Southern African ancient genomes estimate modern human divergence to 350,000 to 260,000 years ago

The Sequence Alignment/Map format and SAMtools

Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041

Fast and accurate short read alignment with Burrows-Wheeler transform

Li, H., & Durbin, R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp324 · Cited by 58,607

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella, K., Altshuler, D., Gabriel, S., Daly, M., et al. (2010) · Genome Research · doi:10.1101/gr.107524.110 · Cited by 27,895

A global reference for human genetic variation

The 1000 Genomes Project Consortium, authors, C., Auton, A., Abecasis, G. R., Steering committee, Altshuler, D. M., Durbin, R. M., Abecasis, G. R., Bentley, D. R., Chakravarti, A., et al. (2015) · Nature · doi:10.1038/nature15393 · Cited by 18,247

The variant call format and VCFtools

Danecek, P., Auton, A., Abecasis, G. R., Albers, C. A., Banks, E., DePristo, M. A., Handsaker, R. E., Lunter, G. A., Marth, G., Sherry, S. T., et al. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr330 · Cited by 16,450

Second-generation PLINK: rising to the challenge of larger and richer datasets

Chang, C. C., Chow, C. C., Tellier, L. C., Vattikuti, S., Purcell, S. M., & Lee, J. J. (2015) · Gigascience · doi:10.1186/s13742-015-0047-8 · Cited by 12,709

Fast and accurate long-read alignment with Burrows-Wheeler transform.

Li, H., & Durbin, R. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btp698 · Cited by 12,063

Principal components analysis corrects for stratification in genome-wide association studies

Price, A. L., Patterson, N. J., Plenge, R. M., Weinblatt, M. E., Shadick, N. A., & Reich, D. (2006) · Nature Genetics · doi:10.1038/ng1847 · Cited by 10,248

Fast model-based estimation of ancestry in unrelated individuals

Alexander, D. H., Novembre, J., & Lange, K. (2009) · Genome Research · doi:10.1101/gr.094052.109 · Cited by 9,898

Bayesian Analysis of Radiocarbon Dates

Bronk Ramsey, C. (2009) · Radiocarbon · doi:10.1017/s0033822200033865 · Cited by 8,725

A map of human genome variation from population-scale sequencing.

The 1000 Genomes Project Consortium (2010) · Nature · doi:10.1038/nature09534 · Cited by 7,877

CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure

Jakobsson, M., & Rosenberg, N. A. (2007) · Bioinformatics · doi:10.1093/bioinformatics/btm233 · Cited by 6,309

Population Structure and Eigenanalysis

Patterson, N., Price, A. L., & Reich, D. (2006) · PLoS Genetics · doi:10.1371/journal.pgen.0020190 · Cited by 5,280

distruct : a program for the graphical display of population structure

Rosenberg, N. A. (2003) · Molecular Ecology Notes · doi:10.1046/j.1471-8286.2003.00566.x · Cited by 4,959

Mitochondrial DNA and human evolution

Cann, R. L., Stoneking, M., & Wilson, A. C. (1987) · Nature · doi:10.1038/325031a0 · Cited by 3,100

ANGSD: Analysis of Next Generation Sequencing Data

Korneliussen, T. S., Albrechtsen, A., & Nielsen, R. (2014) · BMC Bioinformatics · doi:10.1186/s12859-014-0356-4 · Cited by 2,982

Ancient Admixture in Human History

Patterson, N., Moorjani, P., Luo, Y., Mallick, S., Rohland, N., Zhan, Y., Genschoreck, T., Webster, T., & Reich, D. (2012) · Genetics · doi:10.1534/genetics.112.145037 · Cited by 2,848

The complete genome sequence of a Neanderthal from the Altai Mountains

Prüfer, K., Racimo, F., Patterson, N., Jay, F., Sankararaman, S., Sawyer, S., Heinze, A., Renaud, G., Sudmant, P. H., de Filippo, C., et al. (2014) · Nature · doi:10.1038/nature12886 · Cited by 2,254

Association of Trypanolytic ApoL1 Variants with Kidney Disease in African Americans

Genovese, G., Friedman, D. J., Ross, M. D., Lecordier, L., Uzureau, P., Freedman, B. I., Bowden, D. W., Langefeld, C. D., Oleksyk, T. K., Uscinski Knob, A. L., et al. (2010) · Science · doi:10.1126/science.1193032 · Cited by 2,028

A high-coverage genome sequence from an archaic denisovan individual

Meyer, M., Kircher, M., Gansauge, M.-T., Li, H., Racimo, F., Mallick, S., Schraiber, J. G., Jay, F., Prüfer, K., de Filippo, C., et al. (2012) · Science · doi:10.1126/science.1224344 · Cited by 1,967

A Fast and Flexible Statistical Model for Large-Scale Population Genotype Data: Applications to Inferring Missing Genotypes and Haplotypic Phase

Scheet, P. A., & Stephens, M. (2006) · The American Journal of Human Genetics · doi:10.1086/502802 · Cited by 1,959

SHCal13 Southern Hemisphere Calibration, 0–50,000 Years cal BP

Hogg, A. G., Hua, Q., Blackwell, P. G., Niu, M., Buck, C. E., Guilderson, T. P., Heaton, T., Palmer, J., Reimer, P. J., Reimer, R., et al. (2013) · Radiocarbon · doi:10.2458/azu_js_rc.55.16783 · Cited by 1,876

Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation

van Oven, M., & Kayser, M. (2009) · Human Mutation · doi:10.1002/humu.20921 · Cited by 1,810

The Simons Genome Diversity Project: 300 genomes from 142 diverse populations

Mallick, S., Li, H., Lipson, M., Mathieson, I., Gymrek, M., Racimo, F., Zhao, M., Chennagiri, N., Nordenfelt, S., Tandon, A., et al. (2016) · Nature · doi:10.1038/nature18964 · Cited by 1,584

Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments

Dabney, J., Knapp, M., Glocke, I., Gansauge, M.-T., Weihmann, A., Nickel, B., Valdiosera, C., García, N., Pääbo, S., Arsuaga, J.-L., et al. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1314445110 · Cited by 1,443

Ancient human genomes suggest three ancestral populations for present-day Europeans

Lazaridis, I., Patterson, N., Mittnik, A., Renaud, G., Mallick, S., Kirsanow, K., Sudmant, P. H., Schraiber, J. G., Castellano, S., Lipson, M., et al. (2014) · Nature · doi:10.1038/nature13673 · Cited by 1,357

New fossils from Jebel Irhoud, Morocco and the pan-African origin of Homo sapiens.

Hublin, J.-J., Ben-Ncer, A., Bailey, S. E., Freidline, S. E., Neubauer, S., Skinner, M. M., Bergmann, I., Le Cabec, A., Benazzi, S., Harvati, K., et al. (2017) · Nature · doi:10.1038/nature22336 · Cited by 1,347

African Populations and the Evolution of Human Mitochondrial DNA

Vigilant, L., Stoneking, M., Harpending, H. C., Hawkes, K., & Wilson, A. C. (1991) · Science · doi:10.1126/science.1840702 · Cited by 1,338

Inferring human population size and separation history from multiple genome sequences

Schiffels, S., & Durbin, R. (2014) · Nature Genetics · doi:10.1038/ng.3015 · Cited by 1,073

Pleistocene Homo sapiens from Middle Awash, Ethiopia

White, T. D., Asfaw, B., DeGusta, D., Gilbert, H., Richards, G. D., Suwa, G., & Clark Howell, F. (2003) · Nature · doi:10.1038/nature01669 · Cited by 1,032

Stratigraphic placement and age of modern humans from Kibish, Ethiopia

McDougall, I., Brown, F. H., & Fleagle, J. G. (2005) · Nature · doi:10.1038/nature03258 · Cited by 1,023

Patterns of damage in genomic DNA sequences from a neandertal

Briggs, A. W., Stenzel, U., Johnson, P. L. F., Green, R. E., Kelso, J., Prüfer, K., Meyer, M., Krause, J., Ronan, M. T., Lachmann, M., et al. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0704665104 · Cited by 981

Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans

Raghavan, M., Skoglund, P., Graf, K. E., Metspalu, M., Albrechtsen, A., Moltke, I., Rasmussen, S., Stafford Jr, T. W., Orlando, L., Metspalu, E., et al. (2014) · Nature · doi:10.1038/nature12736 · Cited by 963

The genetic history of Ice Age Europe

Fu, Q., Posth, C., Hajdinjak, M., Petr, M., Mallick, S., Fernandes, D., Furtwängler, A., Haak, W., Meyer, M., Mittnik, A., et al. (2016) · Nature · doi:10.1038/nature17993 · Cited by 959

RFMix: A Discriminative Modeling Approach for Rapid and Robust Local-Ancestry Inference

Maples, B. K., Gravel, S., Kenny, E. E., & Bustamante, C. D. (2013) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2013.06.020 · Cited by 900

Tracing the peopling of the world through genomics

Nielsen, R., Akey, J. M., Jakobsson, M., Pritchard, J. K., Tishkoff, S., & Willerslev, E. (2017) · Nature · doi:10.1038/nature21347 · Cited by 728

The African Genome Variation Project shapes medical genetics in Africa

Gurdasani, D., Carstensen, T., Ayele, F. T., Pagani, L., Tachmazidou, I., Hatzikotoulas, K., Karthikeyan, S., Iles, L., Pollard, M., Choudhury, A., et al. (2014) · Nature · doi:10.1038/nature13997 · Cited by 659

Revising the human mutation rate: implications for understanding human evolution

Scally, A., & Durbin, R. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3295 · Cited by 610

A Complete Neandertal Mitochondrial Genome Sequence Determined by High-Throughput Sequencing

Green, R. E., Malaspinas, A., Krause, J., Briggs, A. W., Johnson, P. L. F., Uhler, C., Meyer, M., Good, J. M., Maričić, T., Stenzel, U., et al. (2008) · Cell · doi:10.1016/j.cell.2008.06.021 · Cited by 608

Bayesian inference of ancient human demography from individual genome sequences

Gronau, I., Hubisz, M. J., Gulko, B., Danko, C. G., & Siepel, A. C. (2011) · Nature Genetics · doi:10.1038/ng.937 · Cited by 588

A “Copernican” Reassessment of the Human Mitochondrial DNA Tree from its Root

Behar, D. M., van Oven, M., Rosset, S., Metspalu, M., Loogväli, E., Silva, N. M., Kivisild, T., Torroni, A., & Villems, R. (2012) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2012.03.002 · Cited by 538

Modern human origins: progress and prospects

Stringer, C. (2002) · Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences · doi:10.1098/rstb.2001.1057 · Cited by 534 · cited 2×

Origins and Genetic Legacy of Neolithic Farmers and Hunter-Gatherers in Europe

Skoglund, P., Malmström, H., Raghavan, M., Storå, J., Hall, P., Willerslev, E., Gilbert, M. T. P., Götherström, A., & Jakobsson, M. (2012) · Science · doi:10.1126/science.1216304 · Cited by 521

Accurate sex identification of ancient human remains using DNA shotgun sequencing

Skoglund, P., Storå, J., Götherström, A., & Jakobsson, M. (2013) · Journal of Archaeological Science · doi:10.1016/j.jas.2013.07.004 · Cited by 513

Hunter-gatherer genomic diversity suggests a southern African origin for modern humans

Henn, B. M., Gignoux, C. R., Jobin, M., Granka, J. M., Macpherson, J. M., Kidd, J. M., Rodríguez-Botigué, L., Ramachandran, S., Hon, L., Brisbin, A., et al. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1017511108 · Cited by 502

Harvesting the fruit of the human mtDNA tree

Torroni, A., Achilli, A., Macaulay, V. A., Richards, M. B., & Bandelt, H. (2006) · Trends in Genetics · doi:10.1016/j.tig.2006.04.001 · Cited by 501

The Making of the African mtDNA Landscape

Salas, A., Richards, M. B., Fé, T. D. L., Lareu, M. V., Sobrino, B., Sánchez‐Diz, P., Macaulay, V. A., & Carracedo, Á. (2002) · The American Journal of Human Genetics · doi:10.1086/344348 · Cited by 493

Temporal patterns of nucleotide misincorporations and DNA fragmentation in ancient DNA

Sawyer, S., Krause, J., Guschanski, K., Savolainen, V., & Pääbo, S. (2012) · PLoS ONE · doi:10.1371/journal.pone.0034131 · Cited by 489

A recent bottleneck of Y chromosome diversity coincides with a global change in culturePreprint

Karmin, M., Saag, L., Vicente, M., Sayres, M. A. W., Järve, M., Talas, U. G., Rootsi, S., Ilumäe, A.-M., Mägi, R., Mitt, M., et al. (2015) · Genome Research · doi:10.1101/gr.186684.114 · Cited by 480

Genomic Variation in Seven Khoe-San Groups Reveals Adaptation and Complex African History

Schlebusch, C. M., Skoglund, P., Sjödin, P., Gattepaille, L. M., Hernandez, D. G., Jay, F., Li, S., de Jongh, M., Singleton, A., Blum, M. G. B., et al. (2012) · Science · doi:10.1126/science.1227721 · Cited by 463

The Dawn of Human Matrilineal Diversity

Behar, D. M., Villems, R., Soodyall, H., Blue-Smith, J., Pereira, L., Metspalu, E., Scozzari, R., Makkan, H., Tzur, S., Comas, D., et al. (2008) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2008.04.002 · Cited by 461

Genomic insights into the peopling of the Southwest Pacific

Skoglund, P., Posth, C., Sirak, K., Spriggs, M., Valentin, F., Bedford, S., Clark, G. R., Reepmeyer, C., Petchey, F., Fernandes, D., et al. (2016) · Nature · doi:10.1038/nature19844 · Cited by 414

The global distribution of the Duffy blood group

Howes, R. E., Patil, A. P., Piel, F. B., Nyangiri, O. A., Kabaria, C. W., Gething, P. W., Zimmerman, P. A., Barnadas, C., Beall, C. M., Gebremedhin, A., et al. (2011) · Nature Communications · doi:10.1038/ncomms1265 · Cited by 403

Going global by adapting local: A review of recent human adaptation

Fan, S., Hansen, M. E. B., Lo, Y., & Tishkoff, S. A. (2016) · Science · doi:10.1126/science.aaf5098 · Cited by 387

Genomic Diversity and Admixture Differs for Stone-Age Scandinavian Foragers and Farmers

Skoglund, P., Malmström, H., Omrak, A., Raghavan, M., Valdiosera, C. E., Günther, T., Hall, P. N., Tambets, K., Parik, J., Sjögren, K.-G., et al. (2014) · Science · doi:10.1126/science.1253448 · Cited by 380

Hunters and Herders of Southern Africa

Barnard, A. (1992) · Cambridge University Press eBooks · doi:10.1017/cbo9781139166508 · Cited by 354

The genetic prehistory of southern Africa

Pickrell, J. K., Patterson, N. J., Barbieri, C., Berthold, F., Gerlach, L., Güldemann, T., Kure, B., Mpoloka, S. W., Nakagawa, H., Naumann, C., et al. (2012) · Nature Communications · doi:10.1038/ncomms2140 · Cited by 351

Evolutionary History and Adaptation from High-Coverage Whole-Genome Sequences of Diverse African Hunter-Gatherers

Lachance, J., Vernot, B., Elbers, C. C., Ferwerda, B., Froment, A., Bodo, J.-M., Lema, G., Fu, W., Nyambo, T., Rebbeck, T. R., et al. (2012) · Cell · doi:10.1016/j.cell.2012.07.009 · Cited by 343

Estimating genetic kin relationships in prehistoric populations

Monroy Kuhn, J. M., Jakobsson, M., & Günther, T. (2018) · PLOS ONE · doi:10.1371/journal.pone.0195491 · Cited by 330

On the importance of being structured: instantaneous coalescence rates and human evolution—lessons for ancestral population size inference?

Mazet, O., Rodríguez, W., Grusea, S., Boitard, S., & Chikhi, L. (2015) · Heredity · doi:10.1038/hdy.2015.104 · Cited by 325

Genetic evidence for archaic admixture in Africa

Hammer, M. F., Woerner, A. E., Mendez, F. L., Watkins, J. C., & Wall, J. D. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1109300108 · Cited by 316

Hunters and Herders of Southern Africa. A Comparative Ethnography of the Khoisan Peoples

Klinghardt, G. P., & Barnard, A. (1993) · The South African Archaeological Bulletin · doi:10.2307/3888880 · Cited by 303

Ancient west Eurasian ancestry in southern and eastern Africa

Pickrell, J. K., Patterson, N., Loh, P.-R., Lipson, M., Berger, B., Stoneking, M., Pakendorf, B., & Reich, D. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1313787111 · Cited by 300

Ancient Ethiopian genome reveals extensive Eurasian admixture in Eastern Africa

Gallego-Llorente, M., Jones, E. R., Eriksson, A., Siska, V., Arthur, K. W., Arthur, J. W., Curtis, M. C., Stock, J. T., Coltorti, M., Pieruccini, P., et al. (2015) · Science · doi:10.1126/science.aad2879 · Cited by 296

Dispersals and genetic adaptation of Bantu-speaking populations in Africa and North America

Patin, É., Lopez, M., Grollemund, R., Verdu, P., Harmant, C., Quach, H., Laval, G., Perry, G. H., Barreiro, L. B., Froment, A., et al. (2017) · Science · doi:10.1126/science.aal1988 · Cited by 284

Ancient genomes link early farmers from Atapuerca in Spain to modern-day Basques

Günther, T., Valdiosera, C., Malmström, H., Ureña, I., Rodriguez-Varela, R., Sverrisdóttir, Ó. O., Daskalaki, E. A., Skoglund, P., Naidoo, T., Svensson, E. M., et al. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1509851112 · Cited by 278

History of Click-Speaking Populations of Africa Inferred from mtDNA and Y Chromosome Genetic Variation

Tishkoff, S. A., Gonder, M. K., Henn, B. M., Mortensen, H. M., Knight, A., Gignoux, C. R., Fernandopulle, N. D., Lema, G., Nyambo, T., Ramakrishnan, U., et al. (2007) · Molecular Biology and Evolution · doi:10.1093/molbev/msm155 · Cited by 276

Direct dating of Florisbad hominid

Grün, R., Brink, J. S., Spooner, N. A., Taylor, L., Stringer, C. B., Franciscus, R. G., & Murray, A. S. (1996) · Nature · doi:10.1038/382500a0 · Cited by 270

The Expansion of mtDNA Haplogroup L3 within and out of Africa

Soares, P. A., Alshamali, F., Pereira, J. B., Fernandes, V., Silva, N. M., Afonso, C., Costa, M. D., Musilová, E., Macaulay, V. A., Richards, M. B., et al. (2011) · Molecular Biology and Evolution · doi:10.1093/molbev/msr245 · Cited by 254

Genetic variation reveals large-scale population expansion and migration during the expansion of Bantu-speaking peoples

Li, S., Schlebusch, C. M., & Jakobsson, M. (2014) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2014.1448 · Cited by 246

Analysis of High-Throughput Ancient DNA Sequencing Data

Kircher, M. (2012) · Methods in Molecular Biology · doi:10.1007/978-1-61779-516-9_23 · Cited by 236

Ethiopian Genetic Diversity Reveals Linguistic Stratification and Complex Influences on the Ethiopian Gene Pool

Pagani, L., Kivisild, T., Tarekegn, A., Ekong, R., Plaster, C., Gallego Romero, I., Ayub, Q., Mehdi, S. Q., Thomas, M. G., Luiselli, D., et al. (2012) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2012.05.015 · Cited by 230

mtDNA Variation in the South African Kung and Khwe—and Their Genetic Relationships to Other African Populations

Chen, Y., Olckers, A., Schurr, T. G., Kogelnik, A. M., Huoponen, K., & Wallace, D. C. (2000) · The American Journal of Human Genetics · doi:10.1086/302848 · Cited by 227

Human pigmentation genes under environmental selection

Sturm, R. A., & Duffy, D. L. (2012) · Genome Biology · doi:10.1186/gb-2012-13-9-248 · Cited by 182

Seeing the Wood for the Trees: A Minimal Reference Phylogeny for the Human Y Chromosome

van Oven, M., Geystelen, A. V., Kayser, M., Decorte, R., & Larmuseau, M. (2013) · Human Mutation · doi:10.1002/humu.22468 · Cited by 169

Lactase Persistence Alleles Reveal Partial East African Ancestry of Southern African Khoe Pastoralists

Breton, G., Schlebusch, C. M., Lombard, M., Sjödin, P., Soodyall, H., & Jakobsson, M. (2014) · Current Biology · doi:10.1016/j.cub.2014.02.041 · Cited by 162

Genetic Architecture of Skin and Eye Color in an African-European Admixed Population

Beleza, S., Johnson, N. A., Candille, S. I., Absher, D. M., Coram, M. A., Lopes, J., Campos, J., Araújo, I. I., Anderson, T. M., Vilhjálmsson, B. J., et al. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003372 · Cited by 161

HAPLOFIND: A New Method for High-Throughput mtDNA Haplogroup Assignment

Vianello, D., Sevini, F., Castellani, G., Lomartire, L., Capri, M., & Franceschi, C. (2013) · Human Mutation · doi:10.1002/humu.22356 · Cited by 149

Unraveling the complex maternal history of Southern African Khoisan populations

Barbieri, C., Güldemann, T., Naumann, C., Gerlach, L., Berthold, F., Nakagawa, H., Mpoloka, S. W., Stoneking, M., & Pakendorf, B. (2013) · American Journal of Physical Anthropology · doi:10.1002/ajpa.22441 · Cited by 131

More on Contamination: The Use of Asymmetric Molecular Behavior to Identify Authentic Ancient Human DNA

Malmström, H., Svensson, E., Gilbert, M. T. P., Willerslev, E., Götherström, A., & Holmlund, G. (2007) · Molecular Biology and Evolution · doi:10.1093/molbev/msm015 · Cited by 125

MtDNA control region variation affirms diversity and deep sub-structure in populations from southern Africa

Schlebusch, C. M., Lombard, M., & Soodyall, H. (2013) · BMC Evolutionary Biology · doi:10.1186/1471-2148-13-56 · Cited by 123

Homo naledi and Pleistocene hominin evolution in subequatorial Africa

Berger, L. R., Hawks, J. D., Dirks, P. H. G. M., Elliott, M., & Roberts, E. M. (2017) · eLife · doi:10.7554/elife.24234 · Cited by 122

Population genetic analysis of the DARC locus (Duffy) reveals adaptation from standing variation associated with malaria resistance in humans

McManus, K. F., Oill, A. M. T., Henn, B. M., Bustamante, C. D., Sikora, M., & Cornejo, O. E. (2017) · PLoS Genetics · doi:10.1371/journal.pgen.1006560 · Cited by 116

Genotype–phenotype associations and human eye color

White, D., & Rabago-Smith, M. (2010) · Journal of Human Genetics · doi:10.1038/jhg.2010.126 · Cited by 109

Khoisan hunter-gatherers have been the largest population throughout most of modern-human demographic history

Kim, H. L., Ratan, A., Perry, G. H., Montenegro, Á., Miller, W., & Schuster, S. C. (2014) · Nature Communications · doi:10.1038/ncomms6692 · Cited by 98

Phylogeography of the human mitochondrial haplogroup L3e: a snapshot of African prehistory and Atlantic slave trade

Bandelt, H. J., Alves‐Silva, J., Guimarães, P. E. M., Santos, M., Brehm, A., Pereira, L., Coppa, A., Larruga, J. M., Rengo, C., Scozzari, R., et al. (2001) · Annals of Human Genetics · doi:10.1046/j.1469-1809.2001.6560549.x · Cited by 93

The study of human Y chromosome variation through ancient DNA

Kivisild, T. (2017) · Human Genetics · doi:10.1007/s00439-017-1773-z · Cited by 91

Refining the Y chromosome phylogeny with southern African sequences

Barbieri, C., Hübner, A., Macholdt, E., Ni, S., Lippold, S., Schröder, R., Mpoloka, S. W., Purps, J., Roewer, L., Stoneking, M., et al. (2016) · Human Genetics · doi:10.1007/s00439-016-1651-0 · Cited by 86

Different contributions of ancient mitochondrial and Y-chromosomal lineages in ‘Karretjie people’ of the Great Karoo in South Africa

Schlebusch, C. M., de Jongh, M., & Soodyall, H. (2011) · Journal of Human Genetics · doi:10.1038/jhg.2011.71 · Cited by 86

Phylogeography of the human mitochondrial haplogroup L3e: a snapshot of African prehistory and Atlantic slave trade.

Bandelt, H.-J., Alves‐Silva, J., Guimarães, P. E. M., Santos, M., Brehm, A., Pereira, L., Coppa, A., Larruga, J. M., Rengo, C., Scozzari, R., et al. (2001) · PubMed · doi:10.1017/s0003480001008892 · Cited by 79

Estimation of Population Divergence Times from Non-Overlapping Genomic Sequences: Examples from Dogs and Wolves

Skoglund, P., Götherström, A., & Jakobsson, M. (2010) · Molecular Biology and Evolution · doi:10.1093/molbev/msq342 · Cited by 75

Pleistocene Homo and the updated Stone Age sequence of South Africa

Dusseldorp, G. L., Lombard, M., & Wurz, S. (2013) · South African Journal of Science · doi:10.1590/sajs.2013/20120042 · Cited by 70

Preparation of Next-Generation Sequencing Libraries from Damaged DNA

Briggs, A. W., & Heyn, P. C. (2011) · Methods in molecular biology · doi:10.1007/978-1-61779-516-9_18 · Cited by 61

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Naidoo, T., Schlebusch, C. M., Makkan, H., Patel, P., Mahabeer, R., Erasmus, J. C., & Soodyall, H. (2010) · Investigative Genetics · doi:10.1186/2041-2223-1-6 · Cited by 52

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Morris, A. G., Heinze, A., Chan, E. K. F., Smith, A. B., & Hayes, V. M. (2014) · Genome Biology and Evolution · doi:10.1093/gbe/evu202 · Cited by 50

Evidence for Site-Specific Occupancy of the Mitochondrial Genome by Nuclear Transcription Factors

Marinov, G. K., Wang, Y. E., Chan, D. C., & Wold, B. J. (2014) · PLoS ONE · doi:10.1371/journal.pone.0084713 · Cited by 43

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Mazel, A. D. (2009) · Newcastle University ePrints (Newcastle Univesity) · doi:10.25405/ncl.34119201 · Cited by 38

‘ What is consumed is wasted’: from foraging to herding in the southern African Later Stone Age

Russell, T., & Lander, F. (2015) · Azania Archaeological Research in Africa · doi:10.1080/0067270x.2015.1079082 · Cited by 35

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Chan, E. K. F., Hardie, R., Petersen, D. C., Beeson, K. Y., Bornman, R. M. S., Smith, A. B., & Hayes, V. M. (2015) · PLoS ONE · doi:10.1371/journal.pone.0121223 · Cited by 34

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Schlebusch, C. M., Prins, F. E., Lombard, M., Jakobsson, M., & Soodyall, H. (2016) · Human Genetics · doi:10.1007/s00439-016-1729-8 · Cited by 29

Rock art sequences in uKhahlamba-Drakensberg Park, South Africa

Swart, J. (2004) · Cited by 27

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Bedu‐Addo, G., Meese, S., & Mockenhaupt, F. P. (2013) · The Journal of Infectious Diseases · doi:10.1093/infdis/jit070 · Cited by 26

Population history and economic change in the last 2000 years in KwaZulu-Natal, RSA

Ribot, I., Morris, A. G., Sealy, J. C., & Maggs, T. (2016) · Cited by 20

Two disparate instances of healed cranial trauma from the later stone age of South Africa

Pfeiffer, S. (2012) · The South African Archaeological Bulletin · Cited by 13

Untitled work

Yang, D. Y. (1998) · doi:10.1002/(sici)1096-8644(199804)105:4

Pliocene and Eocene provide best analogs for near-future climates

Burke, K. D., Williams, J. W., Chandler, M. A., Haywood, A. M., Lunt, D. J., & Otto-Bliesner, B. L. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1809600115 · Cited by 624

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Scerri, E. M. L., Thomas, M., Manica, A., Gunz, P., Stock, J. T., Stringer, C. B., Grove, M. L., Groucutt, H. S., Timmermann, A., Rightmire, G. P., et al. (2018) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2018.05.005 · Cited by 514

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Schlebusch, C. M., Malmström, H., Günther, T., Sjödin, P., Coutinho, A., Edlund, H., Munters, A. R., Steyn, M., Soodyall, H., Lombard, M., et al. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/145409 · Cited by 25

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Zahn, L. M. (2017) · Science · doi:10.1126/science.358.6363.604-s

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Pickrell, J. K., Patterson, N. J., Barbieri, C., Berthold, F., Gerlach, L., Güldemann, T., Kure, B., Mpoloka, S. W., Nakagawa, H., Naumann, C., et al. (2012) · Nature Communications · doi:10.1038/ncomms2140 · Cited by 351