Taxonomy: Classification and Naming of Living Things

Milkfish (Fig. 13.1) or bangus in Tagalog dialect.

Different local names: bangrus in Guimaras and Samar awa in Cebu.

Formal System of Naming Species:

Taxonomy vs. Systematics

 Systematics, is the study of diversity of organisms and the evolutionary relationships among them.

 Taxonomy, on the other hand, is the scientific study of describing, naming and classifying living organisms.

Both a systematist and a taxonomist;

 provide scientific names;

 give detailed descriptions of organisms;

 collects and keeps volumes of specimens;

 offer classifications for the organisms by constructing identification keys and data on their occurrence and
distribution.

Systematist investigates on evolutionary histories and considers environmental adaptation of species.

A Swedish botanist, Karl von Linne popularly known in his Latin name as Carolus Linnaeus, “Father of Modern
Taxonomy” created Binomial System of Nomenclature.

This binomial system of nomenclature brings order to a chaotic world of common names. It is universal and
clearly indicates the level of classification involved in any descriptions.

Every species has two-part name: the broader classification genus (plural: genera) with a second word
designates species or specific epithet.

No two kinds of living organisms have the same binomial name, and every organism has only one correct name
as required by various internationally agreed codes of rules.

At present, the following nomenclature codes govern the naming of species, as follows;

 Algae, Fungi, and Plants – International Code of Botanical Nomenclature (ICBN)

 Animals - International Code of Zoological Nomenclature (ICZN)

 Bacteria –International Code of Nomenclature Bacteria (ICNB)

 Viruses - International Committee on Taxonomy of Viruses (ICTV).

Some of the major rules in nomenclature include:

(1) the name should be in Latin;

(2) the genus of an organism begins with a capital letter; the species designation begins with a lowercase letter;
 (3) the entire scientific name is italicized when typewritten or underlined separately when handwritten. Thus, the
scientific name of human is written as Homo sapiens;

(4) ) all taxa must have an author when described. That is, Homo sapiens L., the L stands for Linneaus who first
successfully described and named the organism. When the genus is understood, it can be abbreviated as H.
sapiens.

Taxonomic Hierarchy

Carolus Linnaeus recognized that different species could be grouped into broader categories based on shared
characteristics. Any grouping of organisms that shares a particular set of characteristics forms an assemblage called
taxon.

A taxon, plural (taxa)- any unit used in the science of biological classification. Example: kingdom, phylum

, Linnaeus’s idea is the basis of the taxonomic hierarchy used today (Table.13.1). The three major domains Archaea,
Bacteria, and Eukarya are the most inclusive levels.

Each domain is divided into kingdoms, which in turn are divided into phyla, then classes, orders, families, genera
and species.
Dichotomous Key

Dichotomous means “divided into two parts”, hence the dichotomous keys always provide two choices based on the
key characteristics of the organism in each step.

By correctly selecting the right choice at each stage, the user will be able to identify the name of the organism at
the end of the flow. The further you divide the key, the more you learn about the physical and quantitative characteristic
of the specimen you are trying to identify.

Taxonomic Classification

All living organisms are classified into groups based on very basic, shared characteristics.
 Characteristics such as appearance, reproduction, mobility, and functionality are just a few ways in which living
organisms are grouped together. These specialized groups are collectively called the classification of living things. The
classification of living things includes 7 levels: kingdom, phylum, classes, order, families, genus, and species .

Domain

When Linnaeus was naming and classifying organisms in the 1700s, almost nothing was known of
microorganisms. With the development of powerful microscopes, scientists discovered many single-celled organisms
that did not fit into any of Linnaeus’ kingdoms. As a result, a new taxon was identified- called the domain, was added to
the classification system. The domain is broader than the kingdom.
7 Major Levels of Classification

There are seven major levels of classification: Kingdom, Phylum, Class, Order, Family, Genus, and Species.

The two main kingdoms we think about are plants and animals. Scientists also list four other kingdoms including
bacteria, archaebacteria, fungi, and protozoa.
7 Major Levels of Classification

 Kingdoms- The most basic classification of living things is kingdom. Currently there are five kingdoms. Living
things are placed into certain kingdoms based on how they obtain their food, the types of cells that make up
their body, and the number of cells they contain.

 Phylum- The phylum is the next level following kingdom in the classification of living things. It is an attempt to
find some kind of physical similarities among organisms within a kingdom. These physical similarities suggest
that there is a common ancestry among those organisms in a particular phylum.

 Classes- Classes are way to further divide organisms of a phylum. As you could probably guess, organisms of a
class have even more in common than those in an entire phylum. For example, humans belong to the Mammal
Class because we drink milk in our early years.

 Order- Organisms in each class are further broken down into orders. In this category, a taxonomy key is used to
determine to which order an organism belongs. A taxonomy key is a checklist of characteristics that determines
how organisms are grouped together.

 Families- Orders are divided into families. Organisms within a family have more in common than with organisms
in any classification level above it. Because they share so much characteristics in common, organisms of a family
are said to be related to each other.

 Genus- This describes the generic name for an organism. The genus classification is very specific so there are
fewer organisms within the genus. Because of this, there are a lot of different genera among both animals and
plants. When using taxonomic naming, the genus is used to determine the first part of its two-part name.

 Species- Species is the most specific name os an organisim. It is the last and most strict level of classification of
living things. The main criterion of an organism to be within a particular species is the ability to breed with other
organisms of that same species. The species of an organism determines the second part of its two-part name.
Classification for humans here is an example of how humans are classified.

PHYLOGENETIC TREE

 Phylogeny- is a “tree” which estimates the “historical” connections between species or genes that they carry, it
is the evolutionary history of the relationship between all living things.
 Phylogenetic Tree-is a branching diagram that discusses the evolutionary history of a group of organisms.
The point where a split occurs, a branch point, represents where a single lineage evolved into a distinct new one (new
lineage). We call a lineage that evolved early
from the root that remains unbranched a
basal taxon. We call two lineages stemming
from the same branch point sister taxa. A
branch with more than two lineages is a
polytomy.
BASIC STRUCTURES OF PHYLOGENETIC TREE

Parts of Phylogenetic Tree includes:

-The “tips” of the tree branches represent the taxa in the study.
-Taxa may be at any taxonomic level-orders, species, populations, etc.
-These taxa may be called OTUs, or Operationa-Taxonomic Units- used to classify groups of closely related individuals.
-The lines within the tree are called the “branches”.
-The points at which branches connect, or the tips
of branches are both called nodes. Internal nodes
connect branches: external nodes are the tips
represent taxa.
-Some trees will have a basal node, known as the
“root”.
-A grouping of an ancestor and all its descendants is
known as a clade.

SCALED VS. UNSCALED TREES

The branches of polygenetic tree may be

1. Scaled branches-the branch lengths are

2. Unscaled branches- The branch length is not proportional to the number of changes occurring. Such trees are
called, Cladogram.
ROOTED VS. UNROOTED TREES

 Rooted trees reflect the most basal ancestor of the tree in question.

 have a single lineage at the base representing a common ancestor.

 A rooted phylogenetic tree is a diagram which shows the last common ancestor of the groups. 

 Unrooted trees do not imply a known ancestral root

 A free tree or unrooted tree is a connected undirected graph with no cycles.

 An unrooted phylogenetic tree shows the relationships between organisms without showing the common
ancestor.
TREES AND CLASSIFICATIONS

In the approach to systematics called cladistics, common ancestry is the primary criterion used to classify organisms.

Using this methodology, biologists attempt to place species into groups called clades, each of which includes an
ancestral species and all its descendants.

The most common way to integrate information into phylogenetic trees is called cladistics. Based on features of
ancestor and descendant species, cladistics explains theories about how organisms are linked.

1. Monophyletic group- a monophyletic group is a group of organisms which forms a clade, meaning that it consists of
an ancestor and all its descendants. (from the Greek, meaning “single tribe”)

2. Paraphyletic group-A clade that excludes species that share a common ancestor with its member. (“beside the tribe”)
group.
A paraphyletic group includes a single ancestor and some of its descendants; it is similar to a monophyletic group, but
some descendants are excluded.

The Cladistic System

During the earlier days, systematist constructed phylogenetic tree diagrams by comparing as many
characteristics as possible among species. Those organisms with the most characteristics in common would be placed
close to each other on the tree’s branches. However, a tree based solely on similarities can be misleading.

This problem was solved by using cladistic approach. Beginning in the 1990’s, cladistics is a phylogenetic
system that defines groups by distinguishing between ancestral and derived characteristics.

 Ancestral characters are attributes of species that are old and have been retained from a common ancestor. In
cladistics studies, these ancestral traits are homologies that are common to all members of a group and indicate
a shared ancestry. These common characters are called symplesiomorphies(sym together + plesio, near +
morphe, form).

 Derived characters on the other hand, are attributes different from those found in the group’s ancestor. Derived
characters shared by members of a group are called synapomorphies (syn together + apo, near + morphe, form).

In the 1950s, a scientist named Willi Hennig established cladistics.

Cladistics is derived from the term clade.

A clade is a collection of organisms that include an ancestor species and all of their descendants.

A diagram showing evolutionary relationships is called a cladogram within one or more clades.
A clade is a relative concept. How a clade is described depends on the species that you are interested in classifying.
Small clades may have as few as two species and a shared ancestor. Many more species and their shared ancestors may
be found in the larger clades

Rules in Constructing Cladogram

Rule 1. The branches at every node can be rotated. The branches do not infer any sort of order; they indicate only how
recent are the common descendants (Fig.17.4).
Rule 2. Two lineages branching from a single ancestral node are known as sister taxa. Further specialization after a
branch point is inappropriate. Therefore, it would be improper to say that humans evolved more recently than
chimpanzees or that humans should be placed in their own family simply because they seem so different from
chimpanzees . Note that common ancestry is the main basis of taxonomic groupings and not based on subjective
perceptions of specialization.

Rule 3. There is no such thing as a “most highly evolved species.” All extant species descended from successful
ancestors, and evolved to survive and reproduce in the context of their specific environment. Evolution is a process it
has neither a goal nor a subjective value system.

Rule 4. No extant or extinct taxon is considered ancestral to any other extant or extinct taxon. Nodes represent
hypothetical ancestors, not taxonomic units. When an ancestral lineage diverges to become two separate taxa, the
ancestral lineage (hypothetical ancestor) is considered extinct, even if one of the descendant taxa is virtually the same as
that hypothetical ancestor. When one hears the often repeated yet false argument that "humans evolved from
monkeys," this should be recalled. They did not. A common ancestor is shared by humans and monkeys.