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.

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.

Palaeo-Eskimo genetic ancestry and the peopling of Chukotka and North America.

Much of the American Arctic was first settled 5,000 years ago, by groups of people known as Palaeo-Eskimos. They were subsequently joined and largely displaced around 1,000 years ago by ancestors of the present-day Inuit and Yup'ik1-3. The genetic relationship between Palaeo-Eskimos and Native American, Inuit, Yup'ik and Aleut populations remains uncertain4-6. Here we present genomic data for 48 ancient individuals from Chukotka, East Siberia, the Aleutian Islands, Alaska, and the Canadian Arctic. We co-analyse these data with data from present-day Alaskan Iñupiat and West Siberian populations and published genomes. Using methods based on rare-allele and haplotype sharing, as well as established techniques4,7-9, we show that Palaeo-Eskimo-related ancestry is ubiquitous among people who speak Na-Dene and Eskimo-Aleut languages. We develop a comprehensive model for the Holocene peopling events of Chukotka and North America, and show that Na-Dene-speaking peoples, people of the Aleutian Islands, and Yup'ik and Inuit across the Arctic region all share ancestry from a single Palaeo-Eskimo-related Siberian source.

Molecular analysis of an ancient Thule population at Nuvuk, Point Barrow, Alaska.

OBJECTIVES: The North American archaeological record supports a Holocene origin of Arctic Indigenous peoples. Although the Paleo-Inuit were present for millennia, archaeological and genetic studies suggest that modern peoples descend from a second, more recent tradition known as the Neo-Inuit. Origins of the Neo-Inuit and their relations to the earlier and later Indigenous peoples are an area of active study. Here, we genetically analyze the maternal lineages present at Nuvuk, once the northernmost community in Alaska and located in a region identified as a possible origin point of the Neo-Inuit Thule. The cemetery at Nuvuk contains human remains representing a nearly one thousand year uninterrupted occupation from early Thule to post-contact Iñupiat. MATERIALS AND METHODS: We selected 44 individuals from Nuvuk with calibrated dates between 981 AD and 1885 AD for molecular analysis. We amplified and sequenced the hypervariable segment I of the mitogenome. We compared the Nuvuk data with previously published sequences from 68 modern and ancient communities from across Asia and North America. Phylogeographic analyses suggest possible scenarios of Holocene Arctic and sub-Arctic population movements. RESULTS: We successfully retrieved sequence data from 39 individuals. Haplogroup frequencies in Nuvuk were typed as 66.7% A2b1, 25.6% A2a, and 7.7% D4b1a2a1a. These results suggest that the population at Nuvuk was closest to the ancient Thule and modern Inuit of Canada, and to the Siberian Naukan people. We confirm that haplogroups A2a, A2b1, D2a, and D4b1a2a1a appear at high frequency in Arctic and sub-Arctic populations of North America and Chukotka. Sister clades D2b and D4b1a2a1b are present in Asian and Eastern European populations. DISCUSSION: The ancient mitochondrial sequences from Nuvuk confirm the link between the North Slope and the Thule who later spread east, and the maternal discontinuity between the Neo-Inuit and Paleo-Inuit. We suggest haplogroups A2a, A2b, and D4b1a2a1a are linked to the ancestors of the Thule in eastern Beringia, whereas the D2 and D4b1a2a1 clades appear to have Asian Holocene origins. Further Siberian and Alaskan genomes are necessary to clarify these population migrations beyond a simple two-wave scenario of Neo-Inuit and Paleo-Inuit.

Environmental selection during the last ice age on the mother-to-infant transmission of vitamin D and fatty acids through breast milk.

Because of the ubiquitous adaptability of our material culture, some human populations have occupied extreme environments that intensified selection on existing genomic variation. By 32,000 years ago, people were living in Arctic Beringia, and during the Last Glacial Maximum (LGM; 28,000-18,000 y ago), they likely persisted in the Beringian refugium. Such high latitudes provide only very low levels of UV radiation, and can thereby lead to dangerously low levels of biosynthesized vitamin D. The physiological effects of vitamin D deficiency range from reduced dietary absorption of calcium to a compromised immune system and modified adipose tissue function. The ectodysplasin A receptor (EDAR) gene has a range of pleiotropic effects, including sweat gland density, incisor shoveling, and mammary gland ductal branching. The frequency of the human-specific EDAR V370A allele appears to be uniquely elevated in North and East Asian and New World populations due to a bout of positive selection likely to have occurred circa 20,000 y ago. The dental pleiotropic effects of this allele suggest an even higher occurrence among indigenous people in the Western Hemisphere before European colonization. We hypothesize that selection on EDAR V370A occurred in the Beringian refugium because it increases mammary ductal branching, and thereby may amplify the transfer of critical nutrients in vitamin D-deficient conditions to infants via mothers' milk. This hypothesized selective context for EDAR V370A was likely intertwined with selection on the fatty acid desaturase (FADS) gene cluster because it is known to modulate lipid profiles transmitted to milk from a vitamin D-rich diet high in omega-3 fatty acids.

Beringia and the global dispersal of modern humans.

Until recently, the settlement of the Americas seemed largely divorced from the out-of-Africa dispersal of anatomically modern humans, which began at least 50,000 years ago. Native Americans were thought to represent a small subset of the Eurasian population that migrated to the Western Hemisphere less than 15,000 years ago. Archeological discoveries since 2000 reveal, however, that Homo sapiens occupied the high-latitude region between Northeast Asia and northwest North America (that is, Beringia) before 30,000 years ago and the Last Glacial Maximum (LGM). The settlement of Beringia now appears to have been part of modern human dispersal in northern Eurasia. A 2007 model, the Beringian Standstill Hypothesis, which is based on analysis of mitochondrial DNA (mtDNA) in living people, derives Native Americans from a population that occupied Beringia during the LGM. The model suggests a parallel between ancestral Native Americans and modern human populations that retreated to refugia in other parts of the world during the arid LGM. It is supported by evidence of comparatively mild climates and rich biota in south-central Beringia at this time (30,000-15,000 years ago). These and other developments suggest that the settlement of the Americas may be integrated with the global dispersal of modern humans.

Two contemporaneous mitogenomes from terminal Pleistocene burials in eastern Beringia.

Pleistocene residential sites with multiple contemporaneous human burials are extremely rare in the Americas. We report mitochondrial genomic variation in the first multiple mitochondrial genomes from a single prehistoric population: two infant burials (USR1 and USR2) from a common interment at the Upward Sun River Site in central Alaska dating to ∼11,500 cal B.P. Using a targeted capture method and next-generation sequencing, we determined that the USR1 infant possessed variants that define mitochondrial lineage C1b, whereas the USR2 genome falls at the root of lineage B2, allowing us to refine younger coalescence age estimates for these two clades. C1b and B2 are rare to absent in modern populations of northern North America. Documentation of these lineages at this location in the Late Pleistocene provides evidence for the extent of mitochondrial diversity in early Beringian populations, which supports the expectations of the Beringian Standstill Model.

Ancient DNA perspectives on American colonization and population history.

Ancient DNA (aDNA) analyses have proven to be important tools in understanding human population dispersals, settlement patterns, interactions between prehistoric populations, and the development of regional population histories. Here, we review the published results of sixty-three human populations from throughout the Americas and compare the levels of diversity and geographic patterns of variation in the ancient samples with contemporary genetic variation in the Americas in order to investigate the evolution of the Native American gene pool over time. Our analysis of mitochondrial haplogroup frequencies and prehistoric population genetic diversity presents a complex evolutionary picture. Although the broad genetic structure of American prehistoric populations appears to have been established relatively early, we nevertheless identify examples of genetic discontinuity over time in select regions. We discuss the implications this finding may have for our interpretation of the genetic evidence for the initial colonization of the Americas and its subsequent population history.

The human genetic history of the Americas: the final frontier.

The Americas, the last continents to be entered by modern humans, were colonized during the late Pleistocene via a land bridge across what is now the Bering strait. However, the timing and nature of the initial colonization events remain contentious. The Asian origin of the earliest Americans has been amply established by numerous classical marker studies of the mid-twentieth century. More recently, mtDNA sequences, Y-chromosome and autosomal marker studies have provided a higher level of resolution in confirming the Asian origin of indigenous Americans and provided more precise time estimates for the emergence of Native Americans. But these data raise many additional questions regarding source populations, number and size of colonizing groups and the points of entry to the Americas. Rapidly accumulating molecular data from populations throughout the Americas, increased use of demographic models to test alternative colonization scenarios, and evaluation of the concordance of archaeological, paleoenvironmental and genetic data provide optimism for a fuller understanding of the initial colonization of the Americas.

South from Alaska: a pilot aDNA study of genetic history on the Alaska Peninsula and the eastern Aleutians.

The Aleutian Islands were colonized, perhaps several times, from the Alaskan mainland. Earlier work documented transitions in the relative frequencies of mtDNA haplogroups over time, but little is known about potential source populations for prehistoric Aleut migrants. As part of a pilot investigation, we sequenced the mtDNA first hypervariable region (HVRI) in samples from two archaeological sites on the Alaska Peninsula (the Hot Springs site near Port Moller, Alaska; and samples from a cluster of sites in the Brooks River area near Katmai National Park and Preserve) and one site from Prince William Sound (Mink Island). The sequences revealed not only the mtDNA haplogroups typically found in both ancient and modern Aleut populations (A2 and D2) but also haplogroups B2 and D1 in the Brooks River samples and haplogroup D3 in one Mink Islander. These preliminary results suggest greater mtDNA diversity in prehistoric populations than previously observed and facilitate reconstruction of migration scenarios from the peninsula into the Aleutian archipelago in the past.

Human migrations: the two roads taken.

America was peopled from Asia by at least the end of the last ice age, but the exact timing of entry and the composition of the source population are unclear. A new analysis of two rare mitochondrial haplogroups suggests two separate Asian migrations into the Americas, indicating simultaneous but independent Asian source populations for early American colonists.

Inferring population continuity versus replacement with aDNA: a cautionary tale from the Aleutian Islands.

In The Aleutian and Commander Islands and Their Inhabitants (Philadelphia: Wistar Institute of Anatomy and Biology, 1945), Hrdlicka proposed a population replacement event in the Aleutian Islands approximately 1,000 years ago based on a perceived temporal shift in cranial morphology. However, the archaeological record indicates cultural, and presumed population, continuity for more than 4,000 years. We use mtDNA haplogroup data in the series of prehistoric eastern Aleutian samples (n = 86) studied craniometrically by Hrdlicka to test alternative hypotheses regarding population continuity or replacement in the region. This molecular characterization, in conjunction with direct dating of individual specimens, provided increased resolution for hypothesis testing. Results indicate an apparent shift in mtDNA haplogroup frequencies in the eastern Aleutians approximately 1,000 years ago, in concert with changes in mortuary practices and isotopic signatures reflecting resource acquisition strategies. The earliest Aleut populations were characterized by a high frequency of haplogroup A, as are most modern populations of the North American arctic. Later prehistoric peoples in the Aleutians were characterized by a high frequency of haplogroup D and a correspondingly lower frequency of haplogroup A, a pattern typified by modern Aleut populations.

The late Pleistocene dispersal of modern humans in the Americas.

When did humans colonize the Americas? From where did they come and what routes did they take? These questions have gripped scientists for decades, but until recently answers have proven difficult to find. Current genetic evidence implies dispersal from a single Siberian population toward the Bering Land Bridge no earlier than about 30,000 years ago (and possibly after 22,000 years ago), then migration from Beringia to the Americas sometime after 16,500 years ago. The archaeological records of Siberia and Beringia generally support these findings, as do archaeological sites in North and South America dating to as early as 15,000 years ago. If this is the time of colonization, geological data from western Canada suggest that humans dispersed along the recently deglaciated Pacific coastline.

Inbreeding, heterozygosity, and lymphoma risk among the baboons (Papio hamadryas) of Sukhumi, USSR.

This paper describes the spread of lymphoma through a baboon (Papio hamadryas) colony in the Institute of Experimental Pathology and Therapy at Sukhumi, USSR. In the late 1960s, Soviet scientists inoculated 12 baboons with cells from hospitalized human leukemia patients, causing the death of a total of 135 animals between 1967 and 1978. The death rate from lymphoma averages almost 12 baboons per year in the Sukhumi colony. Genetic investigations of these baboons revealed the following: 1) Six blood protein markers out of 16 systems (38%) tested were polymorphic; 2) the average inbreeding coefficient for the entire colony (N = 1,226) was 0.027 (exclusion of baboons with F values equal to 0.0 raised the mean inbreeding coefficient to 0.096); 3) no relationship between inbreeding and risk of lymphoma was noted; and 4) there was an apparent association between both PGM loci and the incidence of lymphoma at the 0.005 levels of significance. This association was further supported by the significantly lower incidence of PGM2 (2-1) genotype in baboons with high anti-VCA-HVP titers.