A New Method for Genome-wide Marker Development and Genotyping Holds Great Promise for Molecular Primatology
- 1.2k Downloads
Over the last two decades primatologists have benefited from the use of numerous molecular markers to study various aspects of primate behavior and evolutionary history. However, most of the studies to date have been based on a single locus, usually mitochondrial DNA, or a few nuclear markers, e.g., microsatellites. Unfortunately, the use of such markers not only is unable to address successfully important questions in primate population genetics and phylogenetics (mainly because of the discordance between gene tree and species tree), but also their development is often a time-consuming and expensive task. The advent of next-generation sequencing allows researchers to generate large amounts of genomic data for nonmodel organisms. However, whole genome sequencing is still cost prohibitive for most primate species. We here introduce a second-generation sequencing technique for genotyping thousands of genome-wide markers for nonmodel organisms. Restriction site–associated DNA sequencing (RAD-seq) reduces the complexity of the genome and allows inexpensive and fast discovery of thousands of markers in many individuals. Here, we describe the principles of this technique and we demonstrate its application in five primates, Microcebus sp., Cebus sp., Theropithecus gelada, Pan troglodytes, and Homo sapiens, representing some of the major lineages within the order. Despite technical and bioinformatic challenges, RAD-seq is a promising method for multilocus phylogenetic and population genetic studies in primates, particularly in young clades in which a high number of orthologous regions are likely to be found across populations or species.
KeywordsGenotyping Nonmodel organisms Phylogenetics Population genetics Restriction site–associated DNA sequencing Second-generation DNA sequencing Single-nucleotide polymorphisms
The present study was supported by a Leakey Foundation General Grant and an NSF Graduate Research Fellowship. We thank the NYU Langone Medical Center’s Genome Technology Center for assistance with library preparation and sequencing, as well as two anonymous reviewers and the editors for their helpful comments.
- Davey, J. W., Cezard, T., Fuentes-Utrilla, P., Eland, C., Gharbi, K., & Blaxter, M. L. (2012). Special features of RAD sequencing data: Implications for genotyping. Molecular Ecology. doi: 10.1111/mec.12084.
- Etter, P. D., Bassham, S., Hohenlohe, P. A., Johnson, E., & Cresko, W. A. (2011). SNP discovery and genotyping for evolutionary genetics using RAD sequencing. In V. Orgogozo & M. V. Rockman (Eds.), Molecular methods for evolutionary genetics (pp. 157–178). New York: Humana Press.Google Scholar
- Hauser, L., Baird, M., Hilborn, R., Seeb, L. W., & Seeb, J. E. (2011). An empirical comparison of SNPs and microsatellites for parentage and kinship assignment in a wild sockeye salmon (Oncorhynchus nerka) population. Molecular Ecology Resources, 11(Supplement 1), 150–161.PubMedCrossRefGoogle Scholar
- Hohenlohe, P. A., Amish, S. J., Catchen, J. M., Allendorf, F. W., & Luikart, G. (2011). Next-generation RAD sequencing identifies thousands of SNPs for assessing hybridization between rainbow and westslope cutthroat trout. Molecular Ecology Resources, 11(Supplement 1), 117–122.PubMedCrossRefGoogle Scholar
- Human Genome Sequencing Consortium (2001). Initial sequencing and analysis of the human genome. Nature, 409(6822), 860–921.Google Scholar
- Keller, I., Wagner, C. E., Greuter, L., Mwaiko, S., Selz, O. M., Sivasundar, A., et al. (2012). Population genomic signatures of divergent adaptation, gene flow and hybrid speciation in the rapid radiation of Lake Victoria cichlid fishes. Molecular Ecology. doi: 10.1111/mec.12083.
- McCormack, J. E., Hird, S. M., Zellmer, A. J., Carstens, B. C., & Brumfield, R. T. (2012). Applications of next-generation sequencing to phylogeography and phylogenetics. Molecular Phylogenetics and Evolution. doi: 10.1016/j.ympev.2011.12.007.
- Nadeau, N. J., Martin, S. H., Kozak, K. M., Salazar, C., Dasmahapatra, K. K., Davey, J. W., et al. (2012). Genome-wide patterns of divergence and gene flow across a butterfly radiation. Molecular Ecology. doi: 10.1111/j.1365-294X.2012.05730.x.
- Ting, N., & Sterner, K. N. (2012). Primate molecular phylogenetics in a genomic era. Molecular Phylogenetics and Evolution. doi: 10.1016/j.ympev.2012.08.021.
- Wagner, C. E., Keller, I., Wittwer, S., Selz, O. M., Mwaiko, S., Greuter, L., et al. (2012). Genome-wide RAD sequence data provide unprecedented resolution of species boundaries and relationships in the Lake Victoria cichlid adaptive radiation. Molecular Ecology. doi: 10.1111/mec.12023.