State the bioinformatics tool used to obtain the alignment.

State the meaning of the dash (–) in the alignment.

(i) Identify the longest amino acid sequence where there are no differences amongst the five genera.

(ii) Suggest, with a reason, whether the DNA coding for the amino acid sequence identified in (c)(i) must be identical for the five genera.

Describe briefly how the cladogram was obtained.

Determine which two genera are most closely related according to their cytochrome c protein sequence.

BLASTp

Do not allow “BLAST” alone but accept BLASTx.

gap/no amino acid present «for cytochrome c in that organism in that position»
OR
protein is shorter

(i) GLFGR

Can be shown directly on the alignment.

(ii) no, because more than one codon can code for an amino acid/degeneration of the genetic code

ALTERNATIVE 1
a. alignment used to quantify differences and similarities

b. algorithms for cladograms
OR
named algorithms

Named algorithms: least squares, neighbour-joining, parsimony, maximum likelihood or Bayesian inference.
Allow other verifiable algorithms.

c. selection of best model

ALTERNATIVE 2
d. comparing amino acid sequences between organisms

e. more similar sequences correspond to closer evolutionary links/OWTTE
OR
number of differences indicate number of mutations accumulated «over time»
OR
«if mutation rate is assumed to be constant», more mutations imply further evolutionary distance

f. length of lines/position of nodes established by the number of differences/mutations between organisms

Marks should be awarded for statements from only one alternative, not both.

Zea «corn» and Oryza «rice»

Both required.