Initial sequence of the chimpanzee genome and comparison with the human genome

The Chimpanzee Sequencing and Analysis Consortium

doi:10.1038/nature04072

Cited by 2,459Genomics and Phylogenetic StudiesEvolution and Genetic DynamicsPleistocene-Era Hominins and Archaeology

Initial sequence of the chimpanzee genome and comparison with the human genome

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The Chimpanzee Sequencing and Analysis Consortium·2005·Nature

DOI 10.1038/nature04072

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Abstract

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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3.5% of the sequence differences between chimpanzees and humans is due to INDELs.
“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]
The Nucleotide divergence section estimates that indel differences span approximately 3% of both genomes, compared with 1.23% from nucleotide substitutions. That is a percentage of genome sequence, not a finding that indels account for 3.5% of the differences between the genomes; the paper says indels affect more bases than substitutions. (LLM, conf=0.88)
Checked by a reasoning model — may be wrong.
Experimental — accuracy not yet measured
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.
“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]
The gene-evolution discussion (page unavailable in our copy) describes gene-family expansion, recent human-specific duplications, and genes deleted in chimpanzees, supporting the gene-copy-change portion of the claim. It does not identify turnover of protein-domain number or propose that these changes are a major mechanism of adaptive divergence. (LLM, conf=0.77)
Experimental — accuracy not yet measured
Genomic comparisons between closely related species provide insights into the genetic basis of mammalian divergence and adaptation.
“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]
Yak and cattle were estimated to have diverged approximately 4.9 million years ago, comparable to the time at which humans and chimpanzees diverged.
“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]
The number of endogenous retroviruses in chimpanzees may be higher than in humans.
“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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A haplotype map of the human genome
The International HapMap Consortium (2005) · Nature · doi:10.1038/nature04226 · Cited by 5,858 · see citing works
Self-citation
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
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HUMAN MUTATION 28(2),99^130,2007 REVIEW ARTICLE Understanding the Recent Evolution of the Human Genome: Insights from
Comparisons, H. G., Kehrer-sawatzki, H., Cooper, D. N., & Oefner, C. P. (2014)

Authors: The Chimpanzee Sequencing and Analysis Consortium
Corresponding author: The Chimpanzee Sequencing and Analysis Consortium
Venue: Nature
Publisher: Springer Science and Business Media LLC
Published: 2005-09
Volume: 437
Issue: 7055
Pages: 69-87
ISSN: 0028-0836 (ISSN-L)
1476-4687
DOI: 10.1038/nature04072
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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