The DOI matches its Crossref record; 10 of the 10 references it cites were found in a registry or an index.
Using Environmental Correlations to Identify Loci Underlying Local Adaptation
Open accessAbstract
Loci involved in local adaptation can potentially be identified by an unusual correlation between allele frequencies and important ecological variables or by extreme allele frequency differences between geographic regions. However, such comparisons are complicated by differences in sample sizes and the neutral correlation of allele frequencies across populations due to shared history and gene flow. To overcome these difficulties, we have developed a Bayesian method that estimates the empirical pattern of covariance in allele frequencies between populations from a set of markers and then uses this as a null model for a test at individual SNPs. In our model the sample frequencies of an allele across populations are drawn from a set of underlying population frequencies; a transform of these population frequencies is assumed to follow a multivariate normal distribution. We first estimate the covariance matrix of this multivariate normal across loci using a Monte Carlo Markov chain. At each SNP, we then provide a measure of the support, a Bayes factor, for a model where an environmental variable has a linear effect on the transformed allele frequencies compared to a model given by the covariance matrix alone. This test is shown through power simulations to outperform existing correlation tests. We also demonstrate that our method can be used to identify SNPs with unusually large allele frequency differentiation and offers a powerful alternative to tests based on pairwise or global FST. Software is available at http://www.eve.ucdavis.edu/gmcoop/.
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Cites
Phylogenies and the Comparative Method
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Genome-wide detection and characterization of positive selection in human populations
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Robust associations of four new chromosome regions from genome-wide analyses of type 1 diabetes
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SLC24A5, a putative cation exchanger, affects pigmentation in zebrafish and humans
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Genetic determinants of hair, eye and skin pigmentation in Europeans
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Signals of recent positive selection in a worldwide sample of human populations
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Self-citationNatural selection has driven population differentiation in modern humans
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The role of geography in human adaptation
Coop, G., Pickrell, J. K., Novembre, J., Kudaravalli, S., Li, J., Absher, D., Myers, R. M., Cavalli-Sforza, L. L., Feldman, M. W., & Pritchard, J. K. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000500 · Cited by 412
Self-citationGenetic evidence for the convergent evolution of light skin in Europeans and East Asians
Norton, H. L., Kittles, R. A., Parra, E., McKeigue, P., Mao, X., Cheng, K., Canfield, V. A., Bradley, D. G., McEvoy, B., & Shriver, M. D. (2006) · Molecular Biology and Evolution · doi:10.1093/molbev/msl203 · Cited by 410 · cited 3×
“Among our top hits for a European effect are previously identified hits at TLR6 (Todd et al. 2007; Pickrell et al. 2009), SLC45A2 (Norton et al. 2007), and HERC2 (Sulem et al. 2007).”
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Cited by
Inference of population splits and mixtures from genome-wide allele frequency data
Pickrell, J. K., & Pritchard, J. K. (2012) · PLoS Genetics · doi:10.1371/journal.pgen.1002967 · Cited by 2,731
Self-citationFinding the genomic basis of local adaptation: pitfalls, practical solutions, and future directions
Hoban, S., Kelley, J. L., Lotterhos, K. E., Antolin, M. F., Bradburd, G., Lowry, D. B., Poss, M. L., Reed, L. K., Storfer, A., & Whitlock, M. C. (2016) · The American Naturalist · doi:10.1086/688018 · Cited by 876
“There are multiple ways to characterize these covariances, such as co-variance in allele frequencies among populations (Coop et al. 2010; Günther and Coop 2013; Gautier 2015; table A1), a treelike population history (Bonhomme et al. 2010), and re-latedness or other latent factors in a mixed model.”
Fitzpatrick, M. C., & Keller, S. R. (2015) · Ecology Letters · doi:10.1111/ele.12376 · Cited by 699
The trouble with isolation by distance
MEIRMANS, P. G. (2012) · Molecular Ecology · doi:10.1111/j.1365-294x.2012.05578.x · Cited by 624
Fumagalli, M., Sironi, M., Pozzoli, U., Ferrer-Admettla, A., Pattini, L., & Nielsen, R. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1002355 · Cited by 600
Metadata
- Authors
- Coop, G., Witonsky, D., Di Rienzo, A., & Pritchard, J. K.
- Venue
- Genetics
- Publisher
- Oxford University Press (OUP)
- Published
- 2010-08-01
- Volume
- 185
- Issue
- 4
- Pages
- 1411-1423
- ISSN
- 0016-6731 (ISSN-L)
- 1943-2631
- OpenAlex
- W2163980692
- Cited by
- 709
- References
- 10
- FWCI
- 19.11
- Type
- journal article
- Language
- en
- Open access
- bronze
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