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Inferring Nonneutral Evolution from Human-Chimp-Mouse Orthologous Gene Trios
Abstract
Even though human and chimpanzee gene sequences are nearly 99% identical, sequence comparisons can nevertheless be highly informative in identifying biologically important changes that have occurred since our ancestral lineages diverged. We analyzed alignments of 7645 chimpanzee gene sequences to their human and mouse orthologs. These three-species sequence alignments allowed us to identify genes undergoing natural selection along the human and chimp lineage by fitting models that include parameters specifying rates of synonymous and nonsynonymous nucleotide substitution. This evolutionary approach revealed an informative set of genes with significantly different patterns of substitution on the human lineage compared with the chimpanzee and mouse lineages. Partitions of genes into inferred biological classes identified accelerated evolution in several functional classes, including olfaction and nuclear transport. In addition to suggesting adaptive physiological differences between chimps and humans, human-accelerated genes are significantly more likely to underlie major known Mendelian disorders.
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Citations
Cites
Evolutionary trees from DNA sequences: A maximum likelihood approach.
Felsenstein, J. (1981) · Journal of Molecular Evolution · doi:10.1007/bf01734359 · Cited by 14,571
The sequence of the human genome
Venter, J. C., Adams, M. D., Myers, E. W., Li, P. W., Mural, R. J., Sutton, G. G., Smith, H. O., Yandell, M., Evans, C. A., Holt, R. A., et al. (2001) · Science · doi:10.1126/science.1058040 · Cited by 13,909
Self-citationKing, M.-C., & Wilson, A. C. (1975) · Science · doi:10.1126/science.1090005 · Cited by 2,815
A codon-based model of nucleotide substitution for protein-coding DNA sequences.
(1994) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a040153 · Cited by 1,960
Yang, Z., & Nielsen, R. (2002) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a004148 · Cited by 1,374
Self-citation
Cited by
A draft sequence of the Neandertal genome
Green, R. E., Krause, J., Briggs, A. W., Maricic, T., Stenzel, U., Kircher, M., Patterson, N., Li, H., Zhai, W., Fritz, M. H.-Y., et al. (2010) · Science · doi:10.1126/science.1188021 · Cited by 4,318
Self-citationInitial sequence of the chimpanzee genome and comparison with the human genome
The Chimpanzee Sequencing and Analysis Consortium (2005) · Nature · doi:10.1038/nature04072 · Cited by 2,459
Evolutionary and biomedical insights from the rhesus macaque genome.
Gibbs, R. A., Rogers, J., Katze, M. G., Bumgarner, R., Weinstock, G. M., Mardis, E. R., Remington, K. A., Strausberg, R. L., Venter, J. C., Wilson, R. K., et al. (2007) · Science · doi:10.1126/science.1139247 · Cited by 1,403
Self-citationPositive Natural Selection in the Human Lineage
Sabeti, P. C., Schaffner, S. F., Fry, B., Lohmueller, J., Varilly, P., Shamovsky, O., Palma, A., Mikkelsen, T. S., Altshuler, D., & Lander, E. S. (2006) · Science · doi:10.1126/science.1124309 · Cited by 1,157
An RNA gene expressed during cortical development evolved rapidly in humans
Pollard, K. S., Salama, S. R., Lambert, N., Lambot, M.-A., Coppens, S., Pedersen, J. S., Katzman, S., King, B., Onodera, C., Siepel, A., et al. (2006) · Nature · doi:10.1038/nature05113 · Cited by 1,005
Evolution at Two Levels: On Genes and Form
Carroll, S. B. (2005) · PLoS Biology · doi:10.1371/journal.pbio.0030245 · Cited by 882
PANTHER version 10: expanded protein families and functions, and analysis tools
Mi, H., Poudel, S., Muruganujan, A., Casagrande, J. T., & Thomas, P. D. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1194 · Cited by 770
Self-citationThe faculty of language: what's special about it?
Pinker, S., & Jackendoff, R. (2005) · Cognition · doi:10.1016/j.cognition.2004.08.004 · Cited by 631
Patterns of Positive Selection in Six Mammalian Genomes
Kosiol, C., Vinař, T., da Fonseca, R. R., Hubisz, M. J., Bustamante, C. D., Nielsen, R., & Siepel, A. (2008) · PLoS Genetics · doi:10.1371/journal.pgen.1000144 · Cited by 576
Self-citationThe origin of mind: Evolution of brain, cognition, and general intelligence.
Geary, D. C. (2005) · doi:10.1037/10871-000 · Cited by 551
Localizing Recent Adaptive Evolution in the Human Genome.
Williamson, S. H., Hubisz, M. J., Clark, A. G., Payseur, B. A., Bustamante, C. D., & Nielsen, R. (2007) · PLoS Genetics · doi:10.1371/journal.pgen.0030090 · Cited by 507
Self-citationCortical Evolution: Judge the Brain by Its Cover
Geschwind, D. H., & Rakic, P. (2013) · Neuron · doi:10.1016/j.neuron.2013.10.045 · Cited by 519
Evolution of the Human Nervous System Function, Structure, and Development
Sousa, A. M. M., Meyer, K. A., Santpere, G., Gulden, F. O., & Sestan, N. (2017) · Cell · doi:10.1016/j.cell.2017.06.036 · Cited by 517
A Practical Genome Scan for Population-Specific Strong Selective Sweeps That Have Reached Fixation.
Kimura, R., Fujimoto, A., Tokunaga, K., & Ohashi, J. (2007) · PLoS ONE · doi:10.1371/journal.pone.0000286 · Cited by 461
Are splicing mutations the most frequent cause of hereditary disease?
López-Bigas, N., Audit, B., Ouzounis, C., Parra, G., & Guigó, R. (2005) · FEBS Letters · doi:10.1016/j.febslet.2005.02.047 · Cited by 412
Alignment Uncertainty and Genomic Analysis
Wong, K. M., Suchard, M. A., & Huelsenbeck, J. P. (2008) · Science · doi:10.1126/science.1151532 · Cited by 411
Genomic regions exhibiting positive selection identified from dense genotype data
Carlson, C. S., Thomas, D. J., Eberle, M. A., Swanson, J. E., Livingston, R. J., Rieder, M. J., & Nickerson, D. A. (2005) · Genome Research · doi:10.1101/gr.4326505 · Cited by 298
A universal trend of amino acid gain and loss in protein evolution
Jordan, I. K., Kondrashov, F. A., Adzhubei, I. A., Wolf, Y. I., Koonin, E. V., Kondrashov, A. S., & Sunyaev, S. (2005) · Nature · doi:10.1038/nature03306 · Cited by 297
Nuclear receptors CAR and PXR: Molecular, functional, and biomedical aspects
di Masi, A., Marinis, E. D., Ascenzi, P., & Marino, M. (2009) · Molecular Aspects of Medicine · doi:10.1016/j.mam.2009.04.002 · Cited by 288
Possible Ancestral Structure in Human Populations
Plagnol, V., & Wall, J. D. (2006) · PLoS Genetics · doi:10.1371/journal.pgen.0020105 · Cited by 275
Olfactory Receptor Multigene Family in Vertebrates: From the Viewpoint of Evolutionary Genomics
Niimura, Y. (2012) · Current Genomics · doi:10.2174/138920212799860706 · Cited by 263
Uddin, M., Wildman, D. E., Liu, G., Xu, W., Johnson, R. M., Hof, P. R., Kapatos, G., Grossman, L. I., & Goodman, M. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0308725100 · Cited by 238
Dual targeting of p53 and c-MYC selectively eliminates leukaemic stem cells
Abraham, S. A., Hopcroft, L. E. M., Carrick, E., Drotar, M. E., Dunn, K., Williamson, A. J. K., Korfi, K., Baquero, P., Park, L. E., Scott, M. T., et al. (2016) · Nature · doi:10.1038/nature18288 · Cited by 225
Human brain evolution: insights from microarrays
Preuss, T. M., Cáceres, M., Oldham, M. C., & Geschwind, D. H. (2004) · Nature Reviews Genetics · doi:10.1038/nrg1469 · Cited by 215
Anisimova, M., & Yang, Z. (2007) · Molecular Biology and Evolution · doi:10.1093/molbev/msm042 · Cited by 213
CHORLEY, B., WANG, X., CAMPBELL, M., PITTMAN, G., NOUREDDINE, M., & BELL, D. (2008) · Mutation Research/Reviews in Mutation Research · doi:10.1016/j.mrrev.2008.05.001 · Cited by 177
Evolution of genetic and genomic features unique to the human lineage
O'Bleness, M., Searles, V. B., Varki, A., Gagneux, P., & Sikela, J. M. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3336 · Cited by 168
Comparative Genomics Search for Losses of Long-Established Genes on the Human Lineage
Zhu, J., Sanborn, J. Z., Diekhans, M., Lowe, C. B., Pringle, T. H., & Haussler, D. (2007) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0030247 · Cited by 129
A scan for signatures of positive selection in candidate loci for skin pigmentation in humans
Izagirre, N., García, I., Junquera, C., de la Rúa, C., & Alonso, S. (2006) · Molecular Biology and Evolution · doi:10.1093/molbev/msl030 · Cited by 119
Evolution of the pregnane x receptor: adaptation to cross-species differences in biliary bile salts
Krasowski, M. D., Yasuda, K., Hagey, L. R., & Schuetz, E. G. (2005) · Molecular Endocrinology · doi:10.1210/me.2004-0427 · Cited by 115
From trans to cis: transcriptional regulatory networks in neocortical development
Shibata, M., Gulden, F. O., & Sestan, N. (2015) · Trends in Genetics · doi:10.1016/j.tig.2014.12.004 · Cited by 109
Genetic contributions to behavioural diversity at the gene-environment interface
Bendesky, A., & Bargmann, C. I. (2011) · Nature Reviews Genetics · doi:10.1038/nrg3065 · Cited by 103
The role of GC-biased gene conversion in shaping the fastest evolving regions of the human genome
Kostka, D., Hubisz, M. J., Siepel, A., & Pollard, K. S. (2012) · Molecular Biology and Evolution · doi:10.1093/molbev/msr279 · Cited by 102
Genetic basis of human brain evolution
Vallender, E. J., Mekel-Bobrov, N., & Lahn, B. T. (2008) · Trends in Neurosciences · doi:10.1016/j.tins.2008.08.010 · Cited by 102
Involvement of long noncoding RNAs in diseases affecting the central nervous system
Pastori, C., & Wahlestedt, C. (2012) · RNA Biology · doi:10.4161/rna.20482 · Cited by 100
Pervasive positive selection on duplicated and nonduplicated vertebrate protein coding genes
Studer, R. A., Penel, S., Duret, L., & Robinson-Rechavi, M. (2008) · Genome Research · doi:10.1101/gr.076992.108 · Cited by 84
Rapid evolution of BRCA1 and BRCA2in humans and other primates
Lou, D. I., McBee, R. M., Le, U. Q., Stone, A. C., Wilkerson, G. K., Demogines, A. M., & Sawyer, S. L. (2014) · BMC Evolutionary Biology · doi:10.1186/1471-2148-14-155 · Cited by 74
Haplotype Block Structure Is Conserved across Mammals
Guryev, V., Smits, B. M. G., de Belt, J. V., Verheul, M., Hubner, N., & Cuppen, E. (2006) · PLoS Genetics · doi:10.1371/journal.pgen.0020121 · Cited by 69
Goto, H., Watanabe, K., Araragi, N., Kageyama, R., Tanaka, K., Kuroki, Y., Toyoda, A., Hattori, M., Sakaki, Y., Fujiyama, A., et al. (2009) · BMC Evolutionary Biology · doi:10.1186/1471-2148-9-224 · Cited by 16
Specialization Restricts the Evolutionary Paths Available to Yeast Sugar Transporters
Crandall, J. G., Zhou, X., Rokas, A., & Hittinger, C. T. (2024) · Molecular Biology and Evolution · doi:10.1093/molbev/msae228 · Cited by 7
Metadata
- Authors
- Clark, A. G., Glanowski, S., Nielsen, R., Thomas, P. D., Kejariwal, A., Todd, M. A., Tanenbaum, D. M., Civello, D., Lu, F., Murphy, B., Ferriera, S., Wang, G., Zheng, X., White, T. J., Sninsky, J. J., Adams, M. D., & Cargill, M.
- Venue
- Science
- Published
- 2003-12-12
- Volume
- 302
- Issue
- 5652
- Pages
- 1960-1963
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- OpenAlex
- W2117790117
- Cited by
- 668
- References
- 5
- FWCI
- 36.84
- Type
- journal article
- Language
- en
- Open access
- closed
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