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Relevant bibliographies by topics / Nuclear phylogeny

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Academic literature on the topic 'Nuclear phylogeny'

Author: Grafiati

Published: 7 June 2025

Last updated: 2 August 2025

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Journal articles on the topic "Nuclear phylogeny"

1

SAARMA, U., I. JÕGISALU, E. MOKS, et al. "A novel phylogeny for the genus Echinococcus, based on nuclear data, challenges relationships based on mitochondrial evidence." Parasitology 136, no. 3 (2009): 317–28. http://dx.doi.org/10.1017/s0031182008005453.

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SUMMARYThe taxonomic status of Echinococcus, an important zoonotic cestode genus, has remained controversial, despite numerous attempts to revise it. Although mitochondrial DNA (mtDNA) has been the source of markers of choice for reconstructing the phylogeny of the genus, results derived from mtDNA have led to significant inconsistencies with earlier species classifications based on phenotypic analysis. Here, we used nuclear DNA markers to test the phylogenic relationships of members of the genus Echinococcus. The analysis of sequence data for 5 nuclear genes revealed a significantly different

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2

Górniak, Marcin, Dariusz L. Szlachetko, Natalia Olędrzyńska, et al. "Species Phylogeny versus Gene Trees: A Case Study of an Incongruent Data Matrix Based on Paphiopedilum Pfitz. (Orchidaceae)." International Journal of Molecular Sciences 22, no. 21 (2021): 11393. http://dx.doi.org/10.3390/ijms222111393.

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The phylogeny of the genus Paphiopedilum based on the plastome is consistent with morphological analysis. However, to date, none of the analyzed nuclear markers has confirmed this. Topology incongruence among the trees of different nuclear markers concerns entire sections of the subgenus Paphiopedilum. The low-copy nuclear protein-coding gene PHYC was obtained for 22 species representing all sections and subgenera of Paphiopedilum. The nuclear-based phylogeny is supported by morphological characteristics and plastid data analysis. We assumed that an incongruence in nuclear gene trees is caused

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3

Holst-Jensen, Arne, Linda M. Kohn, and Trond Schumacher. "Nuclear rDNA Phylogeny of the Sclerotiniaceae." Mycologia 89, no. 6 (1997): 885. http://dx.doi.org/10.2307/3761109.

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Holst-Jensen, Arne, Linda M. Kohn, and Trond Schumacher. "Nuclear rDNA phylogeny of the Sclerotiniaceae." Mycologia 89, no. 6 (1997): 885–99. http://dx.doi.org/10.1080/00275514.1997.12026859.

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Cameron, Kenneth, and Chengxin Fu. "A Nuclear rDNA Phylogeny of Smilax (Smilacaceae)." Aliso 22, no. 1 (2006): 598–605. http://dx.doi.org/10.5642/aliso.20062201.47.

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Cavalier-Smith, T., J. A. Couch, K. E. Thorsteinsen, et al. "Cryptomonad nuclear and nucleomorph 18S rRNA phylogeny." European Journal of Phycology 31, no. 4 (1996): 315–28. http://dx.doi.org/10.1080/09670269600651541.

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Spooner, David M., Holly Ruess, Philipp Simon, and Douglas Senalik. "Mitochondrial DNA Sequence Phylogeny of Daucus." Systematic Botany 45, no. 2 (2020): 403–8. http://dx.doi.org/10.1600/036364420x15862837791311.

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Abstract—We explored the phylogenetic utility of mitochondrial DNA sequences in Daucus and compared the results with prior phylogenetic results using the same 36 accessions of Daucus (and two additional outgroups) with plastid DNA sequences and with other nuclear results. As in the plastid study we used Illumina HiSeq sequencer to obtain resequencing data of the same accessions of Daucus and outgroups, and analyzed the data with maximum parsimony and maximum likelihood. We obtained data from 47 of 71 total mitochondrial genes but only 17 of these 47 genes recovered major clades that were commo

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Small, Randall L., Richard C. Cronn, and Jonathan F. Wendel. "Use of nuclear genes for phylogeny reconstruction in plants." Australian Systematic Botany 17, no. 2 (2004): 145. http://dx.doi.org/10.1071/sb03015.

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Molecular data have had a profound impact on the field of plant systematics, and the application of DNA-sequence data to phylogenetic problems is now routine. The majority of data used in plant molecular phylogenetic studies derives from chloroplast DNA and nuclear rDNA, while the use of low-copy nuclear genes has not been widely adopted. This is due, at least in part, to the greater difficulty of isolating and characterising low-copy nuclear genes relative to chloroplast and rDNA sequences that are readily amplified with universal primers. The higher level of sequence variation characteristic

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Palmé, A. E., T. Pyhäjärvi, W. Wachowiak, and O. Savolainen. "Selection on Nuclear Genes in a Pinus Phylogeny." Molecular Biology and Evolution 26, no. 4 (2009): 893–905. http://dx.doi.org/10.1093/molbev/msp010.

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Fujita, Matthew K., Tag N. Engstrom, David E. Starkey, and H. Bradley Shaffer. "Turtle phylogeny: insights from a novel nuclear intron." Molecular Phylogenetics and Evolution 31, no. 3 (2004): 1031–40. http://dx.doi.org/10.1016/j.ympev.2003.09.016.

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Dissertations / Theses on the topic "Nuclear phylogeny"

1

Wiswedel, Stefan. "Isolepis (Cyperaceae) revisited : a phylogeny based on plastid and nuclear ribosomal DNA data." Thesis, University of Cape Town, 2006. http://hdl.handle.net/11427/23927.

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Rong, Ying. "Phylogeny of the genus Gossypium and genome origin of its polyploid species inferred from variation in nuclear repetitive DNA sequences." Texas A&M University, 2004. http://hdl.handle.net/1969.1/3161.

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Knowledge of phylogenetic relationships among taxa is essential for comparative and evolutionary genomic research. Here, we report reconstruction of the phylogenetic tree of the genus Gossypium containing cultivated cottons of importance in agriculture by using variation of nuclear repetitive DNA sequences. Genomic DNA was isolated from 87 available accessions of 35 species representing all eight basic genome groups of the genus Gossypium and analyzed to infer phylogeny of the genus and genome origin of its polyploid species. Twenty-two interspersed repeated sequence clones derived from G. hir

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Bateman, Joanna Rosa. "Species Delimitation Predictions Using Mitochondrial and Nuclear DNA Sequences from the Heteromys pictus-spectabilis Species Complex." BYU ScholarsArchive, 2018. https://scholarsarchive.byu.edu/etd/7457.

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Heteromys pictus-spectabilis is a species complex within the subfamily Heteromyinae (Family: Heteromyidae) that is distributed along the western and southern Mexican coast and surrounding environments. Currently, the species complex is accepted as being 2 separate species (H. pictus and H. spectabilis), but this also renders H. pictus paraphyletic. Therefore, the species complex requires re-evaluation in order to resolve the paraphyly. Mitochondrial DNA sequences from a previously existing ~720 specimen database compiled by Victoria Vance were used in conjunction with new nuclear DNA sequences

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Lin, Qianshi. "Using a low-copy nuclear gene (phosphoglycerate kinase; PGK) to explore the phylogeny of the aquatic plant family Hydatellaceae (Nymphaeales)." Thesis, University of British Columbia, 2014. http://hdl.handle.net/2429/50564.

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Hydatellaceae are a small aquatic family of 12 species related to water lilies, part of the ANITA grade of angiosperms. Our current understanding of phylogenetic relationships in the family comes from several plastid genes and nuclear ITS data. These data sets are generally highly congruent, and lend support to the monophyly of multiple species. However, the published nuclear ITS tree was unrooted (outgroups were too distant to align), and there were several minor phylogenetic conflicts between plastid and ITS gene trees for three closely related species, Trithuria bibracteata, T. occidentalis

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Gonzalez, Malinda Wallentine. "Phylogenetic relationship of forest spiny pocket mice (Genus Heteromys) inferred from mitochondrial and nuclear markers with implications for species boundaries." BYU ScholarsArchive, 2005. https://scholarsarchive.byu.edu/etd/263.

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I constructed a best estimate phylogeny based on congruence of multiple data sources. In recent years molecular data has been used both to construct phylogenies of taxonomic groups and to aid in the delimitation of new species. I generated and analyzed sequence data for forest spiny pocket mice (Genus Heteromys) for the mitochondrial gene cyt b (1143 bp) and two nuclear gene segments MYH2 (252 bp) and EN2 (189 bp). I used maximum parsimony and Bayesian analyses to infer relationships among species and to provide a framework for using a species delimitation method to investigate the possibility

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Rossi, Natália. "Revisão das espécies de Macrobrachium, Bate, 1868, pertencentes ao complexo M. olfersii (Crustacea, Palaemonidae): análises morfológicas e moleculares." Universidade de São Paulo, 2012. http://www.teses.usp.br/teses/disponiveis/59/59139/tde-22062012-105613/.

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Pesquisas envolvendo a sistemática e a taxonomia de camarões de água doce do gênero Macrobrachium Bate, 1868 ainda são pouco elucidativas para alguns de seus membros. Este é o caso de Macrobrachium olfersii (Wiegmann, 1836) que ocorre desde o sudeste dos Estados Unidos até o sul do Brasil e é comumente confundido com espécies que ocorrem preferencialmente na América Central (M. faustinum (de Saussure, 1857), M. digueti (Bouvier, 1895), M. crenulatum Holthuis, 1950, M. hancocki Holthuis, 1950 e M. acanthochirus Villalobos, 1967). Em 1969 estas espécies foram designadas por Villalobos como compl

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Liu, Jiarong. "Phylogeny and biogeography or watermelon [Citrullus lanatus (Thunb.) Matsum. & Nakai] based on chloropast, nuclear sequence and AFLP molecular marker data." Auburn, Ala., 2005. http://repo.lib.auburn.edu/2005%20Fall/Thesis/LIU_JIARONG_35.pdf.

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Vasconcelos, RÃgis Fernandes. "Variabilidade da RegiÃo ITS-1 do Cluster RibossÃmico Nuclear em PopulaÃÃes de Ostras de TrÃs EstuÃrios da Costa Cearense." Universidade Federal do CearÃ, 2009. http://www.teses.ufc.br/tde_busca/arquivo.php?codArquivo=2717.

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Conselho Nacional de Desenvolvimento CientÃfico e TecnolÃgico<br>ClassificaÃÃes taxonÃmicas de ostras sÃo problemÃticas, pois estes organismos possuem caracterÃsticas morfolÃgicas pouco informativas. A variabilidade da regiÃo ITS do cluster ibossÃmico tem sido bastante utilizada em estudos filogenÃticos e taxonÃmicos, visto que esta regiÃo apresenta uma variabilidade relativamente elevada e fÃcil amplificaÃÃo por termociclagem. A ostra Crassostrea brasiliana foi, por dÃcadas, confundida com C. rhizophorae, entretanto, estudos recentes indicam que sÃo duas espÃcies biologicamente distintas. Est

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Nguyen, Phi-Nga. "Molecular phylogeny of Southeast Asian Dipterocarps belonging to tribe Dipterocarpeae (family Dipterocarpaceae) based on non-coding sequence data of chloroplast and nuclear DNA /." Göttingen : Optimus Mostafa, 2009. http://d-nb.info/995047812/04.

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Amiri, Neda. "Molecular Phylogeny of Poa L. sensu lato (Poaceae) with a Focus on West Asian Species." Thesis, Université d'Ottawa / University of Ottawa, 2016. http://hdl.handle.net/10393/35018.

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Poa L., is known as a highly diverse cosmopolitan genus with taxonomic difficulties that includes unknown species and species with uncertain affinities mainly in West Asia and North Africa. Poa also exhibits a close relationship with two West Asian genera, Eremopoa Roshev. and Oreopoa H. Scholz & Parolly. This study was conducted to: 1) fill the gap of information on the affinities between Poa species with an emphasis on West Asian Poa; 2) revise and evaluate the accuracy of traditional infrageneric classification of West Asian Poa; and 3) clarify the relationship between Poa and two allied ge

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Books on the topic "Nuclear phylogeny"

1

Peterson, Kristin R. Phylogeny of Cyttaria inferred from nuclear and mitochondrial sequence and morphological data. The Mycological Society of America, 2010.

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2

Sibley, Charles Gald. Phylogeny and classification of birds: A study in molecular evolution. Yale University Press, 1990.

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3

Ward, Wheeler, and American Museum of Natural History., eds. Dynamic homology and phylogenetic systematics: A unified approach using POY. American Museum of Natural History, 2006.

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4

Humpert, Andrea J. Systematics of the genus Ramaria inferred from nuclear large subunit and mitochondrial small subunit ribosomal DNA sequences. 1999.

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5

Wu, Junyuan. Nuclear and mitochondrial DNA polymorphism and phylogeny in the California closed-cone pines. 1998.

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6

Moynihan, Jeremy. Molecular phylogeny of the Caribbean endemic Neolaugeria (Rubiaceae), based on the internal transcribed spacer regions of nuclear ribosomal DNA. 1999.

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Phylogeny and Classification of the Birds: A Study in Molecular Evolution. Yale University Press, 1991.

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8

Sadler, Kay Neuman. An investigation of the phylogeny of the causative agent of bacillary angiomatosis using 16S ribosomal RNA sequence and the design of specific nucleic acid probes. 1992.

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9

(Editor), C.-ting Wu, and Jay C. Dunlap (Editor), eds. Homology Effects (Advances in Genetics, Volume 46) (Advances in Genetics). Academic Press, 2002.

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10

Dunlap, Jay C., and C.-ting Wu. Homology Effects. Elsevier Science & Technology Books, 2002.

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Book chapters on the topic "Nuclear phylogeny"

1

Waltzek, Thomas B., Kuttichantran Subramaniam, and James K. Jancovich. "Ranavirus Taxonomy and Phylogeny." In Ranaviruses. Springer Nature Switzerland, 2024. http://dx.doi.org/10.1007/978-3-031-64973-8_2.

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AbstractThe phylum Nucleocytoviricota, known informally as the Nucleocytoplasmic Large DNA Viruses (NCLDV), is a monophyletic assemblage of viruses that infect eukaryotes, ranging from single-celled organisms to humans, worldwide. The NCLDV phylum encompasses two classes (Megaviricetes, Pokkesviricetes), five orders (Pimascovirales, Imitervirales, Algavirales, Asfuvirales, Chitovirales), and 11 families, including the family Iridoviridae (https://ictv.global/). Members of the NCLDV group have some of the largest known viral genomes. For example, members of the family Mimiviridae have genomes t

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2

Navarro, Elisabeth, Jean Bousquet, André Moiroud, Antonio Munive, Dominique Piou, and Philippe Normand. "Molecular phylogeny of Alnus (Betulaceae), inferred from nuclear ribosomal DNA ITS sequences." In Frankia Symbiosis. Springer Netherlands, 2003. http://dx.doi.org/10.1007/978-94-017-1601-7_22.

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Hoot, Sara B. "Phylogeny of the Ranunculaceae based on preliminary atpB, rbcL and 18S nuclear ribosomal DNA sequence data." In Systematics and Evolution of the Ranunculiflorae. Springer Vienna, 1995. http://dx.doi.org/10.1007/978-3-7091-6612-3_24.

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4

Barbhuiya, A. R., Mohammed Latif Khan, and S. Dayanandan. "Molecular Phylogeny of Citrus species in the Eastern Himalayan Region of Northeast India Based on Chloroplast and Nuclear DNA Sequence Data." In Molecular Genetics and Genomics Tools in Biodiversity Conservation. Springer Singapore, 2022. http://dx.doi.org/10.1007/978-981-16-6005-4_9.

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Kalita, Janmoni, S. Sureshkumar Singh, and Mohammed Latif Khan. "Molecular Characterization and Phylogeny of Clerodendrum Species Occuring in North Eastern Region of India by Internal Transcribed Spacer 2 of Nuclear DNA." In Molecular Genetics and Genomics Tools in Biodiversity Conservation. Springer Singapore, 2022. http://dx.doi.org/10.1007/978-981-16-6005-4_11.

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"Molecular Markers for Phylogenetic Studies and Germplasm Conservation." In Advances in Environmental Engineering and Green Technologies. IGI Global, 2021. http://dx.doi.org/10.4018/978-1-7998-4312-2.ch005.

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Application of molecular markers in phylogenetic studies has become increasingly important in recent times. Availability of fast DNA sequencing techniques and robust statistical analysis methods provided new momentum to this field. Different nuclear encoded genes (16S rRNA, 5S rRNA, 28S rRNA), mitochondrial encoded genes (cytochrome oxidase, mitochondrial 12S, cytochrome b, control region), and few chloroplast encoded genes (rbcL, matK, rpi16) have been used as molecular markers. This method allows researchers to obtain new evidence concerning their phylogeny and biodiversity. Measurement of g

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Kennelly, Peter J., and Arthur M. Edelman. "Protein Serine-Threonine Kinases." In Pre-Equilibrium Nuclear Reactions. Oxford University PressOxford, 1992. http://dx.doi.org/10.1093/oso/9780198517344.003.0003.

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Abstract In nature, a broad range of proteins become modified via the covalent bonding of phosphate to nucleophilic functional groups located on the side-chains of their constituent amino acids. Although numerous amino acids can be modified in this way, by far the most widespread and quantitatively significant phosphorylation events take place on the hydroxyl groups of serine and threonine (Hunter 1991). Protein phosphorylation is a truly ubiquitous phenomenon, both in terms of the range of proteins modified-a murine fibroblast contains several hundred phosphoproteins (Levenson and Blackshear

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SÜLTMANN, HOLGER, and WERNER E. MAYER. "Reconstruction of Cichlid Fish Phylogeny Using Nuclear DNA Markers." In Molecular Systematics of Fishes. Elsevier, 1997. http://dx.doi.org/10.1016/b978-012417540-2/50005-1.

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Doyle, J., and J. Doyle. "Nuclear Protein-coding Genes in Phylogeny Reconstruction and Homology Assessment." In Systematics Association Special Volumes. CRC Press, 1999. http://dx.doi.org/10.1201/9781439833278.ch12.

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ROBLES, RAFAEL, CHRISTOPHER TUDGE, PETER DWORSCHAK, GARY POORE, and DARRYL FELDER. "Molecular Phylogeny of the Thalassinidea Based on Nuclear and Mitochondrial Genes." In Decapod Crustacean Phylogenetics. CRC Press, 2009. http://dx.doi.org/10.1201/9781420092592-c15.

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