Genetics & Ancient DNA

Genetic data for hominin species, including genome sequencing, admixture, divergence times from molecular clock studies, and key gene variants.

Deep Dive: DNA Sequences & Ancient Genomes → Morphology & Specimens → Paleoclimate & Isotopes →

Genetic Divergence Timeline

Molecular Divergence Times

Divergence estimates from published molecular clock studies, compiled by TimeTree 5 (Kumar et al. 2022).

SpeciesDivergence (MYA)95% CIStudiesSource
Homo neanderthalensis 0.70 0.55 – 0.77 15 TimeTree 5
Homo sapiens 6.30 5.10 – 7.60 85 TimeTree 5

Species Genetic Data

Sahelanthropus tchadensis "Toumai"

mtDNA / Nuclear DNANo / No
Divergence Date (fossil calibrated)7.0 MYA

No ancient DNA; Sahelanthropus age ~7–6 Ma (geochronology) used as temporal anchor for comparative rows.

Orrorin tugenensis "Millennium Man"

mtDNA / Nuclear DNANo / No
Divergence Date (fossil calibrated)5.9 MYA

Orrorin: no genome; hominin total-group context only.

Ardipithecus kadabba

mtDNA / Nuclear DNANo / No
Divergence Date (fossil calibrated)5.5 MYA

Ar. kadabba: no DNA; divergence vs chimps per TimeTree-style priors not directly measured.

Ardipithecus ramidus "Ardi"

mtDNA / Nuclear DNANo / No
Divergence Date (fossil calibrated)4.4 MYA

Ar. ramidus: no DNA; node age approximates last common ancestor of Ardipithecus-grade hominins.

Australopithecus anamensis

mtDNA / Nuclear DNANo / No
Divergence Date (fossil calibrated)4.0 MYA

Au. anamensis: no DNA; used in comparative population genomics as fossil anchor.

Australopithecus afarensis "Lucy"

mtDNA / Nuclear DNANo / No
Divergence Date (fossil calibrated)3.5 MYA

Au. afarensis: no DNA; pan-African Pliocene hominin.

Australopithecus deyiremeda

mtDNA / Nuclear DNANo / No
Divergence Date (fossil calibrated)3.4 MYA

Au. deyiremeda: no DNA.

Kenyanthropus platyops "Flat-faced Man"

mtDNA / Nuclear DNANo / No
Divergence Date (fossil calibrated)3.3 MYA

Kenyanthropus: no DNA; phylogenetic position debated.

Australopithecus garhi

mtDNA / Nuclear DNANo / No
Divergence Date (fossil calibrated)2.5 MYA

Au. garhi: no DNA.

Paranthropus aethiopicus "Black Skull"

mtDNA / Nuclear DNANo / No
Divergence Date (fossil calibrated)2.5 MYA

P. aethiopicus: no DNA.

Homo habilis "Handy Man"

mtDNA / Nuclear DNANo / No
Divergence Date (fossil calibrated)2.3 MYA

H. habilis: no genome; early Homo comparative genomics uses modern humans + chimps.

Homo gautengensis

mtDNA / Nuclear DNANo / No
Divergence Date (fossil calibrated)2.0 MYA

H. gautengensis (proposed): no DNA.

Homo georgicus

mtDNA / Nuclear DNANo / No
Divergence Date (fossil calibrated)1.9 MYA

H. georgicus/Dmanisi: ancient DNA not recovered; morphology-only.

Homo antecessor

mtDNA / Nuclear DNANo / No
Divergence Date (fossil calibrated)1.0 MYA

H. antecessor: no genome; protein analysis places deep split (Welker et al. framework).

Homo heidelbergensis "Heidelberg Man"

Genome Coverage0.10%
DNA SourceSima de los Huesos (Spain)
mtDNA / Nuclear DNAYes / Yes
Divergence Date (fossil calibrated)600 KYA
Key Genes/VariantsmtDNA shows Denisovan affinities; nuclear DNA shows Neanderthal affinities

Ancient DNA from ~430 KYA Sima de los Huesos. Oldest nuclear DNA from a hominin. mtDNA closer to Denisovans; nuclear DNA closer to Neanderthals.

Homo bodoensis

mtDNA / Nuclear DNANo / No
Divergence Date (fossil calibrated)600 KYA

H. bodoensis (proposed): no DNA.

Homo neanderthalensis "Neanderthal"

Genome Coverage99.90%
DNA SourceVindija Cave (Croatia), Altai Mountains (Russia)
mtDNA / Nuclear DNAYes / Yes
Admixture with H. sapiens2.5%
Divergence Date (fossil calibrated)550 KYA
Divergence Date (molecular clock) 0.70 MYA (CI: 0.55–0.77)
Key Genes/VariantsFOXP2 gene (human variant), MC1R (red hair variant), TAS2R38 (bitter taste), BNC2 (skin pigmentation), several immune-related HLA variants

First archaic human genome sequenced (Green et al. 2010). High-coverage genome from Altai (Prufer et al. 2014). 1-4% Neanderthal DNA in modern non-Africans.

Homo denisova "Denisovan"

Genome Coverage99.50%
DNA SourceDenisova Cave finger bone (Russia)
mtDNA / Nuclear DNAYes / Yes
Admixture with H. sapiens5.0%
Divergence Date (fossil calibrated)400 KYA
Key Genes/VariantsEPAS1 (high-altitude adaptation passed to Tibetans), WARS2, TBX15 (body fat distribution), immune variants

Known primarily from DNA. Multiple Denisovan populations. Up to 5% DNA in modern Melanesians. Contributed high-altitude adaptation genes to Tibetans.

Homo rhodesiensis "Broken Hill Man"

mtDNA / Nuclear DNANo / No
Divergence Date (fossil calibrated)300 KYA

H. rhodesiensis: no genome; Kabwe age ~299 ka (direct dating attempts contested).

Homo juluensis "Big Head"

mtDNA / Nuclear DNANo / No
Divergence Date (fossil calibrated)300 KYA

H. juluensis (proposed): no DNA.

Homo luzonensis

mtDNA / Nuclear DNANo / No
Divergence Date (fossil calibrated)67 KYA

H. luzonensis: no DNA.

Homo sapiens "Modern Human"

Genome Coverage100.00%
DNA SourceMultiple global populations
mtDNA / Nuclear DNAYes / Yes
Divergence Date (fossil calibrated)0 years ago
Divergence Date (molecular clock) 6.30 MYA (CI: 5.10–7.60)
Key Genes/VariantsFOXP2, ASPM, MCPH1, HAR1, SLC24A5 (skin color), LCT (lactase persistence), AMY1 (amylase copy number)

Human Genome Project completed 2003. Extensive variation documented. Carries 1-4% Neanderthal DNA (non-Africans), up to 5% Denisovan (Melanesians).

Data sources: Divergence time estimates from TimeTree 5 (Kumar S, et al. 2022. Mol Biol Evol 39(8). doi:10.1093/molbev/msac174). Genome and admixture data from primary publications cited on individual species pages.