<p> Evolutionary biologists are supremely interested in the events that cause populations to diverge and speciate, and the mechanisms that maintain divergence over time. Here, I investigate the evolutionary history of a boreal bird species complex. Boreal bird species are co-distributed, diverged during the Pleistocene, and generally have patterns of genetic divergence that are consistent with a single &ldquo;boreal&rdquo; clade in northern and eastern North America. The Gray-cheeked Thrush species complex, however, shows a possible species break in eastern North America between the Bicknell&rsquo;s Thrush (<i> Catharus bicknelli</i>) and Gray-cheeked Thrush (<i>Catharus minimus </i>). Using population genetic and genomic analyses of the largest sampling to-date of either species, I find that the eastern break indeed coincides with a species-level divergence, although low levels of admixture in a few individuals and one probable hybrid hint at the possibility of occasional hybridization. Species distribution models (SDMs) of the Last Glacial Maximum revealed that divergence may have been maintained by residence in different late-Pleistocene refugia. However, because speciation occurred mid-Pleistocene, I examined the geographical context of divergence of the Bicknell&rsquo;s Thrush and Gray-cheeked Thrush using multivariate analyses and ecological niche modeling techniques of local-scale habitat data and broad-scale climate and tree species distributions. Local-scale habitat analyses reveal that the thrushes breed at sites with unique tree species composition, physiognomy (forest structure), and ground cover characteristics; furthermore broad-scale analyses reveal that niche divergence, rather than conservatism, was the predominant pattern for these species, suggesting that ecological divergence has played a role in their speciation. This dissertation supports the hypothesis that the Bicknell&rsquo;s Thrush and Gray-cheeked Thrush are distinctive species that breed in divergent local- and broad-scale niches and emphasizes that this species-level divergence seems unique among boreal bird species.</p>

<p>The decline of the Oregon Spotted Frog (<i>Rana pretiosa</i>), a Pacific Northwest endemic now federally listed as threatened, has been attributed to several aspects of ecosystem alteration, primarily habitat degradation and loss. The introduced American Bullfrog (<i>Rana (Aquarana) catesbeiana </i>) has been widely implicated in those declines, but the basis of that contention has been difficult to characterize. The bullfrog occurring at every site of recent Oregon Spotted Frog extirpation has focused concern about its impact. </p><p> Here, I present a suite of interconnected studies that examine the behavioral ecology of both species to better understand the potential for bullfrog-mediated Oregon Spotted Frog extirpation. I quantified Oregon Spotted Frog anti-predator behavior from the only known population successfully co-occurring with bullfrogs (Conboy Lake) and a population devoid of bullfrog impact (Big Marsh), and compared these behaviors to the predatory traits of the bullfrog. The initial study revealed that captive-reared individuals from the Oregon Spotted Frog population that has successfully co-occurred with bullfrogs respond faster to a predatory stimulus (measured as latency to response) than Oregon Spotted Frogs from a population not to exposed to bullfrogs. Subsequent field investigations of the approach distance allowed by a predator stimulus before taking evasive action (termed the flight initiation distance: FID) conducted with the Oregon Spotted Frog population co-occurring with bullfrogs first demonstrated that FID of recently metamorphosed bullfrogs is consistently greater than that of recently metamorphosed Oregon Spotted Frogs. Further, examination of FID across all post-metamorphic age classes of Oregon Spotted Frogs revealed that older frogs do not allow as close approach as recently metamorphosed Oregon Spotted Frogs. This age class shift in FID did not occur in the Oregon Spotted Frog population not exposed to bullfrogs. In the latter population, FID did not differ among age classes. </p><p> Since the bullfrog might be driving this age-based change in anti-predator behavior, I explored the variation in strike distance of bullfrogs from the site of co-occurrence in both the field and laboratory to determine the extent of overlap with Oregon Spotted Frog FID. I found that the bullfrog strike distance significantly overlaps the FID of all ages of Oregon Spotted Frogs from the bullfrog-free site but only that of youngest (recently metamorphosed) frogs at the site of co-occurrence. Older Oregon Spotted Frogs from the site of co-occurrence generally escaped at distances greater than the strike distance of bullfrogs. </p><p> I also collected > 880 bullfrogs from the site of co-occurrence and analyzed the stomach contents to assess their dietary trends. I found that bullfrogs consume Oregon Spotted Frogs at the site, but do not eat the larger (older) frogs. Moreover, the body size ratio between Oregon Spotted Frogs as prey and bullfrogs as predators suggests that nearly all of the adult size distribution of bullfrogs at Conboy would be incapable of preying on adult Oregon Spotted Frogs. </p><p> Collectively, these studies strongly suggest that bullfrogs have altered the escape behavior of Oregon Spotted Frogs at Conboy Lake and that most adult Oregon Spotted Frogs at Conboy may have a size-based release from predation by bullfrogs. Implicit in this finding is that bullfrogs may pose a real threat via predation to other Oregon Spotted Frog populations with which they might come into contact where the distribution of bullfrog body sizes differ substantially from that at Conboy Lake. </p>

<p> Minimizing inbreeding depression and maintaining genetic diversity are central goals of conservation programs, including the Greenback Recovery Program (GRP), an interagency effort to protect the lineage of trout native to the South Platte River drainage in Colorado. The last remaining population of greenback cutthroat trout consists of about 700 individuals found in a three-mile stretch of stream in the Arkansas drainage, outside its native range. The GRP is committed to reintroducing the greenback into its native range in the South Platte. To do so, they are using a hatchery stock founded by 46 wild individuals. Both wild and hatchery populations have limited genetic diversity and deformities are common in the hatchery population. </p><p> Recovering the fitness of the hatchery population of greenbacks requires variation in fitness upon which selection can act. I performed crosses between individuals to quantify any remaining variation in fitness. The population had high variation in egg production and fertilization but very little variation in overall offspring survival. This suggests that the hatchery managers should consider alternative sources of genetic diversity, such as individuals from the wild or from other subspecies.</p><p> I used a crossing experiment between greenback cutthroat trout and a related subspecies to describe the genomic patterns of recovery of fitness. When greenbacks are crossed with another subspecies, the hybrid offspring have much higher fitness than the pure greenback offspring. I found that the probability of survival has a strong genetic component and that relatedness between the parents is a strong predictor of offspring survival, with offspring from less related greenback parents having higher fitness. This research will help managers decide whether outcrossing is a viable strategy to increase genetic diversity in cutthroat trout.</p><p> I explored the barriers to implementing evolutionary restoration tools, which include a reluctance to disrupt the taxonomic integrity of species. Evolutionary restoration is analogous to ecological restoration: both fields face the challenge of choosing appropriate restoration baselines and setting realistic restoration goals. Active interventions to increase gene flow should be considered as a complement to habitat protection and ecological restoration to prevent species decline.</p><p> I developed a teaching case study based on cutthroat trout research. The case study gives upper division biology students practice in applying evolutionary concepts to a real-world conservation problem by making evidence-based decisions accounting for uncertainty in real data sets. I used the case of cutthroat trout in Colorado because it requires a fundamental understanding of evolutionary processes such as speciation and hybridization and raises questions about the value of native species and the goals of conservation efforts.</p>

<p> Multiple ecological factors (e.g., Bergmann&rsquo;s rule, competition, food quality and quantity) can be responsible for changes in animal body size over time. White-tailed deer <i>(Odocoileus virginianus)</i> serve as an ideal candidate for studying these variables due to their importance today (to hunters and to wildlife enthusiasts), their known phenotypic plasticity in response to ecological factors, and their high frequency in zooarchaeological collections. Using post-cranial, weight-bearing bone measurements as a proxy for body size, this study determines that stunting occurred from prehistoric to modern times in Missouri white-tailed deer. Forage availability and intraspecific competition were the major influences on body size. A diminution event occurred ~1600&ndash;1300 radiocarbon years B.P. and is associated with fluctuating climatic conditions at the time. Modern deer in Missouri are smaller relative to an early prehistoric (ca. 3500 &ndash; 1300 B.P.) sample but smaller than a late prehistoric (ca. 1300 &ndash; 200 B.P.) sample. The historic diminution event seems to stem from modern management goals favoring large population sizes. Advantages of incorporating paleozoological data with modern conservation biology are exemplified by this study.</p>

<p> This project aims to develop a panel of sequence capture baits to use for SNP genotyping for pedigree analysis in Wood Ducks (<i>Aix sponsa </i>) as well as for general population genetic analysis within species in the family Anatidae. SbfI RAD libraries were prepared with samples comprising five duck species (N = 96). Sequenced libraries were aligned to the Mallard (<i>Anas platyrhynchos</i>) reference genome and screened for 120bp regions proximal to the SbfI cutsite that contained SNPs conserved collectively in each species. A series of screenings identified regions which were used to produce 2,508 custom sequence capture baits. These baits were tested in novel individuals from the same species used to design the baits as well as novel species representing different taxonomic ingroup and outgroup levels within Aves. These baits delineate species at various taxonomic scales, even above the taxonomic level that was originally targeted and will prove useful for analyses of population and comparative genetics for species of Anatidae and perhaps more broadly.</p><p>

Habitat modification, when it results in population fragmentation, often results in the loss of genetic diversity due to reduced gene flow, inbreeding, and genetic drift. However, the severity of these effects depends on how diminished dispersal and gene flow become between patches of suitable habitat. An empirical understanding of how habitat change affects dispersal and gene flow within and among patches is essential to predict the effects of increased habitat modification and landscape change on population persistence and processes of divergence. Recent studies in landscape ecology suggest that our understanding of dispersal in a heterogeneous landscape will improve by explicitly considering the heterogeneity of matrix habitats, or unsuitable habitats between patches of suitable habitat. In this dissertation, I describe population genetic structure and dispersal patterns in the Central American Squirrel Monkey (Saimiri oerstedii, Primates: Cebidae), a New World primate threatened with extinction and living in a heterogeneous, human-modified landscape, using analyses that explicitly consider matrix heterogeneity. I focus on the more endangered S. o. citrinellus, whose already restricted distribution in the Central Pacific region of Costa Rica has undergone considerable anthropogenic modification since the early 1900s. I collected non-invasive fecal samples from S. o. citrinellus across the Central Pacific region, obtaining full genotypes from 233 individuals. I also obtained 11 samples from S. o. oerstedii in the Southern Pacific region of Costa Rica from a collaborator, as well as fine-scale landscape data for the Central Pacific. I analyzed the data using molecular systematics, population genetics, and landscape genetic techniques. In this dissertation, first I explore whether molecular genetic support exists for the subspecies distinction between S. o. citrinellus and S. o. oerstedii. Second, I describe population genetic structure and recent migration patterns within S. o. citrinellus using traditional population genetic methods and Bayesian models. I also compare population genetic structure among males versus females to test for sex-biased dispersal patterns in S. o. citrinellus. Then, using landscape genetic approaches, I describe the relationship between landscape heterogeneity and genetic structure in S. o. citrinellus, and inferred which matrix habitats are costly to dispersal. Finally, I offer explicit recommendations for the conservation management of S. oerstedii. My results provide genetic support for S. o. citrinellus and S. o. oerstedii as separate taxa referred to as subspecies. Also, I found evidence of population genetic structure in S. o. citrinellus, with two genetically distinct populations and lower genetic diversity in the western population. I did not find genetic evidence for female-biased dispersal in S. o. citrinellus as expected. Instead, my results suggest that both sexes disperse, with males dispersing over longer distances. The landscape genetic analysis suggests that landscape heterogeneity is important in determining local population genetic structure in S. o. citrinellus in the Central Pacific region of Costa Rica. Specifically, oil palm plantations are moderate barriers to gene flow between populations, but not other matrix habitats. However, these inferences are specific to the composition and configuration of the Central Pacific landscape, and should not be generalized to all S. oerstedii populations. This study generated important information for conservation management. Based on my results, I recommend that conservation managers house the two S. oerstedii subspecies separately in captive facilities, and only transfer, reintroduce, or translocate among groups of the same subspecies. However, transfers, reintroductions, or translocations of either males or females are both likely to be successful for S. o. citrinellus in the Central Pacific region, pending further behavioral study. I also recommend that, in order to augment dispersal to the isolated western population of S. o. citrinellus, conservation efforts should focus on building biological corridors through or around adjacent oil palm plantations. Also, managers should prioritize the maintenance of existing forest connectivity in the Central Pacific region. The results also have important implications for future studies of evolutionary and ecological processes in heterogeneous landscapes. This study contributes to a growing body of research that finds differences in dispersal patterns among local primate populations of the same taxon. My results suggest that predictive models for variation in dispersal patterns should consider both variation among the environments of local populations within a species and temporal variation in local environments (e.g. recent habitat disturbance). Finally, this dissertation also supports the idea that matrix heterogeneity should be considered explicitly in studies of dispersal and gene flow, as opposed to assuming that all non-suitable habitats have a uniform effect on these processes. In the future, agent-based simulation approaches combined with ecological niche models and data on adaptive genetic diversity could expand upon this work to inform predictive models for population divergence and speciation under different climate and landscape change scenarios.

Recent research into the ecological origins and social implications of ecosystem services, the benefits ecosystems provide to society, is predicated on the downward trends observed for many services. Current work increasingly emphasizes how interactions among ecosystem services (synergies and trade-offs) affect the delivery of multiple services, from soil fertility at field scales to watershed-scale hydrological function, to global climate regulation. Meanwhile, research on the relationship between biodiversity and ecosystem functioning has identified substantive linkages between the biodiversity of ecosystems and the services they provide, provoking interest in aligning biodiversity conservation with the sustained delivery of ecosystem services. To better understand the delivery of multiple ecosystem services relevant to smallholder farmer livelihoods in the tropics, the production of wood and livestock forage and the structure and fertility of soils were examined in grazed and improved fallows in western Kenya. The objectives were to investigate fine-scale interactions among ecosystem services, and the potential of fallow plant diversity to enhance levels of multiple services simultaneously, i.e., ecosystem service multi-functionality. To examine influences of fallow vegetation and management on soil structure and fertility, the biomass and functional traits (green tissue N, lignins, polyphenols, lignins+polyphenols) of fallow plants and the condition of soils were quantified. Positive associations of tissue content of lignins+polyphenols with soil organic carbon (SOC) and steady infiltration rates indicated a role of recalcitrant carbon compounds in slowing SOC turnover and supporting soil structural development, while grazed fallows had lower infiltration than improved fallows, likely a result of livestock trampling and soil compaction. To investigate whether woody overstory plants and fallow management generate interactions between the production of wood and livestock forage, the relationships of overstory biomass, overstory diversity as a proxy for niche complementarity, grazing intensity, and soil conditions with the biomass and quality (crude protein:lignin) of forage species were studied. Overstory competition in densely planted improved fallows resulted in an apparent trade-off with forage biomass, however in grazed fallows overstory and forage biomass were positively associated, likely due to negative effects of grazing on both; in addition, reduced forage quality and biomass of quality forage species were attributable to selective grazing. Finally, to assess whether plant diversity enhances joint levels of multiple ecosystem services, two indices of ecosystem multi-functionality were designed for four ecosystem functions: wood biomass, forage biomass, soil base cations, and infiltration. Evidence for positive effects of diversity on multi-functionality was clearer in grazed fallows, while in improved fallows environmental favorability appeared more influential. The difference in the diversity-multi-functionality relationship among fallow types appeared related to contrasting management, disturbance, species composition, and the productivity of vegetation and soils. The results suggest that plant diversity and site productivity can enhance multiple ecosystem services in smallholder fallows, yet diversity effects may vary with management, species composition, and site conditions.

A central aim of conservation science is improving our understanding how different human activities influence the persistence of native biota and associated ecological and evolutionary processes. Meeting this applied biodiversity research challenge requires that we understand (i) patterns in biological responses to anthropogenic environmental change, (ii) what biological mechanisms influence that response, (iii) how the loss of biological diversity will impact important ecological processes, and (iv) how this information can be translated into effective and practical information useful for decision makers. Increasingly, this final translational step is met through the use of ecological indicator assemblages - suites of species whose presence and abundance in a given area provide a useful gauge for measuring and interpreting changing environmental conditions. This thesis aims to improve our understanding of the patterns, causes and consequences of community disassembly for tropical forest insect species. To do this, I have combined systematic literature reviews and empirical approaches to understand how two widespread anthropogenic drivers of environmental change in tropical forest (i.e. land-use change and degradation) influence the community disassembly of Scarabaeine dung beetles in tropical forest, at a variety of spatial scales. I outline the potential for tropical forest defaunation to negatively impact dung beetle communities, summarize the contributions of dung beetles to a range of key ecological processes, provide empirical data demonstrating how dung beetles can serve as a model system to understand terrestrial trophic cascades, discuss the ability of species traits to explain population trends in observed dung beetle community disassembly, and conclude by demonstrating how these various lines of evidence linking dung beetle species with environmental condition strengthen their potential utility as ecological indicator taxa in applied conservation science.

Understanding how plants are spatially and genetically distributed in the environment can be a challenging task given the difficulty to characterize ecological processes, such as gene flow, and to disentangle the relative importance of multiple factors underlying the generation of distinct patterns. In this dissertation, I study different populations of the understory plant Heliconia acuminata L.C. Richard (Heliconiaceae) distributed across 1-ha fragments and continuous forest sites in the Biological Dynamics of Forest Fragments Project (BDFFP), an experimentally fragmented landscape in central Amazonia. I characterize a set of ten microsatellite markers developed for Heliconia acuminata to first evaluate gene flow, which is one of the main processes influencing genetic structure and spatial patterns of plants, and second to assess the potential influence of endogenous (e.g., seed dispersal) and environmental factors on spatial patterns of plants and genetic relatedness distribution. I combine genetic and ecological data in a novel and comprehensive Bayesian model to estimate parentage to more fully characterize the contribution of pollen and seed dispersal to H. acuminata gene flow. I then compare metrics of gene flow between fragments and continuous forest, while taking in consideration the variation in abundance of reproductive plants in each population. I tested the conservation genetics prediction that gene flow is interrupted in fragmented landscapes. Contrary to this hypothesis, I found that that both fragmentation and low population densities were associated with greater immigration rates and longer pollination and seed dispersal distances. My results are one example of how fragmentation does not limit gene dispersal. I suggest that conservation genetics predictions are reformulated by taking in consideration the variation in the behavior of pollinators and seed dispersers across heterogeneous landscapes in response to habitat configuration and to the spatial and temporal availability of food resources. To investigate the influence of endogenous factors (plant - plant interactions) and environmental covariates (light, slope and soil characteristics) on spatial patterns of seedlings and adults, I use a new statistical methodology to model marked point patterns. Using this flexible approach, I also evaluate whether local spatial genetic structure is associated to spatial distribution of plants. The results show that H. acuminata seed dispersal is contagious, but not distance - restricted or genetically structured (presence of highly related plants). The absence of an association between spatial pattern and local genetic structure for adults also suggest the absence of genetic structuring in seedlings over time. Light and zinc availability are positively associated with spatial patterns of seedlings and adults, which may indicate carryover effects of seedlings on recruits over time. Carbon is negatively associated with adults, which may be evidence of competition with large dominant trees. I finally propose a new mechanistic framework to the studies of frugivore - mediated seed dispersal. I conduct a qualitative analysis of existent studies explicitly linking frugivores, fruiting plants and seed shadows and propose a frugivore - centered, process-based view of seed dispersal that integrates animal movement and seed dispersal ecology across multiple spatio - temporal scales. This critical analysis provides the empirical foundation over which we can build a more comprehensive, multi-scaled, research approach to the study of seed dispersal, process which is known to play a crucial role in the dynamics and evolution of plant populations.

In the last two decades, export-oriented crops and timber and fruit plantations have joined small-scale cultivation and pasture as important causes of tropical deforestation. Widespread conversion of tropical forest to agriculture threatens to isolate protected areas, which has led to efforts to maintain functional connectivity in landscapes between protected areas. Relatively few "landscape conservation" efforts have been assessed for their effect on deforestation, but advances in remote sensing now permit detailed monitoring of tropical land uses over time, including mapping of tree crops and plantations. This dissertation evaluates the long-term impact of forest conservation and reforestation policies on tropical forests in a habitat corridor. The following chapters test the capability of remote sensing to monitor tropical conservation efforts and assess whether landscape conservation policies can maintain forest cover and connectivity in the face of rapid agricultural expansion. Costa Rica has one of the most comprehensive landscape conservation policies in the tropics: a 1996 Forest Law banned deforestation and expanded payments for environmental services (PES) to protect forests and plant trees, prioritizing designated habitat corridors between protected areas. The long-term effect of the program on land-use transitions is not well known. To take advantage of this regional policy experiment, I used a time-series of five moderate-resolution Landsat images to track land-use change from 1986 to 2011in the oldest habitat corridor, the San Juan-La Selva Biological Corridor (SJLSBC). Forest conservation policies were associated with a 40% decline in deforestation after 1996 despite a doubling in the area of cropland in the last decade. The proportion of cropland derived from mature forest dropped from 16.4% to 1.9% after 1996, while one fifth of pasture expansion continued to be derived from mature forest. These results suggest that forest conservation policies can successfully lower deforestation, and that they can be more effective with large export producers than small-scale cattle producers. Tree plantations are an important component of Costa Rican PES, but knowledge of their distribution and contribution to connectivity in the corridor region is poor. After reviewing the remote sensing literature, I employed a novel integration of hyperspectral images and a Landsat time-series to create the first regional map of tropical tree plantation species. Including multitemporal data significantly improved overall hyperspectral map accuracy to 91%; the six tree plantation species were classified with 83% mean producer's accuracy. Non-native species made up 89% of tree plantations, and they were cleared more rapidly than native tree plantations and secondary forests. I combined existing land cover maps, field behavioral experiments, and a graph connectivity model to estimate whether landscape conservation policies increased connectivity for understory insectivorous birds, a representative forest-dependent group. The field playback experiments indicated both native and exotic tree plantations with a dense shrubby understory were acceptable dispersal habitat for all species, and that birds traveled readily near secondary forest edges but rarely into forested pasture. Graph model parameters were informed by these results. For all of these bird species, functional connectivity declined by 14-21% with only a 4.9% decline in forest area over time, implying that conservation policies have not caused a net increase in functional connectivity in the SJLSBC region. Despite making up 2% of the region, tree plantations had little effect on regional connectivity because of their placement in the landscape; we demonstrate that spatially-targeted reforestation of 0.1% of the region could increase connectivity by 1.8%. Collectively, the results presented in these chapters underline the potential and limitations of landscape conservation policies and corridor plans in the tropics; combining regulations and PES can lower deforestation over the medium-term, but increased enforcement, improved monitoring with remote sensing, and targeted conservation effort is needed to combat illegal deforestation and restore functional connectivity. Given numerous new tropical corridor and PES programs and the qualified successes of landscape conservation policies in Costa Rica and other tropical countries, our approach to the analysis can be applied to monitor and evaluate connectivity across the tropics.