The DOI matches its Crossref record; 12 of the 12 references it cites were found in a registry or an index.
Population-scale sequencing reveals genetic differentiation due to local adaptation in Atlantic herring
Open accessAbstract
The Atlantic herring ( Clupea harengus ), one of the most abundant marine fishes in the world, has historically been a critical food source in Northern Europe. It is one of the few marine species that can reproduce throughout the brackish salinity gradient of the Baltic Sea. Previous studies based on few genetic markers have revealed a conspicuous lack of genetic differentiation between geographic regions, consistent with huge population sizes and minute genetic drift. Here, we present a cost-effective genome-wide study in a species that lacks a genome sequence. We first assembled a muscle transcriptome and then aligned genomic reads to the transcripts, creating an “exome assembly,” capturing both exons and flanking sequences. We then resequenced pools of fish from a wide geographic range, including the Northeast Atlantic, as well as different regions in the Baltic Sea, aligned the reads to the exome assembly, and identified 440,817 SNPs. The great majority of SNPs showed no appreciable differences in allele frequency among populations; however, several thousand SNPs showed striking differences, some approaching fixation for different alleles. The contrast between low genetic differentiation at most loci and striking differences at others implies that the latter category primarily reflects natural selection. A simulation study confirmed that the distribution of the fixation index F ST deviated significantly from expectation for selectively neutral loci. This study provides insights concerning the population structure of an important marine fish and establishes the Atlantic herring as a model for population genetic studies of adaptation and natural selection.
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Cites
Full-length transcriptome assembly from RNA-Seq data without a reference genome
Grabherr, M. G., Haas, B. J., Yassour, M., Levin, J. Z., Thompson, D. A., Amit, I., Adiconis, X., Fan, L., Raychowdhury, R., Zeng, Q., et al. (2011) · Nature Biotechnology · doi:10.1038/nbt.1883 · Cited by 21,039
Self-citationThe genomic basis of adaptive evolution in threespine sticklebacks
Broad Institute Genome Sequencing Platform & Whole Genome Assembly Team, Jones, F. C., Grabherr, M. G., Chan, Y. F., Russell, P., Mauceli, E., Johnson, J., Swofford, R., Pirun, M., Zody, M. C., et al. (2012) · Nature · doi:10.1038/nature10944 · Cited by 1,777
Self-citationInference of Population Structure using Dense Haplotype Data
Lawson, D. J., Hellenthal, G., Myers, S., & Falush, D. (2012) · PLoS Genetics · doi:10.1371/journal.pgen.1002453 · Cited by 1,188
Gaggiotti, O. E., Bekkevold, D., Jørgensen, H. B. H., Foll, M., Carvalho, G. R., Andre, C., & Ruzzante, D. E. (2009) · Evolution · doi:10.1111/j.1558-5646.2009.00779.x · Cited by 261
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Genome-size evolution in fishes
Hardie, D. C., & Hebert, P. D. (2004) · Canadian Journal of Fisheries and Aquatic Sciences · doi:10.1139/f04-106 · Cited by 155
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Self-citationLarsson, L. C., Laikre, L., Palm, S., André, C., Carvalho, G. R., & Ryman, N. (2006) · Molecular Ecology · doi:10.1111/j.1365-294x.2006.03217.x · Cited by 120
Self-citationCasini, M., Bartolino, V., Molinero, J., et al. (2010) · Marine Ecology Progress Series · doi:10.3354/meps08592 · Cited by 110
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Self-citation
Cited by
Sequencing pools of individuals — mining genome-wide polymorphism data without big funding
Schlötterer, C., Tobler, R., Kofler, R., & Nolte, V. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3803 · Cited by 784
Gagnaire, P., Broquet, T., Aurelle, D., Viard, F., Souissi, A., Bonhomme, F., Arnaud‐Haond, S., & Bierne, N. (2015) · Evolutionary Applications · doi:10.1111/eva.12288 · Cited by 270
Conservation and the Genomics of Populations
Allendorf, F. W., Funk, W. C., Aitken, S. N., Byrne, M., Luikart, G., & Antunes, A. (2022) · doi:10.1093/oso/9780198856566.001.0001 · Cited by 207
Metadata
- Authors
- Lamichhaney, S., Barrio, A. M., Rafati, N., Sundström, G., Rubin, C.-J., Gilbert, E. R., Berglund, J., Wetterbom, A., Laikre, L., Webster, M. T., Grabherr, M., Ryman, N., & Andersson, L.
- Venue
- Proceedings of the National Academy of Sciences
- Published
- 2012-11-07
- Volume
- 109
- Issue
- 47
- Pages
- 19345-19350
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- OpenAlex
- W1980980457
- Cited by
- 281
- References
- 12
- FWCI
- 10.27
- Type
- journal article
- Language
- en
- Open access
- hybrid
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- Lamichhaney, S., Barrio, A. M., Rafati, N., Sundström, G., Rubin, C.-J., Gilbert, E. R., Berglund, J., Wetterbom, A., Laikre, L., Webster, M. T., Grabherr, M., Ryman, N., & Andersson, L. (2012). Population-scale sequencing reveals genetic differentiation due to local adaptation in Atlantic herring. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1216128109
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