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A Revised Timescale for Human Evolution Based on Ancient Mitochondrial Genomes
Open accessAbstract
Background Recent analyses of de novo DNA mutations in modern humans have suggested a nuclear substitution rate that is approximately half that of previous estimates based on fossil calibration. This result has led to suggestions that major events in human evolution occurred far earlier than previously thought.Results Here, we use mitochondrial genome sequences from ten securely dated ancient modern humans spanning 40,000 years as calibration points for the mitochondrial clock, thus yielding a direct estimate of the mitochondrial substitution rate. Our clock yields mitochondrial divergence times that are in agreement with earlier estimates based on calibration points derived from either fossils or archaeological material. In particular, our results imply a separation of non-Africans from the most closely related sub-Saharan African mitochondrial DNAs (haplogroup L3) that occurred less than 62-95 kya.Conclusions Though single loci like mitochondrial DNA (mtDNA) can only provide biased estimates of population divergence times, they can provide valid upper bounds. Our results exclude most of the older dates for African and non-African population divergences recently suggested by de novo mutation rate estimates in the nuclear genome.
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“The mtDNA data provided a contamination estimate with a 95% credibility interval of 0.15%–0.38%18 (SI9).”
From The genome of a Late Pleistocene human from a Clovis burial site in western Montana (2014) · cites this paper as [18]
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Citations
Cites
MUSCLE: multiple sequence alignment with high accuracy and high throughput
Edgar, R. C. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh340 · Cited by 44,662
Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., & Kumar, S. (2011) · Molecular Biology and Evolution · doi:10.1093/molbev/msr121 · Cited by 40,207
BEAST: Bayesian evolutionary analysis by sampling trees
Drummond, A. J., & Rambaut, A. (2007) · BMC Evolutionary Biology · doi:10.1186/1471-2148-7-214 · Cited by 13,104
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
Rate of de novo mutations and the importance of father’s age to disease risk
Kong, A., Frigge, M. L., Masson, G., Besenbacher, S., Sulem, P., Magnusson, G., Gudjonsson, S. A., Sigurdsson, A., Jonasdottir, A., Jonasdottir, A., et al. (2012) · Nature · doi:10.1038/nature11396 · Cited by 2,134
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
Self-citationUpdated 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
Mitochondrial genome variation and the origin of modern humans
Ingman, M., Kaessmann, H., Pääbo, S., & Gyllensten, U. B. (2000) · Nature · doi:10.1038/35047064 · Cited by 1,546
Self-citationAnalysis of Genetic Inheritance in a Family Quartet by Whole-Genome Sequencing
Roach, J. C., Glusman, G., Smit, A. F. A., Huff, C. D., Hubley, R., Shannon, P. T., Rowen, L., Pant, K. P., Goodman, N., Bamshad, M., et al. (2010) · Science · doi:10.1126/science.1186802 · Cited by 1,084
Natural selection shaped regional mtDNA variation in humans
Mishmar, D., Ruiz‐Pesini, E., Golik, P., Macaulay, V. A., Clark, A. G., Hosseini, S., Brandon, M., Easley, K. A., Chen, E., Brown, M. D., et al. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0136972100 · Cited by 1,040
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
Self-citationThe complete mitochondrial DNA genome of an unknown hominin from southern Siberia
Krause, J., Fu, Q., Good, J. M., Viola, B., Shunkov, M. V., Derevianko, A. P., & Pääbo, S. (2010) · Nature · doi:10.1038/nature08976 · Cited by 818
Self-citationCorrecting for Purifying Selection: An Improved Human Mitochondrial Molecular Clock
Soares, P. A., Ermini, L., Thomson, N., Mormina, M., Rito, T., Röhl, A., Salas, A., Oppenheimer, S., Macaulay, V. A., & Richards, M. B. (2009) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2009.05.001 · Cited by 729
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
Self-citationDNA analysis of an early modern human from Tianyuan Cave, China
Fu, Q., Meyer, M., Gao, X., Stenzel, U., Burbano, H. A., Kelso, J., & Pääbo, S. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1221359110 · Cited by 608 · cited 6×
“Tianyuan 1301 [29] a 39,475 6 645 BA-03222 16,559 (99.”
InfluentialSelf-citationTargeted Retrieval and Analysis of Five Neandertal mtDNA Genomes
Briggs, A. W., Good, J. M., Green, R. E., Krause, J., Maričić, T., Stenzel, U., Lalueza‐Fox, C., Rudan, P., Brajković, D., Kućan, Ž., et al. (2009) · Science · doi:10.1126/science.1174462 · Cited by 508
Self-citationFenner, J. N. (2005) · American Journal of Physical Anthropology · doi:10.1002/ajpa.20188 · Cited by 508
Genetic Discontinuity Between Local Hunter-Gatherers and Central Europe’s First Farmers
Bramanti, B., Thomas, M. G., Haak, W., Unterlaender, M., Jores, P., Tambets, K., Antanaitis-Jacobs, I., Haidle, M. N., Jankauskas, R., Kind, C.-J., et al. (2009) · Science · doi:10.1126/science.1176869 · Cited by 504
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
Self-citationPhylogeography of mitochondrial DNA in western Europe
Richards, M. B., Macaulay, V. A., Bandelt, H. J., & Sykes, B. C. (1998) · Annals of Human Genetics · doi:10.1046/j.1469-1809.1998.6230241.x · Cited by 419
A direct characterization of human mutation based on microsatellites
Sun, J. X., Helgason, A., Másson, G., Ebenesersdóttir, S. S., Li, H., Mallick, S., Gnerre, S., Patterson, N. J., Kong, A., Reich, D., et al. (2012) · Nature Genetics · doi:10.1038/ng.2398 · Cited by 348
Self-citationThe evolutionary context of the first hominins
Wood, B. A., & Harrison, T. (2011) · Nature · doi:10.1038/nature09709 · Cited by 329
Using MODELTEST and PAUP * to Select a Model of Nucleotide Substitution
Posada, D. (2003) · Current Protocols in Bioinformatics · doi:10.1002/0471250953.bi0605s00 · Cited by 306
A Complete mtDNA Genome of an Early Modern Human from Kostenki, Russia
Krause, J., Briggs, A. W., Kircher, M., Maricic, T., Zwyns, N., Derevianko, A., & Pääbo, S. (2010) · Current Biology · doi:10.1016/j.cub.2009.11.068 · Cited by 259
Self-citationDirect Measure of the De Novo Mutation Rate in Autism and Schizophrenia Cohorts
Awadalla, P., Gauthier, J., Myers, R. A., Casals, F., Hamdan, F. F., Griffing, A. R., Côté, M., Henrion, É., Spiegelman, D., Tarabeux, J., et al. (2010) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2010.07.019 · Cited by 243
Paleo-Eskimo mtDNA Genome Reveals Matrilineal Discontinuity in Greenland
Gilbert, M. T. P., Kivisild, T., Grønnow, B., Andersen, P. K., Metspalu, E., Reidla, M., Tamm, E., Axelsson, E., Götherström, A., Campos, P. F., et al. (2008) · Science · doi:10.1126/science.1159750 · Cited by 220
Learning about human population history from ancient and modern genomes
Stoneking, M., & Krause, J. (2011) · Nature Reviews Genetics · doi:10.1038/nrg3029 · Cited by 215
Self-citationHobolth, A., Dutheil, J. Y., Hawks, J. D., Schierup, M. H., & Mailund, T. (2011) · Genome Research · doi:10.1101/gr.114751.110 · Cited by 213
The neandertal genome and ancient DNA authenticity
Green, R. E., Briggs, A. W., Krause, J., Prüfer, K., Burbano, H. A., Siebauer, M., Lachmann, M., & Pääbo, S. (2009) · The EMBO Journal · doi:10.1038/emboj.2009.222 · Cited by 190
Self-citationThe relationships of Sivapithecus and Ramapithecus and the evolution of the orang-utan
Andrews, P., & Cronin, J. E. (1982) · Nature · doi:10.1038/297541a0 · Cited by 181
Complete Mitochondrial Genome Sequence of the Tyrolean Iceman
Ermini, L., Olivieri, C., Rizzi, E., Corti, G., Bonnal, R. J. P., Soares, P. A., Luciani, S., Marota, I., Bellis, G. D., Richards, M. B., et al. (2008) · Current Biology · doi:10.1016/j.cub.2008.09.028 · Cited by 130
Evaluating the mitochondrial timescale of human evolution
Endicott, P., Ho, S. Y. W., Metspalu, M., & Stringer, C. B. (2009) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2009.04.006 · Cited by 111
Expanding Southwest Pacific mitochondrial haplogroups P and Q
Friedlaender, J., Schurr, T., Gentz, F., Koki, G., Friedlaender, F., Horvat, G., Babb, P., Cerchio, S., Kaestle, F., Schanfield, M., et al. (2005) · Molecular Biology and Evolution · doi:10.1093/molbev/msi142 · Cited by 107
Les fossiles de Cro-Magnon (Les Eyzies-de-Tayac, Dordogne)
Henry‐Gambier, D. (2002) · Bulletins et Mémoires de la Société d anthropologie de Paris · doi:10.4000/bmsap.459 · Cited by 86
Henry‐Gambier, D. (2002) · Paléo · doi:10.4000/paleo.1424 · Cited by 66
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Haak, W., Lazaridis, I., Patterson, N., Rohland, N., Mallick, S., Llamas, B., Brandt, G., Nordenfelt, S., Harney, E., Stewardson, K., et al. (2015) · Nature · doi:10.1038/nature14317 · Cited by 1,940
Self-citationAncient 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
Self-citationInferring 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
Genome sequence of a 45,000-year-old modern human from western Siberia
Fu, Q., Li, H., Moorjani, P., Jay, F., Slepchenko, S. M., Bondarev, A. A., Johnson, P. L. F., Aximu-Petri, A., Prüfer, K., de Filippo, C., et al. (2014) · Nature · doi:10.1038/nature13810 · Cited by 1,023
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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
Metadata
- Authors
- Fu, Q., Mittnik, A., Johnson, P. L. F., Bos, K., Lari, M., Bollongino, R., Sun, C., Giemsch, L., Schmitz, R., Burger, J., Ronchitelli, A. M., Martini, F., Cremonesi, R. G., Svoboda, J., Bauer, P., Caramelli, D., Castellano, S., Reich, D., Pääbo, S., & Krause, J.
- Affiliations
- Chinese Academy of Sciences (CN)
- University of Tübingen (DE)
- Emory University (US)
- Centre National de la Recherche Scientifique (FR)
- University of Florence (IT)
- Johannes Gutenberg University Mainz (DE)
- Shandong Museum (CN)
- University of Bonn (DE)
- University of Pisa (IT)
- Max Planck Institute for Evolutionary Anthropology (DE)
- Broad Institute (US)
- Corresponding author
- Krause, Johannes
- ORCID
- Venue
- Current Biology
- Publisher
- Elsevier BV
- Published
- 2013-04
- Volume
- 23
- Issue
- 7
- Pages
- 553-559
- ISSN
- 0960-9822 (ISSN-L)
- PMC
- PMC5036973
- OpenAlex
- W2038810697
- Cited by
- 709
- References
- 37
- Citations by year
- 2026: 65 · 2025: 98 · 2024: 48 · 2023: 45 · 2022: 53 · 2021: 63 · 2020: 46 · 2019: 39 · 2018: 56 · 2017: 44 · 2016: 43 · 2015: 47 · 2014: 41 · 2013: 19
- FWCI
- 33.14
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Current Biology (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Florence Research (University of Florence) (submittedVersion, cc-by-nc-nd)
- ASEP (submittedVersion, public-domain)
- MPG.PuRe (Max Planck Society) (submittedVersion, other-oa)
- Use Siena air (University of Siena) (submittedVersion)
- Funders
- National Science Foundation (1032255)
- Deutsche Forschungsgemeinschaft (KR 4015/1-1)
- Chinese Academy of Sciences (XDA05130202)
- Max-Planck-Gesellschaft
- National Institutes of Health
- Social Sciences and Humanities Research Council of Canada
- National Institute of General Medical Sciences (GM100233, R01GM100233)
- National Institute of Allergy and Infectious Diseases (R01AI049334, AI049334)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Social Sciences › Anthropology › Pleistocene-Era Hominins and Archaeology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Keywords
- fossil calibration, divergence time, modern human origins, population divergence
- MeSH terms
- Base Sequence, Bayes Theorem, Demography, Fossils, Haplotypes, Humans, Models, Genetic, Molecular Sequence Data, Phylogeny, Time Factors, Genome, Human, Linear Models, Evolution, Molecular, Genome, Mitochondrial, High-Throughput Nucleotide Sequencing
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