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Microbial phylogeny

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Microbial Phyllogeny.and Classification. Phyllogenetic Tree , Domain and determining technique.

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Microbial Phylogeny: Classification of species in superior taxa and construction of phylogenetic trees based on evolutionary relationships. It is bringing order to the diverse variety of organisms present in nature. So there are two general ways the classification can be constructed. First one is based on the morphological characters (phenetic classification) and second is based on evolutionary relationship (phylogenetic classification) Phenetic classification It is based on the mutual similarity of their phenotypic characteristics. It does not provide any information about phylogenetic relations. Phylogenetic classification- These systems are based on evolutionary relationships rather than external appearance .The term phylogeny [Greek phylon, tribe or race, and genesis, generation or origin] refers to the evolutionary development of a species. It is based on the direct comparison of genetic materials and gene product.
Phylogenetic tree Phylogenetic relationships are illustrated in the form of branched diagrams or trees. A phylogenetic tree is a graph made of branches that connect nodes. The nodes represent taxonomic units such as species or genes; the external nodes, those at the end of the branches, represent living organisms. The tree may have a time scale, or the length of the branches may represent the number of molecular changes that have taken place between the two nodes. Finally, a tree may be unrooted or rooted. An unrooted tree simply represents phylogenetic relationships but does not provide an evolutionary path. Figure (a) shows that A is more closely related to C than it is to either B or D, but does not specify the common ancestor for the four species or the direction of change. In contrast, the rooted tree Figure (b) does give a node that serves as the common ancestor and shows the development of the four species from this root. Fig. 1 . Phylogenetic tree. a) unrooted tree, b) rooted tree.
Domains Advances in genomic DNA sequencing of the microorganisms, biologists are increasingly adapting the classification of living organisms that recognizes three domains, a taxonomic level higher than kingdom. Archaebacteria are in one domain, eubacteria in a second, and eukaryotes in the third. Domain Eukarya is subdivided into four kingdoms plants, animals, fungi, protists. Fig. 2 Three domains based on rRNA sequence analysis. Domain- Archaebacteria The term archaebacteria (Greek, archaio, ancient) refers to the ancient origin of this group of bacteria, which seem to have diverged very early from the eubacteria. They are inhabited mostly in extreme environments. The archaebacteria are grouped (based primarily on the environments in which they live) into three general categories methanogens, extremophiles and non extreme Archaebacteria.
Domain- Bacteria The Eubacteria are the most abundant organisms on earth. It plays critical roles like cycling carbon and sulfur. Much of the world's photosynthesis is carried out by eubacteria. However, certain groups of eubacteria are also responsible for many forms of disease. Domain- Eukarya It consists of four kingdoms. The first of which is protista, mostly unicellular organism like amoeba. The other three kingdoms are plants, fungi, animals. Multicellularity and sexuality are the two unique characters that differentiate from prokaryote and eukaryotes. Fig. 3 - Universal Phylogenetic Tree PHYLOGENIC RELATIONSHIP DETERMINING TECHNIQUE: A)Parsimony Analysis Phylogenetic relationships also can be estimated by techniques such as parsimony analysis. In this approach, relationships are determined by estimating the minimum number of sequence changes required to give the final sequences being compared. It is presumed that evolutionary change occurs along the shortest pathway with the fewest changes or steps from an ancestor to the organism in question.
B)Molecular chronometers This concept, first suggested by Zuckerkandl and Pauling (1965), which is based on thought that the sequences of many rRNAs and proteins gradually change over time without destroying or severely altering their functions. Changes increases with time linearly. If sequences of similar molecules from two organisms differs, it means that they diverged very long time ago. C)Oligonucleotide signature sequences The 16S rRNA of most major phylogenetic groups has one or more characteristic nucleotide sequences called oligonucleotide signatures. Oligonucleotide signature sequences are specific oligonucleotide sequences that occur in most or all members of a particular phylogenetic group. They are rarely or never present in other groups, even closely related ones. Thus signature sequences can be used to place microorganisms in the proper group. Polyphasic Taxonomy Studying phylogeny based on both genotypic and phenotypic information ranging from molecular characteristics to ecological characters.

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Microbial phylogeny

  • 1. Microbial Phylogeny: Classification of species in superior taxa and construction of phylogenetic trees based on evolutionary relationships. It is bringing order to the diverse variety of organisms present in nature. So there are two general ways the classification can be constructed. First one is based on the morphological characters (phenetic classification) and second is based on evolutionary relationship (phylogenetic classification) Phenetic classification It is based on the mutual similarity of their phenotypic characteristics. It does not provide any information about phylogenetic relations. Phylogenetic classification- These systems are based on evolutionary relationships rather than external appearance .The term phylogeny [Greek phylon, tribe or race, and genesis, generation or origin] refers to the evolutionary development of a species. It is based on the direct comparison of genetic materials and gene product.
  • 2. Phylogenetic tree Phylogenetic relationships are illustrated in the form of branched diagrams or trees. A phylogenetic tree is a graph made of branches that connect nodes. The nodes represent taxonomic units such as species or genes; the external nodes, those at the end of the branches, represent living organisms. The tree may have a time scale, or the length of the branches may represent the number of molecular changes that have taken place between the two nodes. Finally, a tree may be unrooted or rooted. An unrooted tree simply represents phylogenetic relationships but does not provide an evolutionary path. Figure (a) shows that A is more closely related to C than it is to either B or D, but does not specify the common ancestor for the four species or the direction of change. In contrast, the rooted tree Figure (b) does give a node that serves as the common ancestor and shows the development of the four species from this root. Fig. 1 . Phylogenetic tree. a) unrooted tree, b) rooted tree.
  • 3. Domains Advances in genomic DNA sequencing of the microorganisms, biologists are increasingly adapting the classification of living organisms that recognizes three domains, a taxonomic level higher than kingdom. Archaebacteria are in one domain, eubacteria in a second, and eukaryotes in the third. Domain Eukarya is subdivided into four kingdoms plants, animals, fungi, protists. Fig. 2 Three domains based on rRNA sequence analysis. Domain- Archaebacteria The term archaebacteria (Greek, archaio, ancient) refers to the ancient origin of this group of bacteria, which seem to have diverged very early from the eubacteria. They are inhabited mostly in extreme environments. The archaebacteria are grouped (based primarily on the environments in which they live) into three general categories methanogens, extremophiles and non extreme Archaebacteria.
  • 4. Domain- Bacteria The Eubacteria are the most abundant organisms on earth. It plays critical roles like cycling carbon and sulfur. Much of the world's photosynthesis is carried out by eubacteria. However, certain groups of eubacteria are also responsible for many forms of disease. Domain- Eukarya It consists of four kingdoms. The first of which is protista, mostly unicellular organism like amoeba. The other three kingdoms are plants, fungi, animals. Multicellularity and sexuality are the two unique characters that differentiate from prokaryote and eukaryotes. Fig. 3 - Universal Phylogenetic Tree PHYLOGENIC RELATIONSHIP DETERMINING TECHNIQUE: A)Parsimony Analysis Phylogenetic relationships also can be estimated by techniques such as parsimony analysis. In this approach, relationships are determined by estimating the minimum number of sequence changes required to give the final sequences being compared. It is presumed that evolutionary change occurs along the shortest pathway with the fewest changes or steps from an ancestor to the organism in question.
  • 5. B)Molecular chronometers This concept, first suggested by Zuckerkandl and Pauling (1965), which is based on thought that the sequences of many rRNAs and proteins gradually change over time without destroying or severely altering their functions. Changes increases with time linearly. If sequences of similar molecules from two organisms differs, it means that they diverged very long time ago. C)Oligonucleotide signature sequences The 16S rRNA of most major phylogenetic groups has one or more characteristic nucleotide sequences called oligonucleotide signatures. Oligonucleotide signature sequences are specific oligonucleotide sequences that occur in most or all members of a particular phylogenetic group. They are rarely or never present in other groups, even closely related ones. Thus signature sequences can be used to place microorganisms in the proper group. Polyphasic Taxonomy Studying phylogeny based on both genotypic and phenotypic information ranging from molecular characteristics to ecological characters.