Human Evolutionary History

A skull from Jebel Irhoud in Morocco has a face you could pass in the street. Its braincase is more elongated than yours. The flints found with it were last heated about 315,000 years ago.

So when did our species begin, and where? And when early members of it met other kinds of humans, what happened? You will answer them with three kinds of evidence, each of which can say some things and not others.

The question: where and when, from three kinds of evidence

Fossils give you shape and a date. But the date usually belongs to something next to the bone, such as a burnt flint or an ash layer, so you ask what was dated and where it lay.

Ancient DNA is genetic sequence recovered from bones tens of thousands of years old. It lets you compare an extinct population, such as the Neanderthals, with living people site by site. Sequencing itself belongs to sequencing and genomes.

Present-day genomes record history in the pattern of shared and unshared variants. In the 1000 Genomes Project’s Phase 3 sample of 2,504 people from 26 populations, individuals from African-ancestry populations carried the greatest numbers of variant sites, and most common variants were shared across the world.

Taken together, this evidence broadly supports an African origin of Homo sapiens. The phrase “our species began 200,000 years ago in one place” does not survive it, for reasons the fossils show first. Populations split and sometimes merge again, which a simple tree cannot draw (see reading phylogenetic trees).

Fossils and their dates

Think of dating a fossil like dating a letter found inside a book. A dated envelope beside it tells you something, and a postmark on the page above it tells you something different.

Jebel Irhoud, Morocco. Fire-heated flints lay with the hominin remains. Thermoluminescence measures the radiation dose a mineral has absorbed since it was last heated, which gives the time since heating. The weighted age of the associated assemblage was 315 +/- 34 thousand years (Richter and colleagues, 2017). The fossils (Hublin and colleagues, 2017) are a mosaic: face, mandible and teeth align with early or recent anatomically modern humans, while the neurocranium and endocranial shape are more primitive. Brain expansion itself is taught in human brain expansion.

Omo I, Ethiopia. Here the age comes from the eruption behind an ash, the KHS Tuff, which lies above the member of the Omo-Kibish Formation that holds the fossil. Vidal and colleagues (2022) matched the ash chemically to a major eruption of the Shala volcano and dated sanidine crystals from its pumice by single-crystal 40Ar/39Ar, giving 233 +/- 22 thousand years at two standard deviations. Because the ash fell after the fossil was buried, 233 thousand years is a minimum: Omo I is at least about that old. It is not a direct date on the bone.

Misliya Cave, Israel. A maxilla with teeth from the Homo sapiens clade was dated to 177,000-194,000 years ago (Hershkovitz and colleagues, 2018), a date whose uranium-series part was challenged and defended in 2018. If the date holds, this shows presence outside Africa long before the roughly 60,000-year dispersal many textbooks taught. Presence is not ancestry: nothing shows that living people descend from this population.

So people with partly modern anatomy lived in north Africa around 300,000 years ago, others in east Africa by at least 233,000 years ago, and some reached western Asia by about 180,000 years ago. That is no single birthplace or birthday.

Reading archaic ancestry in genomes

Suppose two modern genomes and a Neanderthal genome are compared with a chimpanzee as outgroup (a lineage outside the group, used to tell which allele is ancestral). At each site, call the chimpanzee’s allele A (ancestral) and the other B (derived, a newer variant). Order the taxa as P1 (a sampled African genome), P2 (a sampled Eurasian genome), P3 (a Neanderthal) and O (chimpanzee).

An ABBA site has P2 and P3 sharing B. A BABA site has P1 and P3 sharing B. Both disagree with the population tree, in which P1 and P2 are each other’s closest relatives. Both arise without any gene flow, through incomplete lineage sorting: a variant already present in the common ancestor of all three is passed down unevenly, so a gene’s history differs from the population’s (see molecular evolution).

D = (N_ABBA - N_BABA) / (N_ABBA + N_BABA)

Worked problem. These counts are hypothetical. At sites where the Neanderthal carries B, you count ABBA = 600 and BABA = 400.

1. Compute D. D = (600 - 400) / (600 + 400) = 200 / 1,000 = 0.20. D has no units; it runs from -1 to +1.
2. State the null. With no gene flow after the populations split and an ancestor that was one randomly mating population, incomplete lineage sorting makes ABBA and BABA equally likely. The model predicts D = 0. Here the Eurasian genome shares derived alleles with the Neanderthal more often than the African genome does.
3. Test it. Neighbouring sites are inherited together, so you cannot treat each site as independent. A block jackknife drops one large genomic block at a time and recomputes D to get a standard error. If that gives 0.05, then Z = 0.20 / 0.05 = 4. Studies of this kind commonly treat |Z| greater than 3 as significant, so the asymmetry is unlikely to be chance.
4. Do not read D as a percentage. D = 0.20 does not mean 20% Neanderthal ancestry. An ancestry fraction needs a separate estimator.
5. Name the alternative. Durand and colleagues (2011) showed that ancestral population structure can also produce D greater than 0: if the ancestors of Eurasians came from a part of an old, subdivided African population that was closer to the Neanderthal lineage, ABBA would exceed BABA with no interbreeding. A positive D is consistent with gene flow; it is not proof of it.

ABBA sites (P2 + P3 share B) 600 BABA sites (P1 + P3 share B) 400 Block-jackknife standard error 0.05

D = (ABBA − BABA) / (ABBA + BABA)

0.20

Z = D / SE

4.0

|Z| greater than 3?

yes

In this sketch: the counts are hypothetical, and the standard error is set by hand instead of being computed by dropping genomic blocks. P1 is a sampled African genome, P2 a sampled Eurasian genome, P3 a Neanderthal, with a chimpanzee as outgroup.

Rule to keep: D is not percent ancestry, and ancestral structure can also give D above 0.

This is what Green and colleagues found in 2010 with a draft Neanderthal genome from three individuals and five present-day genomes. Neanderthal variants were shared more with the sampled Eurasians than with the sampled sub-Saharan Africans, and they interpreted this as suggesting Neanderthal gene flow into the ancestors of non-Africans. The algebra of gene flow belongs to population genetics; the competing-explanations logic is in drift, gene flow and competing explanations.

Interbreeding made concrete, and adaptive introgression

The structure alternative fails a test that time supplies. Recombination cuts an introgressed segment (a stretch of DNA that entered from another population) into shorter pieces every generation. Old structure leaves only short pieces; recent gene flow leaves long blocks.

The Ust’-Ishim genome, from a Homo sapiens man in western Siberia who lived about 45,000 years ago, carried Neanderthal segments longer than those in present-day people. From their lengths, Fu and colleagues (2014) inferred gene flow 7,000-13,000 years before he lived. Adding 45,000 years puts that roughly 52,000-58,000 years ago, inheriting the uncertainty of both numbers and of the recombination model. All three Initial Upper Palaeolithic individuals studied at Bacho Kiro Cave in Bulgaria had Neanderthal ancestors only a few generations back (Hajdinjak and colleagues, 2021). Using more than 300 ancient and present-day genomes, Iasi and colleagues (2024) attributed most Neanderthal gene flow in their sample to a shared, extended period about 50,500-43,500 years ago.

Then there is a single person. Denisovans are a population known mostly from DNA: a finger-bone genome from Denisova Cave in Siberia placed them as sharing a common origin with Neanderthals (Reich and colleagues, 2010). Denisova 11, a bone fragment from the same cave, had Neanderthal-type mitochondrial DNA, and DNA fragments overlapping sites where Neanderthal and Denisovan genomes differ carried one allele of each. That is the signature of a first-generation offspring: a Neanderthal mother and a Denisovan father, who himself carried some Neanderthal ancestry (Slon and colleagues, 2018).

Reich’s 2010 study inferred a 4-6% Denisovan contribution to the genomes of its sampled present-day Melanesians. Archaic variants were then subject to selection in their new genomic background. At EPAS1, which encodes a transcription factor of the response to low oxygen, the haplotype structure in 40 Tibetans compared with 40 Han Chinese supported introgression from Denisovans or a Denisovan-related population (Huerta-Sánchez and colleagues, 2014). The authors concluded that admixture supplied variation that helped humans adapt to new environments, with Tibetans at high altitude as the case studied. This is adaptive introgression: an allele that entered by interbreeding and then rose in frequency because carriers did better in that environment.

What remains open, and what genetic variation does not show

Several questions are not settled. Where in Africa did Homo sapiens arise, and was it one region at all? Ragsdale and colleagues (2023), fitting models to genomes that included 44 newly sequenced Nama individuals, found that weakly structured stem populations connected by gene flow over hundreds of thousands of years can explain patterns that had been attributed to an unsampled archaic population in Africa. Whether such an archaic contribution happened is open. How many contacts with Neanderthals and Denisovans there were, and where, is open. The Denisovan skeleton is barely known, although protein evidence suggested in 2025 that the Harbin cranium from China belonged to a Denisovan population.

African genomes are not free of Neanderthal ancestry either. Using IBDmix, which finds introgressed sequence without assuming any modern population is unadmixed, Chen and colleagues (2020) detected a stronger signal in sampled Africans than had been recognized, explained partly by migration back into Africa and by earlier gene flow from modern humans into Neanderthals.

All people alive today belong to Homo sapiens. With enough loci, individuals can be assigned to the populations they were sampled from, yet the share of variation between populations is modest and most common variants are shared worldwide (Witherspoon and colleagues, 2007; 1000 Genomes, 2015). The American Association of Physical Anthropologists’ 2019 statement holds that socially recognized races are not discrete biological groups or evolutionarily independent lineages. The categories a study uses are that study’s choices. No ranking of populations follows from any of this evidence.

Design problem

A positive D for (sampled African, sampled Eurasian, Neanderthal, chimpanzee) could come from Neanderthal gene flow into Eurasians or from old structure within Africa. Which evidence would separate them? Name the samples you would use and what each hypothesis predicts.

One way to do it

Start with what each hypothesis predicts about segment length. Gene flow tens of thousands of years ago leaves long Neanderthal-like blocks that recombination has had limited time to break up. Structure dating back hundreds of thousands of years leaves only short pieces.

Then use time. Dated ancient genomes such as Ust’-Ishim (about 45,000 years) and the Bacho Kiro individuals should carry longer segments than present-day genomes if gene flow happened shortly before they lived, and they do. Structure predicts no such change with age.

Next, check divergence. A segment that entered from Neanderthals recently should be very close to the sequenced Neanderthal genome. Under old structure, shared segments should be as divergent from the Neanderthal as the deep split between the lineages implies.

Finally, fit both histories as explicit models to the same data and compare how well each reproduces segment lengths, divergences and D. Keep the conclusion to those samples: the evidence supports Neanderthal gene flow into the ancestors of the sampled non-Africans, and says nothing by itself about other contacts.

Next, life histories turns from ancestry to the trade-offs that shape how organisms grow and reproduce.