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PubMed1993

Evidence for independent acquisition of group I introns in green algae.

We report the occurrence of a group I intron, 452 nucleotides in length, in the nuclear small-subunit ribosomal gene of the benthic seaweed Urospora penicilliformis, a member of the green algal class Ulvophyceae. Group I introns have been reported in fungi, myxomycetes, the ciliate genus Tetrahymena, and recently in five unicellular chlorophycean algae. The sequence of the conserved core of the U. penicilliformis group I intron was aligned with that of 15 other introns of this type, and the evolutionary relationships among these introns were examined. Comparison of the "intron" tree with phylogenetic hypotheses of the intron-harboring organisms shows that nuclear group I introns in green algae have arisen several times and are not lineage specific.

Animals↗
PubMed2002

Inferring the phylogeny of disjunct populations of the azure-winged magpie Cyanopica cyanus from mitochondrial control region sequences.

The azure-winged magpie (AWM), Cyanopica cyanus, is found in Asia and Iberia. This remarkable disjunct distribution has been variously explained by either the sixteenth-century introduction of birds into Iberia from the Far East, or by the loss of individuals from the central part of their range as a result of Pleistocene glaciations. We have used the mitochondrial control region to undertake a molecular phylogenetic analysis of the AWM, with sequences examined from individuals collected from across the current distribution range and incorporating representatives of all currently defined subspecies. The Western birds are genetically distinct from their Asian congeners and their divergence is basal in the phylogenetic tree. This indicates that the AWM is native to Iberia and not the result of a recent introduction from Asia. In Asia, two major mitochondrial DNA lineages were identified. These correspond to an Inland Asia group and a Pacific Seaboard group, and are separated topographically by the Da Hingan Ling mountains and the Yellow Sea. Molecular clock estimates suggest that these divergences are associated with Pleistocene glaciations. Furthermore, our data do not support the current classification of the AWM into 10 subspecies, as defined based on morphology and geographical distribution.

Animals↗
PubMed2001

Molecular epidemiology of dengue type 2 virus in Venezuela: evidence for in situ virus evolution and recombination.

Epidemic outbreaks of dengue fever (DF) were first recorded in Venezuela in 1978 and were followed by the emergence of dengue haemorrhagic fever (DHF) outbreaks in 1989. To gain a better understanding of the nature of these epidemics, the complete envelope (E) gene sequence of 34 Venezuelan dengue type 2 (DEN-2) viruses, isolated between 1997 and 2000 was determined. Of these isolates, 16 were from patients with DF and 17 were from patients diagnosed with DHF. There were no diagnostic sequence differences between them, suggesting that the E gene alone does not determine disease severity. These sequence data were also used in phylogenetic comparisons with a global sample of DEN-2 viruses, including strains collected previously from Venezuela. This analysis revealed that the ancestors of the Venezuelan viruses were Asian in origin, implying that a DEN-2 virus strain from this region was introduced into Venezuela and the wider Caribbean region during the late 1970s or the early 1980s. The phylogenetic trees further indicate that evolution of DEN-2 virus in Venezuela has occurred in situ, with differentiation into a number of distinct but co-circulating lineages, rather than the repeated introduction of new strains from other localities. By incorporating additional sequence data from the virus capsid, premembrane and membrane genes, evidence is provided that a single Venezuelan strain sequenced previously, designated Mara4, is a recombinant virus, incorporating genome sequence from Venezuelan and Asian parental viruses.

Asia↗
PubMed2001

Phylogenetic analysis of tribe Salsoleae (Chenopodiaceae) based on ribosomal ITS sequences: implications for the evolution of photosynthesis types.

Diversity in photosynthetic pathways in the angiosperm family Chenopodiaceae is expressed in both biochemical and anatomical characters. To understand the evolution of photosynthetic diversity, we reconstructed the phylogeny of representative species of tribe Salsoleae of subfamily Salsoloideae, a group that exhibits in microcosm the patterns of photosynthetic variation present in the family as a whole, and examined the distribution of photosynthetic characters on the resulting phylogenetic tree. Phylogenetic relationships were inferred from parsimony analysis of nucleotide sequences of the internal transcribed spacer regions (ITS) of the 18S-26S nuclear ribosomal DNA of 34 species of Salsola and related genera (Halothamnus, Climacoptera, Girgensohnia, Halocharis, and Haloxylon) and representative outgroups from tribes Camphorosmeae (Camphorosma lessingii, Kochia prostrata, and K. scoparia) and Atripliceae (Atriplex spongiosa). A highly resolved strict consensus tree largely agrees with photosynthetic type and anatomy of leaves and cotyledons. The sequence data provide strong support for the origin and evolution of two main lineages of plants in tribe Salsoleae, with NAD-ME and NADP-ME C(4) photosynthesis, respectively. These groups have different C(4) photosynthetic types in leaves and different structural and photosynthetic characteristics in cotyledons. Phylogenetic relationships inferred from ITS sequences generally agree with classifications based on morphological data, but deviations from the existing taxonomy were also observed. The NAD-ME C(4) lineage contains species classified in sections Caroxylon, Malpigipila, Cardiandra, Belanthera, and Coccosalsola, and the NADP-ME lineage comprises species from sections Coccosalsola and Salsola. Reconstruction of photosynthetic characters on the ITS phylogeny indicates separate NAD-ME and NADP-ME lineages and suggests two reversions to C(3) photosynthesis. Reconstruction of geographic distributions suggests Salsoleae originated and diversified in central Asia and subsequently dispersed to Africa, Europe, and Mongolia. Inferred patterns and processes of photosynthetic evolution in Salsoleae should further our understanding of biochemical and anatomical evolution in Chenopodiaceae as a whole.

Journal Article↗
PubMedDate not supplied

The Wilhelmine W. Key 2002 Invitational Lecture. Phylogeography, haplotype trees, and invasive plant species.

The distribution of genetic variants in plant populations is strongly affected both by current patterns of microevolutionary forces, such as gene flow and selection, and by the phylogenetic history of populations and species. Understanding the interplay of shared history and current evolutionary events is particularly confounding in plants due to the reticulating nature of gene exchange between diverging lineages. Certain gene sequences provide historically ordered neutral molecular variation that can be converted to gene genealogies which trace the evolutionary relationships among haplotypes (alleles). Gene genealogies can be used to understand the evolution of specific DNA sequences and relate sequence variation to plant phenotype. For example, in a study of the RPS2 gene in Arabidopsis thaliana, resistant phenotypes clustered in one portion of the gene tree. The field of phylogeography examines the distribution of allele genealogies in an explicit geographical context and, when coupled with a nested clade analysis, can provide insight into historical processes such as range expansion, gene flow, and genetic drift. A phylogeographical approach offers insight into practical issues as well. Here we show how haplotype trees can address the origins of invasive plants, one of the greatest global threats to biodiversity. A study of the geographical diversity of haplotypes in invasive Phragmites populations in the United States indicates that invasiveness is due to the colonization and spread of distinct genotypes from Europe ( Saltonstall 2002). Likewise, a phylogeographical analysis of Tamarix populations indicates that hybridization events between formerly isolated species of Eurasia have produced the most common genotype of the second-worst invasive plant species in the United States.

Biodiversity↗
PubMed2006

Conflicting phylogenetic position of Schizosaccharomyces pombe.

The phylogenetic position of the fission yeast Schizosaccharomyces pombe in the fungal Tree of Life is still controversial. Three alternative phylogenetic positions have been proposed in the literature, namely (1) a position basal to the Hemiascomycetes and Euascomycetes, (2) a position as a sister group to the Euascomycetes with the Hemiascomycetes as a basal branch, or (3) a sister group to the Hemiascomycetes with Euascomycetes as a basal branch. Here we compared 91 clusters of orthologous proteins containing a single orthologue that are shared by 19 eukaryote genomes. The major part of these 91 orthologues supports a phylogenetic position of S. pombe as a basal lineage among the Ascomycota, thus supporting the second proposition. Interestingly, part of the orthologous proteins supported a fourth, not yet described alternative, in which S. pombe is basal to both Basidiomycota and Ascomycota. Both topologies of phylogenetic trees are well supported. We believe that both reflect correctly the phylogenetic history of the species concerned. This apparent paradox may point to a heterogeneous nuclear genome of the fungi. Importantly, this needs to be taken in consideration for a correct understanding of the fungal Tree of Life.

Genetic Speciation↗
PubMed1989

The Deinococcus-Thermus phylum and the effect of rRNA composition on phylogenetic tree construction.

Through comparative analysis of 16S ribosomal RNA sequences, it can be shown that two seemingly dissimilar types of eubacteria Deinococcus and the ubiquitous hot spring organism Thermus are distantly but specifically related to one another. This confirms an earlier report based upon 16S rRNA oligonucleotide cataloging studies (Hensel et al., 1986). Their two lineages form a distinctive grouping within the eubacteria that deserved the taxonomic status of a phylum. The (partial) sequence of T. aquaticus rRNA appears relatively close to those of other thermophilic eubacteria. e.g. Thermotoga maritima and Thermomicrobium roseum. However, this closeness does not reflect a true evolutionary closeness; rather it is due to a "thermophilic convergence", the result of unusually high G+C composition in the rRNAs of thermophilic bacteria. Unless such compositional biases are taken into account, the branching order and root of phylogenetic trees can be incorrectly inferred.

Bacteria↗
PubMed2000

Genetic analysis of wild-type Dobrava hantavirus in Slovenia: co-existence of two distinct genetic lineages within the same natural focus.

Genetic analysis was performed of wild-type (wt) Dobrava hantavirus (DOB) strains from Slovenia, the country where the virus was first discovered and where it was found to cause haemorrhagic fever with renal syndrome (HFRS), with a fatality rate of 12%. Two hundred and sixty mice of the genus APODEMUS:, trapped in five natural foci of DOB-associated HFRS during 1990-1996, were screened for the presence of anti-hantavirus antibodies and 49 APODEMUS: flavicollis and four APODEMUS: agrarius were found to be positive. RT-PCR was used to recover partial sequences of the wt-DOB medium (M) and small (S) genome segments from nine A. flavicollis and one A. agrarius. Sequence comparison and phylogenetic analysis of the Slovenian wt-DOB strains revealed close relatedness of all A. flavicollis-derived virus sequences (nucleotide diversity up to 6% for the M segment and 5% for the S segment) and the geographical clustering of genetic variants. In contrast, the strain harboured by A. agrarius showed a high level of genetic diversity from other Slovenian DOB strains (14%) and clustered together on phylogenetic trees with other DOB strains harboured by A. agrarius from Russia, Estonia and Slovakia. These findings suggest that the DOB variants carried by the two species of APODEMUS: in Europerepresent two distinct genetic lineages.

Animals↗
PubMed2004

Genotypic variation among lineages of Trypanosoma cruzi and its geographic aspects.

Isozyme analysis with 18 enzyme loci was conducted on 146 isolates of Trypanosoma cruzi from Mexico, Guatemala, Colombia, Ecuador, Peru, Brazil, Bolivia, Paraguay and Chile. Forty-four different MLGs (groups of isolates with identical multilocus genotypes) were identified and a phylogeny was constructed. The phylogenetic tree consisted of two main groups (T. cruzi I, T. cruzi II), and the latter was further divided into two subgroups (T. cruzi IIa, T. cruzi IIb-e). Evidence of hybridization between different MLGs of T. cruzi II was found, which means that genetic exchanges seem to have occurred in South American T. cruzi. On the other hand, the persistence of characteristic T. cruzi I and T. cruzi II isozyme patterns in single small villages in Bolivia and Guatemala suggested that genetic exchange is very rare between major lineages. A significant difference in genetic diversity was shown between T. cruzi I and T. cruzi II from several indices of population genetics. Two possibilities could explain this genetic variation in the population: differences in evolutionary history and/or different tendencies to exchange genetic material. Broad-scale geographic distributions of T. cruzi I and T. cruzi IIb-e were different; T. cruzi I occurred in Central America and south to Bolivia and Brazil, while T. cruzi IIb-e occurred in the central and southern areas of South America, overlapping with T. cruzi I in Brazil and Bolivia.

Animals↗
PubMed2003

Lateral gene transfer and ancient paralogy of operons containing redundant copies of tryptophan-pathway genes in Xylella species and in heterocystous cyanobacteria.

BACKGROUND: Tryptophan-pathway genes that exist within an apparent operon-like organization were evaluated as examples of multi-genic genomic regions that contain phylogenetically incongruous genes and coexist with genes outside the operon that are congruous. A seven-gene cluster in Xylella fastidiosa includes genes encoding the two subunits of anthranilate synthase, an aryl-CoA synthetase, and trpR. A second gene block, present in the Anabaena/Nostoc lineage, but not in other cyanobacteria, contains a near-complete tryptophan operon nested within an apparent supraoperon containing other aromatic-pathway genes. RESULTS: The gene block in X. fastidiosa exhibits a sharply delineated low-GC content. This, as well as bias of codon usage and 3:1 dinucleotide analysis, strongly implicates lateral gene transfer (LGT). In contrast, parametric studies and protein tree phylogenies did not support the origination of the Anabaena/Nostoc gene block by LGT. CONCLUSIONS: Judging from the apparent minimal amelioration, the low-GC gene block in X. fastidiosa probably originated by LGT at a relatively recent time. The surprising inability to pinpoint a donor lineage still leaves room for alternative, albeit less likely, explanations other than LGT. On the other hand, the large Anabaena/Nostoc gene block does not seem to have arisen by LGT. We suggest that the contemporary Anabaena/Nostoc array of divergent paralogs represents an ancient ancestral state of paralog divergence, with extensive streamlining by gene loss occurring in the lineage of descent representing other (unicellular) cyanobacteria.

Amino Acid Sequence↗
PubMed2002

Molecular epidemiology of echovirus 30: temporal circulation and prevalence of single lineages.

Echovirus 30 (EV30) is one of the most frequently isolated EVs, causing extensive outbreaks of EV30 aseptic meningitis in temperate climates. EV30 is antigenically heterogeneous, and three major antigenic groups have been defined, although the basis for the antigenic differences is unknown. A reverse transcription-nested PCR which amplifies the 3'-terminal region of the VP1 gene directly from clinical samples was selected for studying EV30 molecular epidemiology, since the major antigenic sites in this region reflect the serotypic pattern of this virus. The different previous approaches to the genetic classification of EV30 were analyzed. A complete study of the EV30 strains was performed by analyzing the sequences from the 112 EV30 strains amplified in this work and the complete set of EV30 strains previously published. A total of 318 strains of EV30 were divided into two broad genotypes (I and II). This classification was supported by the phylogenetic trees obtained from amino acid sequences, and it correlated with the antigenic heterogeneity of the reference strains described in earlier studies. The genotypes could be further divided into subgroups, and these subgroups could be divided into lineages based on their nucleotide distances and levels of bootstrapping. On the other hand, the subgroups and lineages did not result in the same correlation between amino acid and nucleotide differentiation. The molecular epidemiology of EV30 can be compared to influenza virus epidemiology, where prevailing lineages displace the less established lineages on the basis of immune escape. This pattern of evolution is clearly different from that of other enteroviruses. A single lineage at a time appears to be circulating worldwide. This behavior may be related to the epidemic activity of EV30.

Argentina↗
PubMed1994

Molecular evolution of interleukin-3.

Chimpanzee, tamarin, and marmoset interleukin-3 (IL-3) genes were cloned, sequenced, and expressed. Western blot analysis demonstrated that functional genes were isolated. IL-3 sequences were compared with those of mouse, rat, rhesus monkey, gibbon, and man. Multiple alignment of the IL-3 coding regions showed that only a few regions had been conserved during mammalian evolution, which are likely associated with functional domains of the IL-3 protein. Substitution rates for the various lineages were calculated and the numbers of synonymous and nonsynonymous substitutions were estimated separately. Distance matrices of the IL-3 coding regions were used to construct phylogenetic trees which revealed large differences in IL-3 evolution rate as well as a more rapid substitution rate for rodents and a rate slowdown during hominoid evolution. Extremes were rhesus monkey IL-3, which accumulated few synonymous substitutions, and gibbon IL-3, which had almost exclusively synonymous substitutions. In rhesus monkey IL-3, nonsynonymous substitutions outnumbered synonymous substitutions, which could not be readily explained by a random process of substitutions. We assume that during evolution of IL-3, the majority of the amino acid replacements and the impaired interspecies functional cross-reactivity originate from selection mechanisms with the most likely selective force being the structure of the heterodimeric IL.3 cell-surface receptor. Insight into IL-3 architecture and structural analysis of the IL-3 receptor are needed to analyze the unusually fast evolution of IL-3 in more detail.

Animals↗
PubMed1991

Time of the deepest root for polymorphism in human mitochondrial DNA.

A molecular clock analysis was carried out on the nucleotide sequences of parts of the major noncoding region of mitochondrial DNA (mtDNA) from the major geographic populations of humans. Dates of branchings in the mtDNA tree among humans were estimated with an improved maximum likelihood method. Two species of chimpanzees were used as an outgroup, and the mtDNA clock was calibrated by assuming that the chimpanzee/human split occurred 4 million years ago, following our earlier works. A model of homogeneous evolution among sites does not fit well with the data even within hypervariable segments, and hence an additional parameter that represents a proportion of variable sites was introduced. Taking account of this heterogeneity among sites, the date for the deepest root of the mtDNA tree among humans was estimated to be 280,000 +/- 50,000 years old (+/- 1 SE), although there remains uncertainty about the constancy of the evolutionary rate among lineages. The evolutionary rate of the most rapidly evolving sites in mtDNA was estimated to be more than 100 times greater than that of a nuclear pseudogene.

Animals↗
PubMed2002

The evolution of gymnosperms redrawn by phytochrome genes: the Gnetatae appear at the base of the gymnosperms.

Gymnosperms possess two to four phytochrome types which apparently are the result of successive gene duplications in the genomes of their common ancestors. Phytochromes are nuclear-encoded proteins whose genes, contrary to chloroplast, mitochondrion, and rRNA genes, have hitherto rarely been used to examine gymnosperm phylogenies. Since the individual phytochrome gene types implied phylogenies that were not completely congruent to one another, conflicting branching orders were sorted by the number of gene lineages present in a taxon. The Gnetatae (two gene types) branched at the base of all gymnosperms, a position supported by bootstrap sampling (distance and character state trees, maximum likelihood). The Gnetatae were followed by Ginkgo, Cycadatae, and Pinaceae (three gene types) and the remaining conifers (four gene types). Therefore, in phytochrome trees, the most ancient branch of the conifers (Pinatae) seems to be the Pinaceae. The next split appears to have separated Araucariaceae plus Podocarpaceae from the Taxaceae/Taxodiaceae/Cupressaceae group. Structural arrangements in the plastid genomes (Raubeson and Jansen 1992) corroborate the finding that there is no close connection between Pinaceae and Gnetatae as suggested by some publications. The analyses are based on 60 phytochrome genes (579 positions in an alignment of PCR fragments) from 28 species. According to rough divergence time estimates, the last common ancestor of gymnosperms and angiosperms is likely to have existed in the Carboniferous.

Cycadopsida↗
PubMed2003

Possible polyphyletic origin of major histocompatibility complex class I chain-related gene A (MICA) alleles.

Phylogenetic relationships among 23 nonhuman primate (NHP) major histocompatibility complex class I chain-related gene (MIC) sequences, 54 confirmed human MICA alleles, and 16 human MICE alleles were constructed with methods of sequence analysis. Topology of the phylogenetic tree showed separation between NHP MICs and human MICs. For human MICs, the topology indicated monophyly for the MICB alleles, while MICA alleles were separated into two lineages, LI and LII. Of these, LI MICA alleles shared a common ancestry with gorilla (Ggo) MIC. One conservative amino acid difference and two nonconservative amino acid differences in the alpha3 domain were found between the MICA lineages. The nonconservative amino acid differences might imply structural and functional differences. Transmembrane (TM) trinucleotide-repeat variants were found to be specific to the MICA lineages such as A4, A9, and A10 to LI and A5 to LII. Variants such as A5.1 and A6 were commonly found in both MICA lineages. Based on these analyses, we postulate a polyphyletic origin for MICA alleles and their division into two lineages, LI and LII. As such, there would be 30 alleles in LI and 24 alleles in LII, thereby reducing the current level of polymorphism that exists, based on a presumed monophyletic origin. The lower degree of polymorphism in MICA would then be in line with the rest of the human major histocompatibility complex nonclassical class I genes.

Alleles↗
PubMed2006

Genetic variation, population structure, and phylogenetic relationships of Triatoma rubida and T. recurva (Hemiptera: Reduviidae: Triatominae) from the Sonoran Desert, insect vectors of the Chagas' disease parasite Trypanosoma cruzi.

Nucleotide and amino acid sequence data from the mitochondrial cytochrome b (Cytb) and cytochrome c oxidase subunit I (COI) gene segments were used to gain insights into the population biology and phylogenetic relationships of two species of hematophagous kissing bugs (Hemiptera: Reduviidae: Triatominae) from the Sonoran Desert of northwestern Mexico and southern Arizona, USA, Triatoma rubida (Uhler, 1894) and T. recurva (Stål, 1868), both of which are vectors of the protozoan parasite Trypanosoma cruzi responsible for Chagas' disease. Analysis of molecular variance of gene sequences indicated significant structure among populations of both species from widely separated geographic localities. Phylogenetic analyses of gene and amino acid sequences employing both Bayesian and parsimony methods showed that T. recurva clustered within the phyllosoma complex of Triatoma species from central and southern Mexico with high statistical support, and that it was closely related to T. longipennis. Triatoma dimidiata also was shown to be closely related to the phyllosoma complex, as was T. sanguisuga which has historically been assigned to the lecticularia complex. Analyses of gene sequences were unable to confidently resolve relationships of T. rubida, although weak support for a T. nitida+T. rubida clade was seen under certain conditions. A provisional calibration of a mitochondrial DNA molecular clock for T. rubida, based on geological dates for the vicariant separation of the Baja California peninsula from mainland Mexico, suggested that pairwise sequence divergences for the Cytb and COI genes were 1.1-1.8% and 0.6-1.0% per million years, respectively. Two highly supported sympatric lineages of T. rubida uhleri from southern Arizona, which are hypothesized to have diverged approximately 550,000-900,000 years ago, were detected in the Cytb gene trees.

Amino Acid Sequence↗
PubMed2003

Phylogenetic significance of morphological characters in the taxonomy of Pestalotiopsis species.

There has been considerable disagreement regarding the relationships among Pestalotiopsis species and their delimitations. A molecular phylogenetic analysis was conducted on 32 species of Pestalotiopsis in order to evaluate the utility of morphological characters currently used in their taxonomy. Phylogenetic relationships were inferred from nucleotide sequences in the ITS regions and 5.8S gene of the rDNA under four optimality criteria: maximum parsimony, weighted parsimony, maximum likelihood, and neighbor joining. Phylogenies estimated from all analyses yielded trees of essentially similar topology and revealed 3 major groups that correspond with morphology-based classification systems. Molecular data indicated that the genus contains two distinct lineages based on pigmentation of median cells and four distinct groupings based on morphology of apical appendages. The analyses did not support reliability of other phenotypic characters of this genus, such as spore dimensions. Characters with particular phylogenetic significance are discussed in relation to the taxonomy of Pestalotiopsis.

Ascomycota↗
PubMed2001

Phylogeny of Thogoto virus.

Thogoto virus is a tick-borne member of the family Orthomyxoviridae. Previously, based on the similarity in antigenic relationship by cross-neutralization test, all virus strains were concluded to have derived from the same origin. In this study, we obtained partial gene sequences of 4 genes (PB1-like protein, PA-like protein, glycoprotein, and nucleoprotein) of 8 Thogoto virus strains isolated in Africa, Asia, and Europe and studied the genetic variation and phylogeny. Unrooted phylogenetic trees created by both neighbor-joining and maximum likelihood methods based on nucleotide and amino acid sequences for 4 genes were mostly similar and revealed two lineages, Euro-Asian and African. Intra-lineage nucleotide sequence variation was greater in the Euro-Asian lineage than in the African lineage for all 4 genes. Furthermore, for the strains of Euro-Asian lineage, variations for two genes associated with RNA-dependent RNA polymerase activities were greater than those for glycoprotein or nucleoprotein gene, based on both nucleotide and amino acid sequence differences as well as on synonymous and nonsynonymous differences, indicating greater mutation rates for the polymerase activity genes in these strains.

Base Sequence↗