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ARCTIC PREHISTORY THROUGH ANCIENT DNA by Justin C Tackney

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ARCTIC PREHISTORY THROUGH ANCIENT DNA by Justin C Tackney ARCTIC PREHISTORY THROUGH ANCIENT DNA by Justin C Tackney A dissertation submitted to the faculty of The University of Utah in partial fulfillment of the requirements for the degree of Doctor of Philosophy Department of Anthroplogy The University of Utah December 2016 Copyright © Justin C Tackney 2016 All Rights Reserved The University of Utah Graduate School STATEMENT OF DISSERTATION APPROVAL The dissertation of Justin C Tackney has been approved by the following supervisory committee members: Dennis H O’Rourke , Chair 5/4/16 Date Approved Alan R Rogers , Member 5/4/16 Date Approved Lynn B Jorde , Member 5/4/16 Date Approved Anne M Jensen , Member 5/4/16 Date Approved and by Leslie Ann Knapp , Chair/Dean of the Department/College/School of Anthropology and by David B. Kieda, Dean of The Graduate School. ABSTRACT Genetic information from human remains obtained from archaeological excavations can reveal the history of modern peoples, rediscover the signature of prehistoric populations, and track human variation across time and space. The events that led to the colonization of the Americas can be explored by sequencing geographically and temporally appropriate samples. Two distinct phases of Native American migrations are investigated here – the initial Pleistocene movement of people out of Beringia and into North America, and the much later Holocene migrations eastward across the North American Arctic. In the first chapter, whole mitochondrial genomes were sequenced from two contemporaneous human burials at a rare Pleistocene residential site at Upward Sun River in central Alaska, dating to ∼11,500 cal B.P. One individual carried mitochondrial lineage C1b, whereas the other carried a root B2 haplotype. Today C1b and B2 are absent in modern populations of northern North America. These results validate the previously hypothesized expectation of higher levels of genetic diversity in the earlier, and now lost, Beringian gene pool. The second and third chapters concern the origins and migrations of the Neo-Eskimo Thule, the hypothesized ancestors of modern day Iñupiat/Inuit. A population-scale sequencing project was initiated from a cemetery at Nuvuk, a long-term Thule village at Pt. Barrow, AK. The cemetery represents the oldest and largest number of Thule remains ever found in North America. The hypervariable segment I of the mitochondrial genome was amplified and sequenced in 44 individuals, and Arctic haplogroups A2a, A2b, and D4b1a2a1a were identified. The haplogroup frequencies at Nuvuk were compared to populations across Siberia and North America, and were most similar to the modern Inuit communities of Canada and Greenland. This supports the ancient North Slope as the origin point for the Thule migrations. To further investigate phylogenetic relationships, additional human remains were sampled from Igliqtiqsiugvigruaq, a 19th century interior Alaskan site located inside the boundary of Kobuk Valley National Park. Whole mitochondrial genomes were sequenced from three Nuvuk burials and three remains from Igliqtiqsiugvigruaq, and these allowed a refinement of the haplogroup A2b and D4b1a2a1a phylogenies. iv CONTENTS ABSTRACT ....................................................................................................................... iii LIST OF TABLES ............................................................................................................ vii LIST OF FIGURES ......................................................................................................... viii Chapters 1. TWO CONTEMPORANEOUS MITOGENOMES FROM TERMINAL PLEISTOCENE BURIALS IN EASTERN BERINGIA ...............................................1 Abstract ....................................................................................................................2 Results ......................................................................................................................3 Discussion ................................................................................................................6 Conclusion ...............................................................................................................6 Materials and Methods .............................................................................................7 Acknowledgements ..................................................................................................7 References ................................................................................................................7 Supporting Information ............................................................................................8 2. MOLECULAR ANALYSIS OF AN ANCIENT THULE POPULATION AT NUVUK, POINT BARROW, ALASKA.....................................................................18 Introduction ............................................................................................................19 Materials and Methods ...........................................................................................28 Results ....................................................................................................................35 Discussion ..............................................................................................................42 Acknowledgements ................................................................................................51 Literature Cited ......................................................................................................52 3. PHYLOGENETIC RECONSTRUCTION OF BERINGIAN HAPLOGROUPS A2B AND D4B1A2A1A USING DATED NEO-ESKIMO THULE REMAINS ..............70 Introduction ............................................................................................................71 Materials and Methods ...........................................................................................75 Results ....................................................................................................................82 Discussion ..............................................................................................................88 Acknowledgements ................................................................................................94 Literature Cited ......................................................................................................95 vi LIST OF TABLES 1S.1 Library and Torrent Suite sequencing metrics .......................................................17 1S.2 Alternative bioinformatics pipeline metrics...........................................................17 1S.3 Customized oligonucleotides used in this study ....................................................17 2.1 Summary statistics of Nuvuk aDNA samples ........................................................58 2.2 Nuvuk sample HVR-I polymorphisms and dates ..................................................59 2.3 Population sharing of Nuvuk haplotypes ...............................................................60 2S.1 Oligonucleotides ....................................................................................................61 2S.2 Minimum Beringian HVR-I motifs for population selection ................................62 2S.3 Beringian haplogroup frequencies across populations ..........................................63 2S.4 Excluded population frequency data ......................................................................64 2S.5 Chronological appearance of Beringian haplogroups ............................................65 3.1 Oligonucleotides used in this study .......................................................................99 3.2 NGS library workflow .........................................................................................100 3.3 Sequencing and bioinformatics pipeline protocol ...............................................101 3.4 Sequencing and bioinformatics pipeline metrics .................................................102 LIST OF FIGURES 1.1 Geographic map of reported Native American populations with >40% C1 or B2 haplogroup frequencies, as well as locations of archaeological sites discussed ......3 1.2 MP hand-curated phylogenetic trees of (A) C1b and (B) B4 mtDNA haplotypes ..4 1.3 ML phylogenies of (A) haplogroup C1 and (B) haplogroup B2 .............................5 1S.1 Sequence coverage after the Torrent Suite pipeline across the mitochondrial genome for USR1 and USR2 on a 1-base sliding window ....................................12 1S.2 (A) Read-length histograms. (B) Position-specific substitutions from the 5′ end of reads post-Torrent Suite pipeline ...........................................................................13 1S.3 Sequence coverage after the alternative pipeline across the mitochondrial genome for USR1 and USR2 on a 1-base sliding window..................................................14 1S.4 (A) Read-length histograms. (B) Position-specific substitutions from the 5′ end of reads (Upper) and 3′ end of read (Lower) following the alternative bioinformatics pipeline ...................................................................................................................15 1S.5 Plan view of burial and locations of aDNA samples, FS311 (Individual 1) and FS80 (Individual 2) ................................................................................................16 1S.6 aDNA samples, FS311 (Individual 1, Left) and FS80 (Individual 2, Right) .........16 2.1 Beringian haplogroups at Nuvuk across
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