×
van Waaij, Jan; Li, Zilong; Wiuf, Carsten

Estimation of the covariance structure from SNP allele frequencies. (English) Zbl 1494.92074

Stat. Appl. Genet. Mol. Biol. 21, No. 1, Article ID 20220005, 20 p. (2022).

MSC:

92D10 Genetics and epigenetics
62P10 Applications of statistics to biology and medical sciences; meta analysis

Keywords:

admixture model; \(F_2\)-statistics; SNP evolution

Software:

admixturegraph
PDF BibTeX XML Cite
\textit{J. van Waaij} et al., Stat. Appl. Genet. Mol. Biol. 21, No. 1, Article ID 20220005, 20 p. (2022; Zbl 1494.92074)
Full Text: DOI arXiv

References:

[1] DeGiorgio, M., Jakobsson, M., and Rosenberg, N.A. (2009). Out of Africa: modern humanorigins special feature: explaining worldwide patterns of human genetic variation using a coalescent-based serial founder model of migration outward from africa. Proc. Natl. Acad. Sci. U. S. A. 106: 16057-16062. doi:10.1073/pnas.0903341106.
[2] Escalona, M., Rocha, S., and Posada, D. (2016). A comparison of tools for the simulation of genomic next-generation sequencing data. Nat. Rev. Genet. 17: 459-469. doi:10.1038/nrg.2016.57.
[3] Hakemi, S.L. (1962). On realizability of a set of integers as degrees of the vertices of a linear graph. i. J. Soc. Ind. Appl. Math. 10: 496-506. · Zbl 0109.16501
[4] Hudson, R.R. (1983). Properties of a neutral allele model with intragenic recombinationl. Theor. Popul. Biol. 23: 183-201. doi:10.1016/0040-5809(83)90013-8. · Zbl 0505.62090
[5] Hudson, R.R. (2002). Generating samples under a wright-Fisher neutral model of genetic variation. Bioinformatics 18: 337-338. doi:10.1093/bioinformatics/18.2.337.
[6] Korunes, K.L. and Goldberg, A. (2021). Human genetic admixture. PLoS Genet. 17: e1009374. doi:10.1371/journal.pgen.1009374.
[7] Leppala, K., Nielsen, S., and Mailund, T. (2017). admixturegraph: an r package for admixture graph manipulation and fitting. Bioinformatics 33: 1738-1740. doi:10.1093/bioinformatics/btx048.
[8] Lipson, M. (2020). Applying f4-statistics and admixture graphs: theory and examples. Mol. Ecol. Resour. 20: 1658-1667. doi:10.1111/1755-0998.13230.
[9] Nicholson, G., Smith, A.V., Jonsson, F., Gustafsson, O., Stefansson, K., and Donnelly, P. (2002). Assessing population differentiation and isolation from single-nucleotide polymorphism data. J. R. Stat. Soc. Series B Stat. Methodol. 64: 695-715. doi:10.1111/1467-9868.00357. · Zbl 1067.62116
[10] Patterson, N., Moorjani, P., Luo, Y., Mallick, S., Rohland, N., Zhan, Y., Genschoreck, T., Webster, T., and Reich, D. (2012). Ancient admixture in human history. Genetics 192: 1065-1093. doi:10.1534/genetics.112.145037.
[11] Pickrell, J. and Pritchard, J. (2012). Inference of population splits and mixtures from genome-wide allele frequency data. PLoS Genet. 8: 1-17. doi:10.1038/npre.2012.6956.1.
[12] Semple, C. and Steel, M. (2003). Phylogenetics, Oxford lecture series in mathematics and its applications. Oxford University Press, Oxford. · Zbl 1043.92026
This reference list is based on information provided by the publisher or from digital mathematics libraries. Its items are heuristically matched to zbMATH identifiers and may contain data conversion errors. It attempts to reflect the references listed in the original paper as accurately as possible without claiming the completeness or perfect precision of the matching.