Molecular phylogenetics

Question 1

What is molecular phylogenetics?

Answer 1

It is the reconstruction of relationships between taxa based on nucleotids or proteins. This method uses structure and function of molecules and how they change over time to infer evolutionary relationships. It constructs trees based on nucleotid sequences, in which the data is interpreed as a linear chain of multistate K.

Question 2

DNA sequence =

Answer 2

Σ nucleotides

Question 3

What are the four nucleobases, and what are nucleobases used as?

Answer 3

Adenine (A)
Guanine (G)
Thymine (T) or Uracil (U in RNA)
Cytosine (C)

used as character states (4 possible)

Question 4

Gene sequence represent…?
Characters are…?
Character states are…?

Answer 4

represent character data

positions in the sequences

the nucleotides in the sequences (or amino acids in the case of proteins)

Question 5

What three issues that may arrise with molecular phylo analysis?

Answer 5

• probability that two nucleotides are the same by
  mutation is 25%
• what to do with insertions or deletions?
• homoplasy in sequences may cause aligment
  errors

Question 6

What are the five different models of sequence evolution?

Answer 6

• All substitutions have an equal probability, base frequencies are equal
• All substitutions have an equal probability, base frequencies are unequal
• Substitutions have different probabilities, base frequencies are equal
• Substitutions have different probabilities, base frequencies are unequal
• Different probabilities for each substitution, base frequencies are unequal

Question 7

Why do we use a mathmatical model to describe evolution of a sequence over time?

Answer 7

To undersatnd the mechanism of change and to estimate the rate of evolution along with the history of sequences.

Question 8

When comparing gene sequences, it is important to ….

Answer 8

distinguish between identical and
similar genes in different organisms

Question 9

What are Orthologous genes?

Answer 9

homologous genes in
different taxa inherited from a common ancestor

Better to select an homologous gene (ortholog
gene –> having diverged by speciation events rather than by gene duplication events)

Question 10

What are paralogous genes?

Answer 10

similar genes from a gene duplication (gene duplicated to occupy two different positions in the same genome often belong to the same species, but this is not
necessary)

Question 11

What is the step by step method of Molecular phylo?

Answer 11

1. Chromosome extraction: select an homologous gene (i e ortholog) in each studied organism.
2. Electrophoresis: Nucleobases are isolated.
3. Sequence alignment : * for a given gene, sequences often differ in length in different species as a result of insertion and deletion mutations * it is necessary to align the corresponding positions in different sequences * 1 site 1 position 1 character * each nucleobase 1 character state.
4. Select the informative positions: * on 1 position 4 possible character states difficult to identify the plesiomorphic state from the apomorphic states
   * informative position 2 different character states at least, in 2 different taxa
5. Parsimony analysis
6. Determination of the most parsimonious tree

Question 12

configure this problem

Answer 12