Phylogenetically based

Phylogenetically based studies offer the opportunity to reveal additional micro- and macro-evolutionary patterns in the Monogenea, but details on biogeographic ranges, larval development and dispersal, site specificity and phy-logenies of the hosts are needed to complete a broader understanding of their widespread radiation. 

Phylogenetically Based Studies of Microbial Ecosystem Perturbation... 

The following example illustrates how functional occurrence profiles are used in comparative genome analysis. In this example, such a profile is used to examine the presence of a specific pathway (i.e., C02 fixation) in a set of selected organisms, namely in the archaeal class of Methanomicrobium archaea. These organisms can first be selected using IMG s phylogenetic-based Genome Browser as shown in Fig. 3 (i) and then saved in order to focus the analysis context as previously discussed. 

Adachi, J., and Hasegawa, M. (1996). MOLPHY Version 2.3. Programs for Molecular phylogenetics based on maximum likelihood (Tokyo Institute of Statistical Mathematics). 

A phylogenetic base pair was considered correctly predicted if it was identical to a base pair in the structure or if the structure contained a base pair in which one of the two bases was slipped by one nucleotide. That is, given a phylogenetic base pair between nucleotides i and j, then a pair of i—j, (i-1)—j, (i+1)—j, i—(j-1), or i—(j+1) would be counted as a correct base pair. This allows for the common occurrence of helixes that have similar stabilities when slipped by one nucleotide. 

Another method of scoring is to examine whether a phylogenetic base pair occurs in any suboptimal structure. For this database, 98.0% of phylogenetic base pairs are found in at least one suboptimal structure. 

CNG channels are expressed in retinal photoreceptors and olfactory neurons, and play a key role in visual and olfactory signal transduction. In addition, CNG channels are found at low density in some other cell types and tissues such as brain, testis, and kidney. While the function of CNG channels in sensory neurons has been unequivocally demonstrated, the role of these channels in other cell types, where expression has been observed, remains to be established. Based on their phylogenetic relationship, the six CNG channels... 

Histone Deacetylases (HDACs) catalyze the removal of the acetyl groups from lysines (see Fig. 1). Together with the HATs they are responsible for maintaining the level of histone acetylation throughout the genome. The family of HDAC proteins has been divided into four classes based on phylogenetic analysis and sequence comparison. HDACs of the classes I and II share the same Zn2+-based reaction and are evolutionary related. Class IV HDACs also possess a Zn2+-based reaction... 

Figure 1. An unrooted phylogenetic tree of the myosins based on the amino acid sequence comparison of their head domains demonstrating the division of the myosin superfamily into nine classes. The lengths of the branches are proportional to the percent of amino acid sequence divergence and a calibration bar for 5% sequence divergence is shovk n. The different classes of myosins have been numbered using Roman numerals in rough order of their discovery and hypothetical models of the different myosin structures are shown. Question marks indicate either hypothetical or unknown structural features, and only a fraction of the known myosins are shown. (Taken, in modified form, from Cheney et al., 1993).

Fig. 1. (a) Schematic representation of the three types of anoxygenic ([1] and [2]) and oxygenic ([3]) photosynthesis found in plants and bacteria, (b) Phylogenetic tree based on 16S-rRNA sequence comparisons featuring only photo synthetic phyla. 

Fig. 3. Phylogenetic relationship of strain BMEL-2 and related taxa, based on D1/D2 region sequence of the large-subunit rDNA. Bar, 0.01 nucleotide substitution per position.

Matsuura, N., linuma, M. and Tanaka, T. 1994. Phylogenetic analysis in genus Euchresta based on secondary metabolites. Biochem. Syst. Ecol. 22 621-629. 

Nyffeler, R. 2002. Phylogenetic relationships in the cactus family (Cactaceae) based on evidence from tmK/matK and trnL-trnF sequences. Amer. J. Bot. 89 312-326. 

Hibsch-Jetter, C. 2001. Phylogenetic relationships in Chrysosplenium (Saxifragaceae) based on analysis of a combined rbcUmatK sequence data set. Amer. J. Bot. 88 883-893. 

A. Willems, and M. D. Collins, Phylogenetic analysis of rhiz.obia and agrobacteria based on 16S rRNA gene sequences. Int. J. Syst. Bacteriol. 43 305-313 (1993). 

E. F. DeLong, G. S. Wickham, and N. R. Pace, Phylogenetic stains ribosomal RNA-based probes for the identification of single cells. Science 245 1360 (1989). 

Fig. 6.1 Interrelationships of chemoreceptors internal (neurotransmitters) and external chemosignals. Phylogenetic connections for sequences in transmembrane (Fig. 6.2) domains Nos. = bootstrap values from 100 Megaline searches (based on majority consensus tree). Invertebrate — DrOR fruit-fly, CeOR nematode vertebrate — FOR fish, LOR (1 2) lamprey, MOR mouse VR (1 2) vomeronasal (from Dryer and Berghard, 1999).

Fig. 1.1. The phylogenetic structure of the Nematoda revealed by small subunit ribosomal RNA analysis. (A) Neighbour-joining (NJ) analysis of aligned ssu rRNA genes from nematodes. The alignment is based on that of Blaxter etal. (1998), with the addition of sequences from Aleshin etal. (1998), Nadler (1998)...

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