Acoustic communication plays a pivotal role in species recognition across a number of taxa. Species must therefore maintain discrete acoustic signatures to facilitate communication and avoid misidentification. The Acoustic Communication Hypothesis (ACH) thus proposes that in multispecies assemblages, multidimensional acoustic space is partitioned so that each species occupies a discrete acoustic space despite overlap in single parameters (e.g. frequency). Horseshoe bats use echolocation for the purpose of orientation and foraging. However, given the presence of individual and species specific cues in echolocation, it is likely that echolocation also functions to some degree in acoustic communication. This dual function makes echolocation a good model system to investigate the evolution of communication. In support of the ACH recent studies have shown that horseshoe bats are able to discriminate between conspecifics and heterospecifics based on echolocation calls alone even when call frequencies overlap. This suggests that multiple components of echolocation are influential in a bats ability to discriminate between species and indicates a dual function of echolocation in orientation and communication. These multiple components have not until now been identified. Studies have also suggested that preference for echolocation calls in the context of mate choice may influence the evolution of echolocation through sexual selection. Using classical habituation – dishabituation playback experiments, I tested the ability of Geoffroy's horseshoe bat, Rhinolophus clivosus, to discriminate between echolocation calls of heterospecifics with either discrete or overlapping resting frequencies. I subsequently used synthesised calls in which I manipulated individual acoustic parameters, to investigate which call components are involved in discrimination amongst species. Finally, I used a two-alternative choice experiment to investigate preference by R. clivosus to calls of individuals of opposite gender as well as between individuals with high or low body condition during the mating season. Rhinolophus clivosus was able to discriminate readily between echolocation calls with discrete frequencies from different species. When frequencies overlapped, however, the ability of bats to discriminate between species was dependant on additional spectral and temporal components of calls that defined the entire acoustic space occupied by the calls. Consequently, calls that were similar in this multi-parametric acoustic space yielded low levels of discrimination, whereas calls separated in acoustic space yielded high levels of discrimination. This study provides the first experimental evidence of call components, other than frequency, that may play a role in species discrimination and questions earlier reports that bats use echolocation in mate choice. In support of the communicative role of echolocation, bats were also able to discriminate between calls from bats that differed in their body condition, indicating echolocation might represent an honest signal of mate quality and thus a function in mate choice. However, despite this, R. clivosus showed no preference or association based on gender or body condition. The results of this study suggest that despite having the ability to use echolocation to discriminate amongst conspecifics, these bats do not base mate choice on echolocation call components.

Psoraleeae is a tribe of the papilionoid legumes in Fabaceae comprising ca. 223 species in nine genera. Members of Psoraleeae are distributed worldwide, though they mainly occur in the temperate biomes. Of these, ca. 60% of the species (mostly in Otholobium and Psoralea) are endemic to southern Africa predominantly in the Greater Cape Floristic Region (GCFR). The genus Psoralea, consisting of 75 species endemic to southern Africa, is the second most speciose legume in the GCFR after Aspalathus (280 species). This thesis, consisting of a literature review, three research chapters and synthesis, studies the taxonomy, evolutionary history and biogeography of Psoraleeae with an emphasis on Psoralea.

Includes bibliographical references. / As protected areas ultimately aim to successfully conserve natural predator populations, an understanding of the non-anthropogenic drivers of their population change is critical. Both bottom-up (e.g. food limitation, competition) and top-down (e.g. predation, interference) processes play an important role in structuring predator guilds, yet there is a poor understanding of their relative importance. Here, I investigated whether the relative abundance of mesopredators, facultative scavengers, and an apex predator were affected primarily by bottom-up processes (prey abundance) or by top-down processes (predator abundance), or a combination of the two. Central to this study was elucidating the complex relationship between mesopredators and apex predators. Caracal (Caracal caracal), blackbacked jackal (Canis mesomelas), sidestriped jackal (Canis adustus), honey badger (Mellivora capensis) and serval (Leptailurus serval) were classed together as Mesopredators. Facultative scavengers included two hyaena species (spotted Crocuta crocuta and brownhyaena Hyaena brunnea). Leopards (Panthera pardus) were included as an example of an apex predator. Data was obtained from camera-trap surveys conducted in four protected areas located in northern KwaZulu-Natal (South Africa). Results of both a nested analysis of variance and generalised linear mixed models revealed that there was no mesopredator suppression present in protected areas with complete predator guild. In addition, prey and similarly sized predator relative abundance indices (RAIs) had a significant positive effect on mesopredator, hyaena and leopard RAI. The findings suggest that bottom-up drivers are more important than top-down processes in determining the relative abundance of mammalian predators in these protected areas. My study highlights the importance of monitoring prey populations in a protected area when attempting to successfully manage mammalian predator trophic guilds.

In comparison to their ecophysiological and behavioral aspects, the skeletal system of African mole-rats (Bathyergidae) has been relatively understudied. Only a few studies have assessed their skeletal system, but these have mostly focused on their cranial and dental systems, with little attention on their postcranial skeleton. This PhD thesis provides a considerable amount of information about the functional anatomy, morphological diversity and postnatal bone morphogenesis of the appendicular system of these subterranean mammals. African mole-rats are small mammals highly adapted to the hypogeous niche that feed on underground roots and tubers. They forage, mate, breed and to some extent even disperse underground. For this, they build extensive burrow systems primarily with their chisel-like teeth, but also using their forelimbs for scratch-digging. One of the most exceptional features of bathyergids is their wide spectrum of social organization, which is unique among mammals and ranges from solitary, social and eusocial. Here, the eusocial naked mole-rat, Heterocephalus glaber, has been the most studied species. The physiology of African mole-rats is also exceptional among rodents and other mammals, showing low metabolic rates and body temperatures, as well as slow somatic growth rates. They also show enhanced fitness and prolonged longevity, features that have been associated to a life protected from both climatic extremes and predation, as well as to intergenerational transfer of information, communal care of young and shared foraging endeavors in social species. For these reasons, bathyergids represent a unique animal model to explore their skeletal adaptations to fossoriality and life underground. The aim of this research was to assess the patterns of bone growth and development to understand how adults attain their final phenotype. A comprehensive sample (N = 506) of all six bathyergid genera including seven species and comprising individuals of both sexes and of different ontogenetic stages was studied. Stylopodial (humerus and femur) and zeugopodial (ulna and tibia-fibula) bones (n = 1133) were analyzed using multiple quantitative analyses of variance (ANOVA, MANOVA), ordination (PCA, DA) and regression (RMA, OLS, equality of slopes), as well as bone labeling techniques and detailed qualitative descriptions of their midshaft bone histology. Chapter 3 shows that the specialized phenotype of the only scratch-digger bathyergid Bathyergus suillus underwent considerable morphological changes during ontogeny, e.g. juveniles showed externally more robust bones with thin cortical walls, whereas adults presented slender bones with significantly thicker cross-sections. Such changes are probably related to the increased digging demands and agonistic behaviors of the developing young. However, other aspects of their anatomy expressed perinatally, such as greater external epicondylar robustness, well-developed olecranon, teres major and deltoid processes, suggest a major role of genetic factors in their development. This chapter applied for first time the conceptualization of developmental modules to long bones, and showed that the periosteal module had higher variability and tended to grow faster than the endochondral module. Chapter 4 analyzed the morphological diversity within Bathyergidae using comparative anatomy and morpho-functional indices and showed that most species shared a highly specialized fossorial morphology and that only the naked mole-rats were morphologically divergent (having a simplified phenotype), resembling the condition of non-fossorial closest relatives of the Bathyergidae. Nevertheless, the novel inclusion of three ecomorphological categories (solitary scratch-diggers, solitary chisel-tooth diggers and social chisel-tooth diggers) in this study, showed significant differences among the groups. In general, social species appeared to have a phenotype more specialized to increase digging ability and locomotor performance, whereas solitary species showed a relatively less specialized fossorial phenotype, and a diminished locomotor ability. This may contribute to foraging strategies in social species which are known to have more complex and relatively longer burrow systems as compared to solitary species. Chapter 5 assesses the ossification patterns of the endochondral and periosteal modules, and shows that in general most bathyergids have relatively similar endochondral growth rates, irrespective of social behavior or digging strategy, although the periosteal module showed relatively higher growth rates and a higher degree of variation as compared to the endochondral module, thus appearing to be considerably less dependent on body size and genetic factors. Naked mole-rats showed the lowest growth rates among bathyergids. Considering the basal phylogenetic position of H. glaber within the family, a neotenic condition is suggested for this species, and suggests accelerated bone growth rates for the evolution of the other bathyergids. Chapter 6 provides a comprehensive description of the pattern of bone modelling in bathyergids and includes an assessment of their bone dynamics using fluorochrome labeling. All bathyergids analyzed showed increased cortical bone thickening during ontogeny, as well as low rates of endosteal bone resorption. Also, all species showed high histodiversity, limited remodeling (i.e. development of secondary osteons) and they do not ever develop Haversian bone tissues. This thesis concludes that the combination of social strategy and type of excavation had an impact on the evolution of the bathyergid appendicular system. On one hand, it was evidenced that the development of fore- and hindlimbs are not constrained by intrinsic factors (as suggested for other mammals), and that the limbs develop at similar growth rates, resulting in relatively symmetrical limb proportions. This is suggested to improve locomotion within burrows and represents an adaptation to the subterranean lifestyle, which is also observed in other fossorial mammals. This thesis further discusses how environmental factors and specific behaviors and locomotor modes, may represent strong selective pressures on limb adaptation and evolution. Similarly, a proximo-distal pattern of variation was observed, where zeugopodial elements were more variable than stylopodial elements, probably because they are in direct interaction with the substrate, so they can evolve morphological adaptations for particular habitats and locomotor behaviors. Importantly, these adaptations are most likely mediated by heterochronic modifications of their ossification modules, especially intramembranous ossification, which is known to be more responsive to environmental factors, whilst the endochondral modules would be more conservative, perhaps because a stronger genetic regulation in postnatal life. Further research on long bone modules is necessary to understand the specificity of such changes. Despite the comparatively simplified phenotype of H. glaber, they showed a larger morphospace as compared to other bathyergids, indicating a wider intraspecific variability. This agrees with previous observations suggesting skeletal plasticity for this species. It is suggested that living in large colonies results in diminished selective pressures for limb specialization but has an impact on increasing trait variability within members of the colony. This study showed that the integration of multiscale techniques and multivariate analysis of combined skeletal phenotypes (i.e. forelimb + hindlimb) offer a better understanding of adaptations to the hypogeous environment. The findings of this study also highlight the importance of considering developmental modularity of long bones for assessment of bone adaptations, particularly for understanding the differential effects of intrinsic and extrinsic factors regulating endochondral and intramembranous ossification.

Obligate brood parasites lay their eggs in the nests of other species, foisting the costs of parental care onto the host parents. The success of the parasite and host are then at odds, with both parties evolving defences and countermeasures in an evolutionary arms race. This reciprocal influence of acting upon both species' evolution — a process known as coevolution — has forged the natural world around us. Avian brood parasites and their hosts are now model systems for studying such coevolutionary interactions between species, providing striking examples of the adaptations that arise when the life histories of two species become entangled. In this thesis I highlight the adaptations that have arisen in response to coevolutionary selection pressures in a group of understudied avian brood parasites, the honeyguides (Indicatoridae), and their hosts. This study focuses on the greater (Indicator indicator) and lesser (I. minor) honeyguides, and their respective primary hosts, the little bee-eater (Merops pusillus) and the black-collared barbet (Lybius torquatus). The interactions between honeyguides and their cavity-nesting hosts of the Old World tropics are evolutionarily ancient, contrasting with the majority of studies of avian brood parasitism which have predominantly focused on temperate brood-parasitic species targeting open cup-nesting hosts. Therefore, honeyguides and their hosts are an ideal study system in which look for novel adaptations that have not evolved in other systems. Using field observations and experimental manipulations at each stage of the parasitic life cycle — before parasitism, during egg-laying, during incubation, and during chickrearing — I examine how honeyguides and their hosts have evolved in response to the selection pressures they exert on each other. First, in chapter two, I consider whether the nest structure of the little bee-eater – host to the greater honeyguide – can act as a defence against brood parasitism. Experimental manipulation of the size of bee-eater nest tunnels demonstrates that bee-eaters with narrower nest tunnels are less likely to be parasitized by greater honeyguides than those bee-eaters whose nests have wider nest tunnel entrances. This study provides the first experimental evidence of a host nest functioning as a frontline defence against brood parasitism. In chapter three, I take a comparative approach and use a phylogenetic framework to investigate, across multiple avian brood parasite species, the evolutionary drivers of rapid egglaying. This trait is shared by most brood-parasitic birds, but not by non-parasitic birds. I find strong evidence that the egg-laying speed of avian brood parasites is ecologically and physiologically constrained, but find no evidence that variation in the costs incurred duringparasitism events have driven variation in the rapidity of egg-laying among brood-parasitic species. In chapter four, I examine whether there are costs associated with the virulent egg puncturing behaviour of greater honeyguides, and whether honeyguides can adjust their level of virulence in accordance with these costs. I find strong support for the idea that virulence is costly to honeyguides, as bee-eater hosts are more likely to reject clutches that contained eggs punctured by honeyguides. Such punctured clutches are also more likely to be predated. Honeyguides appear to adjust how much they puncture host eggs in accordance with the severity of these costs, providing the first evidence of an avian brood parasite moderating its virulence in response to the associated costs. In chapter five, I examine egg rejection behaviour in the black-collared barbet, a common host of the lesser honeyguide. I consider whether the (smaller) size of a parasitic egg could be used as a cue for egg rejection inside the dark environment of a cavity nest. Through observations of natural parasitism events, and experimental parasitism of host nests using different sized eggs, I demonstrate that barbets are more likely to reject a clutch of eggs when they detect a small egg within the nest. This seems to be achieved through a process of true recognition, a mechanism that involves a specific innate or learnt template of what size eggs a host should reject. Barbets do not appear to rely on discordancy – comparing all eggs within their clutch in order to reject the odd one out – in order to make rejection decisions. Finally, in chapter six I explore whether honeyguides elicit additional provisioning from their foster parents by using vocal mimicry, and investigate why such extra food would be required. I demonstrate that both greater and lesser honeyguides mimic the sound of a brood of chicks of their respective hosts in order to receive higher levels of provisioning from their foster parents. I establish that greater and lesser honeyguides do this for contrasting reasons. Greater honeyguides require higher levels of provisioning to support their fast growth rate to a size much larger than their host siblings, whereas lesser honeyguides require more food in order to offset a sub-optimal diet provided to them by their foster parents.

While leopards (Panthera pardus) currently occupy the most extensive geographic range of all large felids, they are also suffering the highest rate of current range loss amongst large terrestrial carnivores. This is primarily because most leopards still range outside of formally protected areas where they are exposed to the full suite of anthropogenic threats affecting carnivores including habitat loss, prey depletion, conflict with humans, and commercial harvest for body parts. The extensive use of leopard derivatives among traditional healers, royalty, and culturo-religious groups poses a known but poorly understood threat to leopards. Sociopolitical sensitivities surrounding cultural identity and the illegality of much of this use have impeded an objective assessment of both the drivers and impacts of this threat. Through a multi-disciplinary approach, this thesis describes the drivers of illegal leopard skin trade among a significant portion of traditional users in South Africa, quantifies the extent of this trade across the southern African region and assesses its impact on local leopard populations. Together these findings seek to address the lack of conservation- and policy-relevant data regarding the impact and scale of the trade for traditional use in South Africa. Followers of the recently established ‘Shembe' Church, with its estimated membership of over four million in South Africa, represent the foremost culturo-religious users of illegal leopard skins in the world. Following the introduction of a faux skin alternative, I used longitudinal surveys to explore the drivers of authentic skin desirability and possession amongst faux skin recipients. While demand for authentic skins decreased, and faux alternatives were generally considered satisfactory, 27% still expressed a desire for an authentic skin, and 15% had acquired one in the three years since receiving their faux skin. Both desiring and having obtained an authentic skin were best explained by improved economic status and the perceived weakness of law enforcement. The combined demand of all Shembe followers cannot be sustained by the estimated extant leopard population of South Africa, and it is predicted that traders must be sourcing leopards from surrounding range states to meet local demands. To investigate this, I created a genetic reference database of leopards across southern Africa (1,452 individuals) and using DNA-based assignment tests, inferred the geographic origins of illegally traded skins sourced within southern Africa. Smoothed continuous assignment techniques revealed leopard source ‘hotspots' in southwestern Zimbabwe, southern Mozambique and along the eastern borders of South Africa confirming suspicions that the illegal leopard skin trade for traditional use in South Africa is transnational. A similar distribution of leopard source populations was identified from leopard parts obtained in traditional wildlife markets and a large-scale confiscation from a single trader. Together, this suggests the regional trade in leopard parts has been syndicated with predictable harvesting and trade routes into the South African consumer market. Genotyping across all trade samples (237 individuals) revealed a clear bias towards males despite reported sex-ratios being female-biased for natural free-ranging populations. To understand the ecological cost of this sex-biased exploitation of leopards, I compared the spatial, genetic, and demographic data of two South African leopard populations with markedly different histories of anthropogenic mortality. Home-range overlap, parentage assignment, and spatio-genetic autocorrelation showed that extensive historical exploitation, linked to Shembe and other traditional trade, has reduced subadult male dispersal, thereby facilitating opportunistic male natal philopatry. The resultant kinclustering in males is comparable to that of females in the well-protected reserve and has promoted localised inbreeding. Together these results demonstrate novel evidence linking significant ecological consequences to an underestimated, transnational, and syndicated illegal leopard skin trade driven by demand for traditional and religious use in South Africa. These findings are translatable to all leopard populations threatened by exploitation and emphasise the importance of long-term monitoring of leopard populations within protected areas and improving management interventions to mitigate these effects. Interventions such as anti-poaching can be focussed on the ‘hotspots' identified in this study while protected area management should prioritise the maintenance of dispersal corridors to promote in situ recovery of exploited populations. Lastly, demand reduction strategies such as the continued provisioning of suitable alternatives, together with improved education and increased enforcement, are essential to addressing the growing culturo-religious demand for leopard products contributing to the illegal harvest and trade in this iconic large predator. Success will depend on finding the balance between an improved transnational policy which effectively conserves wild leopard populations and maintaining respect for cultural practices

Intertidal ecology research has focused primarily on sandy (grain size < 2mm), granule (2 –< 4mm), pebble (4 –< 64mm) or cobble (64 –< 256mm) shores, and only one on the biota of boulder (256+mm) shores. This study samples intermediate shore types (1 – 256mm) within the Western Cape for the first time and compares these with published data on other Western Cape shores to determine how many distinct habitat types occur across the full spectrum of particle sizes with a focus on describing the unique fauna of pebble and cobble shores. Chapter 1 reviews the literature to date on well-studied shore types including sandy and rocky shores, and explores the limited ecological research on shore types ranging from 1 – 256mm, while both data chapters use sample data to complete the study aim. Sampled shores were surveyed using a 20 x 20cm quadrat placed at eight tidal levels along a transect from low to high shore and species collected were identified, counted and wet-weighed. Chapter 2 also used extractions from previously sampled data which included species presence, biomass and abundance per site (where available). All biomass records were converted to wet weight using published conversion factors. Chapter 2 analyzes data from 58 sites in the South-Western Cape, with data for 42 sites derived from eight previous studies, while 16 sites were sampled as part of this study. Three main groupings of sandy shores (1 – 256mm) and boulder and rocky shores (>256mm) occur. Similar to other shores within the spectrum, shores of intermediate particle grain sizes (1 – 256mm) are affected by heavy wave action, among other driving factors. Heavy wave action against intermediate grain sizes which do not have the stability of larger boulders or rocks, or the compacted nature of smaller grain sizes which can be burrowed into to protect biota, results in rough living conditions only few species can endure, as such these shores have a similar biotic composition. A polarization of species presence occurs amongst the two ends of the spectrum with mobile taxa occurring across particle grain size shores between 0.125 – 256mm, but concentrating on smaller grain sizes (256mm. Chapter 3 examines a total of 12 sites in the South-Western Cape, composed of seven pebble and five cobble shores. Of 39 taxa collected on these shores only 14 species occurred more than once and were thus considered typical of pebble and cobble shores. These were mostly air-breathing species, primarily Arthropoda and a single species of pulmonate Gastropoda. Macroalgae were notable in their absence. Unlike the burrowing species of sandy shores, or the attached species of rocky and boulder shores, pebble and cobble shore species all tended to be motile, no doubt to avoid the rolling grains. Unlike most other intertidal shores, the fauna was also concentrated towards the high shore, where food was available in the form of drift kelp, although, as some airbreathing species were found in the low shore, it is presumed some such species migrated well into the intertidal at low tide, presumably retreating back above the high-water mark at high tide.

Shifting climate patterns are a cause for concern for natural ecosystems globally. Of particular concern is the effect of climate change on fire-prone, Mediterranean-type shrublands globally because of the heightened sensitivity of post-fire vegetation to environmental conditions. In this thesis, I focused on investigating the relationships between rainfall seasonality patterns and post-fire vegetation processes in neighbouring Fynbos and Renosterveld shrubland communities within the mega-diverse Cape Floristic Region of South Africa. I investigated vegetation sensitivity to moisture availability at multiple levels of detail including 1) productivity and community structure, 2) growth form responses and 3) physiological performance over three years. Post-fire rainfall patterns were manipulated by artificially increasing summer rainfall and reducing winter rainfall over permanent, field sites, thus reducing annual seasonality and creating soil moisture contrasts between control and treatment plots over warm and cool seasonal periods. At all levels of investigation, postfire vegetation processes at the Fynbos site were relatively insensitive to variations in moisture availability relative to the Renosterveld site where vegetation processes and community structure were strongly affected. Nutrient limitation and lower soil tension in coarse, sandstone-derived soils of the Fynbos site could strongly limit the influence of soil moisture patterns on post-fire physiology leading to stable growth, community structure and productivity under a variety of moisture regimes. Soil moisture patterns during the first summer had significant and long-term implications for community structure and productivity patterns in the Renosterveld site, highlighting the sensitivity of vegetation patterns to early post-fire processes. Overall this study demonstrates that post-fire rainfall patterns can have strong effects on vegetation recovery processes but that structurally similar shrublands, which are specialised to differing soil types, could show marked differences in their response to climate change due to the mediation of climate responses by soils.

South Africa is known for its highly endemic and remarkably species-rich fauna and flora. The Greater Cape Floristic Region, consisting of the Cape Floristic Region and the Succulent Karoo Region, is home to South Africa's second most diverse plant family, the Aizoaceae. While the Aizoaceae are relatively well studied, there has been little work done on their associated insect fauna. Preliminary observations in recent years revealed a diverse community of gall midges on these plants. This study aimed to investigate the gall midges associated with two speciose genera of Aizoaceae and it is the first of its kind in South Africa. I report five new species of gall midges, three belonging to Asphondylia Loew and two to Lasioptera Meigen. These species are described from several species within the Aizoaceae genera Drosanthemum Schwantes and Malephora N.E.Br., and additional host records were recorded from Lampranthus N.E.Br., Carpobrotus N.E.br., Acrodon N.E.Br., Cephalophyllum Haw. and Jordaaniella H.E.K. Hartmann. The gall midges are described from adults, pupae and larvae and information is provided on their galls, life history and distribution. Morphological attributes of the gall midges support the description of five distinct species. Furthermore, morphological characters of the Lasioptera species described here do not fit entirely with those of the genus, suggesting that a new genus should be established for them. These results provide a mere snapshot of the gall midge diversity that is to be found on Aizoaceae in southern Africa, and much work is still to be done on the Cecidomyiidae of South Africa as a whole. Further targeted sampling may reveal greater distribution ranges and additional host plants for the five species described here, as well as many more undescribed species across the Aizoaceae.

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Biological Engineering, September, 2019 / Cataloged from the PDF version of thesis. / Includes bibliographical references. / Many methods for increasing the optical transparency of non-living brain tissue have come into widespread use because of their utility in enabling better anatomical brain imaging. In the first part of this thesis, we explore whether this is also possible for living brain tissue. We report a general principle for doing so, namely the reduction of refractive index mismatch between cellular membranes and the extracellular space, using high refractive index biocompatible reagents that have high molecular weights, so that they can be used at low concentrations. We implement this via multiple reagents that satisfied these criteria, including the iodinated radiocontrast agent iodixanol, high molecular weight polyethylene glycol (PEG), high molecular weight Dextran, and PEG-ylated Silicon nanoparticles. We achieve ~2x increases in the brightness of cells expressing red fluorescent proteins in vivo in mice, as measured by conventional one-photon epifluorescence imaging, using concentrations of reagents that increased the refractive index of the extracellular space by just 0.01. Lastly, We show that Dextran does not have a statistically significant effect on neural physiology or neural network properties. We expect such strategies to not only facilitate live imaging of the brains of mice and other mammals, but open up a new class of strategies for changing the electromagnetic properties of living systems. We conclude this thesis with two nanotechnologies that may be leveraged for making higher performance reagents for increasing the optical transparency of living brain tissue. (1) A method for the synthesis of high-yield and high-monodispersity nanoparticles of a variety of materials with tailored surface ligands, using common benchtop equipment. This method may be useful for developing nanoparticles with better biosafety, efficacy and performance. (2) A method for the delivery of hydrophobic NVNDs to neural cell membranes using PEG-ylated liposomes. These PEG-ylated liposomes may be used for delivery of hydrophyllic nanoparticles to neural soma and achieve maximal transparency. / by Ishan Gupta. / Ph. D. / Ph.D. Massachusetts Institute of Technology, Department of Biological Engineering