Ecological Epigenetics: Beyond MS-AFLP

Abstract

Ecological Epigenetics studies the relationship between epigenetic variation and ecologically relevant phenotypic variation. As molecular epigenetic mechanisms often control gene expression, even across generations, they may impact many evolutionary processes. Multiple molecular epigenetic mechanisms exist, but methylation of DNA so far has dominated the Ecological Epigenetic literature. There are several molecular techniques used to screen methylation of DNA; here, we focus on the most common technique, methylation-sensitive-AFLP (MS-AFLP), which is used to identify genome-wide methylation patterns. We review studies that used MS-AFLP to address ecological questions, that describe which taxa have been investigated, and that identify general trends in the field. We then discuss, noting the general themes, four studies across taxa that demonstrate characteristics that increase the inferences that can be made from MS-AFLP data; we suggest that future MS-AFLP studies should incorporate these methods and techniques. We then review the short-comings of MS-AFLP and suggest alternative techniques that might address some of these limitations. Finally, we make specific suggestions for future research on MS-AFLP and identify questions that are most compelling and tractable in the short term.

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

“…Moreover, the heterogeneity of microhabitats within each region can increase epigenetic noise masking the direction of epigenetic changes during the invasion. Finally, it is hard to find the few important adaptive loci using a limited number of anonymous loci provided by AFLP and MS‐AFLP (Schrey et al., 2013). For the above reasons, we failed to detect the significant epigenetic divergence independent of genetic variation.…”

“…This epiallele controls leaf senescence and associates with local climates. Moreover, an easy and efficient technique named methylation‐sensitive amplification polymorphism (MS‐AFLP) has been widely used to assess DNA methylation status at a great number of random anonymous loci across the entire genome in nonmodel species without sequenced reference genomes (Alonso, Pérez, Bazaga, Medrano, & Herrera, 2016; Schrey et al., 2013). …”

Genetic and epigenetic variation in Spartina alterniflora following the Deepwater Horizon oil spill

“…In future studies, a reduced‐representation bisulfite sequencing approach would allow the direct comparison of genetic and epigenetic data sets, and at a much finer scale, with substantially increased statistical power to detect epigenetic differences between populations (van Gurp et al., 2016; Robertson & Richards, 2015; Schrey et al., 2013; Trucchi et al., 2016). In addition, sequencing‐based methods provide an increased ability to disentangle the relationship of methylation variation and gene function when fragments overlap with the promoters or coding regions of genes.…”

“…Although there are several epigenetic mechanisms that can alter gene expression (e.g., chromatin remodeling, histone modifications, small interfering RNAs), DNA methylation of cytosines is the most widely studied (Schrey et al., 2013; Verhoeven, Vonholdt, & Sork, 2016) and can have important ecological effects. For example, studies in Taraxacum officinale show that when DNA methylation machinery is disrupted, flowering time differences among populations of these plants are removed (Wilschut, Oplaat, Snoek, Kirschner, & Verhoeven, 2016).…”

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

“…The MSAP technique is useful to identify genome‐wide methylation patterns in ecological epigenetics studies of species without detailed genomic information (Schrey et al. 2013). Frequent experimental demonstration that methylation status of MSAP markers often responds to environmental changes (Alonso et al.…”