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Several hypotheses have been put forward about the origins and evolution of the inhabitants of the Aleutian Islands. Both Hrdlička [The Aleutian and Commander Islands and Their Inhabitants (Philadelphia: Wistar Institute of Anatomy and Biology, 1945)] and Laughlin [“The Alaska gateway viewed from the Aleutian Islands,” in Papers on the Physical Anthropology of the American Indian, W. S. Laughlin, ed. (New York: Viking Fund, 1951), 98–126] analyzed cranial morphology and came to somewhat different conclusions using a typological approach and limited analytical methods. Subsequent investigations using morphological data have not significantly improved our understanding of Aleut prehistory. More recently, radiocarbon dating and mitochondrial DNA analyses have shed light on Aleut genetic variation and changes over time, but better morphological methods using multivariate statistical analysis have not yet been used. We analyzed craniometric data using multivariate procedures and found that Aleuts demonstrate significant changes in cranial morphology over time, and these changes correspond to Hrdlička’s observations but may not necessarily reflect in-migration. The morphological changes were concentrated in the very aspects of morphology that are easily observable and that Hrdlička most often measured, namely, cranial length, breadth, and height, but they were obscured when craniometric variation as a whole was analyzed. Also, we found that the morphological changes over time were not related to the changes in haplogroup frequencies over time, suggesting that migration into the Aleutians did not play a significant role in producing the morphological changes. However, craniometric variability apparently increases over time, suggesting in-migration, localized selection, and/or greater environmental heterogeneity. Our results contradict Laughlin’s observations but may be more in line with his hypothesis of in situ evolutionary changes absent gene flow. In addition to selection, gene flow, and gene drift, however, sociocultural changes must also be considered as a factor in why morphology changed over time.