The DOI matches its Crossref record; 74 of the 74 references it cites were found in a registry or an index.
A Simple and Robust Statistical Test for Detecting the Presence of Recombination
Abstract
Recombination is a powerful evolutionary force that merges historically distinct genotypes. But the extent of recombination within many organisms is unknown, and even determining its presence within a set of homologous sequences is a difficult question. Here we develop a new statistic, Φw, that can be used to test for recombination. We show through simulation that our test can discriminate effectively between the presence and absence of recombination, even in diverse situations such as exponential growth (star-like topologies) and patterns of substitution rate correlation. A number of other tests, Max χ2, NSS, a coalescent-based likelihood permutation test (from LDHat), and correlation of linkage disequilibrium (both r2 and |D′|) with distance, all tend to underestimate the presence of recombination under strong population growth. Moreover, both Max χ2 and NSS falsely infer the presence of recombination under a simple model of mutation rate correlation. Results on empirical data show that our test can be used to detect recombination between closely as well as distantly related samples, regardless of the suspected rate of recombination. The results suggest that Φw is one of the best approaches to distinguish recurrent mutation from recombination in a wide variety of circumstances.
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Cites
The neighbor-joining method: a new method for reconstructing phylogenetic trees.
(1987) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a040454 · Cited by 59,715
Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.
Tajima, F. (1989) · Genetics · doi:10.1093/genetics/123.3.585 · Cited by 13,941
PAUP^* : Phylogenetic Analysis Using Parsimony (and other methods) 4.0b8
Swofford, D. L. (2001) · Cited by 12,789
Application of Phylogenetic Networks in Evolutionary Studies
Huson, D. H., & Bryant, D. (2006) · Molecular Biology and Evolution · doi:10.1093/molbev/msj030 · Cited by 8,830
Self-citationThe Kolmogorov-Smirnov Test for Goodness of Fit
Massey, F. J. (1951) · Journal of the American Statistical Association · doi:10.1080/01621459.1951.10500769 · Cited by 7,210
PAML: a program package for phylogenetic analysis by maximum likelihood
Yang, Z. (1997) · Bioinformatics · doi:10.1093/bioinformatics/13.5.555 · Cited by 5,373
Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations.
Slatkin, M., & Hudson, R. R. (1991) · Genetics · doi:10.1093/genetics/129.2.555 · Cited by 2,351
Kingman, J. F. C. (1982) · Stochastic Processes and their Applications · doi:10.1016/0304-4149(82)90011-4 · Cited by 2,155
Linkage disequilibrium in finite populations
Hill, W. G., & Robertson, A. (1968) · Theoretical and Applied Genetics · doi:10.1007/bf01245622 · Cited by 2,035
THE INTERACTION OF SELECTION AND LINKAGE. I. GENERAL CONSIDERATIONS; HETEROTIC MODELS
Lewontin, R. C. (1964) · Genetics · doi:10.1093/genetics/49.1.49 · Cited by 1,835
Cited by
Croucher, N. J., Page, A. J., Connor, T. R., Delaney, A. J., Keane, J. A., Bentley, S. D., Parkhill, J., & Harris, S. R. (2015) · Nucleic Acids Research · doi:10.1093/nar/gku1196 · Cited by 2,741
Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic
Boni, M. F., Lemey, P., Jiang, X., Lam, T. T.-Y., Perry, B. W., Castoe, T. A., Rambaut, A., & Robertson, D. L. (2020) · Nature Microbiology · doi:10.1038/s41564-020-0771-4 · Cited by 1,014
“%) incompatible splits in Neighbor-Nets (Bryant and Moulton, 2004), and (iii) a near-complete reduction of mosaic signal as identified by 3SEQ.”
BackgroundWhole genome-based population biology and epidemiological surveillance of Listeria monocytogenes
Moura, A., Criscuolo, A., Pouseele, H., Maury, M. M., Leclercq, A., Tarr, C., Björkman, J. T., Dallman, T., Reimer, A., Enouf, V., et al. (2016) · Nature Microbiology · doi:10.1038/nmicrobiol.2016.185 · Cited by 668
Evolution and epidemic spread of SARS-CoV-2 in Brazil
Candido, D. S., Claro, I. M., de Jesus, J. G., Souza, W. M., Moreira, F. R. R., Dellicour, S., Mellan, T. A., du Plessis, L., Pereira, R. H. M., Sales, F. C. S., et al. (2020) · Science · doi:10.1126/science.abd2161 · Cited by 573
Establishment and cryptic transmission of Zika virus in Brazil and the Americas
Faria, N. R., Quick, J., Claro, I. M., Thézé, J., de Jesus, J. G., Giovanetti, M., Kraemer, M. U. G., Hill, S. C., Black, A., da Costa, A. C., et al. (2017) · Nature · doi:10.1038/nature22401 · Cited by 616
Metadata
- Authors
- Bruen, T. C., Philippe, H., & Bryant, D.
- Venue
- Genetics
- Publisher
- Oxford University Press (OUP)
- Published
- 2006-04-01
- Volume
- 172
- Issue
- 4
- Pages
- 2665-2681
- ISSN
- 0016-6731 (ISSN-L)
- 1943-2631
- OpenAlex
- W2155645165
- Cited by
- 1,382
- References
- 74
- FWCI
- 20.68
- Type
- journal article
- Language
- en
- Open access
- closed
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