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Journal articles on the topic 'Phylogenetic analysis'

Author: Grafiati

Published: 4 June 2021

Last updated: 6 September 2023

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1

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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2

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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3

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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4

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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5

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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6

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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7

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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8

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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9

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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10

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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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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11

Otsuka, Yasushi, Chiharu Aoki, and Hiroyuki Takaoka. "Phylogenetic analysis of blackflies." Medical Entomology and Zoology 50, Supplement (1999): 69. http://dx.doi.org/10.7601/mez.50.69.

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12

FINK, W. L. "Microcomputers and Phylogenetic Analysis." Science 234, no. 4780 (November 28, 1986): 1135–39. http://dx.doi.org/10.1126/science.234.4780.1135.

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13

Skupski, Marian P., David A. Jackson, and Donald O. Natvig. "Phylogenetic Analysis of HeterothallicNeurosporaSpecies." Fungal Genetics and Biology 21, no. 1 (February 1997): 153–62. http://dx.doi.org/10.1006/fgbi.1997.0966.

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14

J. Muhaidi, Mohammed, Mohammed A. Hamad, and Noor N. Al-hayani. "Molecular and Phylogenetic Analysis of Sheep Pox Virus in Iraq." Journal of Pure and Applied Microbiology 12, no. 4 (December 30, 2018): 1809–14. http://dx.doi.org/10.22207/jpam.12.4.14.

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15

Vinay, Oraon, Prasad Bhupendra, and Singh Kiran. "16S rDNA-RFLP analysis of phylogenetic tree of Rhizobium bacteria." Indian Journal of Applied Research 3, no. 12 (October 1, 2011): 474–76. http://dx.doi.org/10.15373/2249555x/dec2013/145.

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16

G. D.Sharma, G. D. Sharma, *. Dhritiman Chanda, and D. K. Jha D.K. Jha. "16S rDNA Sequence based Phylogenetic Analysis of Some Bacterial Phytoplasma." International Journal of Scientific Research 3, no. 3 (June 1, 2012): 302–4. http://dx.doi.org/10.15373/22778179/march2014/101.

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17

Ho, Ju-shey. "Phylogenetic Analysis of Copepod Orders." Journal of Crustacean Biology 10, no. 3 (August 1990): 528. http://dx.doi.org/10.2307/1548343.

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18

Hillis, David M., J. J. Bull, Mary E. White, Marty R. Badgett, and Ian J. Molineux. "Experimental Approaches to Phylogenetic Analysis." Systematic Biology 42, no. 1 (March 1993): 90. http://dx.doi.org/10.2307/2992559.

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19

Chadha, Tejpreet, and Adão Alexandre Trindade. "Phylogenetic analysis ofpbpgenes in treponemes." Infection Ecology & Epidemiology 3, no. 1 (January 2013): 18636. http://dx.doi.org/10.3402/iee.v3i0.18636.

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20

Hufford, Larry, and William C. Dickison. "A Phylogenetic Analysis of Cunoniaceae." Systematic Botany 17, no. 2 (April 1992): 181. http://dx.doi.org/10.2307/2419516.

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21

Dean, Deborah, and Kim Millman. "Phylogenetic Analysis of Chlamydia trachomatis." Infection and Immunity 67, no. 2 (February 1999): 1009–10. http://dx.doi.org/10.1128/iai.67.2.1009-1010.1999.

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22

Berčič, Rebeka Lucijana, Krisztián Bányai, Daniel Růžek, Enikő Fehér, Marianna Domán, Vlasta Danielová, Tamás Bakonyi, and Norbert Nowotny. "Phylogenetic Analysis of Lednice Orthobunyavirus." Microorganisms 7, no. 10 (October 13, 2019): 447. http://dx.doi.org/10.3390/microorganisms7100447.

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Lednice virus (LEDV) has been detected in Culex modestus mosquitoes in several European countries within the last six decades. In this study, phylogenetic analyses of the complete genome segments confirm that LEDV belongs to the Turlock orthobunyavirus (Orthobunyavirus, Peribunyaviridae) species and is closely related to Umbre, Turlock, and Kedah viruses.

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23

Rajah.R, Nirmal, and Rufus Auxillia. "Phylogenetic Analysis of Neutral Ceramidase." International Journal of Computer Applications 108, no. 7 (December 18, 2014): 18–23. http://dx.doi.org/10.5120/18923-0271.

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24

Furano, Anthony V., and Karen Usdin. "DNA “Fossils” and Phylogenetic Analysis." Journal of Biological Chemistry 270, no. 43 (October 1995): 25301–4. http://dx.doi.org/10.1074/jbc.270.43.25301.

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25

Paster, B. J., F. E. Dewhirst, W. G. Weisburg, L. A. Tordoff, G. J. Fraser, R. B. Hespell, T. B. Stanton, L. Zablen, L. Mandelco, and C. R. Woese. "Phylogenetic analysis of the spirochetes." Journal of Bacteriology 173, no. 19 (1991): 6101–9. http://dx.doi.org/10.1128/jb.173.19.6101-6109.1991.

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26

Xu, Shizhong. "Phylogenetic Analysis Under Reticulate Evolution." Molecular Biology and Evolution 17, no. 6 (June 1, 2000): 897–907. http://dx.doi.org/10.1093/oxfordjournals.molbev.a026370.

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27

Edwards, S. V. "Natural selection and phylogenetic analysis." Proceedings of the National Academy of Sciences 106, no. 22 (May 26, 2009): 8799–800. http://dx.doi.org/10.1073/pnas.0904103106.

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28

Craig, Walter, and Jonathon Stone. "Information and Phylogenetic Systematic Analysis." Information 6, no. 4 (December 8, 2015): 811–32. http://dx.doi.org/10.3390/info6040811.

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29

Mohammed, Suroor Abood. "Molluscum Contagiosum genome: phylogenetic analysis." Diyala Journal For Pure Science 16, no. 4 (October 1, 2020): 59–73. http://dx.doi.org/10.24237/djps.16.04.534b.

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30

Ives, A. R., and H. C. J. Godfray. "Phylogenetic Analysis of Trophic Associations." American Naturalist 168, no. 1 (July 2006): E1—E14. http://dx.doi.org/10.1086/505157.

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31

Shnyreva, A. A., and A. V. Shnyreva. "Phylogenetic analysis of Pleurotus species." Russian Journal of Genetics 51, no. 2 (February 2015): 148–57. http://dx.doi.org/10.1134/s1022795415020131.

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32

Dunn, C. W., X. Luo, and Z. Wu. "Phylogenetic Analysis of Gene Expression." Integrative and Comparative Biology 53, no. 5 (June 7, 2013): 847–56. http://dx.doi.org/10.1093/icb/ict068.

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33

Koenemann, Stefan, Frederick R. Schram, Mario Hönemann, and Thomas M. Iliffe. "Phylogenetic analysis of Remipedia (Crustacea)." Organisms Diversity & Evolution 7, no. 1 (April 12, 2007): 33–51. http://dx.doi.org/10.1016/j.ode.2006.07.001.

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34

Frickey, Tancred, and Andrei N. Lupas. "Phylogenetic analysis of AAA proteins." Journal of Structural Biology 146, no. 1-2 (April 2004): 2–10. http://dx.doi.org/10.1016/j.jsb.2003.11.020.

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35

Reid, S. M., P. R. Davies, and N. J. Knowles. "117. Phylogenetic analysis of vesiviruses." Research in Veterinary Science 74 (2003): 39. http://dx.doi.org/10.1016/s0034-5288(03)90116-0.

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36

LAKE, J. "Phylogenetic analysis and comparative genomics." Trends in Biotechnology 16 (November 1998): 22–23. http://dx.doi.org/10.1016/s0167-7799(98)00132-2.

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37

Jin-Chan, Wang, Qi Wei-Wei, Zhang Long-Xian, Ning Chang-Shen, Jian Fu-Chun, Zhao Jin-Feng, and Wang Ming. "Phylogenetic analysis ofCryptosporidiumisolates in Henan." Chinese Journal of Agricultural Biotechnology 4, no. 3 (December 2007): 247–52. http://dx.doi.org/10.1017/s1479236207001957.

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AbstractThe functional mitochondrial protein alternative oxidase (AOX) gene was used as a marker to analyse the phylogenetic relationship betweenCryptosporidiumisolates. This gene was characterized, and the phylogentic tree was established fromCryptosporidiumisolates and compared to those generated from 18S rRNA and heat-shock protein 70 (HSP70) gene sequences. The present trial aimed at finding out whether the AOX gene is suitable for phylogenetic analysis of theCryptosporidiumgenus. The results revealed that the genusCryptosporidiumcontained the phylogenetically distinct speciesC. parvum,C. hominis,C. suisandC. baileyi, which were consistent with the biological characterization and host specificity reported earlier.Cryptosporidiumspecies formed two clades: one includedC. hominis,C. suis,C. parvumcattle genotypes andC. parvummouse genotype; and the other comprisedC. meleagridisandC. baileyiisolates. WithinC. parvum, both the mouse genotype and the pig genotype I (also known asC. suis) isolates differed from cattle and human (also known asC. hominis) genotypes, based on the aligned nucleotide sequences. The sequence identity of the AOX gene was higher betweenC. meleagridisandC. baileyithan betweenC. meleagridisandC. parvum. The phylogenetic trees showed thatC. meleagridiswas closer toC. baileyithan toC. parvum. This result was inconsistent with the phylogenetic analysis deduced from 18S rRNA and HSP70 gene sequences, respectively. The present results suggest that the AOX gene is not only equally suitable for the phylogenetic analysis ofCryptosporidium, but also provides an outstanding and new approach in determiningCryptosporidiumheredity.

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38

Liang, Dongmei, and Jianjun Qiao. "Phylogenetic Analysis of Antibiotic Glycosyltransferases." Journal of Molecular Evolution 64, no. 3 (February 26, 2007): 342–53. http://dx.doi.org/10.1007/s00239-006-0110-2.

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39

Forst, Christian V., and Klaus Schulten. "Phylogenetic Analysis of Metabolic Pathways." Journal of Molecular Evolution 52, no. 6 (June 2001): 471–89. http://dx.doi.org/10.1007/s002390010178.

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40

Stein, William E. "Phylogenetic analysis and fossil plants." Review of Palaeobotany and Palynology 50, no. 1-2 (February 1987): 31–61. http://dx.doi.org/10.1016/0034-6667(87)90039-x.

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41

William, J., and O. Ballard. "Combining data in phylogenetic analysis." Trends in Ecology & Evolution 11, no. 8 (August 1996): 334. http://dx.doi.org/10.1016/0169-5347(96)81133-5.

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42

Ramirez-Flandes, S., and O. Ulloa. "Bosque: integrated phylogenetic analysis software." Bioinformatics 24, no. 21 (September 1, 2008): 2539–41. http://dx.doi.org/10.1093/bioinformatics/btn466.

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43

Chappill, Jennifer A. "QUANTITATIVE CHARACTERS IN PHYLOGENETIC ANALYSIS." Cladistics 5, no. 3 (September 1989): 217–34. http://dx.doi.org/10.1111/j.1096-0031.1989.tb00487.x.

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44

Schuchert, P. "Phylogenetic analysis of the Cnidaria." Journal of Zoological Systematics and Evolutionary Research 31, no. 3 (April 27, 2009): 161–73. http://dx.doi.org/10.1111/j.1439-0469.1993.tb00187.x.

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45

Otsuka, Yasushi, Chiharu Aoki, and Hiroyuki Takaoka. "Phylogenetic analysis of blackflies (Simulium)." Medical Entomology and Zoology 49, Supplement (1998): 32. http://dx.doi.org/10.7601/mez.49.32_1.

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46

Prasanna, Arun N., and Sarika Mehra. "Comprehensive Phylogenetic Analysis of Mycobacteria." IFAC Proceedings Volumes 46, no. 31 (2013): 101–6. http://dx.doi.org/10.3182/20131216-3-in-2044.00050.

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47

乔, 战龙. "Phylogenetic Analysis of Rab3A Gene." Bioprocess 08, no. 01 (2018): 1–10. http://dx.doi.org/10.12677/bp.2018.81001.

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48

Behjati, Mohaddeseh, Ibrahim Torktaz, and Amin Rostami. "Phylogenetic analysis of otospiralin protein." Advanced Biomedical Research 5, no. 1 (2016): 41. http://dx.doi.org/10.4103/2277-9175.178787.

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49

Hillis, D. M., J. J. Bull, M. E. White, M. R. Badgett, and I. J. Molineux. "Experimental Approaches to Phylogenetic Analysis." Systematic Biology 42, no. 1 (March 1, 1993): 90–92. http://dx.doi.org/10.1093/sysbio/42.1.90.

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50

Gubser, Caroline, Stéphane Hué, Paul Kellam, and Geoffrey L. Smith. "Poxvirus genomes: a phylogenetic analysis." Journal of General Virology 85, no. 1 (January 1, 2004): 105–17. http://dx.doi.org/10.1099/vir.0.19565-0.

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