Premise Although numerous phylogenetic studies have been conducted in Cactaceae, whole‐plastome datasets have not been employed. We used the chollas to develop a plastome dataset for phylogeny reconstruction to test species relationships, biogeography, clade age, and morphological evolution. Methods We developed a plastome dataset for most known diploid members of the chollas (42 taxa) as well as for other members of Cylindropuntieae. Paired‐end, raw reads from genome skimming were reference‐mapped onto a de novo plastome assembly of one species of cholla, Cylindropuntia bigelovii, and were used to build our plastome dataset, which was analyzed using various methods. Results Our plastome dataset resolved the phylogeny of the chollas, including most interspecific and intraspecific relationships. Tribe Cylindropuntieae arose ~18 mya, during the early Miocene in southern South America, and is supported as sister to the South American clade Tephrocacteae. The (Micropuntia (Cylindropuntia + Grusonia)) clade most likely originated in the Chihuahuan Desert region around 16 mya and then migrated into other North American desert regions. Key morphological characters for recognizing traditional taxonomic series in Cylindropuntia (e.g., spiny fruit) are mostly homoplasious. Conclusions This study provides the first comprehensive plastome phylogeny for any clade within Cactaceae. Although the chollas s.l. are widespread throughout western North American deserts, their most recent common ancestor likely arose in the Chihuahuan Desert region during the mid‐Miocene, with much of their species diversity arising in the early to mid‐Pliocene, a pattern strikingly similar to those found in other western North American desert groups.

A gynodioecious hexaploid {n = 33), Cylindropuntia chuckwallemis M. A. Baker & M. A. Cloud-Hughes, is newly described. Populations of C. chuckwallensis extend from the Eagle Mountains of Joshua Tree National Park, through the Chuckwalla Mountains of Riverside County, to the north side of the Chocolate Mountains in Imperial County, California, USA, and occur on a variety of substrates primarily between 400-1600 m (1312-5250 ft) elevation. Of the flowering individuals studied, 38% produced only pollen-sterile flowers. Flower color in C. chuckwallensis ranges from dark red-purple (33%) through orange (54%) to yellow (13%). For most individuals (93%) the style and filaments are dark red to light pink. Morphological measurements were made for 15 populations of Cylindropuntia, including four of C. chuckwallensis, four of C. echinocarpa, three of C. multigeniculata, and four of C. acanthocarpa. Multivariate analyses indicated that C. chuckwallensis possesses a unique combination of characters. Fewer than 3% of the 121 C chuckwallensis individuals sampled were misclassified by discriminate function analysis, one as C. echinocarpa, and three as C. multigeniculata.

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