SummaryWe report genome-wide ancient DNA from 49 individuals forming four parallel time transects in Belize, Brazil, the Central Andes, and the Southern Cone, each dating to at least ∼9,000 years ago. The common ancestral population radiated rapidly from just one of the two early branches that contributed to Native Americans today. We document two previously unappreciated streams of gene flow between North and South America. One affected the Central Andes by ∼4,200 years ago, while the other explains an affinity between the oldest North American genome associated with the Clovis culture and the oldest Central and South Americans from Chile, Brazil, and Belize. However, this was not the primary source for later South Americans, as the other ancient individuals derive from lineages without specific affinity to the Clovis-associated genome, suggesting a population replacement that began at least 9,000 years ago and was followed by substantial population continuity in multiple regions.

Neanderthals are commonly depicted as leading dangerous lives and permanently13 struggling for survival. This view largely relies on their reported high incidences of 14 trauma 1,2 , variously attributed to violent social behavior 3,4 , highly mobile hunter-15 gatherer lifestyles 2 , or attacks by carnivores 5 . The described Neanderthal pattern of 16 predominantly cranial injuries is further thought to reflect violent, close encounters 17 with large prey mammals resulting from a lack of long-distance hunting weapons 1 . 18 These interpretations directly shape our understanding of Neanderthal lifestyles, health 19 and hunting abilities, yet mainly rest on descriptive, case-based evidence. Quantitative, 20 population-level studies of traumatic injuries are rare. Here we reassess the hypothesis 21 of higher cranial trauma prevalence among Neanderthals using a population-level 22 approach, accounting for preservation bias and other contextual data, and using an 23 exhaustive new fossil database. We show that Neanderthals and Upper Paleolithic 24 modern humans exhibit similar overall incidences of cranial trauma, which are higher 25 for males in both taxa, consistent with patterns shown by later modern human populations. Beyond these similarities we observed species-specific age-related variation 27 in trauma prevalence, suggesting either differences in the timing of injuries during life, 28 or differential mortality risk of trauma survivors in the two groups. Finally, our results 29 highlight the importance of preservation bias in studies of trauma prevalence. 31Neanderthals are commonly depicted as robust hominins leading stressful, dangerous lives 1,6-32 9 . Traumatic injuries, considered common among adult Neanderthal remains 1 , are a major 33 piece of evidence supporting this hypothesis: not only are Neanderthals proposed to suffer 34 from high trauma prevalence 2,3,10,11 , they are also thought to exhibit more traumatic injuries 35 than early modern humans 9,12,13 . Explanations for this include violent social behavior 3,4 , a 36 highly mobile hunter-gatherer-lifestyle in glacial environments 2 , and attacks by carnivores 5 . 37Moreover, Neanderthals are thought to show unusually high levels of head and neck injuries, 38 attributed to their hypothesized reliance on close range hunting, leading to confrontations with 39 large prey mammals 1 . These interpretations have important implications for reconstructions of 40 Neanderthal paleobiology and behavior, and have shaped the prevailing perception of the 41 species. However, they are largely based on anecdotal evidence, since trauma among 42 Paleolithic humans is often reported on a descriptive, case-by-case basis. The few systematic, 43 quantitative studies conducted to date have yielded contradictory results 2,4,11,14,15 , but question 44 the prevailing view of 'the highly traumatized Neandertal' 15 . 45 Current Paleolithic trauma research suffers from several limitations. Most previous work 46 assessed the proportional distribution of lesions throughout...

Objectives: This study characterizes patterns of cranial trauma prevalence in a large sample of Upper Paleolithic (UP) fossil specimens (40,000-10,000 BP). Materials and Methods: Our sample comprised 234 individual crania (specimens), representing 1,285 cranial bones (skeletal elements), from 101 Eurasian UP sites. We used generalized linear mixed models (GLMMs) to assess trauma prevalence in relation to age-at-death, sex, anatomical distribution, and between pre-and post-Last Glacial Maximum (LGM) samples, while accounting for skeletal preservation. Results: Models predicted a mean cranial trauma prevalence of 0.07 (95% CI 0.003-0.19) at the level of skeletal elements, and of 0.26 (95% CI 0.08-0.48) at the level of specimens, each when 76-100% complete. Trauma prevalence increased with skeletal preservation. Across specimen and skeletal element datasets, trauma prevalence tended to be higher for males, and was consistently higher in the old age group. We found no time-specific trauma prevalence patterns for the two sexes or age cohorts when comparing samples from before and after the LGM. Samples showed higher trauma prevalence in the vault than in the face, with vault remains being affected predominantly in males. Discussion: Cranial trauma prevalence in UP humans falls within the variation described for Mesolithic and Neolithic samples. According to our current dataset, UP males and females were exposed to slightly different injury risks and trauma distributions, potentially due to different activities or behaviors, yet both sexes exhibit more trauma among the old. Environmental stressors associated with climatic changes of the LGM are not reflected in cranial trauma prevalence. To analyze trauma in incomplete skeletal remains we propose GLMMs as an informative alternative to crude frequency calculations.