For this study, the flora of the northern section of the Lower Verde River, within the Tonto National Forest in Yavapai and Gila Counties, Arizona was documented and analyzed. The study site, part of the northern leading edge of the Sonoran Desert, encompasses about 16,000 hectares and is located approximately 45 miles north-northeast of Phoenix. The area, extends roughly 28 river miles from the East Verde River in the north to Chalk Mountain in the south and is largely only accessible by foot, or by boat, and as a result was previously extremely under-collected. Over a three-year study period, from August, 2017 to May, 2020, 835 plant specimens were collected and identified, representing 360 species which, combined with earlier herbarium specimens collected by others, resulted in 427 plant species found in the study area. The plant diversity of this remote region reflects three distinct vegetation communities: upland Sonoran Desert, perennial riparian corridor, and semi-desert grasslands. Together, these communities act as an important transition zone between the Sonoran Desert and higher elevation habitats. Perennial streams are biodiversity hotspots within the study area. For example, the 400 hectares of Red Creek that falls within the study boundaries contain 28% of the total species. The study site contains several plants of conservation importance including 12 species endemic to Arizona, 22 vulnerable or imperiled species, five US Forest Service sensitive species, and one Federally Endangered species. In order to compare the diversity of the Lower Verde River Flora to nine other similar/related floras in Arizona, a species-area curve using five different models was generated. The resulting models showed the Lower Verde River flora to be very close to, although slightly below, the species-accumulation curve which may indicate that roughly 50-100 species may yet be added to the flora. This prediction seems realistic, as there were several locations that could not be collected due to remoteness and excessive heat.

Las Cienegas National Conservation Area (LCNCA), located in southeastern Arizona, is a place of ecological and historical value. It is host to rare native, threatened and endangered fauna and flora. as well as the site of the oldest operating ranch in the state. The first chapter of this thesis provides a preliminary flora of vascular plants at LCNCA assembled from field collections, photographs and herbarium specimens, and published through the online database SEINet. This preliminary flora of LCNCA identified 403 species in 76 families. Less than 6% of the flora is non-native, perennial forbs and grasses are the most abundant groups, and over a third of species in the checklist are associated with wetlands. LCNCA has been the target of adaptive management and conservation strategies to preserve its biotic diversity, and results from this study will help inform actions to preserve its rare habitats including cottonwood willow forests, mesquite bosques, sacaton grasslands, and cienegas. The second chapter investigates poorly understood aspects of the life history of the endangered Huachuca Water Umbel (Lilaeopsis schaffneriana subsp. recurva. Apiaceae) (hereafter HWU). This wetland species occurs in scattered cienegas and streams in southeastern Arizona and northern Sonora, Mexico. Three studies were conducted in a greenhouse to investigate seed bank establishment, seed longevity, and drought tolerance. A fourth study compared the reproductive phenology of populations transplanted at LCNCA to populations transplanted at urban sites like the Phoenix Zoo Conservation Center and the Desert Botanical Garden (DBG). Results from the greenhouse studies showed that HWU seeds were capable of germinating 15 years in a dormant state and that HWU seeds are present in the seed banks at sites where populations have been transplanted. Also, greenhouse experiments indicated that colonies of HWU can tolerate up to 3 weeks without flowing water, and up to 2 weeks in dry substrate. Transplanted populations at LCNCA monitored in the fourth study produced a higher abundance of flowers and fruit relative to urban sites (i.e. DBG) suggesting that in-situ conservation efforts may be more favorable for the recovery of HWU populations. Findings from these studies aim to inform gaps in knowledge highlighted in USFWS recovery plan for this species.

There is an ongoing debate around the extent that anthropogenic processes influence both plant species distribution dynamics and plant biodiversity patterns. Past human food use may leave a strong legacy on not only the extent that food plants are dispersed and fill their potential geographic ranges, but also on food plant species richness in areas that have been densely populated by humans through time. The persistent legacy of plant domestication on contemporary species composition has been suggested to be significant in some regions. However, little is known about the effects that past human food use has had on the biogeography of the Sonoran Desert despite its rich cultural diversity and species richness. I used a combination of ecoinformatics, ethnobotanical, and archaeological data sources to quantitatively assess the impacts of pre-Columbian, and in some cases, more recent, human-mediated dispersal of food plants on the Sonoran Desert landscape. I found that (i) food plants do fill more of their potential geographic ranges than their un-used congeners, and that polyploidy, growth form, and life form are correlated with range filling and past food usage. I also found that (ii) both pre-Columbian and contemporary human population presence are correlated with relative food plant species richness. Thus, both past human food use and contemporary human activities may have influenced the geographic distribution of food plants at regional scales as well as species richness patterns. My research emphasizes that there is an interplay between ecological and anthropogenic processes, and that, therefore, humans must be considered as part of the landscape and included in ecological models.

It’s no secret that wetlands have dramatically declined in the arid and semiarid American West, yet the small number of wetlands that persist provide vital ecosystem services. Ciénega is a term that refers to a freshwater arid-land wetland. Today, even in areas where ciénegas are prominent they occupy less than 0.1% of the landscape. This investigation assesses the distribution of vascular plant species within and among ciénegas and address linkages between environmental factors and wetland plant communities. Specifically, I ask: 1) What is the range of variability among ciénegas, with respect to wetland area, soil organic matter, plant species richness, and species composition? 2) How is plant species richness influenced locally by soil moisture, soil salinity, and canopy cover, and regionally by elevation, flow gradient (percent slope), and temporally by season? And 3) Within ciénegas, how do soil moisture, soil salinity, and canopy cover influence plant species community composition? To answer these questions I measured environmental variables and quantified vegetation at six cienegas within the Santa Cruz Watershed in southern Arizona over one spring and two post-monsoon periods. Ciénegas are highly variable with respect to wetland area, soil organic matter, plant species richness, and species composition. Therefore, it is important to conserve the ciénega landscape as opposed to conserving a single ciénega. Plant species richness is influenced negatively by soil moisture, positively by soil salinity, elevation, and flow gradient (percent slope), and is greater during the post-monsoon season. Despite concerns about woody plant encroachment reducing biodiversity, my investigation suggests canopy cover has no significant influence on ciénega species richness. Plant species community composition is structured by water availability at all ciénegas, which is consistent with the key role water availability plays in arid and semiarid regions. Effects of canopy and salinity structuring community composition are site specific. My investigation has laid the groundwork for ciénega conservation by providing baseline information of the ecology of these unique and threatened systems. The high variability of ciénega wetlands and the rare species they harbor combined with the numerous threats against them and their isolated occurrences makes these vanishing communities high priority for conservation.

An understanding of diet habits is crucial in implementing proper management strategies for wildlife. Diet analysis, however, remains a challenge for ruminant species. Microhistological analysis, the method most often employed in herbivore diet studies, is tedious and time consuming. In addition, it requires considerable training and an extensive reference plant collection. The development of DNA barcoding (species identification using a standardized DNA sequence) and the availability of recent DNA sequencing techniques offer new possibilities in diet analysis for ungulates. Using fecal material collected from controlled feeding trials on pygmy goats, (Capra hicus), novel DNA barcoding technology using the P6-loop of the chloroplast trnL (UAA) intron was compared with the traditional microhistological technique. At its current stage of technological development, this study demonstrated that DNA barcoding did not enhance the ability to detect plant species in herbivore diets. A higher mean species composition was reported with microhistological analysis (79%) as compared to DNA barcoding (50%). Microhistological analysis consistently reported a higher species presence by forage class. For affect positive species identification, microhistology estimated an average of 89% correct detection in control diets, while DNA barcoding estimated 50% correct detection of species. It was hypothesized that a number of factors, including variation in chloroplast content in feed species and the effect of rumen bacteria on degradation of DNA, influenced the ability to detect plant species in herbivore diets and concluded that while DNA barcoding opens up new possibilities in the study of plant-herbivore interactions, further studies are needed to standardize techniques and for DNA bar-coding in this context.