DP Biology HL A3.2 Classification and Cladistics

DP Biology HL A3.2 Classification and Cladistics - Full notes

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DP Biology HL | A3.2 Classification and Cladistics

DP BIOLOGY · THEME A: UNITY AND DIVERSITY

A3.2

Classification and Cladistics

Full notes for HL · IB-style

Contents

1	Why classify organisms?
2	The traditional hierarchy of taxa
3	Natural classification and the problem with traditional groups
4	Clades and cladograms
5	Evidence for cladograms: sequences and molecular clocks
6	Reclassification and the three domains
7	Why classify organisms?
8	The three domains
9	Clades and cladistics
10	Reading cladograms
11	Molecular evidence for cladograms
12	The molecular clock
13	Constructing a cladogram from data
14	Homologous and analogous structures
15	Reclassification
16	Traditional versus cladistic classification
17	Mixed review: worked problems
18	Additional exam-style practice
19	Viruses and classification
20	Horizontal gene transfer and the tree of life
21	Kingdoms of eukaryotes
22	Using classification in conservation
23	Common misconceptions and links
24	Exam-style question with markscheme
25	Check your understanding
26	Summary and topic map

These are full teaching notes. Read each section in order, try the Think about it question before you read on, and do every Quick check before moving to the next section.

Before you start

Rate yourself on each statement now, and again after you've worked through the notes. Shade R (not yet), A (getting there) or G (confident).

I can…	R	A	G
explain the need for classification
outline the hierarchy of taxa from domain to species
explain why classification should correspond to evolutionary relationships
define clade and explain how cladograms are constructed and interpreted
explain how base and amino acid sequences are used as evidence
explain molecular clocks and their limitations
explain the reclassification of organisms, including the figwort family and the three domains

A3.2 is an Additional Higher Level (AHL) subtopic. It is studied by HL students only.

Guiding questions

How can we classify millions of species so that the classification reflects their evolutionary history? What do DNA sequences reveal that appearance cannot?

How this topic is examined

A3.2 is an HL-only subtopic and is examined mainly through cladograms: constructing them from data, identifying clades and the most closely related species, and evaluating them using molecular evidence.

Practise reading cladograms carefully: relatedness is shown by the most recent common ancestor (node), not by how close species are on the page.

Command term	What the examiner wants
State / Identify	a brief answer with no explanation needed
Outline	a brief account or summary
Describe	a detailed account, including trends or features, without reasons
Explain	a detailed account including causes, reasons or mechanisms
Distinguish / Compare and contrast	give the differences (and similarities), point by point
Calculate	a numerical answer with working and units
Deduce / Suggest	reach a conclusion from data; propose a reasonable explanation
Evaluate / Discuss	weigh strengths and limitations and reach a judgement

How to use these notes

Each section teaches one part of the syllabus in full. You'll see these boxes throughout; each has one job:

Box	What it's for
Think about it	a question to get you thinking before a section; the answer comes in the section
Key point	the one idea you must not forget
Common mistake	an error examiners see every year, and how to avoid it
In the real world	where the biology shows up outside the classroom
Try this	something quick you can do yourself to test the idea
Worked example	full solutions with IB-style marks (M1 method, A1 answer, R1 reasoning)
Quick check	short questions to test yourself at the end of each section

1 Why classify organisms?

Classification brings order to millions of species.

Think about it

A library sorts its books by subject so you can find related books together. What would a 'library of life' sorted by evolutionary relationships allow biologists to do?

There are about 2 million described species and probably many millions more undescribed. Classification organizes this diversity into groups, giving every species a place and a name. A good classification allows biologists to communicate clearly, store and retrieve information, and make predictions: if a newly discovered plant is closely related to one that contains a useful drug, it may contain similar compounds.

The science of naming and classifying organisms is called taxonomy, and each group is a taxon (plural taxa).

2 The traditional hierarchy of taxa

Groups nested within groups.

Since Linnaeus, organisms have been placed in a hierarchy of taxa, in which each taxon contains one or more taxa from the level below. The main levels are: domain, kingdom, phylum, class, order, family, genus and species. Moving down the hierarchy, groups contain fewer organisms that share more characteristics.

Taxon	Human	Grey wolf	Garden pea
Domain	Eukarya	Eukarya	Eukarya
Kingdom	Animalia	Animalia	Plantae
Phylum	Chordata	Chordata	Angiospermophyta
Class	Mammalia	Mammalia	Magnoliopsida
Order	Primates	Carnivora	Fabales
Family	Hominidae	Canidae	Fabaceae
Genus	Homo	Canis	Pisum
Species	sapiens	lupus	sativum

A mnemonic such as 'Dear King Philip Came Over For Good Soup' helps you remember the order. Note that the hierarchy is a human convention: there is nothing in nature that makes a 'class' equivalent across different groups.

Quick check

1. List the eight main taxa in order.

2. What happens to the number of shared features moving down the hierarchy?

Answers: 1. domain, kingdom, phylum, class, order, family, genus, species 2. it increases

3 Natural classification and the problem with traditional groups

A classification should reflect common ancestry.

A natural classification groups organisms according to their evolutionary relationships: all members of a group share a common ancestor, and all descendants of that ancestor are in the group. Such classifications are predictive, because closely related organisms share many features inherited from their common ancestor.

Traditional classifications based on visible features sometimes produced artificial groups. Organisms can look alike because of convergent evolution (similar adaptations to similar environments) rather than common ancestry: the wings of birds and bats, or the streamlined shapes of sharks and dolphins. Such similar but independently evolved structures are analogous, and grouping by them misleads. Features inherited from a common ancestor are homologous and are the right basis for classification.

Some traditional groups are not natural. 'Reptiles', defined traditionally, excludes birds, yet birds evolved from reptiles (dinosaurs): crocodiles are more closely related to birds than to lizards.

Common mistake

Grouping organisms by analogous structures. Bird and bat wings evolved independently and do not show close relationship.

4 Clades and cladograms

A clade is an ancestor and all its descendants.

A clade is a group of organisms that consists of a common ancestor and all of its descendants. Members of a clade share characteristics inherited from that ancestor. Clades can be large (all vertebrates) or small (a single genus).

A cladogram is a tree diagram showing the evolutionary relationships between clades. Its parts are: terminal branches (the present-day species or groups at the tips); nodes (branch points, each representing a hypothetical common ancestor where lineages split); and the root (the common ancestor of all groups shown).

Reading a cladogram. Two groups are more closely related if they share a more recent common ancestor, that is, a node closer to the tips. The order of species along the tips can be rotated around any node without changing the relationships, so position on the page does not indicate relatedness.

Cladograms are constructed on the principle of parsimony: the best tree is the one that requires the fewest evolutionary changes to explain the observed characteristics.

Figure 1. A cladogram of vertebrates. Each node (blue dot) is a common ancestor; humans and lizards share a more recent ancestor than either does with frogs.

WORKED EXAMPLE 1 Interpreting a cladogram

Using the cladogram of vertebrates, (a) identify the species most closely related to the lizard; (b) state how many clades include the frog; (c) explain why the salmon is more closely related to the frog than to the lamprey.

Solution

(a) Human: they share the most recent common ancestorA1

(b) Count nodes from the root to the frog: the frog is in three clades (including the one containing all five)A1

Quick check

1. Define a clade.

2. What does a node represent?

3. What is the principle of parsimony?

Answers: 1. a common ancestor and all its descendants 2. a hypothetical common ancestor where lineages split 3. the tree with fewest evolutionary changes is preferred

5 Evidence for cladograms: sequences and molecular clocks

DNA and protein sequences reveal relationships directly.

Cladograms were originally based on morphology. Today they are mostly based on base sequences of genes or amino acid sequences of proteins. The more differences between the sequences of two species, the longer ago they diverged from a common ancestor. Sequence data are objective and can be gathered from thousands of genes.

Differences in sequences accumulate gradually as mutations occur. If mutations accumulate at a roughly constant rate, the number of differences can be used as a molecular clock to estimate when two lineages diverged. The clock is calibrated using fossils of known age.

Limitations of molecular clocks: mutation rates differ between genes, between lineages and over time; generation time affects the rate; natural selection can speed up or slow down change; and calibration depends on the fossil record.

Species compared with humans	Differences in cytochrome c (out of 104 amino acids)
Chimpanzee	0
Rhesus monkey	1
Horse	12
Chicken	13
Yeast	44

WORKED EXAMPLE 2 Using sequence data

Using the cytochrome c data, rank the species from most to least closely related to humans and explain your reasoning.

Solution

Chimpanzee, rhesus monkey, horse, chicken, yeastA1

Fewer differences indicate more recent common ancestorR1

Differences accumulate over time as mutations occurR1

Quick check

1. Why do more sequence differences indicate more distant relationships?

2. Give two limitations of molecular clocks.

Answers: 1. more time since divergence for mutations to accumulate 2. variable mutation rates; generation time; selection; calibration

6 Reclassification and the three domains

New evidence changes classifications.

Cladistic analysis has led to the reclassification of many groups. A well-known example is the figwort family (Scrophulariaceae). Traditionally it contained over 5 000 species grouped by flower shape. DNA analysis of chloroplast genes showed that the family was not a clade: its members belonged to several distinct lineages. More than half the genera were moved to other families (such as the plantain family, Plantaginaceae), and some species from other families were added. The figwort family is now a smaller but natural group.

On a larger scale, analysis of ribosomal RNA sequences by Carl Woese in the 1970s showed that prokaryotes are not a single group. Organisms were reclassified into three domains: Bacteria, Archaea and Eukarya. Archaea look like bacteria but differ in their membrane lipids, cell walls and rRNA, and are in some ways more closely related to eukaryotes.

Feature	Bacteria	Archaea	Eukarya
Nucleus	absent	absent	present
Histones with DNA	absent	present in some	present
Cell wall	peptidoglycan	no peptidoglycan	cellulose / chitin / absent
Membrane lipids	ester-linked, unbranched	ether-linked, branched	ester-linked, unbranched
Typical habitats	everywhere	often extreme (hot springs, salt lakes)	everywhere

Key point

Classification is provisional: new evidence, especially from DNA, can show that traditional groups are not clades and should be revised.

Quick check

1. What evidence led to the reclassification of the figwort family?

2. What are the three domains?

Answers: 1. chloroplast DNA sequences showed it was not a clade 2. Bacteria, Archaea, Eukarya

7 Why classify organisms?

Order from diversity.

Classification organizes the enormous diversity of life, aids identification, allows predictions (related organisms share features), and reflects evolutionary relationships. A natural classification groups organisms by common ancestry.

WORKED EXAMPLE 3 Predictive value (standard)

Explain how natural classification can help in drug discovery.

Solution

Related species share biochemical pathwaysR1

If one plant produces a useful compound, relatives may produce similar onesR1

8 The three domains

Archaea, Bacteria, Eukarya.

Woese (1977) proposed the three domains from rRNA sequence comparisons, showing that archaea are as different from bacteria as both are from eukaryotes.

Feature	Bacteria	Archaea	Eukarya
nucleus	no	no	yes
histones	no	yes (some)	yes
membrane lipids	ester-linked	ether-linked	ester-linked
cell wall	peptidoglycan	no peptidoglycan	varies
introns	rare	some	common

WORKED EXAMPLE 4 Evidence (standard)

What evidence led to the three-domain system?

Solution

Comparison of ribosomal RNA sequencesA1

9 Clades and cladistics

Groups with a common ancestor.

A clade is a group containing a common ancestor and all its descendants. Clades are identified by shared derived characteristics (synapomorphies). Cladistics uses these to build cladograms, branching diagrams of evolutionary relationships.

WORKED EXAMPLE 5 Identifying a clade (standard)

Are birds and crocodiles in the same clade? Explain.

Solution

Yes: both descended from a common archosaur ancestorR1

Shared derived features (e.g. four-chambered heart, gizzard)R1

Quick check

1. Define a clade.

Answers: 1. a common ancestor and all its descendants

10 Reading cladograms

Nodes and roots.

Each node represents a common ancestor where lineages split. The root is the common ancestor of all organisms on the cladogram. Species sharing a more recent node are more closely related. Rotating branches around a node does not change relationships.

WORKED EXAMPLE 6 Interpretation (exam level)

On a cladogram, A and B share a node; C joins at an earlier node. Which species is most closely related to A?

Solution

B: most recent common ancestorA1

Common mistake

Reading relatedness from how close species appear at the tips. Relatedness is shown by how recently their lineages branched (the nodes).

Quick check

1. Does a longer branch always mean more change?

Answers: 1. only on cladograms drawn to scale (phylograms)

11 Molecular evidence for cladograms

DNA and protein sequences.

Differences in base sequences (DNA) or amino acid sequences (proteins such as cytochrome c or haemoglobin) between species accumulate over time. Fewer differences mean a more recent common ancestor.

Species compared with humans	Amino acid differences in cytochrome c
chimpanzee	0
rhesus monkey	1
horse	12
chicken	13
yeast	44

WORKED EXAMPLE 7 Interpreting (standard)

Use the table to rank the species by relatedness to humans.

Solution

chimpanzee > rhesus monkey > horse > chicken > yeastA1

12 The molecular clock

Dating divergence.

If mutations accumulate at a roughly constant rate, the number of differences can estimate the time since two species diverged. The clock is calibrated using fossils of known age. Rates vary between genes and lineages, limiting accuracy.

WORKED EXAMPLE 8 Calculation (exam level)

A gene accumulates 1 difference per 2 million years. Two species differ by 14. Estimate the time since divergence.

Solution

14 × 2 million years = 28 million years of total changeM1

Split between two lineages: about 14 million years agoA1

Quick check

1. Give one limitation of the molecular clock.

Answers: 1. mutation rates vary between genes and lineages

13 Constructing a cladogram from data

Shared derived features.

List characteristics for each organism; identify which are shared derived features; group organisms by the number of shared features; the organism sharing the fewest is the outgroup and branches first.

Organism	Vertebrae	Four limbs	Amniotic egg	Hair
lamprey	yes	no	no	no
frog	yes	yes	no	no
lizard	yes	yes	yes	no
mouse	yes	yes	yes	yes

WORKED EXAMPLE 9 Building (exam level)

Describe the cladogram for these organisms.

Solution

Lamprey branches first (fewest derived features)R1

Then frog, then lizard; mouse and lizard share the most recent ancestorR1

14 Homologous and analogous structures

Similarity from ancestry or function.

Homologous structures (pentadactyl limbs) share an evolutionary origin but may have different functions; they support grouping into clades. Analogous structures (wings of insects and birds) have similar functions but different origins (convergent evolution) and can mislead classification.

WORKED EXAMPLE 10 Distinguishing (standard)

Classify bat wings and butterfly wings.

Solution

Analogous: similar function, different originsA1

15 Reclassification

Classification changes with evidence.

Cladistics has led to reclassification. The figwort family (Scrophulariaceae) was split after DNA evidence showed it was not a clade. Birds are now recognized as a clade within reptiles (dinosaurs). The 'reptiles' group excluding birds is paraphyletic.

WORKED EXAMPLE 11 Paraphyletic (exam level)

Explain why 'reptiles' excluding birds is not a clade.

Solution

It includes the common ancestor but not all its descendants (birds excluded)R1

16 Traditional versus cladistic classification

Similarity versus ancestry.

Traditional classification grouped organisms by overall similarity; cladistics groups strictly by common ancestry. Cladistic groups are objective and testable, but some familiar groups (fish, reptiles) are not clades.

WORKED EXAMPLE 12 Comparing (standard)

Give one advantage of cladistic classification.

Solution

Based on evolutionary relationships; testable with DNA evidenceR1

17 Mixed review: worked problems

Bringing the ideas together.

WORKED EXAMPLE 13 Mixed problem (exam level)

Explain how DNA sequence data can be used to construct a cladogram.

Solution

Compare base sequences of a gene between speciesR1

Count differences; fewer differences = more closely relatedR1

Group species by most recent common ancestor; software builds the treeR1

18 Additional exam-style practice

Paper 1 and Paper 2.

WORKED EXAMPLE 14 Paper 1 question (standard)

Which describes a clade? A. organisms that look similar B. an ancestor and all its descendants C. organisms in the same habitat D. an ancestor and some descendants

Solution

BA1

WORKED EXAMPLE 15 Paper 2 question (exam level)

Outline the evidence for the three-domain system.

Solution

rRNA sequences show three distinct groupsR1

Differences in membrane lipids, histones and cell wallsR1

19 Viruses and classification

Outside the tree of life.

Viruses are not included in the three-domain system because they are not cellular and may have multiple origins. They are classified separately by genome type (DNA/RNA, single/double stranded) in the Baltimore classification.

Quick check

1. Why are viruses not placed in a domain?

Answers: 1. they are not cells; uncertain and probably multiple origins

20 Horizontal gene transfer and the tree of life

A web, not a tree?

Bacteria and archaea exchange genes between species by horizontal gene transfer (plasmids, transformation, viruses). This means early evolution may look more like a web than a tree, complicating cladistics for prokaryotes.

Quick check

1. Give one mechanism of horizontal gene transfer.

Answers: 1. conjugation (plasmid transfer)

21 Kingdoms of eukaryotes

Animals, plants, fungi and protists.

Within Eukarya, traditional kingdoms are Animalia, Plantae, Fungi and Protista. 'Protista' is not a clade: it groups unrelated eukaryotes that are not animals, plants or fungi.

Quick check

1. Why is Protista not a natural group?

Answers: 1. it contains organisms from several separate lineages

22 Using classification in conservation

Prioritizing lineages.

Conservation can prioritize evolutionarily distinct species (with few close relatives), such as the tuatara or the platypus, because their loss removes a large amount of unique evolutionary history (the EDGE approach).

Quick check

1. Why is the tuatara considered evolutionarily distinct?

Answers: 1. it is the only surviving member of an ancient reptile order

23 Common misconceptions and links

Students often think…	Actually…
species close together on a cladogram are closely related	relatedness depends on the most recent common node
similar appearance means close relationship	analogous structures arise by convergent evolution
molecular clocks are exact	rates vary between genes and lineages
archaea are a type of bacteria	they form a separate domain

How A3.2 connects to the rest of the course

Topic	Connection
A3.1 Diversity	species and binomial names
A4.1 Evolution	homologous and analogous structures; common ancestry
A1.2 Nucleic acids	sequence data
A2.2 Cell structure	prokaryotes and eukaryotes

24 Exam-style question with markscheme

Try this under exam conditions (about 15 minutes) before reading the markscheme.

Figure 2. Cladogram of five species A to E.

Text A. The cladogram was constructed from differences in the base sequence of a mitochondrial gene.

(a) Define the term clade. [2]

(b) Identify the species most closely related to D. [1]

(d) Outline one limitation of using molecular clocks. [2]

(e) Explain why some traditional groups have been reclassified. [2]

Markscheme

Part	Answer	Marks
(a)	group of organisms with a common ancestor	A1
	and all its descendants	A1
(b)	E	A1
(c)	compare sequences between species	R1
	count differences	R1
	fewer differences = more recent common ancestor; parsimony	R1
(d)	mutation rate not constant	R1
	e.g. differs between genes / lineages / generation time	R1
(e)	DNA showed groups were not clades	R1
	e.g. figwort family members belonged to different lineages	R1

Examiner's comments. In (b), some candidates chose the species printed next to D. Use the nodes, not the position on the page.

25 Check your understanding

Section A: multiple choice

1. A clade includes

A. a common ancestor and all its descendants B. only living species C. organisms that look alike D. one species only

2. On a cladogram, a node represents

A. a living species B. an extinct dead end C. a common ancestor D. a mutation

3. Analogous structures result from

A. common ancestry B. convergent evolution C. mutation D. artificial selection

4. The three domains are

A. Plants, Animals, Fungi B. Prokaryotes, Eukaryotes, Viruses C. Monera, Protista, Fungi D. Bacteria, Archaea, Eukarya

5. The figwort family was reclassified using

A. flower colour B. chloroplast DNA sequences C. leaf shape D. fossil records

6. The correct order of taxa is

A. kingdom, phylum, class, order B. kingdom, class, phylum, order C. phylum, kingdom, order, class D. order, class, phylum, kingdom

Section B: structured

7. Explain how a cladogram is constructed. [4]

8. Distinguish between homologous and analogous structures. [2]

9. Evaluate the use of molecular clocks. [4]

Answers

1. A 2. C 3. B 4. D 5. B 6. A

7. Choose characters/sequences; compare; group by shared derived features; parsimony; nodes as ancestors.

8. Homologous: from common ancestor; analogous: similar function, independent origin.

9. Estimate divergence times objectively; but rates vary; calibration from fossils; selection effects.

26 Summary and topic map

Idea	Remember
Hierarchy	domain, kingdom, phylum, class, order, family, genus, species
Natural classification	based on common ancestry
Clade	ancestor + all descendants
Cladogram	nodes, root, terminal branches; parsimony
Evidence	base and amino acid sequences
Molecular clock	differences estimate divergence time; limitations
Reclassification	figwort family; three domains

Before the exam, make sure you…

•read relatedness from nodes
•define clade with 'all descendants'
•use sequence data to justify relationships
•state limitations of molecular clocks

Classification and Cladistics on one page

Cover this page with a sheet of paper and try to rebuild it from memory. Whatever you can't recall is what to revise next.

Figure 3. Topic map for Classification and Cladistics.

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