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Penalized likelihood analysis of previously published chloroplast DNA (cpDNA) ndhF sequences suggests that the central-southern Andean genus Chaetanthera diverged ca. 16.5 million years (my) ago, well before the uplift of the Andes to their present heights. Penalized likelihood analysis based on new nuclear ribosomal DNA (rDNA) internal transcribed spacer (ITS) sequences indicates that the most relictual lineages occupy high elevation Andean habitats that did not exist until some 10 my later. This result is contrary to the expectation that younger habitats should be occupied by phylogenetically younger lineages. The results are interpreted with respect to the development of aridity in lowland habitats during the Miocene and Pliocene, which presumably extinguished the lowland relatives of the high elevation taxa or, in effect, forced them upwards in search of adequate moisture. As the more northerly lineages were being displaced upward, others diversified in the mediterranean-type climate area of central Chile, giving rise to additional high elevation taxa again, at an early date, as well as lowland taxa. Some species of Chaetanthera from lowland central Chile appear as the phylogenetically youngest taxa, suggesting secondary adaptation to lowland aridity. At the same time, at least two high elevation species, Chaetanthera perliviana and Chaetanthera perpusilla, appear to have been derived recently from a lower elevation ancestor, while some middle to low elevation taxa seem to have evolved recently out of a high elevation complex. The results suggest that the younger high elevation habitats have served as both "cradle" and "museum" for Chaetanthera lineages. (c) 2006 Elsevier Inc. All rights reserved.