DNA Deep Dive - Exploring Human Evolution

Limits of preservation

Ancient DNA (aDNA) survives only where burial chemistry, temperature, and time align. The oldest authenticated hominin DNA comes from sediments and remains far younger than most species in the fossil record. For the majority of hominin taxa, no usable DNA has been sequenced; inferences rely on comparative genomics of living relatives and sparse aDNA from Neanderthals, Denisovans, and early Homo sapiens.

Mitochondrial DNA sequences

Curated GenBank entries associated with hominin comparative genomics. Length reflects the deposited sequence segment (complete mitogenomes vs. partial).

Organism	Accession	Type	Sequence length	Gene name
Homo heidelbergensis	KT780370	Complete Mitogenome	16,573	mitochondrial genome
Homo neanderthalensis	KY751400	Complete Mitogenome	16,572	mitochondrial genome
Homo neanderthalensis	FN673705	Complete Mitogenome	16,570	mitochondrial genome
Homo denisova	NC_013993	Complete Mitogenome	16,570	mitochondrial genome
Homo denisova	FR695060	Partial Mtdna	16,570	mitochondrial genome
Homo sapiens	NC_012920	Complete Mitogenome	16,569	mitochondrial genome
Homo neanderthalensis	KC879692	Complete Mitogenome	16,567	mitochondrial genome
Homo neanderthalensis	NC_011137	Complete Mitogenome	16,565	mitochondrial genome
Homo neanderthalensis	FM865411	Complete Mitogenome	16,565	mitochondrial genome
Homo neanderthalensis	KX198087	Complete Mitogenome	16,565	mitochondrial genome

Evolutionary genes

Genes frequently discussed in human origins research—speech, pigmentation, metabolism, and brain development—with notes on selection signatures and modern human variation.

ASPM Assembly factor for spindle microtubules

Chromosome	1
NCBI Gene ID	259266
Function	Required for normal mitotic spindle function in cerebral cortex neuronal progenitors.
Evolutionary significance	Fastest-evolving gene among microcephaly genes in the primate lineage. New variant arose ~5,800 years ago.
Selection evidence	Accelerated evolution along the lineage leading to humans; strong positive selection.
Human variant notes	Mutations cause primary microcephaly. The selected variant correlates with brain size variation.
Species with data	H. sapiens

DRD4 Dopamine receptor D4

Chromosome	11
NCBI Gene ID	1815
Function	G protein-coupled receptor for dopamine in the mesolimbic system.
Evolutionary significance	7-repeat allele associated with novelty-seeking behavior. Frequency varies geographically and correlates with population migration distance.
Selection evidence	Possible positive selection on long-repeat alleles in migratory populations.
Human variant notes	Associated with ADHD susceptibility. Higher frequency in populations with recent migration history.
Species with data	H. sapiens

EDAR Ectodysplasin A receptor

Chromosome	2
NCBI Gene ID	10913
Function	NF-kB signaling receptor affecting hair thickness, sweat glands, and tooth morphology.
Evolutionary significance	V370A variant under strong positive selection in East Asian and Native American populations (~30,000 ya).
Selection evidence	One of the strongest signals of recent positive selection in human genome.
Human variant notes	V370A: thicker hair shafts, more sweat glands, shovel-shaped incisors in East Asian populations.
Species with data	H. sapiens

EPAS1 Endothelial PAS domain protein 1

Chromosome	2
NCBI Gene ID	2034
Function	Hypoxia-inducible transcription factor regulating erythropoiesis and vascular response to low oxygen.
Evolutionary significance	Tibetan high-altitude adaptation variant introgressed from Denisovans. Unique case of adaptive introgression.
Selection evidence	Denisovan haplotype at near-fixation in Tibetans; virtually absent in lowland populations.
Human variant notes	Tibetans maintain lower hemoglobin at altitude vs. other highland populations. Denisovan origin confirmed.
Species with data	H. sapiens, H. denisova

FOXP2 Forkhead box protein P2

Chromosome	7
NCBI Gene ID	93986
Function	Transcription factor critical for speech and language development.
Evolutionary significance	Neanderthals share the human-derived FOXP2 variant. Mutations cause severe speech disorders in humans. Under positive selection in the human lineage.
Selection evidence	Selective sweep in human lineage; two amino acid changes fixed since divergence from chimps.
Human variant notes	KE family mutation causes verbal dyspraxia. Neanderthal FOXP2 identical to modern human version.
Species with data	H. sapiens, H. neanderthalensis, Pan troglodytes, Gorilla gorilla

HACNS1 Human-accelerated conserved noncoding sequence 1

Chromosome	2
NCBI Gene ID	100271848
Function	Enhancer element active in developing limb and pharyngeal arch.
Evolutionary significance	Gained novel enhancer activity in the human lineage. May contribute to hand and thumb dexterity evolution.
Selection evidence	16 human-specific substitutions in a 546-bp element; among most accelerated noncoding regions.
Human variant notes	Drives gene expression in developing thumb and wrist, potentially linked to precision grip evolution.
Species with data	H. sapiens

HAR1F Human accelerated region 1F

Chromosome	20
NCBI Gene ID	100270894
Function	Non-coding RNA expressed in developing neocortex (Cajal-Retzius neurons).
Evolutionary significance	Most rapidly evolving region in the human genome. 18 changes in human lineage vs. 0 between chicken and chimp.
Selection evidence	18 substitutions in 118 bp since human-chimp split; extreme acceleration.
Human variant notes	Expressed weeks 7-19 of fetal brain development in cortical patterning.
Species with data	H. sapiens

LCT Lactase

Chromosome	2
NCBI Gene ID	3938
Function	Hydrolyzes lactose in the small intestine.
Evolutionary significance	Lactase persistence arose independently multiple times in pastoralist populations (~7,500 ya in Europe, ~3,000 ya in East Africa).
Selection evidence	Among strongest signals of recent positive selection in human populations with dairying history.
Human variant notes	Multiple independent mutations in the MCM6 enhancer region enable adult lactose digestion.
Species with data	H. sapiens

MAOA Monoamine oxidase A

Chromosome	X
NCBI Gene ID	4128
Function	Catalyzes oxidative deamination of serotonin, norepinephrine, and dopamine.
Evolutionary significance	Gene-environment interactions in behavioral studies. Low-activity variant studied in aggression research.
Selection evidence	Frequency variation across populations; complex selection history.
Human variant notes	Brunner syndrome from complete deficiency. Complex gene-environment interactions in behavior.
Species with data	H. sapiens

MCPH1 Microcephalin

Chromosome	8
NCBI Gene ID	79648
Function	Regulates brain size during development; centrosome-associated protein.
Evolutionary significance	Haplogroup D arose ~37,000 years ago and spread rapidly. Mutations cause primary microcephaly.
Selection evidence	Strong positive selection on haplogroup D; possible introgression from archaic humans.
Human variant notes	Loss-of-function mutations cause autosomal recessive primary microcephaly.
Species with data	H. sapiens, H. neanderthalensis

OCA2 OCA2 melanosomal transmembrane protein

Chromosome	15
NCBI Gene ID	4948
Function	Melanin biosynthesis in melanocytes. Major determinant of eye color.
Evolutionary significance	Blue eye color variant arose once ~6,000-10,000 years ago in a single individual near the Black Sea.
Selection evidence	Strong recent positive selection in European populations.
Human variant notes	Mutations cause oculocutaneous albinism type 2. A single SNP (rs12913832) accounts for most blue/brown eye color variation.
Species with data	H. sapiens

SHH Sonic hedgehog signaling molecule

Chromosome	7
NCBI Gene ID	6469
Function	Morphogen essential for craniofacial and brain patterning.
Evolutionary significance	SHH enhancer (HACNS1) shows human-specific changes. Key to understanding facial reduction in human evolution.
Selection evidence	Enhancer region shows human-accelerated evolution.
Human variant notes	Mutations cause holoprosencephaly. Human face shape partially influenced by SHH regulation.
Species with data	H. sapiens, Pan troglodytes, Gorilla gorilla

SLC24A5 Solute carrier family 24 member 5

Chromosome	15
NCBI Gene ID	283652
Function	Potassium-dependent sodium/calcium exchanger affecting melanogenesis.
Evolutionary significance	A111T variant explains ~25-38% of skin color difference between Europeans and West Africans.
Selection evidence	Strongest signal of selection in European genomes. Nearly fixed in Europeans, rare in sub-Saharan Africa.
Human variant notes	Light skin adaptation; likely selected for vitamin D synthesis at northern latitudes.
Species with data	H. sapiens

Ancient DNA samples

Published high-coverage or landmark specimens from the Allen Ancient DNA Resource (AADR) and primary literature. Dates are radiocarbon or contextual age in years before present (BP).

Sample ID	Species	Site	Country	Date (BP)	Coverage	Haplogroup	Sex	Publication DOI
SH_mtDNA	Homo heidelbergensis	Sima de los Huesos	Spain	430,000 ±20,000	0.00	—	unknown	10.1038/nature12788
Denisova8	Homo denisova	Denisova Cave	Russia	136,000 ±20,000	0.01	—	male	10.1126/science.1224344
Denny	Homo denisova	Denisova Cave	Russia	90,000 ±10,000	2.60	—	female	10.1038/s41586-018-0455-x
Mezmaiskaya1	Homo neanderthalensis	Mezmaiskaya Cave	Russia	70,000 ±10,000	0.50	—	male	10.1038/nature08976
Shanidar_Z	Homo neanderthalensis	Shanidar Cave	Iraq	70,000 ±5,000	0.01	—	unknown	10.1016/j.jas.2021.105340
Denisova4	Homo denisova	Denisova Cave	Russia	55,000 ±10,000	0.50	—	male	10.1038/nature09710
AltaiNeandertal	Homo neanderthalensis	Denisova Cave	Russia	52,000 ±5,000	52.00	—	female	10.1038/nature12886
Denisova3	Homo denisova	Denisova Cave	Russia	50,000 ±10,000	30.00	—	female	10.1126/science.1224344
ElSidron1253	Homo neanderthalensis	El Sidron Cave	Spain	49,000 ±3,000	0.30	—	male	10.1126/science.1188021
Ust_Ishim	Homo sapiens	Ust-Ishim	Russia	45,000 ±1,000	42.00	R	male	10.1038/nature13810
Zlatý_kůň	Homo sapiens	Koneprusy Caves	Czech Republic	45,000 ±2,000	3.40	N	female	10.1038/s41559-021-01443-x
Bacho_Kiro_F6-620	Homo sapiens	Bacho Kiro Cave	Bulgaria	45,000 ±2,000	3.30	N	male	10.1038/s41586-021-03335-3
Vindija33.19	Homo neanderthalensis	Vindija Cave	Croatia	44,000 ±5,000	30.00	—	female	10.1126/science.aao1887
LesCottes_Z4-1514	Homo neanderthalensis	Les Cottes	France	42,000 ±3,000	2.70	—	male	10.1073/pnas.1605508113
Oase1	Homo sapiens	Pestera cu Oase	Romania	40,000 ±3,000	0.10	N	male	10.1038/nature14558
Tianyuan	Homo sapiens	Tianyuan Cave	China	40,000 ±1,000	3.90	B	male	10.1073/pnas.1616708114
Kostenki14	Homo sapiens	Kostenki	Russia	38,700 ±2,200	2.80	U2	male	10.1126/science.aaa0114
Sunghir1	Homo sapiens	Sunghir	Russia	34,050 ±600	3.90	U	male	10.1126/science.aao1807
Anzick-1	Homo sapiens	Anzick	United States	12,600 ±100	14.40	D4h3a	male	10.1038/nature13025
Mota	Homo sapiens	Mota Cave	Ethiopia	4,500 ±30	12.50	L3x2a	male	10.1126/science.aad2879

Species DNA coverage

mtDNA and nuclear genome availability from curated species genetics records. Absence does not imply DNA could never be recovered—only that no published sequence met our inclusion criteria.

Ardipithecus kadabba

mtDNA	✗ Not available
Nuclear DNA	✗ Not available

Ardipithecus ramidus

Ardi

mtDNA	✗ Not available
Nuclear DNA	✗ Not available

Australopithecus afarensis

Lucy

mtDNA	✗ Not available
Nuclear DNA	✗ Not available

Australopithecus anamensis

mtDNA	✗ Not available
Nuclear DNA	✗ Not available

Australopithecus deyiremeda

mtDNA	✗ Not available
Nuclear DNA	✗ Not available

Australopithecus garhi

mtDNA	✗ Not available
Nuclear DNA	✗ Not available

Homo antecessor

mtDNA	✗ Not available
Nuclear DNA	✗ Not available

Homo bodoensis

mtDNA	✗ Not available
Nuclear DNA	✗ Not available

Homo denisova

Denisovan

mtDNA	✓ Available
Nuclear DNA	✓ Available

Homo gautengensis

mtDNA	✗ Not available
Nuclear DNA	✗ Not available

Homo georgicus

mtDNA	✗ Not available
Nuclear DNA	✗ Not available

Homo habilis

Handy Man

mtDNA	✗ Not available
Nuclear DNA	✗ Not available

Homo heidelbergensis

Heidelberg Man

mtDNA	✓ Available
Nuclear DNA	✓ Available

Homo juluensis

Big Head

mtDNA	✗ Not available
Nuclear DNA	✗ Not available

Homo luzonensis

mtDNA	✗ Not available
Nuclear DNA	✗ Not available

Homo neanderthalensis

Neanderthal

mtDNA	✓ Available
Nuclear DNA	✓ Available

Homo rhodesiensis

Broken Hill Man

mtDNA	✗ Not available
Nuclear DNA	✗ Not available

Homo sapiens

Modern Human

mtDNA	✓ Available
Nuclear DNA	✓ Available

Kenyanthropus platyops

Flat-faced Man

mtDNA	✗ Not available
Nuclear DNA	✗ Not available

Orrorin tugenensis

Millennium Man

mtDNA	✗ Not available
Nuclear DNA	✗ Not available

Paranthropus aethiopicus

Black Skull

mtDNA	✗ Not available
Nuclear DNA	✗ Not available

Sahelanthropus tchadensis

Toumai

mtDNA	✗ Not available
Nuclear DNA	✗ Not available

Data sources: GenBank imports and gene summaries curated for YourHumanity; ancient sample metadata aligned with the Allen Ancient DNA Resource (AADR) where noted. See individual references on species pages for primary publications.