectly with the ribosomal RNA data: The heterotrichs, which were considered as a late branching lineage, diverge at the base of the ciliate tree and groups formerly thought to represent ancestral lineages now appear as highly derived ciliates.

Amino Acid Sequence↗
PubMed1998

Genetic and antigenic analysis of the G attachment protein of bovine respiratory syncytial virus strains.

Antigenic and genetic studies of bovine respiratory syncytial virus (BRSV) were made on isolates obtained from three continents over 27 years. Antigenic variation between eight isolates was initially determined using protein G-specific monoclonal antibodies. Four distinct reaction patterns were observed, two of which corresponded to the previously established subgroups A and AB. A third pattern was produced by five Scandinavian strains and a fourth was observed from a single Dutch isolate. The genetic diversity of 27 strains of BRSV was investigated by comparative nucleotide sequence analysis of a 731 nucleotide fragment in the G protein gene. Nine of the BRSV strains were analysed by direct sequencing of RT-PCR amplicons whereas sequences of 18 BRSV and three human respiratory syncytial virus (HRSV) strains were obtained from GenBank. The analysis revealed similarities of 88-100% among BRSV strains and 38-41% between BRSV and HRSV. A phylogenetic tree created for BRSV revealed two main branches, one of which divided into five further lineages, each representing a geographic cluster. A correlation was evident between the positions of some strains in the phylogenetic tree and their antigenic pattern. For HRSV strains, a genetic similarity of only 62% allowed the distinction of two antigenic subgroups, A and B, a pattern which was not seen for BRSV. This study showed that genetic analysis was an accurate method for discriminating BRSV strains and that these viruses should be regarded as a single genetic and antigenic group, within which variants can be distinguished.

Amino Acid Sequence↗
PubMed2001

Molecular evolution of Mycobacterium tuberculosis: phylogenetic reconstruction of clonal expansion.

SETTING: M. tuberculosis isolates were collected from patients attending health clinics in a high incidence urban community and in a low incidence rural setting in South Africa. OBJECTIVE: To reconstruct the evolutionary history of a group of closely related M. tuberculosis isolates using IS6110, DRr and MTB484(1) restriction fragment length polymorphism (RFLP) data. DESIGN: Mycobacterium tuberculosis isolates containing an average of ten IS6110 elements, with a similarity index of > or = 65% were genotypically classified by DNA fingerprinting using the IS6110 derived probes IS-3' and IS-5', as well as the DRr and MTB484(1) probes, in combination with PvuII or Hinfl endonuclease digestion. These RFLP data were subjected to phylogenetic analysis using both genetic distance and parsimony algorithms. RESULTS: Phylogenetic analysis predicted the existence of two independently evolving lineages, possibly evolving from a common ancestral strain. The topology of the phylogenetic tree was supported by comprehensive bootstrapping and the specific partitioning of DNA methylation phenotypes. The observed difference in the branch lengths of the two lineages may suggest differential evolutionary rates. Isolates collected from different geographical regions demonstrate independent evolution, suggesting that it is highly unlikely that strains have been recently transmitted between the two regions. The number of evolutionary events identified in this strain family differs significantly from that of previously characterized strain families, implying that evolutionary rate may be strain family dependent. CONCLUSION: Based on this analysis we propose that the algorithm used to calculate recent epidemiological events should be revised to incorporate the evolutionary characteristics of individual strain families, thereby enhancing the accuracy of molecular epidemiological calculations.

Algorithms↗
PubMed1999

Isolation and characterization of simple sequence repeat loci in the gray tree frog, Hyla chrysoscelis.

A gray tree frog (Hyla chrysoscelis) genomic library was constructed and characterized with regard to the incidence and complexity of simple sequence repeat (SSR) loci. The partial genomic library, containing approximately 10,000 clones with an average-sized insert of 350 bp, was screened with six SSR repeat oligonucleotides (AC, AG, ACG, AGC, AAC, and AAG). Screening identified 31 unique positive clones containing 41 SSR loci. Sequences of tandemly arrayed dinucleotide repeats were more common (36 of 41) than trinucleotide repeats. Twenty-six loci were identified using the AC dinucleotide probe, while 7 loci were identified using the AG dinucleotide probe. An additional 3 AT dinucleotide loci were serendipitously identified. The AT repeats generally comprised the longest dinucleotide repeat loci. The SSR repeat loci reported here should provide potent markers for identity, parentage, and short-lineage determinations in large-scale experiments using gray tree frogs.

Animals↗
PubMed2004

Silent nucleotide polymorphisms and a phylogeny for Mycobacterium tuberculosis.

Much remains unknown of the phylogeny and evolution of Mycobacterium tuberculosis, an organism that kills 2 million people annually. Using a population-based approach that analyzes multiple loci around the chromosome, we demonstrate that neutral genetic variation in genes associated with antimicrobial drug resistance has sufficient variation to construct a robust phylogenetic tree for M. tuberculosis. The data describe a clonal population with a minimum of four distinct M. tuberculosis lineages, closely related to M. bovis. The lineages are strongly geographically associated. Nucleotide substitutions proven to cause drug resistance are distributed throughout the tree, whereas nonsynonymous base substitutions unrelated to drug resistance have a restricted distribution. The phylogenetic structure is concordant with all the previously described genotypic and phenotypic groupings of M. tuberculosis strains and provides a unifying framework for both epidemiologic and evolutionary analysis of M. tuberculosis populations.

Amidohydrolases↗
PubMed2003

Phylogenetic relationships in the division Lipastromorphi (Coleoptera, Carabidae) of the world as deduced from mitochondrial ND5 gene sequences.

Phylogenetic trees have been constructed using mitochondrial ND5 gene sequences of 85 specimens representing 40 species belonging to the division Lipastromorphi of the subtribe Carabina (= genus Carabus s. lat.) of the world. In the trees constructed by several methods, there have been recognized a basal split into two lineages, A and B, which are further divided into 2 (A1 and A2) and 9 (B1-B9) sublineages, respectively. Each sublineage and the clustering of the species in the trees are more or less linked to their geographic distribution. Morphology of the species within A1 or A2 in the lineage A is similar, and the species in most of the sublineages in the lineage B are common in a number of important morphological characters in spite of their long evolutionary histories. Whilst such a morphological stability, considerable morphological changes may be recognized upon or after split of lineages and sublineages. Based on the molecular phylogeny together with the morphological data, the pattern of diversification is discussed.

Animals↗
PubMed2005

Heterogeneity in codon usages of sobemovirus genes.

When conventional phylogenetic trees were built using 14 genome sequences of 9 sobemoviruses, two main lineages were apparent: monocot-infecting viruses and dicot-infecting viruses. To investigate whether members of the genus Sobemovirus originated from monocot hosts or from dicot hosts, we constructed relationship trees based on Relative Synonymous Codon Usage (RSCU) of the viruses. The RSCU relationship trees grouped the monocot-infecting and dicot-infecting viruses even better than the genome phylogenetic trees. The RSCU approach also enabled direct comparisons among viral and host species. When host species were added into the RSCU tree, the viral species clustered with the monocot hosts, indicating codon usage homologies to monocots. The stability of the RSCU tree was improved when RSCU values were calculated for individual viral open reading frames (ORFs). Most interestingly, the codon usages of the viral ORF-2 that encodes the replicase showed affinity to that of the plants whereas codon usages of the other viral ORFs were not relevant to the host species. All ORF-2s from 3 monocot viruses and 4 out of 6 dicot viruses had greater RSCU affinities to sequences of ORFs in monocot than to dicot hosts, possibly indicating that ORF-2, and therefore the replicase module of sobemovirus has a monocot origin.

Arabidopsis↗
PubMed2002

Pika and vole mitochondrial genomes increase support for both rodent monophyly and glires.

Complete mitochondrial genomes are reported for a pika (Ochotona collaris) and a vole (Volemys kikuchii) then analysed together with 35 other mitochondrial genomes from mammals. With standard phylogenetic methods the pika joins with the other lagomorph (rabbit) and the vole with the other murid rodents (rat and mouse). In addition, with hedgehog excluded, the seven rodent genomes consistently form a homogeneous group in the unrooted placental tree. Except for uncertainty of the position of tree shrew, the clade Glires (monophyletic rodents plus lagomorphs) is consistently found. The unrooted tree obtained by ProtML (Protein Maximum Likelihood, a program in MOLPHY) is compatible with a reclassification of mammals [Syst. Biol. 48, 1-5 (1999)] which is also supported by other recent studies. However, when this tree is rooted with marsupials plus platypus, the outgroup often joins the lineage leading to the three murid rodents, so the rodents are no longer monophyletic. Apart from misplacing the root, the presence of the outgroups also distorts other parts of the unrooted tree. Either constraining the tree to maintain rodents monophyletic, or omitting murids, maintains the ingroup tree and sees the outgroup join on the edge to Xenarthra, to Afrotheria, or to these two groups together. This emphasises the importance of carrying out both an unrooted and a rooted analysis. It is known from cancer research that murid rodents have reduced activity in some DNA repair mechanisms and this alters their substitution pattern - this may be the case for mitochnodrial DNA as well. Comparing nucleotide compositions may identify taxa that differ in aspects of their DNA repair mechanisms.

Animals↗
PubMed2004

Cloning of IgE from the echidna (Tachyglossus aculeatus) and a comparative analysis of epsilon chains from all three extant mammalian lineages.

In continuation of our evolutionary studies of immunoglobulin (Ig) expression, we present here the cloning of IgE from a monotreme, the short-beaked echidna (Tachyglossus aculeatus). Including echidna IgE, 15 epsilon chain sequences have been isolated and each of the three mammalian lineages (placentals, marsupials and monotremes) is now represented by at least two sequences. Phylogenetic analyses based on all available epsilon chains and a selection of other mammalian Ig isotypes (IgM, IgA and IgG) were generated using three different algorithms. The resulting trees strongly support the Theria hypothesis, which states that the monotreme lineage was the first of the three extant mammalian lineages to appear in evolution. Furthermore, to increase our understanding of IgE we have done a detailed comparative analysis, with focus on primary structure, potential N-glycosylation, charge distribution and conservation of residues in the putative receptor-binding site. The overall structure of IgE, i.e. four constant domains and the positions of putative disulfide-bridge formations, are conserved, as is an N-glycosylation site in the third constant domain. An increased homology was observed in the putative receptor-binding site, which suggests an important function for the IgE/Fc epsilon RI interaction. IgE has been found exclusively in mammals, but it is present in all extant mammalian lineages. This, together with the overall conservation of structure, indicates that IgE appeared as a separate isotype early in mammalian evolution and that structural maintenance may have a selective advantage.

Amino Acid Sequence↗
PubMed2004

Phylogeny and divergence of basal angiosperms inferred from APETALA3- and PISTILLATA-like MADS-box genes.

The B-class MADS-box genes composed of APETALA3 ( AP3) and PISTILLATA ( PI) lineages play an important role in petal and stamen identity in previously studied flowering plants. We investigated the diversification of the AP3-like and PI-like MADS-box genes of eight species in five basal angiosperm families: Amborella trichopoda (Amborellaceae); Brasenia schreberi and Cabomba caroliniana (Cabombaceae); Euryale ferox, Nuphar japonicum, and Nymphaea tetragona (Nymphaeaceae); Illicium anisatum (Illiciaceae); and Kadsura japonica (Schisandraceae). Sequence analysis showed that a four amino acid deletion in the K domain, which was found in all previously reported angiosperm PI genes, exists in a PI homologue of Schisandraceae, but not in six PI homologues of the Amborellaceae, Cabombaceae, and Nymphaeaceae, suggesting that the Amborellaceae, Cabombaceae, and Nymphaeaceae are basalmost lineages in angiosperms. The results of molecular phylogenetic analyses were not inconsistent with this hypothesis. The AP3 and PI homologues from Amborella share a sequence of five amino acids in the 5' region of exon 7. Using the linearized tree and likelihood methods, the divergence time between the AP3 and PI lineages was estimated as somewhere between immediately after to several tens of millions of years after the split between angiosperms and extant gymnosperms. Estimates of the age of the most recent common ancestor of all extant angiosperms range from approximately 140-210 Ma, depending on the trees used and assumptions made.

Amino Acid Sequence↗
PubMed1991

Resolution of the African hominoid trichotomy by use of a mitochondrial gene sequence.

Mitochondrial DNA sequences encoding the cytochrome oxidase subunit II gene have been determined for five primate species, siamang (Hylobates syndactylus), lowland gorilla (Gorilla gorilla), pygmy chimpanzee (Pan paniscus), crab-eating macaque (Macaca fascicularis), and green monkey (Cercopithecus aethiops), and compared with published sequences of other primate and nonprimate species. Comparisons of cytochrome oxidase subunit II gene sequences provide clear-cut evidence from the mitochondrial genome for the separation of the African ape trichotomy into two evolutionary lineages, one leading to gorillas and the other to humans and chimpanzees. Several different tree-building methods support this same phylogenetic tree topology. The comparisons also yield trees in which a substantial length separates the divergence point of gorillas from that of humans and chimpanzees, suggesting that the lineage most immediately ancestral to humans and chimpanzees may have been in existence for a relatively long time.

Animals↗