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Rapid habitat changes are occuring in salt marshes located in the Northeastern United States, including expansion of ponded areas on the marsh platform, die off of coastal forests, and subsequent colonization of 'ghost forests' by marsh vegetation. This work focuses on two main areas: (1) environmental conditions along the marsh forest border undergoing rapid transitions; and (2) environmental conditions and plant stress in marsh platforms with extensive ponding, with three study sites: in Long Island and Southern New England, where there are often significant slope breaks along the upland (slope ~0.01), and in southern New Jersey on the Atlantic Coastal plan (slope ~0.003). To better understand drivers of environmental change in marsh-forest borders undergoing rapid transitions, we measured shallow groundwater levels,  soil salinity, and forest health and structure along the salt marsh-upland border at three sites with varying slopes using installation of shallow groundwater wells, drone imagery and associated image processing, and geophysical methods. To better understand drivers of environmental change on the marsh platform, we measured used piezometers to understand vertical gradients in marsh groundwater levels, and measured photosynthesis and plant biomass and used drone imagery to map plant stress indices, as indicators of plant stress. While we anticipate that this data will be published in journal articles of the next 2 years, we archive collected data to facilitated data sharing, as required by NSF. 

Understanding genome organization requires integration of DNA sequence and three-dimensional spatial context; however, existing genome-wide methods lack either base pair sequence resolution or direct spatial localization. Here, we describe in situ genome sequencing (IGS), a method for simultaneously sequencing and imaging genomes within intact biological samples. We applied IGS to human fibroblasts and early mouse embryos, spatially localizing thousands of genomic loci in individual nuclei. Using these data, we characterized parent-specific changes in genome structure across embryonic stages, revealed single-cell chromatin domains in zygotes, and uncovered epigenetic memory of global chromosome positioning within individual embryos. These results demonstrate how IGS can directly connect sequence and structure across length scales from single base pairs to whole organisms.