Unit 1: Taxonomy

1. Fundamentals of Taxonomy

1.1 Systematics and Taxonomy

Systematics

Systematics is the broad scientific study of the diversity of life and the evolutionary relationships between organisms. It aims to understand the history of life, how organisms have evolved, and how they are related to one another. Systematics includes two main components: taxonomy and phylogeny.

Taxonomy

Taxonomy (from Greek: taxis = arrangement, nomos = law) is the science of naming, describing, and classifying organisms. It is the practical arm of systematics, responsible for creating the organized system (classification) that reflects the evolutionary relationships uncovered by systematics.

Key Distinction: Taxonomy is about classification and naming. Systematics is the broader field that includes taxonomy and also studies evolutionary history (phylogeny). You can think of taxonomy as the "filing system" and systematics as the "family tree research" that determines *why* things are filed together.

1.2 Taxonomic Terms and Concepts

Concept of Classification

Classification is the arrangement of organisms into groups (called taxa, singular: taxon) based on their shared characteristics and evolutionary relationships. This creates an ordered system that is universal, logical, and easy to use for information storage and retrieval.

Taxonomic Hierarchy

This is the nested, ordered system of classification developed by Carolus Linnaeus. It consists of a series of ranks, from broad to specific. Each level includes all the groups in the level below it.

1. Kingdom (e.g., Animalia)
2. Phylum (e.g., Chordata)
3. Class (e.g., Mammalia)
4. Order (e.g., Primates)
5. Family (e.g., Hominidae)
6. Genus (e.g., Homo)
7. Species (e.g., sapiens)

Taxonomic Key

A taxonomic key is a tool used to identify an unknown organism. The most common type is a dichotomous key.

• It works by presenting a series of two contrasting choices (couplets) based on observable characteristics.
• By making a choice at each step, the user is progressively led to a narrower group, until the organism is identified.
• Example Couplet:
  1. (a) Animal has feathers .................... Go to 2
  2. (b) Animal does not have feathers ...... Go to 3

Taxonomic Types (Type Concept)

In formal taxonomy, a "type" is a specific specimen (or group of specimens) to which the scientific name of a species is permanently attached. It serves as the definitive example and reference point for that species name.

• Holotype: A single specimen designated by the original author as the type.
• Paratype: Other specimens from the original collection (besides the holotype) that the author used in the description.
• Neotype: A specimen later designated as the type if the original holotype is lost or destroyed.
• Lectotype: A specimen later selected to be the type from the original collection (syntypes) when no holotype was originally designated.

2. Rules of Nomenclature

2.1 International Code of Zoological Nomenclature (ICZN)

The ICZN is the official rulebook for naming animals. Its primary goal is to ensure stability and universality in scientific names.

Key Objectives of the ICZN:

• Uniqueness: Every animal taxon must have a unique scientific name.
• Universality: The names must be usable and recognized by scientists worldwide, regardless of language.
• Stability: Once a name is established, it should not be changed unnecessarily, to avoid confusion.

2.2 Binomial Nomenclature

This is the system for naming species, introduced by Carolus Linnaeus. Each species is given a two-part scientific name.

Scientific Name = Genus + species
Example: Homo sapiens (Human)

Rules for Writing Scientific Names:

1. Two Parts: The name consists of the Genus name and the specific epithet (species name).
2. Capitalization: The Genus name is always capitalized. The specific epithet is always lowercase.
3. Italics/Underlining: The entire two-part name must be written in italics when typed or underlined when handwritten (e.g., Homo sapiens or Homo sapiens).
4. Author Citation: Often, the name of the author who first described the species and the year of description are written after the name, but not in italics (e.g., Passer domesticus (Linnaeus, 1758)).

2.3 Principle of Priority

This is a foundational rule of the ICZN designed to ensure stability. It states that the oldest validly published name for a taxon is the correct one to use.

• What it means: If an animal is accidentally described and named multiple times by different scientists (creating synonyms), the name that was published first is the one that is retained. All later names are considered junior synonyms and are invalid.
• Starting Point: The official starting point for zoological nomenclature is the 10th edition of Linnaeus's Systema Naturae (1758).
• Example: If Animalia smithii was named in 1850 and Animalia jonesii was named for the same animal in 1860, Animalia smithii is the valid name due to priority.

3. Modern Trends in Systematics

3.1 Newer Trends in Systematics

Traditional taxonomy relied on morphology (physical structures). Modern systematics incorporates a wider range of data:

• Cladistics (Phylogenetic Systematics): This is the dominant modern method. It classifies organisms based on shared derived characteristics (synapomorphies) that indicate common ancestry. It generates branching diagrams called cladograms to represent evolutionary relationships.
• Molecular Systematics: Uses data from DNA, RNA, and proteins to infer relationships.
• Phenetics (Numerical Taxonomy): An older "newer" trend that classifies organisms based on overall similarity, using as many characteristics as possible and giving them equal weight. This has largely been replaced by cladistics.

3.2 Basic Concept of Molecular Taxonomy and DNA Barcoding

Molecular Taxonomy

This approach uses genetic data, primarily DNA sequences, to identify and classify organisms. By comparing the DNA sequences of different organisms, scientists can measure their genetic similarity and infer their evolutionary relatedness with high precision. Common markers include ribosomal RNA genes (like 16S) and mitochondrial DNA.

DNA Barcoding

DNA barcoding is a specific method within molecular taxonomy that uses a short, standardized DNA sequence to identify species, much like a supermarket scanner uses a barcode to identify a product.

• The "Barcode" Region: For most animals, the standard barcode region is a ~650 base-pair segment of the mitochondrial gene Cytochrome c Oxidase I (COI).
• Why COI? This gene is present in most animals, is easily sequenced, and has a "Goldilocks" mutation rate: it's slow enough that it's usually identical within a species, but fast enough that it's different between closely related species.
• Applications:
  • Identifying cryptic species (species that look identical but are genetically distinct).
  • Identifying larval stages or body parts.
  • Detecting food fraud (e.g., mislabeled fish).
  • Monitoring biodiversity in environmental samples (eDNA).