A B DispatchDate: 22.08.2022 · ProofNo: 1875, p.1 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 ANALYSIS https://doi.org/10.1038/s41559-022-01875-z 1 Paleoanthropology section, Senckenberg Centre for Human Evolution and Palaeoenvironment, Institute for Archaeological Sciences, Eberhard Karls Universität Tübingen, Tübingen, Germany. 2 DFG Centre for Advanced Studies ‘Words, Bones, Genes, Tools’, Eberhard Karls Universität Tübingen, Tübingen, Germany. 3 Human Evolution Research Institute, University of Cape Town, Cape Town, South Africa. 4 Department of Archaeology, University of Cape Town, Cape Town, South Africa. ✉ e-mail: katerina.harvati@ifu.uni-tuebingen.de; becky.ackermann@uct.ac.za N atural hybridization promotes evolutionary . m innovation, creating novel and diverse outcomes in subsequent genera- tions, thereby providing a rich substrate on which selection can further act to shape evolutionary trajectories 1,2 . Since 2010, methodological advances allowing unprecedented, high-resolution insights into ancient genomes have provided increasing evidence for hybridization and resultant gene flow among late Pleistocene humans. Currently, indications for gene exchange include move- ment of genes from Neanderthals into early Homo sapiens (conven- tionally called ‘early modern humans’) 3–8 , resulting in approximately 2–3% Neanderthal ancestry of non-African living modern humans 7 ; as well as evidence that H. sapiens contributed to the Neanderthal gene pool as early as 150 to >200 thousand years ago (ka) 9,10 . Gene flow from Denisovans into the ancestors of modern Asian popu- lations 11,12 , from Neanderthals into Denisovans 13,14 , and from some unknown hominin into Denisovans 13 has also been reported, and the genome of a first-generation descendant of a Neanderthal mother and a Denisovan father living ca. 90 ka was recently discov- ered 15 . Finally, genetic exchanges between ancient and recent lin- eages may have also occurred within Africa 9,16–21 . Taken together, these studies indicate that gene flow has been multidirectional, was much more common than previously appreciated by most (but see for example, ref. 22 ), and may have been instrumental in structur- ing genetic diversity across our ancestral lineage over the last half a million years. Given the speed at which new discoveries and meth- odological breakthroughs are occurring, such as the retrieval of Q1 hominin DNA from cave sediments 14 , our expectation is that such evidence will probably continue to accumulate in the future. . m . m . m . m . m Gene flow among hominins has had variable effects, best docu- mented over the last 100 K years. These include genetic evidence for some level of introgression affecting phenotypes in a beneficial manner, including those involved in immunity, spermatogenesis, adaptation to low-oxygen contexts, response to ultraviolet radiation and other traits 23–31 (but see ref. 32 ). For example, Neanderthal genes affecting skin and hair phenotypes are retained in humans living today 27,31 , suggesting that these genes might have been important in the dispersal and adaptation of people emerging from Africa and migrating into environments inhabited by Neanderthals. In other cases, gene exchange may have been detrimental. For example, the existence of chromosomal regions in living humans devoid of Neanderthal-derived alleles, such as the X-chromosome and genes related to testes and therefore reproduction 27,31 , suggests that selection may have acted to purge these genes from descendants. Neanderthal alleles present in living people have also been associ- ated with a range of phenotypes considered detrimental in modern (but not necessarily ancient) contexts, including depression, neu- rodevelopmental disorders, hypercoagulation, altered carbohydrate metabolism and addiction 27,29,33 (but see ref. 32 ). A few recent studies suggest that Neanderthal-derived genetic variation also influences brain phenotypes 29,34,35 and susceptibility to infectious diseases 36,37 . Taken together, the genetic evidence so far indicates that gene flow played an important role in shaping the evolutionary fate of Q2 Q3 Q4 Q5 Q6 Merging morphological and genetic evidence to assess hybridization in Western Eurasian late Pleistocene hominins K. Harvati  1,2 ✉ and R. R. Ackermann  2,3,4 ✉ Previous scientific consensus saw human evolution as defined by adaptive differences (behavioural and/or biological) and the emergence of Homo sapiens as the ultimate replacement of non-modern groups by a modern, adaptively more competitive group. However, recent research has shown that the process underlying our origins was considerably more complex. While archaeological and fossil evidence suggests that behavioural complexity may not be confined to the modern human lineage, recent palaeogenomic work shows that gene flow between distinct lineages (for example, Neanderthals, Denisovans, early H. sapiens) occurred repeatedly in the late Pleistocene, probably contributing elements to our genetic make-up that might have been crucial to our success as a diverse, adaptable species. Following these advances, the prevailing human origins model has shifted from one of near-complete replacement to a more nuanced view of partial replacement with considerable reticulation. Here we provide a brief introduction to the current genetic evidence for hybridization among hominins, its prevalence in, and effects on, comparative mammal groups, and especially how it manifests in the skull. We then explore the degree to which cranial variation seen in the fossil record of late Pleistocene hominins from Western Eurasia corresponds with our current genetic and comparative data. We are especially interested in understanding the degree to which skeletal data can reflect admixture. Our findings indicate some correspondence between these different lines of evidence, flag individual fossils as possibly admixed, and suggest that different cranial regions may preserve hybridization signals differentially. We urge further studies of the phenotype to expand our ability to detect the ways in which migration, interaction and genetic exchange have shaped the human past, beyond what is currently visible with the lens of ancient DNA. NATURE ECOLOGY & EVOLUTION | www.nature.com/natecolevol