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Archaeologists have developed tools to reconstruct the locations of farming and animal herding using ecological and digital modeling of ancient landscapes. The determination of where on a landscape farming and herding took place, however, can remain elusive in environments with evidence for substantial geomorphological and/or ecological change since the period of occupation. Archaeobotanical and geoarchaeological evidence from the site of Gordion, in central Anatolia, indicates substantial landscape change over the last 4000 years, including deforestation, overgrazing, erosion, and alluviation. These have been inferred to be the result of past agricultural practices, but no firm evidence has pointed to specific locations (geographic and temporal) where ancient farming and herding may have caused these changes. Integrating extant archaeobotanical, zooarchaeological, and geoarchaeological evidence with new isotopic data provides a more detailed reconstruction of the sequence of agricultural practices that shaped the present landscape and ecology of the region, offering a model for future archaeological research within substantially transformed landscapes.