The DOI matches its Crossref record; 182 of the 182 references it cites were found in a registry or an index.
Initial sequence of the chimpanzee genome and comparison with the human genome
Open accessAbstract
Here we present a draft genome sequence of the common chimpanzee (Pan troglodytes). Through comparison with the human genome, we have generated a largely complete catalogue of the genetic differences that have accumulated since the human and chimpanzee species diverged from our common ancestor, constituting approximately thirty-five million single-nucleotide changes, five million insertion/deletion events, and various chromosomal rearrangements. We use this catalogue to explore the magnitude and regional variation of mutational forces shaping these two genomes, and the strength of positive and negative selection acting on their genes. In particular, we find that the patterns of evolution in human and chimpanzee protein-coding genes are highly correlated and dominated by the fixation of neutral and slightly deleterious alleles. We also use the chimpanzee genome as an outgroup to investigate human population genetics and identify signatures of selective sweeps in recent human evolution.
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“It has been estimated that 3.5% of the sequence differences between chimpanzees and humans is due to INDELs [34,35] and that this INDEL variation may be of particular evolutionary significance [9].”
From Identification, characterization and comparative genomics of chimpanzee endogenous retroviruses (2006) · cites this paper as [34]
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“Frequent turnover of gene copy and/or protein domain number has been proposed as a major mechanism underlying the adaptive divergence of closely related species 9,[17][18][19] .”
From The yak genome and adaptation to life at high altitude (2012) · cites this paper as [9]
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“Genomic comparisons between closely related species provide insights into the genetic basis of mammalian divergence and adaptation 8,9 .”
From The yak genome and adaptation to life at high altitude (2012) · cites this paper as [9]
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“Yak and cattle were estimated to have diverged approximately 4.9 million years ago, which is comparable to the time at which humans and chimpanzees diverged 9 (Supplementary Fig. 12).”
From The yak genome and adaptation to life at high altitude (2012) · cites this paper as [9]
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“results presented here and elsewhere [34] suggest that the number of endogenous retroviruses in chimpanzees may be higher than in humans.”
From Identification, characterization and comparative genomics of chimpanzee endogenous retroviruses (2006) · cites this paper as [34]
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Initial sequencing and analysis of the human genome
International Human Genome Sequencing Consortium, Whitehead Institute for Biomedical Research, C. F. G. R., Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C., Zody, M. C., Baldwin, J., Devon, K., Dewar, K., et al. (2001) · Nature · doi:10.1038/35057062 · Cited by 24,216
<tt>BLAT</tt> —The <tt>BLAST</tt> -Like Alignment Tool
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Initial sequencing and comparative analysis of the mouse genome
Mouse Genome Sequencing Consortium (2002) · Nature · doi:10.1038/nature01262 · Cited by 7,187
Base-Calling of Automated Sequencer Traces Using Phred. I. Accuracy AssessmentPreprint
Ewing, B., Hillier, L., Wendl, M. C., & Green, P. (1998) · Genome Research · doi:10.1101/gr.8.3.175 · Cited by 6,993
The International HapMap Project
†The International HapMap Consortium, Genotyping centres: Baylor College of Medicine and ParAllele BioScience, Gibbs, R. A., Belmont, J. W., Hardenbol, P., Willis, T. D., Yu, F., Chinese HapMap Consortium, Yang, H., Ch'ang, L.-Y., et al. (2003) · Nature · doi:10.1038/nature02168 · Cited by 6,057
Self-citationFinishing the euchromatic sequence of the human genome
International Human Genome Sequencing Consortium (2004) · Nature · doi:10.1038/nature03001 · Cited by 4,971
The hitch-hiking effect of a favourable gene
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Adaptive protein evolution at the Adh locus in Drosophila
McDonald, J. H., & Kreitman, M. (1991) · Nature · doi:10.1038/351652a0 · Cited by 3,313
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The evolutionary history of human spindle genes includes back-and-forth gene flow with Neandertals
Peyrégne, S., Kelso, J., Peter, B. M., & Pääbo, S. (2022) · eLife · doi:10.7554/elife.75464 · Cited by 24
SINEs, evolution and genome structure in the opossum
Gu, W., Ray, D. A., Walker, J. A., Barnes, E. W., Gentles, A. J., Samollow, P. B., Jurka, J., Batzer, M. A., & Pollock, D. D. (2007) · Gene · doi:10.1016/j.gene.2007.02.028 · Cited by 18
Chintalapati, M., Dannemann, M., & Prüfer, K. (2017) · BMC Evolutionary Biology · doi:10.1186/s12862-017-1018-8 · Cited by 13
Topological Approaches in Animal Comparative Genomics
Schultz, D. T., & Simakov, O. (2026) · Annual Review of Animal Biosciences · doi:10.1146/annurev-animal-030424-084541 · Cited by 1
Metadata
- Authors
- The Chimpanzee Sequencing and Analysis Consortium
- Corresponding author
- The Chimpanzee Sequencing and Analysis Consortium
- Venue
- Nature
- Published
- 2005-09
- Volume
- 437
- Issue
- 7055
- Pages
- 69-87
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- OpenAlex
- W1689369637
- Semantic Scholar
- 21067a3992473f2ba32eeca5d5db5722a696e35d
- Cited by
- 2,459
- References
- 180
- Citations by year
- 2026: 39 · 2025: 69 · 2024: 60 · 2023: 76 · 2022: 60 · 2021: 88 · 2020: 109 · 2019: 60 · 2018: 91 · 2017: 81 · 2016: 89 · 2015: 103 · 2014: 121 · 2013: 129 · 2012: 139
- FWCI
- 84.49
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- CINECA IRIS Institutional Research Information System (University of Bari Aldo Moro) (submittedVersion)
- Funders
- National Science Foundation
- European Molecular Biology Laboratory
- Broad Institute
- National Institutes of Health
- National Human Genome Research Institute
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Social Sciences › Anthropology › Pleistocene-Era Hominins and Archaeology
- Keywords
- chimpanzee genome, chimpanzees, human-chimpanzee divergence, single nucleotide polymorphisms, insertion/deletion polymorphism, chromosomal rearrangements, positive selection, negative selection, deleterious alleles, protein-coding genes, human population genetics, selective sweeps, comparative genomics
- MeSH terms
- Alleles, Animals, Base Composition, Pan troglodytes, Disease, DNA Transposable Elements, Humans, Phylogeny, Polymorphism, Genetic, Recombination, Genetic, Time Factors, Genome, Human, Mutagenesis, Telomere, Sequence Analysis, DNA, Evolution, Molecular, Computational Biology, Alu Elements, Genomics
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