Here's why:
* Synonymous mutations are changes in the DNA sequence that do not alter the amino acid sequence of the protein encoded by the gene. This is because the genetic code is redundant, meaning multiple codons can code for the same amino acid.
* Non-synonymous mutations, on the other hand, change the amino acid sequence, which can potentially alter the protein's function and structure.
* Insertions and deletions (indels) can cause frame shifts, leading to significant changes in the protein sequence and requiring extensive realignment.
Since synonymous mutations do not change the protein sequence, they have minimal impact on the overall structure and function of the gene. This makes them less likely to disrupt the alignment of homologous regions across different species.
Therefore, a synonymous mutation would least require realignment of homologous regions in a gene common to several related species.
