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At least 253 records · Page 14Linked to original sources
PubMed2005

Evolutionary relationships of the cup-fungus genus Peziza and Pezizaceae inferred from multiple nuclear genes: RPB2, beta-tubulin, and LSU rDNA.

To provide a robust phylogeny of Pezizaceae, partial sequences from two nuclear protein-coding genes, RPB2 (encoding the second largest subunit of RNA polymerase II) and beta-tubulin, were obtained from 69 and 72 specimens, respectively, to analyze with nuclear ribosomal large subunit RNA gene sequences (LSU). The three-gene data set includes 32 species of Peziza, and 27 species from nine additional epigeous and six hypogeous (truffle) pezizaceous genera. Analyses of the combined LSU, RPB2, and beta-tubulin data set using parsimony, maximum likelihood, and Bayesian approaches identify 14 fine-scale lineages within Pezizaceae. Species of Peziza occur in eight of the lineages, spread among other genera of the family, confirming the non-monophyly of the genus. Although parsimony analyses of the three-gene data set produced a nearly completely resolved strict consensus tree, with increased confidence, relationships between the lineages are still resolved with mostly weak bootstrap support. Bayesian analyses of the three-gene data, however, show support for several more inclusive clades, mostly congruent with Bayesian analyses of RPB2. No strongly supported incongruence was found among phylogenies derived from the separate LSU, RPB2, and beta-tubulin data sets. The RPB2 region appeared to be the most informative single gene region based on resolution and clade support, and accounts for the greatest number of potentially parsimony informative characters within the combined data set, followed by the LSU and the beta-tubulin region. The results indicate that third codon positions in beta-tubulin are saturated, especially for sites that provide information about the deeper relationships. Nevertheless, almost all phylogenetic signal in beta-tubulin is due to third positions changes, with almost no signal in first and second codons, and contribute phylogenetic information at the "fine-scale" level within the Pezizaceae. The Pezizaceae is supported as monophyletic in analyses of the three-gene data set, but its sister-group relationships is not resolved with support. The results advocate the use of RPB2 as a marker for ascomycete phylogenetics at the inter-generic level, whereas the beta-tubulin gene appears less useful.

Ascomycota↗
PubMed2004

Mitochondrial phylogeny of the Cyprichromini, a lineage of open-water cichlid fishes endemic to Lake Tanganyika, East Africa.

We present a phylogeny of the Cyprichromini, a lineage of cichlid fishes from Lake Tanganyika, showing progressive adaptation towards pelagic life style. Our study is based upon three mitochondrial gene segments, 443 bp of the control region, 402 bp of the cytochrome b gene and the entire NADH dehydrogenase subunit 2 gene (1047 bp). The topologies obtained by different tree building methods subdivide the Cyprichromini into four distinct lineages: the Paracyprichromis-, the Cyprichromis zonatus-, the Cyprichromis microlepidotus-lineage, and a lineage comprising Cyprichromis pavo and Cyprichromis leptosoma. Our study thus corroborates the distinctness of C. zonatus which was recently described formally. Concerning ecology and mating behavior, a clear evolutionary trend towards progressive adaptation to the pelagic zone emerges during the evolution of the Cyprichromini. The linearized tree analysis further shows that the four lineages have split almost contemporaneously. The mean Kimura-2-parameter distance among the four lineages emerging from the primary radiation of the Cyprichromini amounts to 7.21% and is in close agreement to that previously found for the primary radiation of the tribe Tropheini (7.01%), a lineage of rock-dwelling cichlids endemic to Lake Tanganyika. To date, the influence of lake level fluctuations as promoters of diversification has been demonstrated only for rock-dwelling cichlids. Based on the agreement in temporary patterns of diversification, we suggest that Pleistocene lake level changes have left a similar genetic imprint in a group of cichlid fishes that progressively colonized the open water during their radiation.

Africa, Eastern↗
PubMed2001

A multistep process for the dispersal of a Y chromosomal lineage in the Mediterranean area.

In this work we focus on a microsatellite-defined Y-chromosomal lineage (network 1.2) identified by us and reported in previous studies, whose geographic distribution and antiquity appear to be compatible with the Neolithic spread of farmers. Here, we set network 1.2 in the Y-chromosomal phylogenetic tree, date it with respect to other lineages associated with the same movements by other authors, examine its diversity by means of tri- and tetranucleotide loci and discuss the implications in reconstructing the spread of this group of chromosomes in the Mediterranean area. Our results define a tripartite phylogeny within HG 9 (Rosser et al. 2000), with the deepest branching defined by alleles T (Haplogroup Eu10) or G (Haplogroup Eu9) at M172 (Semino et al. 2000), and a subsequent branching within Eu9 defined by network 1.2. Population distributions of HG 9 and network 1.2 show that their occurrence in the surveyed area is not due to the spread of people from a single parental population but, rather, to a process punctuated by at least two phases. Our data identify the wide area of the Balkans, Aegean and Anatolia as the possible homeland harbouring the largest variation within network 1.2. The use of recently proposed tests based on the stepwise mutation model suggests that its spread was associated to a population expansion, with a high rate of male gene flow in the Turkish-Greek area.

Alleles↗
PubMed1989

Lineage effects and the index of dispersion of molecular evolution.

Recent efforts to estimate the index of dispersion [R(t)] of molecular evolution-i.e., the ratio of the variance in the number of substitutions on a lineage to the mean number-have suffered from an inability to adjust the data for lineage effects. These effects may include the generation-time dependency of the rate of evolution or improper assumptions about the branching pattern of a phylogenetic tree. In the present paper a method for correcting for lineage effects in the estimation of R(t) is presented for trees made up of three species. The recent data published by Li et al. for 20 loci in three orders of mammals is examined, and the average R(t), corrected for lineage effects, is shown to be 7.75 for replacement substitutions and 3.3 for silent substitutions. Thus the high values reported earlier may not be dismissed as due to generation-time effects or improper assumptions about phylogenies. Computer simulations are presented to give confidence in the estimate for replacement substitutions but also to demonstrate that the estimate for silent substitutions is sensitive to corrections for multiple substitutions and is not as reliable. This work's implications for our understanding of the mechanism of molecular evolution are discussed, and the arguments in favor of the hypothesis that replacement substitutions are mostly selected while silent substitutions are mostly neutral is presented.

Algorithms↗
PubMed1998

Phylogeny of Nematoda and Cephalorhyncha derived from 18S rDNA.

Phylogenetic relationships of nematodes, nematomorphs, kinorhynchs, priapulids, and some other major groups of invertebrates were studied by 18S rRNA gene sequencing. Kinorhynchs and priapulids form the monophyletic Cephalorhyncha clade that is the closest to the coelomate animals. When phylogenetic trees were generated by different methods, the position of nematomorphs appeared to be unstable. Inclusion of Enoplus brevis, a representative of a slowly evolving nematode lineage, in the set of analyzed species refutes the tree patterns, previously derived from molecular data, where the nematodes appear as a basal bilateral lineage. The nematodes seem to be closer to the coelomate animals than was speculated earlier. According to the results obtained, nematodes, nematomorphs, tardigrades, arthropods, and cephalorhynchs are a paraphyletic association of closely related taxa.

Animals↗
PubMed1996

Molecular evolution of the 14-3-3 protein family.

Members of the highly conserved and ubiquitous 14-3-3 protein family modulate a wide variety of cellular processes. To determine the evolutionary relationships among specific 14-3-3 proteins in different plant, animal, and fungal species and to initiate a predictive analysis of isoform-specific differences in light of the latest functional and structural studies of 14-3-3, multiple alignments were constructed from forty-six 14-3-3 sequences retrieved from the GenBank and SwissProt databases and a newly identified second 14-3-3 gene from Caenorhabditis elegans. The alignment revealed five highly conserved sequence blocks. Blocks 2-5 correlate well with the alpha helices 3, 5, 7, and 9 which form the proposed internal binding domain in the three-dimensional structure model of the functioning dimer. Amino acid differences within the functional and structural domains of plant and animal 14-3-3 proteins were identified which may account for functional diversity amongst isoforms. Protein phylogenic trees were constructed using both the maximum parsimony and neighbor joining methods of the PHYLIP(3.5c) package; 14-3-3 proteins from Entamoeba histolytica, an amitochondrial protozoa, were employed as an outgroup in our analysis. Epsilon isoforms from the animal lineage form a distinct grouping in both trees, which suggests an early divergence from the other animal isoforms. Epsilons were found to be more similar to yeast and plant isoforms than other animal isoforms at numerous amino acid positions, and thus epsilon may have retained functional characteristics of the ancestral protein. The known invertebrate proteins group with the nonepsilon mammalian isoforms. Most of the current 14-3-3 isoform diversity probably arose through independent duplication events after the divergence of the major eukaryotic kingdoms. Divergence of the seven mammalian isoforms beta, zeta, gamma, eta, epsilon, tau, and sigma (stratifin/HME1) occurred before the divergence of mammalian and perhaps before the divergence of vertebrate species. A possible ancestral 14-3-3 sequence is proposed.

14-3-3 Proteins↗
PubMed2004

Molecular taxonomic position of the elephant schistosome, Bivitellobilharzia nairi, newly discovered in Sri Lanka.

Bivitellobilharzia nairi (Mudaliar and Ramanujachar, 1945) Dutt and Srivastava, 1955 was first recorded in India. A number of adult worm specimens of this schistosome species were recovered from a domestic elephant, which died in 1999 in Sri Lanka. This is the first report of this schistosome from Sri Lanka. In the present study, in order to clarify the phylogenetic relationship with other species of schistosomes, sequences from the second internal transcribed spacer (ITS2) of the ribosomal gene repeat, part of the 28S ribosomal RNA gene (28S), and part of the mitochondrial cytochrome c oxidase subunit 1 (CO1) gene from B. nairi were analyzed. Two intraspecific variations were seen within 13 individuals in the ITS2 region. In the CO1 region of the mitochondrial DNA, there were four haplotypes in the nucleotide sequences and two haplotypes in the amino acid sequences. Phylogenetic analysis using the nuclear DNA showed that B. nairi was basal to all of species of the genus Schistosoma. The 28S tree also showed that the mammalian lineage was monophyletic. However, phylogenetic analysis using the mitochondrial DNA showed that B. nairi was nested within the genus Schistosoma. The taxonomical position for this species as well as the contradiction between the results from the nuclear and mitochondrial genes were discussed.

Animals↗
PubMed2005

The beetle gut: a hyperdiverse source of novel yeasts.

We isolated over 650 yeasts over a three year period from the gut of a variety of beetles and characterized them on the basis of LSU rDNA sequences and morphological and metabolic traits. Of these, at least 200 were undescribed taxa, a number equivalent to almost 30% of all currently recognized yeast species. A Bayesian analysis of species discovery rates predicts further sampling of previously sampled habitats could easily produce another 100 species. The sampled habitat is, thereby, estimated to contain well over half as many more species as are currently known worldwide. The beetle gut yeasts occur in 45 independent lineages scattered across the yeast phylogenetic tree, often in clusters. The distribution suggests that the some of the yeasts diversified by a process of horizontal transmission in the habitats and subsequent specialization in association with insect hosts. Evidence of specialization comes from consistent associations over time and broad geographical ranges of certain yeast and beetle species. The discovery of high yeast diversity in a previously unexplored habitat is a first step toward investigating the basis of the interactions and their impact in relation to ecology and evolution.

Animals↗
PubMed2004

Improved resolution on the phylogenetic relationships among Pseudomonas by the combined analysis of atp D, car A, rec A and 16S rDNA.

A study of representatives of the bacterial genus Pseudomonas, analysing a combined data set of four molecular sequences with completely different properties and evolutionary constraints, is reported. The best evolutionary model was obtained with a hierarchical hypothesis testing program to describe each data set and the combined data set is presented and analysed under the likelihood criterion. The resolution among Pseudomonas taxa based on the combined data set analysis of the different lineages increased due to a synergistic effect of the individual data sets. The unresolved fluorescens lineage, as well as other weakly supported lineages in the single data set trees, should be revised in detail at the biochemical and molecular level. The taxonomic status of biovars of P. putida is discussed.

Carbamoyl-Phosphate Synthase (Glutamine-Hydrolyzin↗
PubMed2004

Darwin's abominable mystery: Insights from a supertree of the angiosperms.

Angiosperms are among the major terrestrial radiations of life and a model group for studying patterns and processes of diversification. As a tool for future comparative studies, we compiled a supertree of angiosperm families from published phylogenetic studies. Sequence data from the plastid rbcL gene were used to estimate relative timing of branching events, calibrated by using robust fossil dates. The frequency of shifts in diversification rate is largely constant among time windows but with an apparent increase in diversification rates within the more recent time frames. Analyses of species numbers among families revealed that diversification rate is a labile attribute of lineages at all levels of the tree. An examination of the top 10 major shifts in diversification rates indicates they cannot easily be attributed to the action of a few key innovations but instead are consistent with a more complex process of diversification, reflecting the interactive effects of biological traits and the environment.

Biodiversity↗
PubMed2004

Multiple data sets, high homoplasy, and the phylogeny of softshell turtles (Testudines: Trionychidae).

We present a phylogenetic hypothesis and novel, rank-free classification for all extant species of softshell turtles (Testudines:Trionychidae). Our data set included DNA sequence data from two mitochondrial protein-coding genes and a approximately 1-kb nuclear intron for 23 of 26 recognized species, and 59 previously published morphological characters for a complimentary set of 24 species. The combined data set provided complete taxonomic coverage for this globally distributed clade of turtles, with incomplete data for a few taxa. Although our taxonomic sampling is complete, most of the modern taxa are representatives of old and very divergent lineages. Thus, due to biological realities, our sampling consists of one or a few representatives of several ancient lineages across a relatively deep phylogenetic tree. Our analyses of the combined data set converge on a set of well-supported relationships, which is in accord with many aspects of traditional softshell systematics including the monophyly of the Cyclanorbinae and Trionychinae. However, our results conflict with other aspects of current taxonomy and indicate that most of the currently recognized tribes are not monophyletic. We use this strong estimate of the phylogeny of softshell turtles for two purposes: (1) as the basis for a novel rank-free classification, and (2) to retrospectively examine strategies for analyzing highly homoplasious mtDNA data in deep phylogenetic problems where increased taxon sampling is not an option. Weeded and weighted parsimony, and model-based techniques, generally improved the phylogenetic performance of highly homoplasious mtDNA sequences, but no single strategy completely mitigated the problems of associated with these highly homoplasious data. Many deep nodes in the softshell turtle phylogeny were confidently recovered only after the addition of largely nonhomoplasious data from the nuclear intron.

Animals↗
PubMed2001

The evolutionary history of the coral genus Acropora (Scleractinia, Cnidaria) based on a mitochondrial and a nuclear marker: reticulation, incomplete lineage sorting, or morphological convergence?

This study examines molecular relationships across a wide range of species in the mass spawning scleractinian coral genus Acropora. Molecular phylogenies were obtained for 28 species using DNA sequence analyses of two independent markers, a nuclear intron and the mtDNA putative control region. Although the compositions of the major clades in the phylogenies based on these two markers were similar, there were several important differences. This, in combination with the fact that many species were not monophyletic, suggests either that introgressive hybridization is occurring or that lineage sorting is incomplete. The molecular tree topologies bear little similarity to the results of a recent cladistic analysis based on skeletal morphology and are at odds with the fossil record. We hypothesize that these conflicting results may be due to the same morphology having evolved independently more than once in Acropora and/or the occurrence of extensive interspecific hybridization and introgression in combination with morphology being determined by a small number of genes. Our results indicate that many Acropora species belong to a species complex or syngameon and that morphology has little predictive value with regard to syngameon composition. Morphological species in the genus often do not correspond to genetically distinct evolutionary units. Instead, species that differ in timing of gamete release tend to constitute genetically distinct clades.

Animals↗
PubMed2006

Molecular analysis of gp41 sequences of HIV type 1 subtype C from India.

Sequence polymorphism in HIV type 1 env gene is quite high, and there are little data available for subtype C env gp41 sequences from India. We have presented a molecular sequence analysis for gp41 region of env gene from HIV type 1 subtype C-infected individuals. The samples were obtained from 3 acute seroconverters and 5 seropositive individuals from India, one of whom was a minor. Heteroduplex mobility analysis using V3V5 and gp41 confirmed subtype C infection in all the study subjects. The sequences were analyzed for heterogeneity, polymorphism, and epitope recognition. The phylogenetic and SimPlot analysis showed the monophyletic lineage of Indian sequences. The phylogenetic tree constructed for the 286- to 506-bp region is highly variable and clearly distinguishes the subtype C sequences. The interpatient sequence comparison revealed high genetic diversity ranging from 0.0623 to 2.18 (median, 0.119). This supports the phylogeny where sequences belonging to the 8 study subjects form subclusters within Indian subtype C. A majority of the functional domains of gp41 are well conserved for the seroconverter and seropositive sequences. However, sequence polymorphism is high for the sequences obtained from the minor. The sequences of gp41 would provide valuable information regarding the diversity and its diagnostic implications in HIV/AIDS research.

Adult↗
PubMed2006

Actinoplanes liguriensis sp. nov. and Actinoplanes teichomyceticus sp. nov.

The taxonomic status of 'Actinoplanes liguriae' A/6353 and 'Actinoplanes teichomyceticus' AB8327 was established by using a polyphasic approach. Strains A/6353 and AB8327 form distinct phylogenetic lineages in the 16S rRNA gene tree of members of the genus Actinoplanes and are related moderately and closely to Actinoplanes rectilineatus and Actinoplanes cyaneus, respectively. Morphological, cultural and physiological properties indicated that strains A/6353 and AB8327 represent separate, novel species of the genus Actinoplanes, Actinoplanes liguriensis sp. nov. (type strain A/6353(T)=FH 2244(T)=DSM 43865(T)=ATCC 31048(T)=BCRC 12121(T)=CBS 355.75(T)=IMSNU 22127(T)=JCM 3250(T)=KCTC 9536(T)=KCC A-0250(T)=NBRC 13997(T)=NCIMB 12636(T)=NRRL B-16723(T)=SANK 62178(T)) and Actinoplanes teichomyceticus sp. nov. (type strain AB8327(T)=FH 2149(T)=DSM 43866(T)=ATCC 31121(T)=BCRC 12106(T)=FERM P-3462(T)=IMSNU 20043(T)=IMET 9254(T)=JCM 3252(T)=KCC A-0252(T)=KCTC 9543(T)=NBRC 13999(T)=NCIMB 12640(T)=NRRL B-16726(T)=SANK 60479(T)).

Bacterial Typing Techniques↗
PubMed1980

The unusual karyotype of the lesser kudu, Tragelaphus imberbis.

The chromosome set of the lesser kudu, Tragelaphus imberbis, consists of 38 elements in both sexes. In contrast to most other members of the bovid subfamily Tragelaphinae, both the X and the Y chromosomes are compound, having fused with identical autosomes from ancestors presumed to have higher chromosome numbers. From a comparison of the unusual sex chromosomal rearrangements that have occurred in this family, a hypothetical lineage has been derived. This family tree and the details of various banding studies in the lesser kudu are described.

Animals↗
PubMed2004

Reticulate sympatric speciation in Cameroonian crater lake cichlids.

BACKGROUND: Traditionally the rapid origin of megadiverse species flocks of extremely closely related species is explained by the combinatory action of three factors: Disruptive natural selection, disruptive sexual selection and partial isolation by distance. However, recent empirical data and theoretical advances suggest that the diversity of complex species assemblages is based at least partially on the hybridization of numerous ancestral allopatric lineages that formed hybrids upon invasion of new environments. That reticulate speciation within species flocks may occur under sympatric conditions after the primary formation of species has been proposed but not been tested critically. RESULTS: We reconstructed the phylogeny of a complex cichlid species flock confined to the tiny Cameroonian crater lake Barombi Mbo using both mitochondrial and nuclear (AFLP) data. The nuclear phylogeny confirms previous findings which suggested the monophyly and sympatric origin of the flock. However, discordant intra-flock phylogenies reconstructed from mitochondrial and nuclear data suggest strongly that secondary hybridization among lineages that primarily diverged under sympatric conditions had occurred. Using canonical phylogenetic ordination and tree-based tests we infer that hybridization of two ancient lineages resulted in the formation of a new and ecologically highly distinct species, Pungu maclareni. CONCLUSIONS: Our findings show that sympatric hybrid speciation is able to contribute significantly to the evolution of complex species assemblages even without the prior formation of hybrids derived from allopatrically differentiated lineages.

Journal Article↗
PubMed1987

Nucleotide sequence of the beta-globin genes in gorilla and macaque: the origin of nucleotide polymorphisms in human.

Part of the beta-globin genes of Macaca cynomolgus and Gorilla gorilla has been cloned and sequenced. Ten putatively neutral nucleotide polymorphisms have been described at the beta-globin locus in humans. They are associated in seven combinations, which define seven different haplotypes of the beta-globin gene: four major frameworks--1, 2, 3, and 3--and three minor frameworks, which we term KI1, KA1, and OR1. The nucleotide sequences of these frameworks are compared with those of homologous sequences in chimpanzee, colobus, macaque, and gorilla. This comparison provides strong evidence that framework 2 was the earliest framework in the human lineage. From framework 2, a rooted parsimonious tree for the six other frameworks is constructed. This phylogenetic tree is discussed in terms of the evolution of nucleotide polymorphisms as well as in terms of genetic affinities between human populations. For each position at which there is base difference in comparing human, gorilla, and chimpanzee beta-globin genes, the phyletic lineage where the corresponding substitution occurred has been identified using the maximum parsimony procedure. The data provide evidence that polymorphisms may represent a significant component of differences between closely related species. If so, nucleotide polymorphisms may strongly bias estimates of small evolutionary distances.

Animals↗
PubMed2007

A clade uniting the green algae Mesostigma viride and Chlorokybus atmophyticus represents the deepest branch of the Streptophyta in chloroplast genome-based phylogenies.

BACKGROUND: The Viridiplantae comprise two major phyla: the Streptophyta, containing the charophycean green algae and all land plants, and the Chlorophyta, containing the remaining green algae. Despite recent progress in unravelling phylogenetic relationships among major green plant lineages, problematic nodes still remain in the green tree of life. One of the major issues concerns the scaly biflagellate Mesostigma viride, which is either regarded as representing the earliest divergence of the Streptophyta or a separate lineage that diverged before the Chlorophyta and Streptophyta. Phylogenies based on chloroplast and mitochondrial genomes support the latter view. Because some green plant lineages are not represented in these phylogenies, sparse taxon sampling has been suspected to yield misleading topologies. Here, we describe the complete chloroplast DNA (cpDNA) sequence of the early-diverging charophycean alga Chlorokybus atmophyticus and present chloroplast genome-based phylogenies with an expanded taxon sampling. RESULTS: The 152,254 bp Chlorokybus cpDNA closely resembles its Mesostigma homologue at the gene content and gene order levels. Using various methods of phylogenetic inference, we analyzed amino acid and nucleotide data sets that were derived from 45 protein-coding genes common to the cpDNAs of 37 green algal/land plant taxa and eight non-green algae. Unexpectedly, all best trees recovered a robust clade uniting Chlorokybus and Mesostigma. In protein trees, this clade was sister to all streptophytes and chlorophytes and this placement received moderate support. In contrast, gene trees provided unequivocal support to the notion that the Mesostigma + Chlorokybus clade represents the earliest-diverging branch of the Streptophyta. Independent analyses of structural data (gene content and/or gene order) and of subsets of amino acid data progressively enriched in slow-evolving sites led us to conclude that the latter topology reflects the true organismal relationships. CONCLUSION: In disclosing a sister relationship between the Mesostigmatales and Chlorokybales, our study resolves the long-standing debate about the nature of the unicellular flagellated ancestors of land plants and alters significantly our concepts regarding the evolution of streptophyte algae. Moreover, in predicting a richer chloroplast gene repertoire than previously inferred for the common ancestor of all streptophytes, our study has contributed to a better understanding of chloroplast genome evolution in the Viridiplantae.

Algal Proteins↗