What is the origin of the human species?

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Summary

Modern humans (Homo sapiens) evolved primarily in Africa between ~300 000 and 200 000 years ago, then expanded within and eventually out of the continent, mixing to limited degrees with other hominin lineages such as Neanderthals and Denisovans. While the broad outline—African origin followed by worldwide dispersal—remains widely accepted, recent genomics and fossil discoveries portray a far more reticulated (inter-connected) evolutionary history than the once tidy “single-origin, single-exit” narrative. This emerging view has been described as an “African multiregional” or “metapopulation” model in which semi-isolated populations within Africa exchanged genes over hundreds of thousands of years before giving rise to the lineage that left Africa roughly 60–70 ka (1)(2).

Genomic evidence

Early whole-genome studies showed that present-day humans share most of their ancestry with Africans, pointing to an African origin, and that non-Africans carry ~1–2 % Neanderthal and up to ~5 % Denisovan ancestry obtained after leaving Africa. A 2025 structured-coalescent analysis of >4 000 genomes concluded that all living humans descend from an ancestrally structured African metapopulation that began exchanging genes at least 1 million years ago; lineages later coalesced into the ancestors of modern humans between ~600 ka and 400 ka (1). The same study suggests that what we call “Homo sapiens” never passed through a single, tiny population bottleneck but instead through a prolonged period of subdivided but connected groups.

A 2024 ancient-DNA preprint surveying hundreds of Pleistocene and Holocene genomes finds pervasive directional selection on traits linked to diet, immunity, and pigmentation, highlighting rapid adaptation both within Africa and during the global expansion (3). These results are consistent with a scenario in which small founder groups left Africa repeatedly, with the most successful wave ultimately dominating the ancestry of present-day non-Africans.

Fossil and archaeological evidence

African fossils show a gradual accumulation of modern traits. Jebel Irhoud (Morocco, ~315 ka) exhibits a modern-looking face combined with archaic cranial vaults; Omo Kibish (Ethiopia, ~195 ka) and Herto (Ethiopia, ~160 ka) display more derived features. Toolkits (e.g., Middle Stone Age points, ochre use) appear across Africa by ~300 ka, suggesting behavioural complexity parallel to anatomical change.

Climate reconstructions imply that “green” periods opened corridors across what are now deserts, facilitating gene flow among African populations and later easing exits into Eurasia. One such route, a once-lush Arabian Peninsula, is highlighted in a 2023 synthesis of palaeo-environmental data (4).

Competing or complementary models

Recent African Origin (RAO). Proposes a single, small African population gave rise to all modern humans ~200 ka, with limited admixture outside Africa. This model explains the deepest genetic diversity in Africa but struggles with evidence of deep population structure and repeated contact with archaic groups.

African Multiregional / Metapopulation. Supported by the 2025 Nature Genetics paper, this framework envisions multiple partially isolated African populations connected by intermittent gene flow over long periods. It retains Africa as the main stage of speciation but rejects a single birthplace (1).

Classic Multiregional. Argues that modern humans emerged from continuous gene flow among Homo populations across the Old World. This view has lost traction because genomic data show that most ancestry outside Africa derives from a recent African source, with archaic contributions limited and traceable (1)(2).

Public discourse and points of contention

Razib Khan notes that headlines often ping-pong between “Out of Africa confirmed” and “Single origin shattered,” reflecting how new data are interpreted through older conceptual frames (2). His 2023 essay emphasises that appreciating metapopulation structure need not erase the African origin but does challenge the idea of a clean speciation event. In a separate post he underscores how mosaic fossils and small amounts of archaic introgression complicate binary species distinctions (5).

Debates continue over:

The taxonomic status of early African fossils: are they sapiens, “near-sapiens,” or separate species?

The number and timing of exits from Africa: was there one dominant expansion ~70 ka, or multiple pulses beginning as early as 120 ka?

The extent of admixture within Africa: future ancient-DNA from Africa is expected to clarify whether now-extinct lineages contributed significantly to modern populations.

Despite disagreements, nearly all researchers agree that the genetic, fossil, and archaeological evidence places the deep roots of our species in Africa while highlighting complexity—structured populations, repeated dispersals, and interbreeding—that earlier models failed to anticipate.

Take-away

Homo sapiens originated in a network of African populations hundreds of thousands of years ago. Over time, these populations exchanged genes, developed modern anatomy and behaviour, and eventually expanded across the globe, absorbing small amounts of DNA from other hominin groups they met along the way. The precise geographic focal points and the tempo of divergence remain active areas of research, but the African genesis of our species, tempered by a web of genetic exchanges, is the most robust inference to date.

Sources

1. Ragsdale et al. “A structured coalescent model reveals deep ancestral structure shared by all modern humans.” Nature Genetics, 2025. https://www.nature.com/articles/s41588-025-02117-1
2. Razib Khan. “Current Status: It’s Complicated.” Unsupervised Learning newsletter, 2023. https://www.razibkhan.com/p/current-status-its-complicated
3. Eviston et al. “Pervasive findings of directional selection realize the promise of ancient DNA to elucidate human adaptation.” bioRxiv pre-print, 2024. https://www.biorxiv.org/content/10.1101/2024.09.14.613021v1
4. Phys.org summary of palaeo-environmental research. “Path of early human migrations once lush,” 2023. https://phys.org/news/2023-10-path-early-human-migrations-once-lush.html
5. Razib Khan. “Homo with a side of sapiens: the brainy,” 2023. https://www.razibkhan.com/p/homo-with-a-side-of-sapiens-the-brainy

Suggested Sources

• A structured coalescent model reveals deep ancestral structure shared by all modern humans – Nature Genetics (2025 peer-reviewed research article)
• Current Status: It’s Complicated – Razib Khan’s Unsupervised Learning (2023 newsletter essay / Blog commentary)
• Pervasive findings of directional selection realize the promise of ancient DNA to elucidate human adaptation – bioRxiv (2024 pre-print; Empirical research)
• https://phys.org/news/2023-10-path-early-human-migrations-once-lush.html
• https://www.razibkhan.com/p/homo-with-a-side-of-sapiens-the-brainy