Modern systematics and phylogenetics

Modern systematics and phylogenetics

Microbial Systematics:

This paper focuses on past, present & future of microbial systematic considering different technical & theoretical advancement in the field. Based on molecular & genomics tools, understanding of microbial ecology has been expanded greatly. New prospects of metagenomes astonish taxonomists greatly in the field of microbial systematic. Molecular biology has changed the concept of species & their classification. Conclusively, the articles urges to microbiology, taxonomists, systematists, molecular biologists and all the researchers for the theoretical renaissance on microbial systematic based on advancement of bioinformatics, metagenomics & molecular genetics & focusing on the important of depositing newly described species in culture collection centre for maintaining updated database.

Prokaryotic systematic in the genomics era:

Microbial systematics is the scientific study of the kinds & diversity of microorganisms & of relationships between them. It is a basic scientific discipline that encompasses classification, nomenclature & identification & includes studies on genetics mechanism which underpin evolutionary process & phylogeny. Classification, Nomenclature, & Identification are basic steps of microbial systematic. There are several taxonomic marker used for the basis of identification. Morphology, growth requirements, pathogenic potential, serological traits, physiological characters are conventional techniques used in identification. Study of different chemotaxonomic apparatus, chemical composition of genomic DNA, and DNA-DNA hybridization are the significant approaches in the microbial systematic.

Genomic information, like whole genome sequencing, 16S rRNA sequencing, and  Gene duplication are recent advances in prokaryotic systematics. Prokaryotes have evolved other mechanism for rapid adaptation to newly environmental niches which may leads to speciation. The horizontal gene transfer, chromosomal rearrangement, genomics plasticity, single nucleotides polymorphism, insertion/deletion, may make organism differ from each other.

Prokaryotic speciation can be understood with genomics information. The phylophenetic species concept which is based on these independent approaches DNA-DNA hybridization, phenotype descriptions, & relationship based on the phylogeny of 16S rRNA gene has been considered to be the most universally applicable in the delineation of prokaryotic species.

As a whole, the genomics era has changed the pattern of prokaryotic systematic. The advancement in the techniques challenges systematists to reanalyze the molecular mechanisms underlying the taxonomic characteristics of prokaryotes by drawing the knowledge from studies of genomics & bioinformatics tools.

Molecular Phylogenetics  :

Molecular phylogenetics is the study in which molecular and statistical techniques are combined to infer evolutionary relationship among organisms or genes. Advances in computer tools help molecular phylogenetics to study more effectively. The primary objective of molecular phylogenetics studies is to recover the order of evolutionary events & represent them in evolutionary trees that graphically depict relationships among species or genes overtime.

Darwin’s explain the evolution based on change in traits and molecular techniques explain evolution as a molecular process based on genetics information. This evolutionary mechanism creates basis for the phylogeny which explains all organisms have descended from a common ancestor & the graphical representation of this phylogeny is termed as phylogenetics tree which consists of edge, node & root. Its branches can be grouped into monophyletic, paraphyletic, & polyphyletic group. All members within the group are derived from a common ancestor & have inherited a set of unique common traits is a monophyletic group. A paraphyletic group excludes some of its descendents & a polyphyletic group can be a collection of distantly related operational taxonomic unit (May not directly descendent from a common ancestor. Phylogenetic trees are defined by homologous relationship which can be either paralogs or orthologs. Paralogs are homologous sequences separated by gene duplication event. Orthologs are homologous sequences separated by speciation event.

Phylogenetic tree can be estimated from molecular data which may include biomolecular sequence alignments of DNA, RNA or amino acids. The basic steps in phylogenetic analysis include: assemble & align dataset, building trees from sequences using computational methods & statistically test & assess the estimated tress. Sequence can be align using different software among which ClustalW is widely used. There are several computational methods for building trees after alignment. It includes: Distance Matrix methods & discrete Data methods such as Maximum Parsimony & maximum likelihood. Distance-matrix methods compute pairwise distances between sequences that approximate evolutionary distance. There are several different distance-matrix methods among which Neighbour-Joining method is common. Discrete data methods examine each column of a multiple sequence alignment dataset separately & search for the tree that best represents all this information. Commonly used discrete data methods include Maximum Parsimony & Maximum Likelihood. There are several online phylogenetic tools. These include PANTER, P-Pod PFan, Treefan & the PhyloFacts. Molecular phylogenetics has much diverse application. It can be used to trace the evolution of man, origin of SARS & even required in biological research papers.

In sum up, molecular phylogenetics is a broad, diverse field with many applications, supported by multiple computational & statistical methods. It has become an integral part of biological research, pharmaceutical drug design & bioinformatics techniques.

2016 May11