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Page 1
An extended Tajima's D neutrality test incorporating SNP calling and imputation uncertainties.
Zhang Q, Tyler-Smith C, Long Q. Zhang Q, et al. Stat Interface. 2015 Oct 1;8(4):447-456. doi: 10.4310/SII.2015.v8.n4.a4. Stat Interface. 2015. PMID: 26681995 Free PMC article.
In this work, we propose a modified neutrality test, Extended Tajima's D, which incorporates missing data and SNP-calling uncertainties. Because we do not specify any particular error-generating mechanism, this approach is robust and widely applicable. Simulations s …
In this work, we propose a modified neutrality test, Extended Tajima's D, which incorporates missing data and SNP-calling unce …
Bayesian Estimation of Population Size Changes by Sampling Tajima's Trees.
Palacios JA, Véber A, Cappello L, Wang Z, Wakeley J, Ramachandran S. Palacios JA, et al. Genetics. 2019 Nov;213(3):967-986. doi: 10.1534/genetics.119.302373. Epub 2019 Sep 11. Genetics. 2019. PMID: 31511299 Free PMC article.
Here, we present a new Bayesian approach for inferring past population sizes, which relies on a lower-resolution coalescent process that we refer to as "Tajima's coalescent." Tajima's coalescent has a drastically smaller state space, and hence it is a …
Here, we present a new Bayesian approach for inferring past population sizes, which relies on a lower-resolution coalescent process that we …
Correcting for Bias in Estimates of thetaw and Tajima's D From Missing Data in Next-Generation Sequencing.
Bailey N, Stevison L, Samuk K. Bailey N, et al. Mol Ecol Resour. 2025 Aug;25(6):e14104. doi: 10.1111/1755-0998.14104. Epub 2025 Mar 24. Mol Ecol Resour. 2025. PMID: 40125978 Free PMC article.
Two summary statistics, Watterson's estimator ( thetaw ) of genetic diversity, and Tajima's D , used for detecting non-neutral evolution, are among the most frequently computed statistics utilising this information. ...We found a consequent bias in estimates of T …
Two summary statistics, Watterson's estimator ( thetaw ) of genetic diversity, and Tajima's D , used for detecting non-neutral …
The population genetic test Tajima's D identifies genes encoding pathogen-associated molecular patterns and other virulence-related genes in Ralstonia solanacearum.
Eckshtain-Levi N, Weisberg AJ, Vinatzer BA. Eckshtain-Levi N, et al. Mol Plant Pathol. 2018 Sep;19(9):2187-2192. doi: 10.1111/mpp.12688. Epub 2018 May 23. Mol Plant Pathol. 2018. PMID: 29660239 Free PMC article.
Therefore, we set out to identify additional R. solanacearum PAMPs based on the hypothesis that genes encoding PAMPs are under selection to avoid recognition by plant PRRs. We calculated Tajima's D, a population genetic test statistic which identifies genes that do …
Therefore, we set out to identify additional R. solanacearum PAMPs based on the hypothesis that genes encoding PAMPs are under selection to …
A non-zero variance of Tajima's estimator for two sequences even for infinitely many unlinked loci.
King L, Wakeley J, Carmi S. King L, et al. Theor Popul Biol. 2018 Jul;122:22-29. doi: 10.1016/j.tpb.2017.03.002. Epub 2017 Mar 21. Theor Popul Biol. 2018. PMID: 28341209
We show that for two sequences and n unlinked loci, the variance of Tajima's estimator (theta), which is the average number of pairwise differences, does not vanish even as n. ...
We show that for two sequences and n unlinked loci, the variance of Tajima's estimator (theta), which is the average number of …
Inferring epidemiological dynamics of infectious diseases using Tajima's D statistic on nucleotide sequences of pathogens.
Kim K, Omori R, Ito K. Kim K, et al. Epidemics. 2017 Dec;21:21-29. doi: 10.1016/j.epidem.2017.04.004. Epub 2017 May 1. Epidemics. 2017. PMID: 28552262 Free article.
Here, we propose a new method to estimate epidemiological parameters of outbreaks using the time series change of Tajima's D statistic on the nucleotide sequences of pathogens. To relate the time evolution of Tajima's D to the number of infected indivi …
Here, we propose a new method to estimate epidemiological parameters of outbreaks using the time series change of Tajima's D s …
Recombination and the properties of Tajima's D in the context of approximate-likelihood calculation.
Thornton K. Thornton K. Genetics. 2005 Dec;171(4):2143-8. doi: 10.1534/genetics.105.043786. Epub 2005 Jul 5. Genetics. 2005. PMID: 15998723 Free PMC article.
I show that Tajima's D, a commonly used summary of the site-frequency spectrum for single-nucleotide polymorphism data, is a biased summary of the site-frequency spectrum. ...
I show that Tajima's D, a commonly used summary of the site-frequency spectrum for single-nucleotide polymorphism data, is a b …
Calculation of Tajima's D and other neutrality test statistics from low depth next-generation sequencing data.
Korneliussen TS, Moltke I, Albrechtsen A, Nielsen R. Korneliussen TS, et al. BMC Bioinformatics. 2013 Oct 2;14:289. doi: 10.1186/1471-2105-14-289. BMC Bioinformatics. 2013. PMID: 24088262 Free PMC article.
BACKGROUND: A number of different statistics are used for detecting natural selection using DNA sequencing data, including statistics that are summaries of the frequency spectrum, such as Tajima's D. These statistics are now often being applied in the analysis of Ne …
BACKGROUND: A number of different statistics are used for detecting natural selection using DNA sequencing data, including statistics that a …
Distribution of long-range linkage disequilibrium and Tajima's D values in Scandinavian populations of Norway Spruce (Picea abies).
Larsson H, Källman T, Gyllenstrand N, Lascoux M. Larsson H, et al. G3 (Bethesda). 2013 May 20;3(5):795-806. doi: 10.1534/g3.112.005462. G3 (Bethesda). 2013. PMID: 23550126 Free PMC article.
As in previous studies, we also found that the SFS-based test Tajima's D was highly sensitive to sample size, revealing that care should be taken to draw strong conclusions from this test when sample size is small. In conclusion, the results from this study are in l …
As in previous studies, we also found that the SFS-based test Tajima's D was highly sensitive to sample size, revealing that c …
Correcting estimators of theta and Tajima's D for ascertainment biases caused by the single-nucleotide polymorphism discovery process.
Ramírez-Soriano A, Nielsen R. Ramírez-Soriano A, et al. Genetics. 2009 Feb;181(2):701-10. doi: 10.1534/genetics.108.094060. Epub 2008 Dec 15. Genetics. 2009. PMID: 19087964 Free PMC article.
We also derive the variances and covariances of these estimators and provide a corrected version of Tajima's D statistic. We reanalyze a human genomewide SNP data set and find substantial differences in the results with or without ascertainment bias correction....
We also derive the variances and covariances of these estimators and provide a corrected version of Tajima's D statistic. We r …
10,230 results
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