Jennifer Raff

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.

Two contemporaneous mitogenomes from terminal Pleistocene burials in eastern Beringia.

Significance Beringia gave rise to the first Western Hemisphere colonists, although the genetic characterization of that source population has remained obscure. We report two mitogenomes from human remains within Beringia, with an age (∼11,500 cal B.P.) that postdates the end of the initial colonization by only a few millennia. The mitochondrial lineages identified (B2, C1b) are rare to absent in modern northern populations, indicating greater genetic diversity in early Beringia than in modern populations of the region. The antiquity and geographic location of these two burials, and the combined genomic and archaeological analyses, provide new perspectives on the link between Asia and the Americas, and the genetic makeup of the first Americans. 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.

Comparative analysis of the human saliva microbiome from different climate zones: Alaska, Germany, and Africa

BackgroundAlthough the importance of the human oral microbiome for health and disease is increasingly recognized, variation in the composition of the oral microbiome across different climates and geographic regions is largely unexplored.ResultsHere we analyze the saliva microbiome from native Alaskans (76 individuals from 4 populations), Germans (10 individuals from 1 population), and Africans (66 individuals from 3 populations) based on next-generation sequencing of partial 16S rRNA gene sequences. After quality filtering, a total of 67,916 analyzed sequences resulted in 5,592 OTUs (defined at ≥97% identity) and 123 genera. The three human groups differed significantly by the degree of diversity between and within individuals (e.g. beta diversity: Africans > Alaskans > Germans; alpha diversity: Germans > Alaskans > Africans). UniFrac, network, ANOSIM, and correlation analyses all indicated more similarities in the saliva microbiome of native Alaskans and Germans than between either group and Africans. The native Alaskans and Germans also had the highest number of shared bacterial interactions. At the level of shared OTUs, only limited support for a core microbiome shared across all three continental regions was provided, although partial correlation analysis did highlight interactions involving several pairs of genera as conserved across all human groups. Subsampling strategies for compensating for the unequal number of individuals per group or unequal sequence reads confirmed the above observations.ConclusionOverall, this study illustrates the distinctiveness of the saliva microbiome of human groups living under very different climatic conditions.

Palaeogenomics: Genetic roots of the first Americans

The whole-genome sequence of a human associated with the earliest widespread culture in North America confirms the Asian ancestry of the Clovis people and their relatedness to present-day Native Americans. See Letter p.225 The Clovis complex is an archaeological culture distributed widely in North America. Dating to around 13,000 years ago it is characterized by distinct stone tools including a spear blade known as the Clovis point. Just who made these tools has been a subject of much speculation based on sparse information. There is now more to go on with the publication of the first genome sequence of an ancient North American individual. The genome is that of a male infant (Anzick-1) from the Clovis burial at the Anzick site in Montana. The partial skeleton, buried about 12,600 years ago, was found in association with scores of ochre-painted stone tools. Its genome is from a population from which contemporary Native Americans are descended and is more closely related to all indigenous American populations than to any others. These findings refute the hypothesis that the Clovis people migrated from Europe, are consistent with a human occupation of the Americas a few thousand years before Clovis, and suggest that contemporary Native Americans are descendants of the first people to settle successfully in the Americas.

Does Mitochondrial Haplogroup X Indicate Ancient Trans-Atlantic Migration to the Americas? A Critical Re-Evaluation

It might seem strange for an article to focus largely on the history of a single mitochondrial haplogroup in an era when complete genome sequencing is becoming more common. But as recent publications and film documentaries have shown (Meldrum 2009; Oppenheimer et al. 2014; Smoot et al. 2010; Stanford and Bradley 2012), there is still considerable confusion about what the structure of mitochondrial genetic diversity in the Americas means for Native American population history. Specifically, there are persistent claims that the presence of mitochondrial haplogroup X2a in Native American populations is evidence for ancient trans-Atlantic gene flow from Europe or the Middle East into North America (Meldrum 2009; Oppenheimer et al. 2014; Smoot et al. 2010; Stanford and Bradley 2012). If true, this genetic evidence would lend considerable support to the Solutrean hypothesis, which suggests that the North American Clovis culture (13,300–12,800 cal yr BP) is directly descended from the Solutrean culture of southwestern Europe (23,500–18,000 cal yr BP). The current iteration of the Solutrean hypothesis was developed by Bruce Bradley and Dennis Stanford (Bradley and Stanford 2004; Stanford and Bradley 2012; see Abbott 1877,Greenman 1963 andHibben 1941 for previous iterations of the hypothesis), and it has been heavily critiqued by many archaeologists (Eren et al. 2013, 2015; O’Brien et al. 2014; Philips 2014; Sellet 1998; Straus et al. 2005). The idea that haplogroup X2a is derived from an ancient trans-Atlantic migration to the Americas has been repeatedly considered — and rejected — by anthropological geneticists over the last two decades (Brown et al. 1998; Fagundes et al. 2008; Reidla et al. 2003; Smith et al. 1999, 2005). However, we revisit it here because it continues to be discussed and because recently published genomic data from ancient and contemporary North Americans help clarify the population history of North America and the likely history of this haplogroup.

South from Alaska: A Pilot aDNA Study of Genetic History on the Alaska Peninsula and the Eastern Aleutians

Abstract 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.

Tuberculosis in the New World: a study of ribs from the Schild Mississippian population, West-Central Illinois

Vertebral lesions have been the main evidence for infection by the Mycobacterium tuberculosis complex (MTC) in paleopathology. Skeletal involvement is expected in a small percentage of infected individuals. Recently, several authors report a correlation between rib lesions and tuberculosis (TB) complex infection. This study tests the hypothesis that rib lesions can serve as a useful marker for MTC infection within the Mississippian Schild skeletal collection from West-Central Illinois. Ribs from 221 adults and juveniles were examined, and affected individuals were tested for TB complex infection. DNA from rib samples of affected individuals was amplified with primers targeting the IS6110 insertion element, which is common to all members of the TB complex. Although it cannot allow discrimination between different species of TB, IS6110 is present in many copies within their genomes, and its presence is thus an indication of MTC infection. The results support the use of rib lesions as a marker for TB infection. Additionally, we demonstrate that MTC DNA can be recovered from ribs that lack lesions in individuals who have lesions of other bones. We recommend that an examination of ribs be incorporated into investigations for TB.

Mitochondrial diversity of Iñupiat people from the Alaskan North Slope provides evidence for the origins of the Paleo‐ and Neo‐Eskimo peoples

OBJECTIVES All modern Iñupiaq speakers share a common origin, the result of a recent (∼800 YBP) and rapid trans-Arctic migration by the Neo-Eskimo Thule, who replaced the previous Paleo-Eskimo inhabitants of the region. Reduced mitochondrial haplogroup diversity in the eastern Arctic supports the archaeological hypothesis that the migration occurred in an eastward direction. We tested the hypothesis that the Alaskan North Slope served as the origin of the Neo- and Paleo-Eskimo populations further east. MATERIALS AND METHODS We sequenced HVR I and HVR II of the mitochondrial D-loop from 151 individuals in eight Alaska North Slope communities, and compared genetic diversity and phylogenetic relationships between the North Slope Inupiat and other Arctic populations from Siberia, the Aleutian Islands, Canada, and Greenland. RESULTS Mitochondrial lineages from the North Slope villages had a low frequency (2%) of non-Arctic maternal admixture, and all haplogroups (A2, A2a, A2b, D2a, and D4b1a-formerly known as D3) found in previously sequenced Neo- and Paleo-Eskimos and living Inuit and Eskimo peoples from across the North American Arctic. Lineages basal for each haplogroup were present in the North Slope. We also found the first occurrence of two haplogroups in contemporary North American Arctic populations: D2a, previously identified only in Aleuts and Paleo-Eskimos, and the pan-American C4. DISCUSSION Our results yield insight into the maternal population history of the Alaskan North Slope and support the hypothesis that this region served as an ancestral pool for eastward movements to Canada and Greenland, for both the Paleo-Eskimo and Neo-Eskimo populations.

Ancient DNA from the Schild site in Illinois: Implications for the Mississippian transition in the Lower Illinois River Valley

Archaeologists have long debated whether rapid cultural change in the archaeological record is due to in situ developments, migration of a new group into the region, or the spread of new cultural practices into an area through existing social networks, with the local peoples adopting and adapting practices from elsewhere as they see fit (acculturation). Researchers have suggested each of these explanations for the major cultural transition that occurred at the beginning of the Mississippian period (AD 1050) across eastern North America. In this study, we used ancient DNA to test competing hypotheses of migration and acculturation for the culture change that occurred between the Late Woodland (AD 400-1050) and Mississippian (AD 1050-1500) periods in the Lower Illinois River Valley. We obtained sequences of the first hypervariable segment of the mitochondrial genome (mtDNA) from 39 individuals (17 Late Woodland, 22 Mississippian) interred in the Schild cemetery in western Illinois, and compared these lineages to ancient mtDNA lineages present at other sites in the region. Computer simulations were used to test a null hypothesis of population continuity from Late Woodland to Mississippian times at the Schild site and to investigate the possibility of gene flow from elsewhere in the region. Our results suggest that the Late Woodland to Mississippian cultural transition at Schild was not due to an influx of people from elsewhere. Instead, it is more likely that the transition to Mississippian cultural practices at this site was due to a process of acculturation.

Ancient DNA from the schild site in Illinois

Archaeologists have long debated whether rapid cultural change in the archaeological record is due to in situ developments, migration of a new group into the region, or the spread of new cultural practices into an area through existing social networks, with the local peoples adopting and adapting practices from elsewhere as they see fit (acculturation). Researchers have suggested each of these explanations for the major cultural transition that occurred at the beginning of the Mississippian period (AD 1050) across eastern North America. In this study, we used ancient DNA to test competing hypotheses of migration and acculturation for the culture change that occurred between the Late Woodland (AD 400-1050) and Mississippian (AD 1050-1500) periods in the Lower Illinois River Valley. We obtained sequences of the first hypervariable segment of the mitochondrial genome (mtDNA) from 39 individuals (17 Late Woodland, 22 Mississippian) interred in the Schild cemetery in western Illinois, and compared these lineages to ancient mtDNA lineages present at other sites in the region. Computer simulations were used to test a null hypothesis of population continuity from Late Woodland to Mississippian times at the Schild site and to investigate the possibility of gene flow from elsewhere in the region. Our results suggest that the Late Woodland to Mississippian cultural transition at Schild was not due to an influx of people from elsewhere. Instead, it is more likely that the transition to Mississippian cultural practices at this site was due to a process of acculturation.