The DOI matches its Crossref record.
Statistical tests of neutrality of mutations.
Open accessAbstract
Mutations in the genealogy of the sequences in a random sample from a population can be classified as external and internal. External mutations are mutations that occurred in the external branches and internal mutations are mutations that occurred in the internal branches of the genealogy. Under the assumption of selective neutrality, the expected number of external mutations is equal to theta = 4Ne mu, where Ne is the effective population size and mu is the rate of mutation per gene per generation. Interestingly, this expectation is independent of the sample size. The number of external mutations is likely to deviate from its neutral expectation when there is selection while the number of internal mutations is less affected by the presence of selection. Statistical properties of the numbers of external mutations and of internal mutations are studied and their relationships to two commonly used estimates of theta are derived. From these properties, several new statistical tests based on a random sample of DNA sequences from the population are developed for testing the hypothesis that all mutations at a locus are neutral.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cited by
Detecting recent positive selection in the human genome from haplotype structure
Sabeti, P. C., Reich, D. E., Higgins, J. M., Levine, H. Z. P., Richter, D. J., Schaffner, S. F., Gabriel, S. B., Platko, J. V., Patterson, N. J., McDonald, G. J., et al. (2002) · Nature · doi:10.1038/nature01140 · Cited by 2,106
Positive 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
Blocks of Limited Haplotype Diversity Revealed by High-Resolution Scanning of Human Chromosome 21
Patil, N., Berno, A. J., Hinds, D. A., Barrett, W. A., Doshi, J. M., Hacker, C. R., Kautzer, C. R., Lee, D. H., Marjoribanks, C., McDonough, D. P., et al. (2001) · Science · doi:10.1126/science.1065573 · Cited by 1,145
The Population Genetics of dN/dS
Kryazhimskiy, S., & Plotkin, J. B. (2008) · PLoS Genetics · doi:10.1371/journal.pgen.1000304 · Cited by 962
Detecting Natural Selection in Genomic Data
Vitti, J. J., Grossman, S. R., & Sabeti, P. C. (2013) · Annual Review of Genetics · doi:10.1146/annurev-genet-111212-133526 · Cited by 694
Properties of statistical tests of neutrality for DNA polymorphism data
Simonsen, K. L., Churchill, G. A., & Aquadro, C. F. (1995) · Genetics · doi:10.1093/genetics/141.1.413 · Cited by 681
The hitchhiking effect on the site frequency spectrum of DNA polymorphisms
Braverman, J. M., Hudson, R. R., Kaplan, N. L., Langley, C. H., & Stephan, W. (1995) · Genetics · doi:10.1093/genetics/140.2.783 · Cited by 601
Evidence for archaic adaptive introgression in humans
Racimo, F., Sankararaman, S., Nielsen, R., & Huerta-Sánchez, E. (2015) · Nature Reviews Genetics · doi:10.1038/nrg3936 · Cited by 521
Romeo, S., Pennacchio, L. A., Fu, Y., Boerwinkle, E., Tybjaerg-Hansen, A., Hobbs, H. H., & Cohen, J. C. (2007) · Nature Genetics · doi:10.1038/ng1984 · Cited by 511
Self-citationSupervised Machine Learning for Population Genetics: A New Paradigm
Schrider, D. R., & Kern, A. D. (2018) · Trends in Genetics · doi:10.1016/j.tig.2017.12.005 · Cited by 453
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
Clark, A. G., Weiss, K. M., Nickerson, D. A., Taylor, S. L., Buchanan, A., Stengård, J., Salomaa, V., Vartiainen, E., Perola, M., Boerwinkle, E., et al. (1998) · The American Journal of Human Genetics · doi:10.1086/301977 · Cited by 435
Evolution of primate gene expression
Khaitovich, P., Enard, W., Lachmann, M., & Pääbo, S. (2006) · Nature Reviews Genetics · doi:10.1038/nrg1940 · Cited by 341
Genome-wide scans for footprints of natural selection
Oleksyk, T. K., Smith, M. W., & O'Brien, S. J. (2010) · Philosophical Transactions of the Royal Society B: Biological Sciences · doi:10.1098/rstb.2009.0219 · Cited by 340
McVean, G. A. T., & Charlesworth, B. (2000) · Genetics · doi:10.1093/genetics/155.2.929 · Cited by 336
Natural Selection Favors a Newly Derived timeless Allele in Drosophila melanogaster
Tauber, E., Zordan, M., Sandrelli, F., Pegoraro, M., Osterwalder, N., Breda, C., Daga, A., Selmin, A., Monger, K., Benna, C., et al. (2007) · Science · doi:10.1126/science.1138412 · Cited by 308
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
Voight, B. F., Adams, A. M., Frisse, L. A., Qian, Y., Hudson, R. R., & Di Rienzo, A. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0507325102 · Cited by 262
Korneliussen, T. S., Moltke, I., Albrechtsen, A., & Nielsen, R. (2013) · BMC Bioinformatics · doi:10.1186/1471-2105-14-289 · Cited by 269
Thornton, K., & Andolfatto, P. (2006) · Genetics · doi:10.1534/genetics.105.048223 · Cited by 256
Contrasting demographic history and phylogeographical patterns in two Indo-Pacific gastropods
CRANDALL, E. D., FREY, M. A., GROSBERG, R. K., & BARBER, P. H. (2008) · Molecular Ecology · doi:10.1111/j.1365-294x.2007.03600.x · Cited by 211
Context Dependence, Ancestral Misidentification, and Spurious Signatures of Natural Selection
Hernandez, R. D., Williamson, S. H., & Bustamante, C. D. (2007) · Molecular Biology and Evolution · doi:10.1093/molbev/msm108 · Cited by 169
Mondal, M., Casals, F., Xu, T., Dall'Olio, G. M., Pybus, M., Netea, M. G., Comas, D., Laayouni, H., Li, Q., Majumder, P. P., et al. (2016) · Nature Genetics · doi:10.1038/ng.3621 · Cited by 149
Worldwide distribution of NAT2 diversity: Implications for NAT2 evolutionary history
Sabbagh, A., Langaney, A., Darlu, P., Gérard, N., Krishnamoorthy, R., & Poloni, E. S. (2008) · BMC Genetics · doi:10.1186/1471-2156-9-21 · Cited by 147
Besansky, N. J., Lehmann, T., Fahey, G. T., Fontenille, D., Braack, L. E. O., Hawley, W. A., & Collins, F. H. (1997) · Genetics · doi:10.1093/genetics/147.4.1817 · Cited by 144
Intraspecific variation in symbiont genomes: bottlenecks and the aphid-buchnera association
Funk, D. J., Wernegreen, J. J., & Moran, N. A. (2001) · Genetics · doi:10.1093/genetics/157.2.477 · Cited by 131
Wang, W., Yu, H., & Long, M. (2004) · Nature Genetics · doi:10.1038/ng1338 · Cited by 114
Young inversion with multiple linked QTLs under selection in a hybrid zone
Lee, C.-R., Wang, B., Mojica, J. P., Mandáková, T., Prasad, K. V. S. K., Goicoechea, J. L., Perera, N., Hellsten, U., Hundley, H. N., Johnson, J., et al. (2017) · Nature Ecology & Evolution · doi:10.1038/s41559-017-0119 · Cited by 119
Dahlbäck, M., Rask, T. S., Andersen, P. H., Nielsen, M. A., Ndam, N. T., Resende, M., Turner, L., Deloron, P., Hviid, L., Lund, O., et al. (2006) · PLoS Pathogens · doi:10.1371/journal.ppat.0020124 · Cited by 98
Laval, G., Patin, E., Barreiro, L. B., & Quintana-Murci, L. (2010) · PLoS ONE · doi:10.1371/journal.pone.0010284 · Cited by 93
Characterizing bias in population genetic inferences from low-coverage sequencing data
Han, E., Sinsheimer, J. S., & Novembre, J. (2014) · Molecular Biology and Evolution · doi:10.1093/molbev/mst229 · Cited by 94
Evidence for recent positive selection at the human AIM1 locus in a European population
Soejima, M., Tachida, H., Ishida, T., Sano, A., & Koda, Y. (2006) · Molecular Biology and Evolution · doi:10.1093/molbev/msj018 · Cited by 84
Genetic evidence for unequal effective population sizes of human females and males.
Wilder, J. A. (2004) · Molecular Biology and Evolution · doi:10.1093/molbev/msh214 · Cited by 86
Philippe, R., Courtois, B., McNally, K. L., Mournet, P., El-Malki, R., Le Paslier, M. C., Fabre, D., Billot, C., Brunel, D., Glaszmann, J.-C., et al. (2010) · Theoretical and Applied Genetics · doi:10.1007/s00122-010-1348-z · Cited by 85
JOHN, P. R., MAKOVA, K., LI, W., JENKINS, T., & RAMSAY, M. (2003) · Annals of the New York Academy of Sciences · doi:10.1111/j.1749-6632.2003.tb03193.x · Cited by 72
Self-citationStatham, M. J., Sacks, B. N., Aubry, K. B., Perrine, J. D., & Wisely, S. M. (2012) · Journal of Mammalogy · doi:10.1644/11-mamm-a-033.1 · Cited by 70
DE BRUYN, M., WILSON, J. C., & MATHER, P. B. (2004) · Molecular Ecology · doi:10.1111/j.1365-294x.2004.02348.x · Cited by 67
Herbeck, J. T., Funk, D. J., Degnan, P. H., & Wernegreen, J. J. (2003) · Genetics · doi:10.1093/genetics/165.4.1651 · Cited by 58
Remigereau, M.-S., Lakis, G., Rekima, S., Leveugle, M., Fontaine, M. C., Langin, T., Sarr, A., & Robert, T. (2011) · PLoS ONE · doi:10.1371/journal.pone.0022404 · Cited by 48
Adaptive variation regulates the expression of the human SGK1 gene in response to stress
Luca, F., Kashyap, S., Southard, C., Zou, M., Witonsky, D., Di Rienzo, A., & Conzen, S. D. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000489 · Cited by 45
Baysal, B. E., Lawrence, E. C., & Ferrell, R. E. (2007) · BMC Biology · doi:10.1186/1741-7007-5-12 · Cited by 39
Reconstruction of the colonization of southern Madagascar by introduced Rattus rattus
Hingston, M., Goodman, S. M., Ganzhorn, J. U., & Sommer, S. (2005) · Journal of Biogeography · doi:10.1111/j.1365-2699.2005.01311.x · Cited by 38
Dammannagoda, S. T., Hurwood, D. A., & Mather, P. B. (2011) · Canadian Journal of Fisheries and Aquatic Sciences · doi:10.1139/f10-136 · Cited by 36
Schmegner, C., Hoegel, J., Vogel, W., & Assum, G. (2005) · Human Genetics · doi:10.1007/s00439-005-0056-2 · Cited by 36
PopHuman: the human population genomics browser
Casillas, S., Mulet, R., Villegas-Mirón, P., Hervas, S., Sanz, E., Velasco, D., Bertranpetit, J., Laayouni, H., & Barbadilla, A. (2018) · Nucleic Acids Research · doi:10.1093/nar/gkx943 · Cited by 29
Metadata
- Authors
- Fu, Y. X., & Li, W. H.
- Venue
- Genetics
- Publisher
- Oxford University Press (OUP)
- Published
- 1993-03-01
- Volume
- 133
- Issue
- 3
- Pages
- 693-709
- ISSN
- 0016-6731 (ISSN-L)
- 1943-2631
- OpenAlex
- W2132393729
- Cited by
- 4,034
- References
- 0
- FWCI
- 5.87
- Type
- journal article
- Language
- en
- Open access
- bronze
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
