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Journal articles on the topic 'Phylogeny'

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Published: 4 June 2021
Last updated: 29 July 2024

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1

McKinney, Michael L. "Extinction in Phylogeny, or Phylogeny in Extinction?" Ecology 74, no. 6 (September 1993): 1906–7. http://dx.doi.org/10.2307/1939951.

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2

SMITH, A. B. "Fossils in Phylogeny: Phylogeny Reconstruction in Paleontology." Science 235, no. 4789 (February 6, 1987): 696. http://dx.doi.org/10.1126/science.235.4789.696.

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3

SAARMA, U., I. JÕGISALU, E. MOKS, A. VARCASIA, A. LAVIKAINEN, A. OKSANEN, S. SIMSEK, et al. "A novel phylogeny for the genus Echinococcus, based on nuclear data, challenges relationships based on mitochondrial evidence." Parasitology 136, no. 3 (January 21, 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 phylogeny for Echinococcus from that proposed on the basis of mitochondrial DNA sequence data, but was in agreement with earlier species classifications. The most notable results from the nuclear phylogeny were (1) E. multilocularis was placed as basal taxon, (2) all genotypes of Echinococcus granulosus grouped as a monophyletic entity, and (3) genotypes G8 and G10 clustered together. We conclude that the analysis of nuclear DNA data provides a more reliable means of inferring phylogenetic relationships within Echinococcus than mtDNA and suggest that mtDNA should not be used as the sole source of markers in future studies where the goal is to reconstruct a phylogeny that does not only reflect a maternal lineage, but aims to describe the evolutionary history at species level or higher.
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4

Hubu, Herlin S., Stenly Wullur, Veibe Warouw, Elvy L. Ginting, Robert A. Bara, and Adnan S. Wantasen. "FILOGENI MOLEKULER BAKTERI DARI MEDIA PEMELIHARAAN ROTIFER YANG DIBERI OLAHAN LIMBAH IKAN SEBAGAI SUMBER NUTRISI." JURNAL PESISIR DAN LAUT TROPIS 9, no. 1 (March 29, 2021): 38. http://dx.doi.org/10.35800/jplt.9.1.2021.33574.

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This study aims to identify and construct molecular phylogeny of an isolate bacteria from culture media of rotifer Brachionus rotudiforis supplied with processed fishery waste feed as nutritional source. The use of fish waste-based food for rotifer showed positive effects on growth and nutrient content of the rotifers. Genomic DNA of the isolate bacteria BRLI- 01 was extracted and the 16S rRNA gene was amplified using primers (8F and 1492F) and further sequenced using Sanger sequence technique. The 16S rRNA gene was analysed using SeqScanner® and MEGA® followed with BLAST (Basic Local Alignment Search Tool) analyses in the NCBI (National Centre for Biotechnology Information). Amplification result of 16S rRNA gene bacteria s NCBI site as a reference for identification and phylogeny of bacterial species. BRLI-01 was successfully cultured on rotifer rearing media. The results of the 16S rRNA gene amplification of the isolate bacteria showed a DNA band with a length of 1400 bp. The BLAST result on the NCBI showed that the isolate bacteria BRLI-01 had a percent identity (98.46%) and is in the same phylogony branching position with Vibrio rotiferianus Keywords: Rotifers, Bacteria, Fish waste, 16S rRNA Genes, Phylogeny identification
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5

López, J. Andrés, Wei-Jen Chen, and Guillermo Ortí. "Esociform Phylogeny." Copeia 2004, no. 3 (August 2004): 449–64. http://dx.doi.org/10.1643/cg-03-087r1.

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6

Burgess, George H., and Shigeru Shirai. "Squalean Phylogeny." Copeia 1993, no. 4 (December 28, 1993): 1203. http://dx.doi.org/10.2307/1447121.

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7

Rougler, Guillermo W., John R. Wible, and Michael J. Novacek. "Multituberculate phylogeny." Nature 379, no. 6564 (February 1996): 406. http://dx.doi.org/10.1038/379406a0.

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8

Sereno, Paul C., and Malcolm C. McKenna. "Multituberculate phylogeny." Nature 379, no. 6564 (February 1996): 406–7. http://dx.doi.org/10.1038/379406b0.

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9

Meng, Jin, and Andre R. Wyss. "Multituberculate phylogeny." Nature 379, no. 6564 (February 1996): 407. http://dx.doi.org/10.1038/379407a0.

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10

Telles, Guilherme P., Nalvo F. Almeida, Rosane Minghim, and Maria Emilia M. T. Walter. "Live Phylogeny." Journal of Computational Biology 20, no. 1 (January 2013): 30–37. http://dx.doi.org/10.1089/cmb.2012.0219.

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11

TILLIER, SIMON, and M. G. HARASEWYCH. "MOLLUSCAN PHYLOGENY." Journal of Molluscan Studies 63, no. 3 (August 1997): 299. http://dx.doi.org/10.1093/mollus/63.3.299.

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12

Morris, S. C., B. L. Cohen, A. B. Gawthrop, T. Cavalier-Smith, B. Winnepenninckx;, K. M. Halanych, J. D. Bacheller, et al. "Lophophorate Phylogeny." Science 272, no. 5259 (April 12, 1996): 282–83. http://dx.doi.org/10.1126/science.272.5259.282.

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13

Cottrell, Chris. "Phylogeny: Kitset." Ubiquity: The Journal of Pervasive Media 1, no. 1 (September 6, 2012): 129–32. http://dx.doi.org/10.1386/ubiq.1.1.129_7.

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14

Dodds, Hamer. "Phylogeny introduction." Ubiquity: The Journal of Pervasive Media 1, no. 1 (September 6, 2012): 94–103. http://dx.doi.org/10.1386/ubiq.1.1.94_7.

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15

Roberts, Fred S., and Li Sheng. "Phylogeny numbers." Discrete Applied Mathematics 87, no. 1-3 (October 1998): 213–28. http://dx.doi.org/10.1016/s0166-218x(98)00058-4.

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16

Schram, Frederick R. "Crustacean Phylogeny." Short Courses in Paleontology 3 (1990): 285–302. http://dx.doi.org/10.1017/s2475263000001835.

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Crustacean phylogeny, long the focus of intense speculation, has undergone a renaissance in the last decade. This has been largely propelled by the use of cladistic analyses on the part of several workers, though there are still many who prefer more subjective, evolutionary systematic approaches.
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17

Sidow, Arend, and Barbara H. Bowman. "Molecular phylogeny." Current Opinion in Genetics & Development 1, no. 4 (December 1991): 451–56. http://dx.doi.org/10.1016/s0959-437x(05)80191-1.

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18

Sidow, Arend, and Barbara H. Bowman. "Molecular phylogeny." Current Biology 2, no. 1 (January 1992): 33. http://dx.doi.org/10.1016/0960-9822(92)90422-7.

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19

Telford, Maximilian J. "Animal phylogeny." Current Biology 16, no. 23 (December 2006): R981—R985. http://dx.doi.org/10.1016/j.cub.2006.10.048.

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20

Chu, P. "A Phylogeny." Cladistics 14, no. 1 (March 1998): 1–43. http://dx.doi.org/10.1006/clad.1997.0051.

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21

Cachel, Susan. "Phylogeny triumphant." American Journal of Primatology 38, no. 4 (1996): 365–68. http://dx.doi.org/10.1002/(sici)1098-2345(1996)38:4<365::aid-ajp8>3.0.co;2-x.

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22

Jing, Gongchao, Yufeng Zhang, Ming Yang, Lu Liu, Jian Xu, and Xiaoquan Su. "Dynamic Meta-Storms enables comprehensive taxonomic and phylogenetic comparison of shotgun metagenomes at the species level." Bioinformatics 36, no. 7 (December 3, 2019): 2308–10. http://dx.doi.org/10.1093/bioinformatics/btz910.

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Abstract Motivation An accurate and reliable distance (or dissimilarity) among shotgun metagenomes is fundamental to deducing the beta-diversity of microbiomes. To compute the distance at the species level, current methods either ignore the evolutionary relationship among species or fail to account for unclassified organisms that cannot be mapped to definite tip nodes in the phylogenic tree, thus can produce erroneous beta-diversity pattern. Results To solve these problems, we propose the Dynamic Meta-Storms (DMS) algorithm to enable the comprehensive comparison of metagenomes on the species level with both taxonomy and phylogeny profiles. It compares the identified species of metagenomes with phylogeny, and then dynamically places the unclassified species to the virtual nodes of the phylogeny tree via their higher-level taxonomy information. Its high speed and low memory consumption enable pairwise comparison of 100 000 metagenomes (synthesized from 3688 bacteria) within 6.4 h on a single computing node. Availability and implementation An optimized implementation of DMS is available on GitHub (https://github.com/qibebt-bioinfo/dynamic-meta-storms) under a GNU GPL license. It takes the species-level profiles of metagenomes as input, and generates their pairwise distance matrix. The bacterial species-level phylogeny tree and taxonomy information of MetaPhlAn2 have been integrated into this implementation, while customized tree and taxonomy are also supported. Supplementary information Supplementary data are available at Bioinformatics online.
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23

Mazza, Paul, and Marco Rustioni. "On the phylogeny of Eurasian Bears." Palaeontographica Abteilung A 230, no. 1-3 (January 31, 1994): 1–38. http://dx.doi.org/10.1127/pala/230/1994/1.

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24

Michu, E. "A short guide to phylogeny reconstruction." Plant, Soil and Environment 53, No. 10 (January 7, 2008): 442–46. http://dx.doi.org/10.17221/2194-pse.

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This review is a short introduction to phylogenetic analysis. Phylogenetic analysis allows comprehensive understanding of the origin and evolution of species. Generally, it is possible to construct the phylogenetic trees according to different features and characters (e.g. morphological and anatomical characters, RAPD patterns, FISH patterns, sequences of DNA/RNA and amino acid sequences). The DNA sequences are preferable for phylogenetic analyses of closely related species. On the other hand, the amino acid sequences are used for phylogenetic analyses of more distant relationships. The sequences can be analysed using many computer programs. The methods most often used for phylogenetic analyses are neighbor-joining (NJ), maximum parsimony (MP), maximum likelihood (ML) and Bayesian inference.
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25

Kovtun, M. F., and H. V. Sheverdyukova. "Ontogeny And Phylogeny. To The Problem Of The Relation Of Individual And Historical Development In Organisms." Vestnik Zoologii 49, no. 4 (August 1, 2015): 291–98. http://dx.doi.org/10.1515/vzoo-2015-0030.

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Abstract The theory of filembriogenesis is only an introduction to the problem’s development of ontogeny’ and phylogeny’ relation (hereinafter — «relation»). Discussions as to whether ontogeny creates phylogeny, or vice versa, are devoid of meaning. The opinion of O. Hertwig (Hertwig, 1906) that the ontogeny and phylogeny are two parallel and independent developmental processes is valid only in the first part; thesis about independence distorts the essence of «relation.» According to the authors, one of the essential characteristics of the «relation» is that ontogeny gives the material for phylogeny, and phylogeny renews ontogeny, leading away ontogeny from inbreeding; that ontogeny ensures the life continuity and phylogeny — its differentiation, that is, creates biodiversity; that ontogeny and phylogeny can exist and function only in conjunction or in parallel, changing places (in terms of priority) in the life evolution.
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26

Lauder, George V., R. E. Foreman, A. Gorbman, J. M. Dodd, and R. Olsson. "Phylogeny and Physiology." Evolution 42, no. 5 (September 1988): 1113. http://dx.doi.org/10.2307/2408930.

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27

Poe, Steven. "PHYLOGENY OF ANOLES." Herpetological Monographs 18, no. 1 (2004): 37. http://dx.doi.org/10.1655/0733-1347(2004)018[0037:poa]2.0.co;2.

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28

CABANAC, Michel. "Emotion and Phylogeny." Japanese Journal of Physiology 49, no. 1 (1999): 1–10. http://dx.doi.org/10.2170/jjphysiol.49.1.

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29

Refulio-Rodriguez, Nancy F., and Richard G. Olmstead. "Phylogeny of Lamiidae." American Journal of Botany 101, no. 2 (February 2014): 287–99. http://dx.doi.org/10.3732/ajb.1300394.

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30

Foos, K. Michael, Nicole L. May, Dale L. Beach, Markus Pomper, Kathy B. Sheehan, and Donald G. Ruch. "Phylogeny of Pilobolaceae." Mycologia 103, no. 1 (January 2011): 36–44. http://dx.doi.org/10.3852/09-314.

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31

Bernardet, Jean-François. "Comment: Phylogeny ofFlavobacteriumandFlexibacter." Journal of Aquatic Animal Health 13, no. 1 (March 2001): 69–71. http://dx.doi.org/10.1577/1548-8667(2001)013<0069:cpofaf>2.0.co;2.

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32

Krajewski, Carey. "Phylogeny and Diversity." Science 254, no. 5034 (November 15, 1991): 918. http://dx.doi.org/10.1126/science.254.5034.918.b.

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33

Krajewski, Carey. "Phylogeny and Diversity." Science 254, no. 5034 (November 15, 1991): 918. http://dx.doi.org/10.1126/science.254.5034.918-b.

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34

Baxter, William H. "Mandarin dialect phylogeny." Cahiers de Linguistique Asie Orientale 35, no. 1 (February 27, 2006): 71–114. http://dx.doi.org/10.1163/19606028-03501005.

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This paper investigates the phylogenetic relationships (the relationships of shared ancestry) of ten Chinese dialects: eight generally classified as Mandarin, and two others (Chángshā 長沙 and Hángzhōu 杭州). Using six of the Mandarin dialects, a ‘Proto-Macro-Mandarin’ (PMM) phonological system is reconstructed, from which the other four dialects also appear to be derivable. Taking 29 phonological innovations as a basis, the phylogeny of the ten dialects is estimated using a technique borrowed from biology (Camin-Sokal parsimony). The results suggest that a classification of Chinese dialects based on phylogeny could be rather different from the generally accepted classification.
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35

Palosaari, Jedidiah J. "Ontogeny vs. Phylogeny." Science News 156, no. 4 (July 24, 1999): 51. http://dx.doi.org/10.2307/4011639.

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36

LIVEZEY and ZUSI. "PHYLOGENY OF NEORNITHES." Bulletin of Carnegie Museum of Natural History 37 (June 2006): 1–544. http://dx.doi.org/10.2992/0145-9058(2006)37[1:pon]2.0.co;2.

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37

Baxter, William H. "Mandarin dialect phylogeny." Cahiers de linguistique - Asie orientale 35, no. 1 (2006): 71–114. http://dx.doi.org/10.3406/clao.2006.1748.

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38

Coulardeau, Jacques. "Phylogeny Commands Psychogenesis." Studia Universitatis Babeș-Bolyai Philologia 64, no. 4 (December 15, 2019): 37–58. http://dx.doi.org/10.24193/subbphilo.2019.4.02.

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39

Faith, Daniel P. "Phylogeny and Conservation." Systematic Biology 56, no. 4 (August 1, 2007): 690–94. http://dx.doi.org/10.1080/10635150701475563.

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40

Labiak, Paulo H., and Robbin C. Moran. "Phylogeny ofCampyloneurum(Polypodiaceae)." International Journal of Plant Sciences 179, no. 1 (January 2018): 36–49. http://dx.doi.org/10.1086/694764.

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41

Goldmann, Wilfred, Nora Hunter, Robert Somerville, and James Hope. "Prion phylogeny revisited." Nature 382, no. 6586 (July 1996): 32–33. http://dx.doi.org/10.1038/382032b0.

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42

Vasey, Paul L. "Function and Phylogeny." Journal of Psychology & Human Sexuality 18, no. 2-3 (January 2007): 215–44. http://dx.doi.org/10.1300/j056v18n02_07.

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43

Jeltsch, A. "Phylogeny of Methylomes." Science 328, no. 5980 (May 13, 2010): 837–38. http://dx.doi.org/10.1126/science.1190738.

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44

Wilkinson, Mark, Paul Upchurch, Paul M. Barrett, David J. Gower, and Michael J. Benton. "Robust dinosaur phylogeny?" Nature 396, no. 6710 (December 1998): 423–24. http://dx.doi.org/10.1038/24763.

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45

Van de Peer, Yves. "Phylogeny branches out." Nature 414, no. 6863 (November 2001): 490. http://dx.doi.org/10.1038/35107129.

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46

Bruce Rosenstock. "Phylogeny Recapitulates Ontogeny:." Soundings: An Interdisciplinary Journal 96, no. 1 (2013): 25. http://dx.doi.org/10.5325/soundings.96.1.0025.

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47

Halanych, K. M., J. D. Bacheller, A. M. A. Aguinaldo, S. M. Liva, D. M. Hillis, and J. A. Lake. "Response: Lophophorate Phylogeny." Science 272, no. 5259 (April 12, 1996): 283. http://dx.doi.org/10.1126/science.272.5259.283.

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48

Dolgin, Elie. "Phylogeny: Rewriting evolution." Nature 486, no. 7404 (June 2012): 460–62. http://dx.doi.org/10.1038/486460a.

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49

Lauder, George V. "PHYLOGENY AND PHYSIOLOGY." Evolution 42, no. 5 (September 1988): 1113–14. http://dx.doi.org/10.1111/j.1558-5646.1988.tb02533.x.

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50

Legg, David A., Xiaoya Ma, Joanna M. Wolfe, Javier Ortega-Hernández, Gregory D. Edgecombe, and Mark D. Sutton. "Lobopodian phylogeny reanalysed." Nature 476, no. 7359 (August 10, 2011): E1. http://dx.doi.org/10.1038/nature10267.

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