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In the treeless high\u2010elevation Andean environments, Pleistocene glacial oscillations and niche differentiation are frequently hypothesized diversification mechanisms; however, sufficiently densely sampled population genetic data supporting this are still lacking. Here, we reconstruct the evolutionary history of<jats:italic>Loricaria<\/jats:italic>(Asteraceae), a plant genus endemic to the Andean treeless alpine zone, based on comprehensive population\u2010level sampling of 289 individuals from 67 populations across the entire distribution ranges of its northern Andean species. Partly incongruent AFLP and plastid DNA markers reveal that the distinct genetic structure was shaped by a complex interplay of biogeography (spread along and across the cordilleras), history (Pleistocene glacial oscillations) and local ecological conditions. While plastid variation documents an early split or colonization of the northern Andes by at least two lineages, one of which further diversified, a major split in the AFLP data correlate with altitudinal ecological differentiation. This suggests that niche shifts may be important drivers of Andean diversification not only in forest\u2013alpine transitions, but also within the treeless alpine zone itself. The patterns of genetic differentiation at the intraspecific level reject the hypothesized separation in spatially isolated cordilleras and instead suggest extensive gene flow among populations from distinct mountain chains. Our study highlights that leveraging highly variable markers against extensive population\u2010level sampling is a promising approach to address mechanisms of rapid species diversifications.<\/jats:p>","DOI":"10.1111\/mec.13788","type":"journal-article","created":{"date-parts":[[2016,8,2]],"date-time":"2016-08-02T15:23:26Z","timestamp":1470151406000},"page":"4593-4610","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":36,"title":["Niche shifts and range expansions along cordilleras drove diversification in a high\u2010elevation endemic plant genus in the tropical Andes"],"prefix":"10.1111","volume":"25","author":[{"given":"Filip","family":"Kol\u00e1\u0159","sequence":"first","affiliation":[{"name":"Natural History Museum University of Oslo P.O. 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