Tangled Trees

Question 1

LUCA

Answer 1

• Last universal common ancestor
• Darwin’s theory of evolution implied LUCA
• If all species derive from a single ancestor, drawing out the evolution of all species over time would create a tree shape with LUCA at the root of the tree

Question 2

Tree of Life

Answer 2

First diagram of relatedness in Darwin’s book

-Early trees based on their similarity to man (man at the top)

Question 3

Dark DNA

Answer 3

protein product or RNA transcript is found, but the DNA that codes for it cannot be found

Question 4

Circle of life

Answer 4

the progress of life should be seen more as a circle of related events

• accounts for historic horizontal gene transfer and endosymbiotic theory
• Does not account for modern horizontal gene transfer

Question 5

Coral of life

Answer 5

• Both horizontal and vertical gene transfer occurred during early evolutionary history.
• The relative importance of each has changed over time
• Some genes are so important to life that they are never swapped horizontally -> vertical transfer

Question 6

The 6 deadly sins of the tree of life

Answer 6

1. Placement: Any species on the farthest branches of the tree are implied to be the most evolved (mammals and humans tend to be there)
2. Under-represented prokaryotes (in reality there are many more prokaryotes to eukaryotes)
3. Implying increasing complexity (myth: increasing diversity or complexity, The tree seems to suggest life is becoming more diverse over time)
4. Minor and extinct species excluded
5. Implies punctuated equilibrium (tree cannot be used to infer the WAY a species evolved)
6. Aves is artificial (Birds are often listed as a separate group on the tree of life, but should be classified as dinosaurs)

Question 7

Supertree

Answer 7

a single phylogenetic tree which is assembled from other, smaller phylogenetic trees
-generally has to combine trees which are compiled from completely different datasets

Question 8

Rate of mutation

Answer 8

• Woese and Fox believed they could look at a single universal gene found in every species, and determine the relatedness of all species based on that single gene
• Over an average period of time, a fairly constant number of mutations occur for a specific region of DNA
• Some genes mutate faster than others

Question 9

Ancestral sequence reconstruction

Answer 9

• The determination of ancestral, extinct genes, through reverse engineering from modern species
• type of *synthetic biology
• Heat tolerance of LUCA

Question 10

Modern Development

Answer 10

• used the small subunit rRNA
• found in all life tested
• low and measurable mutation rate
• rarely transported through horizontal gene transfer