Phylogeny of Caragana (Fabaceae) based on DNA sequence data from rbcL, trnS–trnG, and ITS Mingli Zhang a,b , Peter W. Fritsch c, * , Boni C. Cruz c a State Key Lab of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, PR China b Laboratory of Evolution and Biodiversity Conservation in Arid Regions, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, Xinjiang, PR China c Department of Botany, California Academy of Sciences, 55 Music Concourse Drive, Golden Gate Park, San Francisco, CA 94118-4503, USA article info Article history: Received 16 July 2008 Revised 22 November 2008 Accepted 1 December 2008 Available online 8 December 2008 Keywords: Caragana Fabaceae ITS Phylogeny rbcL trnS–trnG abstract Phylogenetic relationships of 48 species of Caragana (Fabaceae: tribe Hedysareae) and one representative each of Astragalus, Calophaca, Halimodendron, and Hedysarum are estimated from DNA sequences of the rbcL gene, trnS–trnG intron and spacer, and ITS region. At least one representative of all five sections and 12 series within Caragana are included. Analyses yielded strongly supported clades corresponding to sections Caragana, Bracteolatae, and Frutescentes. The species of section Jubatae are distributed among three strongly supported clades, i.e., one with the species of section Bracteolatae, another with two spe- cies of section Spinosae, and a third as sister to section Frutescentes. All but the last of these six clades are corroborated by at least one unambiguously traced morphological character. The placement of the other four species of section Spinosae are not well supported and lack unambiguous morphological synapomor- phies, and the samples of Calophaca and Halimodendron nest within Caragana with weak support. Ó 2008 Elsevier Inc. All rights reserved. 1. Introduction Caragana Fabr. (Fabaceae: Papilionoideae; Polhill, 1981; Lock, 2005) comprises about 100 species distributed in northern Eurasia, from the Black Sea to southeastern Siberia, south to eastern and southwestern China, Nepal, Afghanistan, and Turkmenistan. It commonly occurs in cold arid regions, such as the Qinghai–Xizang (Tibet) Plateau, but also is found in forested areas of eastern Asia, especially in northern China. Caragana species often form the dom- inant component of the natural vegetation in cold-temperate dry and arid scrublands, montane meadows, and deserts (Wu, 1980; Zhang et al., 2002). Because of their adaptation to arid conditions, many species of Caragana are widely used as ground covers to con- trol soil erosion in dry areas. They are also used as windbreaks, liv- ing fences, shade trees, and ornamentals. Caragana arborescens is frequently cultivated in North America. Based on morphological similarity, Polhill (1981) placed Carag- ana in subtribe Astragalinae of tribe Galegeae. A phylogenetic esti- mate of the ‘‘temperate herbaceous clade” of Papilionoideae based on DNA sequence data from the internal transcribed spacer (ITS) region of nuclear ribosomal DNA yielded a strongly supported clade (bootstrap value (bt) = 95) comprising the two sampled spe- cies of Caragana, Calophaca Fisch. ex DC., and Halimodendron Fisch ex DC. to the exclusion of the other members of the subtribe (i.e., Alhagi Gagnebin, Astragalus L., Biserrula L., Chesneya Lindl. ex Endl., Gueldenstaedtia Fisch., and Oxytropis DC.) as well as Hedysarum L. and Onobrychis Mill. (Sanderson and Wojciechowski, 1996). A supertree analysis based on sequence data from various genic re- gions also recovered this clade, with a clade comprising Alhagi, Hedysarum L., and Onobrychis Mill. as its sister (Wojciechowski et al., 2000). An analysis based on matK sequences with a subset of these taxa yielded a clade comprising Alhagi, Caragana, Hedysa- rum, and Onobrychis with strong support (bt = 85–92; Bayesian posterior probability (pP) = 1.00), with Caragana as sister to a clade comprising the remaining taxa (bt, pP < 50; Wojciechowski et al., 2004). A subsequent analysis combining matK and ITS data recov- ered the same clade (bt < 50; pP = 1.00) with Caragana as sister (bt = 100; pP = 1.00; Wojciechowski, 2005). Consequently, Lock (2005) transferred these four genera plus Calophaca and Halimo- dendron to tribe Hedysareae. Although there is strong support for a clade comprising Carag- ana, Calophaca, and Halimodendron, molecular phylogenetic studies are thus far inconclusive regarding relationships among these gen- era. An analysis based on ITS sequences, limited to four species of the group, resulted in a clade of Cal. tianschanica (B. Fedtsch.) Bor- iss. and Car. frutex (bt = 73) as sister to Car. arborescens (bt = 79); this larger clade was in turn sister to Halimodendron (Sanderson and Wojciechowski, 1996). A supertree approach based on various genic regions with five samples of the clade resulted in the same 1055-7903/$ - see front matter Ó 2008 Elsevier Inc. All rights reserved. doi:10.1016/j.ympev.2008.12.001 * Corresponding author. Fax: +1 415 379 5737. E-mail address: pfritsch@calacademy.org (P.W. Fritsch). Molecular Phylogenetics and Evolution 50 (2009) 547–559 Contents lists available at ScienceDirect Molecular Phylogenetics and Evolution journal homepage: www.elsevier.com/locate/ympev