Gotowe bibliografie tematyczne / Phylogenetic analyses

Gotowa bibliografia na temat „Phylogenetic analyses”

Autor: Grafiati

Data publikacji: 4 czerwca 2021

Data aktualizacji: 20 lutego 2023

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Artykuły w czasopismach na temat "Phylogenetic analyses"

Sanderson, Michael J., i H. Bradley Shaffer. "Troubleshooting Molecular Phylogenetic Analyses". Annual Review of Ecology and Systematics 33, nr 1 (listopad 2002): 49–72. http://dx.doi.org/10.1146/annurev.ecolsys.33.010802.150509.

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Kuhn, Kristen L., i Thomas J. Near. "Phylogeny of Trematomus (Notothenioidei: Nototheniidae) inferred from mitochondrial and nuclear gene sequences". Antarctic Science 21, nr 6 (grudzień 2009): 565–70. http://dx.doi.org/10.1017/s0954102009990253.

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AbstractThe biota of Antarctica is amazingly rich and highly endemic. The phylogenetics of notothenioid fishes has been extensively investigated through analyses of morphological characters, DNA sequences from mitochondrial genes, and single copy nuclear genes. These phylogenetic analyses have produced reasonably similar phylogenetic trees of notothenioids, however a number of phylogenetic questions remain. The nototheniid clade Trematomus is an example of a group where phylogenetic relationships remain unresolved. In this paper we revisit the phylogenetic relationships of Trematomus using both increased taxon sampling and an expanded dataset which includes DNA sequences from two mitochondrial genes (ND2 and 16S rRNA) and one single-copy nuclear gene (RPS7). The Bayesian phylogeny resulting from the analysis of the combined mitochondrial and nuclear gene datasets was well resolved and contained more interspecific nodes supported with significant Bayesian posteriors than either the mitochondrial or nuclear gene phylogenies alone. This demonstrates that the addition of nuclear gene sequence data to mitochondrial data can enhance phylogenetic resolution and increase node support. Additionally, the results of the combined mitochondrial and nuclear Bayesian analyses provide further support for the inclusion of species previously classified as Pagothenia and Cryothenia in Trematomus.

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LI, JIA-XIN, MAO-QIANG HE i RUI-LIN ZHAO. "Three new species of Micropsalliota (Agaricaceae, Agaricales) from China". Phytotaxa 491, nr 2 (19.03.2021): 167–76. http://dx.doi.org/10.11646/phytotaxa.491.2.6.

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Species diversity of Micropsalliota in China remains poorly known, especially in southwestern China, a hotspot of biodiversity. Based on morphological characteristics and molecular phylogenetic analyses using ITS and nrLSU sequences, three new species named Micropsalliota delicatula, M. dentatomarginata and M. digitatocystis are introduced from China. Phylogenetc analyses results indicated the unique phylogenetic positions of three new species in Micropsalliota. Full descriptions, photo plates, illustrations and a phylogenetic tree to show the placement of three new species are presented.

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Moore, Jenna M., Eijiroh Nishi i Greg W. Rouse. "Phylogenetic analyses of Chaetopteridae (Annelida)". Zoologica Scripta 46, nr 5 (14.03.2017): 596–610. http://dx.doi.org/10.1111/zsc.12238.

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Michu, E. "A short guide to phylogeny reconstruction". Plant, Soil and Environment 53, No. 10 (7.01.2008): 442–46. http://dx.doi.org/10.17221/2194-pse.

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This review is a short introduction to phylogenetic analysis. Phylogenetic analysis allows comprehensive understanding of the origin and evolution of species. Generally, it is possible to construct the phylogenetic trees according to different features and characters (e.g. morphological and anatomical characters, RAPD patterns, FISH patterns, sequences of DNA/RNA and amino acid sequences). The DNA sequences are preferable for phylogenetic analyses of closely related species. On the other hand, the amino acid sequences are used for phylogenetic analyses of more distant relationships. The sequences can be analysed using many computer programs. The methods most often used for phylogenetic analyses are neighbor-joining (NJ), maximum parsimony (MP), maximum likelihood (ML) and Bayesian inference.

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Farmer, Susan. "Phylogenetic Analyses and Biogeography of Trilliaceae". Aliso 22, nr 1 (2006): 579–92. http://dx.doi.org/10.5642/aliso.20062201.45.

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Sullivan, Patrick S., i Alexandra M. Oster. "Phylogenetic analyses of local HIV transmission". Lancet HIV 5, nr 6 (czerwiec 2018): e270-e271. http://dx.doi.org/10.1016/s2352-3018(18)30101-2.

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STUDLEY, WILLIAM KEITH, MUTSUO YAMAGUCHI, YOUSSEF HATEFI i MILTON H. SAIER. "Phylogenetic Analyses of Proton-Translocating Transhydrogenases". Microbial & Comparative Genomics 4, nr 3 (styczeń 1999): 173–86. http://dx.doi.org/10.1089/omi.1.1999.4.173.

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Irinyi, László, György Kövics i Erzsébet Sándor. "Phylogenetic analysis of Phoma species". Acta Agraria Debreceniensis, nr 26 (16.07.2007): 100–107. http://dx.doi.org/10.34101/actaagrar/26/3062.

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The cosmopolitan Phoma genus contains mainly phytopathogenic, opportunistic parasites, and saprophyte fungal species. Up to now, the characterization of Phoma species and other taxa of Phoma has been determined on the basis of morphology on standardized media, and gene sequence analysis was only used as a confirmative or distinctive complement.In this study, we tried to find molecular markers which can be used as phylogenetics markers in the molecular based classification in the Phoma genus.We employed a part of the translation elongation factor 1 subunit alpha (EF-1α=tef1) containing both introns and exons and ITS region containing the internal transcribed spacer regions 1 and 2 and the 5.8S rDNA, as potential genetic markers to infer phylogenetic relationships among different Phoma taxa. Twelve different Phoma species sequences were analysed together with the closely related Ascochyta ones. The constructed phylogenetic trees, based on tef1 and ITS sequences, do not support the traditional Phoma sections based on morphological characterization. However, we managed to distinguish between the Phoma strains and Ascochyta species by comparing their tef1 sequences through parsimony analysis. We proved that a tef1 can be a useful phylogenetic marker to resolve phylogenetic relationships at species level in Phoma genus.Both parsimony sequence analyses confirmed that the Phyllosticta sojicola species is identical to the Phoma exigua var. exigua species as Kövics et al. (1999) claimed. However, the evolutionary distance by ITS sequences within Phoma species is too small to get well based consequences for the phylogenetic relationships of Phoma genus.Further investigations would be necessary to clarify whether the tef1 and ITS sequences as phylogenetic molecular markers are well suited for the classification of Phoma species.

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Mortimer, Sebastian M. E., James Boyko, Jeremy M. Beaulieu i David C. Tank. "Synthesizing Existing Phylogenetic Data to Advance Phylogenetic Research in Orobanchaceae". Systematic Botany 47, nr 2 (15.06.2022): 533–44. http://dx.doi.org/10.1600/036364422x16512564801560.

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Abstract— To date, no comprehensive phylogenetic analyses have been conducted in Orobanchaceae that include both a wide sampling of genera and a large sampling of species. In addition, a lack of fossil evidence in the clade precludes the use of primary fossil calibrations for divergence time estimation, preventing the establishment of a comprehensive temporal framework for use in macroevolutionary studies. Here, we use a recently developed set of tools for synthesizing publicly available data, apply these to reconstruct a comprehensive timetree for Orobanchaceae, and then investigate diversification dynamics in this clade of mostly parasitic plants using two model based methods. The assembled supermatrix included more than 900 species, representing approximately 40% of the known species diversity of the family, and the resulting phylogeny largely confirmed relationships revealed in earlier studies; however, we identified ten non-monophyletic genera that will require focused systematic attention to resolve. Diversification rate analyses found substantial support for character-dependent diversification, with elevated rates in hemiparasitic clades, and evidence for a number of speciation rate changes throughout the tree that are likely linked to other traits. Importantly, our multi-state HiSSE (Hidden State Speciation and Extinction) analysis revealed that transitions to a parasitic lifestyle only occur when there is a prior transition in an unobserved precursor state. For Orobanchaceae, our study provides a new comprehensive framework for the clade that can serve as a stepping-stone for future macroevolutionary studies.

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Rozprawy doktorskie na temat "Phylogenetic analyses"

Fujisawa, Tomochika. "Statistical analyses of genealogical-phylogenetic data". Thesis, Imperial College London, 2012. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.556548.

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Thanks to the recent advancement of the sequence technologies, generating large volumes of DNA sequence data is now becoming more feasible. Sequencing several samples across many species from a range of clades enables us to connect the two fields of study previously separated due to the lack of data: population genetics and phylogenetics. The former has focused on detailed genetic processes in a few species, while the latter has studied large-scale evolutionary relationships across many species. In this thesis, methods to utilize the new type of data, genealogical-phylogenetic data, are explored to tackle the problems lying between the two fields, including how to delimit species with genetic information and how ecological traits affect species genetic properties. First, a method of species delimitation based on single locus gene tree, called the generalized mixed Yule coalescent method (GMYC method), is evaluated. Its statistical properties are assessed on both simulated and real data, and the method is extended to relax some simplifying assumptions and to give a robust confidence measure. The simulation studies showed that the reliability of the delimitation depends on population parameters and patterns of diversification processes. Assessment of the performance on a dataset of 5196 water beetle mitochondrial DNA sequences sampled from across Europe showed that the method accurately delimited half of the studied species. The accuracy was affected by several factors, notably the presence of pseudogenes and potential undersampling of species range. Then, the water beetle data and the GMYC method are used to test the effects of species ecological traits on genetic properties, focusing on species habitat type. Habitat type had significant effects on genetic variation and substitution rate via effects on range size and latitudinal distribution of species. However, direct effects of habitat type on genetic properties were not observed.

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Bandoni, Susan Marie. "Phylogenetic analyses of the Amphilinidea and Gyrocotylidea : (Cercomeria: Brooks, 1982)". Thesis, University of British Columbia, 1985. http://hdl.handle.net/2429/24472.

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The amphilinideans and gyrocotylideans are small groups of monozoic platyhelminths parasitizing fishes and occasionally turtles. They have traditionally been placed with the cestodes because they lack a gut. Systematic relationships of the two groups are poorly understood. Eight species of amphilinideans are considered valid. A phylogenetic analysis of 46 character states comprising 34 homologous series produced a single phylogenetic tree with a consistency index value of 89%, indicating a very low degree of homoplasy. The number of genera has been reduced from six to three, in an attempt to construct a classification which reflects the phylogenetic relationships of the group. The phylogenetic relationships exhibit a fairly high degree of congruence (70%) with a currently accepted hypothesis of phylogenetic relationship of the teleosts. This implies that coevolution has occurred, although with many parasite losses and extinctions. An analysis of the biogeographic distribution of the amphilinideans using the methods of vicariance biogeography produced complete or nearly complete congruence of the distribution of amphilinideans with hypotheses of area relationship, indicating that vicariance is the best explanation for the biogeographic distribution of the group. Ten species of gyrocotylideans are recognized, of which seven were examined in this study. A phylogenetic analysis of 24 character states comprising 13 homologous series produced two trees of equal length. The consistency index for each tree is 88%, indicating a very low degree of homoplasy. The phylogenetic analysis of the gyrocotylideans has provided a summary of the current knowledge of the gyrocotylideans which can serve as a framework for further investigations. Slightly more than half of the observed associations between gyrocotylideans and holocephalans can be attributed to coevolution. Remaining associations can be attributed to colonization, but these represent recolonizations of plesiomorphic hosts. The geographic distribution of gyrocotylideans remains enigmatic, as it does not appear to reflect plate movements. It is suggested that their distribution may be pfe-Pangaean in origin. The phylogenetic analyses of the amphilinideans and gyrocotylideans have provided corroboration for a hypothesis of relationship for the Subphylum Cercomeria. Seven new characters have been identified as autapomorphies for the amphilinideans and gyrocotylideans, while an additional seven new characters support the Subclass Cestodaria and the Infrasubclass Cestoidea. Amphilinideans and gyrocotylideans both appear to be relict groups, but of different types. The amphilinideans were probably more widespread and more numerous than they are at present (i.e. they are geographic and numerical relicts). The gyrocotylideans, on the other hand, appear to have never been diverse or widespread, and are therefore phylogenetic relicts.
Science, Faculty of
Zoology, Department of
Graduate

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Thomas, Gavin Huw. "Sexual conflict, ecology and breeding systems in shorebirds : phylogenetic analyses". Thesis, University of Bath, 2004. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.413066.

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Donati, Beatrice. "Graph models and algorithms in (co-)evolutionary contexts". Thesis, Lyon 1, 2014. http://www.theses.fr/2014LYO10235/document.

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Cette thèse s'inscrit dans le cadre de la bioinformatique. Les outils mathématiques les plus utilisés dans ce travail relèvent de la théorie des graphes, des statistiques, de la théorie des ensembles et des mathématiques discrètes. Ces mathématiques ont permis de développer des modèles de systèmes biologiques ainsi que des algorithmes efficaces dans l'étude concrète de ces modèles. La nécessité d'analyses de jeux de données de très grande taille a rendu critique dans notre démarche cette notion d'efficacité des algorithmes. Il faut enfin remarquer que le champ biologique qui a servi de support à cette thèse nous a conduit à explorer un domaine particulier au sein de la théorie de la complexité, à savoir le développement et l'analyse des algorithmes d'énumération [etc...]
In the results presented in the present manuscripts, graph theory and combinatorial optimizationtecniques, have been used to model and solve biological problems. The manuscript is divided in twoparts, each one containing the mathematical and biological background of a given application and ouroriginal contributions to it.Part I groups a set of results designed for phylogenetics analysis, and in particular for reconstructingthe co-evolution of two groups of organisms (the so called co-phylogeny reconstruction problem).Although the addressed problem was treated in the available there was no method that solved suchproblem in a complete and efficient way. We thus developed and implemented a new one, calledEucalypt, with this purpose in mind. This not only provides a novel and usable software for cophylogenyreconstruction but also allows to investigate how the event-based model performs inpractice in terms of thenumber and quality of the solutions obtained. We compared our method to the available software. Bylooking at the results obtained, some interesting considerations about the advantages anddisadvantages of the commonly accepted mathematical model could be drawn. Finally, we introduceda new version of the problem where the host-switches are distance bounded: the k-bounded-All-MPRproblem. Eucalypt solves both problems in polynomial delay. These results have been accepted forpublication by the jounal Algorithms for Molecular Biology. The relative software is publicyavailable.Our studies show that the 'most parsimonious scenario' approach presents some limitationsthat cannot be ignored. To deal with these problems, we developed a second algorithm, called Coala,based on an approximate Bayesian computation approach for estimating the frequency of the events.The benefits of this method are twofold: it provides more confidence in the set of costs to be used in areconciliation, and it allows to estimate the frequency of the events in the cases where a reconciliationmethod cannot be applied. These results are currently under review by the jounal Systematic Biology.The relative software is publicy available.In Part 2 another set of studies is presented. Our original model for the contig scaffolding problem,and our algorithm MeDuSa, are presented and tested. Unlike traditional software, it does not rely eitheron paired-end information of sequencing reads or on a phylogenetic distance of the microorganismsused in the analysis. This drastically increases the usability of our software and, at the same time,reduces the computational time required for genome scaffolding. We show that the algorithmimplemented in MeDuSa, in most cases, is capable of producing less and longer scaffolds incomparison to commonly used scaffolders, while maintaining high accuracy and correctness of thepredicted joins. These results are currently under revision by the journal Bioinformatics.Finally, during the development of this method we encountered some pure theoretical open problemsand we decided to dedicate part of our job to their analysis. The last chapter is then dedicated to a setof problems, all related to the Implicit Hitting set enumeration problem. After some formal definitions,an original NP-completeness result is presented and the future directions of our work are described

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Milton, Joseph J. "Phylogenetic analyses and taxonomic studies of Senecioninae : southern African Senecio section Senecio". Thesis, St Andrews, 2009. http://hdl.handle.net/10023/701.

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Staron, Anna. "Phylogenetic and functional analyses of stress-responsive bacterial transmembrane signal transducing systems". Diss., lmu, 2012. http://nbn-resolving.de/urn:nbn:de:bvb:19-149558.

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Borner, Janus [Verfasser], i Thorsten [Akademischer Betreuer] Burmester. "Molecular phylogenetic analyses of Ecdysozoa and Haemosporida / Janus Borner ; Betreuer: Thorsten Burmester". Hamburg : Staats- und Universitätsbibliothek Hamburg, 2017. http://d-nb.info/1140166573/34.

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Lehmann, Jörg. "Relative Timing of Intron Gain and a New Marker for Phylogenetic Analyses". Doctoral thesis, Universitätsbibliothek Leipzig, 2014. http://nbn-resolving.de/urn:nbn:de:bsz:15-qucosa-144067.

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Despite decades of effort by molecular systematists, the trees of life of eukaryotic organisms still remain partly unresolved or in conflict with each other. An ever increasing number of fully-sequenced genomes of various eukaryotes allows to consider gene and species phylogenies at genome-scale. However, such phylogenomics-based approaches also revealed that more taxa and more and more gene sequences are not the ultimate solution to fully resolve these conflicts, and that there is a need for sequence-independent phylogenetic meta-characters that are derived from genome sequences. Spliceosomal introns are characteristic features of eukaryotic nuclear genomes. The relatively rare changes of spliceosomal intron positions have already been used as genome-level markers, both for the estimation of intron evolution and phylogenies, however with variable success. In this thesis, a specific subset of these changes is introduced and established as a novel phylogenetic marker, termed near intron pair (NIP). These characters are inferred from homologous genes that contain mutually-exclusive intron presences at pairs of coding sequence (CDS) positions in close proximity. The idea that NIPs are powerful characters is based on the assumption that both very small exons and multiple intron gains at the same position are rare. To obtain sufficient numbers of NIP character data from genomic and alignment data sets in a consistent and flexible way, the implementation of a computational pipeline was a main goal of this work. Starting from orthologous (or more general: homologous) gene datasets comprising genomic sequences and corresponding CDS transcript annotations, the multiple alignment generation is an integral part of this pipeline. The alignment can be calculated at the amino acid level utilizing external tools (e.g. transAlign) and results in a codon alignment via back-translation. Guided by the multiple alignment, the positionally homologous intron positions should become apparent when mapped individually for each transcript. The pipeline proceeds at this stage to output portions of the intron-annotated alignment that contain at least one candidate of a NIP character. In a subsequent pipeline script, these collected so-called NIP region files are finally converted to binary state characters representing valid NIPs in dependence of quality filter constraints concerning, e.g., the amino acid alignment conservation around intron loci and splice sites, to name a few. The computational pipeline tools provide the researcher to elaborate on NIP character matrices that can be used for tree inference, e.g., using the maximum parsimony approach. In a first NIP-based application, the phylogenetic position of major orders of holometabolic insects (more specifically: the Coleoptera-Hymenoptera-Mecopterida trifurcation) was evaluated in a cladistic sense. As already suggested during a study on the eIF2gamma gene based on two NIP cases (Krauss et al. 2005), the genome-scale evaluation supported Hymenoptera as sister group to an assemblage of Coleoptera and Mecopterida, in agreement with other studies, but contradicting the previously established view. As part of the genome paper describing a new species of twisted-wing parasites (Strepsiptera), the NIP method was employed to help to resolve the phylogenetic position of them within (holometabolic) insects. Together with analyses of sequence patterns and a further meta-character, it revealed twisted-wing parasites as being the closest relatives of the mega-diverse beetles. NIP-based reconstructions of the metazoan tree covering a broad selection of representative animal species also identified some weaknesses of the NIP approach that may suffer e.g. from alignment/ortholog prediction artifacts (depending on the depth of range of taxa) and systematic biases (long branch attraction artifacts, due to unequal evolutionary rates of intron gain/loss and the use of the maximum parsimony method). In a further study, the identification of NIPs within the recently diverged genus Drosophila could be utilized to characterize recent intron gain events that apparently involved several cases of intron sliding and tandem exon duplication, albeit the mechanisms of gain for the majority of cases could not be elucidated. Finally, the NIP marker could be established as a novel phylogenetic marker, in particular dedicated to complementarily explore the wealth of genome data for phylogenetic purposes and to address open questions of intron evolution.

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Garcia-Pena, Gabriel Ernesto. "Phylogenetic comparative analyses of breeding systems and life-history strategies in shorebirds". Thesis, University of Bath, 2010. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.527144.

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Long, Peter. "Ecological and life-history basis of wetland bird conservation : phylogenetic and spatial analyses". Thesis, University of Bath, 2008. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.512313.

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Książki na temat "Phylogenetic analyses"

Owen, Robert D. Phylogenetic analyses of the bat subfamily Stenodermatinae (Mammalia:Chiroptera). Lubbock, Tex: Texas Tech University Press, 1987.

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Simone, Luiz Ricardo Lopes de. Phylogenetic analyses of Cerithioidea (Mollusca, Caenogastropoda) based on comparative morphology. São Paulo: Museu de Zoologia da Universidade de São Paulo, 2001.

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Ciochon, Russell L. Evolution of the cercopithecoid forelimb: Phylogenetic and functional implications from morphometric analyses. Berkeley: University of California Press, 1993.

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Weksler, Marcelo. Phylogenetic relationships of oryzomine rodents (Muroidea, Sigmodontinae): Separate and combined analyses of morphological and molecular data. New York, NY: American Museum of Natural History, 2006.

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Voss, Robert S. Phylogenetic studies on didelphid marsupials.: Separate and combined analyses of didelphine relationships with denser taxon samplings. New York, NY: American Museum of Natural History, 2003.

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Reitner, J. Coralline Spongien: Der Versuch einer phylogenetisch-taxonomischen Analyse = Coralline sponges : an attempt of a phylogenetic-taxonomic analysis. Berlin: Selbstverlag Fachbereich Geowissenschaften, 1992.

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Basic phylogenetic combinatorics. New York: Cambridge University Press, 2011.

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Duellman, William Edward. Frogs of the Hyla armata and the Hyla pulchella groups in the Andes of South America, with definitions and analyses of phylogenetic relationships of Andean groups of Hyla. Lawrence, Kan: Natural History Museum, The University of Kansas, 1997.

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J, Wiens John, red. Phylogenetic analysis of morphological data. Washington, D.C: Smithsonian Institution Press, 2000.

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Inc, ebrary, red. Phylogenetics: Theory and practice of phylogenetics systematics. Wyd. 2. Hoboken, N.J: Wiley-Blackwell, 2011.

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Części książek na temat "Phylogenetic analyses"

Bleidorn, Christoph. "Phylogenetic Analyses". W Phylogenomics, 143–72. Cham: Springer International Publishing, 2017. http://dx.doi.org/10.1007/978-3-319-54064-1_8.

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Goloboff, Pablo A. "Summarizing and comparing phylogenetic trees". W Refining Phylogenetic Analyses, 1–51. Boca Raton: CRC Press, 2022. http://dx.doi.org/10.1201/9780367823412-1.

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Goloboff, Pablo A. "Measuring degree of group support". W Refining Phylogenetic Analyses, 119–83. Boca Raton: CRC Press, 2022. http://dx.doi.org/10.1201/9780367823412-3.

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Goloboff, Pablo A. "Morphometric characters". W Refining Phylogenetic Analyses, 185–227. Boca Raton: CRC Press, 2022. http://dx.doi.org/10.1201/9780367823412-4.

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Goloboff, Pablo A. "Scripting". W Refining Phylogenetic Analyses, 229–68. Boca Raton: CRC Press, 2022. http://dx.doi.org/10.1201/9780367823412-5.

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Goloboff, Pablo A. "Character weighting". W Refining Phylogenetic Analyses, 53–117. Boca Raton: CRC Press, 2022. http://dx.doi.org/10.1201/9780367823412-2.

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Fraix-Burnet, Didier. "First Phylogenetic Analyses of Galaxy Evolution". W Astrophysics and Space Science Library, 301–5. Dordrecht: Springer Netherlands, 2004. http://dx.doi.org/10.1007/978-1-4020-2862-5_27.

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Santos, Juan C. "Phylogenetic Analyses of Chemokine Receptors from Sequence Retrieval to Phylogenetic Trees". W Methods in Molecular Biology, 313–43. New York, NY: Springer US, 2020. http://dx.doi.org/10.1007/978-1-0716-0247-8_27.

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May-Collado, Laura J., Carlos Zambrana-Torrelio i Ingi Agnarsson. "Global Spatial Analyses of Phylogenetic Conservation Priorities for Aquatic Mammals". W Biodiversity Conservation and Phylogenetic Systematics, 305–18. Cham: Springer International Publishing, 2016. http://dx.doi.org/10.1007/978-3-319-22461-9_15.

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Sen, Gao, Yuan Zihao, Ning Li, Jiaren Zhang i Zhanjiang Liu. "Determining Sequence Identities: BLAST, Phylogenetic Analysis, and Syntenic Analyses". W Bioinformatics in Aquaculture, 30–42. Chichester, UK: John Wiley & Sons, Ltd, 2017. http://dx.doi.org/10.1002/9781118782392.ch2.

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Streszczenia konferencji na temat "Phylogenetic analyses"

Limbeck, Maggie R., Colin D. Sumrall i Bradley Deline. "PHYLOGENETIC AND MORPHOLOGIC ANALYSES ELUCIDATE RELATIONSHIPS IN PARACRINOIDEA (ECHINODERMATA)". W 67th Annual Southeastern GSA Section Meeting - 2018. Geological Society of America, 2018. http://dx.doi.org/10.1130/abs/2018se-312231.

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Ely, Ricardo Carlos. "PHYLOGENETIC AND GEOMETRIC MORPHOMETRIC ANALYSES OF LYGOSOMINE SKINK MANDIBLES". W GSA Annual Meeting in Indianapolis, Indiana, USA - 2018. Geological Society of America, 2018. http://dx.doi.org/10.1130/abs/2018am-322579.

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Brammer, Grant, i Tiffani L. Williams. "Using decision trees to study the convergence of phylogenetic analyses". W 2010 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB). IEEE, 2010. http://dx.doi.org/10.1109/cibcb.2010.5510326.

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Haiyan Li. "Predicting protein folding cores based on complex network and phylogenetic analyses". W 2009 International Conference on Future BioMedical Information Engineering (FBIE). IEEE, 2009. http://dx.doi.org/10.1109/fbie.2009.5405844.

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Saporetti, Camila M., Leonardo Goliatt, Leonardo C. De Oliveira i Egberto Pereira. "Computational Intelligence Techniques and Phylogenetic Trees for Identification of Sedimentary Petrofacies". W XV Encontro Nacional de Inteligência Artificial e Computacional. Sociedade Brasileira de Computação - SBC, 2018. http://dx.doi.org/10.5753/eniac.2018.4437.

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The heterogeneities are characterized by several sedimentary petro- facies. Petrofacies identification involves manual processes and time-consuming analyses. The study of the diagenesis has been encouraged by petroleum companies, in order to understand the distribution of porosity in sandstones. This work aims to analyze the use of clustering approaches to identify petrofacies and assist the analysis of petrographic data. In addition, this study introduced the use the phylogenetic analysis tools to understand the diagenetic process that occurred during sedimentary rock formation. The proposed methodology reaches similar results to those obtained by the conventional method of individualization while allows for reducing time and cost in the individualization task.

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Oikkonen, Jaana, Nil Campamà Sanz, Antti Häkkinen, Yilin Li, Ingrid Schulman, Mikko Kivikoski, Kaisa Huhtinen i in. "Abstract A60: Phylogenetic analyses reveal variable patterns of tumor evolution in HGSOC". W Abstracts: AACR Special Conference on Advances in Ovarian Cancer Research; September 13-16, 2019; Atlanta, GA. American Association for Cancer Research, 2020. http://dx.doi.org/10.1158/1557-3265.ovca19-a60.

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Nishimura, Yuki, Toshiyuki Amagasa, Yuji Inagaki, Tetsuo Hashimoto i Hiroyuki Kitagawa. "A System for Phylogenetic Analyses over Alignments of Next Generation Sequence Data". W 2016 10th International Conference on Complex, Intelligent, and Software Intensive Systems (CISIS). IEEE, 2016. http://dx.doi.org/10.1109/cisis.2016.51.

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Fedonenko, Yu P., I. M. Ibrahim, E. N. Sigida, V. I. Safronova, M. S. Kokoulin, A. Yu Muratova i S. A. Konnova. "Bioremediation potential of a halophilic bacterium Chromohalobacter salexigens EG1QL3: exopolysaccharide production, crude oil degradation, and heavy metal tolerance". W 2nd International Scientific Conference "Plants and Microbes: the Future of Biotechnology". PLAMIC2020 Organizing committee, 2020. http://dx.doi.org/10.28983/plamic2020.070.

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Based on biochemical and phylogenetic analyses, isolated from a salt sample from Lake Qarun (Egypt) a halophilic strain EG1QL3 was identified as Chromohalobacter salexigens. The abilities of EG1QL3 to produce an extracellular polysaccharide, degrade oil, and resist to heavy metals were revealed.

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McClure, Sheila, Jenna T. Baughman, Jess Pelaez i Justin R. Pardo. "PRELIMINARY GEOHYDROLOGIC APPLICATIONS OF SPATIAL PHYLOGENETIC BIODIVERSITY ANALYSES IN THE MOJAVE NATIONAL PRESERVE". W GSA Annual Meeting in Denver, Colorado, USA - 2016. Geological Society of America, 2016. http://dx.doi.org/10.1130/abs/2016am-283455.

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Zhang, Yunfeng, Yang Zhang i Mingzhu Yang. "Investigating Cultural Macroevolution through Biological Phylogenetic Analyses of Chinese Dai People Costumes Pattern". W 2015 International Conference on Social Science, Education Management and Sports Education. Paris, France: Atlantis Press, 2015. http://dx.doi.org/10.2991/ssemse-15.2015.24.

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Raporty organizacyjne na temat "Phylogenetic analyses"

Perk, Shimon, Maricarmen Garcia, Alexander Panshin, Caroline Banet-Noach, Irina Gissin, Mark W. Jackwood i David Stallknecht. Avian Influenza Virus H9N2: Characterization and Control Strategies. United States Department of Agriculture, czerwiec 2007. http://dx.doi.org/10.32747/2007.7709882.bard.

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Control of Avian Influenza (AI) infection is a highly topical subject of major economicimportance for the worldwide poultry industry at the national level and for international trade.H9N2 viruses are endemic in poultry throughout Asia and the Middle East, causing major losses inproduction. Moreover, these viruses pose wider threats since they have been isolated from bothswine and humans. At the same time, study of the AI viruses affords an opportunity to explore anumber of problems of intriguing scientific interest. The overall goal of this project was to developa sound control strategy for avian influenza subtype H9N2 viruses (AI H9N2) in commercialpoultry in Israel. The one-year feasibility study focused on two main goals, namely: to study themolecular characteristics of AI H9N2 circulating during the last seven years in Israel and todevelop tools enabling differentiation between the immune response to vaccination and infectionwith H9N2.Genetic and phylogenetic characterization of 29 selected AI H9N2 isolates (2000-2006)was performed by complete sequencing of hemagglutinin (HA), neuraminidase (NA), and all sixinternal genes [nucleoprotein (NP), polymerase basic 1 (PB1), polymerase basic 2 (PB2),polymerase acid (PA), matrix (M), and nonstructural (NS) genes]; comparative phylogenetic andgenetic analyses of these sequences; and comparative genetic analyses of deduced amino acidsequences of the HA, NA, NS1, and NS2 proteins. The major conclusions of the molecularanalyses were: (1) Israeli isolates, together with other H9N2 viruses isolated in Middle Eastcountries, comprise a single regional sublineage related to the G1-lineage. In addition, Israeliisolates subdivided into three different subgroups. Genetic analysis of these viruses suggests thatthey underwent divergent evolution paths.

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Pace, Norman R. Phylogenetic Analysis of Marine Picoplankton Using rRNA Sequences. Fort Belvoir, VA: Defense Technical Information Center, czerwiec 1989. http://dx.doi.org/10.21236/ada209595.

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Pace, Norman R. Phylogenetic Analysis of Marine Picoplankton Using Tau RNA Sequences. Fort Belvoir, VA: Defense Technical Information Center, luty 1991. http://dx.doi.org/10.21236/ada254451.

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Biffinger, Justin C., Lisa A. Fitzgerald, Emily R. Petersen, Kristina M. Myers, Jeffrey A. Cramer, Anthony P. Malanoski, Tyler M. Huggins i Robert E. Morris. Analysis of Fatty Acid and Growth Profiles in Ten Shewanella spp. to Associate Phylogenetic Relationships. Fort Belvoir, VA: Defense Technical Information Center, październik 2015. http://dx.doi.org/10.21236/ad1000479.

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Michel Jr., Frederick C., Harry A. J. Hoitink, Yitzhak Hadar i Dror Minz. Microbial Communities Active in Soil-Induced Systemic Plant Disease Resistance. United States Department of Agriculture, styczeń 2005. http://dx.doi.org/10.32747/2005.7586476.bard.

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Induced Systemic Resistance (ISR) is a highly variable property that can be induced by compost amendment of potting media and soils. For example, previous studies showed that only 1 of 79 potting mixes prepared with different batches of mature composts produced from several different types of solid wastes were able to suppress the severity of bacterial leaf spot of radish caused by Xanthomonas campestris pv. armoraciae compared with disease on plants produced in a nonamended sphagnum peat mix. In this project, microbial consortia in the rhizosphere of plants grown in ISR-active compost-amended substrates were characterized. The plants used included primarily cucumber but also tomato and radish. Rhizosphere microbial consortia were characterized using multiple molecular tools including DGGE (Israel) and T -RFLP (Ohio) in both ISR-active field plots and potting media. Universal as well as population-specific bacterial and fungal PCR primers were utilized. T -RFLP analyses using universal bacterial primers showed few significant differences in overall bacterial community composition in ISR-active and inactive substrates (Ohio). In addition, the community members which were significantly different varied when different ISR-activecomposts were used (Ohio). To better characterize the shifts in microbial community structure during the development of ISR, population specific molecular tools were developed (Israel, Ohio).-PCR primers were designed to detect and quantify bacterial groups including Pyrenomycetes, Bacillus, Pan toea, Pseudomonas, Xanthomonas and Streptomyces as well as Trichoderma and Fusarium; two groups of fungi that harbor isolates which are ISR active (Isreal and Ohio). Bacterial consortia associated with cucumber plants grown in compost-amended potting mixtures were shown to be dominated by the phylogenetic taxon Bacteroidetes, including members of the genus Chryseobacterium, which in some cases have been shown to be involved in biocontrol (Israel). Nested-PCR-DGGE analyses coupled with long l6S rDNA sequencing, demonstrated that the Chryseobacteriumspp. detected on seed and the root in compost-amended treatments were derived from the compost itself. The most effective ISR inducing rhizobacterial strains were identified as Bacillus sp. based on partial sequencing of l6S rDNA. However, these strains were significantly less effective in reducing the severity of disease than Trichoderma hamatum382 (T382). A procedure was developed for inoculation of a compost-amended substrate with T -382 which consistently induced ISR in cucumber against Phytophthora blight caused by Phytophthora capsiciand in radish against bacterial spot (Ohio). Inoculation of compost-amended potting mixes with biocontrol agents such as T -382 and other microbes that induce systemic resistance in plants significantly increased the frequency of systemic disease control obtained with natural compost amendments.

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Pace, N. R. Phylogenetic analysis of hyperthermophilic natural populations using ribosomal RNA sequences. Final report, July 15, 1995--July 14, 1996. Office of Scientific and Technical Information (OSTI), czerwiec 1997. http://dx.doi.org/10.2172/491420.

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Wu, Liyou, T. Y. Yi, Joy Van Nostrand i Jizhong Zhou. Phylogenetic Analysis of Shewanella Strains by DNA Relatedness Derived from Whole Genome Microarray DNA-DNA Hybridization and Comparison with Other Methods. Office of Scientific and Technical Information (OSTI), maj 2010. http://dx.doi.org/10.2172/986917.

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Mizrahi, Itzhak, i Bryan A. White. Uncovering rumen microbiome components shaping feed efficiency in dairy cows. United States Department of Agriculture, styczeń 2015. http://dx.doi.org/10.32747/2015.7600020.bard.

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Ruminants provide human society with high quality food from non-human-edible resources, but their emissions negatively impact the environment via greenhouse gas production. The rumen and its resident microorganisms dictate both processes. The overall goal of this project was to determine whether a causal relationship exists between the rumen microbiome and the host animal's physiology, and if so, to isolate and examine the specific determinants that enable this causality. To this end, we divided the project into three specific parts: (1) determining the feed efficiency of 200 milking cows, (2) determining whether the feed- efficiency phenotype can be transferred by transplantation and (3) isolating and examining microbial consortia that can affect the feed-efficiency phenotype by their transplantation into germ-free ruminants. We finally included 1000 dairy cow metadata in our study that revealed a global core microbiome present in the rumen whose composition and abundance predicted many of the cows’ production phenotypes, including methane emission. Certain members of the core microbiome are heritable and have strong associations to cardinal rumen metabolites and fermentation products that govern the efficiency of milk production. These heritable core microbes therefore present primary targets for rumen manipulation towards sustainable and environmentally friendly agriculture. We then went beyond examining the metagenomic content, and asked whether microbes behave differently with relation to the host efficiency state. We sampled twelve animals with two extreme efficiency phenotypes, high efficiency and low efficiency where the first represents animals that maximize energy utilization from their feed whilst the later represents animals with very low utilization of the energy from their feed. Our analysis revealed differences in two host efficiency states in terms of the microbial expression profiles both with regards to protein identities and quantities. Another aim of the proposal was the cultivation of undescribed rumen microorganisms is one of the most important tasks in rumen microbiology. Our findings from phylogenetic analysis of cultured OTUs on the lower branches of the phylogenetic tree suggest that multifactorial traits govern cultivability. Interestingly, most of the cultured OTUs belonged to the rare rumen biosphere. These cultured OTUs could not be detected in the rumen microbiome, even when we surveyed it across 38 rumen microbiome samples. These findings add another unique dimension to the complexity of the rumen microbiome and suggest that a large number of different organisms can be cultured in a single cultivation effort. In the context of the grant, the establishment of ruminant germ-free facility was possible and preliminary experiments were successful, which open up the way for direct applications of the new concepts discovered here, prior to the larger scale implementation at the agricultural level.

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Perl-Treves, Rafael, M. Kyle i Esra Galun. Development and Application of a Molecular Genetic Map for Melon (Cucumis melo). United States Department of Agriculture, październik 1993. http://dx.doi.org/10.32747/1993.7568094.bard.

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This project has generated a systematic survey of DNA polymorphism in Cucumis melo. An RFLP and RAPD survey of the major cultivar groups and botanical varieties of this species has been conducted, with the purpose of assessing the degree of molecular variation and phylogenetic relationships within the melon germplasm and, at the same time, develop sets of markets suitable for mapping the melon genome. Additional activities regarding variation in the melon germplasm in fruit traits and regeneration ability have been initiated as well. The necessary populations required for the development of a molecular map of the C. melo genome have been prepared. An F2 that segregated for 4 viral resistances, powdery mildew resitance and sex type has been derived from a PI 414723 x Topmark cross, and a RILs population has been prepared from it. We have confirmed the resistances in the population and have analyzed the genetic relationships between these resistances. Progress toward the construction of a molecular map of C. melo and the development of markers linked to those traits is described. We have so far screened the first few tens of markers in the F2 population, and many additional ones were screened in DNA bulks prepared from such population.

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Vakharia, Vikram, Shoshana Arad, Yonathan Zohar, Yacob Weinstein, Shamila Yusuff i Arun Ammayappan. Development of Fish Edible Vaccines on the Yeast and Redmicroalgae Platforms. United States Department of Agriculture, luty 2013. http://dx.doi.org/10.32747/2013.7699839.bard.

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Betanodaviruses are causative agents of viral nervous necrosis (VNN), a devastating disease of cultured marine fish worldwide. Betanodavirus (BTN) genome is composed of two single-stranded, positive-sense RNA molecules. The larger genomic segment, RNA1 (3.1 kb), encodes the RNA-dependent RNA polymerase, while the smaller genomic segment, RNA 2 (1.4kb), encodes the coat protein. This structural protein is the host-protective antigen of VNN which assembles to form virus-like particles (VLPs). BTNs are classified into four genotypes, designated red-spotted grouper nervous necrosis virus (RGNNV), barfin flounder nervous necrosis virus (BFNNV), tiger puffer nervous necrosis virus (TPNNV), and striped jack nervous necrosis virus (SJNNV), based on phylogenetic analysis of the coat protein sequences. RGNNV type is quite important as it has a broad host-range, infecting warm-water fish species. At present, there is no commercial vaccine available to prevent VNN in fish. The general goal of this research was to develop oral fish vaccines in yeast and red microalgae (Porphyridium sp.) against the RGNNV genotype. To achieve this, we planned to clone and sequence the coat protein gene of RGNNV, express the coat protein gene of RGNNV in yeast and red microalgae and evaluate the immune response in fish fed with recombinantVLPs antigens produced in yeast and algae. The collaboration between the Israeli group and the US group, having wide experience in red microalgae biochemistry, molecular genetics and large-scale cultivation, and the development of viral vaccines and eukaryotic protein expression systems, respectively, was synergistic to produce a vaccine for fish that would be cost-effective and efficacious against the betanodavirus infection.

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