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.

Chili peppers ( Capsicum spp.) are widely cultivated food plants that arose in the Americas and are now incorporated into cuisines worldwide. Here, we report a genus-specific starch morphotype that provides a means to identify chili peppers from archaeological contexts and trace both their domestication and dispersal. These starch microfossils have been found at seven sites dating from 6000 years before present to European contact and ranging from the Bahamas to southern Peru. The starch grain assemblages demonstrate that maize and chilies occurred together as an ancient and widespread Neotropical plant food complex that predates pottery in some regions.

Study of human adaptation to extreme environments is important for understanding our cultural and genetic capacity for survival. The Pucuncho Basin in the southern Peruvian Andes contains the highest-altitude Pleistocene archaeological sites yet identified in the world, about 900 meters above confidently dated contemporary sites. The Pucuncho workshop site [4355 meters above sea level (masl)] includes two fishtail projectile points, which date to about 12.8 to 11.5 thousand years ago (ka). Cuncaicha rock shelter (4480 masl) has a robust, well-preserved, and well-dated occupation sequence spanning the past 12.4 thousand years (ky), with 21 dates older than 11.5 ka. Our results demonstrate that despite cold temperatures and low-oxygen conditions, hunter-gatherers colonized extreme high-altitude Andean environments in the Terminal Pleistocene, within about 2 ky of the initial entry of humans to South America.

Summary There are many unanswered questions about the population history of the Central and South Central Andes, particularly regarding the impact of large-scale societies, such as the Moche, Wari, Tiwanaku, and Inca. We assembled genome-wide data on 89 individuals dating from ∼9,000-500 years ago (BP), with a particular focus on the period of the rise and fall of state societies. Today’s genetic structure began to develop by 5,800 BP, followed by bi-directional gene flow between the North and South Highlands, and between the Highlands and Coast. We detect minimal admixture among neighboring groups between ∼2,000–500 BP, although we do detect cosmopolitanism (people of diverse ancestries living side-by-side) in the heartlands of the Tiwanaku and Inca polities. We also highlight cases of long-range mobility connecting the Andes to Argentina and the Northwest Andes to the Amazon Basin. Video Abstract

The Younger Dryas Stadial (YDS; ∼12,900-11,600 y ago) in the Northern Hemisphere is classically defined by abrupt cooling and renewed glaciation during the last glacial-interglacial transition. Although this event involved a global reorganization of atmospheric and oceanic circulation [Denton GH, Alley RB, Comer GC, Broecker WS (2005) Quat Sci Rev 24:1159-1182], the magnitude, seasonality, and geographical footprint of YDS cooling remain unresolved and pose a challenge to our understanding of abrupt climate change. Here, we present a deglacial chronology from Scotland, immediately downwind of the North Atlantic Ocean, indicating that the Scottish ice cap disintegrated during the first half of the YDS. We suggest that stratification of the North Atlantic Ocean resulted in amplified seasonality that, paradoxically, stimulated a severe wintertime climate while promoting warming summers through solar heating of the mixed layer. This latter process drove deglaciation of downwind landmasses to completion well before the end of the YDS.

Whether or not tropical climate fluctuated in synchrony with global events during the Late Pleistocene is a key problem in climate research. However, the timing of past climate changes in the tropics remains controversial, with a number of recent studies reporting that tropical ice-age climate is out of phase with global events. Here, we present geomorphic evidence and an in-situ cosmogenic 3 He surface-exposure chronology from Nevado Coropuna, southern Peru, showing that glaciers underwent at least two significant advances during the Late Pleistocene prior to Holocene warming. Comparison of our glacial-geomorphic map at Nevado Coropuna to mid-latitude reconstructions yields a striking similarity between Last Glacial Maximum (LGM) and Late Glacial sequences in tropical and temperate regions. Exposure ages constraining the maximum and end of the older advance at Nevado Coropuna range between 24.5 and 25.3 ka, and between 16.7 and 21.1 ka, respectively, depending on the cosmogenic productionrate scaling model used. Similarly, the mean age of the younger event ranges from 10 to 13 ka. This implies that (1) the LGM and the onset of deglaciation in southern Peru occurred no earlier than at higher latitudes and (2) that a significant Late Glacial event occurred, most likely prior to the Holocene, coherent with the glacial record from mid and high latitudes. The time elapsed between the end of the LGM and the Late Glacial event at Nevado Coropuna is independent of scaling model and matches the period between the LGM termination and Late Glacial reversal in classic mid-latitude records, suggesting that these events in both tropical and temperate regions were in phase.

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Ancient DNA traces the history of hepatitis B Hepatitis B virus (HBV) infections represent a worldwide human health concern. To study the history of this pathogen, Kocher et al . identified 137 human remains with detectable levels of virus dating between 400 and 10,000 years ago. Sequencing and analyses of these ancient viruses suggested a common ancestor between 12,000 and 20,000 years ago. There is no evidence indicating that HBV was present in the earliest humans as they spread out of Africa; however, HBV was likely present in human populations before farming. Furthermore, the virus was present in the Americas by about 9000 years ago, representing a lineage sister to the viral strains found in Eurasia that diverged about 20,000 years ago. —LMZ