The complete genome sequence of a Neanderthal from the Altai Mountains
Tóm tắt
Từ khóa
Tài liệu tham khảo
Meyer, M. et al. A high-coverage genome sequence from an archaic Denisovan individual. Science 338, 222–226 (2012)
Reich, D. et al. Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature 468, 1053–1060 (2010)
Mednikova, M. B. A proximal pedal phalanx of a paleolithic hominin from Denisova cave, Altai. Archaeol. Ethnol. Anthropol. Eurasia 39, 129–138 (2011)
Green, R. E. et al. A complete Neandertal mitochondrial genome sequence determined by high-throughput sequencing. Cell 134, 416–426 (2008)
Briggs, A. W. et al. Targeted retrieval and analysis of five Neandertal mtDNA genomes. Science 325, 318–321 (2009)
Golovanova, L. V., Hoffecker, J. F., Kharitonov, V. M. & Romanova, G. P. Mezmaiskaya cave: A Neanderthal occupation in the Northern Caucasus. Curr. Anthropol. 40, 77–86 (1999)
Gansauge, M. T. & Meyer, M. Single-stranded DNA library preparation for the sequencing of ancient or damaged DNA. Nature Protocols 8, 737–748 (2013)
Kircher, M. Analysis of high-throughput ancient DNA sequencing data. Methods Mol. Biol. 840, 197–228 (2012)
Briggs, A. W. et al. Patterns of damage in genomic DNA sequences from a Neandertal. Proc. Natl Acad. Sci. USA 104, 14616–14621 (2007)
Briggs, A. W. et al. Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA. Nucleic Acids Res. 38, e87 (2010)
Hofreiter, M., Jaenicke, V., Serre, D., von Haeseler, A. & Paabo, S. DNA sequences from multiple amplifications reveal artifacts induced by cytosine deamination in ancient DNA. Nucleic Acids Res. 29, 4793–4799 (2001)
Skinner, A. R. et al. ESR dating at Mezmaiskaya Cave, Russia. Appl. Radiat. Isot. 62, 219–224 (2005)
Kitzman, J. O. et al. Haplotype-resolved genome sequencing of a Gujarati Indian individual. Nature Biotechnol. 29, 59–63 (2011)
Abecasis, G. R. et al. A map of human genome variation from population-scale sequencing. Nature 467, 1061–1073 (2010)
Awadalla, P. et al. Direct measure of the de novo mutation rate in autism and schizophrenia cohorts. Am. J. Hum. Genet. 87, 316–324 (2010)
Roach, J. C. et al. Analysis of genetic inheritance in a family quartet by whole-genome sequencing. Science 328, 636–639 (2010)
Kong, A. et al. Rate of de novo mutations and the importance of father’s age to disease risk. Nature 488, 471–475 (2012)
Campbell, C. D. et al. Estimating the human mutation rate using autozygosity in a founder population. Nature Genet. 44, 1277–1281 (2012)
Li, H. & Durbin, R. Inference of human population history from individual whole-genome sequences. Nature 475, 493–496 (2011)
Prado-Martinez, J. et al. Great ape genetic diversity and population history. Nature 499, 471–475 (2013)
Kirin, M. et al. Genomic runs of homozygosity record population history and consanguinity. PLoS ONE 5, e13996 (2010)
Leffler, E. M. et al. Revisiting an old riddle: what determines genetic diversity levels within species? PLoS Biol. 10, e1001388 (2012)
Reich, D. et al. Denisova admixture and the first modern human dispersals into Southeast Asia and Oceania. Am. J. Hum. Genet. 89, 516–528 (2011)
Skoglund, P. & Jakobsson, M. Archaic human ancestry in East Asia. Proc. Natl Acad. Sci. USA 108, 18301–18306 (2011)
Fu, Q. et al. DNA analysis of an early modern human from Tianyuan Cave, China. Proc. Natl Acad. Sci. USA 110, 2223–2227 (2013)
Wall, J. D. et al. Higher levels of Neanderthal ancestry in East Asians than in Europeans. Genetics 194, 199–209 (2013)
Abi-Rached, L. et al. The shaping of modern human immune systems by multiregional admixture with archaic humans. Science 334, 89–94 (2011)
Waddell, P. J. & Tan, X. New g%AIC, g%AICc, g%BIC, and power divergence fit statistics expose mating between modern humans, Neanderthals and other archaics. Preprint at http://arxiv.org/abs/1212.6820 (2012)
Wegmann, D., Leuenberger, C., Neuenschwander, S. & Excoffier, L. ABCtoolbox: a versatile toolkit for approximate Bayesian computations. BMC Bioinformatics 11, 116 (2010)
Abecasis, G. R. et al. An integrated map of genetic variation from 1,092 human genomes. Nature 491, 56–65 (2012)
Fietz, S. A. & Huttner, W. B. Cortical progenitor expansion, self-renewal and neurogenesis-a polarized perspective. Curr. Opin. Neurobiol. 21, 23–35 (2011)
Kokovay, E. et al. VCAM1 is essential to maintain the structure of the SVZ niche and acts as an environmental sensor to regulate SVZ lineage progression. Cell Stem Cell 11, 220–230 (2012)
Wang, C., Liang, C. C., Bian, Z. C., Zhu, Y. & Guan, J. L. FIP200 is required for maintenance and differentiation of postnatal neural stem cells. Nature Neurosci. 16, 532–542 (2013)
Rios, D. et al. A database and API for variation, dense genotyping and resequencing data. BMC Bioinformatics 11, 238 (2010)
Hublin, J. J. Out of Africa: modern human origins special feature: the origin of Neandertals. Proc. Natl Acad. Sci. USA 106, 16022–16027 (2009)
Sankararaman, S., Patterson, N., Li, H., Pääbo, S. & Reich, D. The date of interbreeding between Neandertals and modern humans. PLoS Genet. 8, e1002947 (2012)
Yang, M. A., Malaspinas, A. S., Durand, E. Y. & Slatkin, M. Ancient structure in Africa unlikely to explain Neanderthal and non-African genetic similarity. Mol. Biol. Evol. 29, 2987–2995 (2012)
Eriksson, A. & Manica, A. Effect of ancient population structure on the degree of polymorphism shared between modern human populations and ancient hominins. Proc. Natl Acad. Sci. USA 109, 13956–13960 (2012)
Krause, J. et al. The complete mitochondrial DNA genome of an unknown hominin from southern Siberia. Nature 464, 894–897 (2010)
Asfaw, B. et al. Remains of Homo erectus from Bouri, Middle Awash, Ethiopia. Nature 416, 317–320 (2002)
Kircher, M., Stenzel, U. & Kelso, J. Improved base calling for the Illumina Genome Analyzer using machine learning strategies. Genome Biol. 10, R83 (2009)
Langergraber, K. E. et al. Generation times in wild chimpanzees and gorillas suggest earlier divergence times in great ape and human evolution. Proc. Natl Acad. Sci. USA 109, 15716–15721 (2012)