The Chuska Mountains, with an elevation of 2,700 m above sea level, are covered with a forest of ponderosa pine punctuated by openings around small lakes. Spruce, fir, Douglas-fir, and aspen are found on the north-facing slopes of canyons. At lower elevations on the mountain flanks, Gambel oak accompanies the ponderosa, and this altitudinal belt gives way below to a woodland or savanna of pinyon pine and juniper, with sagebrush between the trees. The San Juan Basin east of the mountains is dominated by shrub steppe, with various chenopods and composites.

Plots of herbs and shrubs in the various forest belts show an equally clear altitudinal gradient in occurrence and abundance.

The vegetation history is worked out by pollen analysis of sediments of four lakes from the mountain crest. An 11-m core from Dead Man Lake gives the longest record, representing perhaps the last 50,000 yrs. Pollen zone 1, of Holocene age, is only a few decimeters thick. It is dominated by pine pollen, derived from vegetation similar to today's for the area. Pollen zones 2 to 5 are dominated by Artemisia pollen and further characterized by spruce as well as pine pollen. Separation of pine pollen types on the basis of size and shape indicates the past presence of Pinus flexilis (limber pine) in the area, even though this tree is not present there today. This assemblage is interpreted as a record of alpine vegetation of Pleistocene age, with the tree pollen having been blown up to the crest from below. The upper forest limit is believed to have been lowered about 900 m for zones 2 and 4, and even more for zones 3 and 5, so that the upper parts of the mountain flanks were covered with spruce/fir forest. Successively lower forest belts were not depressed so much, however: ponderosa pine did not reach the base of the mountains but was restricted to the lower flanks, and pinyon pine and Artemisia spread across the San Juan Basin. This telescoping of altitudinal belts implies a climatic gradient steeper than that of today.

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