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Hybridization in Human Evolution: Insights from Other Organisms

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Hybridization in Human Evolution: Insights from Other Organisms 1 1 Hybridization in human evolution: insights from other 2 organisms 3 4 RR Ackermann1,2, ML Arnold3, JA Cahill4, L Cortés-Ortiz5, BJ Evans6, BR Grant7, PR 5 Grant7, B Hallgrimsson8, R Humphreys1,2, CJ Jolly9, J Malukiewicz10,11, MD Nidiffer5, CJ 6 Percival8,,12, T Ritzman1,2,13,14, C Roos15, CC Roseman16, L Schroeder2,17, FH Smith18, K 7 Warren1,2, R Wayne19, D Zinner20 8 9 1 Department of Archaeology, University of Cape Town, Rondebosch, South Africa 10 2 Human Evolution Research Institute, University of Cape Town, Rondebosch, South 11 Africa 12 3 Department of Genetics, University of Georgia, Athens, Georgia, USA 13 4 Department of Ecology and Evolutionary Biology, University of California Santa Cruz, 14 Santa Cruz, CA, USA 15 5 Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, 16 MI, USA 17 6 Biology Department, Life Sciences Building, McMaster University, Hamilton, Canada 18 7 Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, 19 USA 20 8 Dept. of Cell Biology & Anatomy and the Alberta Children’s Hospital Research Institute, 21 University of Calgary, Canada 22 9 Center for the Study of Human Origins, Department of Anthropology, New York 23 University, and NYCEP, New York, NY, USA 24 10 Biodesign Institute, Arizona State University, Tempe, AZ, USA 25 11 Federal University of Vicosa, Department of Animal Biology, Vicosa, Brazil 26 12 Department of Anthropology, Stony Brook University, Stony Brook, New York, USA 27 13 Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, 28 USA 29 14 Department of Anthropology, Washington University in St. Louis, McMillan Hall, 1 30 Brookings Dr., St. Louis, MO, USA 31 15 Primate Genetics Laboratory, German Primate Center (DPZ), Leibniz Institute for 32 Primate Research, Göttingen, Germany 33 16 Department of Animal Biology, School of Integrative Biology, University of Illinois at 34 Urbana-Champaign, Illinois, USA 35 17 Department of Anthropology, University of Toronto Mississauga, Mississauga, Canada 36 18 Department of Sociology & Anthropology, Illinois State University, Normal, IL, USA 37 19 Department of Ecology and Evolutionary Biology, UCLA, California, USA 38 20 Cognitive Ethology Laboratory, German Primate Center (DPZ), Leibniz Institute for 39 Primate Research, Göttingen, Germany 40 41 Corresponding author: RR Ackermann, [email protected] 42 43 Funding Information: This manuscript is the product of a symposium entitled 44 “Hybridization in human evolution: what can other organisms tell us?” presented at the 2016 1 2 1 Annual Meeting of the American Association of Physical Anthropologists, in Atlanta, 2 Georgia. The authors are immensely grateful to Wiley-Liss for sponsoring that symposium. 3 RRA research funded by the DST/NRF Centre of Excellence in Palaeosciences (CoE-Pal) 4 and the National Research Foundation of South Africa. 5 6 Abstract 7 8 During the late Pleistocene, genetically isolated lineages of hominins exchanged genes thus 9 influencing genomic variation in humans in both the past and present. However, the 10 dynamics of this genetic exchange and the associated phenotypic consequences through time 11 remain poorly understood. Gene exchange across divergent lineages can result in myriad 12 outcomes arising from the dynamics of the exchange, and the environmental conditions 13 under which it occurs. Here we draw from research across various organisms illustrating 14 some of the ways in which gene exchange can structure genomic/phenotypic diversity 15 within/among species. We present a range of examples relevant to questions about the 16 evolution of our hominin ancestors. These examples illustrate the diverse evolutionary 17 consequences of hybridization and point to potential drivers of human evolution in the 18 context of hybridization with other hominins including: influences on adaptive evolution, 19 climate change, developmental systems, sex-differences in behavior, Haldane’s rule and the 20 large X-effect, transgressive phenotypic variation. 21 22 Keywords: Gene flow, Introgression, Neanderthals, Modern human origins, Model 23 organisms 24 25 26 2 3 1 A shifting paradigm: Introgressive hybridization and human 2 evolution 3 4 Traditionally, the evolution of hominins – humans and our closest relatives since we 5 collectively diverged from the ancestor of chimpanzees – has been represented in two 6 distinct ways. One depicts evolutionary relationships among purported hominin species as a 7 tree describing ancestor-descendant relationships, with evolutionary relatedness depicted by 8 branches that split as one travels upward from the trunk to the leaves and ending in 9 extinction for all those branches not leading to our leaf. Within this set of phylogenetic 10 models lies out of Africa with replacement accounts of recent human evolution.1,2 The out of 11 Africa with replacement models propose that the entirety of the recent non-African 12 components of individuals’ ancestry (ca. 600 years ago, before world empires and 13 colonialism) traces its origins back to Africa sometime between 50 to 100 thousand years ago 14 (ka). As such, non-African human variation in the recent past is a subset of variation that 15 was present in humans in Middle Pleistocene Africa. Under this view, the recent (pre- 16 colonial) genetic variation was initially established by founder effects associated with modern 17 human populations moving out of Africa, and then influenced by recurring gene flow within 18 and among the various regions of the world over tens of millennia. It posits further that 19 these early modern populations did not interbreed with resident groups of archaic humans 20 such as Neanderthals, and that differentiation between them was generated by drift and 21 natural selection acting in more or less independently evolving lineages. 22 In contrast, multiregional continuity evolutionary models emphasize sustained gene 23 flow, as opposed to replacement and extinction. In the case of recent human evolution, this 24 includes sustained gene flow across the entirety of the human inhabited world at all points 25 throughout the Pleistocene and into the present day.3,4 The neutral component of the 26 multiregional model came to be identified as isolation by distance.3,5 Under isolation by 27 distance, the local reduction of genomic variation by random genetic drift is counteracted by 28 the addition of new variation to local groups via gene flow. Left unperturbed by major 29 evolutionary events such as range expansions and local replacement of populations, this 30 balance between gene flow and random genetic drift leads to an equilibrium between within 31 group and among group genetic variation. In this treatment, adaptation to regional 32 conditions by natural selection leads to more pronounced differences among groups. A key 33 distinguishing factor between the multiregional continuity model of recent human evolution 34 and the out of Africa with replacement model is that the former postulates that Homo sapiens 35 populations outside of Africa became established far earlier (~1 million years ago (Ma) or 36 more) than the latter model (~100ka or less). 37 These two models have occupied the extreme ends of a continuum of possible 38 accounts of recent human evolution. Other models of recent human evolution combined 39 features of both renditions and allowed for a combination of long periods of isolation 40 interrupted by bouts of gene flow between groups.6,7 These models were often subsumed 41 under the general multiregional view in the 1990s and 2000s,8 although sometimes Bräuer’s 42 model (Afro European sapiens hypothesis) was lumped together with out of Africa.9 43 A striking realization in the last decade is that neither of the scenarios at the extreme 44 poles of this continuum is in fact supported by new genetic and genomic evidence.10-15 Clear 45 evidence for reticulation among diverged lineages/populations (Neanderthals, Denisovans, 46 H. sapiens) falsifies the predictions of branching phylogenetic models without reticulation, 3 4 1 while evidence for periods of substantial isolation among these same groups is inconsistent 2 with the multiregional continuity model. Further studies of the phenotypic consequences of 3 hybridization across taxa show that it may have provided genetic variation that was then 4 favored by natural selection to drive evolutionary innovation in our hominin ancestors, and 5 perhaps contributed to bursts of exceptional phenotypic diversification, not only in our 6 recent past (e.g. emergence of Homo sapiens16), but also deeper in time. 7 Introgression via hybridization, together with natural selection and drift, plays an 8 important role in speciation and the evolution of diversity in animal taxa.17-24 This recent 9 body of research validates the work of earlier evolutionary biologists (e.g.25,26), who 10 emphasized the significance of introgressive hybridization (e.g. ‘divergence-with-gene- 11 flow’27), and the phenotypic variation it can produce, to adaptive evolution and 12 biodiversification. Evolutionary biologists can now move past the question of whether 13 lineages can diverge while undergoing gene exchange with other lineages towards 14 investigating how such exchange affects the interacting groups of organisms (Figure 1).28 15 With the survival of admixed genetic lineages, extinction of a recognized species or 16 lineage should no longer necessarily be viewed as the disappearance without issue of a 17 species. Rather it may be a circumstance of extinction by hybridization.29 In such cases, some 18 genetic characteristics of a lineage continue even when anatomical morphs disappear. Key 19 examples of this are the extinction of the Neanderthals and Denisovans as distinct 20 evolutionary lineages, and probably other archaic Eurasian and African groups as well. 21 We argue four points about the importance of hybridization and introgression in 22 human evolution. 23 24 1. The human genome shows ample signs of introgression and hybridization, which is 25 also not unusual in other organisms, including amphibians, birds, and myriad 26 terrestrial mammals, including primates.
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