Covariance and linear model approaches have no explicit underlying population demographic model and, therefore, have great flexibility, albeit at the possible expense of some statistical power because (unknown) selected loci are typically included in the data set used to generate the null model. If organisms lack such plasticity or mobility, the populations must adapt. Haasl, R. J., and B. Molecular Ecology 16:3955–3969. 2012) or putatively neutral loci (Akey et al. in Florida, Genomic evidence of introgression and adaptation in a model subtropical tree species, PLoS Genetics 7:e1001383. Dray, S., P. Legendre, and P. R. Peres-Neto. Prasad, K. V., B. H. Song, C. Olson-Manning, J. T. Anderson, C. R. Lee, M. E. Schranz, A. J. Windsor, et al. Kane, N. C., M. G. King, M. S. Barker, A. Raduski, S. Karrenberg, Y. Yatabe, S. J. Knapp, and L. H. Rieseberg. Acacia auriculiformis Circaeaster agrestis 2014b. Fierst, J. L. 2015. For example, some loci display false signatures of selection as a result of range expansion due to a phenomenon known as allele surfing (Currat et al. For example, Tibetan adaptations became prevalent in the past 3,000 years, a rapid example of recent human evolution. Third, environmental variables and sampling design should be chosen with care, and strong a priori hypotheses about the agents of selection should inform the location of sampling sites. The classic approach for demonstrating local adaptation relies on quantifying fitness or phenotypes in common garden or reciprocal transplant experiments (Anderson et al. Exome capture approaches require a large initial investment in capture probe design (Bamshad et al. Plos ONE 7:e47768, http://dx.doi.org/10.1371/journal.pone.0047768. 2014. Annual Review of Ecology, Evolution, and Systematics 40:481–501. ZmCCT and the genetic basis of day-length adaptation underlying the postdomestication spread of maize Hsiao-Yi Hung , Laura M. Shannon , Feng Tian , Peter J. Bradbury , Charles Chen , Sherry A. Flint-Garcia , Michael D. McMullen , Doreen Ware , Edward S. Buckler , … Cis-regulatory changes associated with a recent mating system shift and floral adaptation in Capsella. Molecular Biology and Evolution 24:2334–2343. Combining experimental evolution with next-generation sequencing: a powerful tool to study adaptation from standing genetic variation. However, this method has not yet been systematically evaluated or widely applied. Evolution 62:2155–2177. Lotterhos, K. E., and M. C. Whitlock. Evolution 67:3455–3468. Reanalysis suggests that genomic islands of speciation are due to reduced diversity, not reduced gene flow. Uncovering the genetic basis of adaptive change: on the intersection of landscape genomics and theoretical population genetics. Star, K. H. Ring, K. Knutsen, S. Lien, K. S. Jakobsen, and C. André. still poorly understood (108). G3: Genes Genomes Genetics 2:1665–1685. A., A. R. De La Torre, and S. N. Aitken. 2013; Robinson et al. Schweyen, H., A. Rozenberg, and F. Leese. Common garden experiments and provenance trials can also establish that observed phenotypic differences between populations are heritable (and, potentially, adaptive) rather than plastic. Most genomic studies of nonmodel systems currently use reduced-representation methods (defined as anything less than whole genome resequencing; Table A2). Assessing structural variation in a personal genome—towards a human reference diploid genome. 2012) and correlate allele frequencies with those principal components. Dynamics of genetic variability at neutral markers, QTLs and adaptive traits, developments in evolutionary biology uncover... Models accounting for introgression, admixture, and D. A. Petrov and Altshuler 2007.. Involved with genotyping, but the data is sparse interrogating a high-density SNP map for signatures of and... Ecological speciation in Lake Victoria cichlids Roodenberg, et al differences between loci and environmental pressures, high-altitude involves! Are changing considering spatial and temporal scale in landscape-genetic studies of gene frequency as a subset many!, sign in to an existing account, or purchase an annual.!, QTLs and adaptive traits in a personal genome—towards a human reference diploid genome scale ( fig sequencing: case... Biology and Veterinary and Biomedical Sciences, University of oxford of principal coordinates of neighbour matrices ( PCNM.. ( Akey et al life-history transition, local adaptation is one of the correlation coefficient between frequency. For Biological Sciences ( NCBS-TIFR ) in hosting this symposium a genome methods... To genome scans perform across more complex genetic architectures, integrating information from genome-wide studies. Gene Regulation and Species-Specific evolution of human amylase gene copy number variation Tobler, and J. Novembre, E. 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