Evolutionary history and phylogeography of Encelia farinosa (Asteraceae) from the Sonoran, Mojave, and Peninsular Deserts Shannon D. Fehlberg a, * , Tom A. Ranker b a Desert Botanical Garden, 1201 N. Galvin Pkwy., Phoenix, AZ 85008-3437, USA b Department of Botany, University of Hawai’i at Manoa, 3190 Maile Way, Room 101, Honolulu, HI 96822-2279, USA article info Article history: Received 19 June 2008 Revised 13 November 2008 Accepted 13 November 2008 Available online 27 November 2008 Keywords: Encelia farinosa North American Deserts Phylogeography Pleistocene glaciation Population structure Refugia abstract Pleistocene glaciations have had a profound influence on the genetic structure of plant species through- out the Northern Hemisphere because of range contractions, fragmentations, and expansions. Phylogeo- graphic studies have contributed to our knowledge of this influence in several geographic regions of North America, however, very few phylogeographic studies have examined plant species in the Sonoran, Mojave, and Peninsular deserts. In this study, we used sequence data from the chloroplast DNA psbA–trnH intergenic spacer to obtain information on phylogeographic patterns among 310 individuals from 21 pop- ulations of Encelia farinosa (‘‘brittlebush”; Asteraceae) across its range. We applied several population and spatial genetic analyses that allowed us to interpret our data with respect to Pleistocene climate change. These analyses indicate that E. farinosa displays patterns of genetic differentiation and geographic struc- turing consistent with postglacial range expansion. Populations of E. farinosa are characterized by distinct haplotype lineages significantly associated with geography. Centers of genetic diversity for the species occur in southwestern Arizona, the plains of Sonora, and Baja California Sur, all of which are putative sites of glacial refugia as predicted by analyses of macrofossil and pollen data. Nested clade analysis suggests that genetic structure in E. farinosa has been affected by past fragmentation followed by range expansion. Range expansion in several locations is further supported by significant departures from neutrality for values of Fu’s F S and Tajima’s D, and mismatch analyses. Ó 2008 Elsevier Inc. All rights reserved. 1. Introduction Phylogeography is the study of principles and processes govern- ing the geographic distribution of genealogical lineages, especially those at the intraspecific level or among closely related species (Avise, 2000). Some of the most notable studies of phylogeography in plants have examined genealogical lineages in the context of Quaternary climate oscillations, including range contractions, frag- mentations, expansions, and postglacial migrations from refugia. These studies suggest that Pleistocene glaciations have had a pro- found influence on the genetic structure of plant species through- out the Northern Hemisphere (Hewitt, 2000). In temperate Europe (e.g., Hewitt, 1996, 2000, 2004; Taberlet et al., 1998), northwestern North America (e.g., Brunsfeld et al., 2001; Steele and Storfer, 2006), and eastern North America (e.g., Avise et al., 1987; Avise, 2000; Soltis et al., 2006), genetic data indicate that plants and ani- mals persisted in one to several glacial refugia during periods of glacial maximum. When these periods ended, species re-estab- lished continuous distributions, but now exhibit geographically structured genetic variation that reflects glacial history (Soltis et al., 1997). While phylogeographic research has contributed to our knowledge of the influence of Pleistocene glaciation on the ge- netic structure of plant species in several geographic regions of North America, few phylogeographic studies have examined the influence of Pleistocene glaciation on the genetic structure of plant species in the Sonoran, Mojave, and Peninsular Deserts (see Nason et al., 2002). The Sonoran, Mojave, and Peninsular Deserts in southwestern North America provide an excellent context for studying the genet- ic effects of Pleistocene glaciation because independent paleoenvi- ronmental data are available for these deserts through the examination of macrofossils found in packrat middens, or nests built by packrats in the genus Neotoma (Spaulding, 1990; Van Dev- ender, 1990). These macrofossils are well-preserved fragments of plants and animals that were accumulated locally by packrats and eventually encased in amber-like, crystallized urine, and pre- served for up to tens of thousands of years (Betancourt et al., 1990). Analyses of macrofossils indicate that periods of Pleistocene cooling increased the frequency of winter freezes and decreased summer precipitation relative to warmer periods (Van Devender, 1990). Such changes in climate allowed the expansion of northern woodland vegetation into current desert regions, while desert veg- etation was only able to persist in southern refugia. Pleistocene 1055-7903/$ - see front matter Ó 2008 Elsevier Inc. All rights reserved. doi:10.1016/j.ympev.2008.11.011 * Corresponding author. Fax: +1 480 481 8156. E-mail address: sfehlberg@dbg.org (S.D. Fehlberg). Molecular Phylogenetics and Evolution 50 (2009) 326–335 Contents lists available at ScienceDirect Molecular Phylogenetics and Evolution journal homepage: www.elsevier.com/locate/ympev