Phylogenetic and Phylogenomic Analysis

BioCodeKb - Bioinformatics Knowledgebase

Phylogenomics is the intersection of the fields of evolution and genomics. The term has been used in multiple ways to refer to analysis that involves genome data and evolutionary reconstructions. It is a group of techniques within the larger fields of phylogenetics and genomics.

Phylogenetic analysis is the study of evolutionary development of a species or a group of organisms or a particular characteristic of an organism. In phylogenetic analysis, branching diagrams are made to represent the evolutionary history or relationship between different species, organisms, or characteristics of an organism (genes, proteins, organs, etc.) that are developed from a common ancestor.

The diagram is known as a phylogenetic tree. Phylogenetic analysis is important for gathering information on biological diversity, genetic classifications, as well as learning developmental events that occur during evolution. With the advancement in genetic sequencing techniques, phylogenetic analysis now involves the sequence of a gene to understand the evolutionary relationships among species. DNA being the hereditary material can now be sequenced easily, rapidly, and cost-effectively, and the data obtained from genetic sequencing is very informative and specific. Morphological estimates can also be used to infer evolutionary developments, especially in cases where genetic material is not available (fossils). Phylogenetic analysis provides an in-depth understanding of how species evolve through genetic changes. Using phylogenetics, scientists can evaluate the path that connects a present-day organism with its ancestral origin, as well as can predict the genetic divergence that may occur in the future. Phylogenetics has many applications in medical and biological fields, including forensic science, conservation biology, epidemiology, drug discovery and drug design, prediction of protein structure and function, and gene function prediction. In a molecular phylogenetic analysis using gene sequencing data, a more accurate estimation of the evolutionary relationship among species is now possible. Regarding public health applications, molecular phylogenetic analysis can be employed to gather information about pathogen outbreaks. In conservation biology, phylogenetic analysis can be used to predict which species are becoming extinct, and thus, should be taking care of. Phylogenetic analysis can be useful in comparative genomics, which studies the relationship between genomes of different species. In microbiology, phylogenetic analysis can be used to identify and classify various microorganisms, including bacteria. Moreover, phylogenetics can be used to evaluate the reciprocal evolutionary interaction between microorganisms, as well as to identify mechanisms (horizontal gene transfer) responsible for the rapid adaptation of pathogens in an ever-changing host microenvironment. Whole-genome, SNP-based method have been discovered for subtyping and preliminary phylogenomic analysis of bacterial isolates, that circumvent the known limitations of current gene- and SNP-based approaches.

Phylogenomic analyses with larger datasets across a wider spectrum of taxa are becoming more and more computationally tractable as methods of identifying potential phylogenetic markers on a genome-wide scale (e.g., identification and reconstruction of orthologous gene phylogenies in super tree analysis) and genome-scale reconstruction improve.

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We are providing “Phylogenetic and Phylogenomic Analysis” service to the bioinformatics community, scientists and researchers through our expertise to make evolutionary connections between organisms using morphologic and molecular data to identify homologous characteristics and genes and make their research powerfull.

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