The evolution of mitochondria

Mitochondria descend from a bacterial endosymbiont related to the Alphaproteobacteria that was acquired more than 1.5 billion years ago, before the last eukaryotic common ancestor. Two questions organise this site: where exactly among bacteria the mitochondrial lineage comes from, and how its genome subsequently diversified across the eukaryotic tree — from the bacteria-like, ~100-gene mtDNAs of jakobid flagellates to the 6 kb, three-gene remnants of apicomplexan parasites and the multi-megabase genomes of flowering plants.

For each question the site shows two things side by side: a curated summary of the literature (hypotheses, key studies, what they used and what they found) and a de novo analysis that is re-run automatically from public data (NCBI RefSeq mitochondrial genomes and RefSeq bacterial proteomes) on a monthly schedule, so that trees, tables and charts track the growth of the databases. Every automated run is logged with data versions, tool versions and model details in the changelog.

Current de novo results

Origin: mitochondria among Alphaproteobacteria

103 taxa

10,199 aligned sites · 35 markers

method: IQ-TREE LG+F+G4
support: SH-aLRT
log-likelihood: -821,164.9
rooted on: outgroup (Betaproteobacteria, Gammaproteobacteria, Bacteria)
run: 2026-08-16 · profile ci · 2 min

view tree →

Diversification: mitochondrial genomes across eukaryotes

618 taxa

4,030 aligned sites · 13 markers

method: FastTree LG GAMMA
support: SH-like local support (FastTree)
log-likelihood: -2,095,922.6
rooted on: outgroup (Jakobida)
run: 2026-08-16 · profile ci · 2 min

view tree →

RefSeq mitochondrial genomes

17,720

complete mitogenomes parsed · release files: mitochondrion.1.genomic.gbff.gz (Thu, 09 Jul 2026 18:20:43 GMT)

sampled for tree: 618
size range: 5,150 bp (Hypnea edeniana) – 2,290,019 bp (Selenicereus monacanthus)
most annotated CDS: 2190 (Utricularia reniformis; includes ORFs)

Headline from the current automated origin tree: mitochondria are monophyletic and their sister group is the Rickettsiales(support at that node: 98.9). Under a site-homogeneous LG+F+G4 model this is expected to be biased towards Rickettsiales-sister — see the Origin page for why.

What is on this site

Origin

Competing hypotheses for the position of mitochondria relative to Alphaproteobacteria (sister to Rickettsiales; sister to all Alphaproteobacteria; within Alphaproteobacteria with Rickettsiales + marine Alpha-II lineages; the refuted SAR11 hypothesis), a table of what differs between studies, and the automated concatenated-protein tree of mitochondrion-encoded proteins with their bacterial homologs.

Diversification

A consensus tree of eukaryote supergroups annotated with what mitochondrial genomes look like in each lineage, a gene-retention matrix for representative genomes, and an automated tree of ~600 taxonomically balanced RefSeq mitogenomes with genome-size, gene-content and genetic-code statistics over all ~17,000 complete mitogenomes.

Data & Methods

Marker genes and synonyms, taxon lists, sampling rules, ortholog assignment, alignment/trimming/tree-inference settings, tool versions and download links for all alignments, trees and tables.