Reconstructing the Phylogeny

07/10/22

Cladistics

Biological classification system that involves the categorisation of organisms based on their shared traits.

Distance methods

Determine a distance matrix and a minimal distance tree

Character methods

Evaluate multiple trees to find the most likely or most parsimonious tree

Parsimonious

Least number of changes

Plesiomorphy

An ancestral character state

Symplesiomorphy

A character state shared by several groups, but inherited from ancestors older than the last common ancestor.

Apomorphy

Derived character state

Autopomorphy

Apomorphy unique to one group

Synapomorphy

Apomorphy shared by two or more groups which originated in their last common ancestor. Helpful in constructing a tree.

Homoplasy

Development of bodily structures within different species, which resemble each other and have the same functions, but no common ancestral origin

Inter-species crossing

Exchange of genetic material between closely related, but distinct, species

Different rates of evolution

Rate of evolution for the character can differ between clades

Homoplasies

* Similar character states that evolved independently


* Parallel evolution or convergence


* Can happen due to adaption to a similar ecological niche/environment,

Cladistic Method: Character Matrix

* Records the number of differences between each pair of species
* Closely related species will have fewer differences


* The 0 shows they don’t have the character state
* The tree can show when derived states first emerged

Maximum Parsimony Method

* The tree construction relies on the correct interpretation of characters,
* It can help find the correct tree topology

Tree construction using sequences

* Sequence methods compare homologous positions
* Mutations can include insertions and deletions
* Sequences need to be aligned
* A character matrix can be made using DNA sequences

Homoplasies in sequence evidence

* DNA sequences are likely to show homoplasies
* This is because only 4-character states are possible for any given position
* Wobble makes the 3rd codon positions uninformative
* In deep time signal, saturation quickly happens