Phylogeny molecular

Galtier, N., Gouy, M., and Gautier, C. (1996). SEAVIEW and PHYLO WIN two graphic tools for sequence alignment and molecular phylogeny. Comp. Appl. Biosci. 12, 543-548. 

Li, W.-H., and Gouy, M. (1990). Statistical tests of molecular phylogenies. In Molecular Evolution Computer Analysis of Protein and Nucleic Acid Sequences. (Doolittle, R. F., ed.) Methods Enzymol. 183, 645-659. 

Molecular phylogeny is a discipline that studies species differences between DNA or protein sequences. Its basic tenet is that during evolution, the sequences have drifted apart by mutation and selection as well as by random drift and fixation of variants in certain positions. The earlier two species separated the more differences became fixed. Phylogenetic trees are constructed on the basis of mutual differences of protein and/or DNA sequence. Comparison of intraspecies variation with between-species variation may in the future yield information on the neutralist/selectionist alternative. McDonald and Kreitman (1991) devised an interesting test against neutrality that compared the ratio of silent/replacement mutation of a given locus within a species with the same ratio between two related species. Under the neutral theory this should be equal (corrected for sample size), but in fact it is not (see Li, 1997, and Hudson, 1993, for a discussion). 

Wink, M. and Mohamed, G. 1. A. 2003. Evolution of chemical defense traits in the Leguminosae Mapping of distribution patterns of secondary metabolities on a molecular phylogeny inferred from nucleotide sequences of the rbcL gene. Biochemical Systematics and Ecology, 31 8 897-917. 

Yamazaki, M Saito, A., Saito, K. and Murakoshi, I. 1993. Molecular phylogeny based on RFLP and its relation with alkaloid patterns in Lupinus plants. Biology and Pharmacology Bulletin, 16 1182-1184. 

Wink M, Waterman P. Chemotaxonomy in relation to molecular phylogeny of plants. In Wink, M. (ed.), Biochemistry of plant secondary metabolism. Annual Plant Reviews. Boca Raton Sheffield Academic Press and CRC Press. 1999 300-341. 

Molecular phylogeny and floral fragrances of male euglossine bee-pollinated orchids a study of Stanhopea (Orchidaceae). Plant Species Biology 14 ... 

Sapp J (2007) Mitochondria and their host Morphology to molecular phylogeny. In Martin W, Muller M (eds) Origin of Mitochondria and Hydrogenosomes. Springer, Berlin Heidelberg New York, pp 57-84... 

Paquin B, Forget L, Roewer I, Lang BF (1995) Molecular phylogeny of Allomyces macrog-ynus—congruency between nuclear ribosomal RNA and mitochondrial protein-based trees. J Mol Evol 41 657-665... 

Cavalier-Smith T, Chao EEY, Oates (2004) Molecular phylogeny of Amoebozoa and the evolutionary significance of the unikont Phalansterium. Eur J Protistol 40 21-48 Chavez LA, Balamuth W, Gong T (1986) A light and electron-microscopic study of a new, polymorphic free-living amoeba, Phreatamoeba balamuthi n. g., n. sp. J Euk Microbiol 33 397-404... 

Rokas, A., Williams, B.L., King, N., Carroll, S.B. (2003) Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 425, 798-804. 

Baguna, J. and Riutort, M. (2004) Molecular phylogeny of the Platyhelminthes. Canadian Journal of Zoology 82, 168-193. 

Simkova, A., Morand, S., Jobet, E., Gelnar, M. and Verneau, O. (2004) Molecular phylogeny of congeneric monogenean parasites (Dactylogyrus) a case of intrahost speciation. Evolution 58, 1001 -1 01 8. 

Barker, S.C. and Blair, D. (1996) Molecular phylogeny of Schistosoma species supports traditional groupings within the genus. Parasitology 82, 292-298. 

Bell, A.S., Sommerville, C. and Valtonen, E.T. (2001) A molecular phylogeny of the genus Ichthyocotylurus (Digenea, Strigeidae). InternationalJournal for Parasitology 31, 833-842. 

Donald, K.M., Kennedy, M., Poulin, R. and Spencer, H.G. (2004) Host specificity and molecular phylogeny of larval Digenea isolated from New Zealand and Australian topshells (Gastropoda Trochidae). International Journal for Parasitology 34, 557-568. 

Jousson, O., Bartoli, P. and Pawlowski, J. (1998) Molecular phylogeny of Mesometridae (Trematoda, Digenea) with its relation to morphological changes in parasites. Parasite 5, 365. 

Plaisance, L., Littlewood, D.T.J., Olson, P.D. and Morand, S. (2005) Molecular phylogeny of gill monogeneans (platyhelminthes, Monogenea, Dactylogyridae) and colonization of Indo-west Pacific butterfly fish hosts (Perciformes, Chaetodontidae). Zoologica scripta 34, 425-436. 

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