GENE 222 Mod 4 - Phylogenetics

What is a clade in phylogeny?

A determined grouping within a hiearchal classification, supported by genetic similarity evidence. Also known as a monophyletic grouping, the most common

What are some methods used to construct phylogenetic trees?

• Distance method - overall similarity of species (assumes a relatively similar rate of evolution)

• Character based methods - based on tracking evolutionary events, and common ancestry.

Outline the cladistic method of phylogeny

Makes an assumption that genes are either ancestral or ‘derived’ (new in the organism) and usually must hypothesize a way to differentiate them. Used on a genome/gene level or a morphological level to identify differences in organisms and form a tree from there.

Outline the Maximum parsimony method of forming phylogenetic trees?

Constructing a phylogenetic tree by finding the differences between similar species via base-pair changes in select conserved protein-coding genes. Maximum parsimony means choosing the possible phylogenetic tree that would form from the least single-nucleotide mutations.

From there, different weightings could be assigned to different SNPs just like the UPGMA method.

What problem does insertion/deletion events pose to DNA alignment analysis?

It makes it difficult to align the sequences, this becomes exponentially more difficult for more different species, enough so that it becomes computationally expensive. It brings up a potential problem of overfitting of the analysis data as the algorithm may misalign very different sequence to maximise base-pair homology.