12.1 Phylogenetic trees

Phylogenetic trees represent the evolutionary relationships between samples. When comparing genetic sequences, we construct trees based on shared mutations between sequences – with the caveat that sometimes the same mutation can arise independently on different lineages.

Human vs. viral phylogenies

Constructing a phylogeny for human sequences is complicated by recombination (as well as diploidy and sex chromosomes), which means that every non-recombined segment of the genome has its own phylogenetic history.

Viral phylogenies are simpler to construct because they recombine less frequently than human chromosomes do. While the frequency of recombination varies by virus, ~3% of SARS-CoV-2 lineages show evidence of recombination (as opposed to 100% of human lineages, since recombination is an essential component of human meiosis).

Similar to the human Y chromosome, viral genomes typically accumulate mutations without recombination to split up haplotypes.