Готові списки джерел за темами / Phylogenetic analysis

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Добірка наукової літератури з теми "Phylogenetic analysis"

Автор: Grafiati

Опубліковано: 4 червня 2021

Оновлено: 6 вересня 2023

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Статті в журналах з теми "Phylogenetic analysis"

Petersen, G., and O. Seberg. "Phylogenetic Analysis of allopolyploid species." Czech Journal of Genetics and Plant Breeding 41, Special Issue (July 31, 2012): 28–37. http://dx.doi.org/10.17221/6129-cjgpb.

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Brower, A. V. "Phylogenetic Analysis." Science 276, no. 5317 (May 30, 1997): 1317b—1321. http://dx.doi.org/10.1126/science.276.5317.1317b.

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Hillis, David M. "Phylogenetic analysis." Current Biology 7, no. 3 (March 1997): R129—R131. http://dx.doi.org/10.1016/s0960-9822(97)70070-8.

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Wiesemüller, Bernhard, and Hartmut Rothe. "Interpretation of Bootstrap Values in Phylogenetic Analysis." Anthropologischer Anzeiger 64, no. 2 (June 21, 2006): 161–65. http://dx.doi.org/10.1127/anthranz/64/2006/161.

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Mecham, Jesse, Mark Clement, Quinn Snell, Todd Freestone, Kevin Seppi, and Keith Crandall. "Jumpstarting phylogenetic analysis." International Journal of Bioinformatics Research and Applications 2, no. 1 (2006): 19. http://dx.doi.org/10.1504/ijbra.2006.009191.

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Tolkoff, Max R., Michael E. Alfaro, Guy Baele, Philippe Lemey, and Marc A. Suchard. "Phylogenetic Factor Analysis." Systematic Biology 67, no. 3 (August 7, 2017): 384–99. http://dx.doi.org/10.1093/sysbio/syx066.

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Zavada, Michael S., and Muyeol Kim. "Phylogenetic analysis ofUlmaceae." Plant Systematics and Evolution 200, no. 1-2 (1996): 13–20. http://dx.doi.org/10.1007/bf00984745.

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Adams, Dean C. "PHYLOGENETIC META-ANALYSIS." Evolution 62, no. 3 (March 2008): 567–72. http://dx.doi.org/10.1111/j.1558-5646.2007.00314.x.

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Caldwell, Michael W. "Ichthyosauria: A preliminary phylogenetic analysis of diapsid affinities." Neues Jahrbuch für Geologie und Paläontologie - Abhandlungen 200, no. 3 (July 31, 1996): 361–86. http://dx.doi.org/10.1127/njgpa/200/1996/361.

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Irinyi, László, György Kövics, and Erzsébet Sándor. "Phylogenetic analysis of Phoma species." Acta Agraria Debreceniensis, no. 26 (July 16, 2007): 100–107. http://dx.doi.org/10.34101/actaagrar/26/3062.

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Анотація:

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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Дисертації з теми "Phylogenetic analysis"

Krig, Kåre. "Methods for phylogenetic analysis." Thesis, Linköping University, Department of Mathematics, 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-56814.

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Анотація:

In phylogenetic analysis one study the relationship between different species. By comparing DNA from two different species it is possible to get a numerical value representing the difference between the species. For a set of species, all pair-wise comparisons result in a dissimilarity matrix d.

In this thesis I present a few methods for constructing a phylogenetic tree from d. The common denominator for these methods is that they do not generate a tree, but instead give a connected graph. The resulting graph will be a tree, in areas where the data perfectly matches a tree. When d does not perfectly match a tree, the resulting graph will instead show the different possible topologies, and how strong support they have from the data.

Finally I have tested the methods both on real measured data and constructed test cases.

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Gottschling, Marc. "Phylogenetic analysis of selected Boraginales." [S.l. : s.n.], 2003. http://www.diss.fu-berlin.de/2003/30/index.html.

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Boudko, Ekaterina. "Phylogenetic Analysis of Subtribe Alopecurinae (Poaceae)." Thèse, Université d'Ottawa / University of Ottawa, 2014. http://hdl.handle.net/10393/30696.

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Subtribe Alopecurinae (Poeae, Poaceae) sensu lato‘s seven genera share interesting morphological similarities (dense spicate panicles and one-flowered spikelets) that were widely thought to have a common origin. However, recent molecular evidence for three of the genera has suggested that the subtribe may be polyphyletic. To test this, five DNA regions were sequenced and analyzed using phylogenetic methods. Results confirm that Alopecurinae s.l. as presently treated is polyphyletic and should be dissolved. Additionally, the genus Cornucopiae may be just another Alopecurus. Limnas and Pseudophleum are not closely allied to Alopecurus or each other, and are even further from Phleum. Phleum is a distinct lineage that is not closely allied to any other included Alopecurinae genus. Evidence for revising infrageneric classifications of Alopecurus and Phleum is presented, as is evidence for separating A. magellanicus into two or more subspecies.

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Williams, Annette Mary. "Phylogenetic analysis of the genus Streptococcus." Thesis, University of Reading, 1992. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.333267.

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Högnabba, Filip. "Phylogenetic studies of cyanobacterial lichens /." Helsinki : Yliopistopaino, 2007. http://ethesis.helsinki.fi.

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Yu, Junjie, and 于俊杰. "Phylogenetic tree reconstruction with protein linkage." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2012. http://hub.hku.hk/bib/B49618167.

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Анотація:

Phylogenetic tree reconstruction for a set of species is an important problem for understanding the evolutionary history of the species. Existing algorithms usually represent each species as a binary string with each bit indicating whether a particular gene/protein exists in the species. Given the topology of a phylogenetic tree with each leaf representing a species (a binary string of equal length) and each internal node representing the hypothetical ancestor, the Fitch-Hartigan algorithm and the Sankoff algorithm are two polynomial-time algorithms which assign binary strings to internal nodes such that the total Hamming distance between adjacent nodes in the tree is minimized. However, these algorithms oversimplify the evolutionary process by considering only the number of protein insertions/deletions (Hamming distance) between two species and by assuming the evolutionary history of each protein is independent. Since the function of a protein may depend on the existence of other proteins, the evolutionary history of these functionally dependent proteins should be similar, i.e. functionally dependent proteins should usually be present (or absent) in a species at the same time. Thus, in addition to the Hamming distance, the protein linkage distance for some pairs/sets of proteins: whole block linkage distance, partial block linkage distance, pairwise linkage distance is introduced. It is proved that the phylogenetic tree reconstruction problem to find the binary strings for the internal nodes of a phylogenetic tree that minimizes the sum of the Hamming distance and the linkage distance is NP-hard. In this thesis, a general algorithm to solve the phylogenetic tree reconstruction with protein linkage problem which runs in O(4^m⋅n) time for whole/partial block linkage distance and O(4^m⋅⋅ (m+n)) time for pairwise linkage distance (compared to the straight-forward O(4^m⋅ m⋅ n) or O(4^m⋅ m^2⋅⋅ n) time algorithm) is introduced where n is the number of species and m is the length of the binary string (number of proteins). It is further shown, by experiments, that our algorithm using linkage information can construct more accurate trees (better matches with the trees constructed by biologists) than the algorithms using only Hamming distance.
published_or_final_version
Computer Science
Master
Master of Philosophy

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Paquette, Lance. "Phylogenetic analysis of the bryozoan Suborder Rhabdomesina." Diss., Connect to online resource - MSU authorized users, 2008.

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Park, Hyun Jung. "Large-scale analysis of phylogenetic search behavior." [College Station, Tex. : Texas A&M University, 2007. http://hdl.handle.net/1969.1/ETD-TAMU-1452.

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Msimanga, Wela Patrick. "Phylogenetic analysis of HIV-1 in Mpumalanga." Thesis, Stellenbosch : Stellenbosch University, 2013. http://hdl.handle.net/10019.1/80344.

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Thesis (MScMedSc)--Stellenbosch University, 2013.
The diversity of HIV-1 sequences derived from patients in Bushbuckridge, Mpumalanga, was investigated. The gag p24, pol p10 and p66/p51, pol p31 and env gp41 gene fragments from 51 patients were amplified and sequenced. Quality control on the sequences was carried out using the LANL QC online tool. HIV-1 subtype was assigned using the LANL QC (RIP), REGA and jpHMM online tools. Subtype for the pol gene fragment was further designated using the SCUEAL online tool. Most of the sequences, that is 89%, belonged to HIV-1 subtype C. LANL QC (RIP), REGA, jpHMM also detected recombinants in 11% of the sequences. One of the isolates could only have the env gp41 gene fragment amplified and sequenced, which was determined to be HIV-1 subtype B. Phylogenetic analysis using the Neighbor-Joining and Maximum Likelihood methods from MEGA v 5 showed that, except for the env gp41 designated as a subtype B, all sequences in the study clustered with HIV-1 subtype C. Significantly, phylogenetic analysis showed that not only are the Bushbuckridge, Mpumalanga sequences related to HIV-1 subtype C sequences from southern Africa, India, Ethiopia and Brazil, but it is possible there has been multiple introductions of HIV-1 in the province. SDRMs were observed in two samples.

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Couto, Diogo Ribeiro do. "A PHYLOGENETIC ANALYSIS OF FASCIOLARIIDAE (GASTROPODA: BUCCINOIDEA)." Universidade de São Paulo, 2017. http://www.teses.usp.br/teses/disponiveis/38/38131/tde-08022017-214445/.

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The neogastropod family Fasciolariidae comprise of important representatives of tropical and subtropical molluscan assemblages, with over 500 species in the subfamilies Fasciolariinae, Fusininae and Peristerniinae. Fasciolariids with many well-known species such as tulip shells, horse-conchs, spindles, among others have a long complicated taxonomical history, with several genus names being used to group heterogeneous contingents of many unrelated species. Recently, however, taxonomical revisions have begun to set straight its taxonomy. The present work aims to resolve the phylogeny of the family Fasciolariidae, through: 1) a morphological phylogenetic parsimony analysis in TnT based on 95 characters and 53 taxa which revealed a monophyletic Fasciolariidae, with the genera Dolicholatirus and Teralatirus representing the first split in the family, followed by three splits that correspond to a fusinine grade, which also include the genus Pseudolatirus (Peristerniinae); a last split groups the peristerniine genera Peristernia and Fusolatirus, while the last group comprises of fasciolariines and the remaining peristerniines. None of these clades correspond to the present-day accepted circumscription of the three recognized subfamilies. 2) Complementing the work of Couto et al. (2016), which used a five-gene molecular dataset to analyze the phylogeny of the family. To this dataset, the previous morphological matrix was added, generating a total evidence dataset that was implemented in POY. This analysis revealed a non-monophyletic family with the genera Dolicholatirus and Teralatirus as non-fasciolariids; the remaining fasciolariids are well-supported, with the first split a monophyletic Fusininae and Pseudolatirus; a second split groups Peristernia and Fusolatirus; while the last, the remaining peristerniines and fasciolariines. Total evidence was congruent with the morphological data with the exception of the Fusininae that appeared as a crown-group and not as a grade; Lamellilatirus lamyi (Peristerniinae) nested within the fasciolariines. Finally, 3) supplement the phylogenetic analysis of Simone (2011), inserting the analyzed taxa from the morphological analysis in the same dataset. This resulted in a monophyletic Buccinoidea superfamily, a monophyletic Fasciolariidae, despite low resolution of relationship for internal taxa; Dolicholatirus nested within Fasciolariidae and the fusinines with Pseudolatirus appeared as a monophyletic crown-group.
A família de neogastrópodes Fasciolariidae é composta por representantes significativos da malacofauna em mares tropicais e subtropicais, com mais de 500 espécies descritas nas subfamílias Fasciolariinae, Fusininae e Peristerniinae. Os fasciolarídeos possuem um longo e confuso histórico taxonômico, com muitas espécies sendo alocados em gêneros claramente heterogêneos, resultando em agrupamentos que não refletem relação de parentesco. O presente estudo tem como objetico gerar hipóteses de filogenia da família Fasciolariidae; dessa maneira, foi realizada: 1) uma análise filogenética através de parcimonia no programa TnT, baseada em 95 caracteres morfológicos e 53 espécies, na qual demostrou a monofilia da família. Em relação aos arranjos internos dos fasciolarídeos, as subfamílias que compõem esse clado não são monofiléticas. Segundo a topologia obtida, observou-se que a primeira divergência separa um grupo com os gêneros Dolicholatirus e Teralatirus; a seguir, três divisões que correspondem a um grado de fusiníneos, que também inclui o gênero Pseudolatirus (Peristerniinae); uma última divisão, na qual se observa uma dicotomia que agrupa os gêneros de peristerníneos Peristernia e Fusolatirus, e os demais peristerníneos e fasciolaríneos. 2) Complementar o trabalho de Couto et al. (2016), que utilizaram dados moleculares de cinco genes para analisar a filogenia da família. A esses dados, foram incluídos também a matriz da análise morfológica, a fim de realizar uma análise de evidência total implementada no programa POY. O resultado dos dados concatenados corrobora com a análise molecular evidenciando a família Fasciolariidae como um clado não monofilético, uma vez que os gêneros Dolicholatirus e Teralatirus não estão incluídos na família; os demais fasciolarídeos formam um clado com uma primeira divisão que separa os fusiníneos e Pseudolatirus dos demais; uma segunda divisão compondo os peristerníneos Peristernia e Fusolatirus e a última agrupa os demais peristerníneos e fasciolaríneos. Dados de evidência total foram congruentes com a análise morfológica, com exceção dos fusiníneos, que apareceram como um grupo monofilético e Lamellilatirus lamyi (Peristerniinae) dentro dos fasciolaríneos. Finalmente, 3) inserir as espécies analisadas na análise morfológica, na matriz de dados de Simone (2011). Esta última análise resultou um uma superfamília Buccinoidea monofilética, a família Fasciolariidae sendo monofilético apesar de com uma topologia com pouca resolução interna para os táxons internos; Dolicholatirus e Teralatirus estão incluídos na família e os fusiníneos mais o gênero Pseudolatirus como um grupo monofilético.

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Книги з теми "Phylogenetic analysis"

M, Miyamoto Michael, and Cracraft Joel, eds. Phylogenetic analysis of DNA sequences. New York: Oxford University Press, 1991.

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

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1968-, Salemi Marco, Vandamme Anne-Mieke 1960-, and Lemey Philippe, eds. The phylogenetic handbook: A practical approach to phylogenetic analysis and hypothesis testing. 2nd ed. Cambridge, UK: Cambridge University Press, 2009.

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

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Burns-Balogh, Pamela. A phylogenetic analysis of the Orchidaceae. City of Washington: Smithsonian Institution Press, 1986.

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Scotland, Robert W. Homology and systematics: Coding characters for phylogenetic analysis. London: Taylor & Francis, 2000.

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E, MacPhee R. D., ed. Primates and their relatives in phylogenetic perspective. New York: Plenum Press, 1993.

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Coates, Kathryn. Phylogenetic analysis of some Enchytraeidae (Annelida: Oligochaeta): Parsimony analysis of structural characters. [Victoria, B.C.]: The author, 1987.

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O, Wiley E., and University of Kansas. Museum of Natural History., eds. The Compleat cladist: A primer of phylogenetic procedures. Lawrence, Kan: Museum of Natural History, University of Kansas, 1991.

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Частини книг з теми "Phylogenetic analysis"

Brinkman, Fiona S. L., and Detlef D. Leipe. "Phylogenetic Analysis." In Methods of Biochemical Analysis, 323–58. New York, USA: John Wiley & Sons, Inc., 2002. http://dx.doi.org/10.1002/0471223921.ch14.

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Hershkovitz, Mark A., and Detlef D. Leipe. "Phylogenetic Analysis." In Methods of Biochemical Analysis, 189–230. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2006. http://dx.doi.org/10.1002/9780470110607.ch9.

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Gupta, Manoj Kumar, Gayatri Gouda, S. Sabarinathan, Ravindra Donde, N. Rajesh, Pallabi Pati, Sushil Kumar Rathore, Lambodar Behera, and Ramakrishna Vadde. "Phylogenetic Analysis." In Bioinformatics in Rice Research, 179–207. Singapore: Springer Singapore, 2021. http://dx.doi.org/10.1007/978-981-16-3993-7_9.

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Akhøj, Morten, Xavier Pennec, and Stefan Sommer. "Tangent Phylogenetic PCA." In Image Analysis, 77–90. Cham: Springer Nature Switzerland, 2023. http://dx.doi.org/10.1007/978-3-031-31438-4_6.

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Subbotin, Sergei A. "Phylogenetic analysis of DNA sequence data." In Techniques for work with plant and soil nematodes, 265–82. Wallingford: CABI, 2021. http://dx.doi.org/10.1079/9781786391759.0265.

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Abstract The goal of phylogenetics is to construct relationships that are true representations of the evolutionary history of a group of organisms or genes. The history inferred from phylogenetic analysis is usually depicted as branching in tree-like diagrams or networks. In nematology, phylogenetic studies have been applied to resolve a wide range of questions dealing with improving classifications and testing evolution processes, such as co-evolution, biogeography and many others. There are several main steps involved in a phylogenetic study: (i) selection of ingroup and outgroup taxa for a study; (ii) selection of one or several gene fragments for a study; (iii) sample collection, obtaining PCR products and sequencing of gene fragments; (iv) visualization, editing raw sequence data and sequence assembling; (v) search for sequence similarity in a public database; (vi) making and editing multiple alignment of sequences; (vii) selecting appropriate DNA model for a dataset; (viii) phylogenetic reconstruction using minimum evolution, maximum parsimony, maximum likelihood and Bayesian inference; (ix) visualization of tree files and preparation of tree for a publication; and (x) sequence submission to a public database. Molecular phylogenetic study requires particularly careful planning because it is usually relatively expensive in terms of the cost in reagents and time.

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Lamprecht, Anna-Lena. "Phylogenetic Analysis Workflows." In Lecture Notes in Computer Science, 65–88. Berlin, Heidelberg: Springer Berlin Heidelberg, 2013. http://dx.doi.org/10.1007/978-3-642-45389-2_3.

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Thioulouse, Jean, Stéphane Dray, Anne-Béatrice Dufour, Aurélie Siberchicot, Thibaut Jombart, and Sandrine Pavoine. "Analysing Phylogenetic Structures." In Multivariate Analysis of Ecological Data with ade4, 261–80. New York, NY: Springer New York, 2018. http://dx.doi.org/10.1007/978-1-4939-8850-1_13.

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Paradis, Emmanuel. "Phylogenetic Data in R." In Analysis of Phylogenetics and Evolution with R, 29–80. New York, NY: Springer New York, 2011. http://dx.doi.org/10.1007/978-1-4614-1743-9_3.

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Moret, Bernard M. E. "Phylogenetic Analysis of Whole Genomes." In Bioinformatics Research and Applications, 4–7. Berlin, Heidelberg: Springer Berlin Heidelberg, 2011. http://dx.doi.org/10.1007/978-3-642-21260-4_3.

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Тези доповідей конференцій з теми "Phylogenetic analysis"

Berry, Vincent, and David Bryant. "Faster reliable phylogenetic analysis." In the third annual international conference. New York, New York, USA: ACM Press, 1999. http://dx.doi.org/10.1145/299432.299457.

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Blackburn, Michael B. "Phylogenetic analysis of insecticidalChromobacterium." In 2016 International Congress of Entomology. Entomological Society of America, 2016. http://dx.doi.org/10.1603/ice.2016.112826.

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Halgaswaththa, Thilini, Ajantha S. Atukorale, Mahen Jayawardena, and Jagathpriya Weerasena. "Neural network based phylogenetic analysis." In 2012 International Conference on Biomedical Engineering (ICoBE). IEEE, 2012. http://dx.doi.org/10.1109/icobe.2012.6178974.

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Lameri, Silvia, Paolo Bestagini, and Stefano Tubaro. "Video alignment for phylogenetic analysis." In 2016 24th European Signal Processing Conference (EUSIPCO). IEEE, 2016. http://dx.doi.org/10.1109/eusipco.2016.7760650.

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Lu, Wei, and Mike Hanrahan. "Phylogenetic analysis using Bayesian model." In 2014 Zone 1 Conference of the American Society for Engineering Education (ASEE Zone 1). IEEE, 2014. http://dx.doi.org/10.1109/aseezone1.2014.6820677.

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Das, Bilitcr, and Suat Toroman. "Deep Learning Based Phylogenetic Analysis." In 2020 5th International Conference on Computer Science and Engineering (UBMK). IEEE, 2020. http://dx.doi.org/10.1109/ubmk50275.2020.9219386.

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Jilcott, Steven. "Scalable malware forensics using phylogenetic analysis." In 2015 IEEE International Symposium on Technologies for Homeland Security (HST). IEEE, 2015. http://dx.doi.org/10.1109/ths.2015.7225311.

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MIZUTANI, SAYAKA, MICHIHIRO TANAKA, CRAIG E. WHEELOCK, MINORU KANEHISA, and SUSUMU GOTO. "PHYLOGENETIC ANALYSIS OF LIPID MEDIATOR GPCRs." In Proceedings of the 10th Annual International Workshop on Bioinformatics and Systems Biology (IBSB 2010). IMPERIAL COLLEGE PRESS, 2010. http://dx.doi.org/10.1142/9781848166585_0010.

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Verde, Sebastiano, Simone Milani, and Giancarlo Calvagno. "Phylogenetic Analysis of Multimedia Codec Software." In 2018 26th European Signal Processing Conference (EUSIPCO). IEEE, 2018. http://dx.doi.org/10.23919/eusipco.2018.8553158.

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Verde, Sebastiano, Simone Milani, Paolo Bestagini, and Stefano Tubaro. "Audio phylogenetic analysis using geometric transforms." In 2017 IEEE Workshop on Information Forensics and Security (WIFS). IEEE, 2017. http://dx.doi.org/10.1109/wifs.2017.8267650.

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Звіти організацій з теми "Phylogenetic analysis"

Pace, Norman R. Phylogenetic Analysis of Marine Picoplankton Using rRNA Sequences. Fort Belvoir, VA: Defense Technical Information Center, June 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, February 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, and 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, October 2015. http://dx.doi.org/10.21236/ad1000479.

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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), June 1997. http://dx.doi.org/10.2172/491420.

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Wu, Liyou, T. Y. Yi, Joy Van Nostrand, and 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), May 2010. http://dx.doi.org/10.2172/986917.

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Perk, Shimon, Maricarmen Garcia, Alexander Panshin, Caroline Banet-Noach, Irina Gissin, Mark W. Jackwood, and David Stallknecht. Avian Influenza Virus H9N2: Characterization and Control Strategies. United States Department of Agriculture, June 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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Mizrahi, Itzhak, and Bryan A. White. Uncovering rumen microbiome components shaping feed efficiency in dairy cows. United States Department of Agriculture, January 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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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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Hulata, Gideon, Thomas D. Kocher, and Micha Ron. Elucidating the molecular pathway of sex determination in cultured Tilapias and use of genetic markers for creating monosex populations. United States Department of Agriculture, January 2007. http://dx.doi.org/10.32747/2007.7695855.bard.

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The objectives of this project were to: 1) Identify genetic markers linked to sex-determining genes in various experimental and commercial stocks of O. niloticusand O. aureus, as well as red tilapias; 2) Develop additional markers tightly linked to these sex determiners, and develop practical, non-destructive genetic tests for identifying genotypic sex in young tilapia; A third aim, to map sex modifier loci, was removed during budget negotiations at the start of the project. Background to the topic. A major obstacle to profitable farming of tilapia is the tendency of females to reproduce at a small size during the production cycle, diverting feed and other resources to a large population of small, unmarketable fish. Several approaches for producing all-male fingerlings have been tried, including interspecific hybridization, hormonal masculinization, and the use of YY-supermale broodstock. Each method has disadvantages that could be overcome with a better understanding of the genetic basis of sex determination in tilapia. The lack of sex-linked markers has been a major impediment in research and development of efficient monosex populations for tilapia culture. Major conclusions, solutions, achievements. We identified DNA markers linked to sex determining genes in six closely related species of tilapiine fishes. The mode of sex determination differed among species. In Oreochromis karongaeand Tilapia mariaethe sex-determining locus is on linkage group (LG) 3 and the female is heterogametic (WZ-ZZ system). In O. niloticusand T. zilliithe sex-determining locus is on LG1 and the male is heterogametic (XX-XY system). We have nearly identified the series of BAC clones that completely span the region. A more complex pattern was observed in O. aureus and O. mossambicus, in which markers on both LG1 and LG3 were associated with sex. We found evidence for sex-linked lethal effects on LG1, as well as interactions between loci in the two linkage groups. Comparison of genetic and physical maps demonstrated a broad region of recombination suppression harboring the sex-determining locus on LG3. We also mapped 29 genes that are considered putative regulators of sex determination. Amhand Dmrta2 mapped to separate QTL for sex determination on LG23. The other 27 genes mapped to various linkage groups, but none of them mapped to QTL for sex determination, so they were excluded as candidates for sex determination in these tilapia species. Implications, both scientific and agricultural. Phylogenetic analysis suggests that at least two transitions in the mode of sex determination have occurred in the evolution of tilapia species. This variation makes tilapias an excellent model system for studying the evolution of sex chromosomes in vertebrates. The genetic markers we have identified on LG1 in O. niloticusaccurately diagnose the phenotypic sex and are being used to develop monosex populations of tilapia, and eliminate the tedious steps of progeny testing to verify the genetic sex of broodstock animals.

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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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