New approaches for ecological adaptation study: from population genetics to landscape genomics

Abstract

Ecological adaptation or local adaptation is one of the most important responses of species to the changing environment. Understanding the molecular mechanism of local adaptation provides a theoretical foundation for the protection and utilization of the species. Landscape genomics studies the interaction between the genetic variation of species and landscape characteristics on the genomic level which quantify the response of genetic variation caused by environmental changes at the genomic level, and can provide new insights for local adaptation research as compared with the classic population genetics methods. In this review, we first summarized series methods for local adaptation research, with particular emphasis on the introduction of generalized linear mixed models, multivariate statistical analysis, non-linear models, and calculation tools involved in genotype-environment associations (GEAs), and we also compared the advantages and disadvantages of these methods. Next, we introduced the newly developed method “risk of non-adaptedness (RONA)”, which evaluates the current and predicts future adaptability of species by combining the allele frequency and the changes in environmental factors. Finally, using case studies of tree local adaptation, we provided suggestions for the future study directions on tree local adaptation.