Using AFLP and MS-AFLP to compare genetic and epigenetic variation in Spartina alterniflora

Spartina alterniflora is a keystone species to salt marsh communities along the Atlantic and Gulf of Mexico coasts. Spartina alterniflora is significant to these regions because within its ecosystem it filters toxins and pollutants, protects the coastline from erosion and supports the wildlife by providing habitat and nutrients. Spartina alterniflora flourishes in intertidal areas because of its tolerance to inundation from tides and changes in salinity, but these environmental factors can trigger changes in gene expression, which might be heritable. Epigenetics is the study of heritable changes in gene expression and function that cannot be explained by changes in DNA sequence. These heritable changes include variation in methylation patterns, which can be measured with methylation sensitive AFLP. By analyzing methylation variation compared to genetic variation, we can begin to understand if epigenetic variation contributes to ecological success. My hypothesis is that methylation patterns will change predictably in response to different habitats within a population of Spartina alterniflora. If there are methylation differences associated with different habitats, then epigenetic effects may contribute to local adaptation