A3.2Theme A — Unity and diversity
Classification and cladistics — IB Biology HL Revision Notes & Topical Questions
10 min read 11 parts Lesson 11 of 14 2 quizzes
Curriculum Equation Key قوانين الرقم الهيدروجيني والاتزان الأيوني - pH & Acid-Base Equilibrium FormulasFast Exam Solution
pH = -log[H⁺] | pOH = -log[OH⁻] | pH + pOH = 14 | [H⁺][OH⁻] = 10⁻¹⁴
Word Equation & Conditions: الرقم الهيدروجيني = -لوغاريتم تركيز أيون الهيدروجين | pH + pOH = 14
Location & Specifications: الاتزان الأيوني، كيمياء 3 ثانوي، التحصيلي، و AP Chemistry.
Lesson summary
A3.2 Classification and cladistics — IB BIOLOGY HL notes: Explain the taxonomic hierarchy, the three-domain system, cladistics, cladograms and reclassification using sequence data.Global biodiversity — it is vast and only estimated, with many species undiscovered.Taxonomy = the s…
- Order of taxa from largest
- Morphology
- Taxonomic rank
- Species boundaries
- Nature of science
- Monophyletic
Section 1 of 11Why organisms are classified
Why organisms are classified
Global biodiversity
- Global biodiversity it is vast and only estimated, with many species undiscovered.
Taxonomy
Taxonomy the science of classification, carried out by taxonomists, who place organisms in taxa and name them.
Method
- Method observable characteristics were used historically and are now combined with genome sequencing.
Benefits of accurate classification
- It gives an accurate count of known species and avoids recording a species twice or merging several species.
- It shows evolutionary relationships and common ancestry.
- It targets conservation, because several species wrongly treated as one could be lost together.
- It speeds medical research, because relatives of a medicinal plant can be tested first.
- It speeds work on new diseases, for example the COVID-19 virus was quickly classified as a coronavirus, which informed vaccine development.
Section 2 of 11Taxonomic hierarchy
Hierarchy
Hierarchy larger groups containing smaller groups with no overlap.
Order of taxa from largest
- Order of taxa from largest domain, kingdom, phylum, class, order, family, genus, species.
- (mnemonic: Dear King Phillip Came Over For Great Soup)
| Rank | Wolf | Hibiscus |
|---|---|---|
| Domain | Eukaryote | Eukaryote |
| Kingdom | Animalia | Plantae |
| Phylum | Chordata | Angiospermae |
| Class | Mammalia | Dicotyledonae |
| Order | Carnivora | Malvales |
| Family | Canidae | Malvaceae |
| Genus | Canis | Hibiscus |
| Species | lupus | rosa-sinensis |
Section 3 of 11Difficulties with classification
Morphology
- Morphology similar appearance does not show recent common ancestry.
- Dolphins (mammals) and sharks (fish) have similar streamlined shapes that evolved separately.
- Genome sequencing reduces this problem but does not solve every challenge.
Taxonomic rank
- Taxonomic rank hybrids between plants in distant taxa are hard to place,
- and moving one group between taxa may force all groups in the taxon to shift rank.
Species boundaries
- Species boundaries the point at which populations become different species is subjective.
- Introgression = fertile hybrid offspring breeding back with only one parent species, so descendants fit neither species fully.
- Example — early humans bred with Neanderthals and the offspring bred with early humans, so some modern humans carry Neanderthal genes.
Nature of science
- Nature of science the fixed ranking is arbitrary because variation is gradual.
- Species must be clearly distinct and obey breeding rules to fit ranks, which is not true in nature.
- A good system follows the evidence, and genome data often lead to reclassification.
Section 4 of 11Cladistics and clades
1Clade
Clade a group of organisms that all descended from a common ancestor, which can include extinct species and the extinct ancestor.
2Monophyletic
Monophyletic containing a common ancestor and all of its descendants.
3Common ancestor
- Common ancestor the most recent common ancestor of siblings is their parents and of cousins is their grandparents.
4Taxonomy versus cladistics
- Taxonomy versus cladistics taxonomy classifies and names, while cladistics identifies evolutionary relationships.
- A taxon should be a clade if taxonomy is correct, but historical errors mean it is not always so.
5Advantages
- Advantages clades hold close relatives and share characteristics inherited from the ancestor.
- Care is needed not to group organisms by analogous characteristics.
6Errors to avoid
- Errors to avoid splitting descendants of one ancestor into different clades and including organisms from a different ancestor.
Section 5 of 11Identifying clade members
1
Sequence data
- Sequence data the most objective method uses DNA, mRNA or amino acid sequences, and more similar sequences mean more closely related species.
- Species separated for longer have accumulated more mutations.
2
Morphology
- Morphology close relatives are more likely to look alike, but this is subjective and has caused errors.
- Similar morphology can come from convergent evolution.
- Bats could be grouped with birds by wings or with mammals by fur.
3
Primitive and derived traits
- Primitive traits arose early in a lineage and are found in all members, for example the spinal cord in vertebrates and six legs in insects.
- Derived traits arose later and differ between members, for example feathers in birds and fur in mammals.
- A trait can be derived in one clade and primitive in another, and closer relatives share more derived traits.
Section 6 of 11Molecular clock and DNA hybridisation
1Sequence differences
- Sequence differences more differences mean the species diverged longer ago.
2
DNA hybridisation
Molecular clock and DNA hybridisation
Take single-stranded DNA from the same part of the genome of two species.
Allow the complementary strands to bind to each other.
Unbound points show base differences, and their number is recorded.
- Molecular clock
- mutations occur at a roughly constant rate, so the number of differences estimates the time since divergence.
- The assumed rate does not always match the real rate, so results are estimates.
- Generation time, population size and selection pressure affect the rate.
Section 7 of 11Constructing and analysing cladograms
Cladogram
Cladogram an evolutionary tree showing the probable order of divergence and relationships.
Data
- Data base or amino acid sequences are used because observable traits can mislead.
- Several genes give a more reliable cladogram than one gene.
Parsimony
- Parsimony computers build the shortest cladogram with the fewest divergence events, because the simplest explanation is preferred.
- Fur is more likely to have evolved once than twice, so mammals share one ancestor.
- Cladograms show the most probable relationships and may change with new evidence.
Nature of science
- Nature of science different criteria can lead to different hypotheses, and a cladogram is a hypothesis.
Reading a cladogram
- A node is where two branches separate and represents a common ancestor.
- Clades that join at an adjacent node are more closely related than to any other clade.
- Needing many nodes before two clades join shows a distant relationship.
- The root at the base is the common ancestor of all organisms in the cladogram.
- A terminal branch is the most recent species in a lineage.
- Numbers on branches give base or amino acid changes, which can be used as a molecular clock, and some cladograms have a time scale.
Primate example
- Primate example humans are most closely related to chimps and bonobos, then gorillas, and diverged from chimps and bonobos 5–7 million years ago.
Section 8 of 11Reclassification: the figwort family
Reclassification: the figwort family
Original group
- Scrophulariaceae, once the 8th largest angiosperm family, was defined in the late 1700s with 16 genera and grew to 275 genera.
- Classification used traits such as a tube-shaped flower, with foxgloves and yellow rattle as members.
DNA evidence
- DNA evidence analysis of three chloroplast genes showed the family was not a true clade.
- It was paraphyletic because it did not contain all descendants of one ancestor and included separate lineages.
Outcome
- New families were created and some genera moved to existing families.
- The remaining genera plus two previously missed genera formed a new Scrophulariaceae, less than half its original size.
Nature of science
- Nature of science theories can be falsified.
- Shared flower traits were due to convergent evolution, so the old classification was falsified.
- New DNA and computer analysis provides a new theory, and further evidence can lead to further reclassification.
Types of change
- Types of change species are moved between groups, groups are split and groups are merged.
Section 9 of 11Three domains
History of kingdoms
- Plants and animals were the first kingdoms, and fungi were first wrongly placed in plants.
- Microscopes showed prokaryotes and eukaryotes,
- giving five kingdoms of plants, animals, fungi, protoctists and prokaryotes.
- (mainly single-celled eukaryotes)
- giving five kingdoms of plants, animals, fungi, protoctists and prokaryotes.
- rRNA analysis showed two distinct prokaryote groups, leading to the three-domain system of Archaea, Eubacteria and Eukarya.
Archaea
- Archaea single-celled organisms, some in extreme habitats such as thermophiles in hot springs and methanophiles that metabolise methane.
- They were first grouped with bacteria because they have a circular chromosome, a cell wall and 70S ribosomes.
- Woese showed in 1977 that their cell walls, membrane lipids and small ribosomal subunit differ from bacteria,
- and that methanogens lack some bacterial DNA sequences.
- They are thought to be more closely related to eukaryotes than to eubacteria.
| Feature | Archaea | Eubacteria | Eukaryotes |
|---|---|---|---|
| Cell type | Prokaryotic | Prokaryotic | Eukaryotic |
| Chromosome | Circular | Circular | Linear, with circular mitochondrial and chloroplast DNA |
| Membrane lipids | Glycerol-ether | Glycerol-ester | Glycerol-ester |
| Ribosomes | 70S, small subunit like eukaryotes | 70S | 80S in cytoplasm, 70S in mitochondria and chloroplasts |
| Cell walls | Always, without peptidoglycan | Always, with peptidoglycan | Sometimes, with or without peptidoglycan |
| Histones | Yes | No | Yes |
| Introns | Sometimes | Rarely | Yes |
Section 10 of 11Key terms
| Term | Meaning |
|---|---|
| Taxonomy | the science of classifying and naming organisms. |
| Clade | a group of organisms that descended from a common ancestor. |
| Monophyletic | a group containing an ancestor and all its descendants. |
| Paraphyletic | a group that does not include all descendants of its common ancestor. |
| Cladogram | an evolutionary tree showing probable order of divergence. |
| Parsimony | the principle that the simplest explanation, with fewest changes, is preferred. |
| Derived trait | a trait that evolved later in a lineage and differs between clade members. |
| Introgression | fertile hybrids breeding back with one parent species. |
| Molecular clock | estimating divergence time from the constant rate of mutation. |
Section 11 of 11Exam technique
1
A taxon and a clade are always identical — a taxon is a named group and may not contain all descendants of an ancestor.
2
Similar appearance shows close relationship — convergent evolution can produce similar features in unrelated organisms.
3
Archaea are a type of bacteria — they form their own domain with features closer to eukaryotes in some respects.
4
The molecular clock gives exact dates — it gives estimates because mutation rates vary.
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