A3.2.6 Base sequences of genes or amino acid sequences of proteins (HL) Notes

Cladograms Represent Evolutionary Relationships

1. Cladograms are branching diagrams showing evolutionary relationships between species.
2. They're built using DNA sequences or protein amino acid sequences, which objectively reveal shared ancestry.
3. More similar sequences mean species diverged more recently.
4. Greater sequence differences mean species diverged longer ago.

Why Use Base and Amino Acid Sequences?

1. DNA and proteins accumulate changes over time as a result of mutations.
2. These changes occur at a roughly measurable rate, allowing scientists to infer how long ago two species diverged.

Base Sequence Comparisons

1. DNA base sequences provide the most direct genetic evidence.
2. Mutations alter the order of bases (A, T, C, G) over evolutionary time.
3. Sequence alignment software compares stretches of DNA from two or more species, identifying similarities and differences.
4. Closely related species show long stretches of identical sequences.

Amino Acid Sequence Comparisons

1. Mutations in DNA can lead to changes in amino acids in proteins.Comparing amino acid sequences allows us to estimate evolutionary distance between species.
2. Conserved proteins like cytochrome c (respiration) or haemoglobin (oxygen transport) are commonly used because they evolve slowly.
3. Slow evolution makes these proteins ideal for studying distant evolutionary relationships across large groups (e.g., mammals, birds, reptiles).

Parsimony and Cladogram Construction

1. Computers analyse sequence data using the principle of parsimony, which selects the cladogram requiring the fewest evolutionary changes.
2. This assumes the simplest explanation is most likely.
3. Multiple cladograms can be generated from the same data, but the most parsimonious one is chosen as most probable.

Simple Example 1: DNA Base Sequences

1. Consider three species, A, B, and C, with the following DNA sequences for a specific gene:
   1. Species A: ATGCTACG
   2. Species B: ATGCTGCG
   3. Species C: ATGATACG
2. Step 1: Compare Sequences
   1. A vs. B: 1 difference (C vs. G at position 6).
   2. A vs. C: 2 differences (C vs. A at position 3, C vs. G at position 6).
   3. B vs. C: 2 differences (C vs. A at position 3, G vs. C at position 6).
3. Step 2: Group Based on Similarity
   1. Species A and B have the fewest differences (1), so they are more closely related.
   2. Species C has more differences, so it diverged earlier.

        ── A  
    ──┤  
        ── B  
───┤  
        ── C  

Simple Example 2: Amino Acid Sequences

1. Here are amino acid sequences for the same protein in three species:
   1. Species X: MET-ALA-GLY-VAL
   2. Species Y: MET-ALA-GLY-ILE
   3. Species Z: MET-SER-GLY-ILE
2. Step 1: Compare Sequences
   1. X vs. Y: 1 difference (VAL vs. ILE).
   2. X vs. Z: 2 differences (ALA vs. SER, VAL vs. ILE).
   3. Y vs. Z: 1 difference (ALA vs. SER).
3. Step 2: Group Based on Similarity
   1. Species X and Y are more closely related (1 difference), while Z has more differences and diverged earlier.

        ── X  
    ──┤  
        ── Y  
───┤  
        ── Z