Phylogenetics

Question 1

What is a phylogeny

Answer 1

• a diagram showing evolutionary relationships among species/taxa
• based on genetic and morphological traits

Question 2

What is the different tree terminology

Answer 2

• root or base
  -branch
• branch length (can tell you how closely related species are)
• nodes
• bootstrap support (show how strongly supported relationship is by data)
• tips or leaves (species at end)
• monophyletic clade (all species come from a single common ancestor)
• sister taxa (two most closely related taxa on a tree)
• ## outgroup (most distantly related species on a tree show root and direction)

Question 3

What is a cladogram

Answer 3

• shows the relationship among taxa
• branch lengths are all the same so don’t know how closely related species are

Question 4

What is a phylograph

Answer 4

• shows relationship among taxa and how similar/different to eachother they are
• different lengths of branches show how related species are

Question 5

Rooting a phylogeny

Answer 5

• rotating the nodes has no effect on topology (relationships)

but rooting the tree at different points can cause a different topologies
- we need other information to decide the root of a tree eg. fossils will tell us age so provide direction

Question 6

How to make a tree

Answer 6

• must use a shared derived character
• using homolgous characters ( character from a common ancestor)

Question 7

How to make a tree using DNA

Answer 7

• use DNA sequence from homologous genes
• each base that varies is a character
• input data is a DNA alignment

can make a phylogeny by
- neighbour-joining
- maximum likelihood
- bayesian inference