Abstract
Demographic events are important in shaping the population genetic structure and exon variation can play roles in adaptive divergence. Twelve nuclear genes were used to investigate the species-level phylogeography of Rhododendron oldhamii, test the difference in the average GC content of coding sites and of third codon positions with that of surrounding non-coding regions, and test exon variants associated with environmental variables. Spatial expansion was suggested by R2 index of the aligned intron sequences of all genes of the regional samples and sum of squared deviations statistic of the aligned intron sequences of all genes individually and of all genes of the regional and pooled samples. The level of genetic differentiation was significantly different between regional samples. Significantly lower and higher average GC contents across 94 sequences of the 12 genes at third codon positions of coding sequences than that of surrounding non-coding regions were found. We found seven exon variants associated strongly with environmental variables. Our results demonstrated spatial expansion of R. oldhamii in the late Pleistocene and the optimal third codon position could end in A or T rather than G or C as frequent alleles and could have been important for adaptive divergence in R. oldhamii.
Highlights
Spatial and temporal patterns underlie population demographic processes of plant species and the phylogenetic relationship between and within species can be revealed by using chloroplast and nuclear DNA sequence d ata[1,2,3]
R. oldhamii discontinuously distributed in a wide geographic range makes it an excellent exemplar endemic subtropical forest tree species occurring in Taiwan for investigating the population divergence associated with environmental differences, and the phylogeographic history related to the current genetic structure of this species
Our results in the present study found that environmental factors such as BIO1, BIO7, WSmean, RH, and slope strongly associated with coding sequence variation in natural populations of R. oldhamii suggestive of local adaptation in consistence with the findings of previous studies[4,5]
Summary
Spatial and temporal patterns underlie population demographic processes of plant species and the phylogenetic relationship between and within species can be revealed by using chloroplast and nuclear DNA sequence d ata[1,2,3] Molecular techniques, such as amplified fragment length polymorphisms (AFLPs), expressed sequence tag simple sequence repeats (EST-SSRs), and methylation-sensitive amplification polymorphisms (MSAPs) have been commonly employed in investigation testing for environmentally dependent local adaptation[4,5,6]. R. oldhamii discontinuously distributed in a wide geographic range makes it an excellent exemplar endemic subtropical forest tree species occurring in Taiwan for investigating the population divergence associated with environmental differences, and the phylogeographic history related to the current genetic structure of this species
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