151
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Szpak M, Xue Y, Ayub Q, Tyler‐Smith C. How well do we understand the basis of classic selective sweeps in humans? FEBS Lett 2019; 593:1431-1448. [DOI: 10.1002/1873-3468.13447] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 04/29/2019] [Accepted: 05/17/2019] [Indexed: 12/14/2022]
Affiliation(s)
| | - Yali Xue
- The Wellcome Sanger Institute Hinxton UK
| | - Qasim Ayub
- School of Science Monash University Malaysia Bandar Sunway Malaysia
- Tropical Medicine and Biology Multidisciplinary Platform Monash University Malaysia Genomics Facility Bandar Sunway Malaysia
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152
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Ragsdale AP, Gravel S. Models of archaic admixture and recent history from two-locus statistics. PLoS Genet 2019; 15:e1008204. [PMID: 31181058 PMCID: PMC6586359 DOI: 10.1371/journal.pgen.1008204] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 06/20/2019] [Accepted: 05/17/2019] [Indexed: 11/18/2022] Open
Abstract
We learn about population history and underlying evolutionary biology through patterns of genetic polymorphism. Many approaches to reconstruct evolutionary histories focus on a limited number of informative statistics describing distributions of allele frequencies or patterns of linkage disequilibrium. We show that many commonly used statistics are part of a broad family of two-locus moments whose expectation can be computed jointly and rapidly under a wide range of scenarios, including complex multi-population demographies with continuous migration and admixture events. A full inspection of these statistics reveals that widely used models of human history fail to predict simple patterns of linkage disequilibrium. To jointly capture the information contained in classical and novel statistics, we implemented a tractable likelihood-based inference framework for demographic history. Using this approach, we show that human evolutionary models that include archaic admixture in Africa, Asia, and Europe provide a much better description of patterns of genetic diversity across the human genome. We estimate that an unidentified, deeply diverged population admixed with modern humans within Africa both before and after the split of African and Eurasian populations, contributing 4 - 8% genetic ancestry to individuals in world-wide populations.
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Affiliation(s)
- Aaron P Ragsdale
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Simon Gravel
- Department of Human Genetics, McGill University, Montreal, QC, Canada
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153
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Prendergast ME, Lipson M, Sawchuk EA, Olalde I, Ogola CA, Rohland N, Sirak KA, Adamski N, Bernardos R, Broomandkhoshbacht N, Callan K, Culleton BJ, Eccles L, Harper TK, Lawson AM, Mah M, Oppenheimer J, Stewardson K, Zalzala F, Ambrose SH, Ayodo G, Gates HL, Gidna AO, Katongo M, Kwekason A, Mabulla AZP, Mudenda GS, Ndiema EK, Nelson C, Robertshaw P, Kennett DJ, Manthi FK, Reich D. Ancient DNA reveals a multistep spread of the first herders into sub-Saharan Africa. Science 2019; 365:science.aaw6275. [PMID: 31147405 DOI: 10.1126/science.aaw6275] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 05/13/2019] [Indexed: 12/31/2022]
Abstract
How food production first entered eastern Africa ~5000 years ago and the extent to which people moved with livestock is unclear. We present genome-wide data from 41 individuals associated with Later Stone Age, Pastoral Neolithic (PN), and Iron Age contexts in what are now Kenya and Tanzania to examine the genetic impacts of the spreads of herding and farming. Our results support a multiphase model in which admixture between northeastern African-related peoples and eastern African foragers formed multiple pastoralist groups, including a genetically homogeneous PN cluster. Additional admixture with northeastern and western African-related groups occurred by the Iron Age. These findings support several movements of food producers while rejecting models of minimal admixture with foragers and of genetic differentiation between makers of distinct PN artifacts.
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Affiliation(s)
- Mary E Prendergast
- Division of Humanities, Saint Louis University, 28003 Madrid, Spain. .,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Mark Lipson
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
| | - Elizabeth A Sawchuk
- Department of Anthropology, Stony Brook University, Stony Brook, NY 11790, USA.
| | - Iñigo Olalde
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Christine A Ogola
- Department of Earth Sciences, National Museums of Kenya, Nairobi, Kenya
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Kendra A Sirak
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Nicole Adamski
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Rebecca Bernardos
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Nasreen Broomandkhoshbacht
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Kimberly Callan
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Brendan J Culleton
- Institutes for Energy and the Environment, Pennsylvania State University, University Park, PA 16802, USA
| | - Laurie Eccles
- Department of Anthropology, Pennsylvania State University, University Park, PA 16802, USA
| | - Thomas K Harper
- Department of Anthropology, Pennsylvania State University, University Park, PA 16802, USA
| | - Ann Marie Lawson
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Matthew Mah
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA.,Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Jonas Oppenheimer
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Kristin Stewardson
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Fatma Zalzala
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Stanley H Ambrose
- Department of Anthropology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - George Ayodo
- Department of Public and Community Health, School of Health Sciences, Jaramogi Oginga Odinga University of Science and Technology, Bondo, Kenya
| | - Henry Louis Gates
- Hutchins Center for African and African American Research, Harvard University, Cambridge, MA 02138, USA
| | | | | | | | | | | | - Emmanuel K Ndiema
- Department of Earth Sciences, National Museums of Kenya, Nairobi, Kenya
| | - Charles Nelson
- Academy for Lifelong Learning, Western Washington University, Bellingham, WA 98225, USA
| | - Peter Robertshaw
- Department of Anthropology, California State University, San Bernardino, CA 92407, USA
| | - Douglas J Kennett
- Department of Anthropology, University of California, Santa Barbara, CA 93106, USA
| | - Fredrick K Manthi
- Department of Earth Sciences, National Museums of Kenya, Nairobi, Kenya
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. .,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA.,Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
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154
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Isern N, Fort J. Assessing the importance of cultural diffusion in the Bantu spread into southeastern Africa. PLoS One 2019; 14:e0215573. [PMID: 31067220 PMCID: PMC6506142 DOI: 10.1371/journal.pone.0215573] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 04/05/2019] [Indexed: 11/18/2022] Open
Abstract
The subsistence of Neolithic populations is based on agriculture, whereas that of previous populations was based on hunting and gathering. Neolithic spreads due to dispersal of populations are called demic, and those due to the incorporation of hunter-gatherers are called cultural. It is well-known that, after agriculture appeared in West Africa, it spread across most of subequatorial Africa. It has been proposed that this spread took place alongside with that of Bantu languages. In eastern and southeastern Africa, it is also linked to the Early Iron Age. From the beginning of the last millennium BC, cereal agriculture spread rapidly from the Great Lakes area eastwards to the East African coast, and southwards to northeastern South Africa. Here we show that the southwards spread took place substantially more rapidly (1.50–2.27 km/y) than the eastwards spread (0.59–1.27 km/y). Such a faster southwards spread could be the result of a stronger cultural effect. To assess this possibility, we compare these observed ranges to those obtained from a demic-cultural wave-of-advance model. We find that both spreads were driven by demic diffusion, in agreement with most archaeological, linguistic and genetic results. Nonetheless, the southwards spread seems to have indeed a stronger cultural component, which could lead support to the hypothesis that, at the southern areas, the interaction with pastoralist people may have played a significant role.
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Affiliation(s)
- Neus Isern
- Complex Systems Laboratory, University of Girona, Girona, Catalonia, Spain
| | - Joaquim Fort
- Complex Systems Laboratory, University of Girona, Girona, Catalonia, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Catalonia, Spain
- * E-mail:
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155
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Lorente-Galdos B, Lao O, Serra-Vidal G, Santpere G, Kuderna LFK, Arauna LR, Fadhlaoui-Zid K, Pimenoff VN, Soodyall H, Zalloua P, Marques-Bonet T, Comas D. Whole-genome sequence analysis of a Pan African set of samples reveals archaic gene flow from an extinct basal population of modern humans into sub-Saharan populations. Genome Biol 2019; 20:77. [PMID: 31023378 PMCID: PMC6485163 DOI: 10.1186/s13059-019-1684-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 03/28/2019] [Indexed: 12/30/2022] Open
Abstract
Background Population demography and gene flow among African groups, as well as the putative archaic introgression of ancient hominins, have been poorly explored at the genome level. Results Here, we examine 15 African populations covering all major continental linguistic groups, ecosystems, and lifestyles within Africa through analysis of whole-genome sequence data of 21 individuals sequenced at deep coverage. We observe a remarkable correlation among genetic diversity and geographic distance, with the hunter-gatherer groups being more genetically differentiated and having larger effective population sizes throughout most modern-human history. Admixture signals are found between neighbor populations from both hunter-gatherer and agriculturalists groups, whereas North African individuals are closely related to Eurasian populations. Regarding archaic gene flow, we test six complex demographic models that consider recent admixture as well as archaic introgression. We identify the fingerprint of an archaic introgression event in the sub-Saharan populations included in the models (~ 4.0% in Khoisan, ~ 4.3% in Mbuti Pygmies, and ~ 5.8% in Mandenka) from an early divergent and currently extinct ghost modern human lineage. Conclusion The present study represents an in-depth genomic analysis of a Pan African set of individuals, which emphasizes their complex relationships and demographic history at population level. Electronic supplementary material The online version of this article (10.1186/s13059-019-1684-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Belen Lorente-Galdos
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (UPF/CSIC), Universitat Pompeu Fabra, 08003, Barcelona, Spain.,Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Oscar Lao
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, 08028, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Gerard Serra-Vidal
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (UPF/CSIC), Universitat Pompeu Fabra, 08003, Barcelona, Spain
| | - Gabriel Santpere
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (UPF/CSIC), Universitat Pompeu Fabra, 08003, Barcelona, Spain.,Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Lukas F K Kuderna
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (UPF/CSIC), Universitat Pompeu Fabra, 08003, Barcelona, Spain
| | - Lara R Arauna
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (UPF/CSIC), Universitat Pompeu Fabra, 08003, Barcelona, Spain
| | - Karima Fadhlaoui-Zid
- College of Science, Department of Biology, Taibah University, Al Madinah, Al Monawarah, Saudi Arabia.,Higher Institute of Biotechnology of Beja, University of Jendouba, Avenue Habib Bourguiba, BP, 382, 9000, Beja, Tunisia
| | - Ville N Pimenoff
- Oncology Data Analytics Program, Bellvitge Biomedical Research Institute (ICO-IDIBELL), Consortium for Biomedical Research in Epidemiology and Public Health, Hospitalet de Llobregat, Barcelona, Spain.,Department of Archaeology, University of Helsinki, Helsinki, Finland
| | - Himla Soodyall
- Division of Human Genetics, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and National Health Laboratory Service, Johannesburg, South Africa
| | - Pierre Zalloua
- School of Medicine, The Lebanese American University, Beirut, 1102-2801, Lebanon
| | - Tomas Marques-Bonet
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (UPF/CSIC), Universitat Pompeu Fabra, 08003, Barcelona, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, 08028, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats, ICREA, 08003, Barcelona, Spain
| | - David Comas
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (UPF/CSIC), Universitat Pompeu Fabra, 08003, Barcelona, Spain.
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156
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Fan S, Kelly DE, Beltrame MH, Hansen MEB, Mallick S, Ranciaro A, Hirbo J, Thompson S, Beggs W, Nyambo T, Omar SA, Meskel DW, Belay G, Froment A, Patterson N, Reich D, Tishkoff SA. African evolutionary history inferred from whole genome sequence data of 44 indigenous African populations. Genome Biol 2019; 20:82. [PMID: 31023338 PMCID: PMC6485071 DOI: 10.1186/s13059-019-1679-2] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 03/22/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Africa is the origin of modern humans within the past 300 thousand years. To infer the complex demographic history of African populations and adaptation to diverse environments, we sequenced the genomes of 92 individuals from 44 indigenous African populations. RESULTS Genetic structure analyses indicate that among Africans, genetic ancestry is largely partitioned by geography and language, though we observe mixed ancestry in many individuals, consistent with both short- and long-range migration events followed by admixture. Phylogenetic analysis indicates that the San genetic lineage is basal to all modern human lineages. The San and Niger-Congo, Afroasiatic, and Nilo-Saharan lineages were substantially diverged by 160 kya (thousand years ago). In contrast, the San and Central African rainforest hunter-gatherer (CRHG), Hadza hunter-gatherer, and Sandawe hunter-gatherer lineages were diverged by ~ 120-100 kya. Niger-Congo, Nilo-Saharan, and Afroasiatic lineages diverged more recently by ~ 54-16 kya. Eastern and western CRHG lineages diverged by ~ 50-31 kya, and the western CRHG lineages diverged by ~ 18-12 kya. The San and CRHG populations maintained the largest effective population size compared to other populations prior to 60 kya. Further, we observed signatures of positive selection at genes involved in muscle development, bone synthesis, reproduction, immune function, energy metabolism, and cell signaling, which may contribute to local adaptation of African populations. CONCLUSIONS We observe high levels of genomic variation between ethnically diverse Africans which is largely correlated with geography and language. Our study indicates ancient population substructure and local adaptation of Africans.
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Affiliation(s)
- Shaohua Fan
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Present Address: State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai, China
| | - Derek E Kelly
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Marcia H Beltrame
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Matthew E B Hansen
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Alessia Ranciaro
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Jibril Hirbo
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Present Address: Division of Genetic Medicine, Vanderbilt University Medical Center, Vanderbilt University, Nashville, TN, 37232, USA
| | - Simon Thompson
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - William Beggs
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Thomas Nyambo
- Department of Biochemistry, Muhimbili University of Health and Allied Sciences, Dares Salaam, Tanzania
| | - Sabah A Omar
- Center for Biotechnology Research and Development, Kenya Medical Research Institute, Nairobi, Kenya
| | | | - Gurja Belay
- Department of Biology, Addis Ababa University, Addis Ababa, Ethiopia
| | | | - Nick Patterson
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Sarah A Tishkoff
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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157
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Abstract
Hominin evolution is characterized by progressive regional differentiation, as well as migration waves, leading to anatomically modern humans that are assumed to have emerged in Africa and spread over the whole world. Why or whether Africa was the source region of modern humans and what caused their spread remains subject of ongoing debate. We present a spatially explicit, stochastic numerical model that includes ongoing mutations, demic diffusion, assortative mating and migration waves. Diffusion and assortative mating alone result in a structured population with relatively homogeneous regions bound by sharp clines. The addition of migration waves results in a power-law distribution of wave areas: for every large wave, many more small waves are expected to occur. This suggests that one or more out-of-Africa migrations would probably have been accompanied by numerous smaller migration waves across the world. The migration waves are considered "spontaneous", as the current model excludes environmental or other extrinsic factors. Large waves preferentially emanate from the central areas of large, compact inhabited areas. During the Pleistocene, Africa was the largest such area most of the time, making Africa the statistically most likely origin of anatomically modern humans, without a need to invoke additional environmental or ecological drivers.
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158
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Enamel pearls: Their occurrence in recent human populations and earliest manifestation in the modern human lineage. Arch Oral Biol 2019; 101:147-155. [PMID: 30939297 DOI: 10.1016/j.archoralbio.2019.03.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 02/22/2019] [Accepted: 03/04/2019] [Indexed: 12/28/2022]
Abstract
OBJECTIVE To document and describe the occurrence of an enamel pearl on the distal root surface of the maxillary M3 of the fossil hominin specimen from Florisbad, South Africa that is dated to ca. 259,000 years B.P., and is an early representative of Homo sapiens or as a member of the evolutionary line that was directly ancestral to modern humans. DESIGN The molar was examined macroscopically and by micro-computed tomography (μCT) to enable accurate measurement and visualization of the structure of the enamel pearl. RESULTS The single pearl has a diameter of 0.97 mm; it is a Type 2 "composite" pearl comprising an enamel cap and dentine core without pulp chamber involvement. The size of the Florisbad pearl falls within or just below the size ranges of this anomaly in modern human samples. Type 2 pearls are most commonly encountered in recent human populations, and the location of the pearl on the distal root surface of the Florisbad M3 is consistent with its most frequent location in recent humans. Pearls in recent human populations affect between 0.2-4.8% of individuals, and 1.7-6.8% of permanent molars. Pearls have been documented in several prehistoric human dentitions, and all examples are less than 4000 years old. CONCLUSIONS Enamel pearls have been associated with periodontal disease, but it is not possible to relate its presence to the advanced periodontal inflammation and alveolar bone loss in the Florisbad fossil. Florisbad presents the earliest evidence of this anomaly in the fossil record pertaining to modern humans.
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159
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Vyas DN, Mulligan CJ. Analyses of Neanderthal introgression suggest that Levantine and southern Arabian populations have a shared population history. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2019; 169:227-239. [PMID: 30889271 DOI: 10.1002/ajpa.23818] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 01/11/2019] [Accepted: 02/21/2019] [Indexed: 01/31/2023]
Abstract
OBJECTIVES Modern humans are thought to have interbred with Neanderthals in the Near East soon after modern humans dispersed out of Africa. This introgression event likely took place in either the Levant or southern Arabia depending on the dispersal route out of Africa that was followed. In this study, we compare Neanderthal introgression in contemporary Levantine and southern Arabian populations to investigate Neanderthal introgression and to study Near Eastern population history. MATERIALS AND METHODS We analyzed genotyping data on >400,000 autosomal SNPs from seven Levantine and five southern Arabian populations and compared these data to those from populations from around the world including Neanderthal and Denisovan genomes. We used f4 and D statistics to estimate and compare levels of Neanderthal introgression between Levantine, southern Arabian, and comparative global populations. We also identified 1,581 putative Neanderthal-introgressed SNPs within our dataset and analyzed their allele frequencies as a means to compare introgression patterns in Levantine and southern Arabian genomes. RESULTS We find that Levantine and southern Arabian populations have similar levels of Neanderthal introgression to each other but lower levels than other non-Africans. Furthermore, we find that introgressed SNPs have very similar allele frequencies in the Levant and southern Arabia, which indicates that Neanderthal introgression is similarly distributed in Levantine and southern Arabian genomes. DISCUSSION We infer that the ancestors of contemporary Levantine and southern Arabian populations received Neanderthal introgression prior to separating from each other and that there has been extensive gene flow between these populations.
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Affiliation(s)
- Deven N Vyas
- Department of Anthropology, University of Florida, Gainesville, Florida.,Genetics Institute, University of Florida, Gainesville, Florida
| | - Connie J Mulligan
- Department of Anthropology, University of Florida, Gainesville, Florida.,Genetics Institute, University of Florida, Gainesville, Florida
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160
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Positive selection in Europeans and East-Asians at the ABCA12 gene. Sci Rep 2019; 9:4843. [PMID: 30890716 PMCID: PMC6424970 DOI: 10.1038/s41598-019-40360-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 02/07/2019] [Indexed: 11/17/2022] Open
Abstract
Natural selection acts on genetic variants by increasing the frequency of alleles responsible for a cellular function that is favorable in a certain environment. In a previous genome-wide scan for positive selection in contemporary humans, we identified a signal of positive selection in European and Asians at the genetic variant rs10180970. The variant is located in the second intron of the ABCA12 gene, which is implicated in the lipid barrier formation and down-regulated by UVB radiation. We studied the signal of selection in the genomic region surrounding rs10180970 in a larger dataset that includes DNA sequences from ancient samples. We also investigated the functional consequences of gene expression of the alleles of rs10180970 and another genetic variant in its proximity in healthy volunteers exposed to similar UV radiation. We confirmed the selection signal and refine its location that extends over 35 kb and includes the first intron, the first two exons and the transcription starting site of ABCA12. We found no obvious effect of rs10180970 alleles on ABCA12 gene expression. We reconstructed the trajectory of the T allele over the last 80,000 years to discover that it was specific to H. sapiens and present in non-Africans 45,000 years ago.
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161
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A dispersal of Homo sapiens from southern to eastern Africa immediately preceded the out-of-Africa migration. Sci Rep 2019; 9:4728. [PMID: 30894612 PMCID: PMC6426877 DOI: 10.1038/s41598-019-41176-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 02/19/2019] [Indexed: 01/08/2023] Open
Abstract
Africa was the birth-place of Homo sapiens and has the earliest evidence for symbolic behaviour and complex technologies. The best-attested early flowering of these distinctive features was in a glacial refuge zone on the southern coast 100–70 ka, with fewer indications in eastern Africa until after 70 ka. Yet it was eastern Africa, not the south, that witnessed the first major demographic expansion, ~70–60 ka, which led to the peopling of the rest of the world. One possible explanation is that important cultural traits were transmitted from south to east at this time. Here we identify a mitochondrial signal of such a dispersal soon after ~70 ka – the only time in the last 200,000 years that humid climate conditions encompassed southern and tropical Africa. This dispersal immediately preceded the out-of-Africa expansions, potentially providing the trigger for these expansions by transmitting significant cultural elements from the southern African refuge.
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162
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Gelabert P, Ferrando-Bernal M, de-Dios T, Mattorre B, Campoy E, Gorostiza A, Patin E, González-Martín A, Lalueza-Fox C. Genome-wide data from the Bubi of Bioko Island clarifies the Atlantic fringe of the Bantu dispersal. BMC Genomics 2019; 20:179. [PMID: 30841922 PMCID: PMC6404284 DOI: 10.1186/s12864-019-5529-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 02/13/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Bioko is one of the few islands that exist around Africa, the most genetically diverse continent on the planet. The native Bantu-speaking inhabitants of Bioko, the Bubi, are believed to have colonized the island about 2000 years ago. Here, we sequenced the genome of thirteen Bubi individuals at high coverage and analysed their sequences in comparison to mainland populations from the Gulf of Guinea. RESULTS We found that, genetically, the closest mainland population to the Bubi are Bantu-speaking groups from Angola instead the geographically closer groups from Cameroon. The Bubi possess a lower proportion of rainforest hunter-gatherer (RHG) ancestry than most other Bantu-speaking groups. However, their RHG component most likely came from the same source and could have reached them by gene flow from the mainland after island settlement. By studying identity by descent (IBD) genomic blocks and runs of homozygosity (ROHs), we found evidence for a significant level of genetic isolation among the Bubi, isolation that can be attributed to the island effect. Additionally, as this population is known to have one of the highest malaria incidence rates in the world we analysed their genome for malaria-resistant alleles. However, we were unable to detect any specific selective sweeps related to this disease. CONCLUSIONS By describing their dispersal to the Atlantic islands, the genomic characterization of the Bubi contributes to the understanding of the margins of the massive Bantu migration that shaped all Sub-Saharan African populations.
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Affiliation(s)
- Pere Gelabert
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | | | - Toni de-Dios
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Benedetta Mattorre
- Laboratory of Anthropology, Department of Biology, University of Florence, Florence, Italy
| | - Elena Campoy
- Department of Biodiversity, Ecology and Evolution, Complutense University of Madrid, Madrid, Spain
| | - Amaya Gorostiza
- Forensic Genetics Laboratory, GENOMICA S.A.U., Pharma Mar Group, Madrid, Spain
| | - Etienne Patin
- Unit of Human Evolutionary Genetics, Department of Genomics & Genetics, Institut Pasteur, Paris, France
- CNRS UMR 2000, Paris, France
- Center of Bioinformatics, Biostatistics and Integrative Biology, Institut Pasteur, Paris, France
| | - Antonio González-Martín
- Department of Biodiversity, Ecology and Evolution, Complutense University of Madrid, Madrid, Spain
| | - Carles Lalueza-Fox
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
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163
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Pinhasi R, Fernandes DM, Sirak K, Cheronet O. Isolating the human cochlea to generate bone powder for ancient DNA analysis. Nat Protoc 2019; 14:1194-1205. [DOI: 10.1038/s41596-019-0137-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 01/10/2019] [Indexed: 12/21/2022]
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164
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Vai S, Sarno S, Lari M, Luiselli D, Manzi G, Gallinaro M, Mataich S, Hübner A, Modi A, Pilli E, Tafuri MA, Caramelli D, di Lernia S. Ancestral mitochondrial N lineage from the Neolithic 'green' Sahara. Sci Rep 2019; 9:3530. [PMID: 30837540 PMCID: PMC6401177 DOI: 10.1038/s41598-019-39802-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 01/30/2019] [Indexed: 11/16/2022] Open
Abstract
Because Africa's climate hampers DNA preservation, knowledge of its genetic variability is mainly restricted to modern samples, even though population genetics dynamics and back-migrations from Eurasia may have modified haplotype frequencies, masking ancient genetic scenarios. Thanks to improved methodologies, ancient genetic data for the African continent are now increasingly available, starting to fill in the gap. Here we present newly obtained mitochondrial genomes from two ~7000-year-old individuals from Takarkori rockshelter, Libya, representing the earliest and first genetic data for the Sahara region. These individuals carry a novel mutation motif linked to the haplogroup N root. Our result demonstrates the presence of an ancestral lineage of the N haplogroup in the Holocene "Green Sahara", associated to a Middle Pastoral (Neolithic) context.
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Affiliation(s)
- Stefania Vai
- Department of Biology, University of Florence, Florence, Italy
| | - Stefania Sarno
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Martina Lari
- Department of Biology, University of Florence, Florence, Italy
| | - Donata Luiselli
- Department of Cultural Heritage, University of Bologna, Ravenna, Italy
| | - Giorgio Manzi
- Department of Environmental Biology, Sapienza University of Rome, Rome, Italy
| | - Marina Gallinaro
- Department of Ancient World Studies, Sapienza University of Rome, Rome, Italy
| | - Safaa Mataich
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Alexander Hübner
- Max-Planck-Institute for Evolutionary Anthropology, Department Evolutionary Genetics, Leipzig, Germany
| | - Alessandra Modi
- Department of Biology, University of Florence, Florence, Italy
| | - Elena Pilli
- Department of Biology, University of Florence, Florence, Italy
| | - Mary Anne Tafuri
- Department of Environmental Biology, Sapienza University of Rome, Rome, Italy
| | - David Caramelli
- Department of Biology, University of Florence, Florence, Italy.
| | - Savino di Lernia
- Department of Ancient World Studies, Sapienza University of Rome, Rome, Italy.
- School of Geography, Archaeology and Environmental Studies, University of the Witwatersrand, Johannesburg, South Africa.
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165
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Human Immunology through the Lens of Evolutionary Genetics. Cell 2019; 177:184-199. [DOI: 10.1016/j.cell.2019.02.033] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 02/19/2019] [Accepted: 02/20/2019] [Indexed: 01/04/2023]
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166
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Pfeiffer S, Harrington L, Lombard M. The people behind the samples: Biographical features of Past Hunter-Gatherers from KwaZulu-Natal who yielded aDNA. INTERNATIONAL JOURNAL OF PALEOPATHOLOGY 2019; 24:158-164. [PMID: 30399480 DOI: 10.1016/j.ijpp.2018.10.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 10/18/2018] [Accepted: 10/25/2018] [Indexed: 05/25/2023]
Abstract
PURPOSE Skeletons sampled for ancient human DNA analysis are sometimes complete enough to provide information about the lives of the people they represent. We focus on three Later Stone Age skeletons, ca. 2000 B.P., from coastal KwaZulu-Natal, South Africa, whose ancient genomes have been sequenced (Schlebusch et al., 2017). METHODS Bioarchaeological approaches are integrated with aDNA information. RESULTS All skeletons are male. Dental development shows that the boy, with prominent cribra orbitalia, died at age 6-7 years. Two men show cranial and spinal trauma, extensive tooth wear, plus mild cribra orbitalia in one. CONCLUSIONS Dental wear and trauma of the adults are consistent with hunter-gatherer lives. Even partial aDNA evidence contributes to sex determination. Parasitic infection such as schistosomiasis is the best-fit cause for the child's anemia in this case. CONTRIBUTION TO KNOWLEDGE The convergence of genomic and bioarchaeological approaches expands our knowledge of the past lives of a boy and two men whose lives as hunter-gatherers included episodes of trauma and disease. LIMITATIONS The skeletons are incomplete, in variable condition, and from poorly characterized local cultural contexts. SUGGESTIONS FOR FURTHER RESEARCH Thorough osteobiographic analysis should accompany paleogenomic investigations. Such disciplinary collaboration enriches our understanding of the human past.
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Affiliation(s)
- Susan Pfeiffer
- Department of Anthropology, University of Toronto, 19 Russell Street, Toronto, M5S 2S2, Canada; Department of Archaeology, University of Cape Town, Rondebosch 7701, South Africa; Department of Anthropology, George Washington University, D.C., USA.
| | - Lesley Harrington
- Department of Anthropology, University of Alberta, 13-15 H.M. Tory Building, Edmonton, T6G 2H4, Canada
| | - Marlize Lombard
- Centre for Anthropological Research, University of Johannesburg, P.O. Box 524, Auckland Park, 2006, South Africa
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167
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Bentley AR, Callier S, Rotimi C. The Emergence of Genomic Research in Africa and New Frameworks for Equity in Biomedical Research. Ethn Dis 2019; 29:179-186. [PMID: 30906167 DOI: 10.18865/ed.29.s1.179] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Individuals with African ancestry have the greatest genomic diversity in the world, yet they have been underrepresented in genomic research. To advance our understanding of human biology and our ability to trace human history, we must include more samples from Africans in genomic research. Additionally, inclusion of more samples from participants of recent African descent is imperative to provide equitable health care as genomics is increasingly used for diagnosis, treatment, and to understand disease risk. The Human Heredity and Health in Africa initiative (H3Africa) seeks to expand the number of Africans included in genomic research and to do so by expanding the research capacity on the continent. In this article, we discuss how H3Africa is endeavoring to achieve these goals while promoting equitable research collaborations.
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Affiliation(s)
- Amy R Bentley
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Shawneequa Callier
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD.,Department of Clinical Research and Leadership, The George Washington University School of Medicine and Health Sciences, Washington, DC
| | - Charles Rotimi
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
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168
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Petr M, Pääbo S, Kelso J, Vernot B. Limits of long-term selection against Neandertal introgression. Proc Natl Acad Sci U S A 2019; 116:1639-1644. [PMID: 30647110 PMCID: PMC6358679 DOI: 10.1073/pnas.1814338116] [Citation(s) in RCA: 109] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Several studies have suggested that introgressed Neandertal DNA was subjected to negative selection in modern humans. A striking observation in support of this is an apparent monotonic decline in Neandertal ancestry observed in modern humans in Europe over the past 45,000 years. Here, we show that this decline is an artifact likely caused by gene flow between modern human populations, which is not taken into account by statistics previously used to estimate Neandertal ancestry. When we apply a statistic that avoids assumptions about modern human demography by taking advantage of two high-coverage Neandertal genomes, we find no evidence for a change in Neandertal ancestry in Europe over the past 45,000 years. We use whole-genome simulations of selection and introgression to investigate a wide range of model parameters and find that negative selection is not expected to cause a significant long-term decline in genome-wide Neandertal ancestry. Nevertheless, these models recapitulate previously observed signals of selection against Neandertal alleles, in particular the depletion of Neandertal ancestry in conserved genomic regions. Surprisingly, we find that this depletion is strongest in regulatory and conserved noncoding regions and in the most conserved portion of protein-coding sequences.
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Affiliation(s)
- Martin Petr
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Svante Pääbo
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Janet Kelso
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Benjamin Vernot
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
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169
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Approximate Bayesian computation with deep learning supports a third archaic introgression in Asia and Oceania. Nat Commun 2019; 10:246. [PMID: 30651539 PMCID: PMC6335398 DOI: 10.1038/s41467-018-08089-7] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 12/12/2018] [Indexed: 01/24/2023] Open
Abstract
Since anatomically modern humans dispersed Out of Africa, the evolutionary history of Eurasian populations has been marked by introgressions from presently extinct hominins. Some of these introgressions have been identified using sequenced ancient genomes (Neanderthal and Denisova). Other introgressions have been proposed for still unidentified groups using the genetic diversity present in current human populations. We built a demographic model based on deep learning in an Approximate Bayesian Computation framework to infer the evolutionary history of Eurasian populations including past introgression events in Out of Africa populations fitting the current genetic evidence. In addition to the reported Neanderthal and Denisovan introgressions, our results support a third introgression in all Asian and Oceanian populations from an archaic population. This population is either related to the Neanderthal-Denisova clade or diverged early from the Denisova lineage. We propose the use of deep learning methods for clarifying situations with high complexity in evolutionary genomics.
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170
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Zou X, Wang Z, He G, Wang M, Su Y, Liu J, Chen P, Wang S, Gao B, Li Z, Hou Y. Population Genetic Diversity and Phylogenetic Characteristics for High-Altitude Adaptive Kham Tibetan Revealed by DNATyper TM 19 Amplification System. Front Genet 2018; 9:630. [PMID: 30619458 PMCID: PMC6304359 DOI: 10.3389/fgene.2018.00630] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 11/26/2018] [Indexed: 11/13/2022] Open
Abstract
Tibetans residing in the high-altitude inhospitable environment have undergone significant natural selection of their genetic architecture. Recently, highly mutational autosomal short tandem repeats were widely used not only in the anthropology and population genetics to investigate the genetic structure and relationships, but also in the medical genetics to explore the pathogenesis of multiple genetic diseases and in the forensic science to identify individual and parentage relatedness. However, genetic variants and forensic efficiency of DNATyperTM 19 amplification system and genetic background of Kham Tibetan remain uncharacterized. Thus, we genotyped 19 forensic genetic markers in 11,402 Kham Tibetans to gain insight into the genetic diversity of Chinese high-altitude adaptive population. Highly discriminating and polymorphic forensic measures were observed, which indicated that this new-developed DNATyper 19 PCR amplification is suitable for routine forensic identification purposes and Chinese national DNA database establishment. Pairwise genetic distances among the comprehensive population comparisons suggested that this high-altitude adaptive Kham Tibetan has genetically closer relationships with lowlanders of Tibeto-Burman-speaking populations (Chengdu Tibetan, Liangshan Tibetan, and Liangshan Yi). Genetic substructure analyses via phylogenetic reconstruction, principal component analysis, and multidimensional scaling analysis in both nationwide and worldwide contexts suggested that the genetic proximity exists along the linguistic, ethnic, and continental geographical boundary. Further studies with whole-genome sequencing of modern or archaic Kham Tibetans would be useful in reconstructing the Tibetan population history.
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Affiliation(s)
- Xing Zou
- Institute of Forensic Medicine, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Zheng Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Guanglin He
- Institute of Forensic Medicine, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Mengge Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Yongdong Su
- Forensic Identification Center, Public Security Bureau of Tibet Autonomous Region, Lhasa, China
| | - Jing Liu
- Institute of Forensic Medicine, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Pengyu Chen
- Center of Forensic Expertise, Affiliated Hospital of Zunyi Medical University, Zunyi, China.,School of Forensic Medicine, Zunyi Medical University, Zunyi, China
| | - Shouyu Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Bo Gao
- Institute of Forensic Science, Yili Public Security Bureau of Xinjiang, Kuytun, China
| | - Zhao Li
- Department of Criminal Investigation, Mianyang Public Security Bureau, Mianyang, China
| | - Yiping Hou
- Institute of Forensic Medicine, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
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171
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Montinaro F, Capelli C. The evolutionary history of Southern Africa. Curr Opin Genet Dev 2018; 53:157-164. [PMID: 30522870 DOI: 10.1016/j.gde.2018.11.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 10/12/2018] [Accepted: 11/06/2018] [Indexed: 01/15/2023]
Abstract
The genomic variability of Southern African groups is characterized by an exceptional degree of diversity, which is the result of long-term local evolutionary history, migrations and gene-flow. Over the last few years several investigations have identified and described signatures related to these processes, revealing how ancient and more recent events have shaped the structure and ancestry composition of local populations. Here we discuss recent insights into the genetic history of the Southernmost part of the African continent provided by the analysis of modern and ancient genomes. Future work is expected to clarify the population dynamics associated with the emergence of Homo sapiens across Africa and the details of the process of dispersion and admixture associated with the arrival of Bantu-speaking groups in the region.
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Affiliation(s)
- Francesco Montinaro
- Department of Zoology, University of Oxford, UK; Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
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172
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Molinaro L, Pagani L. Human evolutionary history of Eastern Africa. Curr Opin Genet Dev 2018; 53:134-139. [DOI: 10.1016/j.gde.2018.10.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 08/31/2018] [Accepted: 10/08/2018] [Indexed: 01/16/2023]
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173
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Henn BM, Steele TE, Weaver TD. Clarifying distinct models of modern human origins in Africa. Curr Opin Genet Dev 2018; 53:148-156. [PMID: 30423527 DOI: 10.1016/j.gde.2018.10.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 10/09/2018] [Accepted: 10/15/2018] [Indexed: 11/29/2022]
Abstract
Accumulating genomic, fossil and archaeological data from Africa have led to a renewed interest in models of modern human origins. However, such discussions are often discipline-specific, with limited integration of evidence across the different fields. Further, geneticists typically require explicit specification of parameters to test competing demographic models, but these have been poorly outlined for some scenarios. Here, we describe four possible models for the origins of Homo sapiens in Africa based on published literature from paleoanthropology and human genetics. We briefly outline expectations for data patterns under each model, with a special focus on genetic data. Additionally, we present schematics for each model, doing our best to qualitatively describe demographic histories for which genetic parameters can be specifically attached. Finally, it is our hope that this perspective provides context for discussions of human origins in other manuscripts presented in this special issue.
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Affiliation(s)
- Brenna M Henn
- Department of Anthropology, University of California, Davis, CA, 95616, United States; UC Davis Genome Center, University of California, Davis, CA, 95616, United States.
| | - Teresa E Steele
- Department of Anthropology, University of California, Davis, CA, 95616, United States
| | - Timothy D Weaver
- Department of Anthropology, University of California, Davis, CA, 95616, United States
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174
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Maxmen A. Rare genetic sequences illuminate early humans’ history in Africa. Nature 2018; 563:13-14. [DOI: 10.1038/d41586-018-07164-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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175
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de Filippo C, Meyer M, Prüfer K. Quantifying and reducing spurious alignments for the analysis of ultra-short ancient DNA sequences. BMC Biol 2018; 16:121. [PMID: 30359256 PMCID: PMC6202837 DOI: 10.1186/s12915-018-0581-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 09/27/2018] [Indexed: 04/25/2023] Open
Abstract
BACKGROUND The study of ancient DNA is hampered by degradation, resulting in short DNA fragments. Advances in laboratory methods have made it possible to retrieve short DNA fragments, thereby improving access to DNA preserved in highly degraded, ancient material. However, such material contains large amounts of microbial contamination in addition to DNA fragments from the ancient organism. The resulting mixture of sequences constitutes a challenge for computational analysis, since microbial sequences are hard to distinguish from the ancient sequences of interest, especially when they are short. RESULTS Here, we develop a method to quantify spurious alignments based on the presence or absence of rare variants. We find that spurious alignments are enriched for mismatches and insertion/deletion differences and lack substitution patterns typical of ancient DNA. The impact of spurious alignments can be reduced by filtering on these features and by imposing a sample-specific minimum length cutoff. We apply this approach to sequences from four ~ 430,000-year-old Sima de los Huesos hominin remains, which contain particularly short DNA fragments, and increase the amount of usable sequence data by 17-150%. This allows us to place a third specimen from the site on the Neandertal lineage. CONCLUSIONS Our method maximizes the sequence data amenable to genetic analysis from highly degraded ancient material and avoids pitfalls that are associated with the analysis of ultra-short DNA sequences.
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Affiliation(s)
- Cesare de Filippo
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Matthias Meyer
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Kay Prüfer
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
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176
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Bradbury C, Köttgen A, Staubach F. Off-target phenotypes in forensic DNA phenotyping and biogeographic ancestry inference: A resource. Forensic Sci Int Genet 2018; 38:93-104. [PMID: 30391626 DOI: 10.1016/j.fsigen.2018.10.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 08/27/2018] [Accepted: 10/13/2018] [Indexed: 01/04/2023]
Abstract
With recent advances in DNA sequencing technologies it has become feasible and cost effective to genotype larger marker sets for forensic purposes. Two technologies that make use of the larger marker sets have come into focus in forensic research and applications; inference of biogeographic ancestry (BGA) and forensic DNA phenotyping (FDP). These methods hold the promise to reveal information about a yet unknown perpetrator from a DNA sample. In contrast, DNA-profiling, that is a standard practice in case work, relies on matching DNA-profiles between crime scene material and suspects on a database of DNA-profiles. Markers for DNA-profiling were developed under the premise to reveal as little additional information about the human source of the profile as possible, the rationale being that personal privacy rights have to be balanced against the public interest in solving a crime. The same argument holds for markers used in BGA and FDP; these markers might also reveal information on off-target phenotypes (OTPs), that go beyond BGA and the phenotypes targeted in FDP. In particular, health related OTPs might shift the balance between privacy protection and public interest. However, to our knowledge, there is currently no convenient resource available to incorporate knowledge on OTPs in BGA and FDP assay design and application. In order to provide such a resource, we performed a systematic search for OTPs associated with a comprehensive set of markers (1766 SNPs) used or suggested to be used for BGA inference and FDP. In this set, we identified a relatively small number of 27 SNPs (1.53%) that convey information on diverse health related OTPs such as cancer risk, induced asthma, or risk of alcoholism. Some of these SNPs are commonly used for FDP and BGA across different marker sets. We conclude that the effects of SNP markers used in FDP and BGA on OTPs are currently limited, with few exceptions that should be considered in a balanced decision on assay design and application.
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Affiliation(s)
- Cedric Bradbury
- University College Freiburg, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Anna Köttgen
- Institute of Genetic Epidemiology, Dept. of Biometry, Epidemiology and Medical Bioinformatics, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Fabian Staubach
- Institute of Biology I, Dept. of Evolutionary Biology and Ecology, Albert-Ludwigs-University Freiburg, Freiburg, Germany.
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177
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Bajić V, Barbieri C, Hübner A, Güldemann T, Naumann C, Gerlach L, Berthold F, Nakagawa H, Mpoloka SW, Roewer L, Purps J, Stoneking M, Pakendorf B. Genetic structure and sex-biased gene flow in the history of southern African populations. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2018; 167:656-671. [PMID: 30192370 PMCID: PMC6667921 DOI: 10.1002/ajpa.23694] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 07/13/2018] [Accepted: 07/15/2018] [Indexed: 12/31/2022]
Abstract
Objectives We investigated the genetic history of southern African populations with a special focus on their paternal history. We reexamined previous claims that the Y‐chromosome haplogroup E1b1b (E‐M293) was brought to southern Africa by pastoralists from eastern Africa, and investigated patterns of sex‐biased gene flow in southern Africa. Materials and methods We analyzed previously published complete mtDNA genome sequences and ∼900 kb of NRY sequences from 23 populations from Namibia, Botswana, and Zambia, as well as haplogroup frequencies from a large sample of southern African populations and 23 newly genotyped Y‐linked STR loci for samples assigned to haplogroup E1b1b. Results Our results support an eastern African origin for Y‐chromosome haplogroup E1b1b (E‐M293); however, its current distribution in southern Africa is not strongly associated with pastoralism, suggesting more complex demographic events and/or changes in subsistence practices in this region. The Bantu expansion in southern Africa had a notable genetic impact and was probably a rapid, male‐dominated expansion. Our finding of a significant increase in the intensity of the sex‐biased gene flow from north to south may reflect changes in the social dynamics between Khoisan and Bantu groups over time. Conclusions Our study shows that the population history of southern Africa has been complex, with different immigrating groups mixing to different degrees with the autochthonous populations. The Bantu expansion led to heavily sex‐biased admixture as a result of interactions between Khoisan females and Bantu males, with a geographic gradient which may reflect changes in the social dynamics between Khoisan and Bantu groups over time.
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Affiliation(s)
- Vladimir Bajić
- Department of Evolutionary Genetics, MPI for Evolutionary Anthropology, Leipzig, Germany
| | - Chiara Barbieri
- Department of Linguistic and Cultural Evolution, MPI for the Science of Human History, Jena, Germany.,Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Alexander Hübner
- Department of Evolutionary Genetics, MPI for Evolutionary Anthropology, Leipzig, Germany
| | - Tom Güldemann
- Department of Linguistic and Cultural Evolution, MPI for the Science of Human History, Jena, Germany.,Institute of Asian and African Studies, Humboldt University, Berlin, Germany
| | - Christfried Naumann
- Institute of Asian and African Studies, Humboldt University, Berlin, Germany
| | - Linda Gerlach
- Department of Human Behavior, Ecology and Culture, MPI for Evolutionary Anthropology, Leipzig, Germany
| | - Falko Berthold
- Max Planck Research Group on Comparative Population Linguistics, MPI for Evolutionary Anthropology, Leipzig, Germary
| | - Hirosi Nakagawa
- Institute of Global Studies, Tokyo University of Foreign Studies, Tokyo, Japan
| | - Sununguko W Mpoloka
- Department of Biological Sciences, University of Botswana, Gaborone, Botswana
| | - Lutz Roewer
- Charité - Universitätsmedizin Berlin, Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Berlin, Germany
| | - Josephine Purps
- Charité - Universitätsmedizin Berlin, Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Berlin, Germany
| | - Mark Stoneking
- Department of Evolutionary Genetics, MPI for Evolutionary Anthropology, Leipzig, Germany
| | - Brigitte Pakendorf
- Laboratoire «Dynamique du Langage», CNRS & Université de Lyon, Lyon, France
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178
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Abstract
The first decade of ancient genomics has revolutionized the study of human prehistory and evolution. We review new insights based on prehistoric modern human genomes, including greatly increased resolution of the timing and structure of the out-of-Africa expansion, the diversification of present-day non-African populations, and the earliest expansions of those populations into Eurasia and America. Prehistoric genomes now document population transformations on every inhabited continent—in particular the effect of agricultural expansions in Africa, Europe, and Oceania—and record a history of natural selection that shapes present-day phenotypic diversity. Despite these advances, much remains unknown, in particular about the genomic histories of Asia (the most populous continent) and Africa (the continent that contains the most genetic diversity). Ancient genomes from these and other regions, integrated with a growing understanding of the genomic basis of human phenotypic diversity, will be in focus during the next decade of research in the field.
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Affiliation(s)
| | - Iain Mathieson
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19103, USA
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179
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Schlebusch CM, Jakobsson M. Tales of Human Migration, Admixture, and Selection in Africa. Annu Rev Genomics Hum Genet 2018; 19:405-428. [DOI: 10.1146/annurev-genom-083117-021759] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In the last three decades, genetic studies have played an increasingly important role in exploring human history. They have helped to conclusively establish that anatomically modern humans first appeared in Africa roughly 250,000–350,000 years before present and subsequently migrated to other parts of the world. The history of humans in Africa is complex and includes demographic events that influenced patterns of genetic variation across the continent. Through genetic studies, it has become evident that deep African population history is captured by relationships among African hunter–gatherers, as the world's deepest population divergences occur among these groups, and that the deepest population divergence dates to 300,000 years before present. However, the spread of pastoralism and agriculture in the last few thousand years has shaped the geographic distribution of present-day Africans and their genetic diversity. With today's sequencing technologies, we can obtain full genome sequences from diverse sets of extant and prehistoric Africans. The coming years will contribute exciting new insights toward deciphering human evolutionary history in Africa.
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Affiliation(s)
- Carina M. Schlebusch
- Human Evolution, Department of Organismal Biology, Uppsala University, SE-752 36 Uppsala, Sweden;,
- Centre for Anthropological Research and Department of Anthropology and Development Studies, University of Johannesburg, 2006 Johannesburg, South Africa
- SciLifeLab, SE-751 23 Uppsala, Sweden
| | - Mattias Jakobsson
- Human Evolution, Department of Organismal Biology, Uppsala University, SE-752 36 Uppsala, Sweden;,
- Centre for Anthropological Research and Department of Anthropology and Development Studies, University of Johannesburg, 2006 Johannesburg, South Africa
- SciLifeLab, SE-751 23 Uppsala, Sweden
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180
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Archaeogenomic evidence from the southwestern US points to a pre-Hispanic scarlet macaw breeding colony. Proc Natl Acad Sci U S A 2018; 115:8740-8745. [PMID: 30104352 DOI: 10.1073/pnas.1805856115] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Hundreds of scarlet macaw (Ara macao cyanoptera) skeletons have been recovered from archaeological contexts in the southwestern United States and northwestern Mexico (SW/NW). The location of these skeletons, >1,000 km outside their Neotropical endemic range, has suggested a far-reaching pre-Hispanic acquisition network. Clear evidence for scarlet macaw breeding within this network is only known from the settlement of Paquimé in NW dating between 1250 and 1450 CE. Although some scholars have speculated on the probable existence of earlier breeding centers in the SW/NW region, there has been no supporting evidence. In this study, we performed an ancient DNA analysis of scarlet macaws recovered from archaeological sites in Chaco Canyon and the contemporaneous Mimbres area of New Mexico. All samples were directly radiocarbon dated between 900 and 1200 CE. We reconstructed complete or near-complete mitochondrial genome sequences of 14 scarlet macaws from five different sites. We observed remarkably low genetic diversity in this sample, consistent with breeding of a small founder population translocated outside their natural range. Phylogeographic comparisons of our ancient DNA mitogenomes with mitochondrial sequences from macaws collected during the last 200 years from their endemic Neotropical range identified genetic affinity between the ancient macaws and a single rare haplogroup (Haplo6) observed only among wild macaws in Mexico and northern Guatemala. Our results suggest that people at an undiscovered pre-Hispanic settlement dating between 900 and 1200 CE managed a macaw breeding colony outside their endemic range and distributed these symbolically important birds through the SW.
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181
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Ancient DNA from Chalcolithic Israel reveals the role of population mixture in cultural transformation. Nat Commun 2018; 9:3336. [PMID: 30127404 PMCID: PMC6102297 DOI: 10.1038/s41467-018-05649-9] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 06/29/2018] [Indexed: 02/01/2023] Open
Abstract
The material culture of the Late Chalcolithic period in the southern Levant (4500–3900/3800 BCE) is qualitatively distinct from previous and subsequent periods. Here, to test the hypothesis that the advent and decline of this culture was influenced by movements of people, we generated genome-wide ancient DNA from 22 individuals from Peqi’in Cave, Israel. These individuals were part of a homogeneous population that can be modeled as deriving ~57% of its ancestry from groups related to those of the local Levant Neolithic, ~17% from groups related to those of the Iran Chalcolithic, and ~26% from groups related to those of the Anatolian Neolithic. The Peqi’in population also appears to have contributed differently to later Bronze Age groups, one of which we show cannot plausibly have descended from the same population as that of Peqi’in Cave. These results provide an example of how population movements propelled cultural changes in the deep past. The Late Chalcolithic material culture in the southern Levant has unique attributes that suggest spread of people or culture. Here, the authors use genome-wide ancient DNA data from 22 individuals from a Chalcolithic site and show evidence of complex population movements and turnovers.
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182
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Larmuseau MHD, Ottoni C. Mediterranean Y-chromosome 2.0-why the Y in the Mediterranean is still relevant in the postgenomic era. Ann Hum Biol 2018; 45:20-33. [PMID: 29382278 DOI: 10.1080/03014460.2017.1402956] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
CONTEXT Due to its unique paternal inheritance, the Y-chromosome has been a highly popular marker among population geneticists for over two decades. Recently, the advent of cost-effective genome-wide methods has unlocked information-rich autosomal genomic data, paving the way to the postgenomic era. This seems to have announced the decreasing popularity of investigating Y-chromosome variation, which provides only the paternal perspective of human ancestries and is strongly influenced by genetic drift and social behaviour. OBJECTIVE For this special issue on population genetics of the Mediterranean, the aim was to demonstrate that the Y-chromosome still provides important insights in the postgenomic era and in a time when ancient genomes are becoming exponentially available. METHODS A systematic literature search on Y-chromosomal studies in the Mediterranean was performed. RESULTS Several applications of Y-chromosomal analysis with future opportunities are formulated and illustrated with studies on Mediterranean populations. CONCLUSIONS There will be no reduced interest in Y-chromosomal studies going from reconstruction of male-specific demographic events to ancient DNA applications, surname history and population-wide estimations of extra-pair paternity rates. Moreover, more initiatives are required to collect population genetic data of Y-chromosomal markers for forensic research, and to include Y-chromosomal data in GWAS investigations and studies on male infertility.
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Affiliation(s)
- Maarten H D Larmuseau
- a KU Leuven, Forensic Biomedical Sciences , Department of Imaging & Pathology , Leuven , Belgium.,b KU Leuven, Laboratory of Socioecology and Social Evolution , Department of Biology , Leuven , Belgium
| | - Claudio Ottoni
- c Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences , University of Oslo , Oslo , Norway
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183
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Choudhury A, Aron S, Sengupta D, Hazelhurst S, Ramsay M. African genetic diversity provides novel insights into evolutionary history and local adaptations. Hum Mol Genet 2018; 27:R209-R218. [PMID: 29741686 PMCID: PMC6061870 DOI: 10.1093/hmg/ddy161] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 04/27/2018] [Accepted: 04/27/2018] [Indexed: 12/22/2022] Open
Abstract
Genetic variation and susceptibility to disease are shaped by human demographic history and adaptation. We can now study the genomes of extant Africans and uncover traces of population migration, admixture, assimilation and selection by applying sophisticated computational algorithms. There are four major ethnolinguistic divisions among present day Africans: Hunter-gatherer populations in southern and central Africa; Nilo-Saharan speakers from north and northeast Africa; Afro-Asiatic speakers from north and east Africa; and Niger-Congo speakers who are the predominant ethnolinguistic group spread across most of sub-Saharan Africa. The enormous ethnolinguistic diversity in sub-Saharan African populations is largely paralleled by extensive genetic diversity and until a decade ago, little was known about detailed origins and divergence of these groups. Results from large-scale population genetic studies, and more recently whole genome sequence data, are unravelling the critical role of events like migration and admixture and environmental factors including diet, infectious diseases and climatic conditions in shaping current population diversity. It is now possible to start providing quantitative estimates of divergence times, population size and dynamic processes that have affected populations and their genetic risk for disease. Finally, the availability of ancient genomes from Africa provides historical insights of unprecedented depth. In this review, we highlight some key interpretations that have emerged from recent African genome studies.
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Affiliation(s)
- Ananyo Choudhury
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Shaun Aron
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Dhriti Sengupta
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Scott Hazelhurst
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- School of Electrical & Information Engineering, University of the Witwatersrand, Johannesburg, South Africa
| | - Michèle Ramsay
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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184
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Willoughby PR, Compton T, Bello SM, Bushozi PM, Skinner AR, Stringer CB. Middle Stone Age human teeth from Magubike rockshelter, Iringa Region, Tanzania. PLoS One 2018; 13:e0200530. [PMID: 30063742 PMCID: PMC6067719 DOI: 10.1371/journal.pone.0200530] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 06/28/2018] [Indexed: 11/18/2022] Open
Abstract
In 2006, six isolated hominin teeth were excavated from Middle Stone Age (MSA) deposits at the Magubike rockshelter in southern Tanzania. They comprise two central incisors, one lateral incisor, one canine, one third premolar, and one fourth premolar. All are fully developed and come from the maxilla. None of the teeth are duplicated, so they may represent a single individual. While there is some evidence of post-depositional alteration, the morphology of these teeth clearly shares features with anatomically modern Homo sapiens. Both metric and non-metric traits are compared to those from other African and non-African dental remains. The degree of biological relatedness between eastern and southern African Stone Age hunter-gatherers has long been a subject of interest, and several characteristics of the Magubike teeth resemble those of the San of southern Africa. Another notable feature is that the three incisors are marked on the labial crown by scratches that are much coarser than microwear striations. These non-masticatory scratches on the Magubike teeth suggest that the use of the front teeth as tools included regularly repeated activities undertaken throughout the life of the individual. The exact age of these teeth is not clear as ESR and radiocarbon dates on associated snail shells give varying results, but a conservative estimate of their minimum age is 45,000 years.
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Affiliation(s)
| | - Tim Compton
- Department of Earth Sciences, Natural History Museum, London, United Kingdom
| | - Silvia M. Bello
- Department of Earth Sciences, Natural History Museum, London, United Kingdom
| | - Pastory M. Bushozi
- Department of History and Archaeology, College of Humanities, University of Dar es Salaam, Dar es Salaam, Tanzania
| | - Anne R. Skinner
- Department of Chemistry, Williams College, Williamstown, Massachusetts, United States of America
| | - Chris B. Stringer
- Department of Earth Sciences, Natural History Museum, London, United Kingdom
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185
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Did Our Species Evolve in Subdivided Populations across Africa, and Why Does It Matter? Trends Ecol Evol 2018; 33:582-594. [PMID: 30007846 PMCID: PMC6092560 DOI: 10.1016/j.tree.2018.05.005] [Citation(s) in RCA: 130] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 05/15/2018] [Accepted: 05/17/2018] [Indexed: 01/27/2023]
Abstract
We challenge the view that our species, Homo sapiens, evolved within a single population and/or region of Africa. The chronology and physical diversity of Pleistocene human fossils suggest that morphologically varied populations pertaining to the H. sapiens clade lived throughout Africa. Similarly, the African archaeological record demonstrates the polycentric origin and persistence of regionally distinct Pleistocene material culture in a variety of paleoecological settings. Genetic studies also indicate that present-day population structure within Africa extends to deep times, paralleling a paleoenvironmental record of shifting and fractured habitable zones. We argue that these fields support an emerging view of a highly structured African prehistory that should be considered in human evolutionary inferences, prompting new interpretations, questions, and interdisciplinary research directions. The view that Homo sapiens evolved from a single region/population within Africa has been given primacy in studies of human evolution. However, developments across multiple fields show that relevant data are no longer consistent with this view. We argue instead that Homo sapiens evolved within a set of interlinked groups living across Africa, whose connectivity changed through time. Genetic models therefore need to incorporate a more complex view of ancient migration and divergence in Africa. We summarize this new framework emphasizing population structure, outline how this changes our understanding of human evolution, and identify new research directions.
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186
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Gokcumen O. The Year In Genetic Anthropology: New Lands, New Technologies, New Questions. AMERICAN ANTHROPOLOGIST 2018. [DOI: 10.1111/aman.13032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Omer Gokcumen
- Department of Biological Sciences University of Buffalo NY 14260 USA
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187
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van de Loosdrecht M, Bouzouggar A, Humphrey L, Posth C, Barton N, Aximu-Petri A, Nickel B, Nagel S, Talbi EH, El Hajraoui MA, Amzazi S, Hublin JJ, Pääbo S, Schiffels S, Meyer M, Haak W, Jeong C, Krause J. Pleistocene North African genomes link Near Eastern and sub-Saharan African human populations. Science 2018; 360:548-552. [PMID: 29545507 DOI: 10.1126/science.aar8380] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 02/28/2018] [Indexed: 12/22/2022]
Abstract
North Africa is a key region for understanding human history, but the genetic history of its people is largely unknown. We present genomic data from seven 15,000-year-old modern humans, attributed to the Iberomaurusian culture, from Morocco. We find a genetic affinity with early Holocene Near Easterners, best represented by Levantine Natufians, suggesting a pre-agricultural connection between Africa and the Near East. We do not find evidence for gene flow from Paleolithic Europeans to Late Pleistocene North Africans. The Taforalt individuals derive one-third of their ancestry from sub-Saharan Africans, best approximated by a mixture of genetic components preserved in present-day West and East Africans. Thus, we provide direct evidence for genetic interactions between modern humans across Africa and Eurasia in the Pleistocene.
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Affiliation(s)
- Marieke van de Loosdrecht
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History (MPI-SHH), Jena, Kahlaische Strasse 10, D-07745, Germany
| | - Abdeljalil Bouzouggar
- Origin and Evolution of Homo sapiens in Morocco Research Group, Institut National des Sciences de l'Archéologie et du Patrimoine, Hay Riad, Madinat Al Irfane, Angle rues 5 et 7, Rabat-Instituts, 10 000 Rabat, Morocco. .,Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology (MPI-EVA), Leipzig, Deutscher Platz 6, D-04103, Germany
| | - Louise Humphrey
- Department of Earth Sciences, The Natural History Museum, London SW7 5BD, UK
| | - Cosimo Posth
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History (MPI-SHH), Jena, Kahlaische Strasse 10, D-07745, Germany
| | - Nick Barton
- Institute of Archaeology, University of Oxford, 36 Beaumont Street, Oxford OX1 2PG, UK
| | - Ayinuer Aximu-Petri
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology (MPI-EVA), Leipzig, Deutscher Platz 6, D-04103, Germany
| | - Birgit Nickel
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology (MPI-EVA), Leipzig, Deutscher Platz 6, D-04103, Germany
| | - Sarah Nagel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology (MPI-EVA), Leipzig, Deutscher Platz 6, D-04103, Germany
| | - El Hassan Talbi
- Faculté des Sciences, Campus d'Al Qods, Université Mohammed Premier, B.P. 717 Oujda, Morocco
| | - Mohammed Abdeljalil El Hajraoui
- Origin and Evolution of Homo sapiens in Morocco Research Group, Institut National des Sciences de l'Archéologie et du Patrimoine, Hay Riad, Madinat Al Irfane, Angle rues 5 et 7, Rabat-Instituts, 10 000 Rabat, Morocco
| | - Saaïd Amzazi
- Mohammed V University, Avenue Ibn Batouta, Rabat, Morocco
| | - Jean-Jacques Hublin
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology (MPI-EVA), Leipzig, Deutscher Platz 6, D-04103, Germany
| | - Svante Pääbo
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology (MPI-EVA), Leipzig, Deutscher Platz 6, D-04103, Germany
| | - Stephan Schiffels
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History (MPI-SHH), Jena, Kahlaische Strasse 10, D-07745, Germany
| | - Matthias Meyer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology (MPI-EVA), Leipzig, Deutscher Platz 6, D-04103, Germany
| | - Wolfgang Haak
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History (MPI-SHH), Jena, Kahlaische Strasse 10, D-07745, Germany
| | - Choongwon Jeong
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History (MPI-SHH), Jena, Kahlaische Strasse 10, D-07745, Germany.
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History (MPI-SHH), Jena, Kahlaische Strasse 10, D-07745, Germany.
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188
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Abstract
The Sahara was once fertile; a recent study identifies human Y-chromosomal lineages that flourished in this Green Sahara and their relation to present-day populations.
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Affiliation(s)
- Yali Xue
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK.
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189
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190
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Loreille O, Ratnayake S, Bazinet AL, Stockwell TB, Sommer DD, Rohland N, Mallick S, Johnson PLF, Skoglund P, Onorato AJ, Bergman NH, Reich D, Irwin JA. Biological Sexing of a 4000-Year-Old Egyptian Mummy Head to Assess the Potential of Nuclear DNA Recovery from the Most Damaged and Limited Forensic Specimens. Genes (Basel) 2018; 9:genes9030135. [PMID: 29494531 PMCID: PMC5867856 DOI: 10.3390/genes9030135] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 02/06/2018] [Accepted: 02/06/2018] [Indexed: 12/17/2022] Open
Abstract
High throughput sequencing (HTS) has been used for a number of years in the field of paleogenomics to facilitate the recovery of small DNA fragments from ancient specimens. Recently, these techniques have also been applied in forensics, where they have been used for the recovery of mitochondrial DNA sequences from samples where traditional PCR-based assays fail because of the very short length of endogenous DNA molecules. Here, we describe the biological sexing of a ~4000-year-old Egyptian mummy using shotgun sequencing and two established methods of biological sex determination (RX and RY), by way of mitochondrial genome analysis as a means of sequence data authentication. This particular case of historical interest increases the potential utility of HTS techniques for forensic purposes by demonstrating that data from the more discriminatory nuclear genome can be recovered from the most damaged specimens, even in cases where mitochondrial DNA cannot be recovered with current PCR-based forensic technologies. Although additional work remains to be done before nuclear DNA recovered via these methods can be used routinely in operational casework for individual identification purposes, these results indicate substantial promise for the retrieval of probative individually identifying DNA data from the most limited and degraded forensic specimens.
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Affiliation(s)
- Odile Loreille
- DNA Support Unit, FBI Laboratory, 2501 Investigation Parkway, Quantico, VA 22135, USA.
| | - Shashikala Ratnayake
- National Biodefense Analysis and Countermeasures Center, 8300 Research Plaza, Fort Detrick, MD 21702, USA.
| | - Adam L Bazinet
- National Biodefense Analysis and Countermeasures Center, 8300 Research Plaza, Fort Detrick, MD 21702, USA.
| | - Timothy B Stockwell
- National Biodefense Analysis and Countermeasures Center, 8300 Research Plaza, Fort Detrick, MD 21702, USA.
| | - Daniel D Sommer
- National Biodefense Analysis and Countermeasures Center, 8300 Research Plaza, Fort Detrick, MD 21702, USA.
| | - Nadin Rohland
- Department of Genetics Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.
| | - Swapan Mallick
- Department of Genetics Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.
| | - Philip L F Johnson
- Department of Biology, University of Maryland, 1210 Biology-Psychology Building, 4094 Campus Drive, College Park, MD 20742, USA.
| | - Pontus Skoglund
- The Francis Crick Institute, 1 Midland Rd, London NW1 1AT, UK.
| | - Anthony J Onorato
- DNA Support Unit, FBI Laboratory, 2501 Investigation Parkway, Quantico, VA 22135, USA.
| | - Nicholas H Bergman
- National Biodefense Analysis and Countermeasures Center, 8300 Research Plaza, Fort Detrick, MD 21702, USA.
| | - David Reich
- Department of Genetics Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA.
| | - Jodi A Irwin
- DNA Support Unit, FBI Laboratory, 2501 Investigation Parkway, Quantico, VA 22135, USA.
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191
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Yang MA, Fu Q. Insights into Modern Human Prehistory Using Ancient Genomes. Trends Genet 2018; 34:184-196. [DOI: 10.1016/j.tig.2017.11.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 11/26/2017] [Accepted: 11/29/2017] [Indexed: 01/05/2023]
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192
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Abstract
The mammalian placenta shows an extraordinary degree of variation in gross and fine structure, but this has been difficult to interpret in physiological terms. Transcriptomics offers a path to understanding how structure relates to function. This essay examines how studies of gene transcription can inform us about placental evolution in eutherian and marsupial mammals and more broadly about convergent evolution of viviparity and placentation in vertebrates. Thus far, the focus has been on the chorioallantoic placenta of eutherians at term, the reproductive strategies of eutherians and marsupials, and the decidual response of the uterus at implantation. Future work should address gene expression during early stages of placental development and endeavor to cover all major groups of mammals. Comparative studies across oviparous and viviparous vertebrates have centered on the chorioallantoic membrane and yolk sac. They point to the possibility of defining a set of genes that can be recruited to support commonalities in reproductive strategies. Further advances can be anticipated from single-cell transcriptomics if those techniques are applied to a range of placental structures and in species other than humans and mice.
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Affiliation(s)
- Anthony M Carter
- Cardiovascular and Renal Research, Institute of Molecular Medicine, University of Southern Denmark, J. B. Winsloews Vej 21, DK-5000 Odense, Denmark
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193
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Putilov AA, Dorokhov VB, Poluektov MG. How have our clocks evolved? Adaptive and demographic history of the out-of-African dispersal told by polymorphic loci in circadian genes. Chronobiol Int 2017; 35:511-532. [DOI: 10.1080/07420528.2017.1417314] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Arcady A. Putilov
- Research Group for Math-Modeling of Biomedical Systems, the Research Institute for Molecular Biology and Biophysics, Novosibirsk, Russia
| | - Vladimir B. Dorokhov
- Laboratory of Sleep/Wake Neurobiology, The Institute of Higher Nervous Activity and Neurophysiology of the Russian Academy of Sciences, Moscow, Russia
| | - Michael G. Poluektov
- Department of Nervous Diseases, Institute of Professional Education, I.M. Sechenov 1-st Moscow State Medical University, Moscow, Russia
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