Lodgepole pine has been a component of the western North America flora throughout recent geological history although its present widespread distribution may be a relatively recent phenomenon (Late Pleistocene). The differentiation of populations within and between subspecies, and the distribution of rare alleles, both suggest that at the time of maximal Wisconsin glacial advance lodgepole pine was restricted to a number of refugia in the western United States, the islands along the north Pacific coast, and in an unglaciated region of the west-central Yukon. Subsequent to glacial retreat, logepole pine migrated to its present range with northern and southern interior populations meeting in northern British Columbia, possibly within the last 4000 years.
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