CHAPTER 2

CLASSIFICATION OF LIVING
THINGS
INTRODUCTION
To trace phylogeny or the evolutionary history
of life, biologists use evidence from
paleontology, molecular data, comparative
anatomy and other approaches.
Tracing phylogeny is one of the main goals of
systematics, the study of biological diversity in an
evolutionary context.
Systematics includes taxanomy, which is the naming
and classification of species and groups of species.
Taxanomy employs a hierarchical system of
classification
Taxonomy is the branch of biology dealing with the
identification, naming and classifying the diverse form
of life.
Taxonomy is the science of the classification of living
things, and phylogeny is evolutionary history.
The Linnean system, first formally proposed by Carolus
Linnaeus in Systema naturae in the 18
th
century, it has
two main characteristics.
i) each species has a two-part name.
ii) species are organized hierarchically into broader
and broader groups of organisms.
Binomial System of Nomenclature
The Linnaean system of naming species is
referred to as the binomial system of
nomenclature because each species is assigned to
a two-part name.
The first part of the name is a genus, and the
second part, the species epithet, designates a
particular species belonging to that genus.
The generic name is always capitalized; the
species epithet is not capitalized.
Both names are always italicized or underlined.

Under the binomial system, each species is
assigned a two-part latinized name, a
binomial.
The first part, the genus, is the closest group to
which a species belongs.
The second part, the specific epithet, refers to one
species within each genus.
The first letter of the genus is capitalized and both
names are italicized and latinized.
e.g Homo sapiens, Panthera tigris, Mimosa pudica
etc.
A hierarchical classification will group species
into broader taxonomic categories.
Species that appear to be closely related are
grouped into the same genus.

e.g. The leopard, Panthera pardus, belongs to a
genus that includes the African lion (Panthera leo)
and the tiger (Panthera tigris)
Biologys taxonomic scheme formalizes our
tendency to group related objects.
Phylogenetic trees reflect the hierarchical classification
of taxonomic groups nested within more inclusive
group.
SYSTEMATICS AND PHYLOGENETIC
BIOLOGY
Taxonomy is part of a larger division of biology known
as systematic, which is the study of the diversity of
organisms at all levels of organization.
In Greek, systematics comes from work systema, an
orderly arrangement. Determination of phylogeny is a
goal of systematics. This is done by the construction of
phylogenetic tree.
Phylogenetic tree is a branching diagram that shows a
hypothesis about evolutionary relationships among
organisms. To build these phylogenetic trees, we must
have data that comes from the characteristics used in
classification.

Modern phylogenetic systematics is based
on cladistic analysis
A phylogeny is determined by a variety of
evidence including fossils, molecular data,
anatomy and other features.
Most systematists use cladistic analysis,
developed by a German entomologist Willi
Hennig to analyze the data.
A phylogenetic diagram or cladogram is
constructed from a series of dichotomies.
cladogram
Genera are
grouped into
progressively
broader
categories :
family, order,
class, phylum,
kingdom and
domain.
Each taxonomic level is more comprehensive
than the previous one.
as an example, all species of cats are mammals, but
not all mammals are cats.
The named taxonomic unit at the genus level,
the generic name for various species of pine
trees.
e.g: Pinus is a taxon at the genus level, the generic
name for various species of pine trees.
Mammalia, a taxon at the class level, includes all the
many orders of mammals.
Determining which similarities between
species are relevant to group the species in a
clade is a challenge.
It is important to distinguish similarities that
are based on shared ancestry or homology
from those that are based on convergent
evolution or analogy.
As a general rule, the more homologous parts
that two species share, the more closely related
they are.
- Adaptation can obscure homology and convergence can
create misleading analogies.

Also, the more complex two structures are, the
less likely that they evolved independently.
e.g. the skulls of a human and chimpanzee are
composed not of a single bone, but a fusion of
multiple bones that match almost perfectly.
Constructing Phylogenies
Systematists collect various data so as to discover the
evolutionary relationship between species.
They depend on a combination of data from many
sources such as fossil record, homology, structure and
behavior, molecular data in order to determine the right
sequence of common ancestors in any particular group of
organisms.
Biologists are interested in the phylogenetic relationships among
organisms for many reasons.
- To understand the evolution of structures they need to know
which traits are ancestral and which are derived.
- They need a good phylogeny in order to determine how fast
various traits have evolved in different lineages.
- Phylogenetic information is essential for the study of nearly all
aspects of adaptation.

Homology
Homologies are anatomical features of different
organisms that have a similar appearance or
function because they were inherited from a
common ancestor.
For example, the forelimb of a bear, the wing of a bird, and human
arm have the same functional types of bones as did our shared
reptilian ancestor where these bones are homologous structures.
Homologous structures are structures that are
similar in different species of common
ancestry.
The more homologies two organisms possess, the more likely
it is that they have a close genetic relationship.

Homology
Homology indicates similarity in different
species that results from their derivation from
a common ancestor. The features that exhibit
such similarity are called homologous
features.

Nonhomology
Nonhomologous structural similarities
between species.
In these cases, the common ancestor did not
have the same anatomical structures as its
descendants.
Misleading similarities are called
homoplasies.
Homoplastic structures can be the result of
parallelism, convergence, analogies, or mere
chance.

Homoplasies
Parallelism, or parallel evolution, is a similar evolutionary
development in different species lines after divergence from a
common ancestor that had the initial anatomical feature that
led to it.
Convergent evolution, distantly related groups may come to
resemble one another in structure and function as they
become adapted to similar modes of life.
Analogies are anatomical features that have the same form or
function in different species that have no known common
ancestor.
- the wings of a bird and a butterfly are analogous structures because they seem similar
in appearance and function. However, their wings are quite different on the inside. Bird
wings have an internal framework consisting of bones, while butterfly wings do not
have any bones at all and are kept rigid mostly through fluid pressure.

Homoplasy
Homoplasy indicates similarity in the
characters in different species that is due to
convergent evolution, not common descent.
The features that exhibit such similarity are
called homoplastic features.

Both parallelism and convergence are thought to be due primarily
to separate species lines experiencing the same kinds of natural
selection pressures over long periods of time.
These dichotomous branching diagrams can
include more taxa.
The sequence of branching symbolizes
historical chronology.
Each branch or clade can be nested within
larger clades.
A clade consists of an ancestral species and all
its descendants, a monophyletic group.
Groups that do not fit this definition are
unacceptable in cladistics.
Polyphyletic groups
Phylogenetic taxa
Monophyletic taxon
A group of organisms made up of a common
ancestor and all of its descendants.

Example : Birds sole descendants of a group of
arboreal Triassic reptile.

Paraphyletic taxon
A group of organisms made up of a common
ancestor and some, but not all of its
descendants are included in the grouping.

Example : Modern reptiles because their
amphibian ancestor also give rise to the birds
and mammals.
Polyphyletic taxon
A group made up of organisms that evolved
from two or more different ancestors.

Example : The group including all
insectivorous animals.
Shared derived characters
originate in a recent common ancestor and are
present in its descendants.
Species that share derived characters form a
clade.
Systematists use shared derived characters to
identify points where groups diverged from one
another.
More recent common ancestor is indicated by
classification into less inclusive taxonomic groups
with more specific shared derived characters.


Example :
If we compare dogs, goats and dolphins (all of
which are mammals), only dogs and goats
have hair whereas dolphins do not have hair.
Hair is an ancestral trait in mammals and
cannot be used as evidence that dogs and
goats share a more recent common ancestor.
In contrast, the virtual absence of hair in
mature dolphins is a derived character within
mammals.
For example, the presence of hair is a good character to distinguish
the clade of mammals from other tetrapods.
- It is a shared derived character that uniquely identifies mammals.

However, the presence of a backbone can qualify as a shared
derived character, but at a deeper branch point that distinguishes all
vertebrates from other mammals.
- Among vertebrates, the backbone is a shared primitive character
because if evolved in the ancestor common to all vertebrates.
Shared derived characters are useful in establishing a
phylogeny, but shared primitive characters are not.

The status of a character as analogous versus
homologous or shared versus primitive may depend on
the level at which the analysis is being performed.
All similar character

homologies analogies

Primitive derived
(ancestral) (unique to a clade)
For example, the forelimbs of bats and birds are analogous
adaptations for flight because the fossil record shows that both
evolved independently from the walking forelimbs of different
ancestors.
- Their common specializations for flight are convergent, not
indications of recent common ancestry.

The presence of forelimbs in both birds and bats is homologous,
through, at a higher level of the cladogram, at the level of tetrapods.

The question of homology versus analogy often depends on the
level of the clade that is being examined.
Systematists must sort through homologous features of characters
to separate shared derived characters from shared primitive
characters.

A shared derived character is uniquely to a particular clade.

A shared primitive character is found not only in the clade being
analyzed, but older clades too.

Shared derived characters are useful in establishing a phylogeny,
but shared primitive characters are not.
In an outgroup analysis, the assumption is that any homologies
shared by the ingroup and outgroup must be primitive characters
already present in the ancestor common to both groups.

Homologies present in some or all of the ingroup taxa must have
evolved after the divergence of the ingroup and outgroup taxa.
- In our example, a notochord, present in lancets and in the embryos
of the ingroup, would be a shared primitive character and not useful.

- The presence of a vertebral column, shared by all members of the
ingroup but not the outgroup, is a useful character for the whole
ingroup.

- Similarly, the presence of jaws, absent in lampreys and present in
the other ingroup taxa, helps to identify the earliest branch in the
vertebrate cladogram.
A key step in cladistic analysis is outgroup comparison which is
used to differentiate shared primitive characters from shared derived
ones.

To do this we need to identify an outgroup:
- a species or group of species that is closely related to the species
that we are studying,
- but known to be less closely related than any study-group
members are to each other.
To study the relationships among five vertebrates ( the ingroup): a
leopard, a turtle, a salamander, a tuna, and a lamprey, on a
cladogram, then an animal called the lancet would be a good
choice.
- The lancet is closely related to the most primitive vertebrates
based on other evidence and other lines of analysis.
- These other analyses also show that the lancet is not more closely
related to any of the ingroup taxa.
Systematists can use cladograms to place species in the taxonomic
hierarchy.
- For example, using turtles as the outgroup, we can assign
increasing exclusive clades to finer levels of the hierarchy of taxa.
However, some systematists argue that the hierarchical system is
antiquated because such a classification must be rearranged when
a cladogram is revised based on new evidence.
- These systematists propose replacing the Linneaen system with a
strictly cladistic classification called phylocode that drops the
hierarchical tags, such as class, order, and family.
- So far, biologists still prefer a hierarchical system of taxonomic
levels as a more useful way of organizing the diversity of life.
Analyzing the taxonomic distribution of homologies enables us to
identify the sequence in which derived characters evolved during
vertebrate phylogeny.

A cladogram presents the chronological sequence of branching
during the evolutionary history of a set of organisms.
- However, this chronology does not indicate the time of origin of the
species that we are comparing, only the groups to which they
belong.
- For example, a particular species in an old group may have
evolved more recently than a second species that belongs to a
newer group.
Most molecular systematics is based on a comparison of nucleotide
sequences in DNA, or RNA.
- Each nucleotide position along a stretch of DNA represents an
inherited character as one of the four DNA bases: A (adenine), G
(guanine), C (cytosine), and T (thymine).
- Systematists may compare hundreds or thousands of adjacent
nucleotide positions and among several DNA regions to assess
the relationship between two species.
- This DNA sequence analysis provides a quantitative tool for
constructing cladograms with branch points defined by mutations
in DNA sequence.
The rates of change in DNA sequences varies from one part of the
genome to another.
- Some regions (e.g., rRNA) that change relatively slowly are useful
in investigating relationships between taxa that diverged hundreds
of millions of years ago.
- Other regions (e.g., mtDNA) evolve relatively rapidly and can be
employed to assess the phylogeny of species that are closely
related or even populations of the same species.
3. Systematists can infer phylogeny from
molecular evidence

The application of molecular methods and data for comparing
species and tracing phylogenies has accelerated revision of
taxonomic trees.
- If homology reflects common ancestry, then comparing genes and
proteins among organisms should provide insights into their
evolutionary relationships.
- The more recently two species have branced from a common
ancestor, the more similar their DNA and amino acid sequences
should be.
These data for many species are available via the internet.
Molecular systematics makes it possible to assess phylogenetic
relationships that cannot be measured by comparative anatomy and
other non-molecular methods.
- This includes groups that are too closely related to have
accumulated much morphological divergence.
- At the other extreme, some groups (e.g., fungi, animals, and
plants) have diverged so much that little morphological homolgy
remains.
In 1969, R.H Whittaker argued for a five-kingdom system: Monera,
Protista, Plantae, Fungi, and Animalia.

The five-kingdom system recognizes that there are two
fundamentally different types of cells: prokaryotic (the kingdom
Monera) and eukaryotic (the other four kingdoms).

Three kingdoms of multicellular eukaryotes were distinguished by
nutrition, in part.
- Plant are autotrophic, making organic food by photosynthesis.
- Most fungi are decomposers with extracellular digestion.
- Most animals digest food within specialized cavities.
The first step in DNA comparisons is to align homologous DNA
sequences for the species we are comparing.
- Two closely related species may differ only in which base is
present at a few sites.
- Less closely related species may not only differ in bases at many
sites, but there may be insertions and deletions that alter the length
of genes.
- This creates problems for establishing homology.
4. The five-kingdom system reflected
increased knowledge of lifes diversity
Traditionally, systematists have considered kingdom as the highest
taxonomic category.

As a product of a long tradition, beginning with Linnaeus organisms
were divided into only two kingdoms of life-animal or plant.
- Bacteria, with rigid cell walls, were placed with plants.
- Even fungi, not photosynthetic and sharing little with green plants,
were considered in the plant kingdom.
- Photosynthetic, mobile microbes were claimed by both botanists
and zoologists.
Many microbiologists have divided the two prokaryotic domains into
multiple kingdoms based on cladistic analysis of molecular data.
A second challenge to the five kingdom system comes from
systematists who are sorting out the phylogeny of the former
members of the kingdom Protista.
- Molecular systematics and cladistics have shown that the Protista
is not monophyletic.
- Some of these organisms have been split among five or more new
kingdoms.
- Others have been assigned to the Plantae, Fungi, or Animalia.
In Whittakers system, the Protista consisted of all eukaryotes that
did not fit the definition of plants, fungi, or animals.
- Most protists are unicellular.
- However, some multicellular organisms, such as seaweeds, were
included in the Protista because of their relationships to specific
unicellular protists.
- The five-kingdom system prevailed in biology for over 20 years.
5. Arranging the diversity of life into the
highest taxa is a work in progress
During the last three decades, systematists applying cladistic
analysis, including the construction of cladograms based on
molecular data, have been identifying problems with the five-
kingdom system.
- One challenge has been evidence that there are two distinct
lineages of prokaryotes.
- These data led to the three-domain system: Bacteria, Archaea, and
Eukarya, as superkingdoms.
Different approach in classifying organism
How data are analyzed and interpreted depends on the
systematists approach

1. Phenetic
2. Cladistic
3. Classical evolutionary taxonomy
Phenetics
Phenetics is based on measurable phenotypic similarities and
differences.

A comparison is made of as many characters (atonomical
characteristics) as possible without attempting to sort homology from
analogy.

The phenetic approach is also called numerical taxonomy.

Pheneticists do not attempt to distinguish between homoplastic and
homologus characteristics.

The inclusion of homoplastic characteristics may lead to inaccurate
taxonomic classifications.
Clearly, taxonomy at the highest level is a work in progress.
- It may seem ironic that systematists are generally more confident
in their groupings of species into lower tax than they are about
evolutionary relationships among the major groups of organisms.
- Tracing phylogeny at the kingdom level takes us back to the
evolutionary branching that occurred in Precambrian seas a billion
or more years ago.
There will be much more research before there is anything close to
a new consensus for how the three domains of life are related and
how many kingdoms there are.
- New data will undoubtedly lead to further taxonomic modeling.
- Keep in mind that phylogenetic trees and taxonomic groupings are
hypotheses that fit the best available data.
Cladistics
Phylogenetic systematics (cladistics) emphasizes phylogeny.

Cladists use shared derived characters to reconstruct phylogenies
by outgroup analysis.

Cladograms illustrate branching between taxa.

Ancestral and derived characters are used to construct cladograms
Classical evolutionary taxonomy
Allows paraphyletics group which attempts to balance the extent of
divergence and the branching sequence.

Predates both phenetics and cladistics, but now incorporates some
ideas from both.

In cases of systematic conflict, a subjective judgement is made
about which type of information receives the highest priority.



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