Evolutionary and Medical Consequences of Archaic Introgression into Modern Human Genomes

Jul 7, 2026

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Demographic history of anatomically modern humans reflects repeated migration, local extinctions and genetic adaptation, with genome-wide sequencing now enabling direct study of introgression from extinct lineages. Modern non-African genomes contain archaic fragments, confirming that AMH interbred with Neanderthals and Denisovans after leaving Africa. This review analyzes fitness consequences of archaic interbreeding, addressing how selection shapes introgressed variants and how to test health- and disease-related hypotheses using present-day genomic data.

LanguageEnglish

CategoryResearch & Report

FormatPDF

Pages12

Reading Time30 min

Abstract

Widespread Interbreeding between Hominins

Out of Africa and early migration challenges

Ancient DNA evidence for Neanderthal and Denisovan admixture

Introgression within Africa and “ghost” archaic populations

Selection against Introgressed Regions at the Level of Genomes and Individual Loci

G C A T T A C G G C A T genes Review Evolutionary and Medical Consequences of Archaic Introgression into Modern Human Genomes Olga Dolgova * and Oscar Lao * Population Genomics Group, Centre Nacional d'An lisi Genámica, Centre de Regulaciâ Genámica (CRG-CNAG), Parc Cient½fic de Barcelona, Baldiri Reixac 4, 08028 Barcelona, Catalonia, Spain * Correspondence: [olga.dolgova@cnag.crg.eu](olga.dolgova@cnag.crg.eu) (O.D.); [oscar.lao@cnag.crg.eu](oscar.lao@cnag.crg.eu) (O.L.); Tel.: +34-934-037-276 (O.D. & O.L.) Received: 15 June 2018; Accepted: 11 July 2018; Published: 18 July 2018 􀀁􀀂􀀃􀀁􀀄 􀀆􀀇􀀈 􀀁􀀂􀀃􀀄􀀅􀀆􀀇 Abstract: The demographic history of anatomically modern humans (AMH) involves multiple migration events, population extinctions and genetic adaptations. As genome-wide data from complete genome sequencing becomes increasingly abundant and available even from extinct hominins, new insights of the evolutionary history of our species are discovered. It is currently known that AMH interbred with archaic hominins once they left the African continent. Current non-African human genomes carry fragments of archaic origin. This review focuses on the ﬁtness consequences of archaic interbreeding in current human populations. We discuss new insights and challenges that researchers face when interpreting the potential impact of introgression on ﬁtness and testing hypotheses about the role of selection within the context of health and disease. Keywords: archaic introgression; ﬁtness; natural selection; Neanderthal; Denisovan; anatomically modern humans 1. Widespread Interbreeding between Hominins The demographic history of anatomically modern humans (AMH) is complex, and involves a large number of migrations, genetic admixtures and introgressions, population extinctions and genetic adaptations, which overlap both in time and in space (see Figure 1) . Due to this complexity, the evolutionary history of humankind is still far from being fully understood [1] During the last 30 years, the most accepted demographic scenario for explaining recent evolution of AMH has been the Out of Africa model (OOA) . According to this model, AMH evolved in Africa around 100–200 thousand years ago (kya) in East Africa [2,3] and migrated to the rest of the world around 50–60 kya [4–7] . This widely accepted dating of Homo sapience emergence was recently challenged by Hublin et al. [8], who found AMH fossils of 300 kya at Jebel Irhoud in Morocco [9] . Similarly, Herschkovitz et al. [10] described a Homo sapiens maxilla of 177 to 194 kya in Misliya Cave, Israel. All these studies suggest that the members of the H. sapiens clade left Africa earlier than previously thought, probably in several waves of OOA migration at different stages of evolution. Classical “pure”OOA assumes that admixture with other archaic populations such as Neanderthals or Denisovans, present at the time of the rise of AMH, either did not occur or was negligible [11] . Genes 2018, 9, 358; [doi:10.3390/genes9070358 www.mdpi.com/journal/genes](doi:10.3390/genes9070358 www.mdpi.com/journal/genes) Figure 1. Family tree of the four groups of early humans living in Eurasia 50,000 years ago and the inferred gene ﬂow between the groups due to interbreeding (based on [12–16]) . The direction and estimated magnitude of inferred gene ﬂow events are shown. Branch lengths and timing of gene ﬂows are not scaled. The dashed line indicates that it is uncertain whether Denisovan gene ﬂow into modern humans in mainland Asia occurred directly or via Oceania. Light violet color indicates introgression events from unknown archaic populations (Ghost) . However, genomic studies of ancient DNA have revealed that AMH interbred with other hominid lineages, such as Neanderthals and Denisovans, present in Eurasia since 300 kya up to 30–50 kya. The admixture with Neanderthals occurred around 37–86 kya, and most likely between 47 and 65 kya [17–20] . The event of admixture with Denisovan took plac

FAQs

What is the key evolutionary evidence that archaic introgression occurred in modern humans?

Genome-wide data from current and ancient samples show that anatomically modern humans interbred with archaic hominins after leaving Africa. Non-African genomes carry measurable Neanderthal and Denisovan ancestry fragments.

How do Neanderthal and Denisovan contributions differ across modern populations?

Estimates report roughly 1.8%–2.6% Neanderthal DNA outside Oceania, with higher fractions in East Asians than in Western Eurasia. Denisovan ancestry is found mainly in Australo-Melanesians, and to a lesser extent in South Asians and East Asians.

Why is detecting archaic introgression in African modern genomes especially challenging?

The difficulty stems from the lack of preserved genetic material from African archaic remains that could serve as a proxy. Despite this, evidence suggests introgression events also occurred within Africa, implying additional unknown archaic sources.

Jul 7, 2026

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