Late Pleistocene exploration and settlement of the Americas by modern humans

Taguatagua 3: A new late Pleistocene settlement in a highly suitable lacustrine habitat in central Chile (34°S)

We present the results of the excavations and analyses of the diverse and exceptional archaeological assemblage of Taguatagua 3, a new late Pleistocene site located in the ancient Tagua Tagua lake in Central Chile (34°S). The anthropogenic context is constrained in a coherently dated stratigraphic deposit which adds new information about the mobility, subsistence strategies, and settlement of the early hunter-gatherers of southern South America. The age model constructed, as well as radiocarbon dates obtained directly from a combustion structure, indicate that the human occupation occurred over a brief time span around 12,440-12,550 cal yr BP. Considering taphonomic, geoarchaeological, lithic, archaeobotanical, and zooarchaeological evidence, as well as the spatial distribution combined with ethnographic data, we interpret Taguatagua 3 as a logistic and temporary camp associated mainly with gomphothere hunting and butchering. Nevertheless, several other activities were carried out here as well, such as hide and/or bone preparation, small vertebrate and plant processing and consumption, and red ochre grinding. Botanical and eggshell remains suggest that the anthropic occupation occurred during the dry season. Considering the contemporaneous sites recorded in the basin, we conclude that the ancient Tagua Tagua lake was a key location along the region's early hunter-gatherer mobility circuits. In this context, it acted as a recurrent hunting/scavenging place during the Late Pleistocene due to its abundant, diverse, and predictable resources.

New age constraints for human entry into the Americas on the north Pacific coast

The timing of the initial peopling of the Americas is unresolved. Because the archaeological record necessitates discussion of human entry from Beringia into southern North America during the last glaciation, addressing this problem routinely involves evaluating environmental parameters then targeting areas suitable for human settlement. Vertebrate remains indicate landscape quality and are a key dataset for assessing coastal migration theories and the viability of coastal routes. Here, radiocarbon dates on vertebrate specimens and archaeological sites are calibrated to document species occurrences and the ages of human settlements across the western expansion and decay of the Cordilleran Ice Sheet (CIS) during the Late Wisconsin Fraser Glaciation in four subregions of the north Pacific coast of North America. The results show archaeological sites occur after glacial maxima and are generally consistent with the age of other securely dated earliest sites in southern North America. They also highlight gaps in the vertebrate chronologies around CIS maxima in each of the subregions that point to species redistributions and extirpations and signal times of low potential for human settlement and subsistence in a key portion of the proposed coastal migration route. This study, therefore, defines new age constraints for human coastal migration theories in the peopling of the Americas debate.

Peopling of the Americas: A new approach to assessing dental morphological variation in Asian and Native American populations

OBJECTIVES

Through biodistance analyses, anthropologists have used dental morphology to elucidate how people moved into and throughout the Americas. Here, we apply a method that focuses on individuals rather than sample frequencies through the application rASUDAS2, based on a naïve Bayes' algorithm.

MATERIALS AND METHODS

Using the database of C.G. Turner II, we calculated the probability that an individual could be assigned to one of seven biogeographic groups (American Arctic, North & South America, East Asia, Southeast Asia & Polynesia, Australo-Melanesia, Western Eurasia, & Sub-Saharan Africa) through rASUDAS2. The frequency of classifications for each biogeographic group was determined for 1418 individuals from six regions across Asia and the Americas.

RESULTS

Southeast Asians show mixed assignments but rarely to American Arctic or "American Indian." East Asians are assigned to East Asia half the time while 30% are assigned as Native American. People from the American Arctic and North & South America are assigned to Arctic America or non-Arctic America 75%-80% of the time, with 10%-15% classified as East Asian.

DISCUSSION

All Native American groups have a similar degree of morphological affinity to East Asia, as 10%-15% are classified as East Asian. East Asians are classified as Native American in 30% of cases. Individuals in the Western Hemisphere are decreasingly classified as Arctic the farther south they are located. Equivalent levels of classification as East Asian across all Native American groups suggests one divergence between East Asians and the population ancestral to all Native Americans. Non-arctic Native American groups are derived from the Arctic population, which represents the Native American founder group.

Dating the arrival of humans in the Americas

A debate about the age of ancient footprints continues.

Pre-Younger Dryas megafaunal extirpation at Rancho La Brea linked to fire-driven state shift

The cause, or causes, of the Pleistocene megafaunal extinctions have been difficult to establish, in part because poor spatiotemporal resolution in the fossil record hinders alignment of species disappearances with archeological and environmental data. We obtained 172 new radiocarbon dates on megafauna from Rancho La Brea in California spanning 15.6 to 10.0 thousand calendar years before present (ka). Seven species of extinct megafauna disappeared by 12.9 ka, before the onset of the Younger Dryas. Comparison with high-resolution regional datasets revealed that these disappearances coincided with an ecological state shift that followed aridification and vegetation changes during the Bølling-Allerød (14.69 to 12.89 ka). Time-series modeling implicates large-scale fires as the primary cause of the extirpations, and the catalyst of this state shift may have been mounting human impacts in a drying, warming, and increasingly fire-prone ecosystem.

The role of Beringia in human adaptation to Arctic conditions based on results of genomic studies of modern and ancient populations

The results of studies in Quaternary geology, archeology, paleoanthropology and human genetics demonstrate that the ancestors of Native Americans arrived in mid-latitude North America mainly along the Pacific Northwest Coast, but had previously inhabited the Arctic and during the last glacial maximum were in a refugium in Beringia, a land bridge connecting Eurasia and North America. The gene pool of Native Americans is represented by unique haplogroups of mitochondrial DNA and the Y chromosome, the evolutionary age of which ranges from 13 to 22 thousand years. The results of a paleogenomic analysis also show that during the last glacial maximum Beringia was populated by human groups that had arisen as a result of interaction between the most ancient Upper Paleolithic populations of Northern Eurasia and newcomer groups from East Asia. Approximately 20 thousand years ago the Beringian populations began to form, and the duration of their existence in relative isolation is estimated at about 5 thousand years. Thus, the adaptation of the Beringians to the Arctic conditions could have taken several millennia. The adaptation of Amerindian ancestors to high latitudes and cold climates is supported by genomic data showing that adaptive genetic variants in Native Americans are associated with various metabolic pathways: melanin production processes in the skin, hair and eyes, the functioning of the cardiovascular system, energy metabolism and immune response characteristics. Meanwhile, the analysis of the existing hypotheses about the selection of some genetic variants in the Beringian ancestors of the Amerindians in connection with adaptation to the Arctic conditions (for example, in the FADS, ACTN3, EDAR genes) shows the ambiguity of the testing results, which may be due to the loss of some traces of the "Beringian" adaptation in the gene pools of modern Native Americans. The most optimal strategy for further research seems to be the search for adaptive variant.

Trans-Holocene Bayesian chronology for tree and field crop use from El Gigante rockshelter, Honduras

El Gigante rockshelter in western Honduras provides a deeply stratified archaeological record of human-environment interaction spanning the entirety of the Holocene. Botanical materials are remarkably well preserved and include important tree (e.g., ciruela (Spondias), avocado (Persea americana)) and field (maize (Zea mays), beans (Phaseolus), and squash (Cucurbita)) crops. Here we provide a major update to the chronology of tree and field crop use evident in the sequence. We report 375 radiocarbon dates, a majority of which are for short-lived botanical macrofossils (e.g., maize cobs, avocado seeds, or rinds). Radiocarbon dates were used in combination with stratigraphic details to establish a Bayesian chronology for ~9,800 identified botanical samples spanning the last 11,000 years. We estimate that at least 16 discrete intervals of use occurred during this time, separated by gaps of ~100-2,000 years. The longest hiatus in rockshelter occupation was between ~6,400 and 4,400 years ago and the deposition of botanical remains peaked at ~2,000 calendar years before present (cal BP). Tree fruits and squash appeared early in the occupational sequence (~11,000 cal BP) with most other field crops appearing later in time (e.g., maize at ~4,400 cal BP; beans at ~2,200 cal BP). The early focus on tree fruits and squash is consistent with early coevolutionary partnering with humans as seed dispersers in the wake of megafaunal extinction in Mesoamerica. Tree crops predominated through much of the Holocene, and there was an overall shift to field crops after 4,000 cal BP that was largely driven by increased reliance on maize farming.

Tracing the evolutionary history of hepatitis B virus genotype H endemic to Mexico

Hepatitis B virus (HBV) spreads efficiently among all human populations worldwide. HBV is classified into ten genotypes (A to J) with their geographic distribution and clinical features. In Mexico, HBV genotype H is the leading cause of hepatitis B and has been detected in indigenous populations, suggesting that HBV genotype H may be native to Mexico. However, little is known about the evolutionary history of HBV genotype H. Thus, we aimed to determine the age of HBV genotype H in Mexico using molecular dating techniques. Ninety-two HBV sequences of the reverse transcriptase (RT) domain of the polymerase gene (~1,251 bp) were analyzed; 48 were genotype H, 43 were genotype F, and the oldest HBV sequence from America was included as the root. All sequences were aligned, and the most recent common ancestor (TMRCA) time was calculated using the Bayesian Skyline Evolutionary Analysis. Our results estimate a TMRCA for the genotype H in Mexico of 2070.9 (667.5-4489.2) years before the present (YBP). We identified four major diversification events in genotype H, named H1, H2, H3, and H4. The TMRCA of H1 was 1213.0 (253.3-2638.3) YBP, followed by H2 1175.5 (557.5-2424.2) YBP, H3 949.6 (279.3-2105.0) YBP, and H4 1230.5 (336.3, 2756.7) YBP. We estimated that genotype H diverged from its sister genotype F around 8140.8 (1867.5-18012.8) YBP. In conclusion, this study found that genotype H in Mexico has an estimated age of 2070.9 (667.5-4489.2) YBP and has experienced at least four major diversification events since then.

The multifaceted genomic history of Ashaninka from Amazonian Peru

Despite its crucial location, the western side of Amazonia between the Andes and the source(s) of the Amazon River is still understudied from a genomic and archaeogenomic point of view, albeit possibly harboring essential information to clarify the complex genetic history of local Indigenous groups and their interactions with nearby regions,^{1,2,3,4,5,6,7,8} including central America and the Caribbean.^9,10,11,12 Focusing on this key region, we analyzed the genome-wide profiles of 51 Ashaninka individuals from Amazonian Peru, observing an unexpected extent of genomic variation. We identified at least two Ashaninka subgroups with distinctive genomic makeups, which were differentially shaped by the degree and timing of external admixtures, especially with the Indigenous groups from the Andes and the Pacific coast. On a continental scale, Ashaninka ancestors probably derived from a south-north migration of Indigenous groups moving into the Amazonian rainforest from a southeastern area with contributions from the Southern Cone and the Atlantic coast. These ancestral populations diversified in the variegated geographic regions of interior South America, on the eastern side of the Andes, differentially interacting with surrounding coastal groups. In this complex scenario, we also revealed strict connections between the ancestors of present-day Ashaninka, who belong to the Arawakan language family,¹³ and those Indigenous groups that moved further north into the Caribbean, contributing to the early Ceramic (Saladoid) tradition in the islands.^14,15.

Late Pleistocene osseous projectile point from the Manis site, Washington-Mastodon hunting in the Pacific Northwest 13,900 years ago

Bone fragments embedded in a rib of a mastodon (Mammut americanum) from the Manis site, Washington, were digitally excavated and refit to reconstruct an object that is thin and broad, has smooth, shaped faces that converge to sharp lateral edges, and has a plano-convex cross section. These characteristics are consistent with the object being a human-made projectile point. The 13,900-year-old Manis projectile point is morphologically different from later cylindrical osseous points of the 13,000-year-old Clovis complex. The Manis point, which is made of mastodon bone, shows that people predating Clovis made and used osseous weapons to hunt megafauna in the Pacific Northwest during the Bølling-Allerød.

Beringia and the peopling of the Western Hemisphere

Did Beringian environments represent an ecological barrier to humans until less than 15 000 years ago or was access to the Americas controlled by the spatial-temporal distribution of North American ice sheets? Beringian environments varied with respect to climate and biota, especially in the two major areas of exposed continental shelf. The East Siberian Arctic Shelf ('Great Arctic Plain' (GAP)) supported a dry steppe-tundra biome inhabited by a diverse large-mammal community, while the southern Bering-Chukchi Platform ('Bering Land Bridge' (BLB)) supported mesic tundra and probably a lower large-mammal biomass. A human population with west Eurasian roots occupied the GAP before the Last Glacial Maximum (LGM) and may have accessed mid-latitude North America via an interior ice-free corridor. Re-opening of the corridor less than 14 000 years ago indicates that the primary ancestors of living First Peoples, who already had spread widely in the Americas at this time, probably dispersed from the NW Pacific coast. A genetic 'arctic signal' in non-arctic First Peoples suggests that their parent population inhabited the GAP during the LGM, before their split from the former. We infer a shift from GAP terrestrial to a subarctic maritime economy on the southern BLB coast before dispersal in the Americas from the NW Pacific coast.

Genomic evidence for ancient human migration routes along South America's Atlantic coast

An increasing body of archaeological and genomic evidence has hinted at a complex settlement process of the Americas by humans. This is especially true for South America, where unexpected ancestral signals have raised perplexing scenarios for the early migrations into different regions of the continent. Here, we present ancient human genomes from the archaeologically rich Northeast Brazil and compare them to ancient and present-day genomic data. We find a distinct relationship between ancient genomes from Northeast Brazil, Lagoa Santa, Uruguay and Panama, representing evidence for ancient migration routes along South America's Atlantic coast. To further add to the existing complexity, we also detect greater Denisovan than Neanderthal ancestry in ancient Uruguay and Panama individuals. Moreover, we find a strong Australasian signal in an ancient genome from Panama. This work sheds light on the deep demographic history of eastern South America and presents a starting point for future fine-scale investigations on the regional level.

Theoretical analysis of principal components in an umbrella model of intraspecific evolution

Principal component analysis (PCA) is one of the most frequently-used approach to describe population structure from multilocus genotype data. Regarding geographic range expansions of modern humans, interpretations of PCA have, however, been questioned, as there is uncertainty about the wave-like patterns that have been observed in principal components. It has indeed been argued that wave-like patterns are mathematical artifacts that arise generally when PCA is applied to data in which genetic differentiation increases with geographic distance. Here, we present an alternative theory for the observation of wave-like patterns in PCA. We study a coalescent model - the umbrella model - for the diffusion of genetic variants. The model is based on genetic drift without any particular geographical structure. In the umbrella model, splits from an ancestral population occur almost continuously in time, giving birth to small daughter populations at a regular pace. Our results provide detailed mathematical descriptions of eigenvalues and eigenvectors for the PCA of sampled genomic sequences under the model. When variants uniquely represented in the sample are removed, the PCA eigenvectors are defined as cosine functions of increasing periodicity, reproducing wave-like patterns observed in equilibrium isolation-by-distance models. Including singleton variants in the analysis, the eigenvectors corresponding to the largest eigenvalues exhibit complex wave shapes. The accuracy of our predictions is further investigated with coalescent simulations. Our analysis supports the hypothesis that highly structured wave-like patterns could arise from genetic drift only, and may not always be artificial outcomes of spatially structured data. Genomic data related to the peopling of the Americas are reanalyzed in the light of our new theory.

A genomic perspective on South American human history

It has generally been accepted that the current indigenous peoples of the Americas are derived from ancestors from northeastern Asia. The latter were believed to have spread into the American continent by the end of the Last Glacial Maximum. In this sense, a joint and in-depth study of the earliest settlement of East Asia and the Americas is required to elucidate these events accurately. The first Americans underwent an adaptation process to the Americas' vast environmental diversity, mediated by biological and cultural evolution and niche construction, resulting in enormous cultural diversity, a wealth of domesticated species, and extensive landscape modifications. Afterward, in the Late Holocene, the advent of intensive agricultural food production systems, sedentism, and climate change significantly reshaped genetic and cultural diversity across the continent, particularly in the Andes and Amazonia. Furthermore, starting around the end of the 15th century, European colonization resulted in massive extermination of indigenous peoples and extensive admixture. Thus, the present review aims to create a comprehensive picture of the main events involved in the formation of contemporary South American indigenous populations and the dynamics responsible for shaping their genetic diversity by integrating current genetic data with evidence from archeology, linguistics and other disciplines.

Late quaternary biotic homogenization of North American mammalian faunas

Biotic homogenization—increasing similarity of species composition among ecological communities—has been linked to anthropogenic processes operating over the last century. Fossil evidence, however, suggests that humans have had impacts on ecosystems for millennia. We quantify biotic homogenization of North American mammalian assemblages during the late Pleistocene through Holocene (~30,000 ybp to recent), a timespan encompassing increased evidence of humans on the landscape (~20,000–14,000 ybp). From ~10,000 ybp to recent, assemblages became significantly more homogenous (>100% increase in Jaccard similarity), a pattern that cannot be explained by changes in fossil record sampling. Homogenization was most pronounced among mammals larger than 1 kg and occurred in two phases. The first followed the megafaunal extinction at ~10,000 ybp. The second, more rapid phase began during human population growth and early agricultural intensification (~2,000–1,000 ybp). We show that North American ecosystems were homogenizing for millennia, extending human impacts back ~10,000 years.

Biotic homogenization, which is increased similarity in the composition of species among communities, is rising due to human activities. Using North American mammal fossil records from the past 30,000 years, this study shows that this phenomenon is ancient, beginning between 12,000 and 10,000 years ago with the extinction of the mammal megafauna.

Human Occupation of the North American Colorado Plateau ∼37,000 Years Ago

Calibrating human population dispersals across Earth’s surface is fundamental to assessing rates and timing of anthropogenic impacts and distinguishing ecological phenomena influenced by humans from those that were not. Here, we describe the Hartley mammoth locality, which dates to 38,900–36,250 cal BP by AMS 14C analysis of hydroxyproline from bone collagen. We accept the standard view that elaborate stone technology of the Eurasian Upper Paleolithic was introduced into the Americas by arrival of the Native American clade ∼16,000 cal BP. It follows that if older cultural sites exist in the Americas, they might only be diagnosed using nuanced taphonomic approaches. We employed computed tomography (CT and μCT) and other state-of-the-art methods that had not previously been applied to investigating ancient American sites. This revealed multiple lines of taphonomic evidence suggesting that two mammoths were butchered using expedient lithic and bone technology, along with evidence diagnostic of controlled (domestic) fire. That this may be an ancient cultural site is corroborated by independent genetic evidence of two founding populations for humans in the Americas, which has already raised the possibility of a dispersal into the Americas by people of East Asian ancestry that preceded the Native American clade by millennia. The Hartley mammoth locality thus provides a new deep point of chronologic reference for occupation of the Americas and the attainment by humans of a near-global distribution.

Evolutionary Medicine Perspectives: Helicobacter pylori, Lactose Intolerance, and 3 Hypotheses for Functional and Inflammatory Gastrointestinal and Hepatobiliary Disorders

Many clinicians have suboptimal knowledge of evolutionary medicine. This discipline integrates social and basic sciences, epidemiology, and clinical medicine, providing explanations, especially ultimate causes, for many conditions. Principles include genetic variation from population bottleneck and founder effects, evolutionary trade-offs, and coevolution. For example, host-microbe coevolution contributes to the inflammatory and carcinogenic variability of Helicobacter pylori. Antibiotic-resistant strains are evolving, but future therapy could target promutagenic proteins. Ancient humans practicing dairying achieved survival and reproduction advantages of postweaning lactase persistence and passed this trait to modern descendants, delegitimizing lactose intolerance as "disease" in people with lactase nonpersistence. Three evolutionary hypotheses are each relevant to multiple diseases: (i) the polyvagal hypothesis posits that prehistoric adaptation of autonomic nervous system reactions to stress is beneficial acutely but, when continued chronically, predisposes individuals to painful functional gastrointestinal disorders, in whom it may be a biomarker; (ii) the thrifty gene hypothesis proposes genetic adaptation to feast-famine cycles among Pleistocene migrants to America, which is mismatched with Indigenous Americans' current diet and physical activity, predisposing them to obesity, nonalcoholic fatty liver disease, and gallstones and their complications; and (iii) the hygiene hypothesis proposes alteration of the gut microbiome, with which humans have coevolved, in allergic and autoimmune disease pathogenesis; for example, association of microbiome-altering proton pump inhibitor use with pediatric eosinophilic esophagitis, early-life gastrointestinal infection with celiac disease, and infant antibiotic use and an economically advanced environment with inflammatory bowel disease. Evolutionary perspectives broaden physicians' understanding of disease processes, improve care, and stimulate research.

The age of the opening of the Ice-Free Corridor and implications for the peopling of the Americas

The Ice-Free Corridor (IFC) has long played a key role in hypotheses about the peopling of the Americas. Earlier assessments of its age suggested that the IFC was available for a Clovis-first migration, but subsequent developments now suggest a pre-Clovis occupation of the Americas that occurred before the opening of the IFC, thus supporting a Pacific coastal migration route instead. However, large uncertainties in existing ages from the IFC cannot preclude its availability as a route for the first migrations. Resolving this debate over migration route is important for addressing the questions of when and how the first Americans arrived. We report cosmogenic nuclide exposure ages that show that the final opening of the IFC occurred well after pre-Clovis occupation.

The Clovis-first model for the peopling of the Americas by ∼13.4 ka has long invoked the Ice-Free Corridor (IFC) between the retreating margins of the Cordilleran and Laurentide ice sheets as the migration route from Alaska and the Yukon down to the Great Plains. Evidence from archaeology and ancient genomics, however, now suggests that pre-Clovis migrations occurred by at least ∼15.5 to 16.0 ka or earlier than most recent assessments of the age of IFC opening at ∼14 to 15 ka, lending support to the use of a Pacific coast migration route instead. Uncertainties in ages from the IFC used in these assessments, however, allow for an earlier IFC opening which would be consistent with the availability of the IFC as a migration route by ∼15.5 to 16.0 ka. Here, we use 64 cosmogenic (¹⁰Be) exposure ages to closely date the age of the full opening of the IFC at 13.8 ± 0.5 ka. Our results thus clearly establish that the IFC was not available for the first peopling of the Americas after the Last Glacial Maximum, whereas extensive geochronological data from the Pacific coast support its earlier availability as a coastal migration route.

Earliest evidence for human use of tobacco in the Pleistocene Americas

Current archaeological research on cultigens emphasizes the protracted and intimate human interactions with wild species that defined paths to domestication and, with certain plants, profoundly impacted humanity. Tobacco arguably has had more impact on global patterns in history than any other psychoactive substance, but how deep its cultural ties extend has been widely debated. Excavations at the Wishbone site, directed at the hearth-side activities of the early inhabitants of North America's desert west, have uncovered evidence for human tobacco use approximately 12,300 years ago, 9,000 years earlier than previously documented. Here we detail the preservation context of the site, discuss its cultural affiliation and suggest ways that the tobacco may have been used. The find has implications for our understanding of deep-time human use of intoxicants and its sociocultural intersection with food crop domestication.

Archaeometric studies on rock art at four sites in the northeastern Great Basin of North America

Rock art originated some 46,000 years ago and can provide unique insights into the minds of our human ancestors. However, dating of these ancient images, especially of petroglyphs, remains a challenge. In this study, we explore the potential of deriving age estimates from measurements of the areal densities of manganese (D_Mn) and iron (D_Fe) in the rock varnish on petroglyphs, based on the concept that the amount of varnish that has regrown on a petroglyph since its creation, relative to the surrounding intact varnish, is a measure of its age. We measured D_Mn and D_Fe by portable X-ray fluorescence (pXRF) on dated Late Pleistocene and Holocene rock surfaces, from which we derived accumulation rates of Mn and Fe in the rock varnish. The observed rates were comparable to our previous findings on basalt surfaces in North America. We derived age estimates for the rock art at four sites in the northern Great Basin region of North America based on D_Mn measurements on the petroglyphs and intact varnish. They suggest that rock art creation in this region began around the Pleistocene/Holocene transition and continued into the Historic Period, encompassing a wide range of styles and motifs. Evidence of reworking of the rock art at various times by Indigenous people speaks of the continued agency of these images through the millennia. Our results are in good agreement with chronologies based on archeological and other archaeometric techniques. While our method remains subject to significant uncertainty with regard to the absolute ages of individual images, it provides the unique opportunity to obtain age estimates for large ensembles of images without the need for destructive sampling.

Overview of the Americas’ First Peopling from a Patrilineal Perspective: New Evidence from the Southern Continent

Uniparental genetic systems are unique sex indicators and complement the study of autosomal diversity by providing landmarks of human migrations that repeatedly shaped the structure of extant populations. Our knowledge of the variation of the male-specific region of the Y chromosome in Native Americans is still rather scarce and scattered, but by merging sequence information from modern and ancient individuals, we here provide a comprehensive and updated phylogeny of the distinctive Native American branches of haplogroups C and Q. Our analyses confirm C-MPB373, C-P39, Q-Z780, Q-M848, and Q-Y4276 as the main founding haplogroups and identify traces of unsuccessful (pre-Q-F1096) or extinct (C-L1373*, Q-YP4010*) Y-chromosome lineages, indicating that haplogroup diversity of the founder populations that first entered the Americas was greater than that observed in the Indigenous component of modern populations. In addition, through a diachronic and phylogeographic dissection of newly identified Q-M848 branches, we provide the first Y-chromosome insights into the early peopling of the South American hinterland (Q-BY104773 and Q-BY15730) and on overlying inland migrations (Q-BY139813).

Ten millennia of hepatitis B virus evolution

[Figure: see text].

Evidence of humans in North America during the Last Glacial Maximum

[Figure: see text].

Agricultural intensification and climate change are rapidly decreasing insect biodiversity

Major declines in insect biomass and diversity, reviewed here, have become obvious and well documented since the end of World War II. Here, we conclude that the spread and intensification of agriculture during the past half century is directly related to these losses. In addition, many areas, including tropical mountains, are suffering serious losses because of climate change as well. Crops currently occupy about 11% of the world's land surface, with active grazing taking place over an additional 30%. The industrialization of agriculture during the second half of the 20th century involved farming on greatly expanded scales, monoculturing, the application of increasing amounts of pesticides and fertilizers, and the elimination of interspersed hedgerows and other wildlife habitat fragments, all practices that are destructive to insect and other biodiversity in and near the fields. Some of the insects that we are destroying, including pollinators and predators of crop pests, are directly beneficial to the crops. In the tropics generally, natural vegetation is being destroyed rapidly and often replaced with export crops such as oil palm and soybeans. To mitigate the effects of the Sixth Mass Extinction event that we have caused and are experiencing now, the following will be necessary: a stable (and almost certainly lower) human population, sustainable levels of consumption, and social justice that empowers the less wealthy people and nations of the world, where the vast majority of us live, will be necessary.

The genomics of rapid climatic adaptation and parallel evolution in North American house mice

Parallel changes in genotype and phenotype in response to similar selection pressures in different populations provide compelling evidence of adaptation. House mice (Mus musculus domesticus) have recently colonized North America and are found in a wide range of environments. Here we measure phenotypic and genotypic differentiation among house mice from five populations sampled across 21° of latitude in western North America, and we compare our results to a parallel latitudinal cline in eastern North America. First, we show that mice are genetically differentiated between transects, indicating that they have independently colonized similar environments in eastern and western North America. Next, we find genetically-based differences in body weight and nest building behavior between mice from the ends of the western transect which mirror differences seen in the eastern transect, demonstrating parallel phenotypic change. We then conduct genome-wide scans for selection and a genome-wide association study to identify targets of selection and candidate genes for body weight. We find some genomic signatures that are unique to each transect, indicating population-specific responses to selection. However, there is significant overlap between genes under selection in eastern and western house mouse transects, providing evidence of parallel genetic evolution in response to similar selection pressures across North America.

Archaeogenomic distinctiveness of the Isthmo-Colombian area

The recently enriched genomic history of Indigenous groups in the Americas is still meager concerning continental Central America. Here, we report ten pre-Hispanic (plus two early colonial) genomes and 84 genome-wide profiles from seven groups presently living in Panama. Our analyses reveal that pre-Hispanic demographic events contributed to the extensive genetic structure currently seen in the area, which is also characterized by a distinctive Isthmo-Colombian Indigenous component. This component drives these populations on a specific variability axis and derives from the local admixture of different ancestries of northern North American origin(s). Two of these ancestries were differentially associated to Pleistocene Indigenous groups that also moved into South America, leaving heterogenous genetic footprints. An additional Pleistocene ancestry was brought by a still unsampled population of the Isthmus (UPopI) that remained restricted to the Isthmian area, expanded locally during the early Holocene, and left genomic traces up to the present day.

24.0 kyr cal BP stone artefact from Vale da Pedra Furada, Piauí, Brazil: Techno-functional analysis

Current archaeological paradigm proposes that the first peopling of the Americas does not exceed the Last Glacial Maximum period. In this context, the acceptance of the anthropogenic character of the earliest stone artefacts generally rests on the presence of projectile points considered no more as typocentric but as typognomonic, since it allows, by itself, to certify the human character of the other associated artefacts. In other words, without this presence, nothing is certain. Archaeological research at Piauí (Brazil) attests to a Pleistocene human presence between 41 and 14 cal kyr BP, without any record of lithic projectile points. Here, we report the discovery and interpretation of an unusual stone artefact in the Vale da Pedra Furada site, in a context dating back to 24 cal kyr BP. The knapping stigmata and macroscopic use-wear traces reveal a conception centred on the configuration of double bevels and the production in the same specimen of at least two successive artefacts with probably different functions. This piece unambiguously presents an anthropic character and reveals a technical novelty during the Pleistocene occupation of South America.

Understanding the Adaptive Evolutionary Histories of South American Ancient and Present-Day Populations via Genomics

The South American continent is remarkably diverse in its ecological zones, spanning the Amazon rainforest, the high-altitude Andes, and Tierra del Fuego. Yet the original human populations of the continent successfully inhabited all these zones, well before the buffering effects of modern technology. Therefore, it is likely that the various cultures were successful, in part, due to positive natural selection that allowed them to successfully establish populations for thousands of years. Detecting positive selection in these populations is still in its infancy, as the ongoing effects of European contact have decimated many of these populations and introduced gene flow from outside of the continent. In this review, we explore hypotheses of possible human biological adaptation, methods to identify positive selection, the utilization of ancient DNA, and the integration of modern genomes through the identification of genomic tracts that reflect the ancestry of the first populations of the Americas.

An early dog from southeast Alaska supports a coastal route for the first dog migration into the Americas

The oldest confirmed remains of domestic dogs in North America are from mid-continent archaeological sites dated approximately 9900 calibrated years before present (cal BP). Although this date suggests that dogs may not have arrived alongside the first Native Americans, the timing and routes for the entrance of New World dogs remain uncertain. Here, we present a complete mitochondrial genome of a dog from southeast Alaska, dated to 10 150 ± 260 cal BP. We compared this high-coverage genome with data from modern dog breeds, historical Arctic dogs and American precontact dogs (PCDs) from before European arrival. Our analyses demonstrate that the ancient dog belongs to the PCD lineage, which diverged from Siberian dogs around 16 700 years ago. This timing roughly coincides with the minimum suggested date for the opening of the North Pacific coastal (NPC) route along the Cordilleran Ice Sheet and genetic evidence for the initial peopling of the Americas. This ancient southeast Alaskan dog occupies an early branching position within the PCD clade, indicating it represents a close relative of the earliest PCDs that were brought alongside people migrating from eastern Beringia southward along the NPC to the rest of the Americas. The stable isotope δ¹³C value of this early dog indicates a marine diet, different from the younger mid-continent PCDs' terrestrial diet. Although PCDs were largely replaced by modern European dog breeds, our results indicate that their population decline started approximately 2000 years BP, coinciding with the expansion of Inuit peoples, who are associated with traditional sled-dog culture. Our findings suggest that dogs formed part of the initial human habitation of the New World, and provide insights into their replacement by both Arctic and European lineages.

Disentangling Domestication from Food Production Systems in the Neotropics

The Neolithic Revolution narrative associates early-mid Holocene domestications with the development of agriculture that fueled the rise of late Holocene civilizations. This narrative continues to be influential, even though it has been deconstructed by archaeologists and geneticists in its homeland. To further disentangle domestication from reliance on food production systems, such as agriculture, we revisit definitions of domestication and food production systems, review the late Pleistocene–early Holocene archaeobotanical record, and quantify the use, management and domestication of Neotropical plants to provide insights about the past. Neotropical plant domestication relies on common human behaviors (selection, accumulation and caring) within agroecological systems that focus on individual plants, rather than populations—as is typical of agriculture. The early archaeobotanical record includes numerous perennial and annual species, many of which later became domesticated. Some of this evidence identifies dispersal with probable cultivation, suggesting incipient domestication by 10,000 years ago. Since the Pleistocene, more than 6500, 1206 and 6261 native plant species have been used in Mesoamerica, the Central Andes and lowland South America, respectively. At least 1555, 428 and 742 are managed outside and inside food production systems, and at least 1148, 428 and 600 are cultivated, respectively, suggesting at least incipient domestication. Full native domesticates are more numerous in Mesoamerica (251) than the Andes (124) and the lowlands (45). This synthesis reveals that domestication is more common in the Neotropics than previously recognized and started much earlier than reliance on food production systems. Hundreds of ethnic groups had, and some still have, alternative strategies that do involve domestication, although they do not rely principally on food production systems, such as agriculture.

Acoustic Mapping of Submerged Stone Age Sites—A HALD Approach

Acoustic response from lithics knapped by humans has been demonstrated to facilitate effective detection of submerged Stone Age sites exposed on the seafloor or embedded within its sediments. This phenomenon has recently enabled the non-invasive detection of several hitherto unknown submerged Stone Age sites, as well as the registration of acoustic responses from already known localities. Investigation of the acoustic-response characteristics of knapped lithics, which appear not to be replicated in naturally cracked lithic pieces (geofacts), is presently on-going through laboratory experiments and finite element (FE) modelling of high-resolution 3D-scanned pieces. Experimental work is also being undertaken, employing chirp sub-bottom systems (reflection seismic) on known sites in marine areas and inland water bodies. Fieldwork has already yielded positive results in this initial stage of development of an optimised Human-Altered Lithic Detection (HALD) method for mapping submerged Stone Age sites. This paper reviews the maritime archaeological perspectives of this promising approach, which potentially facilitates new and improved practice, summarizes existing data, and reports on the present state of development. Its focus is not reflection seismics as such, but a useful resonance phenomenon induced by the use of high-resolution reflection seismic systems.

Potato Virus A Isolates from Three Continents: Their Biological Properties, Phylogenetics, and Prehistory

Forty-seven potato virus A (PVA) isolates from Europe, Australia, and South America's Andean region were subjected to high-throughput sequencing, and 46 complete genomes from Europe (n = 9), Australia (n = 2), and the Andes (n = 35) obtained. These and 17 other genomes gave alignments of 63 open reading frames 9,180 nucleotides long; 9 were recombinants. The nonrecombinants formed three tightly clustered, almost equidistant phylogroups; A comprised 14 Peruvian potato isolates; W comprised 37 from potato in Peru, Argentina, and elsewhere in the world; and T contained three from tamarillo in New Zealand. When five isolates were inoculated to a potato cultivar differential, three strain groups (= pathotypes) unrelated to phylogenetic groupings were recognized. No temporal signal was detected among the dated nonrecombinant sequences, but PVA and potato virus Y (PVY) are from related lineages and ecologically similar; therefore, "relative dating" was obtained using a single maximum-likelihood phylogeny of PVA and PVY sequences and PVY's well-supported 157 CE "time to most common recent ancestor". The PVA datings obtained were supported by several independent historical coincidences. The PVA and PVY populations apparently arose in the Andes approximately 18 centuries ago, and were taken to Europe during the Columbian Exchange, radiating there after the mid-19th century potato late blight pandemic. PVA's phylogroup A population diverged more recently in the Andean region, probably after new cultivars were bred locally using newly introduced Solanum tuberosum subsp. tuberosum as a parent. Such cultivars became widely grown, and apparently generated the A × W phylogroup recombinants. Phylogroup A, and its interphylogroup recombinants, might pose a biosecurity risk.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Identification of New Helicobacter pylori Subpopulations in Native Americans and Mestizos From Peru

Region-specific Helicobacter pylori subpopulations have been identified. It is proposed that the hspAmerind subpopulation is being displaced from the Americans by an hpEurope population following the conquest. Our study aimed to describe the genomes and methylomes of H. pylori isolates from distinct Peruvian communities: 23 strains collected from three groups of Native Americans (Asháninkas [ASHA, n = 9], Shimaas [SHIM, n = 5] from Amazonas, and Punos from the Andean highlands [PUNO, n = 9]) and 9 modern mestizos from Lima (LIM). Closed genomes and DNA modification calls were obtained using SMRT/PacBio sequencing. We performed evolutionary analyses and evaluated genomic/epigenomic differences among strain groups. We also evaluated human genome-wide data from 74 individuals from the selected Native communities (including the 23 H. pylori strains donors) to compare host and bacterial backgrounds. There were varying degrees of hspAmerind ancestry in all strains, ranging from 7% in LIM to 99% in SHIM. We identified three H. pylori subpopulations corresponding to each of the Native groups and a novel hspEuropePeru which evolved in the modern mestizos. The divergence of the indigenous H. pylori strains recapitulated the genetic structure of Native Americans. Phylogenetic profiling showed that Orthogroups in the indigenous strains seem to have evolved differentially toward epigenomic regulation and chromosome maintenance, whereas OGs in the modern mestizo (LIM) seem to have evolved toward virulence and adherence. The prevalence of cagA⁺/vacA s1i1m1 genotype was similar across populations (p = 0.32): 89% in ASHA, 67% in PUNO, 56% in LIM and 40% in SHIM. Both cagA and vacA sequences showed that LIM strains were genetically differentiated (p < 0.001) as compared to indigenous strains. We identified 642 R-M systems with 39% of the associated genes located in the core genome. We found 692 methylation motifs, including 254 population-specific sequences not previously described. In Peru, hspAmerind is not extinct, with traces found even in a heavily admixed mestizo population. Notably, our study identified three new hspAmerind subpopulations, one per Native group; and a new subpopulation among mestizos that we named hspEuropePeru. This subpopulation seems to have more virulence-related elements than hspAmerind. Purifying selection driven by variable host immune response may have shaped the evolution of Peruvian subpopulations, potentially impacting disease outcomes.

The age of Clovis-13,050 to 12,750 cal yr B.P

Thirty-two radiocarbon ages on bone, charcoal, and carbonized plant remains from 10 Clovis sites range from 11,110 ± 40 to 10,820 ± 10 ¹⁴C years before the present (yr B.P.). These radiocarbon ages provide a maximum calibrated (cal) age range for Clovis of ~13,050 to ~12,750 cal yr B.P. This radiocarbon record suggests that Clovis first appeared at the end of the Allerød and is one of at least three contemporary archaeological complexes in the Western Hemisphere during the terminal Pleistocene. Stemmed projectile points in western North America are coeval and even older than Clovis, and the Fishtail point complex is well established in the southern cone of South America by ~12,900 cal yr B.P. Clovis disappeared ~12,750 cal yr B.P. at the beginning of the Younger Dryas, coincident with the extinction of the remaining North American megafauna (Proboscideans) and the appearance of multiple North American regional archaeological complexes.

Generations of genomes: advances in paleogenomics technology and engagement for Indigenous people of the Americas

For decades, scientists have collected genomic information from Indigenous peoples and their ancestors with the goal of elucidating human migration events, understanding ancestral origins, and identifying ancestral variants contributing to disease. However, such studies may not have offered much benefit to the Indigenous groups who contributed DNA, and many have instead perpetuated stereotypes and other harms. With recent advances in genomic technology facilitating the study of both ancient and present-day DNA, researchers and Indigenous communities have new opportunities to begin collaboratively addressing important questions about human health and history. Yet, while there are increased efforts to ethically engage Indigenous communities, more work is still needed as the discipline struggles to absolve itself of the racialized science and extractive biocolonialism that defined its past.