
An R Framework for the Partitioning of Linkage Disequilibrium between and Within Populations
References
- Vitti, J J, Grossman, S R and Sabeti, P C 2013 Detecting Natural Selection in Genomic Data. Annual Review of Genetics, 47(1): 97–120. DOI: 10.1146/annurev-genet-111212-133526
- Maynard, J and Haigh, J 1974 The hitch-hiking effect of a favourable gene. Genetics Research, 89(5–6): 391–403. DOI: 10.1017/S0016672308009579
- Ohta, T 1982 Linkage disequilibrium due to random genetic drift in finite subdivided populations. Proceedings of the National Academy of Sciences of the United States of America, 79(6): 1940–1944. DOI: 10.1073/pnas.79.6.1940
- Wright, S 1922 Coefficients of Inbreeding and Relationship. The American Naturalist, 56(645): 330–338. DOI: 10.1086/279872
- Miyashita, N T, Aguadé, M and Langley, C H 1993 Linkage disequilibrium in the white locus region of Drosophila melanogaster. Genetical Research, 62(2): 101. DOI: 10.1017/S0016672300031694
- Beissinger, T M, Gholami, M, Erbe, M, et al. 2016 Using the variability of linkage disequilibrium between subpopulations to infer sweeps and epistatic selection in a diverse panel of chickens. Heredity, 116(2): 158–166. DOI: 10.1038/hdy.2015.81
- Song, B-H, Windsor, A J, Schmid, K J, et al. 2009 Multilocus Patterns of Nucleotide Diversity, Population Structure and Linkage Disequilibrium in Boechera stricta, a Wild Relative of Arabidopsis. Genetics, 181(3): 1021–1033. DOI: 10.1534/genetics.108.095364
- Black, W C and Krafsur, E S 1985 A FORTRAN program for the calculation and analysis of two-locus linkage disequilibrium coefficients. Theoretical and Applied Genetics, 70(5): 491–496. DOI: 10.1007/BF00305981
- Garnier-Gere, P and Dillmann, C 1992 A Computer Program for Testing Pairwise Linkage Disequilibria in Subdivided Populations. Journal of Heredity, 83(3): 239–239. DOI: 10.1093/oxfordjournals.jhered.a111204
- Yeh, F 1997 Population genetic analysis of co-dominant and dominant marker and quantitative traits. Belgian J Bot, 130: 129–157.
- R Core Team 2018
R: A language and environment for statistical computing . Vienna, Austria: R Foundation for Statistical Computing. - Sarkar, D 2008
Lattice: Multivariate Data Visualization with R . New York. Springer. DOI: 10.1007/978-0-387-75969-2 - Jette, M A, Yoo, A B and Grondona, M 2002
SLURM: Simple Linux Utility for Resource Management . In: Lect. Notes Comput. Sci. Proc. Job Sched. Strateg. Parallel Process, 44–60. JSSPP 2003. Springer-Verlag. - Raymond, M and Rousset, F 1995 GENEPOP (Version 1.2): Population Genetics Software for Exact Tests and Ecumenicism. Journal of Heredity, 86(3): 248–249. DOI: 10.1093/oxfordjournals.jhered.a111573
- Voight, B F, Kudaravalli, S, Wen, X and Pritchard, J K 2006 A Map of Recent Positive Selection in the Human Genome. PLOS Biology, 4(3): e72. DOI: 10.1371/journal.pbio.0040072
- Sabeti, P C, Reich, D E, Higgins, J M, et al. 2002 Detecting recent positive selection in the human genome from haplotype structure. Nature, 419(6909): 832–837. DOI: 10.1038/nature01140
DOI: https://doi.org/10.5334/jors.250 | Journal eISSN: 2049-9647
Language: English
Submitted on: Oct 24, 2018
Accepted on: Apr 2, 2019
Published on: Apr 30, 2019
Published by: Ubiquity Press
In partnership with: Paradigm Publishing Services
Publication frequency: 1 issue per year
© 2019 Paul F. Petrowski, Elizabeth G. King, Timothy M. Beissinger, published by Ubiquity Press
This work is licensed under the Creative Commons Attribution 4.0 License.