Relevant bibliographies by topics / Phylogenetic position

Contents

  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers
  6. Reports

Academic literature on the topic 'Phylogenetic position'

Author: Grafiati
Published: 6 September 2023

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Journal articles on the topic "Phylogenetic position"

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Wolf, Matthias, Lothar Krienitz, and Dominik Hepperle. "Phylogenetic position of Actinastrum hantzschii LAGERHEIM 1882 (Chlorophyta, Trebouxiophyceae)." Algological Studies/Archiv für Hydrobiologie, Supplement Volumes 104 (March 28, 2002): 59–67. http://dx.doi.org/10.1127/algol_stud/104/2002/59.

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Mounce, Ross C. P., and Matthew A. Wills. "Phylogenetic position of Diania challenged." Nature 476, no. 7359 (August 10, 2011): E1. http://dx.doi.org/10.1038/nature10266.

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Zeng, Zhao-Qing, and Wen-Ying Zhuang. "Phylogenetic position of Pseudohypocrea (Hypocreales)." Mycoscience 58, no. 4 (July 2017): 274–81. http://dx.doi.org/10.1016/j.myc.2017.04.005.

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Kearney, Maureen. "The phylogenetic position ofSineoamphisbaena hexatabularisreexamined." Journal of Vertebrate Paleontology 23, no. 2 (June 17, 2003): 394–403. http://dx.doi.org/10.1671/0272-4634(2003)023[0394:tpposh]2.0.co;2.

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Tourova, T. P., B. B. Kuznetsov, T. V. Kalganova, and E. A. Bonch-Osmolovskaya. "Phylogenetic position of desulfurococcus amylolyticus." Microbiology 69, no. 3 (May 2000): 369–70. http://dx.doi.org/10.1007/bf02756750.

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Young, Nathan M., and Laura MacLatchy. "The phylogenetic position of Morotopithecus." Journal of Human Evolution 46, no. 2 (February 2004): 163–84. http://dx.doi.org/10.1016/j.jhevol.2003.11.002.

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Cao, Y., N. Okada, and M. Hasegawa. "Phylogenetic position of guinea pigs revisited." Molecular Biology and Evolution 14, no. 4 (April 1, 1997): 461–64. http://dx.doi.org/10.1093/oxfordjournals.molbev.a025782.

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PATIL, VISHWANATH, JON BRÅTE, KAMRAN SHALCHIAN-TABRIZI, and KJETILL S. JAKOBSEN. "Revisiting the Phylogenetic Position ofSynchroma grande." Journal of Eukaryotic Microbiology 56, no. 4 (July 2009): 394–96. http://dx.doi.org/10.1111/j.1550-7408.2009.00389.x.

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Lieckfeldt, Elke, Cornelia M. Kullnig, Christian P. Kubicek, Gary J. Samuels, and Thomas Börner. "Trichoderma aureoviride: phylogenetic position and characterization." Mycological Research 105, no. 3 (March 2001): 313–22. http://dx.doi.org/10.1017/s0953756201003616.

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Kuramae, Eiko E., Vincent Robert, Berend Snel, and Teun Boekhout. "Conflicting phylogenetic position of Schizosaccharomyces pombe." Genomics 88, no. 4 (October 2006): 387–93. http://dx.doi.org/10.1016/j.ygeno.2006.07.001.

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Dissertations / Theses on the topic "Phylogenetic position"

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Bales, Ashley. "The phylogenetic position of Proconsul and catarrhine ancestral morphotypes." Thesis, New York University, 2017. http://pqdtopen.proquest.com/#viewpdf?dispub=10192021.

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There continues to be a lack of agreement concerning the precise phylogenetic placement of Proconsul despite the wealth of fossil material and the extensiveness of its study. The difficulty in resolving the phylogenetic status of this important and well represented Miocene catarrhine is a consequence of its apparent basal position relative to crown catarrhines. This position complicates the inference of character polarities. This dissertation tests three previously proposed hypotheses concerning the phylogenetic position of Proconsul: (1) Proconsul is a stem catarrhine; (2) Proconsul is a stem hominoid; and (3) Proconsul is a basal hominid, most closely related to extant great apes and humans. A phylogenetic analysis based on 719 characters drawn from the skull, forelimb, pelvis and foot, and sampling a diversity of extant anthropoid taxa, offers no compelling support for a hominoid clade that includes Proconsul. The radiation of crown catarrhines involved rapid evolutionary changes from the ancestral catarrhine morphotype, resulting in stem catarrhines appearing much more similar to each other, even where there are key synapomorphies linking them with crown clades. As a result, systematic analyses alone are insufficient to confidently support a single optimal phylogenetic hypothesis. Further exploration of the data, by combining inferred ancestral morphotypes with phenetic visualizations of character evolution, demonstrated that inclusion of Proconsul among Hominoidea or Hominidae pushed the ancestral catarrhine morphotype closer to these clades, respectively. Given a more comprehensive analysis of character evolution under each hypothesis, this dissertation supports the hypothesis that Proconsul is a stem catarrhine. In addition to helping clarify the long-running debate about the phylogenetic status of Proconsul, the results offer fresh insights into the early stages of hominoid evolution and demonstrate the importance of comprehensive phylogenetic analyses in helping to resolve the relationships of problematic stem taxa.

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Bleidorn, Christoph, Lars Podsiadlowski, Min Zhong, Igor Eeckhaut, Stefanie Hartmann, Kenneth M. Halanych, and Ralph Tiedemann. "On the phylogenetic position of Myzostomida : can 77 genes get it wrong?" Universität Potsdam, 2009. http://opus.kobv.de/ubp/volltexte/2010/4489/.

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Background: Phylogenomic analyses recently became popular to address questions about deep metazoan phylogeny. Ribosomal proteins (RP) dominate many of these analyses or are, in some cases, the only genes included. Despite initial hopes, hylogenomic analyses including tens to hundreds of genes still fail to robustly place many bilaterian taxa. Results: Using the phylogenetic position of myzostomids as an example, we show that phylogenies derived from RP genes and mitochondrial genes produce incongruent results. Whereas the former support a position within a clade of platyzoan taxa, mitochondrial data recovers an annelid affinity, which is strongly supported by the gene order data and is congruent with morphology. Using hypothesis testing, our RP data significantly rejects the annelids affinity, whereas a platyzoan relationship is significantly rejected by the mitochondrial data. Conclusion: We conclude (i) that reliance of a set of markers belonging to a single class of macromolecular complexes might bias the analysis, and (ii) that concatenation of all available data might introduce conflicting signal into phylogenetic analyses. We therefore strongly recommend testing for data incongruence in phylogenomic analyses. Furthermore, judging all available data, we consider the annelid affinity hypothesis more plausible than a possible platyzoan affinity for myzostomids, and suspect long branch attraction is influencing the RP data. However, this hypothesis needs further confirmation by future analyses.
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Eitel, Michael Sebastian [Verfasser]. "Phylogenetic position, biodiversity, phylogeography and biology of the Placozoa / Michael Sebastian Eitel." Hannover : Technische Informationsbibliothek und Universitätsbibliothek Hannover (TIB), 2010. http://d-nb.info/1036525228/34.

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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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Starr, Julian Richard. "The origin and phylogenetic position of Carex section Phyllostachys in the genus Carex, Cyperaceae." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1997. http://www.collectionscanada.ca/obj/s4/f2/dsk2/ftp04/mq23510.pdf.

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Ozdemir, Degirmenci Funda. "Molecular Phylogenetic Position Of Turkish Abies(pinaceae)based On Noncoding Trn Regions Of Chloroplast Genome." Master's thesis, METU, 2011. http://etd.lib.metu.edu.tr/upload/12613590/index.pdf.

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Abies is the second largest genus of family Pinaceae (after Pinus), consisting of about 51 species, all native to the Northern Hemisphere. There are six native taxa belonging to this genus growing in pure and mixed stands in Turkey. Abies cilicica subsp. isaurica, Abies nordmanniana subsp. bornmü
lleriana, Abies nordmanniana subsp. equi-trojani, Abies x olcayana are endemic and considered as lower risk (LR) species. To determine the genetic relationships in Turkish firs, 18 populations of different subspecies of Abies were collected from different regions of Turkey and non-coding trn regions of chloroplast DNA were sequenced to assess the genetic structure of the studied species. trnL, trnF and trnV region were examined. All the trn regions of Abies species in the world (aproximately 300 species that found in the IPNI (The International Plant Names Index) were investigated in the database of NCBI. The available trn sequences of 23 Abies species worldwide included into the analyses. All analyses to estimate molecular diversity parameters were carried out with the MEGA software. The constructed phylogenetic tree with the trn sequences revealed that Turkish firs formed a monophyletic group with almost no sequence divergence. v Since sequence data for all three sectors of trn were not available from the NCBI data base, the phylogentic analysis with the sequence data of trnL regions were compartively analyzed in all firs. The results showed that Turkish- European species formed a single clade, which clearly differentiated them from the others, such as Japanese species, A. veitchii. Similarly, according to the sequence data of trnF, Turkish fir species were grouped together and distinctly separated from Asian-American Fir species. The results suggest that all Turkish firs may have evolved from single ancestral fir species, most likely from Abies nordmanniana.
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Villavicencio, José Eduardo Serrano. "Taxonomy of the genus Brachyteles Spix, 1823 and its phylogenetic position within the subfamily Atelinae Gray, 1825." Universidade de São Paulo, 2016. http://www.teses.usp.br/teses/disponiveis/38/38131/tde-16112016-150803/.

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Muriquis, genus Brachyteles Spix, 1823, are the largest of the extant New World primates, and they are one of the three extant genera of the subfamily Atelinae along with Ateles (spider monkeys) and Lagothrix (wooly monkeys). The taxonomy of Brachyteles has constantly changed since its first description in the 19th century. First treated as a monotypic genus, and after several modifications in the number of species, Brachyteles currently contains two species, B. arachnoides (Southern muriqui) and B. hypoxanthus (Northern muriqui). The morphological evidence for this taxonomic arrangement relies on two diagnostic characters: the occurrence of a black-pigmented face and the absence of the first digit (thumb) in Southern muriqui populations vs. mottled face and fully-developed thumb in Northern muriqui populations. In addition, the phylogenetic relationship between atelines is disputed: on the one hand, the molecular evidence suggests an (Ateles (Brachyteles + Lagothrix)) clade and, on the other, most morphological evidence supports a clade (Lagothrix (Ateles + Brachyteles)) based on the high degree of postcranial and locomotory resemblances between Ateles and Brachyteles. My aims here are: 1) to verify how many taxa at the species level group there are in Brachyteles, and 2) to estimate the phylogenetic relationships among Atelinae using morphological characters. To achieve these goals, I have performed a qualitative analysis of external morphological characters as the presence or absence of the thumb, pelage coloration, and face pigmentation to test sexual dimorphism or dichromatism and intrapopulational variation. I also performed linear and geometric morphometrics analyses to test sexual dimorphism and geographical variation in both size and shape of the skull. Finally, I carried out a morphological phylogeny using 74 discrete morphological characters, two ecological and one karyological. This analysis includes 11 species of extant and fossil atelids and the outgroup was composed of Sapajus nigritus and Callicebus personatus. The analysis of the pelage coloration reveals that there is no sexual dimorphism or dichromatism in Brachyteles; besides, the pelage presents a high degree of individual variation. The development of the thumb and the facial pigmentation do not exhibit uniformity; thus, they have no taxonomic meaning. Linear and geometric morphometrics failed on to discriminate between sexes and populations based on the size and shape of the skull. For these reasons, I consider Brachyteles as a monotypic genus with no subspecies. Lastly, the morphologic phylogenetic analysis shows that Brachyteles is more closely related to Lagothrix than to Ateles, suggesting that the postcranial similarities between muriquis and spider monkeys could be a plesiomorphic condition in Atelidae, and the arboreal quadrupedalism of Alouatta and Lagothrix evolved convergently in alouattines and atelines.
Os muriquis ou monos-carvoeiros, gênero Brachyteles Spix, 1823, são os maiores primatas existentes do Novo Mundo, fazendo parte da subfamília Atelinae, juntamente com os gêneros Ateles (macaco-aranha) e Lagothrix (macaco-barrigudo). A taxonomia de Brachyteles tem sofrido constantes alterações desde sua primeira descrição no século XIX. Inicialmente foi tratado como um gênero monotípico, entretanto, após diversas alterações no número de espécies, atualmente considera-se composto por duas espécies, B. arachnoides (muriqui-do-sul) and B. hypoxanthus (muriqui-do-norte). O suporte para este arranjo taxonômico baseia-se em dois caracteres diagnósticos: a ocorrência de face com coloração preta e a ausência do primeiro dígito (polegar) nos muriquis-do-sul vs. face com manchas e polegar totalmente desenvolvido em populações de muriquis-do-norte. Adicionalmente, as relações filogenéticas entre os atelinos é contestada: por um lado, a evidência molecular sugere o clado formado por (Ateles (Brachyteles + Lagothrix)), por outro, a evidência morfológica suporta o clado (Lagothrix (Ateles + Brachyteles)), baseando-se na grande similaridade pós-craniana e locomotora. Desta forma, o meus objetivos neste trabalho são: 1) verificar quantos taxa do grupo da espécie existem em Brachyteles, e 2) estabelecer as relações filogenéticas entre os Atelinae utilizando caracteres morfológicos. Para isso, analisei qualitativamente os caracteres morfológicos externos, como a presença ou ausência de polegar, a coloração da pelagem, e a pigmentação facial, a fim de testar a ocorrência de dimorfismo sexual ou dicromatismo e a variação intraespecífica. Além disso, realizei análises morfométricas lineares e geométricas para testar o dimorfismo sexual e a variação geográfica do tamanho e forma do crânio. Por fim, realizei uma filogenia morfológica utilizando 74 caracteres morfológicos, dois ecológicos e um cariotípico. Estas análises incluíram 11 espécies de atelídeos viventes e fósseis e um grupo-externo composto por Sapajus nigritus e Callicebus personatus. A análise da coloração da pelagem revela que não há dimorfismo sexual ou dicromatismo em Brachyteles; além disso, a pelagem apresenta um alto grau de variação individual. O desenvolvimento do polegar e a pigmentação facial não apresentam uniformidade, assim, não tem relevância taxonômica. A morfometria linear e geométrica falharam em discriminar entre os sexos e as populações com base no tamanho e forma do crânio. Finalmente, as análises filogenéticas mostraram que Brachyteles está mais estreitamente relacionado com Lagothrix do que com Ateles, sugerindo que a similaridade pós-craninana entre os muriquis e os macacos-aranha poderia ser uma condição plesiomórfico dos atelídeos, e o quadrupedalismo arborícola de Alouatta e Lagothrix teria evoluído convergentemente em alouatíneos e atelíneos.
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Müller, Johannes. "A revision of Askeptosaurus italicus and other thalattosaurs from the European Triassic, the interrelationships of thalattosaurs, and their phylogenetic position within diapsid reptiles (Amniota, Eureptilia)." [S.l. : s.n.], 2002. http://ArchiMeD.uni-mainz.de/pub/2002/0127/diss.pdf.

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Gontang, Erin Ann. "Phylogenetic diversity of gram-positive bacteria and their secondary metabolite genes." Diss., Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 2008. http://wwwlib.umi.com/cr/ucsd/fullcit?p3324374.

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Thesis (Ph. D.)--University of California, San Diego, 2008.
Title from first page of PDF file (viewed October 3, 2008). Available via ProQuest Digital Dissertations. Vita. Includes bibliographical references.
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Fujimoto, Masaki Stanley. "The OGCleaner: Detecting False-Positive Sequence Homology." BYU ScholarsArchive, 2017. https://scholarsarchive.byu.edu/etd/6410.

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Within bioinformatics, phylogenetics is the study of the evolutionary relationships between different species and organisms. The genetic revolution has caused an explosion in the amount of raw genomic information that is available to scientists for study. While there has been an explosion in available data, analysis methods have lagged behind. A key task in phylogenetics is identifying homology clusters. Current methods rely on using heuristics based on pairwise sequence comparison to identify homology clusters. We propose the Orthology Group Cleaner (the OGCleaner) as a method to evaluate cluster level verification of putative homology clusters in order to create higher quality phylogenetic tree reconstruction.
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Books on the topic "Phylogenetic position"

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Bertelli, Sara. Earliest tinamous (Aves: Palaeognathae) from the Miocene of Argentina and their phylogenetic position. Los Angeles: Natural History Museum of Los Angeles County, 2005.

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Vasconcellos, Alberto Corrêa de. Hennigan phylogenetic analysis of the rugose clades Cystiphyllida and Stauriida and their position within Zoantharia. Portsmouth: University of Portsmouth, School of Earth and Environmental Sciences, 2002.

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Corti, Claudia, Pietro Lo Cascio, and Marta Biaggini, eds. Mainland and insular lacertid lizards. Florence: Firenze University Press, 2007. http://dx.doi.org/10.36253/978-88-8453-523-8.

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Lacertid lizards have long been a fruitful field of scientific enquiry with many people working on them over the past couple of hundred years. The scope of the field has steadily increased, beginning with taxonomy and anatomy and gradually spreading so that it includes such topics as phylogenetics, behaviour, ecology, and conservation. Since 1992, a series of symposia on lacertid lizards of the Mediterranean basin have taken place every three years. The present volume stems from the 2004 meeting in the Aeolian Islands. In the volume a wide range of island topics are considered, including the systematics of the species concerned, from both morphological and molecular viewpoints, interaction with other taxa, and conservation. The last topic is especially important, as island lizards across the world have often been vulnerable to extinction, after they came into contact with people and the animals they introduced. The volume also has papers on the more positive aspects of human influence, specifically the benign effects of traditional agriculture on at least some reptile species. Olive trees, cork oaks and the banks and walls of loose rocks that crisscross the Mediterranean scene all often contribute to elevated lizard populations. Nor is more basic biology neglected and there are articles on morphology, reproduction, development and thermoregulation. Finally, it is good to see one paper on non-Mediterranean species is included. For, to fully understand the lacertids of this region, it is necessary to appreciate their close relatives in Africa, Asia and the archipelagos of the northeastern Atlantic Ocean. (From Preface by E. Nicholas Arnold & Wolfgang Böhme)
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CRYAN. New World Treehopper Tribe Microcentrini: Monographic Revision And Phylogenetic Position. Entomological Society of Amer, 2003.

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Howes, G. J. Phylogenetic Position of the Yugoslavian Cyprinid Fish Genus Aulopyge Heckel, 1841, with an Appraisal of the Genus Barbus Cuvier and Cloquet, 1816 and the Subfamily Cyprininae (Zoology Bulletins). Intercept Ltd, 1987.

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Book chapters on the topic "Phylogenetic position"

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Kluge, Nikita. "Systematic position of Ephemeroptera." In The Phylogenetic System of Ephemeroptera, 17–20. Dordrecht: Springer Netherlands, 2004. http://dx.doi.org/10.1007/978-94-007-0872-3_2.

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Nielsen, C. "The phylogenetic position of the Arthropoda." In Arthropod Relationships, 11–22. Dordrecht: Springer Netherlands, 1998. http://dx.doi.org/10.1007/978-94-011-4904-4_2.

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Seckbach, Joseph, and Franklyn D. Ott. "Systematic position and phylogenetic status of Cyanidium Geitler 1933." In Evolutionary Pathways and Enigmatic Algae: Cyanidium caldarium (Rhodophyta) and Related Cells, 133–43. Dordrecht: Springer Netherlands, 1994. http://dx.doi.org/10.1007/978-94-011-0882-9_8.

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Middelhoven, Wouter J. "History, Habitat, Variability, Nomenclature and Phylogenetic Position ofHansenula polymorpha." In Hansenula polymorpha, 1–7. Weinheim, FRG: Wiley-VCH Verlag GmbH & Co. KGaA, 2005. http://dx.doi.org/10.1002/3527602356.ch1.

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Miao, Hongmei, Yamin Sun, Wenchao Lin, Lei Wang, and Haiyang Zhang. "Genome Synteny Analysis and Phylogenetic Position of S. indicum." In Compendium of Plant Genomes, 267–73. Cham: Springer International Publishing, 2021. http://dx.doi.org/10.1007/978-3-319-98098-0_16.

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Škaloud, Pavel, Fabio Rindi, Christian Boedeker, and Frederik Leliaert. "Phylogenetic position of the Ulvophyceae and evolutionary relationships among its main lineages." In Freshwater Flora of Central Europe, Vol 13: Chlorophyta: Ulvophyceae (Süßwasserflora von Mitteleuropa, Bd. 13: Chlorophyta: Ulvophyceae), 15–16. Berlin, Heidelberg: Springer Berlin Heidelberg, 2018. http://dx.doi.org/10.1007/978-3-662-55495-1_4.

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Ferraguti, Marco, and Barrie G. M. Jamieson. "Spermiogenesis in Bythonomus lemani and the phylogenetic position of the Lumbriculidae (Oligochaeta, Annelida)." In Aquatic Oligochaeta, 123–34. Dordrecht: Springer Netherlands, 1987. http://dx.doi.org/10.1007/978-94-009-3091-9_13.

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Ramon-Mateu, Julia, Allison Edgar, Dorothy Mitchell, and Mark Q. Martindale. "Studying Ctenophora WBR Using Mnemiopsis leidyi." In Methods in Molecular Biology, 95–119. New York, NY: Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2172-1_5.

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AbstractCtenophores, also known as comb jellies, are a clade of fragile holopelagic, carnivorous marine invertebrates, that represent one of the most ancient extant groups of multicellular animals. Ctenophores show a remarkable ability to regenerate in the adult form, being capable of replacing all body parts (i.e., whole-body regeneration) after loss/amputation. With many favorable experimental features (optical clarity, stereotyped cell lineage, multiple cell types), a full genome sequence available and their early branching phylogenetic position, ctenophores are well placed to provide information about the evolution of regenerative ability throughout the Metazoa. Here, we provide a collection of detailed protocols for use of the lobate ctenophore Mnemiopsis leidyi to study whole-body regeneration, including specimen collection, husbandry, surgical manipulation, and imaging techniques.
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Böttger-Schnack, Ruth, and Rony Huys. "Taxonomy of Oncaeidae (Copepoda, Poecilostomatoida) from the Red Sea. III. Morphology and phylogenetic position of Oncaea subtilis Giesbrecht, 1892." In Copepoda: Developments in Ecology, Biology and Systematics, 467–81. Dordrecht: Springer Netherlands, 2001. http://dx.doi.org/10.1007/0-306-47537-5_40.

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Danilov, Igor G., Vladimir B. Sukhanov, and Elena V. Syromyatnikova. "Redescription of Zangerlia dzamynchondi (Testudines: Nanhsiungchelyidae) from the Late Cretaceous of Mongolia, with a Reassessment of the Phylogenetic Position and Relationships of Zangerlia." In Vertebrate Paleobiology and Paleoanthropology, 407–17. Dordrecht: Springer Netherlands, 2012. http://dx.doi.org/10.1007/978-94-007-4309-0_22.

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Conference papers on the topic "Phylogenetic position"

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Toan, Le Chi, Nguyen Thi Phuong Thao, Nguyen Thi Anh Duong, Pham Thi Minh Anh, Pham Thi Bich Ha, Hoang Nguyen Tuan Phuong, Tran My Linh, et al. "STUDY ON PHYLOGENETIC POSITION AND GENETIC RELATIONSHIP OF ALTINGIA EXCELSA NORONHA FROM LAO CAI, VIETNAM BY MOLECULAR DATA." In NGHIÊN CỨU VÀ GIẢNG DẠY SINH HỌC Ở VIỆT NAM - BIOLOGICAL RESEARCH AND TEACHING IN VIETNAM. Nhà xuất bản Khoa học tự nhiên và Công nghệ, 2022. http://dx.doi.org/10.15625/vap.2022.0038.

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Schiffbauer, James D., Tara Selly, Tara Selly, Sarah M. Jacquet, Sarah M. Jacquet, Michael A. Strange, Michael A. Strange, et al. "NEW DATA ON CLOUDINIDS FROM THE TERMINAL EDIACARAN OF NEVADA: POSSIBLE SOFT-TISSUE PRESERVATION MAY PROVIDE CLUES ONTO PHYLOGENETIC POSITION." In GSA Annual Meeting in Indianapolis, Indiana, USA - 2018. Geological Society of America, 2018. http://dx.doi.org/10.1130/abs/2018am-317349.

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"SYSTEMATIC POSITION AND PHYLOGENETIC RELATIONSHIPS OF THE CYCLOPHYLLIDEAN CESTODES - An In-silico Study using ITS2 rDNA and Sequence-structure Alignment." In International Conference on Bioinformatics. SciTePress - Science and and Technology Publications, 2010. http://dx.doi.org/10.5220/0002690500050012.

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López-Solano, Alfonso, Silvia Perea, Ignacio Doadrio, and Tessa Lynn Nester. "Complete Mitochondrial Genome of the Spanish Toothcarp, Apricaphanius iberus (Valenciennes, 1846) (Actinopterygii, Aphaniidae) and Its Phylogenetic Position within the Cyprinodontiformes Order †." In SIBIC 2022. Basel Switzerland: MDPI, 2022. http://dx.doi.org/10.3390/blsf2022013029.

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Mesquita, Laércio, Antônio De C. Filho, Alcilene De Sousa, and Patrícia Drumond. "Redução de falsos positivos em imagens de mamografias digitais usando os índices phylogenetic species variability, phylogenetic species richness e múltiplos classificadores." In XVI Simpósio Brasileiro de Computação Aplicada à Saúde. Sociedade Brasileira de Computação - SBC, 2020. http://dx.doi.org/10.5753/sbcas.2016.9895.

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Os sistemas CADx têm ganhado cada vez mais atenção devido sua importância na área médica, tornando o diagnóstico por parte dos especialistas mais preciso. Para criação dessas ferramentas são utilizados métodos computacionais, processamento digital de imagens e conhecimentos sobre a doença. Neste trabalho utilizam-se índices de diversidade filogenética para extração de características baseada na textura. Tais índices são utilizados como características para os classificadores: Support Vector Machine, Random Forest, Random Basis Function e MultiLayer Perceptron identificando em tecidos de mamografias a presença de massa e não massa, perfazendo assim parte de um Computer-Aided Diagnosis. Para validação da metodologia, foram utilizadas 200 imagens de mamografia, onde 100 contêm massa e as demais não massa. Os resultados mostram-se promissores, pois os melhores resultados alcançam uma acurácia de 91,5%, sensibilidade de 89,5%, especificidade de 94% e uma taxa de falsos positivos de 0,085 por exame.
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Bandeira, Larissa Melo, Ana Rita Motta-Castro, Marco Puga, Silvia Uehara, João Domingos, Grazielli Rezende, Gabriela Alves Cesar, and Tayana Tanaka. "Human T-cell leukemia virus type 1 infection among Japanese immigrants and their descendants living in Southeast Brazil: a call for preventive and control responses." In XIII Congresso da Sociedade Brasileira de DST - IX Congresso Brasileiro de AIDS - IV Congresso Latino Americano de IST/HIV/AIDS. Zeppelini Editorial e Comunicação, 2021. http://dx.doi.org/10.5327/dst-2177-8264-202133p012.

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Introduction: Human T-cell leukemia virus type 1 (HTLV-1) has worldwide distribution and is considered endemic in southwestern Japan. HTLV-1 infection has been associated with adult T-cell leukemia/lymphoma (ATL) and HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP) besides other diseases. Objective: This cross-sectional study aimed to investigate the prevalence, risk factors, and molecular characterization of HTLV-1, among the world´s largest population of Japanese immigrants and their descendants outside Japan, in São Paulo, Southeast Brazil, as well as to analyze the phylogenetic relationship among isolates of HTLV-1. Methods: From July to December 2017, 2,139 individuals from five Japanese associations were interviewed and submitted to blood collection. All serum samples were first tested for the presence of anti-HTLV-1/2 antibodies by ELISA and then peripheral blood from individuals with positive serological results were analyzed for the presence of HTLV-1 5ʹLTR proviral DNA. Partial sequencing of the 5ʹLTR region of HTLV-1 proviral DNA was performed by Sanger. Results: The prevalence of HTLV-1 infection was 5.1% (95% CI 4.2-6.0). In the multiple logistic regression model, HTLV-1 infection was associated with age 45 years, female sex, first- and second-generation Japanese immigrants, and having sexual partners with a history of blood transfusion. The phylogenetic analysis revealed that all HTLV-1 were classified as Cosmopolitan (1a) subtype. Of them, 47.8% were classified as Transcontinental (A) subgroup and 52.2% as belonging to the Japanese (B) subgroup. Although most HTLV-1-infected patients were asymptomatic (97.3%), the blurred vision was associated with HTLV-1 infection. Conclusion: The high prevalence of HTLV-1 infection found in this study population and especially the intrafamily and interfamily HTLV-1 transmission presents an urgent need for preventive and control responses of this infection in Brazil.
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Castro, Ana Rita Motta, Livia Lima, Larissa Bandeira, Selma Gomes, Barbara Lago, Grazielli Rezende, and Gabriela Alves Cesar. "Hepatitis B: changes in epidemiological features of Afrodescendant communities in Central Brazil." In XIII Congresso da Sociedade Brasileira de DST - IX Congresso Brasileiro de AIDS - IV Congresso Latino Americano de IST/HIV/AIDS. Zeppelini Editorial e Comunicação, 2021. http://dx.doi.org/10.5327/dst-2177-8264-202133p142.

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Introduction: Hepatitis B virus (HBV) infection is still a concern in vulnerable populations. In a study performed by our team in 1999–2003 in two Afro-Brazilian communities, Furnas dos Dionísios (FD) and São Benedito (SB), high prevalence rates of HBV exposure (42.7% and 16.0%, respectively), high susceptibility to HBV (55.3% and 63.0%, respectively) and low HBV vaccination like profile rates (2.0% and 21.0%, respectively) were observed. Objective: In 2015–2016, we reassessed epidemiological and molecular features of HBV in these two communities to verify the impact of health actions adopted in the past years. Methods: Serum samples were screened by enzyme-linked immunosorbent assay (ELISA) for the presence of HBsAg, hepatitis B core antibody (total anti-HBc), and hepatitis B surface antibody (anti-HBs) (Biokit S.A., Barcelona, Spain). Cobas® e601 analyzer (Roche Diagnostics, Mannheim, Germany) was used to test the presence of HBeAg, anti- -HBe, and anti-HBc IgM in HBsAg-positive samples. The complete pre-S/S HBV region (nt 2826–nt 841) was amplified by semi-nested polymerase chain reaction (PCR). Results: The prevalence rate of HBV exposure among the enrolled 331 subjects was 35.3% in FD and 21.8% in SB. HBV chronic infection (5.8% in FD, 4.9% in SB) remained high. The rate of HBV vaccination like profile rate increased from 10.7% to 43.5% (2.0%–45.9% in FD, 21.0%–39.5% in SB), while susceptible subjects declined from 58.9% to 26.3% (55.3%– 18.8% in FD, 63.0%–38.7% in SB). Among 18 HBsAg-positive samples, 13 were successfully sequenced (pre-S/S region). Phylogenetic analyses showed that all isolates belong to HBV subgenotype A1, clustering within the Asian-American clade. Conclusion: Despite the maintenance of high prevalence rate of HBV exposure over these 13 years of surveillance, significant improvements were observed, reinforcing the importance of facilitated HBV vaccination to difficult-to-access population to close gaps in prevention.
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Mathew, Shilu M., Malak Ibrahim, Asmaa Al Thani, Khalid Al Ansari, Hassan Zaraket, and Hadi M. Yassine. "Antigenica and Genetic Characterization of Identified Rotavirus Strains in Qatar in Response to Rotarix Vaccine Usage." In Qatar University Annual Research Forum & Exhibition. Qatar University Press, 2020. http://dx.doi.org/10.29117/quarfe.2020.0114.

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To identify genetic and antigenic variation in RV in response to vaccine usage. Methods: A total of 231 RV-positive fecal samples were collected from children suffering from AGE during three-year study period between June 2016 and June 2019. The age of the subjects ranged between 2 months and 14 years (median of 16 months). RV genotyping and neutralizing regions, which include both VP4 (Ptype) and VP7 (G type), were amplified and sequenced. We characterized amino acid sequence variability and predicted antigenicity compared to the Rotarix vaccine strain. Phylogenetic analyses were performed using MEGA7.0. Fisher’s exact test was used to run the statistical analysis for the clinical and demographical characteristics of circulating strains. Results: RV infection was most common in children between 3-36 months of age. Among the RV-positive cases, 135 (59.3%) had been vaccinated using either of the RV vaccines available. The number of children vaccinated with one and two-dose was 53 (39.2%) and 82 (60.8%), respectively. The percentage reduction of disease in a vaccinated group of pediatrics compared to an unvaccinated group of pediatrics was 25%. Of these, 108 (78.2%) experienced diarrhea for less than three days, and only eight (6.7%) had diarrhea for more than five days. All vaccinated children showed mild to moderate dehydration except for ten children who were then treated with intravenous fluids. G3 strains were the most strains detected (40%) followed by G2 (17.7%), G4 (16.8%), G9 (15%), G1 (9%), and G8 (0.9%). The dominant RV strains during the study period were G3P [8] (30.8%), G2P [8] (12.3%), G4P [8] (11.7%) and G1P[8] (10.4%). Comparisons of the amino acid residues defining the VP7 and VP4 antigenic domains revealed several mismatches between G1P [8] strains and the G1 and P [8] strains contained in the currently licensed rotavirus vaccines Rotarix. Eighty percent (n=8) of the G1 genotype specimens harbored three amino acid substitutions (N94S, S123N, and M217T) in 7‐ 1a and 7‐ 2b antigenic sites in comparison to the Rotarix vaccine. The P [8] strains with G4 and G9 counterparts showed the highest degree of variation among all specimens with known G genotype. These viruses had 15 and 13 substitutions in their VP4 antigenic epitopes when compared with the P [8] component of the Rotarix vaccines. Conclusion: This study suggests genetic variability in G1 genotype specimens to escape the vaccine-derived immune response. It also identified the wide diversity of circulating RV genotypes in Qatar.
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Reports on the topic "Phylogenetic position"

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Lance, Richard, and Xin Guan. Variation in inhibitor effects on qPCR assays and implications for eDNA surveys. Engineer Research and Development Center (U.S.), August 2021. http://dx.doi.org/10.21079/11681/41740.

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Aquatic environmental DNA (eDNA) surveys are sometimes impacted by polymerase chain reaction (PCR) inhibitors. We tested varying concentrations of different inhibitors (humic, phytic, and tannic acids; crude leaf extracts) for impacts on quantitative PCR (qPCR) assays designed for eDNA surveys of bighead and silver carp (Hypophthalmichthys nobilis and Hypophthalmichthys molitrix). We also tested for inhibition by high concentrations of exogenous DNA, hypothesizing that DNA from increasingly closely related species would be increasingly inhibitory. All tested inhibitors impacted qPCR, though only at very high concentrations — likely a function, in part, of having used an inhibitor-resistant qPCR solution. Closer phylogenetic relatedness resulted in inhibition at lower exogenous DNA concentrations, but not at relatively close phylogenetic scales. Inhibition was also influenced by the qPCR reporter dye used. Importantly, different qPCR assays responded differently to the same inhibitor concentrations. Implications of these results are that the inclusion of more than one assay for the same target taxa in an eDNA survey may be an important countermeasure against false negatives and that internal positive controls may not, in the absence of efforts to maximize inhibition compatibility, provide useful information about the inhibition of an eDNA assay.
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Vakharia, Vikram, Shoshana Arad, Yonathan Zohar, Yacob Weinstein, Shamila Yusuff, and Arun Ammayappan. Development of Fish Edible Vaccines on the Yeast and Redmicroalgae Platforms. United States Department of Agriculture, February 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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Malkinson, Mertyn, Irit Davidson, Moshe Kotler, and Richard L. Witter. Epidemiology of Avian Leukosis Virus-subtype J Infection in Broiler Breeder Flocks of Poultry and its Eradication from Pedigree Breeding Stock. United States Department of Agriculture, March 2003. http://dx.doi.org/10.32747/2003.7586459.bard.

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Objectives 1. Establish diagnostic procedures to identify tolerant carrier birds based on a) Isolation of ALV-J from blood, b) Detection of group-specific antigen in cloacal swabs and egg albumen. Application of these procedures to broiler breeder flocks with the purpose of removing virus positive birds from the breeding program. 2. Survey the AL V-J infection status of foundation lines to estimate the feasibility of the eradication program 3. Investigate virus transmission through the embryonated egg (vertical) and between chicks in the early post-hatch period (horizontal). Establish a model for limiting horizontal spread by analyzing parameters operative in the hatchery and brooder house. 4. Compare the pathogenicity of AL V-J isolates for broiler chickens. 5. Determine whether AL V-J poses a human health hazard by examining its replication in mammalian and human cells. Revisions. The: eradication objective had to be terminated in the second year following the closing down of the Poultry Breeders Union (PBU) in Israel. This meant that their foundation flocks ceased to be available for selection. Instead, the following topics were investigated: a) Comparison of commercial breeding flocks with and without myeloid leukosis (matched controls) for viremia and serum antibody levels. b) Pathogenicity of Israeli isolates for turkey poults. c) Improvement of a diagnostic ELISA kit for measuring ALV-J antibodies Background. ALV-J, a novel subgroup of the avian leukosis virus family, was first isolated in 1988 from broiler breeders presenting myeloid leukosis (ML). The extent of its spread among commercial breeding flocks was not appreciated until the disease appeared in the USA in 1994 when it affected several major breeding companies almost simultaneously. In Israel, ML was diagnosed in 1996 and was traced to grandparent flocks imported in 1994-5, and by 1997-8, ML was present in one third of the commercial breeding flocks It was then realized that ALV-J transmission was following a similar pattern to that of other exogenous ALVs but because of its unusual genetic composition, the virus was able to establish an extended tolerant state in infected birds. Although losses from ML in affected flocks were somewhat higher than normal, both immunosuppression and depressed growth rates were encountered in affected broiler flocks and affected their profitability. Conclusions. As a result of the contraction in the number of international primary broiler breeders and exchange of male and female lines among them, ALV-J contamination of broiler breeder flocks affected the broiler industry worldwide within a short time span. The Israeli national breeding company (PBU) played out this scenario and presented us with an opportunity to apply existing information to contain the virus. This BARD project, based on the Israeli experience and with the aid of the ADOL collaborative effort, has managed to offer solutions for identifying and eliminating infected birds based on exhaustive virological and serological tests. The analysis of factors that determine the efficiency of horizontal transmission of virus in the hatchery resulted in the workable solution of raising young chicks in small groups through the brooder period. These results were made available to primary breeders as a strategy for reducing viral transmission. Based on phylogenetic analysis of selected Israeli ALV-J isolates, these could be divided into two groups that reflected the countries of origin of the grandparent stock. Implications. The availability of a simple and reliable means of screening day old chicks for vertical transmission is highly desirable in countries that rely on imported breeding stock for their broiler industry. The possibility that AL V-J may be transmitted to human consumers of broiler meat was discounted experimentally.
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