Africa from MIS 6–2: Population Dynamics and Paleoenvironments Sacha C
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Supplementary Information
doi: 10.1038/nature08795 SUPPLEMENTARY INFORMATION Supplementary Discussion Population naming In some contexts, the indigenous hunter-gatherer and pastoralist peoples of southern Africa are referred to collectively as the Khoisan (Khoi-San) or more recently Khoesan (Khoe-San) people. This grouping is based on the unique linguistic use of click-consonants1. Many names, often country-specific, have been used by Bantu pastoralists and European settlers to describe the hunter-gatherers, including San, Saan, Sonqua, Soaqua, Souqua, Sanqua, Kwankhala, Basarwa, Batwa, Abathwa, Baroa, Bushmen, Bossiesmans, Bosjemans, or Bosquimanos. In addition, group-specific names such as !Kung and Khwe are often used for the broader population. The two most commonly used names, “San” and “Bushmen”, have both been associated with much controversy due to derogatory connotations2. “San” has become the more popular term used in Western literature, although “Bushmen” is arguably the more commonly recognized term within the communities. Since they have no collective name for themselves, the term Bushmen was selected for use in this paper as the term most familiar to the participants themselves. Regarding identification of individuals The five men identified in this study have all elected to have their identity made public knowledge. Thus we present two complete personal genomes (KB1 and ABT), a low-coverage personal genome (NB1), and personal exomes for all five men. On a scientific level, identification allows for current and future correlation of genetic data with demographic and medical histories. On a social level, identification allows for maximizing community benefit. For !Gubi, G/aq’o, D#kgao and !Aî, their name represents not only themselves, but importantly their extended family unit and a way of life severely under threat. -
Bayesian Coalescent Inference of Major Human Mitochondrial DNA Haplogroup Expansions in Africa Quentin D
Downloaded from http://rspb.royalsocietypublishing.org/ on July 28, 2017 Proc. R. Soc. B (2009) 276, 367–373 doi:10.1098/rspb.2008.0785 Published online 30 September 2008 Bayesian coalescent inference of major human mitochondrial DNA haplogroup expansions in Africa Quentin D. Atkinson1,*, Russell D. Gray2 and Alexei J. Drummond3 1Institute of Cognitive and Evolutionary Anthropology, University of Oxford, 64 Banbury Road, Oxford OX2 6PN, UK 2Department of Psychology, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand 3Bioinformatics Institute and Department of Computer Science, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand Past population size can be estimated from modern genetic diversity using coalescent theory. Estimates of ancestral human population dynamics in sub-Saharan Africa can tell us about the timing and nature of our first steps towards colonizing the globe. Here, we combine Bayesian coalescent inference with a dataset of 224 complete human mitochondrial DNA (mtDNA) sequences to estimate effective population size through time for each of the four major African mtDNA haplogroups (L0–L3). We find evidence of three distinct demographic histories underlying the four haplogroups. Haplogroups L0 and L1 both show slow, steady exponential growth from 156 to 213 kyr ago. By contrast, haplogroups L2 and L3 show evidence of substantial growth beginning 12–20 and 61–86 kyr ago, respectively. These later expansions may be associated with contemporaneous environmental and/or cultural changes. The timing of the L3 expansion—8–12 kyr prior to the emergence of the first non-African mtDNA lineages—together with high L3 diversity in eastern Africa, strongly supports the proposal that the human exodus from Africa and subsequent colonization of the globe was prefaced by a major expansion within Africa, perhaps driven by some form of cultural innovation. -
Models and Methods of Tectonic Geomorphology and the Reconstruction of Hominin Landscapes
This is a repository copy of Landscapes of human evolution : models and methods of tectonic geomorphology and the reconstruction of hominin landscapes. White Rose Research Online URL for this paper: http://eprints.whiterose.ac.uk/11178/ Version: Accepted Version Article: Bailey, G.N. orcid.org/0000-0003-2656-830X, Reynolds, Sally and King, G.C.P. (2011) Landscapes of human evolution : models and methods of tectonic geomorphology and the reconstruction of hominin landscapes. Journal of Human Evolution. pp. 257-80. ISSN 0047-2484 https://doi.org/10.1016/j.jhevol.2010.01.004 Reuse Items deposited in White Rose Research Online are protected by copyright, with all rights reserved unless indicated otherwise. They may be downloaded and/or printed for private study, or other acts as permitted by national copyright laws. The publisher or other rights holders may allow further reproduction and re-use of the full text version. This is indicated by the licence information on the White Rose Research Online record for the item. Takedown If you consider content in White Rose Research Online to be in breach of UK law, please notify us by emailing [email protected] including the URL of the record and the reason for the withdrawal request. [email protected] https://eprints.whiterose.ac.uk/ This is an author-created pdf. Cite as: In press, J Hum Evol (2010), doi:10.1016/j.jhevol.2010.01.004 Landscapes of human evolution: models and methods of tectonic geomorphology and the reconstruction of hominin landscapes Geoffrey N. Bailey 1 Sally C. Reynolds 2, 3 Geoffrey C. -
Pleistocene Palaeoart of Africa
Arts 2013, 2, 6-34; doi:10.3390/arts2010006 OPEN ACCESS arts ISSN 2076-0752 www.mdpi.com/journal/arts Review Pleistocene Palaeoart of Africa Robert G. Bednarik International Federation of Rock Art Organizations (IFRAO), P.O. Box 216, Caulfield South, VIC 3162, Australia; E-Mail: [email protected]; Tel.: +61-3-95230549; Fax: +61-3-95230549 Received: 22 December 2012; in revised form: 22 January 2013 / Accepted: 23 January 2013 / Published: 8 February 2013 Abstract: This comprehensive review of all currently known Pleistocene rock art of Africa shows that the majority of sites are located in the continent’s south, but that the petroglyphs at some of them are of exceptionally great antiquity. Much the same applies to portable palaeoart of Africa. The current record is clearly one of paucity of evidence, in contrast to some other continents. Nevertheless, an initial synthesis is attempted, and some preliminary comparisons with the other continents are attempted. Certain parallels with the existing record of southern Asia are defined. Keywords: rock art; portable palaeoart; Pleistocene; figurine; bead; engraving; Africa 1. Introduction Although palaeoart of the Pleistocene occurs in at least five continents (Bednarik 1992a, 2003a) [38,49], most people tend to think of Europe first when the topic is mentioned. This is rather odd, considering that this form of evidence is significantly more common elsewhere, and very probably even older there. For instance there are far less than 10,000 motifs in the much-studied corpus of European rock art of the Ice Age, which are outnumbered by the number of publications about them. -
The Aurignacian Viewed from Africa
Aurignacian Genius: Art, Technology and Society of the First Modern Humans in Europe Proceedings of the International Symposium, April 08-10 2013, New York University THE AURIGNACIAN VIEWED FROM AFRICA Christian A. TRYON Introduction 20 The African archeological record of 43-28 ka as a comparison 21 A - The Aurignacian has no direct equivalent in Africa 21 B - Archaic hominins persist in Africa through much of the Late Pleistocene 24 C - High modification symbolic artifacts in Africa and Eurasia 24 Conclusions 26 Acknowledgements 26 References cited 27 To cite this article Tryon C. A. , 2015 - The Aurignacian Viewed from Africa, in White R., Bourrillon R. (eds.) with the collaboration of Bon F., Aurignacian Genius: Art, Technology and Society of the First Modern Humans in Europe, Proceedings of the International Symposium, April 08-10 2013, New York University, P@lethnology, 7, 19-33. http://www.palethnologie.org 19 P@lethnology | 2015 | 19-33 Aurignacian Genius: Art, Technology and Society of the First Modern Humans in Europe Proceedings of the International Symposium, April 08-10 2013, New York University THE AURIGNACIAN VIEWED FROM AFRICA Christian A. TRYON Abstract The Aurignacian technocomplex in Eurasia, dated to ~43-28 ka, has no direct archeological taxonomic equivalent in Africa during the same time interval, which may reflect differences in inter-group communication or differences in archeological definitions currently in use. Extinct hominin taxa are present in both Eurasia and Africa during this interval, but the African archeological record has played little role in discussions of the demographic expansion of Homo sapiens, unlike the Aurignacian. Sites in Eurasia and Africa by 42 ka show the earliest examples of personal ornaments that result from extensive modification of raw materials, a greater investment of time that may reflect increased their use in increasingly diverse and complex social networks. -
An Overview of the Independent Histories of the Human Y Chromosome and the Human Mitochondrial Chromosome
The Proceedings of the International Conference on Creationism Volume 8 Print Reference: Pages 133-151 Article 7 2018 An Overview of the Independent Histories of the Human Y Chromosome and the Human Mitochondrial chromosome Robert W. Carter Stephen Lee University of Idaho John C. Sanford Cornell University, Cornell University College of Agriculture and Life Sciences School of Integrative Plant Science,Follow this Plant and Biology additional Section works at: https://digitalcommons.cedarville.edu/icc_proceedings DigitalCommons@Cedarville provides a publication platform for fully open access journals, which means that all articles are available on the Internet to all users immediately upon publication. However, the opinions and sentiments expressed by the authors of articles published in our journals do not necessarily indicate the endorsement or reflect the views of DigitalCommons@Cedarville, the Centennial Library, or Cedarville University and its employees. The authors are solely responsible for the content of their work. Please address questions to [email protected]. Browse the contents of this volume of The Proceedings of the International Conference on Creationism. Recommended Citation Carter, R.W., S.S. Lee, and J.C. Sanford. An overview of the independent histories of the human Y- chromosome and the human mitochondrial chromosome. 2018. In Proceedings of the Eighth International Conference on Creationism, ed. J.H. Whitmore, pp. 133–151. Pittsburgh, Pennsylvania: Creation Science Fellowship. Carter, R.W., S.S. Lee, and J.C. Sanford. An overview of the independent histories of the human Y-chromosome and the human mitochondrial chromosome. 2018. In Proceedings of the Eighth International Conference on Creationism, ed. J.H. -
Genetic Inferences on Human Evolutionary History in Southern Arabia and the Levant
GENETIC INFERENCES ON HUMAN EVOLUTIONARY HISTORY IN SOUTHERN ARABIA AND THE LEVANT By DEVEN N. VYAS A DISSERTATION PRESENTED TO THE GRADUATE SCHOOL OF THE UNIVERSITY OF FLORIDA IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY UNIVERSITY OF FLORIDA 2017 © 2017 Deven N. Vyas To my parents, sisters, and nephews and in memory of my grandmother, Ba. ACKNOWLEDGMENTS First, I would also like to thank my parents and sisters and the rest of my family for all their love and support. I want to thank my advisor and mentor, Dr. Connie J. Mulligan for all her advice, support, and guidance throughout my graduate career. I would also like to thank my other committee members, Dr. Steven A. Brandt, Dr. John Krigbaum, and Dr. David L. Reed for their input and guidance. I would also like to thank the many former and current postdocs, graduate students, and undergraduate students from the Mulligan lab including Dr. David A. Hughes, Dr. Laurel N. Pearson, Dr. Jacklyn Quinlan, Dr. Aida T. Miró-Herrans, Dr. Tamar E. Carter, Dr. Peter H. Rej, Christopher J. Clukay, Kia C. Fuller, Félicien M. Maisha, and Chu Hsiao for all their advice throughout the years as well as prior lab members Dr. Andrew Kitchen and Dr. Ryan L. Raaum who gave me much advice and guidance from afar. Finally, I would like to express thank the Yemeni people without whose participation none of this research would have been possible. 4 TABLE OF CONTENTS page ACKNOWLEDGMENTS .................................................................................................. 4 LIST OF TABLES ............................................................................................................ 7 LIST OF FIGURES .......................................................................................................... 8 LIST OF OBJECTS ...................................................................................................... -
Analysis of Y-Chromosome Polymorphisms in Pakistani
ANALYSIS OF Y-CHROMOSOME POLYMORPHISMS IN PAKISTANI POPULATIONS Thesis submitted to the Sindh Institute of Medical Sciences for the degree of Doctor of Philosophy. BY Sadaf Firasat Centre of Human Genetics and Molecular Medicine Sindh Institute of Medical Sciences Sindh Institute of Urology and Transplantation (SIUT) Karachi, Pakistan 2010 TABLE OF CONTENTS Title page Acknowledgements ii List of Tables iii List of Figures iv Summary vi Introduction 1 Literature Review 19 Materials and Methods 34 Results Phylogeography of Pakistani ethnic groups. 51 Comparison between the Pakistani and Greek populations 73 Discussion 86 Comparison within Pakistan 88 Comparison between the Pakistani and Greek population 94 Comparison with world populations 98 Insight in to populations origins 111 Conclusions 121 References 122 Appendix a i ACKNOWLEDGEMENT I thank Prof. Dr. Syed Qasim Mehdi H.I. S.I., for his support, encouragement and for providing all the facilities for doing scientific work in his laboratory. The work presented in this thesis was done under the supervision of Dr. Qasim Ayub T.I. It is great pleasure for me to acknowledge the keen interest, advice, patient guidance and kindness that I have received from him during the course of this work. I would like to thank Dr. Shagufta Khaliq, (PoP), for teaching all the molecular genetics lab techniques and also to Dr Aiysha Abid for comments on this manuscript and suggestion for its improvement. I am also grateful to Mrs. Ambreen Ayub for her help in making the contour map. I thank my colleague Ms. Sadia Ajaz for her help and cooperation in proof reading the thesis. -
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The Role of Selection in the Evolution of Human Mitochondrial Genomes
Genetics: Published Articles Ahead of Print, published on September 19, 2005 as 10.1534/genetics.105.043901 The role of selection in the evolution of human mitochondrial genomes Toomas Kivisild*,1,4,5, Peidong Shen†,4, Dennis Wall‡3, Bao Do†, Raphael Sung†, Karen Davis†, Giuseppe Passarino§, Peter A. Underhill*, Curt Scharfe†, Antonio Torroni**, Rosaria Scozzari††,David Modiano‡‡, Alfredo Coppa§§, Peter de Knijff***, Marcus Feldman‡, Luca L. Cavalli-Sforza*, Peter J. Oefner†,2,4 *Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA. †Stanford Genome Technology Center, Palo Alto, California 94304, USA. ‡Department of Biological Sciences, Stanford University, Stanford, California 94305, USA. §Dipartimento di Biologia Cellulare, Università della Calabria, Rende, Italy. **Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia, Italy. ††Dipartimento di Genetica e Biologia Molecolare, Università "La Sapienza", Rome, Italy. ‡‡Dipartimento di Scienze di Sanità Pubblica, Sezione di Parassitologia, Università "La Sapienza", Rome, Italy. §§Dipartimento di Biologia Animale e dell'Uomo, Università "La Sapienza", Rome, Italy. ***Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands. Present addresses: 1Department of Evolutionary Biology, Tartu University and Estonian Biocenter, 51010 Tartu, Estonia. 2 Institute of Functional Genomics, University of Regensburg, Josef-Engert-Str. 9, 93053 Regensburg, Germany. 3 Department of Systems Biology, Harvard Medical School, -
Excavations at Mlambalasi Rockshelter: a Terminal Pleistocene to Recent Iron Age Record in Southern Tanzania
Afr Archaeol Rev DOI 10.1007/s10437-017-9253-3 RESEARCH REPORT Excavations at Mlambalasi Rockshelter: a Terminal Pleistocene to Recent Iron Age Record in Southern Tanzania K. M. Biittner & E. A. Sawchuk & J. M. Miller & J. J. Werner & P. M. Bushozi & P. R. Willoughby # The Author(s) 2017. This article is an open access publication Abstract The Mlambalasi rockshelter in the Iringa Re- millennia as diverse human groups were repeatedly gion of southern Tanzania has rich artifactual deposits attracted to this fixed feature on the landscape. spanning the Later Stone Age (LSA), Iron Age, and historic periods. Middle Stone Age (MSA) artifacts are Résumé L'abri sous roche Mlambalasi dans la région also present on the slope in front of the rockshelter. d'Iringa au sud de la Tanzanie est riche en artéfacts du Extensive, systematic excavations in 2006 and 2010 Paléolithique supérieur jusqu'à l'âge du fer et la by members of the Iringa Region Archaeological Project période historique. Des artéfacts du Paléolithique (IRAP) illustrate a complex picture of repeated occupa- moyen sont présents sur le versant en face de l'abri. tions and reuse of the rockshelter during an important Des fouilles extensives et systématiques réalisées par time in human history. Direct dates on Achatina shell l’équipe d’Iringa Region Archaeological Project and ostrich eggshell (OES) beads suggest that the earli- (IRAP) révèlent une image complexe de l’utilisation est occupation levels excavated at Mlambalasi, which et de la réutilisation de l'abri sous roche pendant un are associated with human burials, are terminal Pleisto- moment important dans l'histoire de l'humanité. -
A War-Prone Tribe Migrated out of Africa to Populate the World
A war-prone tribe migrated out of Africa to populate the world. Eduardo Moreno1. 1 CNIO, Melchor Fernández Almagro, 3. Madrid 28029, Spain. Of the tribal hunter gatherers still in existence today, some lead lives of great violence, whereas other groups live in societies with no warfare and very little murder1,2,3,4,5. Here I find that hunter gatherers that belong to mitochondrial haplotypes L0, L1 and L2 do not have a culture of ritualized fights. In contrast to this, almost all L3 derived hunter gatherers have a more belligerent culture that includes ritualized fights such as wrestling, stick fights or headhunting expeditions. This appears to be independent of their environment, because ritualized fights occur in all climates, from the tropics to the arctic. There is also a correlation between mitochondrial haplotypes and warfare propensity or the use of murder and suicide to resolve conflicts. This, in the light of the “recent out of Africa” hypothesis”6,7, suggests that the tribe that left Africa 80.000 years ago performed ritualized fights. In contrast to the more pacific tradition of non-L3 foragers, it may also have had a tendency towards combat. The data implicate that the entire human population outside Africa is descended from only two closely related sub-branches of L3 that practiced ritual fighting and probably had a higher propensity towards warfare and the use of murder for conflict resolution. This may have crucially influenced the subsequent history of the world. There is little evidence for the practice of war before the late Paleolithic3,4.