Investigation 3: Comparing DNA Sequences with BLAST

DNA that codes for the same gene tends to look alike across species that share a recent common ancestor, because there hasn't been much time for mutations to pile up. BLAST (Basic Local Alignment Search Tool) takes a query sequence and lines it up against sequences in a database, letter by letter, to see how well they match. The output is a percent identity: the fraction of bases or amino acids that are identical once the two sequences are aligned. A 98% identity means almost every position matches; a 65% identity means the sequences have drifted apart over a longer evolutionary stretch. Because mutations accumulate roughly over time, percent identity works as a rough molecular clock for relatedness.

To build a cladogram from a table of percent identities, rank the species from highest to lowest identity relative to your sequence of interest. The species with the highest percent identity branches off most recently, closest to your organism on the tree, because its DNA has changed the least since the split. Lower identity scores push a species further down the tree, onto an earlier-branching lineage, since more time (and more mutations) separates it. The actual numbers don't have to mean much on their own; what matters is their order relative to each other.

This investigation connects directly to the practice of using quantitative data to support a claim about common ancestry, the same logic behind morphological cladograms built from physical traits elsewhere in the course. BLAST just swaps traits for sequence data, which is more precise but works on the same principle: more shared characteristics, more recent shared ancestry.