Systematics and taxonomy

CLASSIFICATION
1. Definition and Concepts of Classification

■ Placement of organisms and objects into groups and categories for a clear
understanding, proper study and effective organization.
■ Arrangement of group of organisms [plants] with particular circumscription by
rank and position according to artificial criteria, phenetic similarities, or
phylogenetic relationships (Radford, 1986)
PRINCIPLES OF CLASSIFICation
2. Radford et al. (1986) as mentioned by Malabrigo (2016)
 1. Classification is based on character
correlations and discontinuities of
variation, which are necessary for
characterizations and delimitations of
taxa.

2. Classification is the the ordering

of organisms into a hierarchy of taxa
with the species being the
fundamental basic unit, rank or
category.
 3. Classification results in an orderly
arrangement of system designed to express
interrelationships in a particular or
natural way

4. Classification provides a system

for efficient and effective
information storage
 5. NO CHARACTER perse, is more important
than another in classification, but one
character may be more significant within
group

6. THE LIMITS of taxon cannot usually

be defined quantitatively or
qualitatively by a single
characteristic
7. ASSIGNMENTS of natural populations or
of population systems to taxa and
hierarchical arrangements of those
involve judgement
DEVELOPMENT OF CLASSIFICation
SYSTEMS
Malabrigo (2016)
 development
of classification
POST - LINNAEN PERIOD 03 (1760-1880)

LINNAEN PERIOD 02 (1735-1760)

(300 BC – 1700)
PRE-LINNAEN PERIOD 01 use of habit and important to man as
characters
DEVELOPMENT OF CLASSIFICATION
SYSTEMS
Malabrigo (2016)

PRE-LINNAEN PERIOD (300 BC – 1700)

•use of habit and important to man as characters

ANCIENT CLASSIFICATION SYSTEMS

•classification based on habit
 Pre-linnaen period
ANCIENT CLASSIFICATION SYSTEM
ARISTOTLE THEOPHRASTUS
established the earliest classification
was first to write down a
scheme
classification in permanent and logical
wrote extensively on plants form in his De Historia Plantarum
and animals classified plants into trees,
shrubs, undershrubs, etc
DIOSCORIDES
separated medicinal herbs from those
used in making perfumes
wrote De Materia Medica
where he wrote 600 kinds of
plants
 Pre-linnaen period
THE HERBALIST

O. Brunfels (1530) J. Bock (1539) M. de L’Obel (1570)

motivated by medicinal/ commercial considerations

 PRE-LINNAEN PERIOD
MECHANICAL CLASSIFICATION SYSTEMS

ANDREA CAESALPINO CASPAR BAUHIN

■ was called the first plant taxonomist
■ first to classify plants primarily according to
structural characteristics
■ Wrote De Plantis (classified about 1500 species)
■ recognized distinction between genera and
species as major taxonomic levels;
■ wrote Pinax Theatri Botanici listing 6000 plant
species
LINNAEN PERIOD
SYSTEMA NATURAE
✔was an important publication that
introduced the binomial system of
nomenclature

Simplification and standardization of

taxonomic names:
Physalis annua ramosissima, ramis
angulosis glabris, foliis dentato-serratis was
transformed to Physalis angulata
LINNAEAN PERIOD
CAROLUS LINNAEUS (1707-1778)
✔founder of modern taxonomy
✔ developed formal rules that provided
consistency for a two-name system in
common use (binomial system of
nomenclature)

Genera Plantarum (1737)

Species Plantarum (1753) codification of
European folk taxonomies; 1350 genera
and descriptions of 8550 species
 POST-LINNAEN PERIOD
NATURAL SYSTEMS

M. ADANSON J. LINDLEY
■ a French that rejected artificial classifications ■ published first comprehensive natural system in
English
■ emphasized equal weighing of characters

■ Grand father of Numerical Taxonomy

 POST-LINNAEN PERIOD
NATURAL SYSTEMS

S.L. ENDLICHER G. BENTHAM and J.D. HOOKER

■ produced Genera Plantarum ■ produced Genera Plantarum

■ which separated the Thallophyta from the higher ■ dealing only with seed plants and described 200
plants families and 7569 genera
Post - LINNAEN PERIOD
PHYLOGENETIC SYSTEMS
✔attempted to integrate evolutionary
history to natural systems
✔arranged plant groups according to their
routes of descent

A.W. EICHLER
proposed the first phylogenetic system of
classification for plants in the third edition of his
Syllabus de Vorlesungeuber Specielle und Medicinish
– Pharmaceutische Botanik
 TRADITIONAL AND MODERN
APPROACHES TO Classification
Malabrigo (2016)
 UTILITARIAN - people based classification
based on how they are used; the most
conventional and perhaps the simplest
way to make demarcations among
organisms

ARTIFICIAL OR ANALYTIC classification

is based on a number of characters so
that those that are likely to be
related share common morphological
traits
 PHYLETIC OR EVOLUTIONARY - rose after the
publication of Darwin’s Theory of Evolution
that made biologists realize that the
reason taxonomic groups shared certain
traits was because those groups have
evolutionary relationships

PHYLOGENETIC - classification is based

from cladistic theory and the
construction of phylogenies, the
patterns of lineage branching produced
by the true evolutionary history of the
organisms
 The relationships that provide the cohesion of
1 living and extinct organisms are genealogical
relationships.

FIVE BASIC IDEAS 2

Such relationships exist for individuals within
populations, populations within species, and
between species themselves

THAT BEGAN THE 3

All other types of relationships have maximum
relevance when understood within the context of

SYSTEMATICS genealogical descent

The genealogical descent among species may be

REVOLUTION 4 recovered by searching for particular characters

that document these relationships

Of the many possible ways to classify organisms,

5 the best general reference system is one that

exactly reflects the genealogical relationships of
the species classified

Wiley and Lieberman (2011)

PHENETICS versus PHYLOGENETICS
Wiley and Lieberman (2011)

EVOLUTIONARY
PHENETICS TAXONOMY is a moderate
PHYLOGENETICS
highlights evolutionary
highlights degree field by looking into
relationships based on a
similarities and inferring
of similarity evolutionary relationships cladistic approach

Classification spectrum
 CLADISTICS PHENETICS PHYLOGENETICS

method of study of relationships

reconstructing among a group of broad study of
evolutionary trees to organisms on the basis evolutionary
reflect evolutionary of the degree of relationships among
relationships or by similarity (phenogram) organisms
which organisms
diverge to form clades
(cladogram)
CLADOGRAM
• the graphical representation of the hypothetical relationship
(phylogenetic relationship) between different groups of organisms. It
is used in the phylogenetic analysis of organisms to determine the
evolutionary relationship between them.
Root
•A root is the initial common ancestors of all the organisms in a cladogram.
•A root is the starting point for any given cladogram. However, the root might also
indicate that it comes from some other larger clades.

Nodes
•Each node is a hypothetical ancestor that gives rise to two or more daughter taxa.
•Nodes indicate the bifurcating branch point of divergence in all cladograms.
•Thus, a node exists in each point where a group of organisms divides or separate into
further different groups.
Clades
• Clades are groups of organisms or genes that include the most recent common ancestor
of all of its members and all of the descendants of that most recent common ancestor.
• A clade is made up of an ancestor and all its descendants.
• It includes a particular node and all of its connected branches.
Taxon / Outgroup
• A taxon or an outgroup is the most distantly related group of animals that isn’t
necessarily a clade.
• This functions as a point of reference or comparison for the rest of the cladogram.
Branches
• A branch in a cladogram is a line that connects all the other parts of the cladogram.
• The branch length in some cases represents the extent of divergence or the extent of
the relationship among different taxa.
ORGANISMS
8. Terms and Concepts
AND GROUPINGS
MONOPHYLETIC GROUP
• is a taxon composed of two or more species that includes the ancestral species
and all and only the descendants of the ancestor

PARA AND POLYPHYLETIC GROUPS

• are incomplete groups in which one or more of the descendants of the common
ancestor are not included in the group

SISTER GROUP
• is a single species or a monophyletic group that is the closest genealogical
relative of another species or monophyletic group of species
ORGANISMS
8. Terms and Concepts
AND GROUPINGS
TYPES OF CLADOGRAM
Monophyletic group-

Paraphyletic group-

Polyphyletic group-
How to make a CLADOGRAM?
Two ways:
A. Using morphological/ structural characters
Step 1: Determine the defined characters to be used
• The first step in phylogenetic analysis is to determine whether a character is derived or primitive
(innate).
• In this case, the characters that are not influenced by environmental factors are to be selected.
• The outgroup comparison method is the primary method in use for the construction of cladograms or
other trees.
• In the outgroup method, a character of an organism is selected where the organisms is not a member of
the group of animals to be classified, but the selected character is the same as some of the organisms in
the group, then such a character can be used as a defined character.
• Here, the outside organism is called the outgroup, and the organisms being classified are the ingroup.
• Now, within the group, other characters are selected to separate the organisms in the ingroup further.
How to make a CLADOGRAM?
Two ways:
A. Using morphological/ structural characters
How to make a CLADOGRAM?
Two ways:
A. Using morphological/ structural characters
Step 2: Classify the organisms according to the shared characteristics
• For the grouping of the organisms, a Venn diagram can be constructed prior to developing
a cladogram.
• In the Venn diagram, begin with the character that is common in all groups and place it on
the outside.
Example of Venn Diagram
Cladogram from the Venn diagram
B. Using molecular characters
Step 1: Selection of the molecular evidence common
among the selected organisms
• The first step in phylogenetic construction using molecular evidence
is to decide whether to use DNA sequences or protein sequences.
• Protein sequences are preferable in most cases.
• However, for studying very recent evolution, DNA is the marker of
choice.
• Some examples of proteins that are common in many organisms are
hemoglobin and cytochrome c.
B. Using molecular characters

Step 2: Collect and run the multiple sequence alignment to compare the
molecular sequences (DNA or amino acid) for each of the organisms
selected
• Multiple sequence alignment software like Clustal Omega can be used to

align multiple DNA or amino acid sequences to determine similarities and

dissimilarities.
• The closely related organisms will have a higher degree of similarity in

the sequences compared to the organisms that are distantly related.

B. Using molecular characters

Step 3: Generate a cladogram from the obtained data of the multiple

sequence alignment
• The next step is to select a proper substitution model that provides

estimates of the relationship between the organisms by taking into

account the results of multiple sequence alignment.
• The commonly used nucleotide substitution models are the Jukes-Cantor

and Kimura models.

• The commonly used amino acid substitution models are the PAM and JTT

models.
• In the cladogram samples, four phylogenetic characters are studied.
• This represents that humans and kangaroo are more closely related than
humans and bullfrogs.
• The extent of the relationship cannot be determined by this cladogram as it is
an unscaled diagram.
• The orientation of the lines and the order of the animals also don’t matter.
• Similarly, in the cladogram, as we move towards the right of the diagram, the
organisms become less related to each other. Sharks and humans are more
distantly related than bulldog and humans.
• Characteristic to all cladograms, the ancestors of the organisms are
hypothetical and thus are not indicated.
• In the above diagram, the shark is the outgroup, whereas human and
kangaroo form a clade.
 ORGANISMS
8. Terms and Concepts
AND GROUPINGS

OUTGROUP
• is a species or higher
taxon used in
phylogenetic analysis
to evaluate which
presumed homologs
indicate genealogical
relationships within the
group being studied
and which are simply
primitive characters
 ORGANISMS
8. Terms and Concepts
AND GROUPINGS

INGROUP
•is the group being
analyzed by the
investigator;
ingroups
sometimes are
shown as polytomy
prior to analysis
PHYLOGENETIC HISTORY AND
EVOLUTION
8. Terms and Concepts

RELATIONSHIP in a phylogenetic system refers to genealogical

relationships
GENEALOGY AND GENEALOGICAL DESCENT are graphic
representations of a hypothesis of the descent relationships of
one or more organisms from one or more ancestors
CLADOGENESIS refers to branching or divergent evolution
(individual or population level
ANAGENESIS synonym of phyletic evolution; evolution within the
lineage through population genetic phenomena
PHYLOGENETIC HISTORY AND
EVOLUTION
8. Terms and Concepts

SPECIATION
• is an array of processes leading to the origin of one or more new species

SPECIATION EVENT
• refers to a particular and historically unique event for the ancestor species
in question; could be instantaneous or protracted

VICARIANCE EVENT
• is a geographic separation of a once continuous biota such that the biota
becomes two or more geographically separated biota
SPECIATION EVENT
VICARIANCE EVENT
ATTRIBUTES
8. Terms and Concepts
OF ORGANISMS
CHARACTER refers to the property of the organism. A character
state is a feature, attribute, or observable part of the organism as
interpreted by an investigator
MATCH OR CHARACTER MATCH is a shared character state
EVOLUTIONARY NOVELTY refers to an inherited change from a
previously existing character state
TAXIC HOMOLOGIES are character states shared by two taxa
and are the same state inherited from a common ancestral
species
TRANSFORMATIONAL HOMOLOGIES are different states, one
character being the ancestral state
ATTRIBUTES
8. Terms and Concepts
OF ORGANISMS

HOMOPLASY
is a similarity
achieved by
independent
evolution in
different parts
of the tree of
life
ATTRIBUTES
8. Terms and Concepts
OF ORGANISMS

•refers to traits that differ significantly in

ANALOGY structure but perform similar functions

•is the total spectrum of characters exhibited

HOLOMORPHOLOGY by that organism during its lifetime

•refers to the characters of an organism at any

EPIPHENOTYPE particular time it is inspected during its life
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