Community phylogenetics

After establishing a phylogenetic tree, further analysis can be pursued to determine patterns in diversity within and across communities. Phylogenetic diversity (PD) can be determined with the aid of programs like DOTUR (84), and DIVERSITY (85). DOTUR calculates the Shannon-Weiner index, a calculation of diversity based on how predictable the community is, and the Simpson diversity index, a calculation based on both the number of different samples in a community and their proportions in addition to several richness estimators. DIVERSITY calculates PD a diversity index that summates... 

Yoshida N, N Takahashi, A Hiraishi (2005) Phylogenetic characterization of polychlorinated-dioxin-dechlorinating microbial community by use of microcosm studies. Appl Environ Microbiol 71 4325-4334. 

Rossetti S, LL Blackall, M Majone, P Hugenholtz, JJ Plumb, V Tandoi (2003) Kinetic and phylogenetic characterization of an anaerobic dechlorinating microbial community. Microbiology (UK) 149 459-469. 

L. Marilley and M. Aragno, Phylogenetic diversity of bacterial communities differing in degree of proximity of Lolium perenne and Trifolium repens roots. Applied Soil Ecology 73 127 (1999). 

The function of peptides as first messengers is evolu-tionarily very old. In phylogenetic terms, neuropeptides were established very early as molecules effecting intercellular communication. In coelenterates, such as Hydra, there are many peptides used in neurotransmission, but many of the conventional neurotransmitter systems, such as acetylcholine (ACh), catecholamines and serotonin,... 

Eomeris E, Binda C, Vanoni MA, BattagUoli E, Mattevi A (2005) Human histone demethylase LSDl reads the histone code. J Biol Chem 280 41360-41365 Erye RA (2000) Phylogenetic classification of prokaryotic and eukaryotic Sir2-like proteins. Biochem Biophys Res Commun 273 793—798... 

The universal phylogenetic tree, therefore, is not an organismal tree at its base but gradually becomes one as its peripheral branchings emerge. The Universal Ancestor is not a distinct entity. It is, rather, a diverse community of cells that survives and evolves as... 

Frye, R.A. (2000) Phylogenetic classification of prokaryotic and eukaryotic Sir2-like proteins. Biochemical el Biophysical Research Communications, 273, 793-798. 

Suzuki T, Hashimoto T, Yabu Y, Kido Y, Sakamoto K, Nihei C, Hato M, Suzuki S, Amano Y, Nagai K, Hosokawa T, Minagawa N, Ohta N, Kita (2004) Direct evidence for cyanide-insensitive quinol oxidase (alternative oxidase) in the apicomplexan parasite Cryptosporidium parvum phylogenetic and therapeutic implications. Biochem Biophys Res Commun 313 1044-1052... 

Crump B. C., E. V. Armbrust, and J. A. Baross. 1999. Phylogenetic analysis of particle-attached and free-living bacterial communities in the Columbia River, its estuary, and the adjacent coastal ocean. Applied and Environmental Microbiology 65 3192-3204. 

Fuhrman, J. A., K. McCallum, and A. A. Davis. 1993. Phylogenetic diversity of subsurface marine microbial communities from the Atlantic and Pacific Oceans. Applied and Environmental Microbiology 59 1294-1302. 

Boutros PC, Moffat ID, Franc MA, Tijet N, Tuomisto J, Pohjanvirta R, Okey AB. Dioxin-responsive AHRE-II gene battery identification by phylogenetic footprinting. Biochem Biophys Res Commun 2004 321 707-715. 

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