The DOI matches its Crossref record; 45 of the 45 references it cites were found in a registry or an index.
Restriction site‐associated DNA sequencing, genotyping error estimation and de novo assembly optimization for population genetic inference
Abstract
Restriction site‐associated DNA sequencing (RAD seq) provides researchers with the ability to record genetic polymorphism across thousands of loci for nonmodel organisms, potentially revolutionizing the field of molecular ecology. However, as with other genotyping methods, RAD seq is prone to a number of sources of error that may have consequential effects for population genetic inferences, and these have received only limited attention in terms of the estimation and reporting of genotyping error rates. Here we use individual sample replicates, under the expectation of identical genotypes, to quantify genotyping error in the absence of a reference genome. We then use sample replicates to (i) optimize de novo assembly parameters within the program Stacks, by minimizing error and maximizing the retrieval of informative loci; and (ii) quantify error rates for loci, alleles and single‐nucleotide polymorphisms. As an empirical example, we use a double‐digest RAD data set of a nonmodel plant species, B erberis alpina, collected from high‐altitude mountains in M exico.
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Cited by
O'Leary, S. J., Puritz, J. B., Willis, S. C., Hollenbeck, C. M., & Portnoy, D. S. (2018) · Molecular Ecology · doi:10.1111/mec.14792 · Cited by 434
Next-generation data filtering in the genomics era
Hemstrom, W., Grummer, J. A., Luikart, G., & Christie, M. R. (2024) · Nature Reviews Genetics · doi:10.1038/s41576-024-00738-6 · Cited by 77
Chang, J.-T., Chao, C.-T., Nakamura, K., Liu, H.-L., Luo, M.-X., & Liao, P.-C. (2022) · Frontiers in Plant Science · doi:10.3389/fpls.2022.824158 · Cited by 20
Metadata
- Authors
- Mastretta‐Yanes, A., Arrigo, N., Alvarez, N., Jorgensen, T. H., Piñero, D., & Emerson, B. C.
- Venue
- Molecular Ecology Resources
- Publisher
- Wiley
- Published
- 2014-07-03
- Volume
- 15
- Issue
- 1
- Pages
- 28-41
- ISSN
- 1755-098X (ISSN-L)
- 1755-0998
- OpenAlex
- W2091450548
- Cited by
- 391
- References
- 45
- FWCI
- 16.64
- Type
- journal article
- Language
- en
- Open access
- closed
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