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.

For over thirty years archaeologists have provided evidence that southern Arizona pre-Columbian Native Americans, the Hohokam, extensively cultivated agave. However, no archeologists reported finding living agaves growing in the rock-piled or gridded Hohokam fields, therefore researchers could only speculate about the species cultivated. Our work expands upon a recent publication noting several agaves growing in prehistoric dry-farmed fields on terraces overlooking the San Pedro River. These agaves have affinities to A. phillipsiana W. C. Hodgs. and A. palmeri Engelm. based on flower color but differ by their gray-green leaves with thick bases and conspicuous bud imprinting. They are extremely rare, reproduce asexually via rhizomatous offsets with no apparent fruit set, have relatively uniform intra-and inter-population morphology, grow only with archaeological features and are unknown from natural settings: all characteristics expected in a domesticated crop. Here we describe Agave sanpedroensis, provide a key to distinguish it from other agaves in south-central Arizona and propose that it is a clonal, relictual crop grown from ca. A.D. 800-1450 by the Hohokam, and thus represents a 'lost crop' as sought by archaeologists. The extensive size and wide distribution of Hohokam agave fields that transformed the landscape and are still visible today indicates the crop's importance in the Hohokam economy. The question of where and when this agave originated has implications for North American domestication centers. Our discovery emphasizes the importance of collaborative research between archaeologists and botanists whose distinctive data can provide a richer understanding of how the Hohokam developed and then sustained one of the American Southwest's largest prehistoric populations.

The seed oil of Lesquerella and the closely related genus Physaria (Brassicaceae) is rich in hydroxy fatty acids (HFAs). HFAs and their derivatives are used to produce a variety of industrial products including lubricants, nylon-11, plastics, drying agents, protective coatings, surfactants, cosmetics, and pharmaceuticals. Lesquerella fendleri is being developed as a new crop for arid regions of the southwestern United States as an alternative source of HFAs. Between 1995 and 2001, 66 accessions from 28 species of Lesquerella were collected in the United States, 33 accessions from four species were collected in Mexico, and 41 accessions from 15 species of Physaria were collected from the southwestern United States. Mean seed mass ranged from 0.54 to 2.30 mg for Lesquerella compared to 1.70 to 5.80 mg for Physaria. Seed oil content ranged from a high of 32.2% in Lesquerella to a high of 35.4% in Physaria. The fatty acid profile of all species of Physaria and most of the lesquerolic-acid-rich species of Lesquerella contained from 30 to 55% lesquerolic acid, although several species contained Ͼ60%. These collections of wild germplasm provide a diverse gene pool that should enhance our breeding program in developing a domestic source of HFAs.

Cactaceae comprise a diverse and iconic group of flowering plants which are almost exclusively indigenous to the New World. The wide variety of growth forms found amongst the cacti have led to the trafficking of many species throughout the world as ornamentals. Despite the evolution and physiological properties of these plants having been extensively studied, little research has focused on cactus-associated viral communities. While only single-stranded RNA viruses had ever been reported in cacti, here we report the discovery of cactus-infecting single-stranded DNA viruses. These viruses all apparently belong to a single divergent species of the family Geminiviridae and have been tentatively named Opuntia virus 1 (OpV1). A total of 79 apparently complete OpV1 genomes were recovered from 31 different cactus plants (belonging to 20 different cactus species from both the Cactoideae and Opuntioideae clades) and from nine cactus-feeding cochineal insects (Dactylopius sp.) sampled in the USA and Mexico. These 79 OpV1 genomes all share > 78.4% nucleotide identity with one another and < 64.9% identity with previously characterized geminiviruses. Collectively, the OpV1 genomes display evidence of frequent recombination, with some genomes displaying up to five recombinant regions. In one case, recombinant regions span ~40% of the genome. We demonstrate that an infectious clone of an OpV1 genome can replicate in Nicotiana benthamiana and Opuntia microdasys. In addition to expanding the inventory of viruses that are known to infect cacti, the OpV1 group is so distantly related to other known geminiviruses that it likely represents a new geminivirus genus. It remains to be determined whether, like its cactus hosts, its geographical distribution spans the globe.