Microbial Phylogeny

A phylogenetic tree represents evolutionary relationships among microorganisms and often relies on DNA, RNA, or protein sequences.

In phylograms, species appear at the tips, and branch lengths reflect the amount of sequence change.

Rooted trees mark common ancestors and divergence points, while unrooted trees show links without evolutionary direction.

Phylogenetic trees use homologous sequences, especially orthologs, which are homologous genes separated by speciation.

Highly conserved small subunit rRNA genes, like the 16S rRNA gene, serve as universal markers for microbial comparisons.

The DNA for these marker genes in the samples is sequenced.

Sequences are aligned to identify mismatches and gaps from insertions or deletions.

Then, evolutionary distance is measured as the ratio of nucleotide differences to the total number of aligned positions.

Phylogenetic trees can sometimes be misleading when similar traits evolve independently or when horizontal gene transfer introduces genes across unrelated lineages, producing gene histories that do not reflect the actual evolutionary history of the organisms.