Genome‐wide DNA methylation alterations of Alternanthera philoxeroides in natural and manipulated habitats: implications for epigenetic regulation of rapid responses to environmental fluctuation and phenotypic variation

Abstract

Alternanthera philoxeroides (alligator weed) is an invasive weed that can colonize both aquatic and terrestrial habitats. Individuals growing in different habitats exhibit extensive phenotypic variation but little genetic differentiation in its introduced range. The mechanisms underpinning the wide range of phenotypic variation and rapid adaptation to novel and changing environments remain uncharacterized. In this study, we examined the epigenetic variation and its correlation with phenotypic variation in plants exposed to natural and manipulated environmental variability. Genome-wide methylation profiling using methylationsensitive amplified fragment length polymorphism (MSAP) revealed considerable DNA methylation polymorphisms within and between natural populations. Plants of different source populations not only underwent significant morphological changes in common garden environments, but also underwent a genome-wide epigenetic reprogramming in response to different treatments. Methylation alterations associated with response to different water availability were detected in 78.2% (169/216) of common garden induced polymorphic sites, demonstrating the environmental sensitivity and flexibility of the epigenetic regulatory system. These data provide evidence of the correlation between epigenetic reprogramming and the reversible phenotypic response of alligator weed to particular environmental factors.

Epigenetics in natural animal populations

“…Herrera & Bazaga, 2010), and principal coordinate analyses (PCoA) can be equally useful in describing population differentiation at the epigenetic level (e.g. Gao et al, 2010;Wenzel & Piertney, 2014;Preite et al, 2015). Correlations between population statistics for genetic vs. epigenetic variation can potentially be analysed using a Mantel test (e.g.…”

Genetic and epigenetic changes during the invasion of a cosmopolitan species (Phragmites australis)

“…Unlike many invasive clonal species spreading mostly by vegetative reproduction (Gao, Geng, Li, Chen, & Yang, 2010; Lambertini et al., 2010; Richards et al., 2012), the invasion of P. australis in North America contributes to a reproduction strategy combining sexual and vegetative propagation (Albert, Brisson, Belzile, Turgeon, & Lavoie, 2015; McCormick, Kettenring, Baron, & Whigham, 2010). The high genetic diversity in P. australis makes it more difficult to detect the epigenetic changes during the invasion.…”

“…Given that the climate in the introduced range was more advantageous than that in the original range for the survival of common reed because of abundant precipitation and warm temperature, the introduced environment did not provide enough selection pressures to shape the stable genetic and epigenetic structure of introduced populations. Therefore, we cannot ignore the potential effect of preadaptation and ecological fitting based on the inherently high phenotypic plasticity during the invasion process of common reed (Guo, Lambertini, Nguyen, Li, & Brix, 2014; Guo et al., 2016), which may be correlated with plastic epigenetic mechanisms (Gao et al., 2010). …”

Genetic and epigenetic divergence between disturbed and undisturbed subpopulations of a Mediterranean shrub: a 20‐year field experiment

“…Indirect support for positing a relationship between ecological disturbance and epigenetic characteristics of populations includes: (1) theoretical models documenting the significance of nongenetic inheritance systems for population persistence in fluctuating environments (Furrow and Feldman 2013; Geoghegan and Spencer 2013); (2) empirical results showing that epigenetic diversity may broaden the ecological niche and enhance the colonizing ability, expanding potential and resistance to perturbations of plant populations (Gao et al. 2010; Richards et al. 2012; Latzel et al.…”

“…Furthermore, the flexibility and short‐term responsiveness of epigenetic variation to alterations in the biotic and abiotic environment (Gao et al. 2010; Lira‐Medeiros et al. 2010; Herman et al.…”