Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “structural phylogenetics”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 217 records · Page 12Linked to original sources
PubMed2000

Comparative molecular phylogeography of North American softshell turtles (Apalone): implications for regional and wide-scale historical evolutionary forces.

We use a comparative analysis of partial cytochrome b sequences to evaluate the evolutionary forces shaping wide-scale phylogeographic patterns of all three North American softshell turtles (Apalone ferox, A. mutica, and A. spinifera). The overall phylogeographic patterns are concordant with results from both extensive regional studies of southeastern species, implicating historical vicariant processes during the Pliocene and Pleistocene, and investigations of more northerly distributed species, indicating a bottleneck effect of recent dispersal into postglacial habitat. We also resolved a novel, shared genetic break between northern-western and southeastern populations within both A. mutica and A. spinifera, demonstrating the value of using widespread taxa to evaluate both regional and wider scale phylogeographic patterns. The extensive phylogenetic structure and sequence divergences within both A. mutica and A. spinifera contrast sharply with most previous studies of turtles and with the hypothesis that turtles in general have slow rates of mtDNA evolution.

Animals↗
PubMed2001

Variation in the nrDNA ITS of Pinus subsection Cembroides: implications for molecular systematic studies of pine species complexes.

The pinyon pines (Pinus subsection Cembroides), distributed in semiarid regions of the western United States and Mexico, include a mixture of relictual and more recently evolved taxa. To investigate relationships among the pinyons, we screened and partially sequenced 3000-bp clones of the nuclear ribosomal DNA internal transcribed spacer (ITS) region for 16 taxa from subsect. Cembroides and nine representatives from four other subsections of subgenus Strobus. Restriction digests of clones reveal within-individual heterogeneity, suggesting that concerted evolution is operating slowly on the ITS in pine species. Two ITS clones were identified as pseudogenes. Tandem subrepeats in the ITS1 form stem loops comparable to those in other genera of Pinaceae and may be promoting recombination between rDNA repeats, resulting in ITS1 chimeras. Within the pinyon clade, phylogenetic structure is present, but different clones from the same (or different) individuals of a species are polyphyletic, indicating that coalescence of ITS copies within individual genomes predates evolutionary divergence in the group. At the level of subsection and above, the ITS region corresponds well with morphological and cpDNA evidence. Except for P. nelsonii, the pinyons are monophyletic, with both subsect. Cembroides and P. nelsonii forming a clade with the foxtail and bristlecone pines (subsect. Balfourianae) of western North America.

Base Sequence↗
PubMed2005

Phylogeography of Australia's king brown snake (Pseudechis australis) reveals Pliocene divergence and Pleistocene dispersal of a top predator.

King brown snakes or mulga snakes (Pseudechis australis) are the largest and among the most dangerous and wide-ranging venomous snakes in Australia and New Guinea. They occur in diverse habitats, are important predators, and exhibit considerable morphological variation. We infer the relationships and historical biogeography of P. australis based on phylogenetic analysis of 1,249 base pairs from the mitochondrial cytochrome b, NADH dehydrogenase subunit 4 and three adjacent tRNA genes using Bayesian, maximum-likelihood, and maximum-parsimony methods. All methods reveal deep phylogenetic structure with four strongly supported clades comprising snakes from New Guinea (I), localities all over Australia (II), the Kimberleys of Western Australia (III), and north-central Australia (IV), suggesting a much more ancient radiation than previously believed. This conclusion is robust to different molecular clock estimations indicating divergence in Pliocene or Late Miocene, after landbridge dispersal to New Guinea had occurred. While members of clades I, III and IV are medium-sized, slender snakes, those of clade II attain large sizes and a robust build, rendering them top predators in their ecosystems. Genetic differentiation within clade II is low and haplotype distribution largely incongruent with geography or colour morphs, suggesting Pleistocene dispersal and recent ecomorph evolution. Significant haplotype diversity exists in clades III and IV, implying that clade IV comprises two species. Members of clade II are broadly sympatric with members of both northern Australian clades. Thus, our data support the recognition of at least five species from within P. australis (auct.) under various criteria. We discuss biogeographical, ecological and medical implications of our findings.

Animals↗
PubMed1999

Vacuolating cytotoxin (vacA) alleles of Helicobacter pylori comprise two geographically widespread types, m1 and m2, and have evolved through limited recombination.

Vacuolating cytotoxin (vacA) alleles of Helicobacter pylori vary, particularly in their mid region (which may be type m1 or m2) and their signal peptide coding region (type s1 or s2). We investigated nucleotide diversity among vacA alleles in strains from several locales in Asia, South America, and the USA. Phylogenetic analysis of vacA mid region sequences from 18 strains validated the division into two main groups (m1 and m2) and showed further significant divisions within these groups. Informative site analysis demonstrated one example of recombination between m1 and m2 alleles, and several examples of recombination among alleles within these groups. Recombination was not sufficiently extensive to destroy phylogenetic structure entirely. Synonymous nucleotide substitution rates were markedly different between regions of vacA, suggesting different evolutionary divergence times and implying horizontal transfer of genetic elements within vacA. Non-synonymous/synonymous rate ratios were greater between m1 and m2 sequences than among m1 sequences, consistent with m1 and m2 alleles encoding functions fitting strains for slightly different ecological niches.

Alleles↗
PubMed2001

Fish retroposons related to the Penelope element of Drosophila virilis define a new group of retrotransposable elements.

Poseidon and Neptune are two ancient lineages of retroposons related to the Penelope element from Drosophila virilis. They have been identified in various teleost fish species, including the medakafish (Oryzias latipes), and the pufferfishes Fugu rubripes and Tetraodon nigroviridis, whose genomes are currently being sequenced. Some of these elements are highly reiterated in fish genomes. Penelope-related elements were also identified in blood fluke, shrimp, sea urchin, cichlid fish and frog, showing that they are widespread in animals. Penelope-related retroposons were not detected among sequences from the Drosophila melanogaster and human genome projects, suggesting that they have been lost from certain animal lineages. A sequence encoding a putative Uri (also called GIY-YIG) endonuclease domain was detected downstream from the gene for reverse transcriptase. To the best of our knowledge, this type of endonuclease sequence has previously been identified in group I introns and in genes for prokaryotic excinucleases but not in retrotransposable elements. Penelope-related elements are frequently truncated at their 5' ends and can also be flanked by long terminal repeat-like structures. Phylogenetic analysis of the reverse transcriptase domain failed to assign Penelope-related retroposons to one of the major groups of retroelements. Overall, therefore, the evidence strongly suggests that these sequences represent a new group of retrotransposable elements.

Amino Acid Sequence↗
PubMed2005

Human F7 sequence is split into three deep clades that are related to FVII plasma levels.

It is widely accepted that FVII levels are strongly, consistently, and independently related to cardiovascular risk. These levels are influenced by genetic and environmental factors. Among the genetic factors, only a limited number of polymorphisms in the F7 gene have been reported, and they explain only a small proportion of the genetic variability. Recently, we have accomplished the complete dissection of the F7 quantitative trait locus responsible for all of the genetic variability observed in FVII levels. Now, we present the thorough study of the haplotype organization of F7 DNA sequence variation among individuals and the evolutionary processes that produced this variation, by sequencing 15 kb of genomic DNA sequence from the F7 locus in 40 unrelated individual (80 chromosomes) from the genetic analysis of idiopathic thrombophilia (GAIT) project as well as four non-human primate species. Our study revealed 49 polymorphisms, of which 39 SNPs were further considered. Genotyping of these DNA variations in the whole family-based GAIT sample helped resolve linkage phases, and a total of 37 distinct haplotypes were identified.Tajima's D was significantly positive in this sample, suggesting balancing selection. This parameter was a reflection of the phylogenetic structure of F7 haplotype, which was deeply split into three well-supported clades or haplogroups, suggesting that functional differences among F7 variants do not depend on a few single-site variations. Moreover, haplogroup 2 was associated with high FVII levels and haplogroup 3 with low levels. In this study, we have for the first time established a clear relation between genotypic variability structure and phenotypic variability of a particular quantitative trait involved in a complex disease.

Animals↗
PubMed2006

Dietary specialization in European species groups of seed beetles (Coleoptera: Bruchidae: Bruchinae).

Because of their particular biology, seed beetles exhibit a strong relationship with their larval host plants. In Europe, however, field data have long been scarce and unreliable. The results of Legume seed collections of nearly 1,000 samples belonging to 292 species from various locations in Europe are summarized. The status of current Bruchidius species groups is amended on morphological and phylogenetic bases. Recent advances in the knowledge of phylogenetic structures of both Fabaceae and Bruchinae provide a new picture of Bruchinae-Fabaceae interactions. It reveals a certain level of host conservatism. The hypothesis of radiative adaptation seems the most compatible with observed data.

Adaptation, Physiological↗
PubMed2005

Complete nucleotide sequence of the RNA-2 of grapevine deformation and Grapevine Anatolian ringspot viruses.

The nucleotide sequence of RNA-2 of Grapevine Anatolian ringspot virus (GARSV) and Grapevine deformation virus (GDefV), two recently described nepoviruses, has been determined. These RNAs are 3753 nt (GDefV) and 4607 nt (GARSV) in size and contain a single open reading frame encoding a polyprotein of 122 kDa (GDefV) and 150 kDa (GARSV). Full-length nucleotide sequence comparison disclosed 71-73% homology between GDefV RNA-2 and that of Grapevine fanleaf virus (GFLV) and Arabis mosaic virus (ArMV), and 62-64% homology between GARSV RNA-2 and that of Grapevine chrome mosaic virus (GCMV) and Tomato black ring virus (TBRV). As previously observed in other nepoviruses, the 5' non-coding regions of both RNAs are capable of forming stem-loop structures. Phylogenetic analysis of the three proteins encoded by RNA-2 (i.e. protein 2A, movement protein and coat protein) confirmed that GDefV and GARSV are distinct viruses which can be assigned as definitive species in subgroup A and subgroup B of the genus Nepovirus, respectively.

5' Untranslated Regions↗
PubMed1983

Sequences of three transfer RNAs from mosquito mitochondria.

The sequences of three transfer RNAs from mosquito cell mitochondria, tRNAArgUCG, tRNAAspGUC, and tRNAIleGAU, determined using a combination of rapid ladder and fingerprinting procedures are reported. These were compared with hamster mitochondrial tRNAArgUCG and tRNAAspGUC determined similarly, and a bovine mitochondrial tRNAIleGAU determined using a somewhat different approach. The primary sequences of the mosquito tRNAs were 35 to 65% homologous to the corresponding mammalian mitochondrial species, and bore little homology to "conventional" (bacterial or eucaryotic cytoplasmic) tRNA. The modification status of the mosquito mitochondrial tRNAs resembled that of mammalian mitochondrial tRNA. The results contribute to the generalization that metazoan mitochondrial tRNA constitutes a distinctive, albeit loosely structured, phylogenetic group.

Aedes↗
PubMed2006

Diversity and evolution of Ty1-copia and Ty3-gypsy retroelements in the non-photosynthetic flowering plants Orobanche and Phelipanche (Orobanchaceae).

We present the first study on the diversity and evolution of Ty1-copia and Ty3-gypsy retroelements in a group of non-photosynthetic flowering plants. To this end partial sequences of the reverse transcriptase (rt) gene were obtained from 20 clones for each retroelement type from seven and six accessions of Orobanche and Phelipanche (Orobanchaceae), respectively. Overall sequence similarity is higher in Ty3-gypsy elements than in Ty1-copia elements in agreement with the results from other angiosperm groups. Higher sequence diversity and stronger phylogenetic structure, especially of Ty1-copia sequences, in Orobanche species compared to Phelipanche species support the previously suggested hypothesis (based on karyological and cytological data) that genomes of Orobanche species are more dynamic than those of Phelipanche species. No evidence was found for intraspecific differences of retroelement diversity nor for differences between pest taxa and their putative wild relatives, e.g., O. crenata and O. owerini. The occurrence of a few sequences from Phelipanche species in clades otherwise comprising sequences from Orobanche species might be due to horizontal gene transfer, but the alternative of vertical transmission cannot be rejected unambiguously.

Chromosome Mapping↗
PubMed2006

Minimization of genetic distances by the consensus, ancestral, and center-of-tree (COT) sequences for HIV-1 variants within an infected individual and the design of reagents to test immune reactivity.

Eliciting maximal immune responses to highly divergent viruses is a challenge and a focus in AIDS vaccine development. Another challenge is to identify the immune correlates of protective immunity. Recent AIDS vaccine design approaches attempt to use reconstructed centralized viral sequences that minimize genetic differences to circulating viruses. Using these approaches, we derive and analyze consensus (CON), ancestral (ANC), and center-of-tree (COT) sequences to represent intra-individual HIV-1 env variants encoding a range of diversities and phylogenetic structures. Each reconstructed sequence significantly minimized genetic distances to extant sequences throughout the first 5 years of infection of an individual. Interestingly, ANC sequences diverged and were not significantly better than extant sequences in minimizing genetic distances at later stages of infection and disease, likely due to the development of a substantially asymmetric phylogeny. COT or CON sequences derived from autologous virus samplings may be useful for increasing the sensitivity of assessments of immune reactivity against HIV.

Amino Acid Sequence↗
PubMed2005

Phylogenetic relationships and evolutionary history of the reef fish family Labridae.

The family Labridae (including scarines and odacines) contains 82 genera and about 600 species of fishes that inhabit coastal and continental shelf waters in tropical and temperate oceans throughout the world. The Labridae (the wrasses) is the fifth largest fish family and second largest marine fish family, and is one of the most morphologically and ecologically diversified families of fishes in size, shape, and color. Labrid phylogeny is a long-standing problem in ichthyology that is part of the larger question of relationships within the suborder Labroidei. A phylogenetic analysis of labrids was conducted to investigate relationships among the six classical tribes of wrasses, the affinities of the wrasses to the parrotfishes (scarines), and the broad phylogenetic structure among labrid genera. Four gene fragments were sequenced from 98 fish species, including 84 labrid fishes and 14 outgroup taxa. Taxa were chosen from all major labrid clades and most major global ocean regions where labrid fishes exist, as well as cichlid, pomacentrid, and embiotocid outgroups. From the mitochondrial genome we sequenced portions of 12S rRNA (1000 bp) and 16S rRNA (585 bp), which were aligned by using a secondary structure model. From the nuclear genome, we sequenced part of the protein-coding genes RAG2 (846 bp) and Tmo4C4 (541 bp). Maximum likelihood, maximum parsimony, and Bayesian analyses on the resulting 2972 bp of DNA sequence produced similar topologies that confirm the monophyly of a family Labridae that includes the parrotfishes and butterfishes and strong support for many previously identified taxonomic subgroups. The tribe Hypsigenyini (hogfishes, tuskfishes) is the sister group to the remaining labrids and includes odacines and the chisel-tooth wrasse Pseudodax moluccanus, a species previously considered close to scarines. Cheilines and scarines are sister-groups, closely related to the temperate Labrini, and pseudocheilines and cheilines are split in all phylogenies. The razorfishes (novaculines) and temperate pseudolabrines form successive sister clades to the large crown group radiation of the Julidini. The cleaner wrasses (Labrichthyini) are nested within this radiation and several julidine genera do not appear to be monophyletic (e.g., Coris and Halichoeres). Invasion of temperate water by this predominantly tropical group has occurred multiple times and the reconstruction of biogeography assuming an Indo-Pacific ancestor results in five different lineages invading the Atlantic/Caribbean region. Functional novelties in the feeding apparatus have allowed labrid fishes to occupy nearly every feeding guild in reef environments, and trophic variation is a central axis of diversification in this family.

Animals↗
PubMed2000

Oncomelania hupensis (Gastropoda: rissooidea) in eastern China: molecular phylogeny, population structure, and ecology.

The rissooidean snail genus Oncomelania is of medical interest as various taxa are hosts for the human blood fluke Schistosoma and the lung fluke Paragonimus; because of close co-evolved host-parasite-relationships, snail diversity may reflect parasite diversity. There is a considerable amount of confusion regarding the identity of smooth- and ribbed-shelled populations of Oncomelania hupensis in eastern China. We therefore studied the genetic variation, population structure, phylogenetic relationships and ecology of five smooth- and five ribbed-shelled populations in Hubei, Hunan, Anhui, Zhejiang, and Jiangsu provinces. Based on sequencing data of a fragment of the mitochondrial gene for cytochrome oxidase I from 80 individuals, we found little genetic variability within the ingroup-individuals studied here (average pi=0.01922). Moreover, within the ingroup, smooth-shelled individuals cluster together with ribbed-shelled individuals. We therefore consider all smooth- and ribbed-shelled populations of Oncomelania throughout the lower Yangtze River basin to belong to the subspecies O. hupensis hupensis. Our data indicate that ribbing in O. h. hupensis is associated with the annual floods of the Yangtze River. The greatest haplotype (d(H)) and nucleotide diversities (pi) are found in aggregates of ribbed-shelled snails along areas of the Yangtze River drainage subject to flooding. In areas not affected by flooding, the shells are smooth and genetic diversity decreases significantly.

Animals↗
PubMed2003

Phylogenies, the comparative method and parasite evolutionary ecology.

A growing number of comparative analyses in the field of parasite evolution and ecology have used phylogenetically based comparative methods. However, the comparative approach has not been used much by parasitologists. We present the rationale for the use of phylogenetic information in comparative studies, and we illustrate the use of several phylogenetically based comparative methods with case studies in parasite evolutionary ecology. The independent contrasts method is the most popular one, but presents some problems for studying co-adaptation between host and parasite life traits. The eigenvector method has been recently proposed as a new method to estimate and correct for phylogenetic inertia. We illustrate this method with an investigation of patterns of helminth parasite species richness across mammalian host species. This method seems to perform well in situations where host and parasite phylogenies are not perfectly congruent, but one might still want to correct for the effects of both. Finally, we present a method recently proposed for variation partitioning in a phylogenetic context, i.e. the phylogenetically structured environmental variation.

Animals↗
PubMed2006

Cloning and characterization of four B-hordein genes from Tibetan hull-less barley (Hordeum vulgare subsp. vulgare).

Four B-hordein genes, designated BH1-BH4, were cloned using PCR amplification from two hull-less barley cultivars, ZQ7239 and ZQ148, collected from Tibet. The results of sequencing indicated that BH1-BH4 contained complete open reading frames (ORFs). Comparison of their predicted polypeptide sequences with the published sequences suggested that they all share the same basic protein structure. Phylogenetic analysis indicated that the deduced amino-acid sequences of BH1-BH4 genes were more closely related to B-hordeins from cultivated barley (Hordeum vulgare L.) than to any other prolamins from wild barley and Aegilops tauschii. Comparison of the coding regions of BH1-BH4 genes showed that BH1 had a lower sequence identity to other previously published B-hordeins than the other three B-hordeins obtained in this study. BH1 was then cloned in a bacterial expression vector based on bacteriophage T7 RNA polymerase. The resulting plasmid produced a 28.15 kDa protein in Escherichia coli. The potential value of B-hordein genes in grain quality improvement of hull-less barley has been discussed.

Cloning, Molecular↗
PubMed2003

Using matK sequence data to unravel the phylogeny of Casuarinaceae.

Casuarinaceae are a Gondwanic family with a unique combination of morphological characters not comparable to any other family. Until recently, the 96 species in the family were classified in a single genus, Casuarina s.l. A recent morphological revision of the family resulted in the splitting of Casuarina s.l. into four genera-Allocasuarina, Casuarina s.s., Ceuthostoma, and Gymnostoma. This study uses matK sequence data from 76 species of Casuarinaceae and eight outgroup taxa to examine the phylogenetic structure within the Casuarinaceae. The study demonstrates the monophyly of the four genera and examines the relationships within the family; it tests the validity of the infra-generic subdivision of Allocasuarina; it discovers geography-based infra-generic subdivisions within Gymnostoma and Casuarina; and, finally, provides a molecular framework on which to trace the evolution of xeromorphy in the Casuarinaceae.

Base Sequence↗
PubMed2000

Comparison of papillomavirus and immunodeficiency virus evolutionary patterns in the context of a papillomavirus vaccine.

In contemplating a vaccine for human papillomaviruses (HPVs), it is important to consider the evolutionary context in which such a vaccine would be deployed. The human immunodeficiency virus, having been the subject of even more extensive study than HPV, shares certain salient features with regards to phylogenetic structure, and may serve as a model for contemplation of possible difficulties with HPV vaccination. However, there are also striking differences in the evolutionary potentials and histories of the viruses that permit an optimistic outlook for HPV. These similarities and differences, as well as their implications for vaccination studies, are reviewed.

Animals↗
PubMed1999

Symbiomonas scintillans gen. et sp. nov. and Picophagus flagellatus gen. et sp. nov. (Heterokonta): two new heterotrophic flagellates of picoplanktonic size.

Two new oceanic free-living heterotrophic Heterokonta species with picoplanktonic size (< 2 microm) are described. Symbiomonas scintillans Guillou et Chrétiennot-Dinet gen. et sp. nov. was isolated from samples collected both in the equatorial Pacific Ocean and the Mediterranean Sea. This new species possesses ultrastructural features of the bicosoecids, such as the absence of a helix in the flagellar transitional region (found in Cafeteria roenbergensis and in a few bicosoecids), and a flagellar root system very similar to that of C. roenbergensis, Acronema sippewissettensis, and Bicosoeca maris. This new species is characterized by a single flagellum with mastigonemes, the presence of endosymbiotic bacteria located close to the nucleus, the absence of a lorica and a R3 root composed of a 6+3+x microtubular structure. Phylogenetical analyses of nuclear-encoded SSU rDNA gene sequences indicate that this species is close to the bicosoecids C. roenbergensis and Siluania monomastiga. Picophagus flagellatus Guillou et Chrétiennot-Dinet gen. et sp. nov. was collected in the equatorial Pacific Ocean. Cells are naked and possess two flagella. This species is characterized by the lack of a transitional helix and lateral filaments on the flagellar tubular hairs, the absence of siliceous scales, two unequal flagella, R1 + R3 roots, and the absence of a rhizoplast. SSU rDNA analyses place this strain at the base of the Chrysophyceae/Synurophyceae lineages.

Animals↗