Interactive Mitochondrial DNA Analysis visualized with D3.js
Unlike nuclear DNA, which recombines from both parents, Mitochondrial DNA (mtDNA) is inherited strictly maternally. This allows computational biologists to trace unbroken, direct evolutionary lineages without the noise of genetic mixing.
Biologically, the Cheetah is the true outgroup here. However, look at the base of our tree (Inner4)—the algorithm placed the Lion as the outgroup! This happens because UPGMA assumes a constant mutation rate. If the Lion's mtDNA mutated slightly faster or slower, the algorithm gets tripped up. This proves why data scientists test multiple models!
This tree was calculated using UPGMA (Unweighted Pair Group Method with Arithmetic Mean). It is a rapid hierarchical clustering method used in bioinformatics to create phenograms based on pairwise distance matrices.
Click the orange ancestral nodes (Inner1, Inner2, etc.) to collapse and expand evolutionary branches in real-time. This dynamic scaling is critical when analyzing massive genomes with thousands of variations.