BIOL1030 Chap.1 Phylogeny, Prokaryotes and Protists
Phylogeny, Prokaryotes and Protists
Phylogeny, Prokaryotes and Protists covers the first three lectures of Unit 5 in Week 1. It begins with how to read a phylogenetic tree: roots, branches and nodes, ancestors placed at nodes, and the difference between monophyletic, paraphyletic and polyphyletic groups, shown with whales and their hoofed relatives.
It separates ancestral from derived characters, gene trees from species trees, and orthologues from paralogues, and explains when DNA or protein alignments suit a comparison.
The chapter then turns to bacteria and archaea, their membranes, differentiation and three recombination routes, before tracing eukaryotes to Asgard archaea and to the engulfed bacteria that became mitochondria and plastids, including secondary endosymbiosis and the nucleomorph.
What this chapter covers
- 01
Roots, branches and nodes on a phylogenetic tree
- 02
Monophyletic, paraphyletic and polyphyletic groups
- 03
Plesiomorphies, synapomorphies and gene versus species trees
- 04
Bacteria and archaea: membranes, differentiation and recombination
- 05
Asgard archaea and the origin of eukaryotes
- 06
Primary and secondary endosymbiosis and the nucleomorph
- 07
Protists as symbionts and pathogens
Worked example · free
Classify three groupings on the whale and hoofed mammal tree
- 1State the rule: a monophyletic group holds one ancestor and every descendant of it.
- 1(a) Cetartiodactyla includes the shared ancestor of camels, pigs, cattle, hippos and whales and all of its descendants, so it is monophyletic.
- 1(b) Artiodactyla keeps that ancestor but drops the whales, one branch of its descendants, so it is paraphyletic.
- 1(c) Whales and seals reached the sea separately; no node unites only them, so marine mammals are polyphyletic.
Key terms
- Monophyletic group
- A group made of one ancestor and all of its descendants, also called a clade.
- Synapomorphy
- A shared derived character that identifies the members of a particular clade.
- Paralogue
- One of two gene copies within a genome that arose by gene duplication rather than by speciation.
- Nucleomorph
- The strongly reduced remnant nucleus of an engulfed alga left inside a secondary plastid.
- Holobiont
- A host organism together with the symbionts living in or on it, treated as one unit.
Phylogeny, Prokaryotes and Protists FAQ
How do you tell whether a group on a tree is monophyletic?
Find the most recent node that joins all the members. If every lineage descending from that node is included, the group is monophyletic. If some descendants are left out it is paraphyletic, and if the members only come together through separate origins of a shared trait, with no single node of their own, it is polyphyletic.
Why can a tree built from one gene give the wrong species relationships?
A single gene records the history of its own copies. If the gene duplicated, copies from different species may be paralogues, which split at the duplication, not at speciation. Species trees therefore combine many orthologous genes, copies separated only by speciation, often thousands of them.
Where did mitochondria and chloroplasts come from?
Both descend from bacteria engulfed and kept by a host cell. The host was related to Asgard archaea, the mitochondrion to alpha-proteobacteria and the plastid of algae and plants to cyanobacteria. Some algae later gained plastids secondhand by swallowing another alga, sometimes leaving its reduced nucleus behind.
How do bacteria gain new genes without sex?
Besides mutation, they recombine DNA in three ways. Transformation takes up free DNA from the surroundings, transduction moves DNA inside a bacteriophage, and conjugation passes genetic material directly between two cells that are in contact. None of these routes needs sexual reproduction, so they add variation alongside mutation in single-celled populations.
Exam move
Start by drawing one tree of your own from memory each day and labelling the root, two nodes and a clade, then circle a paraphyletic and a polyphyletic grouping on it. Pair every term with its opposite: plesiomorphy and synapomorphy, orthologue and paralogue, gene tree and species tree, LUCA and FUCA.
For the cell story, practise sketching the engulfment sequence from host to mitochondrion to plastid to secondary plastid without notes, and add the nucleomorph at the last step. Finish by sorting each protist or prokaryote the lecture mentions into partner, pathogen or free-living, and test yourself with the weekly quiz before moving on to the plants.
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