Local adaptation in the flowering-time gene network of balsam poplar, Populus balsamifera L

• Published in: Molecular biology and evolution Vol. 29; no. 10; pp. 3143 - 3152
• Main Authors: Keller, Stephen R, Levsen, Nicholas, Olson, Matthew S, Tiffin, Peter
• Format: Journal Article
• Language: English
• Published: United States Oxford University Press 01-10-2012
• Subjects: Abscisic acid; Adaptability; Adaptation, Physiological - genetics; Adaptations; Arabidopsis; Cellular biology; Circadian Rhythm - genetics; Circadian rhythms; CLOCK Proteins - genetics; Data processing; Fitness; Flowers - genetics; Flowers - physiology; Gene frequency; Gene Regulatory Networks - genetics; Gene-Environment Interaction; Genes, Plant - genetics; Genetic Variation; Genetics; Genetics, Population; Linkage Disequilibrium - genetics; Models, Genetic; Phenology; Photoreceptors; phytochromes; Polymorphism; Polymorphism, Single Nucleotide - genetics; Population differentiation; Population genetics; Populus - genetics; Populus - physiology; Populus balsamifera; Precipitation; Single-nucleotide polymorphism; Temperature effects; Time Factors; Trees
• ISSN: 0737-4038; 1537-1719
• DOI: 10.1093/molbev/mss121

Identifying the signature and targets of local adaptation is an increasingly important goal in empirical population genetics. Using data from 443 balsam poplar Populus balsamifera trees sampled from 31 populations, we tested for evidence of geographically variable selection shaping diversity at 27 homologues of the Arabidopsis flowering-time network. These genes are implicated in the control of seasonal phenology, an important determinant of fitness. Using 335 candidate and 412 reference single nucleotide polymorphisms (SNPs), we tested for evidence of local adaptation by searching for elevated population differentiation using F(ST)-based outlier analyses implemented in BayeScan or a Hierarchical Model in Arelquin and by testing for significant associations between allele frequency and environmental variables using BAYENV. A total of 46 SNPs from 14 candidate genes had signatures of local adaptation-either significantly greater population differentiation or significant covariance with one or more environmental variable relative to reference SNP distributions. Only 11 SNPs from two genes exhibited both elevated population differentiation and covariance with one or more environmental variables. Several genes including the abscisic acid gene ABI1B and the circadian clock genes ELF3 and GI5 harbored a large number of SNPs with signatures of local adaptation-with SNPs in GI5 strongly covarying with both latitude and precipitation and SNPs in ABI1B strongly covarying with temperature. In contrast to several other systems, we find little evidence that photoreceptors, including phytochromes, play an important role in local adaptation. Our results additionally show that detecting local adaptation is sensitive to the analytical approaches used and that model-based significance thresholds should be viewed with caution.