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Classification and Cladistics

It covers the need for classifying organisms, the challenges associated with traditional taxonomic hierarchies, and the advantages of evolutionary-based classification methods. Detailed discussions on clades, cladograms, molecular clocks, and the three-domain system are included. The presentation provides IB-specific guiding questions, key terms, and activities to reinforce understanding of evolutionary relationships and phylogenetic methods.

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100% found this document useful (1 vote)
131 views57 pages

Classification and Cladistics

It covers the need for classifying organisms, the challenges associated with traditional taxonomic hierarchies, and the advantages of evolutionary-based classification methods. Detailed discussions on clades, cladograms, molecular clocks, and the three-domain system are included. The presentation provides IB-specific guiding questions, key terms, and activities to reinforce understanding of evolutionary relationships and phylogenetic methods.

Uploaded by

43660
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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First Exams 2025

A3.2
Classification
and Cladistics
Theme: Unity and Diversity

Level of Organisation: Organisms


Additional
HL
Content
HL Content Only
From
IB Guiding Questions the IB

What tools are used to classify organisms into taxonomic


groups?
How do cladistic methods differ from traditional
taxonomic methods?
HL Content Only
From
Additional HL Content - the IB

A3.2 Classification and Cladistics


A3.2.1: Need for classification of organisms
A3.2.2: Difficulties classifying organisms into the traditional hierarchy of
taxa
A3.2.3: Advantages of classification corresponding to evolutionary
relationships
A3.2.4: Clades as groups of organisms with common ancestry and shared
characteristics
HL Content Only
From
Additional HL Content - the IB

A3.2 Classification and Cladistics


A3.2.5: Gradual accumulation of sequence differences as the basis for
estimates of when clades diverged from a common ancestor
A3.2.6: Base sequences of genes or amino acid sequences of proteins as
the basis for constructing cladograms
A3.2.7: Analysing cladograms
A3.2.8: Using cladistics to investigate whether the classification of groups
corresponds to evolutionary relationships
HL Content Only
From
Additional HL Content - the IB

A3.2 Classification and Cladistics


A3.2.9: Classification of all organisms into three domains using evidence
from rRNA base sequences
HL Content Only

HL Only Key Terms

Taxonomy Node Common Ancestor


Taxon / Taxa Terminal Branch Domain
Cladistics Evolution Archaea
Clade Morphology
Eubacteria
Cladogram Molecular Clock
Eukarya
Root (of a cladogram) Parsimony Analysis
HL Content Only
From
A3.2.1: Need for classification of the IB

organisms

Classification is needed because of the immense diversity of species.


After classification is completed, a broad range of further study is
facilitated.
HL Content Only

Classification of Organisms:
Taxonomy
Taxonomy is the
science of classifying
organisms into groups.

Traditional taxonomy
classifies organisms
into groups, known as
taxa, based on
observable physical
traits.
HL Content Only

Classification of Organisms:
Taxonomy
Classification is needed because of the immense
diversity of species.
There are estimated to be around 8.7 million
different species on Earth.
Once an organism is classified, this facilitates a
broad range of further studies.
If you know the characteristics of known mammals
(Class Mammalia), then you know the common
characteristics of all mammals, including all
undiscovered mammals. Class Mammalia
HL Content Only
From
A3.2.2: Difficulties classifying the IB
organisms into the traditional
hierarchy of taxa
The traditional hierarchy of kingdom, phylum, class, order, family, genus
and species does not always correspond to patterns of divergence
generated by evolution.
Nature of Science: A fixed ranking of taxa (kingdom, phylum and so on)
is arbitrary because it does not reflect the gradation of variation.
Cladistics offers an alternative approach to classification using unranked
clades.
This is an example of the paradigm shift that sometimes occurs in
scientific theories.
HL Content Only

Traditional Taxonomy
A taxon is a group of any rank
such as species, order or
kingdom.
Taxa are traditionally
organised from the broadest
taxon, domain, to the most
specific taxon, species.
Traditional classification,
developed by Linnaeus,
placed organisms into taxa
based on observable physical
Classification of the red fox (Vulpes vulpes)
traits.
HL Content Only

Hierarchy of Taxa

IB students should be able to recall the Mnemonic Taxon


hierarchy of taxa. Dashing Domain
There are many mnemonics to help King Kingdom
remember the sequence from domain to Philip Phylum
species such as: Came Class
Over Order
The traditional hierarchy of kingdom, phylum,
class, order, family, genus and species does For Family
not always correspond to patterns of Great Genus
divergence generated by evolution. Soup Species
HL Content Only

Reptiles Do Not Exist


Read the linked article.

1. Explain why cladistics is


the “most widely accepted
method” of classification.
2. State what is true for all
members of a clade.
3. Explain why reptiles do not
exist according to
cladistics. Tetrapod cladogram
HL Content Only

Cladistics - A Paradigm Shift


Nature of Science: A paradigm shift is a fundamental change in understanding.

Changing from a traditional classification system based on arbitrary taxa, to


classifying organisms into clades with all members having a common ancestor
is an example of a paradigm shift.
Traditional classification grouped reptiles into a single taxon (Class Reptilia),
but this does not correspond to patterns of divergence by evolution.
Cladistics groups organisms into clades, where all members of a clade share a
common ancestor. Birds are more closely related to crocodiles and turtles than
other reptiles, therefore birds, crocodiles and turtles are classified into a single
clade.
HL Content Only
From
A3.2.3: Advantages of classification the IB

corresponding to evolutionary
relationships
The ideal classification follows evolutionary relationships, so all the
members of a taxonomic group have evolved from a common ancestor.
Characteristics of organisms within such a group can be predicted
because they are shared within a clade.
HL Content Only

Evolution

Evolution is the
change in the
heritable
characteristics of
populations of a
species over time.
HL Content Only

Classification and Evolution

The ideal classification system follows


evolutionary relationships, so all the
members of a taxonomic group have evolved
from a common ancestor as suggested by
Darwin’s sketch of the tree of life.
Traditional methods of classification, based
on observable traits, do not always group
organisms into groups which share a
common ancestor.
Darwin’s Tree of Life
HL Content Only

Cladistics
Cladistics is a method of classifying organisms
into groups called clades, based on shared
traits.
A clade is a group of organisms (or viruses)
that have all evolved from a common
ancestor. Characteristics of organisms can be
predicted according to the clades that they are
classified into.
Clades can be organised into cladograms,
which are tree diagrams that show the most
Cladogram of the great apes
probably divergence between species.
HL Content Only
From
A3.2.4: Clades as groups of the IB

organisms with common ancestry


and shared characteristics.

The most objective evidence for placing organisms in the same clade
comes from base sequences of genes or amino acid sequences of
proteins.
Morphological traits can be used to assign organisms to clades.
HL Content Only

Clades

Clades are groups of


organisms (or viruses) with
a common ancestry and
shared traits.
Morphological traits can be
used to assign organisms to
clades.
HL Content Only

Classifying Organisms into Clades


The most objective evidence for placing organisms in the same clade comes
from base sequences of genes or amino acid sequences of proteins.
Scientists can estimate these relationships by comparing DNA, RNA or
protein sequences.
As the organisms evolve and diverge, their DNA sequences accumulate
mutations. Scientists compare these mutations using sequence alignments
to reconstruct evolutionary history. (HHMI Biointeractive)
Students should complete the activity on “
Creating Phylogenetic Trees from DNA Sequences” from HHMI
Biointeractive.
HL Content Only
From
A3.2.5: Gradual accumulation of the IB

sequence differences as the basis for


estimates of when clades diverged
from a common ancestor

This method of estimating times is known as the “molecular clock”. The


molecular clock can only give estimates because mutation rates are
affected by the length of the generation time, the size of a population,
the intensity of selective pressure and other factors.
HL Content Only

Molecular Clock
Differences in the
base sequence of DNA
(and therefore
proteins) are the
result of mutations.
Mutations accumulate
gradually over long
periods of time at a
constant rate, so they
can be used as
molecular clocks.
HL Content Only

Molecular Clock
Molecular clocks are based on the gradual accumulation of sequence
differences, due to mutations, over time.
Molecular clocks can be used to estimate when clades diverged from a
common ancestor
Read the linked article on molecular clocks.

1. Explain why closely related organisms will have few differences in


gene or protein sequences.
2. Explain why the number of mutations will be higher in species which
have older common ancestors.
HL Content Only

Limits to Molecular Clocks


Molecular clocks only allow scientists to estimate when species diverged as
the following factors affect mutation rates within a population.
Limitations of molecular clocks include:
● Generation time - Species with shorter generation times provide more
opportunities for mutations to occur, resulting in faster molecular
clocks than species with longer generation times.
● Population size - Mutations are more likely to be fixed in small
populations, resulting in faster molecular clocks.
● Selective pressure - Under strong selective pressure (high intraspecies
competition), mutations are more likely to be fixed in a population.
HL Content Only

A3.2.6: Base sequences of genes From


the IB
or amino acid sequences of
proteins as the basis for
constructing
Examples can be simple andcladograms
based on sample data to illustrate the tool.
Nature of Science: Students should recognize that different criteria for
judgement can lead to different hypotheses. Here, parsimony analysis is
used to select the most probable cladogram, in which observed
sequence variation between clades is accounted for with the smallest
number of sequence changes.
Consider the consequences for treating diseases caused by rapidly
evolving viruses.
HL Content Only

Cladograms

Cladograms are tree diagrams


which show the most probable
sequence of divergence
between clades.

Nodes on a cladogram occur


where two or more species
diverge from a common ancestor.
Examples of nodes include
Canine Cladogram
HL Content Only

Constructing Cladograms

Cladograms can be
constructed by
grouping organisms
according to shared
characteristics.
HL Content Only

Constructing Cladograms
Comparing base sequences of genes or amino
acid sequences in proteins is the preferred
method of constructing cladograms, as the data
is objective.
Nucleotide sequences or amino acid sequences
are compared to determine the number of
differences in the gene/protein between species.
The fewer differences in the sequence, the more
closely related two species are.
Amniota Cladogram
HL Content Only

Parsimony Analysis of Cladograms

An analysis of differences between organisms can produce a number of


different cladograms
Parsimony analysis is used to select the most probable cladogram, in
which observed sequence variation between clades is accounted for
with the smallest number of sequence changes.
The assumption of parsimony analysis is that a simple hypothesis with a
small number of evolutionary changes is more likely to be true than a
complex hypothesis.
Read the linked article for more information on parsimony analysis
HL Content Only

Treating Rapidly Evolving Viruses


Rapidly evolving viruses can quickly develop resistance
to existing drugs and treatment, requiring more
research and development of new drugs.
The mutations often produce novel subtypes of the
virus, which are no longer recognised by the immune
system. The novel viruses will also impact the
effectiveness of current vaccines, which may no longer
confer immunity. COVID Virus

If the rapidly evolving viruses are not contained, it can


result in epidemics or pandemics.
HL Content Only
From
A3.2.7: Analysing cladograms the IB

Students should be able to deduce evolutionary relationships, common


ancestors and clades from a cladogram.
They should understand the terms “root”, “node” and “terminal branch”
and also that a node represents a hypothetical common ancestor.
HL Content Only

Clades on a Cladogram

A clade is a group of
organisms which have evolved
from a common ancestor.
A branch on a cladogram that
includes a single common
ancestor, a node, and all of its
descendants represents a
clade.
HL Content Only

Cladogram Definitions

Terminal Branch - is an
endpoint of a cladogram
representing one group.
Example: Birds

Node - is the point on a


cladogram where a common
Tetrapod Cladogram
ancestor diverges into two
Root - is the node on the cladogram that or more groups.
represents the theoretical last common
ancestor of all groups on the cladogram.
HL Content Only

Analysing Cladograms

1. Identify all of the organisms


within the cladogram with a
common ancestor at the
highlighted node.

2. Identify the animal that is


the closest relative of the
gray wolf.

Canine Cladogram
HL Content Only

Analysing Cladograms

The further back a node occurs on the


cladogram, the older the common
ancestor.

1. Identify the animal most closely


related to manatees and dugongs.

2. Identify the animals most closely


related to humans.

Mammals Cladogram
HL Content Only

Analysing Primate Cladograms

1. Identify members of the


primate clade with the most
recent common ancestor.

2. Identify the animals most


distantly related to humans.

Primate Cladogram
HL Content Only

Neanderthals and Modern Humans


Complete the linked activity on the relationship
between modern humans and Neanderthals Svante Pääbo was
awarded the Nobel
Prize in Physiology or
Medicine in 2022 “for
his discoveries
concerning the
genomes of extinct
hominins and human
evolution” (
❓ Deduce, with reason, if Neanderthals can be
NobelPrize.org)
classified into the same clade as modern humans.
HL Content Only
From
A3.2.8: Using cladistics to the IB

investigate whether the


classification of groups corresponds
to evolutionary relationships
A case study of transfer of plant species between families could be used
to develop understanding, for example the reclassification of the figwort
family (Scrophulariaceae). However, students are not required to
memorize the details of the case study.
HL Content Only
From
A3.2.8: Using cladistics to the IB

investigate whether the


classification of groups corresponds
to evolutionary relationships
Nature of Science: Students should appreciate that theories and other
scientific knowledge claims may eventually be falsified.
In this example, similarities in morphology due to convergent evolution
rather than common ancestry suggested a classification that by cladistics
has been shown to be false.
HL Content Only

The Figwort Family


Scrophulariaceae is a family of plants,
that are commonly known as the
figworts.
The figwort family were first
described and classified by Antoine
de Jussieu in 1879.
The figworts were classified based on
morphology, using similar traits.

Scrophularia nodosa
HL Content Only

Reclassification of the Figwort


Family
Plants that were originally placed into the
figwort family were reclassified using cladistics.
Scientists compared the nucleotide sequence
of three chloroplast genes for all members of
the figwort family and some of the plants that
were considered close relatives within the
same order of plants.
The result of the cladistic analysis was the
reclassification of many original members of
the figwort family.
Scrophularia californica
HL Content Only

Reclassification of the Figwort


Family
The results of the reclassification of the figwort family were:

● Fifty genera were reclassified into the plantain family (Plantaginaceae).


● Twelve genera were reclassified into the broomrape family
(Orobanchaceae).
● Thirteen genera were classified into a new family, lindernia
(Linderniaceae)
● Two genera were were reclassified into a new family, calceolaria (
Calceolariaceae).
● Two small families of other plants were reclassified into the figwort
family.
HL Content Only

Scientific Knowledge Can Be


Nature of Science Falsified
Theories and other scientific knowledge claims may eventually be
falsified by evidence. This means that the evidence shows the original
theory or claim is no longer valid.

Figworts were originally classified based on their morphology.


The analysis of the gene sequences of the plants required many plants to
be reclassified into different families.
The morphology of the plants was similar due to convergent evolution
rather than recent common ancestors.
HL Content Only
From
A3.2.9: Classification of all the IB

organisms into three domains


using evidence from rRNA base
sequences
This is the revolutionary reclassification with an extra taxonomic level
above kingdoms that was proposed in 1977.
HL Content Only

The Three Domains


Carl Woese proposed
adding an additional
taxonomic level, domain,
in 1977 after analysing
ribosomal RNA found in
prokaryotes.
Archaea rRNA is more
similar to eukaryotic
rRNA than bacterial rRNA,
suggesting that archaea
and eukarya have a more
recent common ancestor.
HL Content Only

The Three Domains

All organisms are


classified into one of
three domains:
● Archaea (archaeans)
● Eubacteria (bacteria)
● Eukarya (eukaryotes)
Note that Archaea have a more recent common
ancestor with Eukarya than with bacteria.
HL Content Only

The Three Domains


❓ Contrast eubacteria, archaea and eukarya by completing the table
(Research may be required).

Feature Eubacteria Archaea Eukarya


Chromosome shape
Histone proteins
associated with DNA
Presence of Introns
Component in cell walls
Nucleus
Lipid in plasma
membrane
Environment
HL Content Only
The Three Domains
Feature Eubacteria Archaea Eukarya
Chromosome shape Circular Circular Linear
Proteins associated Proteins associated Histone proteins
None
with DNA with DNA associated with DNA
Presence of Introns Seldom present Usually present Always present
Component in cell Peptidoglycan Not peptidoglycan Cellulose in plants
walls Chitin in fungi
Not present in
animals
Nucleus Not present Not present Present
Lipid in plasma Unbranched ester Branched ether Unbranched ester
membrane linked hydrocarbon linked hydrocarbon linked hydrocarbon
fatty acid chains fatty acid chains fatty acid chains
Environment type Not extreme Extreme Not extreme
HL Content Only

HL Only Key Terms

Taxonomy Node Common Ancestor


Taxon / Taxa Terminal Branch Domain
Cladistics Evolution Archaea
Clade Morphology
Eubacteria
Cladogram Molecular Clock
Eukarya
Root (of a cladogram) Parsimony analysis
HL and SL Content
From
A3.2 Viruses - IB Linking the IB

Questions

What mechanisms contribute to convergent evolution?


To what extent is the natural history of life characterized by increasing
complexity or simplicity?
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