Since anatomically modern humans dispersed Out of Africa, the evolutionary history of Eurasian populations has been marked by introgressions from presently extinct hominins. Some of these introgressions have been identified using sequenced ancient genomes (Neanderthal and Denisova). Other introgressions have been proposed for still unidentified groups using the genetic diversity present in current human populations. We built a demographic model based on deep learning in an Approximate Bayesian Computation framework to infer the evolutionary history of Eurasian populations including past introgression events in Out of Africa populations fitting the current genetic evidence. In addition to the reported Neanderthal and Denisovan introgressions, our results support a third introgression in all Asian and Oceanian populations from an archaic population. This population is either related to the Neanderthal-Denisova clade or diverged early from the Denisova lineage. We propose the use of deep learning methods for clarifying situations with high complexity in evolutionary genomics.
Conflict of interest statement
The authors declare no competing interests.
Archaic Hominin Introgression Into Modern Human GenomesO Gokcumen. Am J Phys Anthropol. PMID 31702050.Ancient genomes from multiple Neanderthal and the Denisovan individuals, along with DNA sequence data from diverse contemporary human populations strongly support the pre …
Neanderthal and Denisova Genetic Affinities With Contemporary Humans: Introgression Versus Common Ancestral PolymorphismsRK Lowery et al. Gene 530 (1), 83-94. PMID 23872234.Analyses of the genetic relationships among modern humans, Neanderthals and Denisovans have suggested that 1-4% of the non-Sub-Saharan African gene pool may be Neandertha …
Analysis of Human Sequence Data Reveals Two Pulses of Archaic Denisovan AdmixtureSR Browning et al. Cell 173 (1), 53-61.e9. PMID 29551270.Anatomically modern humans interbred with Neanderthals and with a related archaic population known as Denisovans. Genomes of several Neanderthals and one Denisovan have b …
Evolutionary and Medical Consequences of Archaic Introgression Into Modern Human GenomesO Dolgova et al. Genes (Basel) 9 (7). PMID 30022013. - ReviewThe demographic history of anatomically modern humans (AMH) involves multiple migration events, population extinctions and genetic adaptations. As genome-wide data from c …
Searching for Archaic Contribution in AfricaC Santander et al. Ann Hum Biol 46 (2), 129-139. PMID 31163991. - ReviewContext: Africa's role in the narrative of human evolution is indisputably emphasised in the emergence of Homo sapiens. However, once humans dispersed beyon …
Cited by 2 PubMed Central articles
Using Hominin Introgression to Trace Modern Human DispersalsJC Teixeira et al. Proc Natl Acad Sci U S A 116 (31), 15327-15332. PMID 31300536.The dispersal of anatomically modern human populations out of Africa and across much of the rest of the world around 55 to 50 thousand years before present (ka) is record …
Whole-genome Sequence Analysis of a Pan African Set of Samples Reveals Archaic Gene Flow From an Extinct Basal Population of Modern Humans Into sub-Saharan PopulationsB Lorente-Galdos et al. Genome Biol 20 (1), 77. PMID 31023378.The present study represents an in-depth genomic analysis of a Pan African set of individuals, which emphasizes their complex relationships and demographic history at pop …