An ecologist's guide to ecogenomics

1 Currently, plant ecologists are increasingly adopting approaches and techniques from molecular biology. The new field of ecogenomics aims at understanding the mechanistic basis for adaptation and phenotypic variation by using genomic techniques to investigate the mechanistic and evolutionary basis of species interactions, and focuses on identifying the genes affected by evolution. 2 While the entire toolbox of genomics is only available for model species such as Arabidopsis thaliana, we describe the options open to ecologists interested in pursuing an ecogenomics research program on ecologically relevant traits or phenomena in non-model species, for which part of the genomic toolbox may be currently unavailable. In these non-model species, a viable ecogenomics research program is possible with relatively modest effort. 3 Four challenges to further development of ecogenomics are described and discussed: (i) the ecogenomic study of non-model species; (ii) reconciliation of experimental languages of ecology and evolutionary biology with molecular biology; (iii) development of specific ecogenomic data analysis tool; and (iv) adoption of a multidisciplinary cooperative research culture. 4 An important task for ecologists is to provide the necessary ecological input (the 'eco' part) to ecogenomics.