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Pollen analysis is frequently used to build climate and environmental histories. A distinct Holocene pollen series exists for Chaco Canyon, New Mexico. This study reports linear modeling and hypothesis testing of long distance dispersal pollen from radiocarbon-dated packrat middens which reveal strong relationships between piñon pine (Pinus edulis) and ponderosa pine (Pinus ponderosa). Ponderosa pollen dominates midden pollen assemblages during the early Holocene, while a rapid shift to a much higher proportion of piñon to ponderosa pine pollen between c. 5440 and 5102 cal. yr BP points to an aridization episode. This shift is associated with higher δ18O values in Southwest speleothem records relative to the preceding millennium. The period of aridization is followed by a sharp increase in El Niño/Southern Oscillation events that would have caused highly variable precipitation and lasted until c. 4200 cal. yr BP. Bayesian change-point analysis suggests that this aridization episode led to stable ecotonal boundaries for at least 3000 years. The piñon/ponderosa transition may have been caused by punctuated multiyear droughts, analogous to those in the 20th century. The earliest documented instance of Zea mays cultivation on the Colorado Plateau is around c. 3940 14C yr BP (c. 4364 cal. yr BP) (Hall SA (2010) Early maize pollen from Chaco Canyon, New Mexico, USA. Palynology 34(1): 125–137) in Chaco Canyon. The introduction of this labor-intensive cultigen from Mesoamerica may have been facilitated by changes in the regional ecosystems, specifically by an increase in piñon trees, that promoted increasing human territoriality. Linear modeling and hypothesis testing can complement traditional palynological techniques by adding greater resolution in vegetation patterning to climate/environmental histories. [ABSTRACT FROM AUTHOR]