Loren G. Davis

Genomic evidence for the Pleistocene and recent population history of Native Americans

Genetic history of Native Americans Several theories have been put forth as to the origin and timing of when Native American ancestors entered the Americas. To clarify this controversy, Raghavan et al. examined the genomic variation among ancient and modern individuals from Asia and the Americas. There is no evidence for multiple waves of entry or recurrent gene flow with Asians in northern populations. The earliest migrations occurred no earlier than 23,000 years ago from Siberian ancestors. Amerindians and Athabascans originated from a single population, splitting approximately 13,000 years ago. Science, this issue 10.1126/science.aab3884 Genetic variation within ancient and extant Native American populations informs on their migration into the Americas. INTRODUCTION The consensus view on the peopling of the Americas is that ancestors of modern Native Americans entered the Americas from Siberia via the Bering Land Bridge and that this occurred at least ~14.6 thousand years ago (ka). However, the number and timing of migrations into the Americas remain controversial, with conflicting interpretations based on anatomical and genetic evidence. RATIONALE In this study, we address four major unresolved issues regarding the Pleistocene and recent population history of Native Americans: (i) the timing of their divergence from their ancestral group, (ii) the number of migrations into the Americas, (iii) whether there was ~15,000 years of isolation of ancestral Native Americans in Beringia (Beringian Incubation Model), and (iv) whether there was post-Pleistocene survival of relict populations in the Americas related to Australo-Melanesians, as suggested by apparent differences in cranial morphologies between some early (“Paleoamerican”) remains and those of more recent Native Americans. We generated 31 high-coverage modern genomes from the Americas, Siberia, and Oceania; 23 ancient genomic sequences from the Americas dating between ~0.2 and 6 ka; and SNP chip genotype data from 79 present-day individuals belonging to 28 populations from the Americas and Siberia. The above data sets were analyzed together with published modern and ancient genomic data from worldwide populations, after masking some present-day Native Americans for recent European admixture. RESULTS Using three different methods, we determined the divergence time for all Native Americans (Athabascans and Amerindians) from their Siberian ancestors to be ~20 ka, and no earlier than ~23 ka. Furthermore, we dated the divergence between Athabascans (northern Native American branch, together with northern North American Amerindians) and southern North Americans and South and Central Americans (southern Native American branch) to be ~13 ka. Similar divergence times from East Asian populations and a divergence time between the two branches that is close in age to the earliest well-established archaeological sites in the Americas suggest that the split between the branches occurred within the Americas. We additionally found that several sequenced Holocene individuals from the Americas are related to present-day populations from the same geographical regions, implying genetic continuity of ancient and modern populations in some parts of the Americas over at least the past 8500 years. Moreover, our results suggest that there has been gene flow between some Native Americans from both North and South America and groups related to East Asians and Australo-Melanesians, the latter possibly through an East Asian route that might have included ancestors of modern Aleutian Islanders. Last, using both genomic and morphometric analyses, we found that historical Native American groups such as the Pericúes and Fuego-Patagonians were not “relicts” of Paleoamericans, and hence, our results do not support an early migration of populations directly related to Australo-Melanesians into the Americas. CONCLUSION Our results provide an upper bound of ~23 ka on the initial divergence of ancestral Native Americans from their East Asian ancestors, followed by a short isolation period of no more than ~8000 years, and subsequent entrance and spread across the Americas. The data presented are consistent with a single-migration model for all Native Americans, with later gene flow from sources related to East Asians and, indirectly, Australo-Melanesians. The single wave diversified ~13 ka, likely within the Americas, giving rise to the northern and southern branches of present-day Native Americans. Population history of present-day Native Americans. The ancestors of all Native Americans entered the Americas as a single migration wave from Siberia (purple) no earlier than ~23 ka, separate from the Inuit (green), and diversified into “northern” and “southern” Native American branches ~13 ka. There is evidence of post-divergence gene flow between some Native Americans and groups related to East Asians/Inuit and Australo-Melanesians (yellow). How and when the Americas were populated remains contentious. Using ancient and modern genome-wide data, we found that the ancestors of all present-day Native Americans, including Athabascans and Amerindians, entered the Americas as a single migration wave from Siberia no earlier than 23 thousand years ago (ka) and after no more than an 8000-year isolation period in Beringia. After their arrival to the Americas, ancestral Native Americans diversified into two basal genetic branches around 13 ka, one that is now dispersed across North and South America and the other restricted to North America. Subsequent gene flow resulted in some Native Americans sharing ancestry with present-day East Asians (including Siberians) and, more distantly, Australo-Melanesians. Putative “Paleoamerican” relict populations, including the historical Mexican Pericúes and South American Fuego-Patagonians, are not directly related to modern Australo-Melanesians as suggested by the Paleoamerican Model.

Clovis Age Western Stemmed Projectile Points and Human Coprolites at the Paisley Caves

They Walked Together Paisley Cave in Oregon provides some of the earliest evidence for humans in North America. Jenkins et al. (p. 223) provide a wide variety of additional evidence of early human occupation of this site, including a series of radiocarbon ages extending back to nearly 12,500 radiocarbon years ago (about 14,500 calendar years ago). The find includes examples of projectile points representative of the Western Stemmed Tradition dating to about 11,100 radiocarbon years ago. The Western Stemmed Tradition has been thought to have evolved after the dominant Clovis technology, but the find suggests that the two cultures overlapped in time. The age of a Western Stemmed projectile point implies that this culture overlapped with the Clovis culture in North America. The Paisley Caves in Oregon record the oldest directly dated human remains (DNA) in the Western Hemisphere. More than 100 high-precision radiocarbon dates show that deposits containing artifacts and coprolites ranging in age from 12,450 to 2295 14C years ago are well stratified. Western Stemmed projectile points were recovered in deposits dated to 11,070 to 11,340 14C years ago, a time contemporaneous with or preceding the Clovis technology. There is no evidence of diagnostic Clovis technology at the site. These two distinct technologies were parallel developments, not the product of a unilinear technological evolution. “Blind testing” analysis of coprolites by an independent laboratory confirms the presence of human DNA in specimens of pre-Clovis age. The colonization of the Americas involved multiple technologically divergent, and possibly genetically divergent, founding groups.

A Late Pleistocene Occupation on the Southern Coast of Oregon

Abstract Geoarchaeological research on the southern coast of Oregon brought to light archaeological evidence of early human occupation in the late Pleistocene. Indian Sands (35CU67) lies on a highly eroded deflated headland on the Oregon coast where previous surveys had found and dated surficial cultural materials as early as 8250 b.p. (uncalibrated radiocarbon years). Prior to excavation of Indian Sands, sediment and stratigraphic analysis, along with radiocarbon and thermoluminescence dates, established the existence of late Pleistocene deposits. The excavations confirmed the presence of buried cultural deposits containing lithic artifacts, charcoal, and fire-cracked rock. Dispersed charcoal from the floor of an artifactbearing level was dated to 10,430 b.p., more than 2000 l4C years older than any other Oregon coastal site.

Context, Provenance and Technology of a Western Stemmed Tradition Artifact Cache from the Cooper's Ferry Site, Idaho

Abstract The discovery of an artifact cache containing Western Stemmed Tradition (WST) projectile points in a clearly defined pit feature at the Cooper’s Ferry site offers a unique perspective on early lithic technology and logistical organization in western North America. A description and analysis of the cache feature reveals several new insights, including: a rocky cairn capped the surface of the pit feature; some of the artifacts were made from cryptocrystalline silicates found 16 km away; debitage analysis, including aggregate and attribute based measures, identified two distinct lithic reduction stages present in the cache; new radiocarbon assays suggest that the cache is probably not early Holocene in age and may date to associated age estimates of 11,410–11,370 radiocarbon years before present (B.P.). Unlike Clovis caches, the Pit Feature A2 cache at Cooper’s Ferry appears to be a generalized toolkit that was probably placed at the site for future use. If the 11,410–11,370 radiocarbon years B.P. assays date the creation of the Pit Feature A2 cache, then its creators were probably not pioneers in the lower Salmon River canyon but possessed local knowledge about the landscape and raw material sources; these patterns suggest greater time depth for WST foragers.

Differential response of vegetation to postglacial climate in the Lower Salmon River Canyon, Idaho

Late Pleistocene to Holocene terrestrial climate and vegetation records in the Lower Salmon River Canyon of Idaho are interpreted from the stable isotopic composition of soil carbonates and from aeolian sedimentation frequencies. Carbonate and sediment samples from six sections were processed and analyzed, with the resulting isotopic and grainsize data organized in relation to a normalized time series developed from an associated radiocarbon chronology. This record is interpreted in regards to changes in aridity, temperature and wind speed during the Late Quaternary and is further compared with regional paleoenvironmental records. Lowered N 18 O and N 13 C concentrations before 20 000 yr BP are interpreted as reflecting Late Wisconsinan cold conditions. After 18 000 yr BP, climatic conditions show warmer periods punctuated by sharp returns to colder temperatures and increased C3 flora by 12 000 yr BP. Higher resolution data show very unstable climatic conditions across the Pleistocene^Holocene boundary, reflected in wide variations in N 18 O and N 13 C and aeolian sand deposition. During the period between 12 000 and 9000 yr BP, the Lower Salmon River Canyon is thought to have experienced marked seasonality with summers and winters, respectively, warmer and colder than today. This climatic scenario was accompanied by an initial instability in canyon vegetation. Following the establishment of a low-energy floodplain in the canyon after 10 000 yr BP, a pattern of C3-dominant riparian flora appears. During the middle Holocene, climatic and vegetative variability is much reduced from the preceding period. After 4000 yr BP, soil carbonate isotopes reflect a trend toward cooler climate conditions and more mesic vegetation populations. ; 2002 Elsevier Science B.V. All rights reserved.

Trekking the Shore

The sea is central to the lives of contemporary coastal Aboriginal and Torres Strait Islander people across northeast Australia. Indigenous histories and documentary sources show the sea to be a vital source of subsistence, raw materials, spirituality and connection with other peoples. Coasts, and especially islands, were a focus of occupation, with high population densities linked to low mobility along the length of the Queensland coast. But what are the antecedents of these people–sea relationships? In this review, the archaeological evidence for coastal foraging across northeast Australia from the late Pleistocene is explored and the main themes and challenges in developing an understanding of how coastal resources figured in the lives of ancient Australians are discussed.

The North American Paleocoastal Concept Reconsidered

The Pleistocene archaeological record of North America’s Pacific coast is understood from only a handful of sites that postdate the continent’s earliest interior sites by at least 500 radiocarbon years. Like other coastal regions of the world, the reasons that early North American Pacific coastal sites are so few in number relate to late Quaternary environmental history: postglacial marine transgression submerged older coastal terrains and sites, leaving behind only a small portion of a previously larger coastal and pericoastal landscape and any sites it might contain (cf. Davis et al. 2009). Although many early continental sites were also surely destroyed or concealed by periglacial and postglacial geomorphic processes, few regions, such as those parts of the Pacific Northwest’s Columbia River drainage that were affected by the catastrophic outburst floods of Glacial Lake Missoula and Pluvial Lake Bonneville, share the same extremes of postdepositional history as the world’s coastal zones. In spite of these difficulties of site preservation, a small number of late Pleistocene-aged North American Pacific coastal sites are known from British Columbia to Baja California Sur.

RADIOCARBON, SOIL, AND ARTIFACT CHRONOLOGIES FOR AN EARLY SOUTHERN OREGON COASTAL SITE

Radiocarbon dates together with geoarchaeological, soil, and lithic analyses are presented to describe archaeological site 35-CS-9 in Bandon Ocean Wayside State Park, Oregon, northwestern USA. One of the few Oregon middle- Holocene coastal sites that includes sediments and artifacts dating to the early Holocene and possibly to the late Pleistocene, it was recorded in 1951 and surface surveyed by archaeologists in 1975, 1986, and 1991, but its depth and antiquity were not tested. In February 2002, we studied the sites stratigraphy and sediments and described 8 strata from the aeolian surface to bedrock at 350 cm depth. Soil samples taken from a cut bank for texture classification, particle size analysis, pH, carbon content, and chemical analysis suggested that the site represented a complete history of Holocene deposits. Excavation of 2 test units in August 2002 uncovered substantial lithic and charcoal remains that confirm a protracted middle-Holocene occupation and suggest that human occupation began in the early Holocene. Charcoal recovered at 235245 cm dated to 11,000 14C BP, and the deepest lithic artifact was recovered in a level at 215225 cm. Whether the human occupation was continuous throughout the Holocene, and whether it began in the early Holocene or in the late Pleistocene, can only be determined with further excavations.

GLIMR: A GIS-BASED METHOD FOR THE GEOMETRIC MORPHOMETRIC ANALYSIS OF ARTIFACTS

Abstract Archaeologys participation in the digital renaissance of the twenty-first century requires adequate operationalization of technological methods, such as three-dimensional scanning. Here, we describe and demonstrate a geographic information systems-based lithic morphometric research (GLiMR) software approach. GLiMR accurately and rapidly handles a sequence of ArcGIS procedures to extract geometric morphometric data from 2D and 3D scan files that are impractical to record by hand, opening new doors to the analysis of lithic artifacts. GLiMR generates three main types of geometric properties: shape data, topographic data, and domain aggregate data. These data can be extracted in ways that support other analyses of artifact form, including generalized Procrustes analysis, principal components analysis, and cluster analyses. We illustrate the use of GLiMR by presenting a basic case study that compares the geometric morphometry of Western Stemmed Tradition projectile points found in two cache features at Idahos Coopers Ferry site and from other sites in the Columbia River Plateau region of the Pacific Northwest. Cluster analyses of the generalized Procrustes analysis of 3D landmarks from Coopers Ferry cache points fail to separate the two caches from one another on the basis of their geometric morphometric attributes. We interpret these results to suggest that these stemmed projectile points were probably created by persons who shared a specific set of technological production guidelines for the manufacture of Western Stemmed Tradition projectile points. Cluster analyses indicate that Coopers Ferry Western Stemmed Tradition projectile points can be morphometrically separated from stemmed points found at other regional sites; however, significant overlaps were seen among stemmed projectile points from the Pilcher Creek site, which may suggest the existence of contemporaneous information sharing networks or macroband territorial movements.

PALEOSEISMICITY, ECOLOGICAL CHANGE, AND PREHISTORIC EXPLOITATION OF ANADROMOUS FISHES IN THE SALMON RIVER BASIN, WESTERN IDAHO, USA

By the middle Holocene, Native American groups developed semi-sedentary villages in the Columbia River basin of the Pacific Northwest. The economic basis for these villages is thought to have been predicated on the acquisition of bulk food resources, such as salmon and camas, for delayed consumption during the winter. In Idahos lower Salmon River canyon, semi-sedentary pit house villages are absent until after 2000 14C yr BP. Floodplain geochronology shows channel incision and terrace formation occurred at ca. 2000 14C yr BP, caused by fluvial response to neotectonic displacement along a normal fault. The delayed appearance of pit house sites and other markers of the Winter Village Pattern in the canyon is argued to be directly related to neotectonically-induced changes in fluvial conditions after 2000 14C yr BP, which significantly improved aquatic habitats for anadromous fishes and led to the development of a predictable, productive salmon fishery.