Although snakes have a nearly worldwide distribution and are a speciose (>4000 taxa) and important group of predators of seed-eating animals, few studies have explored their potential role in diploendozoochory. Here, we use two widespread species of the Sonoran Desert, the foothill palo verde tree (Parkinsonia microphylla) and captive-held western diamondback rattlesnakes (Crotalus atrox), to determine if seeds that have passed through the snakes' digestive tract remain viable and capable of germination up to 1 year post gut transit. Additionally, we tested whether the presence of rattlesnake excrement (faeces and urates) influenced seed germination success. Germination trials were conducted in natural summer conditions in Phoenix, Arizona. We found seeds exposed to snake gut-transit can remain viable and that seeds planted with excrement from which they were recovered had higher germination (40.07%) than seeds planted without excrement (28.95%) and compared to control seeds with no snake exposure (28.2%). These findings suggest that snake excrement may facilitate germination and that western diamondback rattlesnakes have the potential to act as seed rescue and secondary dispersal agents. In light of the emerging global seed dispersal crisis, our results highlight the need for broader studies into the role of diploendozoochory in snakes worldwide.

The increase in human-mediated introduction of plant species to new regions has resulted in a rise of invasive exotic plant species (IEPS) that has had significant effects on biodiversity and ecosystem processes. One commonly accepted mechanism of invasions is that proposed by the enemy release hypothesis (ERH), which states that IEPS free from their native herbivores and natural enemies in new environments can outcompete indigenous species and become invasive. We here propose the virome release hypothesis (VRH) as a virus-centered variant of the conventional ERH that is only focused on enemies. The VRH predicts that vertically transmitted plant-associated viruses (PAV, encompassing phytoviruses and mycoviruses) should be co-introduced during the dissemination of the IEPS, while horizontally transmitted PAV of IEPS should be left behind or should not be locally transmitted in the introduced area due to a maladaptation of local vectors. To document the VRH, virome richness and composition as well as PAV prevalence, co-infection, host range, and transmission modes were compared between indigenous plant species and an invasive grass, cane bluestem (Bothriochloa barbinodis), in both its introduced range (southern France) and one area of its native range (Sonoran Desert, Arizona, USA). Contrary to the VRH, we show that invasive populations of B. barbinodis in France were not associated with a lower PAV prevalence or richness than native populations of B. barbinodis from the USA. However, comparison of virome compositions and network analyses further revealed more diverse and complex plant-virus interactions in the French ecosystem, with a significant richness of mycoviruses. Setting mycoviruses apart, only one putatively vertically transmitted phytovirus (belonging to the Amalgaviridae family) and one putatively horizontally transmitted phytovirus (belonging to the Geminiviridae family) were identified from B. barbinodis plants in the introduced area. Collectively, these characteristics of the B. barbinodis-associated PAV community in southern France suggest that a virome release phase may have immediately followed the introduction of B. barbinodis to France in the 1960s or 1970s, and that, since then, the invasive populations of this IEPS have already transitioned out of this virome release phase, and have started interacting with several local mycoviruses and a few local plant viruses.

BACKGROUND AND SCOPE:Agaves played a central role as multi-use plants providing food, fibre and beverage to pre-contact and historical Mesoamerican cultures. However, their importance to Indigenous Peoples in the Southwest USA and northern Mexico, where they occur because of adaptations such as CAM photosynthesis, is less well known. Archaeological research indicates the Hohokam and other pre-contact Southwestern agrarian people increased agricultural potential in this region by engineering riverine terraces and bajadas for agave dry farming. Agricultural features such as terraces and rock piles were especially characteristic of post-1000 CE with the increase of dense, aggregated populations. We present an overview of six pre-contact agave domesticates (PCADs) the Hohokam and other cultures cultivated, and their ecological and cultural attributes. These PCADs are Agave murpheyi, A. delamateri, A. phillipsiana, A. sanpedroensis, A. verdensis and A. yavapaiensis.CONCLUSION:Pre-contact agriculturists cultivated at least six once cryptic domesticated agave species in the modern Arizona landscape associated with pre-contact agricultural features, such as rock structures. Because of the longevity and primarily asexual reproduction of these agaves, relict clones have persisted to the present day, providing an opportunity to study pre-contact nutrition, trade, migration and agricultural practices. Taxonomic data imply that pre-contact farmers selected desirable attributes, initiating domestication processes that resulted in discrete lineages. These agaves are morphologically and genetically distinct from Southwest US and northern Mexico wild agaves and Mesoamerican wild and domesticated species. Additionally, the remnant clones present a rare opportunity to examine domesticates virtually unchanged since they were last cultivated prehistorically. These discoveries underline the need to view landscapes and some plant species from a cultural, rather than 'natural', perspective and discern potential cryptic species veiled by traditional taxonomic treatments. Protecting and understanding the distribution, and ecological and cultural roles of these plants require interdisciplinary collaboration between botanists, archaeologists, federal agencies and Indigenous Peoples.

The determination of the chromosome numbers of species of Physaria (Brassicaceae) are of interest as part of a breeding program to develop new industrial oilseeds and to further our knowledge of the genus in general. Polyploid plants could be useful in generating novel and improved breeding populations. We report 47 meiotic chromosome number determinations for 19 species of Physaria. The first chromosome number is reported for P. kingii subsp. kaibabensis as 2n = 5 II, and the first report of polyploidy in Physaria kingii susbsp. latifolia with a tetraploid determination of 2n = 10 II. A determination of 2n = 23 II is reported for Physaria mendocina, which was previously reported as 2n = ca. 50, which results in a new base number for the genus of x = 23.

The importance of vertebrate animals as seed dispersers (zoochory) has received increasing attention from researchers over the past 20 years, yet one category in particular, diploendozoochory, remains understudied. As the term implies, this is a two-phase seed dispersal system whereby a secondary seed predator (carnivorous vertebrate) consumes a primary seed predator or granivore (rodent and bird) with undamaged seeds in their digestive tract (mouth, cheek pouch, crop, stomach, or other organ), which are subsequently eliminated with feces. Surprisingly, although snakes are among the most abundant predators of granivorous vertebrates, they are the least studied group insofar as our knowledge of seed rescue and secondary dispersal in a diploendozoochorous system. Here, using live snake subjects of the Sonoran Desert (one viperid and two colubrid species) and seeds of the Foothill Palo Verde ( Parkinsonia microphylla ), a dominant tree of the same region, we experimentally tested germination frequency and rate, and seedling viability. Specifically, to mimic rodents with seed-laden cheek pouches, we tested whether wild-collected P. microphylla seeds placed in the abdomen of thawed laboratory mice and ingested by the snakes would retain their germination viability. Second, we examined whether seeds exposed to gut transit germinated at a greater frequency and rate than the controls. While we found strong statistical support for our first hypothesis, both aspects of the second one were not significant. Accordingly, we provide an explanation for these results based on specific life-history traits (dormant and non-dormant seeds) of P . microphylla. Our study provides support for the role of snakes as important agents of seed rescue and dispersal in nature, their potential as ecosystem engineers, and crucial evidence for the investment of field-based studies on diploendozoochorous systems in deserts and other ecosystems.

Thirteen meiotic chromosome number determinations are reported for seven species of Paysonia O’Kane & Al-Shehbaz (Brassicaceae). Our counts are in agreement with previous published numbers and we make new chromosome number reports for five counties.

The family Cactaceae comprises a diverse group of typically succulent plants that are native to the American continent but have been introduced to nearly all other continents, predominantly for ornamental purposes. Despite their economic, cultural, and ecological importance, very little research has been conducted on the viral community that infects them. We previously identified a highly divergent geminivirus that is the first known to infect cacti. Recent research efforts in non-cultivated and asymptomatic plants have shown that the diversity of this viral family has been under-sampled. As a consequence, little is known about the effects and interactions of geminiviruses in many plants, such as cacti. With the objective to expand knowledge on the diversity of geminiviruses infecting cacti, we used previously acquired high-throughput sequencing results to search for viral sequences using BLASTx against a viral RefSeq protein database. We identified two additional sequences with similarity to geminiviruses, for which we designed abutting primers and recovered full-length genomes. From 42 cacti and five scale insects, we derived 42 complete genome sequences of a novel geminivirus species that we have tentatively named Opuntia virus 2 (OpV2) and 32 genomes of an Opuntia-infecting becurtovirus (which is a new strain of the spinach curly top Arizona virus species). Interspecies recombination analysis of the OpV2 group revealed several recombinant regions, in some cases spanning half of the genome. Phylogenetic analysis demonstrated that OpV2 is a novel geminivirus more closely related to viruses of the genus Curtovirus, which was further supported by the detection of three recombination events between curtoviruses and OpV2. Both OpV2 and Opuntia becurtoviruses were identified in mixed infections, which also included the previously characterized Opuntia virus 1. Viral quantification of the co-infected cactus plants compared with single infections did not show any clear trend in viral dynamics that might be associated with the mixed infections. Using experimental Rhizobium-mediated inoculations, we found that the initial accumulation of OpV2 is facilitated by co-infection with OpV1. This study shows that the diversity of geminiviruses that infect cacti is under-sampled and that cacti harbor diverse geminiviruses. The detection of the Opuntia becurtoviruses suggests spill-over events between viruses of cultivated species and native vegetation. The threat this poses to cacti needs to be further investigated.

Geminiviruses are a group of plant-infecting viruses with single-stranded DNA genomes. Within this family, viruses in the genus Begomovirus are known to have a worldwide distribution causing a range of severe diseases in a multitude of dicotyledonous plant species. Begomoviruses are transmitted by the whitefly Bemisia tabaci, and their ssDNA genomes can be either monopartite or bipartite. As part of a viral survey, various plants including those in the families Alliaceae, Amaranthaceae, Apiaceae, Asteraceae, Brassicaceae, Cactaceae, Cucurbitaceae, Lamiaceae, Lauraceae, Malvaceae, Oleaceae and Solanaceae were sampled and screened for begomoviruses using both a high-throughput sequencing and a begomovirus-specific primer pair approach. Based on the sequences derived using these approaches, the full-length genome of various begomoviruses were amplified from plants using abutting primers. Squash leaf curl virus (SLCV) and watermelon chlorotic stunt virus (WCSV) were identified in Cactaceae (n = 25), Solanaceae (n = 7), Cucurbitaceae (n = 2) and Lamiaceae (n = 1) samples. WCSV is an Old World bipartite begomovirus that has only recently been discovered infecting watermelons in the Americas. Our discovery of WCSV in the USA is the first indication that it has reached this country and indicates that this virus might be widespread throughout North America. Phylogenetic analysis suggests WCSV was introduced to the New World twice. The detection of begomoviruses in cactus plants suggests possible spillover events from agricultural areas into native vegetation. Since WCSV and SLCV have previously been found in mixed infections, pseudo-recombination infection experiments were conducted. We demonstrate that WCSV DNA-B is successfully trans-replicated by SLCV DNA-A despite very low degree of similarity between the replication-associated iterative sequences present in their common region, an essential feature for binding of the replication associated protein. This study highlights the importance of viral surveys for the detection of spillover events into native vegetation, but also suggests the need for more surveillance of WCSV in the USA, as this virus is a serious threat to watermelon cultivation in the Middle East.

Aim: Climate is usually regarded as the main determinant of plant species distributions. However, past human use of species for food might also have influenced distributions. We hypothesized that human- mediated dispersal has resulted in food plants occupying more of their potential geographical range. We also hypothesized that key ecological traits could predispose a species to occupy more of its potential climatic geographical range and be selected by humans for food. Location: The Sonoran Desert of south- western North America. Time period: Present day. Major taxa studied: Food plants. Methods: We used ethnobotanical data and data from large botanical ecoinformatics databases to estimate realized (dispersal- and climate- constrained) and potential (climate- constrained) ranges for food plants and their used and unused congeners. Results: We found that food plants fill more of their potential geographical ranges than their unused congeners. We also found that succulence and annual growth in-teracted with food usage to increase range filling. Main conclusions: Human food use has expanded the distribution of many plant species in the Sonoran Desert.

Genomoviruses (family Genomoviridae) are circular single-stranded DNA viruses that have been mainly identified through metagenomics studies in a wide variety of samples from various environments. Here, we describe 98 genomes of genomoviruses found associated with members of 19 plant families from Australia, Brazil, France, South Africa and the USA. These 98 genomoviruses represent 29 species, 26 of which are new, in the genera Gemykolovirus (n = 37), Gemyduguivirus (n = 9), Gemygorvirus (n = 8), Gemykroznavirus (n = 6), Gemycircularvirus (n = 21) and Gemykibivirus (n = 17).

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.

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.

Cactaceae are native to the new world and have undergone adaptive radiation into diverse morphological shapes and a wide variety of environments. In 1885, the first cacti-infecting virus was described, since then, very little research has been undertaken to explore their associated viral community, with only a few single-stranded RNA viruses having been identified. Here, we investigate the diversity of DNA viruses associated with cacti, using a high-throughput sequencing approach. Cacti samples were collected in Argentina, Bolivia, Brazil, France, Lebanon, Mexico, Spain, Tunisia, and the United States. A novel divergent geminivirus, tentatively named Opuntia virus 1 (OpV1) was identified in a range of cacti species but most commonly in Opuntia spp from the United States (Arizona, Utah, New Mexico, Texas, and Colorado) and Mexico. OpV1 genomes range from 2941 to 2962 nucleotides in length and encode a replication-associated protein (Rep), a capsid protein (CP), a replication enhancer protein, a transactivator protein, an AC4 and a movement protein (MP). The OpV1 genome is significantly different from the presently known and classified geminiviruses, sharing 77% genome pairwise identity amongst themselves. Prevalence of OpV1 appears to be highest at the Phoenix Desert Botanical Garden, with the oldest genome being isolated from herbarium samples dating back to 2002 originally from Mexico. Infectious clones with two in tadem copies of genomes were generated and agroinfiltrated into Nicotiana benthamiana and four different Opuntia spp. The infection was shown to be systemic in N. benthamiana; however only one Opuntia microdasys thus far has been detected as positive post-infection. No specific symptoms were identified with OpV1 infection in either of the plants. This is the first report of geminivirus infecting cacti and these findings demonstrate the broader diversity of their viral community. These findings highlight the relevance of viral surveys for plant species such as cacti, which are unique and ecologically important to specific ecosystems; such information is essential for conservation, and informed management and cultivation practices.

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.

ABSTRACT This research considers the applicability of different vegetation indices at 30 m resolution for mapping and monitoring desert wetland (cienega) health and spatial extent through time at Cienega Creek in southeastern Arizona, USA. Multiple stressors including the risk of decadal-scale drought, the effects of current and predicted global warming, and continued anthropogenic pressures threaten aquatic habitats in the southwest and cienegas are recognized as important sites for conservation and restoration efforts. However, cienegas present a challenge to satellite-imagery based analysis due to their small size and mixed surface cover of open water, exposed soils, and vegetation. We created time series of five well-known vegetation indices using annual Landsat Thematic Mapper (TM) images retrieved during the April–June dry season, from 1984 to 2011 to map landscape-level distribution of wetlands and monitor the temporal dynamics of individual sites. Indices included the Normalized Difference Vegetation Index (NDVI), the Soil-Adjusted Vegetation Index (SAVI), the Normalized Difference Water Index (NDWI), and the Normalized Difference Infrared Index (NDII). One topographic index, the Topographic Wetness Index (TWI), was analyzed to examine the utility of topography in mapping distribution of cienegas. Our results indicate that the NDII, calculated using Landsat TM band 5, outperforms the other indices at differentiating cienegas from riparian and upland sites, and was the best means to analyze change. As such, it offers a critical baseline for future studies that seek to extend the analysis of cienegas to other regions and time scales, and has broader applicability to the remote sensing of wetland features in arid landscapes.

A new species, Mosiera nipensis (Myrtaceae), from the crest of the Sierra de Nipe, Cuba, is described and illustrated. This species is readily distinguished from all other species of Mosiera by two diagnostic characters: four-angled, slightly four-winged young twigs, and calyx lobes that are valvate in the bud. We suspect that this species grows on a serpentine substrate. It is known only from the holotype, a collection made in 1941. An assessment of its conservation status is urgently needed.