Plant Molecular Evolution - Answers

Question 1: What is the E-value for the top match?
> 0 (in other words, infinitely improbable by chance).

Question 2: In what ways are some sequence sites dissimilar?
> Mismatches, transitions, transversions and indels.

Question 3: What domains are indicated by the annotations for this sequence?
> 18S, 5.8S and 2.8S ribosomal RNA + internal transcribed spacer (ITS) 1 & 2 along with the location of the BLAST hit.

Question 4: Where have most of the gaps been placed?
> In the ITS regions.

Question 5: Which domains show the most variability and the least variability among all of the sequences?
> ITS regions are most variable and the ribosomal DNA is least variable.

Question 6: What is the pairwise % similarity of the sequences and the percentage of sites that are identical?
> Pairwise similarity is 93.3% and 65.5% of sites are identical.

Question 7: Why do these two numbers differ?
> Identical sites are identical across all sequences in the alignment, whereas pairwise similarity is the average number of times sites are identical in pairwise comparisons.

Question 8: What is the sum of branch lengths between the two most closely related species?
>Medicago tornata and Medicago littorals are the two most closely related species, and adding their branch lengths (7.57x10-4) gives 0.001514

Question 9: What is the genetic distance between the two most closely related species?
> 0.001514

Question 10: How does this value compare to the sum of branch lengths between the two most closely related species?
> The genetic distance is approximately equal to the sum of branch lengths.