What is a Taxonomy?

It is the branch of biology that works with the identification of organisms at first, then naming, and classification of them into phenetic or phylogenetic groups (a classification system). In other words, it is the scientific study of biological diversity and a part of systematic biology.

Levels of Taxonomy

It is a process to classify different genus based on their natural relationships and shared behaviours and properties.

There are three levels.

• First one is alpha which deals with findings organisms, describing, and naming them.
• Second one is beta which identifies natural groups and biological classes.
• Third one is gamma that includes the study of evolutionary processes and patterns.

History of Taxonomical Classification

In the eighteenth century, Swedish naturalist and taxonomist Carl Linnaeus brought modern biological classification by establishing a simple taxonomic system for the classification and naming of plants or animals. He developed a hierarchy or a ranking system for the taxonomical classification of plants and animals which is the basis of modern taxonomy.

Naming

It is the formal naming of a particular group of individuals or new species according to some standardized system. The fundamental principle behind it is that each individual of different species (plants, animals, or microbes) must have only one scientifically given name. They have their common names also which are used by common people to identify them within a limited geographic region (scientific classification).

Criteria

Presently, the criteria for scientific naming of plants, fungi, or algae are based on the rule and recommendations of the international code of nomenclature (ICN). The scientific names are binomials. The binomial nomenclature includes two names in which the first name is the genus name and the second name is the species name.

What is Classification?

It is an arrangement of taxa into some type of order. The purpose of it is to prove a system for cataloguing and expressing the relationship between them. It is not a single-step process. It involves a hierarchy of steps and each step represents a category termed rank.

How Classification works?

Every organism can be classified into seven taxonomic ranks on the basis of its evolutionary history. Each rank contains organisms with similar characteristics. The kingdom is the largest unit. It splits into smaller units called phyla. Phyla split into classes, classes into orders, orders into families, families into genera, and genera into species. Various units to classify are called taxonomic categories. Together they make up the taxonomic hierarchy. A taxon is a defined group typically treated as a given rank.

Biological Species Concept

All the biologists universally agree that the specie is a fundamental natural unit but they have not been able to agree on their definition. Taxonomists practically define them taxonomically by means of morphological and phonetic properties. If one group (species) consistently differs from another, it will be a separate definition.

How is it described?

According to this concept, they are groups of natural populations who interbreed and reproductively isolated from other such groups. Reproductively isolated means that the members of one group do not interbreed with the members of others. It explains why the members of a group resemble each other and differ from other groups. When two organisms of the same group breed, their genes pass into their offspring. As this process repeats, the genes of different individuals shuffle around the gene pool. The shared gene pool gives one group its identity. By contrast, genes are not transferred to other groups and different groups exhibit different appearances. 

Subspecies

It is a taxonomic subdivision, often distinguished by special phenotypic characters and by its origin or localization in a given geographical region.  A unique, geographic locale is shared by the members of a subspecies. Subspecies are not isolated reproductively, but they are normally allopatric and exhibit phylogenetic partitioning which is recognizable. The terms race and subspecies are potentially misleading are most often used synonymously. Although race is normally used in the case of the human population, it generally implies a lower level of differentiation. A group of the single uniform population, devoid of differentiated and semi-isolated local populations(subspecies) are monotypic and if it is subdivided into two or more subspecies, it is polytypic. 

Phenetic and Phylogenetic Principles of the Classification

Two main methods used for the classification of species are phenetic and phylogenetic.

Phenetics

Phenetics or taximeters is an attempt to distinguish individuals on the basis of overall similarity in morphology, or other observable traits, and does not depend on their phylogeny or evolutionary relationship. Phenetic characters are all the observable and measurable properties. The phenetic classification scheme does not distinguish between homologous characters and analogous characters. The result is often summarized with a tree-like network called a phonogram. 

Determination of the phenetic relationship between operational taxonomic units (OTUs)

The following operations are involved in the determination of the phenetic relationship.

1. Selection of individuals (species) for study.
2. Selection of traits.
3. Description of character states.
4. Comparison of character states.

Numerical Taxonomy

It is a common misconception equating phenetics. It is a system that developed as a part of multivariate analysis. It aims to create a systematic study using numeric algorithms like cluster analysis rather than using subjective evaluation of their properties. 

Phylogenetics

Phylogenetics is the scientific study that concerns how various groups of individuals are related at an evolutionary level. Basically, this is the study of phylogeny. It finds the relationship between various individuals based on their evolutionary similarities, and differences. The phylogenetic principle classifies individuals according to how recently, they share a common ancestor.

Cladistics

It can be defined as the concepts and methods for the determination of branching patterns of evolution. Cladistic relationship describes the branching sequence of the ancestral lineages. Some scientists preferred the term Phylogenetic taxonomy. This is the most widely used method used to distinguish various plants and animals today. This approach focuses on the branching of different lineages from each other in the evolutionary background. Biologists distinguished two parts of traits: homoplasy and homology.  

Homoplasy

Homoplasy (analogous character) is a character shared through convergent evolution. It is a similarity in outer look but dissimilarity in origin. The wings of birds and bats are examples of homoplasy. Groups of individuals who did not share the common ancestor have homoplasious character. They are not an indicator of phylogenetic relationships.

Homology

Homology (Homologous character) includes similarity in origin. Groups of individuals that shared a common ancestor have homologous characters. They are divided into shared derived and shared ancestral characters. A shared ancestral character or symplesiomorphic character is shared with the groups of individuals ancestral to more than one group. A shared derived or synapomorphic character is a trait that is shared by two or more groups of individuals and their most recent common ancestor.

Cladistic approach 

The cladistic approach attempts to identify monophyletic groups. A monophyletic or clade means a group of individuals containing a single common ancestor and all its descendants. The converse of monophyly is paraphyly. Paraphyletic means a group of individuals who do not include all the descendants of a common ancestor. If the group includes some or all of the descendants, but not the common ancestor, be called polyphyletic. 

Cladogram

A branching diagram constructed by cladistic principle and method is called a cladogram. Any branching of the cladogram represents a divergence in lineage and one common ancestor from two separate lineages. It is represented by nodes and branches. Nodes can be internal or external. The last common ancestor of the two lineages is represented by each internal node. External nodes or terminal nodes represent the tip of the tree or extant unit of taxonomy under consideration. Branches can be internal o external also. Two nodes are connected by internal branches, whereas a tip and a node are connected by external branches.

Evolutionary taxonomy

It incorporates both phenetic and phylogenetic elements. Paraphyletic and monophyletic are recognized by evolutionary classification, but polyphyletic groups are not recognized. Regarding the kinds of traits used to infer phylogeny, it forms groups by the homologies rather than homoplasies but does not distinguish ancestral from derived homologies.

Formulas

Simple matching coefficient (SMC)

(M₀₀ + M₁₁)/ (M₀₀ + M₀₁ + M₁₀ + M₁₁)

Jaccard's coefficient

M₁₁ / (M₀₁ + M₁₀ + M₁₁)

where,

• M₁₁= The total number of characters positive for two OTUs
• M₀₁= The total number of characters that are negative for the first OTU and positive for the second
• M₁₀= The total number of characters that are positive for the first OTU and negative for the second
• M₀₀= The total number of characters negative for both OTUs

Context and Applications

This topic is significant in the professional exams for both under-graduate and post-graduate courses, especially for:

• B.Sc. in Zoology
• M.Sc. in Zoology
• M.Sc. in Genetics

Related Concepts

• Diversity of life
• Systematics
• Carl Woese Principle
• Plesiomorphy