The Mexican tussilaginioid group consists of 13 diverse genera of sunflowers (Asteraceae: Senecioneae) distributed from the USA to Panama, with most species occurring in montane regions from Central Mexico to Guatemala. Presently, 140 species in 13 genera are recognized with many of these species considered to be endemic to threatened pine-oak forest or cloud forest ecosystems. Sixty-two species within the study group were included in a combined phylogenetic analysis of two regions of the nuclear ribosomal repeat, the internal and external transcribed spacers. Fifty-two of these taxa were analyzed in a phylogenetic framework for the first time. The results from the combined nrDNA analysis (62 species in 12 genera in the combined analysis) strongly support the monophyly of the Mexican tussilaginioid group, however, the topology and hypothesis testing using constraint models indicate that the genera Pittocaulon, Psacaliopsis, and Roldana are not monophyletic. Telanthophora s.s. is monophyletic, although this genus is nested within Roldana s.s. Endemism is abundant among the clade with over half of the species restricted to relatively small geographic areas. Moreover, most members of the group (ca. 120 species, or 87%) are present in montane regions under immense pressure from human land use practices at or above 1500 meters in Mexico and Guatemala. Two of the genera from my study group, Pippenalia and Psacaliopsis were taxonomically assessed based on their morphological characters and the nrDNA results. A single species, Psacaliopsis purpusii, remains in the genus, while Pippenalia delphinifolia, Psacaliopsis macdonaldii, and P. pudica are transferred to Psacalium. Funstonia gen. nov. is here erected a new genus encompassing a single species with two varieties. Chloroplast genomes of Arnoglossum atriplicifolium, Roldana aschenborniana, R. barba-johannis, and Telanthophora grandifolia were sequenced with next generation sequencing in order to identify regions of variation and to compare the assemblies produced via de novo and reference-based methods. The reference-based assemblies were more complete than the de novo assemblies, and therefore the former sequences were utilized for phylogenetic analyses. / text

In this thesis I investigated the importance of plant-animal mutualisms to the reproductive success of three West African mistletoe species in two genera, Globimetula braunii, Agelanthus brunneus and A. djurensis, in Ngel Nyaki Forest Reserve, Nigeria. The flowers of all three mistletoes were visited by 3 - 4 species of sunbird. Agelanthus flowers were also visited by honeybees (Apis mellifera) and a small social wasp species (Vespinae). A. mellifera appeared to be robbing nectar from the flowers of A. brunneus. To investigate the relative role of pollinators, I compared flower opening and fruit set amongst bagged, caged, natural, hand-selfed and hand-crossed treatments. The flowers of G. braunii were able to selfopen on average 66% of the time when pollinators were excluded, whereas pollinators were essential to the flower opening mechanism of both Agelanthus spp. Insects were as effective at opening the flowers of Agelanthus spp. as sunbirds. However, flower opening ability did not translate directly into pollination effectiveness, as insect access alone did not result in significantly higher fruit set than that observed under the bagged condition. There was no significant evidence for autonomous selfing within any of the three mistletoes and thus reproduction was almost entirely reliant on 3 – 4 species of sunbird. Hand-pollinations of all three species indicated a high level of self-compatibility, and in one species, G. braunii, pollen limitation was evident (PLI = 0.504). To investigate dispersal mutualisms amongst the three mistletoe species, fruit ripening and removal were monitored. The fruits of all three mistletoe species appeared to be removed rapidly from plants as they ripened, with few ripe or overripe fruits present on the branches at any time. Dispersal efficiency, or the total proportion of fruit crop removed across the fruiting season, was also very high (>90%) for the Agelanthus spp. but lower in G. braunii, for which almost a third of the total fruit crop was recorded undispersed in fruit nets beneath plants. Mistletoes are an important component of West African montane forests. Disruption to mistletoe reproductive mutualisms may affect not only mistletoes and their mutualists directly, but also an entire network of species, all linked within a web of interactions. To protect these ecosystems from further degradation, increased community involvement and greater enforcement of laws set out to manage montane forest habitat across the region is essential. Without this support, the future of these ecosystems and the web of interacting species within remains tenuous.

Forest edges created by scattered-patch clear-cutting have become a common landscape feature in tropical montane forests, including pine-oak and evergreen cloud forests. Forest-edge-pasture gradients were characterised with respect to changes in vegetation structure and ecological function in the Highlands of Chiapas, Mexico. In this study two edge types were recognised by assessing vegetation structure and floristic composition along a gradient from adjacent clearings into the forest interior. The influence of edge type (either “hard” or “soft”) was investigated with respect to acorn production, predation, dispersal and germination, seedling establishment and abundance of small mammals during two consecutive years. There was no significant difference between the forest interior and the edge in plant density and basal area. Floristic richness and composition did not vary with depth-of edge influence. Edge type influenced the relationship between probability of acorn removal by small mammals and distance from the edge in both mast fruiting and non-mast fruiting years. Movements of metal-tagged acorns supported the hypothesis that soft edges are permeable to acorn predators and/or dispersers, and that rodents move acorns up to 15 m into the grasslands in soft edges. In hard edges, acorn dispersal and removal was greater within the forest. Peromyscus spp. were the main acorn predators and/or dispersers of acorns. The intensity and rate of acorn removal varied with the year, demonstrating that in mast-fruiting years some seeds may escape predation by animals, according to the predator satiation hypothesis. Grasslands presented fewer insect damaged acorns and higher seedling emergence than the edge and the forest, emphasising the importance of acorn dispersal. Seedling survival and growth were higher for 12 m into grassland from the soft edges, suggesting that the probability of oak expansion into the grassland increases when the grasslands have been abandoned and have a scattered cover of shrubs. The results indicate that edge structure alters edge function (edge permeability), which determines the probabilities of tree invasion into old-fields. These findings have implications for the conservation of montane forest in Mexico where scattered patch clear-cutting is widespread. Recommendations are made for different restoration practices to accelerate tree colonisation into the grasslands across hard and soft edges.

Climate change is expected to disproportionately impact high elevation ecosystems by disrupting current temperature and precipitation regimes. The future carbon balance of these systems is uncertain, given the interplay between longer growing season length and the potential for increased drought. Currently, the most robust inferences about ecosystem responses to changing climate come from the integration of experimental and observational methods. In this thesis, I utilize evidence from a warming experiment and an elevational gradient to gain insights into how aspects of ecosystem productivity and community functional composition change in response to the abiotic environment. First, I show that ecosystem productivity was similar in the heated and ambient treatment groups of the warming experiment. Net ecosystem productivity (NEP) was similar between treatments with only slightly increased NEP in the early season in the heated treatment. Important leaf functional traits (leaf mass per area, LMA; leaf dry matter content, LDMC) shifted with heating in directions associated with higher productivity, both at the community level and within species. While these results are counterintuitive, potential insight was provided by a soil cooling effect found in the heated plots in the early season. Second, I investigate ecosystem productivity across spatial and temporal gradients using phenology cameras. I show strong relationships between greenness indices generated from camera images and on-the-ground measurements of gross primary productivity (GPP). I also used changes in greenness indices early season to infer green-up rates, and found a strong pattern of increasing green-up rate with increasing elevation. Together, these studies highlight the importance of comparing experimental and gradient methods to assess how different spatial and temporal scales influence our conclusions about the effect of climate change on ecosystems.

Only a small body of work currently exists regarding the geomorphology of humid tropical montane rivers. The research that does exist reports rapid geomorphic processes and high sediment loads compared to other montane rivers. This research applies traditional field survey methods combined with new applications of remote sensing techniques to examine the geomorphology and sediment dynamics of the montane portions of the Rio Pacuare in Costa Rica. A suite of geomorphic components (channel slope and width, lateral contributions and planform) are examined and a model presented that illustrates the complexity of the Rio Pacuare’s geomorphology and how the distribution of alluvial sediment varies in relation to geology (tectonics and lithology) and flow hydraulics (stream power). Next, average annual bedload sediment transport capacity is estimated using fifty-one years of daily discharge data at six different locations within the study area, including the temporal (monthly) variability of sediment flux due to dry versus wet season discharge regimes. Then, a time-step hydraulic model is created that simulates observed (modern) and potential future discharge scenarios based on regional climate change model results. The simulated discharge data for two locations within the study area is then integrated into the sediment transport model to examine how sediment flux, and thus channel geomorphology, is likely to change in response to changes in the river’s discharge regime.

The Amazon rainforest along the Andean foothills contains exceptionally high diversity, much of it recent. The complex geology of the Andes and paleoclimate fluctuations preclude complex dispersal scenarios. This, in turn, has contributed to idiosyncratic speciation modes among shallowly-diverged Amazonian taxa. The poison frog genus Ameerega recently radiated throughout the Andes and Amazon (MRCA ~8.7 mya), with some taxa diverging as recently as the late Pliocene and early Pleistocene. Some species-level relationships remain poorly resolved, especially among recently diverged taxa. Here, I define ancestral populations and address the phylogenetic relationships among three recently diverged Peruvian Ameerega species (A. cainarachi, A. petersi, and A. smaragdina), using multiple species tree methods, including one that accounts for reticulate evolution. I complement species tree inference with assessments of behavioral divergence and niche overlap to better resolve species boundaries. I further explore the phylogeographic history of these species of Ameerega with demographic inference, considering evidence for population expansions. These analyses provide the basis to address speciation hypotheses in the Andean lowlands, including the refugial hypothesis and dispersal-vicariance hypothesis. I find support to synonymize A. smaragdina with A. petersi, and that divergent and convergent reticulation processes and historical range expansion impacted the A. petersi group’s speciation history. In addition, I use species distribution modeling (SDM) to infer the A. petersi group’s range dynamics since the mid-Pleistocene (785 kya). SDMs reveal periods of range expansion, contraction, and shifts, tracking climate fluctuations during the Pleistocene. In order to explicitly consider the relative roles of climate and geography in structuring genetic diversity at different time periods, I use a landscape genetics approach and consider 21 isolation-by-resistance hypotheses. These hypotheses include climatic resistance layers from five time periods in the Pleistocene, a stability layer, two geographic layers that reflect the two species’ natural history (distance-from-river and mid-elevation resistance), and composite layers that pair geographic and environmental layers. I find that climate stability and river proximity best explain gene flow. I find that phylogeographic, niche modeling, and landscape genetic evidence supports a dispersal-vicariance model of speciation in the A. petersi group.

Data on rates of atmospheric deposition is limited in many montane ecosystems, where high spatial variability in meteorological, topographic, and vegetation factors contributes to elevated atmospheric inputs and to the creation of deposition hotspots. Addressing the ecological consequences of increasing deposition in these areas will require a better understanding of surface controls influencing atmospheric deposition rates at both large and small-scales. The overarching objective of this thesis research was to understand the influence of vegetation structure and canopy exposure on small-scale patterns of atmospheric sulfate, nitrate, and chloride deposition inputs to a conifer forest in the Santa Cruz Mountains, California. Throughfall ion fluxes (i.e., ions delivered in water that pass from the forest canopy to the forest floor), bulk deposition (i.e., primarily wet deposition), and rainfall data were collected during the rainy period from October 2012 to May 2013. Throughfall SO42-, Cl-, and NO3- fluxes were measured beneath eight clusters of Douglas fir (Pseudotsuga menziesii) trees (three trees per cluster) differing in tree size (i.e., diameter at breast height; DBH) and canopy exposure. In each cluster, a throughfall collector was placed 1-meter from the bole of an individual tree, for a total of 24 individual collectors. The position of each throughfall collector was recorded with a Trimble® GPS. In addition, tree height, tree diameter, and leaf area index, were measured for all trees. LiDAR data were obtained from GeoEarthScope’s Northern California Airborne LiDAR project and used to model the elevation (DEM), canopy surface height (DSM), tree height (CHM), slope, and curvature of the canopy surface across the entire study area. Over the rainy season, total throughfall flux of SO42--S, a conservative tracer of total deposition (wet + dry + fog), to Douglas fir clusters ranged from 1.44 - 3.84 kg S ha-1 wet season-1, while dry and fog deposition ranged from 0.13 -2.37 kg S ha-1 wet season-1. Total deposition to exposed mature tree clusters was 1.7-2.7 times higher than other clusters. Patterns of total Cl- fluxes (17.10 – 54.14 kg Cl- ha-1 wet season-1) resembled patterns of total SO42--S inputs. Overall, net throughfall fluxes (throughfall – bulk deposition) to Douglas fir trees clusters were more variable than total throughfall fluxes. Net SO42--S and Cl- fluxes to individual collectors increased with tree DBH and the convexity of the canopy surface. Compared to SO42--S and Cl- in throughfall, total NO3--N fluxes (0.17 - 4.03 kg N ha-1 wet season-1) were low and appeared to vary with small-scale changes in elevation. Geospatial technologies and remote sensing tools, such as LiDAR, are promising in the study of relationships between atmospheric deposition and topography (including vegetation), and in scaling-up estimates of atmospheric deposition to larger spatial scales. Understanding small-scale surface controls on atmospheric deposition has implications for different areas of research within geography, including modeling the spread of emerging infectious disease and assessing the effects of nitrogen cycling on native and invasive plant species composition.

This research considers human impacts on three components of biodiversity (composition, spatial structure and function). Given the relict character and unusual biogeochemical balance of tropical montane cloud forests in Mexico, logging poses a pressing threat to their survival. Specifically, this thesis explores the effect of selective logging and above-ground secondary succession on the biogeochemical cycling and soil macroinvertebrate community in a cloud forest in Oaxaca, Mexico. The research investigates: (1) whether the above-ground chain of successional changes in tree dominance, litterfall, litter diversity and soil microenvironmental conditions are coupled with a below-ground succession of soil nutrient availability and macroinvertebrate communities, (2) the role of spatial structuring of environmental conditions and litter resources as determinates of the nutrient availability and macroinvertebrate taxa abundance, (3) the implications of successional changes for decomposition and (4) whether the local influence of single trees explains the spatial structure of macroinvertebrate communities in late successional forests. The work was carried out in three chronosequences (c.15, 45, 75 and 100 year-old stages) of high altitude (1500-2000m) tropical montane cloud forest, two recently logged sites and two pristine sites. the macroinvertebrates in the litter and mineral soil were hand sorted from monoliths. Parametric statistics and canonical correspondance analysis were used to determine mean successional trends, and Spatial Analysis by Distance Indices and geostatistical methods were used in combination to determine spatial patterns. Two decompositional experiments were performed to explore the relationship between decompositional rate, litter quality and macroinvertebrate community higher taxa composition in different successional stages and under the canopy of different tree species. The research showed that: 1. The macroinvertebrate community composition in both recently logged sites and pristine forests were distinct compared to secondary successional stages. A decrease in soil temperature and nutrient availablity but increase in litter diversity and soil organic matter recorded through succession were accompanied by an increase in the number of macroinvertebrate taxa in the soil. For exampl, Collembola were most abundant in recently logged sites and earthworms (Megascolecidae) were almost excluvely found in pristine forests. 2. The oldest secondary forest (100 year-old) showed the highest frequency of aggregation in the abundance of individual macroinvertebrate taxa, and the highest and most uniform value of Shannon's diversity. This suggests that high levels of diversity in litter resources and soil chemistry in late succession are associated with complex spatial structuring of highly diverse macroinvertebrate communities. 3. The leaves of a late successional species (Persea americana)decomposed at a slightly slower rate than an early successional species (Pinus chiapensis) in all successional stages, yet the number and Shannon's diversity of macroinvertebrate taxa that invaded decomposing P.Americana leaves was consistently higher. The preference of macroinvertebrate taxa for the late-successional leaves was ultimately explained by differences in leaf quality during decomposition. P.americana leaves had higher concentrations of cations throughout decomposition and their concentration of lignin and nitrogen became higher. 4. In the 100-year-old forest, the effect of seasonal variation on soil microenvironmental conditions and litter availability was different under the canopy of different tree species. Furthermore, the chemical evolution of the same leaf type (e.g. Oreopanax xalapensis) was differentwhen decomposing under different canopies. The highly diverse and spatially complex macroinvertebrate community found in late succession (and experimental litter) was largely explained by the interactive effects of seasonal variation, tree species, litter quality and availability of the decomposing leaf type. The results provide the first analysis of the relationship between soil biodiversity and the tight biogeochemical cycling in this relict ecosystem type. Overall the results indicate that mature cloud forests sustain a diverse and spatially heterogenous macroinvertebrate community. The compositional and spatial components of soil biodiversity are compromised by logging and full recovery may take mopre than 100 years.

As bison are considered to be ecologically extinct, and negative interactions between bison and cattle are perceived to limit bison restoration and cattle production, I designed a series of studies to test for potential competition between bison (Bison bison) and cattle (Bos taurus) for forage on the Henry Mountains in southern Utah. These studies provide insight into key information gaps previously identified by the Utah Division of Wildlife Resources (UDWR), Bureau of Land Management, and the local grazing association. The results indicate that bison and cattle are not strong competitors for forage on the Henry Mountains. Jackrabbits (Lepus californicus) emerged as the strongest competitive threat to cattle, consuming more than twice the amount of forage consumed by bison. Further, bison habitat preferences did not match with cattle habitat needs as reported by a survey of the local ranching community. This suggests that negative impacts on cattle due to bison have been overstated. Still, any potential negative impacts of bison will be felt by a small group of local individuals. This prompted me to design a new management scheme, which has the potential to increase the number of bison on the Henry Mountains while also compensating local ranchers for reducing the number of cattle they graze in the area. This system should be mutually beneficial for the local ranching community and the UDWR, and easily implemented by taking advantage of the currently exiting conservation license program.

The mountainous areas in the Intermountain West (IMW) of the North America are considered as the major water reservoir for the Western US. Summer evapotranspiration (ET) and soil moisture are key factors affecting the annual water yield in the montane region of the IMW. This research estimated ET of four common vegetation types (aspen, conifer, grass, and sage) and areal soil moisture in an advanced instrumentation site located at the T.W. Daniel Experimental Forest (TWDEF). Among instrumented forest research sites worldwide, TWDEF is one of a few with triplicate measures of meteorological parameters, radiation, and soil moisture within four common vegetation types in the IMW. This unique dataset enables study and understanding of the ecological and hydrological responses to climate change in Utah and the IMW region. In a second phase of this study, summer water uses from the four common vegetation types were simulated using a numerical simulation model, Hydrus-1D. The simulation was informed by soil moisture measurements at three depths (0.1 m, 0.25 m, and 0.5 m) and by ET measured from an eddy covariance tower. The results confirmed the value of numerical simulations as a viable alternate method to estimated ET where no direct ET measurements are available. It also provided comparison of water use by these vegetation species including both high and low water years. In the third phase of this study, a comparison was made between the intermediate-scale areal soil moisture measured by a Cosmic-ray neutron probe (CRNP) and the in situ TDT soil moisture network at the TWDEF site. Improved correlations were obtained, especially after shallow rainfall events, by including numerically simulated soil moisture above 0.1 m where no measurements were available. The original CRNP calibration exhibited a dry bias during spring/early summer, leading to the need for a site-specific enhanced calibration, which improved the accuracy of the CRNP soil moisture estimate at the TWDEF site.