Introduction
To carry out this lab, we will use GIS software (Quantum GIS; OpenGeoDa → download4mac, → download4windows) and a specific landscape genomic software implementing a correlative approach to detect signatures of natural selection and spatial statistics named SamBada (Linux, Mac and Windows versions available).
Instructions: Landscape genomic analysis of large datasets
Data used
The main dataset we will use was made available by Andrew Eckert and is about loblolly pine (Pinus taeda L.). The dataset was published in two papers:
- Eckert, A. J., A. D. Bower, S. C. González-Martínez, J. L. Wegrzyn, G. Coop and D. B. Neale. 2010. Back to nature: Ecological genomics of loblolly pine (Pinus taeda, Pinaceae). Molecular Ecology 19: 3789-3805.
- Eckert, A. J., J. van Heerwaarden, J. L. Wegrzyn, C. D. Nelson, J. Ross-Ibarra, S. C. González-Martínez and D. B. Neale. 2010. Patterns of population structure and environmental associations to aridity across the range of loblolly pine (Pinus taeda L., Pinaceae). Genetics 185: 969-982.
Data necessary for the exercices are available here.
Useful references
- Colli L., Joost S., Negrini R., Nicoloso L., Crepaldi P., Ajmone-Marsan P. & Consortium E. (2014) Assessing The Spatial Dependence of Adaptive Loci in 43 European and Western Asian Goat Breeds Using AFLP Markers. Plos One 9.
- Jones M.R., Forester B.R., Teufel A.I., Adams R.V., Anstett D.N., Goodrich B.A., Landguth E.L., Joost S. & Manel S. (2013) Integrating Landscape Genomics and Spatially Explicit Approaches to Detect Loci under Selection in Clinal Populations. Evolution 67, 3455-68.
- Joost S., Colli L., Baret P.V., Garcia J.F., Boettcher P.J., Tixier-Boichard M., Ajmone-Marsan P. & Consortium G. (2010) Integrating geo-referenced multiscale and multidisciplinary data for the management of biodiversity in livestock genetic resources. Animal Genetics 41, 47-63.
- Joost S., Vuilleumier S., Jensen J.D., Schoville S., Leempoel K., Stucki S., Widmer I., Melodelima C., Rolland J. & Manel S. (2013) Uncovering the genetic basis of adaptive change: on the intersection of landscape genomics and theoretical population genetics. Molecular Ecology 22, 3659-65.
- Manel S., Joost S., Epperson B.K., Holderegger R., Storfer A., Rosenberg M.S., Scribner K.T., Bonin A. & Fortin M.J. (2010) Perspectives on the use of landscape genetics to detect genetic adaptive variation in the field. Molecular Ecology 19, 3760-72.
- Manel S. & Holderegger R. (2013) Ten years of landscape genetics. Trends in Ecology & Evolution 28, 614-21.