Methods and sources

What MitoAge is

MitoAge is a database for comparative analysis of mitochondrial DNA (mtDNA), with a special focus on animal longevity. For each of 2,335 species it combines the complete mitochondrial genome from NCBI RefSeq with the maximum recorded lifespan and other life-history traits from AnAge, and computes base composition, strand skews and codon usage for the whole genome and for every gene.

How the numbers are computed

• Base composition counts A, C, G and T on the reference (L) strand as deposited in RefSeq, for the whole genome, each of the 13 protein-coding genes, the 12S and 16S rRNA genes, all tRNA genes together and the control region (D-loop). Ambiguous bases are counted separately.
• GC content is (G + C) divided by all bases, in percent.
• GC skew is (G − C) / (G + C) and AT skew is (A − T) / (A + T), both on the L strand.
• Codon usage counts codons of each protein-coding gene in frame. Amino acids are assigned with the mitochondrial genetic code of the species (vertebrate, invertebrate or echinoderm code).
• Correlations with lifespan use log10 of the trait. Pearson and Spearman coefficients are reported for all species and within each class and order that has enough species; p-values are corrected with the Benjamini–Hochberg procedure within each trait and scope. Where a dated phylogeny is available, phylogenetically independent contrasts correct for shared ancestry.

Sources

Data notes

Problems found in the source data while building 2 (2026-11-13), and how they were handled.

• The build 1 CSV export has 923 species but the published release has 922: Loxioides bailleui (HAGRID 1598, NC_025626.1) is excluded: RefSeq NC_025626.1 is titled 'complete genome' but is only 9,243 bp (about 7 kb short of a complete avian mtDNA).
• EURING: not retrieved. The EURING longevity list (list of 2023-09-01) is not in the cache (data/cache/build2/sources/euring/2023-09-01/euring_longevity_2023-09-01.csv); euring.org was in maintenance on 2026-11-13. No EURING values are used; bird lifespans from USGS BBL are provisional because EURING outranks them.
• 6 records used from release 237 (mitochondrion.1.genomic.gbff.gz, file date 2026-09-03) carry only a CONTIG line (no sequence) in the release file; their sequence and features were taken from the same accession.version retrieved with NCBI efetch (rettype gbwithparts), checked to have the release's length: NC_053523.1, NC_054728.1, NC_059324.1, NC_059325.1, NC_080739.1, NC_091244.1.
• Dated tree: topology from the Open Tree of Life synthetic tree (opentree16.1, induced subtree of 2305 of 2335 species, polytomies kept); node ages from the TimeTree 5 API for 2045 of 2229 internal nodes; 184 undated nodes placed midway between parent and oldest child, 61 ages raised to keep parents older than children. 30 species are not in the tree: their PIC contribution is unknown (they are left out of PIC, not given values). PIC (Felsenstein 1985) correlations are computed during the site build on this tree.
• Build 2 (2026-11-13): 2335 species = 922 from build 1 + 1413 new. Record status: updated 465, original 392, renamed 46, retired 19, new 1413. Every value of a build 1 species that changed is in changelog.parquet with its old value and the reason; build 1 itself is frozen in build1/.
• Genome values (region statistics, codon usage, genome features) of every live species are computed from the RefSeq record in release 237 (mitochondrion.1.genomic.gbff.gz, file date 2026-09-03); for build 1 species that is the same accession.version they cited (or its newer version, or a live successor when the record was suppressed). Retired species keep their build 1 values.
• Base-label bug of build 1: in every MitoAge CSV file the base columns are complement-labelled ("G" holds C on the RefSeq strand, "C" holds G, "A" holds T, "T" holds A). All a/c/g/t here are on the RefSeq strand as deposited; GC% is unaffected, GC and AT skews change sign relative to the old site.
• Lifespan: AnAge build 15 always first; when AnAge has no value, fish take FishBase v26.06, aquatic invertebrates SeaLifeBase v26.06 and birds EURING (not retrieved) then USGS BBL v2025.1. Every value from every source is in lifespan_observations.parquet. Values from FishBase and SeaLifeBase are CC BY-NC 4.0 (non-commercial).
• Class labels follow the build 1 scheme (AnAge build 12-era: Actinopterygii, Reptilia, ...) for every species, so correlation scopes stay comparable with the 2016 paper; AnAge build 15's fish reclassification (Teleostei, ...) is not adopted.

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