The DOI matches its Crossref record; 9 of the 9 references it cites were found in a registry or an index.
Using Population Genomics to Detect Selection in Natural Populations: Key Concepts and Methodological Considerations
Open accessAbstract
Natural selection shapes patterns of genetic variation among individuals, populations, and species, and it does so differentially across genomes. The field of population genomics provides a comprehensive genome-scale view of the action of selection, even beyond traditional model organisms. However, even with nearly complete genomic sequence information, our ability to detect the signature of selection on specific genomic regions depends on choosing experimental and analytical tools appropriate to the biological situation. For example, processes that occur at different timescales, such as sorting of standing genetic variation, mutation-selection balance, or fixed interspecific divergence, have different consequences for genomic patterns of variation. Inappropriate experimental or analytical approaches may fail to detect even strong selection or falsely identify a signature of selection. Here we outline the conceptual framework of population genomics, relate genomic patterns of variation to evolutionary processes, and identify major biological factors to be considered in studies of selection. As data-gathering technology continues to advance, our ability to understand selection in natural populations will be limited more by conceptual and analytical weaknesses than by the amount of molecular data. Our aim is to bring critical biological considerations to the fore in population genomics research and to spur the development and application of analytical tools appropriate to diverse biological systems.
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Citations
Cites
Genome-wide detection and characterization of positive selection in human populations
The International HapMap Consortium, Sabeti, P. C., Varilly, P., Fry, B., Lohmueller, J., Hostetter, E., Cotsapas, C., Xie, X., Byrne, E. H., McCarroll, S. A., et al. (2007) · Nature · doi:10.1038/nature06250 · Cited by 2,131
Detecting recent positive selection in the human genome from haplotype structure
Sabeti, P. C., Reich, D. E., Higgins, J. M., Levine, H. Z. P., Richter, D. J., Schaffner, S. F., Gabriel, S. B., Platko, J. V., Patterson, N. J., McDonald, G. J., et al. (2002) · Nature · doi:10.1038/nature01140 · Cited by 2,106
Gutenkunst, R. N., Hernandez, R. D., Williamson, S. H., & Bustamante, C. D. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000695 · Cited by 1,906 · cited 1×
“For example, Gutenkunst et al. (2010) present a method for estimating from genomic data the parameters of a population model that can include combinations of expansion, contraction, migration, and admixture.”
MethodPersonal genomes: The case of the missing heritability
Maher, B. (2008) · Nature · doi:10.1038/456018a · Cited by 1,737
Linkage disequilibrium--understanding the evolutionary past and mapping the medical future.
Slatkin, M. (2008) · Nature Reviews Genetics · doi:10.1038/nrg2361 · Cited by 1,614
Human genetic variation and its contribution to complex traits
Frazer, K. A., Murray, S. S., Schork, N. J., & Topol, E. J. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2554 · Cited by 1,073
The genetics of human adaptation: hard sweeps, soft sweeps, and polygenic adaptation
Pritchard, J. K., Pickrell, J. K., & Coop, G. (2010) · Current Biology · doi:10.1016/j.cub.2009.11.055 · Cited by 932
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
Genome-wide scans for footprints of natural selection
Oleksyk, T. K., Smith, M. W., & O'Brien, S. J. (2010) · Philosophical Transactions of the Royal Society B: Biological Sciences · doi:10.1098/rstb.2009.0219 · Cited by 340
Cited by
Harnessing genomics for delineating conservation units
Funk, W. C., McKay, J. K., Hohenlohe, P. A., & Allendorf, F. W. (2012) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2012.05.012 · Cited by 1,117
Finding 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
“In cases where selection on new mutations or recently introduced alleles has been rapid, the genomic signatures of selective sweeps can be used to identify genomic regions with population-speci fi c signatures of selection (table 1; selective sweeps reviewed in Hohenlohe et al. 2010).”
Lotterhos, K. E., & Whitlock, M. C. (2015) · Molecular Ecology · doi:10.1111/mec.13100 · Cited by 566
Evolutionary genetics of plant adaptation
Anderson, J. T., Willis, J. H., & Mitchell-Olds, T. (2011) · Trends in Genetics · doi:10.1016/j.tig.2011.04.001 · Cited by 434
A field guide to whole‐genome sequencing, assembly and annotation
Ekblom, R., & Wolf, J. B. W. (2014) · Evolutionary Applications · doi:10.1111/eva.12178 · Cited by 428
Metadata
- Venue
- International Journal of Plant Sciences
- Publisher
- University of Chicago Press
- Published
- 2010-11
- Volume
- 171
- Issue
- 9
- Pages
- 1059-1071
- ISSN
- 1058-5893 (ISSN-L)
- 1537-5315
- OpenAlex
- W2139974331
- Cited by
- 221
- References
- 9
- FWCI
- 5.36
- Type
- journal article
- Language
- en
- Open access
- green
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