Search results for "phylogenetic tree"

Molecular Evolution and the Phylogenetic Relationships of the African Toad, Bufo danielae PERRET, 1977 (Salientia : Bufonidae)

1980

Abstract Phylogenetic relationships of the African toad Bufo danielae are investigated using a variety of biochemical approaches. Nuclear DNA content was assayed and compared to representatives of three species groups of African Bufo. Cellogel electrophoresis of plasma proteins was performed and patterns of B. danielae compared with those of representatives of the African B. regularis species complex. Finally microcomplement fixation analyses of albumin relationships of B. danielae and African Bufo were carried out. The strengths of the varied approaches for phylogenetic analysis are discussed. B. danielae appears most closely related to B. maculatus and B. pusillus, it being some 5-6 mill…

Salicornia L. (Amaranthaceae) in South Africa and Namibia: rapid spread and ecological diversification of cryptic species

2013

In Salicornia, morphology does not provide reliable diagnostic characters supporting the true extent of evolutionary divergence in the genus, and species concepts have been challenged by molecular analyses. Here, we report the results of an analysis of 91 accessions of the S. meyeriana complex from South Africa and Namibia using the measurements of 38 morphological traits and external transcribed spacer (ETS) sequence data. Morphological data were analysed using discriminant analysis, principal coordinate analysis and nonmetric multidimensional scaling. Phylogenetic divergence was compared with the geographical and ecological diversity of the sampled populations. Tree topology corresponds t…

New insights into the taxonomy and phylogeny of social voles inferred from mitochondrial cytochrome b sequences

2012

We sequenced the entire cytochrome b gene in Microtus paradoxus from Turkmenistan and Microtus socialis from Crimea and Kalmykia. Phylogenetic relationships among social voles were reconstructed by the inclusion into analyses of a further 23 published haplotypes belonging to six species. The two probabilistic methods which were used in phylogenetic analyses, the Bayesian inference and Maximum Likelihood, yielded very similar results. Both trees showed two highly divergent lineages which were further subdivided into seven species. The socialis lineage encompassed four species (M. socialis, M. irani, M. anatolicus, and M. paradoxus), and the remaining three species clustered into the guenther…

Rapid differentiation between livestock-associated and livestock-independent Staphylococcus aureus CC398 clades.

2013

Staphylococcus aureus clonal complex 398 (CC398) isolates cluster into two distinct phylogenetic clades based on single-nucleotide polymorphisms (SNPs) revealing a basal human clade and a more derived livestock clade. The scn and tet(M) genes are strongly associated with the human and the livestock clade, respectively, due to loss and acquisition of mobile genetic elements. We present canonical single-nucleotide polymorphism (canSNP) assays that differentiate the two major host-associated S. aureus CC398 clades and a duplex PCR assay for detection of scn and tet (M). The canSNP assays correctly placed 88 S. aureus CC398 isolates from a reference collection into the human and livestock clade…

Reducing the effect of the data order in algorithms for constructing phylogenetic trees.

1988

Metagenomics reveals our incomplete knowledge of global diversity

2008

Metagenomic sequencing obtains huge amounts of sequences from environmental and clinical samples, thus providing a glimpse of the global prokaryotic diversity of both species and genes in these sources. The current trend in metagenomic analysis follows the so-called gene-centric approach, focused on describing the environments by the study of the functional roles of the proteins encoded in the sequenced genes. In this way, it is clear that metagenomic analysis relies heavily on the accurate knowledge of the universe of proteins stored in the databases. Nevertheless, it is known that some biases exist in the composition of databases (which are rich in sequences from common, cultivable and ea…

Marinifilum flexuosum sp. nov., a new Bacteroidetes isolated from coastal Mediterranean Sea water and emended description of the genus Marinifilum Na…

2012

Abstract A facultatively anaerobe, moderately halophilic, Gram-negative, filamentous, non motile and unpigmented bacterium, designated M30 T , was isolated from coastal Mediterranean Sea water in Valencia, Spain. Phylogenetic analysis based on 16S rRNA sequences placed this strain in the phylum “ Bacteroidetes ” with Marinifilum fragile JC2469 T as its closest relative with 97% sequence similarity. Average nucleotide identity (ANI) values between both strains were far below the 95% threshold value for species delineation (about 89% using BLAST and about 90% using MUMmer). A comprehensive polyphasic study, including morphological, biochemical, physiological, chemotaxonomic and phylogenetic d…

An 18S rDNA-Based Molecular Phylogeny of Aphidiinae (Hymenoptera: Braconidae)

2000

We have obtained a molecular phylogeny of the subfamily Aphidiinae (Hymenoptera: Braconidae) by sequencing the 18S rDNA in 37 aphidiine taxa. Approximately 1857 nucleotides were sequenced in each species. Evolutionary relationships were established by comparing the results of maximum-parsimony, maximum-likelihood, and distance analyses. The most variable region of this gene, V4 (approx 403 nucleotides), was employed to establish the basality of the tribe Ephedrini within this subfamily. All phylogenetic reconstructions yielded trees with very similar topologies that confirmed the existence of two of the four traditionally accepted tribes, Ephedrini and Praini, but questioned the existence o…

Systematic position of Dinidoridae within the superfamily Pentatomoidea (Hemiptera: Heteroptera) revealed by the Bayesian phylogenetic analysis of th…

2012

Mitochondrial 12S and 16S rDNA sequences of five species of Dinidoridae Stål, 1868, a largely Paleotropical family, and 16 other shield bugs (Pentatomoidea) were studied. This was the first molecular examination of the systematic position of this family within the superfamily Pentatomoidea using more than a single dinidorid species. Phylogenetic trees obtained from the Bayesian inference of 12S and 16S sequences of these mitochondrial DNA, identified Dinidoridae as the monophylum and a sister group to the Tessaratomidae. Moreover, results of the study suggested a close molecular affinity of the genus Eumenotes to representatives of the subfamily Dinidorinae, which contradicts all previous m…

Evolution of the Secondary Symbiont “Candidatus Serratia symbiotica” in Aphid Species of the Subfamily Lachninae ▿†

2008

ABSTRACT Buchnera aphidicola BCc, the primary endosymbiont of the aphid Cinara cedri (subfamily Lachninae), is losing its symbiotic capacity and might be replaced by the coresident “ Candidatus Serratia symbiotica.” Phylogenetic and morphological analyses within the subfamily Lachninae indicate two different “ Ca . Serratia symbiotica” lineages and support the longtime coevolution of both symbionts in C. cedri .