Publications by authors named "Jennifer Raff"

15 Publications

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Race reconciled II: Interpreting and communicating biological variation and race in 2021.

Am J Phys Anthropol 2021 06 27;175(2):313-315. Epub 2021 Apr 27.

Department of Anthropology, University of Florida, Gainesville, Florida, USA.

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http://dx.doi.org/10.1002/ajpa.24291DOI Listing
June 2021

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

Nature 2019 06 5;570(7760):236-240. Epub 2019 Jun 5.

Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.

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'ik. The genetic relationship between Palaeo-Eskimos and Native American, Inuit, Yup'ik and Aleut populations remains uncertain. 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 techniques, 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.
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http://dx.doi.org/10.1038/s41586-019-1251-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6942545PMC
June 2019

Comparing signals of natural selection between three Indigenous North American populations.

Proc Natl Acad Sci U S A 2019 05 15;116(19):9312-9317. Epub 2019 Apr 15.

Department of Anthropology, University of Connecticut, Storrs, CT 06269-1176.

While many studies have highlighted human adaptations to diverse environments worldwide, genomic studies of natural selection in Indigenous populations in the Americas have been absent from this literature until very recently. Since humans first entered the Americas some 20,000 years ago, they have settled in many new environments across the continent. This diversity of environments has placed variable selective pressures on the populations living in each region, but the effects of these pressures have not been extensively studied to date. To help fill this gap, we collected genome-wide data from three Indigenous North American populations from different geographic regions of the continent (Alaska, southeastern United States, and central Mexico). We identified signals of natural selection in each population and compared signals across populations to explore the differences in selective pressures among the three regions sampled. We find evidence of adaptation to cold and high-latitude environments in Alaska, while in the southeastern United States and central Mexico, pathogenic environments seem to have created important selective pressures. This study lays the foundation for additional functional and phenotypic work on possible adaptations to varied environments during the history of population diversification in the Americas.
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http://dx.doi.org/10.1073/pnas.1819467116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6511053PMC
May 2019

Advancing the ethics of paleogenomics.

Science 2018 04 26;360(6387):384-385. Epub 2018 Apr 26.

All affiliations and members of the SING Consortium are listed in the supplementary materials.

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http://dx.doi.org/10.1126/science.aaq1131DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6150602PMC
April 2018

Genetics: Ancient DNA Clarifies Population Histories of the Northeastern Margin of North America.

Authors:
Jennifer Raff

Curr Biol 2017 10;27(20):R1116-R1118

Department of Anthropology, University of Kansas, Lawrence, KS 66045, USA. Electronic address:

A new study of ancient mitochondrial DNA from Newfoundland and Labrador indicates that this region at the northeastern margin of North America was populated three times in succession by different indigenous groups. This research helps shed light on the movement of populations across the continent, following the initial peopling of the Americas.
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http://dx.doi.org/10.1016/j.cub.2017.09.036DOI Listing
October 2017

Genome of the Ancient One (a.k.a. Kennewick Man).

Authors:
Jennifer Raff

Hum Biol 2015 Apr;87(2):132-3

1 Department of Anthropology, University of Kansas, 614 Fraser Hall, 1415 Jayhawk Blvd, Lawrence, KS 66045. E-mail: .

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http://dx.doi.org/10.13110/humanbiology.87.2.0132DOI Listing
April 2015

Two contemporaneous mitogenomes from terminal Pleistocene burials in eastern Beringia.

Proc Natl Acad Sci U S A 2015 Nov 26;112(45):13833-8. Epub 2015 Oct 26.

Department of Anthropology, University of Utah, Salt Lake City, UT 84112;

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.
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http://dx.doi.org/10.1073/pnas.1511903112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4653186PMC
November 2015

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

Am J Phys Anthropol 2015 Aug 17;157(4):603-14. Epub 2015 Apr 17.

Division of Endocrinology, Metabolism and Molecular Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611.

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.
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http://dx.doi.org/10.1002/ajpa.22750DOI Listing
August 2015

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

BMC Microbiol 2014 Dec 17;14:316. Epub 2014 Dec 17.

Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103, Leipzig, Germany.

Background: Although 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.

Results: Here 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.

Conclusion: Overall, this study illustrates the distinctiveness of the saliva microbiome of human groups living under very different climatic conditions.
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http://dx.doi.org/10.1186/s12866-014-0316-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4272767PMC
December 2014

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

Am J Phys Anthropol 2015 Mar 24;156(3):434-48. Epub 2014 Nov 24.

Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712; Department of Anthropology, University of Texas at Austin, Austin, TX, 78712.

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.
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http://dx.doi.org/10.1002/ajpa.22668DOI Listing
March 2015

Palaeogenomics: genetic roots of the first Americans.

Nature 2014 Feb;506(7487):162-3

Department of Anthropology, University of Texas at Austin, Austin, Texas 78712-1723, USA.

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http://dx.doi.org/10.1038/506162aDOI Listing
February 2014

Ancient DNA perspectives on American colonization and population history.

Am J Phys Anthropol 2011 Dec 13;146(4):503-14. Epub 2011 Sep 13.

Department of Anthropology, University of Utah, Salt Lake City, UT, USA.

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.
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http://dx.doi.org/10.1002/ajpa.21594DOI Listing
December 2011

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

Hum Biol 2010 Dec;82(5-6):677-93

Department of Anthropology, University of Utah, Salt Lake City, UT, USA.

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.
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http://dx.doi.org/10.3378/027.082.0510DOI Listing
December 2010

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

Curr Biol 2010 Feb;20(4):R202-7

Department of Anthropology, University of Utah, 270 S. 1400 E., Rm. 102, Salt Lake City, UT 84112, USA.

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.
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http://dx.doi.org/10.1016/j.cub.2009.11.051DOI Listing
February 2010

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

Mem Inst Oswaldo Cruz 2006 Dec;101 Suppl 2:25-7

Departments of Anthropology and Biology, Indiana University, Bloomington, Indiana 47405-7100, USA.

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.
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http://dx.doi.org/10.1590/s0074-02762006001000005DOI Listing
December 2006