Search results for "phylogeny"
showing 10 items of 1398 documents
Phylointeractomics reconstructs functional evolution of protein binding
2017
Molecular phylogenomics investigates evolutionary relationships based on genomic data. However, despite genomic sequence conservation, changes in protein interactions can occur relatively rapidly and may cause strong functional diversification. To investigate such functional evolution, we here combine phylogenomics with interaction proteomics. We develop this concept by investigating the molecular evolution of the shelterin complex, which protects telomeres, across 16 vertebrate species from zebrafish to humans covering 450 million years of evolution. Our phylointeractomics screen discovers previously unknown telomere-associated proteins and reveals how homologous proteins undergo functiona…
Ancient proteins resolve the evolutionary history of Darwin's South American ungulates.
2015
No large group of recently extinct placental mammals remains as evolutionarily cryptic as the approximately 280 genera grouped as 'South American native ungulates'. To Charles Darwin, who first collected their remains, they included perhaps the 'strangest animal[s] ever discovered'. Today, much like 180 years ago, it is no clearer whether they had one origin or several, arose before or after the Cretaceous/Palaeogene transition 66.2 million years ago, or are more likely to belong with the elephants and sirenians of superorder Afrotheria than with the euungulates (cattle, horses, and allies) of superorder Laurasiatheria. Morphology-based analyses have proved unconvincing because convergences…
Response of rainbow trout transcriptome to model chemical contaminants.
2004
We used high-density cDNA microarray in studies of responses of rainbow trout fry at sublethal ranges of beta-naphthoflavone, cadmium, carbon tetrachloride, and pyrene. The differentially expressed genes were grouped by the functional categories of Gene Ontology. Significantly different response to the studied compounds was shown by a number of classes, such as cell cycle, apoptosis, signal transduction, oxidative stress, subcellular and extracellular structures, protein biosynthesis, and modification. Cluster analysis separated responses to the contaminants at low and medium doses, whereas at high levels the adaptive reactions were masked with general unspecific response to toxicity. We fo…
Adaptative biochemical pathways and regulatory networks in Klebsiella oxytoca BAS-10 producing a biotechnologically relevant exopolysaccharide during…
2012
Abstract Background A bacterial strain previously isolated from pyrite mine drainage and named BAS-10 was tentatively identified as Klebsiella oxytoca. Unlikely other enterobacteria, BAS-10 is able to grow on Fe(III)-citrate as sole carbon and energy source, yielding acetic acid and CO2 coupled with Fe(III) reduction to Fe(II) and showing unusual physiological characteristics. In fact, under this growth condition, BAS-10 produces an exopolysaccharide (EPS) having a high rhamnose content and metal-binding properties, whose biotechnological applications were proven as very relevant. Results Further phylogenetic analysis, based on 16S rDNA sequence, definitively confirmed that BAS-10 belongs t…
The Globin Gene Repertoire of Lampreys: Convergent Evolution of Hemoglobin and Myoglobin in Jawed and Jawless Vertebrates
2014
Agnathans (jawless vertebrates) occupy a key phylogenetic position for illuminating the evolution of vertebrate anatomy and physiology. Evaluation of the agnathan globin gene repertoire can thus aid efforts to reconstruct the origin and evolution of the globin genes of vertebrates, a superfamily that includes the well-known model proteins hemoglobin and myoglobin. Here, we report a comprehensive analysis of the genome of the sea lamprey (Petromyzon marinus )w hich revealed 23 intact globin genes and two hemoglobin pseudogenes. Analyses of the genome of the Arctic lamprey (Lethenteron camtschaticum) identified 18 full length and five partial globin gene sequences. The majority of the globin …
Molecular barcoding for central-eastern European Crioceris leaf-beetles (Coleoptera: Chrysomelidae)
2011
Abstract Among Crioceris leaf-beetles, the two most widespread species (Crioceris asparagi and C. duodecimpunctata) are serious invasive plant pests, while another two (C. quatuordecimpunctata and C. quinquepunctata) are rare species restricted to steppe-like habitats in Eurasia. The aim of the research was to check the genetic distinctiveness of these four species and develop barcodes for their molecular identification using the mitochondrial Cytochrome Oxidase I (COI) gene and two nuclear markers: Elongation Factor 1-α (EF1-α) and Internal Transcribed Spacer 1 (ITS1). The identification of each species was possible and reliable with the use of COI and ITS1 markers. EF1-α was omitted in an…
Optimizing auditory images and distance metrics for self‐organizing timbre maps*
1996
Abstract The effect of using different auditory images and distance metrics on the final configuration of a self‐organized timbre map is examined by comparing distance matrices, obtained from simulations, with a similarity rating matrix, obtained using the same set of stimuli as in the simulations. Gradient images, which are intended to represent idealizations of physiological gradient maps in the auditory pathway, are constructed. The optimal auditory image and distance metric, with respect to the similarity rating data, are searched using the gradient method.
Simultaneous occurrence of covert infections with small RNA viruses in the lepidopteran Spodoptera exigua
2014
Viral covert infections in invertebrates have been traditionally attributed to sublethal infections that were not able to establish an acute infection. Recent studies are revealing that, although true for some viruses, other viruses may follow the strategy of establishing covert or persistent infections without producing the death of the host. Recently, and due to the revolution in the sequencing technologies, a large number of viruses causing covert infections in all type of hosts have been identified.The beet armyworm, Spodoptera exigua (Lepidoptera: Noctuidae) is a worldwide pest that causes significant losses to agricultural and ornamental plant industries. In a previous project we used…
An unusually high substitution rate in transplant-associated BK polyomavirus in vivo is further concentrated in HLA-C-bound viral peptides
2018
Infection with human BK polyomavirus, a small double-stranded DNA virus, potentially results in severe complications in immunocompromised patients. Here, we describe the in vivo variability and evolution of the BK polyomavirus by deep sequencing. Our data reveal the highest genomic evolutionary rate described in double-stranded DNA viruses, i.e., 10−3–10−5 substitutions per nucleotide site per year. High mutation rates in viruses allow their escape from immune surveillance and adaptation to new hosts. By combining mutational landscapes across viral genomes with in silico prediction of viral peptides, we demonstrate the presence of significantly more coding substitutions within predicted cog…
First Data on the Molecular Phylogeography of Scincid Lizards of the Genus Mabuya
2000
A 487-bp fragment of the mitochondrial 16S rRNA gene was sequenced in 26 species of the circumtropical lizard genus Mabuya and used to analyze phylogenetic relationships within the genus. The species from Africa and Madagascar formed a monophyletic group relative to the included Asian and South American taxa. The Malagasy species included (M. elegans, M. cf. dumasi, and M. comorensis) did not appear as a monophylum. Combined and separate analysis of the 16S data and additional sequences of the mitochondrial 12S rRNA, ND4, and cytochrome b genes (a total of 2255 bp) in one Asian, two Malagasy, and two African species also did not result consistently in a monophyletic grouping of the Malagasy…