DOCSLIB.ORG

Inferring the Characteristics of Ancient Populations Using Bioinformatic Analysis of Genome-Wide DNA Sequencing Data

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Inferring the Characteristics of Ancient Populations Using Bioinformatic Analysis of Genome-Wide DNA Sequencing Data Inferring the Characteristics of Ancient Populations using Bioinformatic Analysis of Genome-wide DNA Sequencing Data Graham Gower Australian Centre for Ancient DNA School of Biological Sciences Faculty of Sciences University of Adelaide Thesis submitted in fulfilment of the requirements for the degree of Doctor of Philosophy February 2019 Contents 1 Introduction1 1.1 Evolution and population dynamics................ 2 1.2 Inference based on modern data.................. 3 1.2.1 Detecting gene flow..................... 3 1.2.2 Coalescent theory and population size inference..... 4 1.3 Direct observation using ancient DNA .............. 6 1.3.1 What is ancient DNA?................... 6 1.3.2 Challenges for ancient DNA studies............ 7 1.3.3 Ancient DNA analyses................... 8 1.4 Thesis overview........................... 9 1.4.1 Motivation & Aims..................... 9 1.4.2 Early cave art and ancient DNA record the origin of European bison....................... 10 1.4.3 Population size history from short scaffolds: how short is too short?......................... 10 1.4.4 Widespread male sex bias in mammal fossil and museum collections.......................... 11 1.4.5 PP5mC: preprocessing hairpin-ligated bisulfite-treated DNA sequences....................... 12 1.5 References.............................. 12 2 Early cave art and ancient DNA record the origin of European bison 25 2.1 Authorship statement........................ 25 2.2 Manuscript ............................. 34 2.3 Supplementary Information .................... 42 2.4 Supplementary Data 1: sample details . 112 3 Population size history from short scaffolds: how short is too short? 125 3.1 Authorship statement........................125 3.2 Manuscript .............................128 4 Widespread male sex bias in mammal fossil and museum collections 143 4.1 Authorship statement........................143 4.2 Manuscript .............................146 4.3 Supplementary Information ....................167 5 PP5mC: preprocessing hairpin-ligated bisulfite-treated DNA sequences 175 5.1 Authorship statement........................175 5.2 Manuscript .............................177 5.3 Supplementary Figures.......................192 6 Discussion 197 6.1 Research summary .........................198 6.2 Primary outcomes..........................198 6.2.1 European bison ancestry..................198 6.2.2 PSMC and MSMC with short scaffolds . 199 6.2.3 A male bias is ubiquitous in mammal collections . 199 6.2.4 More efficient processing of HBS-seq data . 200 6.3 Synthesis...............................201 6.4 Limitations and future directions . 202 6.4.1 Models for the origin of European bison . 202 6.4.2 SMC-based population size inference . 202 6.4.3 Drivers of male-biased sex ratios . 204 6.4.4 Prospects for paleo-epigenetics . 205 6.4.5 PP5mC computational performance . 205 6.5 Concluding remarks.........................206 6.6 References..............................206 Abstract In this thesis, I apply, evaluate, and develop methods for learning about past populations from genome-wide sequencing data. Specifically, I: apply methods based on random genetic drift between populations, to • determine that pre-Holocene gene flow occurred between the ancestors of domestic cattle (Bos primigenius) and European bison (Bison priscus), and that the contribution of Bos genealogy to the bison lineage was less than 10 %; use simulations to assess the impact of short genomic scaffolds when • inferring past populations sizes with the pairwise sequentially Markov coalescent, and show that population size inferences can be robust for scaffold lengths as short as 100 kb; perform genetic sex determination of ancient DNA specimens to show • that bison (Bison spp.) and brown bear (Ursus arctos) specimens are approximately 75 % male, and that male-biased observations likely stem from the ecological and social structures of the populations; and develop a suite of software tools for processing hairpin bisulfite • sequencing data, which can be used to investigate genome-wide DNA methylation levels in ancient DNA. Acknowledgements This thesis would not have been possible without the ongoing support of my su- pervisors Alan Cooper, Bastien Llamas, Julien Soubrier, and Kieren Mitchell. You provided me with an opportunity, and the freedom, to learn a great deal about a broad range of interesting biological phenomena. Thank you for your time, energy, criticism, and many motivating ideas. I also wish to thank all the members of ACAD, for enjoyable journal club discussions, social events, and sporadic tomfoolery. And speaking of tomfoolery, it’s been a pleasure to col- laborate with our friends in the School of Mathematical Sciences—Nigel, Jono, and Ben, you’ve inspired me to spend my leisure time reading maths books. Finally, to my partner Saskia; thank you for being there for me no matter what, and thank you for listening to my long winded and overly-detailed ex- planations with far too many digressions before sometimes finally getting to the point. Chapter 1 Introduction 1 2 CHAPTER 1. INTRODUCTION 1.1 Evolution and population dynamics Evolutionary biologists wish to learn about organisms living now, and those that lived in the past. Motivations are diverse and include understanding evolutionary processes, conservation of species, or characterising the etiology of diseases. How are living things related to each other? How did their form and function come to be? What causes them to go extinct? What processes that are occurring now, have also occurred in the past? Can the past and the present tell us about the future? Such ideas have a long history in biology, starting with Darwin, who was immensely influenced by the uniformitarianism of Lyell(1835). By comparing living species with those that are extinct, we can derive hypotheses about the circumstances for extinction, and why similar species did not suffer the same fate. Using what we learn of the past we can try to predict, and hopefully pacify, current and future extinction risk. Population parameters such as spatial distribution, age-specific mortality, sex ratios, migration rates between populations, and population size can all be informative regarding behavioural and ecological characteristics. Changes to these population parameters over time can further pinpoint responses to the environment, with regard to large-scale disruptions from geological and climatic events. Demographic parameters of past populations have often been discussed by comparing the morphology of extant species, in the context of morphological assessments of fossils (Robson & Wood, 2008). This is made possible by a wealth of reference material for hominid remains, for example, to morphologically determine a specimen’s sex (Frayer & Wolpoff, 1985; Rehg & Leigh, 1999), and age at death (Dean & Liversidge, 2015; Dean, 2016). Increasingly, genetic data are being used in addition to, or in place of, mor- phological data. This is particularly important where remains are fragmentary or rare, such as for Denisovans, a hominin group originally described from a finger bone and a tooth (Reich et al., 2010). But genetics also offers to answer questions that were previously difficult or impossible to answer, such as de- termining average generation times (Moorjani et al., 2016), inferring ancestral population sizes (Li & Durbin, 2011), quantifying past gene flow (Patterson et al., 2012), or clarifying that distinct morphological forms are different sexes of a single species (Bunce et al., 2003; Huynen et al., 2003; Bover et al., 2018). Like for morphological data, two complementary approaches exist for investig- ating past populations with genetic data: use the data from modern individuals to infer things about their ancestors; or observe the populations directly from the DNA of subfossil remains. 1.2. INFERENCE BASED ON MODERN DATA 3 1.2 Inference based on modern data 1.2.1 Detecting gene flow The ancestors of modern populations leave extensive signatures in the genomes of their descendents. Phylogenetic relationships can be used to infer population split times (Bouckaert et al., 2014; Molak et al., 2013) and evolutionary rates of change (Bouckaert et al., 2014; Rabosky, 2014). But relationships between in- dividuals within a population are rarely tree-like, and similarly, speciation may not be characterised by clean separation into reciprocally monophyletic groups (Mallet, 2005). To detect gene flow in past populations, a four-population test statistic (F4) has been developed (Reich et al., 2009; Patterson et al., 2012), which is sensitive to even small quantities of gene flow. The principal idea of the test is that in a phylogeny, the components of random genetic drift along two distinct branches are uncorrelated, whereas if gene flow existed between the two branches then genetic drift will be correlated. A B C D Figure 1.1: A four taxon phylogenetic tree with branches representing random genetic drift. The expected difference in allele frequencies between and ( and ) is due to drift occurring along the path shown in blue (red).A B C D Consider the four populations ; ; and in Figure 1.1, and suppose we wish to test for gene flow betweenA B C and D (or and ) that occurred after and split. If a, b, c, and d areA the respectiveC B alleleC frequencies in A B populations ; ; ; and , then Patterson’s F4 = cov(a b; c d). When the four populationsA B C haveD a strictly tree-like relationship,− then− the A B drift is uncorrelated with the drift, so F4 = 0. In contrast, if gene flow has occurred between
Load more

Recommended publications
  • Past Climate Changes, Population Dynamics and the Origin of Bison in Europe Diyendo Massilani1†, Silvia Guimaraes1†, Jean-Philip Brugal2,3, E
    Massilani et al. BMC Biology (2016) 14:93 DOI 10.1186/s12915-016-0317-7 RESEARCHARTICLE Open Access Past climate changes, population dynamics and the origin of Bison in Europe Diyendo Massilani1†, Silvia Guimaraes1†, Jean-Philip Brugal2,3, E. Andrew Bennett1, Malgorzata Tokarska4, Rose-Marie Arbogast5, Gennady Baryshnikov6, Gennady Boeskorov7, Jean-Christophe Castel8, Sergey Davydov9, Stéphane Madelaine10, Olivier Putelat11,12, Natalia N. Spasskaya13, Hans-Peter Uerpmann14, Thierry Grange1*† and Eva-Maria Geigl1*† Abstract Background: Climatic and environmental fluctuations as well as anthropogenic pressure have led to the extinction of much of Europe’s megafauna. The European bison or wisent (Bison bonasus), one of the last wild European large mammals, narrowly escaped extinction at the onset of the 20th century owing to hunting and habitat fragmentation. Little is known, however, about its origin, evolutionary history and population dynamics during the Pleistocene. Results: Through ancient DNA analysis we show that the emblematic European bison has experienced several waves of population expansion, contraction, and extinction during the last 50,000 years in Europe, culminating in a major reduction of genetic diversity during the Holocene. Fifty-seven complete and partial ancient mitogenomes from throughout Europe, the Caucasus, and Siberia reveal that three populations of wisent (Bison bonasus)and steppe bison (B. priscus) alternately occupied Western Europe, correlating with climate-induced environmental changes. The Late Pleistocene European steppe bison originated from northern Eurasia, whereas the modern wisent population emerged from a refuge in the southern Caucasus after the last glacial maximum. A population overlap during a transition period is reflected in ca. 36,000-year-old paintings in the French Chauvet cave.
    [Show full text]
  • Comments on Mezmaiskaya"
    Eurasian Prehistory, 5 (1) : 131- 136. GETTING BACK TO BASICS: A RESPONSE TO OTTE "COMMENTS ON MEZMAISKAYA" Lubov Golovanova, Vladimir Doronichev and Naomi Cleghorn Marcel Otte recently argued (In "Comments Jar to the Ahmarian tradition, and particularly the on Mezmaiskaya, North Caucasus", Eurasian lithic assemblages from Abu Noshra and the La­ Prehistory, this issue) that the Early Upper Paleo­ gaman, dating between 30 and 35 ky BP (Gilead, lithic (EUP) at Mezmaiskaya Cave can be defined 1991 ). This preliminary conclusion is based on as Aurignacian (versus Golovanova et al., 2006). the prevalence of micro-laminar (bladelet) debi­ This raises an old methodological problem con­ tage, a high percentage of tools made on bladelets cerning the correct use of scientific terms and the (compared with 45 .7 percent at Lagama), and a definition of the Aurignacian. Lithic definitions rather low representation (about 20 percent) of such as Aurignacian and Gravettian, which were endscrapers and burins. It is important to note that ori ginally based on specific materials, have been only the later Ahmarian assemblages provided a rather more loosely applied to assemblages dis­ basis for this comparison. Moreover, despite tant in time and space. We believe that the wider many similarities, the EUP industry from Layer application of these original terms not only sim­ 1C at Mezmaiskaya is not identical to the Ahmar­ plifies them by a subjective reduction of their pri­ ian. mary determining attributes, but also confuses our Ongoing excavations of EUP levels in Mez­ understanding of cultural processes within and maiskaya Cave now permit a more accurate com­ between various regions.
    [Show full text]
  • Comments on Mezmaiskaya"
    EllrasianPrehistory, 5 (I): 13/-136. GETTING BACK TO BASICS: A RESPONSETO OTTE "COMMENTS ON MEZMAISKAYA" Lubov Golovanova, Vladimir Doronichev and Naomi Cleghorn MarcelOtte recently argued (In "Comments lar to the Ahrnarian tradition, and particularly the f onMezmaiskaya,North Caucasus", Eurasian lithic assemblages from Abu Noshra and the La- Prehistory, thisissue)that the Early Upper Paleo- gaman, dating between 30 and 35 ky BP (Gilead, Iilhic(EDP)atMezmaiskayaCave can be defined 1991). This preliminary conclusion is based on asAurignacian(versus Golovanova et al., 2006). the prevalence of micro-laminar (bladelet) debi- Ihisraisesan old methodological problem con- tage, a high percentage of tools made on bladelets cerningthecorrectuse of scientific terms and the (compared with 45.7 percent at Lagama), and a definitionof the Aurignacian. Lithic definitions rather low representation (about 20 percent) of suchasAurignacianand Gravettian which were endscrapers and burins. It is important to note that originallybasedon specific materials, have been only the later Ahmarian assemblages provided a rathermoreloosely applied to assemblages dis- basis for this comparison. Moreover, despite tantintimeand space. We believe that the wider many similarities, the EUP industry from Layer ap.plicationof these original terms not only sim- l C at Mezmaiskaya is not identical to the Ahmar- plifiesthemby a subjective reduction of their pri- tan. mary determiningattributes, but also confuses our Ongoing excavations of EUP levels in Mez- understandingof cultural processes within and maiskaya Cave now permit a more accurate com- betweenvariousregions. parison with the Ahmarian. Typical el-Wad To get hack to the basic definition of the points with fine lateral retouch, which are very ~urignacian,it is necessary to return to Sonne- characteristic of the Ahmarian assemblages from Ville-Bordes'(1950) classic publication on this Lagama (Bar-Yosefand Belfer 1977: fig.
    [Show full text]
  • Paleoecology and Land-Use of Quaternary Megafauna from Saltville, Virginia Emily Simpson East Tennessee State University
    East Tennessee State University Digital Commons @ East Tennessee State University Electronic Theses and Dissertations Student Works 5-2019 Paleoecology and Land-Use of Quaternary Megafauna from Saltville, Virginia Emily Simpson East Tennessee State University Follow this and additional works at: https://dc.etsu.edu/etd Part of the Paleontology Commons Recommended Citation Simpson, Emily, "Paleoecology and Land-Use of Quaternary Megafauna from Saltville, Virginia" (2019). Electronic Theses and Dissertations. Paper 3590. https://dc.etsu.edu/etd/3590 This Thesis - Open Access is brought to you for free and open access by the Student Works at Digital Commons @ East Tennessee State University. It has been accepted for inclusion in Electronic Theses and Dissertations by an authorized administrator of Digital Commons @ East Tennessee State University. For more information, please contact [email protected]. Paleoecology and Land-Use of Quaternary Megafauna from Saltville, Virginia ________________________________ A thesis presented to the faculty of the Department of Geosciences East Tennessee State University In partial fulfillment of the requirements for the degree Master of Science in Geosciences with a concentration in Paleontology _______________________________ by Emily Michelle Bruff Simpson May 2019 ________________________________ Dr. Chris Widga, Chair Dr. Blaine W. Schubert Dr. Andrew Joyner Key Words: Paleoecology, land-use, grassy balds, stable isotope ecology, Whitetop Mountain ABSTRACT Paleoecology and Land-Use of Quaternary Megafauna from Saltville, Virginia by Emily Michelle Bruff Simpson Land-use, feeding habits, and response to seasonality by Quaternary megaherbivores in Saltville, Virginia, is poorly understood. Stable isotope analyses of serially sampled Bootherium and Equus enamel from Saltville were used to explore seasonally calibrated (δ18O) patterns in megaherbivore diet (δ13C) and land-use (87Sr/86Sr).
    [Show full text]
  • The Appendicular Remains of the Kiik-Koba 2 Neandertal Infant
    The Appendicular Remains of the Kiik-Koba 2 Neandertal Infant ERIK TRINKAUS Department of Anthropology, Washington University, St. Louis, MO 63130, USA; [email protected] MARIA B. MEDNIKOVA Institute of Archaeology, Russian Academy of Sciences, Dm. Ulianova str. 19, Moscow 117036, RUSSIA; [email protected] LIBBY W. COWGILL Department of Anthropology, University of Missouri, Columbia, MO 65201, USA; [email protected] submitted: 9 August 2016; revised 21 November 2016; accepted 7 December 2016 ABSTRACT The appendicular skeleton (scapula, humerus, ulnae, radii, metacarpals, pollical phalanges, hip bone, femora, tibiae and fibula) of the Neandertal infant from Kiik-Koba (Crimea), Kiik-Koba 2, are reassessed in the context of Late Pleistocene archaic and modern human infant remains. Based on long bone lengths, it should have been 4–6 months old at death, of indeterminate sex. The infant resembles (most) older Neandertals in its scapular dorsal sulcus axillary border, medially oriented radial tuberosity, radial curvature, large pollical opponens flange, and low crural index. It lacks the mediolateral pubic elongation seen in some older Neandertals, its brachial index is average for a Late Pleistocene or recent human, and its femoral neck-shaft angle is low for its developmental age. The percent cortical areas of its humerus and especially femur are average for its age, but its tibial one is unusually low. Yet, when scaled to intermetaphyseal lengths, the midshaft rigidities of all three long bones are unexceptional for a Late Pleistocene or non-mechanized recent human infant. The Kiik-Koba 2 infant limb bones thus provide additional data and inferences concerning the mosaic of Neandertal early postnatal development of postcranial features and appendicular hypertrophy, when assessed in the broader context of both Late Pleistocene and recent human infant remains.
    [Show full text]
  • Occurrence of the Musk Ox, Symbos Cavifrons, from Southeastern Idaho and Comments on the Genus Bootherium
    Great Basin Naturalist Volume 47 Number 2 Article 9 4-30-1987 Occurrence of the musk ox, Symbos cavifrons, from southeastern Idaho and comments on the genus Bootherium Michael E. Nelson Fort Hays State University, Hays, Kansas James H. Madsen Jr. Antiquities Section, Utah Division of State History, Salt Lake City Follow this and additional works at: https://scholarsarchive.byu.edu/gbn Recommended Citation Nelson, Michael E. and Madsen, James H. Jr. (1987) "Occurrence of the musk ox, Symbos cavifrons, from southeastern Idaho and comments on the genus Bootherium," Great Basin Naturalist: Vol. 47 : No. 2 , Article 9. Available at: https://scholarsarchive.byu.edu/gbn/vol47/iss2/9 This Article is brought to you for free and open access by the Western North American Naturalist Publications at BYU ScholarsArchive. It has been accepted for inclusion in Great Basin Naturalist by an authorized editor of BYU ScholarsArchive. For more information, please contact [email protected], [email protected]. OCCURRENCE OF THE MUSK OX, SYMBOS CAVIFRONS, FROM SOUTHEASTERN IDAHO AND COMMENTS ON THE GENUS BOOTHERIUM Michael E. Nelson' and James H. Madsen, Jr." Abstract.—A set of ovibovine horn cores collected from Pleistocene sediments in southeastern Idaho provides additional evidence for sexual dimorphism in the helmeted musk ox, Symhos cavifrons. Specimens previously assigned to Boothchum sargenti are placed in synonomy with Symbos cavifrons as sexual dimorphs (females). Bootherium bomhifrons is a \alid taxon and is probably not closely related to Symbos. The taxonomic status of the e.xtinct musk figures and descriptions, pronounced that ox, Bootherium, has been questioned since Bootherium cavifrons (= Symbos cavifrons) Leidy (1852a, 1852b) proposed the name for was a male and B.
    [Show full text]
  • Ahead of the Game: Middle and Upper Palaeolithic Hunting Behaviors in the Southern Caucasus
    Ahead of the Game: Middle and Upper Palaeolithic Hunting Behaviors in the Southern Caucasus The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Adler, Daniel S., Guy Bar#Oz, Anna Belfer#Cohen, and Ofer Bar# Yosef. 2006. Ahead of the Game: Middle and Upper Palaeolithic Hunting Behaviors in the Southern Caucasus. Current Anthropology 47, no. 1: 89–118. Published Version doi:10.1086/432455 Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:12242824 Terms of Use This article was downloaded from Harvard University’s DASH repository, and is made available under the terms and conditions applicable to Other Posted Material, as set forth at http:// nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#LAA Current Anthropology Volume 47, Number 1, February 2006 89 Ahead of the Game Middle and Upper Palaeolithic Hunting Behaviors in the Southern Caucasus by Daniel S. Adler, Guy Bar-Oz, Anna Belfer-Cohen, and Ofer Bar-Yosef Over the past several decades a variety of models have been proposed to explain perceived behavioral and cognitive differences between Neanderthals and modern humans. A key element in many of these models and one often used as a proxy for behavioral “modernity” is the frequency and nature of hunting among Palaeolithic populations. Here new archaeological data from Ortvale Klde, a late Middle–early Upper Palaeolithic rockshelter in the Georgian Republic, are considered, and zooar- chaeological methods are applied to the study of faunal acquisition patterns to test whether they changed significantly from the Middle to the Upper Palaeolithic.
    [Show full text]
  • An Anthropological Assessment of Neanderthal Behavioural Energetics
    DEPARTMENT OF ARCHAEOLOGY, CLASSICS & EGYPTOLOGY An Anthropological Assessment of Neanderthal Behavioural Energetics. Thesis submitted in accordance with the requirements of the University of Liverpool for the Degree of Doctor in Philosophy by Andrew Shuttleworth. April, 2013. TABLE OF CONTENTS……………………………………………………………………..i LIST OF TABLES……………………………………………………………………………v LIST OF FIGURES…………………………………………………………………………..vi ACKNOWLEDGMENTS…………………………………………………………………...vii ABSTRACT…………………………………………………………………………………viii TABLE OF CONTENTS 1. INTRODUCTION...........................................................................................................1 1.1. Introduction..............................................................................................................1 1.2. Aims and Objectives................................................................................................2 1.3. Thesis Format...........................................................................................................3 2. THE NEANDERTHAL AND OXYEGN ISOTOPE STAGE-3.................................6 2.1. Discovery, Geographic Range & Origins..............................................................7 2.1.1. Discovery........................................................................................................7 2.1.2. Neanderthal Chronology................................................................................10 2.2. Morphology.............................................................................................................11
    [Show full text]
  • Haplogroup Relationships Between Domestic and Wild Sheep Resolved Using a Mitogenome Panel
    Heredity (2011) 106, 700–706 & 2011 Macmillan Publishers Limited All rights reserved 0018-067X/11 www.nature.com/hdy ORIGINAL ARTICLE Haplogroup relationships between domestic and wild sheep resolved using a mitogenome panel JRS Meadows1,3, S Hiendleder2 and JW Kijas1 1CSIRO Livestock Industries, St Lucia, Queensland, Australia and 2School of Agriculture, Food and Wine & Research Centre for Reproductive Health, School of Animal and Veterinary Science, University of Adelaide, Roseworthy, South Australia, Australia Five haplogroups have been identified in domestic sheep 920 000±190 000 years ago based on protein coding through global surveys of mitochondrial (mt) sequence sequence. The utility of various mtDNA components to inform variation, however these group classifications are often the true relationship between sheep was also examined with based on small fragments of the complete mtDNA sequence; Bayesian, maximum likelihood and partitioned Bremmer sup- partial control region or the cytochrome B gene. This study port analyses. The control region was found to be the mtDNA presents the complete mitogenome from representatives of component, which contributed the highest amount of support to each haplogroup identified in domestic sheep, plus a sample the tree generated using the complete data set. This study of their wild relatives. Comparison of the sequence success- provides the nucleus of a mtDNA mitogenome panel, which can fully resolved the relationships between each haplogroup be used to assess additional mitogenomes and serve as a and provided insight into the relationship with wild sheep. reference set to evaluate small fragments of the mtDNA. The five haplogroups were characterised as branching Heredity (2011) 106, 700–706; doi:10.1038/hdy.2010.122; independently, a radiation that shared a common ancestor published online 13 October 2010 Keywords: Ovis aries; domestication; mitochondria; genome; diversity Introduction Pedrosa et al., 2005; Pereira et al., 2006; Tapio et al., 2006; Meadows et al., 2007).
    [Show full text]
  • Early Cave Art and Ancient DNA Record the Origin of European Bison
    ARTICLE Received 22 Apr 2016 | Accepted 9 Sep 2016 | Published 18 Oct 2016 DOI: 10.1038/ncomms13158 OPEN Early cave art and ancient DNA record the origin of European bison Julien Soubrier1,*, Graham Gower1,*, Kefei Chen1, Stephen M. Richards1,BastienLlamas1,KierenJ.Mitchell1,SimonY.W.Ho2, Pavel Kosintsev3, Michael S.Y. Lee4,5, Gennady Baryshnikov6, Ruth Bollongino7, Pere Bover1,8, Joachim Burger7, David Chivall9,EvelyneCre´gut-Bonnoure10,11,Jared E. Decker12, Vladimir B. Doronichev13,KaterinaDouka9,DamienA.Fordham14, Federica Fontana15,CaroleFritz16, Jan Glimmerveen17, Liubov V. Golovanova13, Colin Groves18, Antonio Guerreschi15, Wolfgang Haak1,19,TomHigham9, Emilia Hofman-Kamin´ska20, Alexander Immel19, Marie-Anne Julien21,22, Johannes Krause19, Oleksandra Krotova23, Frauke Langbein24,GregerLarson25, Adam Rohrlach26, Amelie Scheu7, Robert D. Schnabel12,JeremyF.Taylor12, Małgorzata Tokarska20, Gilles Tosello27, Johannes van der Plicht28, Ayla van Loenen1, Jean-Denis Vigne29, Oliver Wooley1, Ludovic Orlando30,31, Rafał Kowalczyk20, Beth Shapiro32,33 & Alan Cooper1 The two living species of bison (European and American) are among the few terrestrial megafauna to have survived the late Pleistocene extinctions. Despite the extensive bovid fossil record in Eurasia, the evolu- tionary history of the European bison (or wisent, Bison bonasus) before the Holocene (o11.7 thousand years ago (kya)) remains a mystery. We use complete ancient mitochondrial genomes and genome-wide nuclear DNA surveys to reveal that the wisent is the product of hybridization between the extinct steppe bison (Bison priscus) and ancestors of modern cattle (aurochs, Bos primigenius) before 120 kya, and contains up to 10% aurochs genomic ancestry. Although undetected within the fossil record, ancestors of the wisent have alternated ecological dominance with steppe bison in association with major environmental shifts since at least 55 kya.
    [Show full text]
  • Life and Extinction of Megafauna in the Ice-Age Arctic
    Life and extinction of megafauna in the ice-age Arctic Daniel H. Manna,1, Pamela Grovesb, Richard E. Reanierc, Benjamin V. Gagliotid, Michael L. Kunze, and Beth Shapirof,1 aGeosciences Department, University of Alaska, Fairbanks, AK 99775; bInstitute of Arctic Biology, University of Alaska, Fairbanks, AK 99775; cReanier & Associates, Inc., Seattle, WA 98166; dWater and Environmental Research Center, University of Alaska, Fairbanks, AK 99775; eCooperative Extension and Resources, University of Alaska, Fairbanks, AK 99775; and fDepartment of Ecology and Evolutionary Biology and University of California, Santa Cruz Genomics Institute, University of California, Santa Cruz, CA 95064 Edited by Richard G. Klein, Stanford University, Stanford, CA, and approved September 23, 2015 (received for review June 29, 2015) Understanding the population dynamics of megafauna that in- The study area is Alaska’s North Slope, the tundra region habited the mammoth steppe provides insights into the causes of bordered to the south by the Brooks Range and to the north by extinctions during both the terminal Pleistocene and today. Our the Arctic Ocean (Fig. 1). The North Slope is a particularly in- study area is Alaska’s North Slope, a place where humans were teresting place to study end-Pleistocene extinctions for several rare when these extinctions occurred. After developing a statisti- reasons. First, its ice-age megafauna included iconic species like cal approach to remove the age artifacts caused by radiocarbon woolly mammoth (Mammuthus primigenius), steppe bison (Bison priscus), and cave lion (Panthera spelaea) (14). Second, the local calibration from a large series of dated megafaunal bones, we ’ compare the temporal patterns of bone abundance with climate extinctions of megafauna on Alaska s North Slope occurred at a records.
    [Show full text]
  • Evidence of Pre-Clovis Sites in the Eastern United States Albert C
    University of South Carolina Scholar Commons Archaeology and Anthropology, South Carolina Faculty & Staff ubP lications Institute of 2005 Evidence of Pre-Clovis Sites in the Eastern United States Albert C. Goodyear University of South Carolina - Columbia, [email protected] Follow this and additional works at: https://scholarcommons.sc.edu/sciaa_staffpub Part of the Anthropology Commons Publication Info Published in Paleoamerican Origins: Beyond Clovis, 2005, pages 103-112. http://csfa.tamu.edu/ © 2005 by Center for the Study of the First Americans This Book Chapter is brought to you by the Archaeology and Anthropology, South Carolina Institute of at Scholar Commons. It has been accepted for inclusion in Faculty & Staff ubP lications by an authorized administrator of Scholar Commons. For more information, please contact [email protected]. Paleoamerican Origins: Beyond Clovis A Peopling of the Americas Publication Evidence for Pre-Clovis Sites in the Eastern United States Albert C. Goodyear is believed that they sufficiently meet these criteria and thus con- stitute evidence. Truth is the daughter of time. –John Trapp, 17th-century Puritan writer Meadowcroft Rockshelter, Pennsylvania Abstract The most long-standing case for archaeological evidence of pre- Over the past 25 years, a number of archaeological sites in east- Clovis (earlier than 11,500 RCYBP) humans in the eastern United ern North America have manifested evidence of human occupa- States is the famous Meadowcroft Rockshelter, located about 48 tions dating earlier than 11,500 RCYBP. These sites include km southwest of Pittsburgh, Pennsylvania (Figure 1). Meadowcroft Meadowcroft Rockshelter, Penn.; Cactus Hill, Va.; Saltville-2, Va.; Rockshelter is within the Cross Creek drainage, a tributary of the and Topper, S.C.
    [Show full text]