There are different methods of studying a species.

Taxonomy is the branch of biology which deals with description, identification and naming of organisms. Systematics refers to the study of diversity and differentiation of organisms which existed in the past as well as present times.It tries to analyze and identify the relationships that exist between the different species. Nomenclature is the procedure of naming the organism up to the species level. Phylogenetics refers to the deciphering of evolutionary history and relationship among the different organisms.

The most popular notation of the species is the 'Biological species concept' which is based on the principles of population genetics. There are other types of species in use like the morphospecies which is based on the morphological or type species of the group. Another is the phylogenetic species which is based on evolutionary history of the organism.

The basis for all these biological classification is the predictivity or predictive value. The predictivity is the probability of a feature of an organism to be found in the other member of the same class. If the members share more characters in common and a new feature is found in one of the members, then the predicivity of the feature to be found in the other members of the species is also higher.

Phenetic classification utilizes any other data such as chemical, cytological, and embryological similarities among species to classify them into a common class. These resemblances are collectively called as paltristic similarity. It can be either primitive paltristic similarity or derived paltristic similarity. When these similarities are due to convergence or parallelism, it is termed as homoplasy.

The process of speciation can either be
• Anagenesis - It is the process of accumulation of gradual changes over the development of an organism over evolutionary history. This is the basis of Darwin's principle of microevolution. Species diversity shows little changes due to the slow and gradual changes.
• Cladogenesis - In this type of speciation, the evolutionary lineages diverge into two or more new species forming a branched evolution. The changes in species diversity are more pronounced and evident.
• Radiation - is essentially cladogenesis repeated with many diverging branches occurring at the same time in evolutionary history.

The current methods of systematics are based on a mixed approach utilizing the similarities in morphology, biochemical parameters, molecular comparisons etc. to derive at the phylogenetic relationship.

In general, such approaches result in a reliable indication of evolutionary relationship among different species derived from fossil evidences and DNA sequence similarity. However, convergent evolution or parallelism which results in analogous features (homoplasy) can often be misleading. This is usually attributed to the similarity in environmental pressures and natural selection.

The recent systematic studies employ software and algorithms to compare DNA sequences from different organisms. The result of such studies is a cladogram which exhibits the shared characteristics among the different species. A clade refers to an ancestral species and its descendents. The resemblances among the clades are the basis of cladistic researches.

An ideal clade is monophyletic consisting of the ancestral species and all its descendents. When one or more descendent species are eliminated/ missing from the study, the clade is referred to as paraphyletic. When the ancestral species is missing, the clade is referred to as polyphyletic.

The resultant phylogenetic trees are rather relative in representation of the time of divergence of the different species. A Phylogram solves this by depicting the nucleotide sequence changes from the ancestor as the length of the branch in the cladogram. An ultrametric tree has all the branches of equal length from the ancestral species and the same branching as of the phylogram.

When studying the evolutionary relationships among the different species, systematists use either the maximum likelihood method or maximum parsimony method to find the best tree that fits the data. The tree with the maximum parsimony is constructed by having the least number of evolutionary events for achieving the shared derived characters among the different species under consideration.

The maximum likelihood method uses a set of predefined rules on DNA base changes over generations to construct a tree which can represent the evolutionary events in the best way.

The resultant evolutionary tree is compared with other evidences and similarities for better conclusion. Paralogous genes resulting from Gene duplication can occur in more than one copy in a genome and can diverge in different ways within a single clade adding further new functions in organisms and technical difficulties in deciphering evolutionary relations.

Applications
1. to analyze evolutionary changes and finding the similarities of evolution among different species.
2. Detecting orthologous genes.
3. Follow the changes of genes and genomes in species that show higher diversity.

Software

PHYLIP is a free Phylogenetic inference package used in detecting phylogenetic relations. PAUP carries out the phylogenetic analysis using maximum parsimony method.
The data used is mostly DNA and protein sequences. The methods employed range from the simple distance measures, maximum likelihood method, bootstrap methods and using algorithms.

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