NEWS AND VIEWS PERSPECTIVE Triangulating the genetic basis of adaptation to multifarious selection M. E. PFRENDER Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA Understanding how natural populations adapt to their local environments is a major research theme for ecologi- cal genomics. This endeavour begins by sleuthing for shared genetic similarities among unrelated natural pop- ulations sharing adaptive traits to documented selective pressures. When the selective pressures have low dimen- sionality, and the genetic response is localized to a few genes of major effect, this detective work is relatively straightforward. However, in the real world, populations face a complex mixture of selective pressures and many adaptive responses are the result of changes in quantita- tive traits that have a polygenic genetic basis. This com- plex relationship between environment and adaptation presents a significant challenge. How can we begin to identify drivers of adaptation in natural settings? In this issue of Molecular Ecology, Orsini et al. (2012) take advantage of the biological attributes of the freshwater microcrustacean Daphnia (Fig. 1) to disentangle multidi- mensional selection’s signature on the genome of popula- tions that have repeatedly evolved adaptive responses to isolated selective pressures including predation, parasit- ism and anthropogenic changes in land use. Orsini et al. (2012) leverage a powerful combination of spatially struc- tured populations in a geographic mosaic of environmen- tal stressors, the historical archive of past genotypes preserved in lake-bottom sediments and selection experi- ments to identify sets of candidate genomic regions asso- ciated with adaptation in response to these three environmental stressors. This study provides a template for future investigation in ecological genomics, combin- ing multiple experimental approaches with the genomic investigation of a well-studied ecological model species. Keywords: adaptation, Daphnia, experimental evolution, genome scans, paleogenetic, selection Received 25 December 2011; accepted 9 January 2012 A common objective for evolutionary biologists and ecolo- gists is the ability to infer the consequences of changing environments to natural populations. How do populations respond to novel selective pressures? How do anthropo- genic alterations to the environment interact with existing demographic and selective forces? Developing a prospec- tive view of adaptation requires an understanding of the selective forces at play, the genetic underpinnings of adap- tive traits and the origins of genetic variation. Unfortu- nately, the complexity of both selection and the genetic basis of adaptation alone forms a daunting barrier to pro- gress in many systems. Often researchers are much like real-life versions of Detective Hercule Poirot in Agatha Christie’s novels, sifting through clues using ‘order and method’ to establish causal connections without a conven- tional path to this goal. Progress at finding causality requires a detailed understanding of the ecological context that natural populations are exposed to and a combination of empirical approaches and analytical tools to link local environmental conditions to genes. Because of these inher- ent complexities, many of the most well-documented stud- ies demonstrating the genetic basis of adaptation come from discovering a direct connection between strong low- dimensional selection and an adaptive response mediated by a few genes of major effect (e.g. Storz et al. 2007; Feld- man et al. 2009; van’t Hof et al. 2011). In many cases, selec- tion and the genetic basis of adaptation are often far more complicated. Fortunately, we are now entering an arena where solving this type of mystery is increasingly tractable. The recent development of genomic tools in traditionally non-model systems, and the increasing availability of high- throughput sequencing, has spurred ecological genomic studies. This area of investigation and studies combining genome-wide genetic markers are now a significant compo- nent of recent articles in Molecular Ecology (Rieseberg et al. 2012). Disentangling the various elements of natural selection is one of the primary challenges. Orsini et al. (2012) tackle this central problem in a multifaceted study of Daphnia populations taking advantage of extensive previous work documenting patterns of land-use intensity (Michels 2008) and rapid micro-evolutionary responses to fish predation (Cousyn et al. 2001) and parasite exposure (Decaestecker et al. 2007). By examining a spatially structured set of pop- ulations embedded in a geographic mosaic of environmen- tal gradients and implementing a replicated design, they are able to isolate orthogonal environmental factors. This analysis, using a genome scan strategy (Storz 2005) based on a combination of 84 microsatellite loci (Jansen et al. 2011) and 82 SNPs (Orsini et al. 2011), allows the authors to identify a set of candidate markers linked to the envi- ronmental stressors. By itself, this spatially structured study with a genome scan demonstrating repeated local adaptation would be Correspondence: M. E. Pfrender, Fax: 574-631-7413; E-mail: michael.pfrender.1@nd.edu Ó 2012 Blackwell Publishing Ltd Molecular Ecology (2012) 21, 2051–2053