The distinctiveness of brain structures and circuits depends on interacting gene products, yet the organization of these molecules (the "transcriptome") within and across brain areas remains unclear. High-throughput, neuroanatomically-specific gene expression datasets such as the Allen Human Brain Atlas (AHBA) and Allen Mouse Brain Atlas (AMBA) have recently become available, providing unprecedented opportunities to quantify molecular neuroanatomy. This dissertation seeks to clarify how transcriptomic organization relates to conventional neuroanatomy within and across species, and to introduce the use of gene expression data as a bridge between genotype and phenotype in complex behavioral disorders. The first part of this work examines large-scale, regional transcriptomic organization separately in the mouse and human brain. The use of dimensionality reduction methods and cross-sample correlations both revealed greater similarity between samples drawn from the same brain region. Sample profiles and differentially expressed genes across regions in the human brain also showed consistent anatomical specificity in a second human dataset with distinct sampling properties. The frequent use of mouse models in clinical research points to the importance of comparing molecular neuroanatomical organization across species. The second part of this dissertation describes three comparative approaches. First, at genome scale, expression profiles within homologous brain regions tended to show higher similarity than those from non-homologous regions, with substantial variability across regions. Second, gene subsets (defined using co-expression relationships or shared annotations), which provide region-specific, cross-species molecular signatures were identified. Finally, brain-wide expression patterns of orthologous genes were compared. Neuron and oligodendrocyte markers were more correlated than expected by chance, while astrocyte markers were less so. The localization and co-expression of genes reflect functional relationships that may underlie high-level functions. The final part of this dissertation describes a database of genes that have been implicated in speech and language disorders, and identifies brain regions where they are preferentially expressed or co-expressed. Several brain structures with functions relevant to four speech and language disorders showed co-expression of genes associated with these disorders. In particular, genes associated with persistent developmental stuttering showed stronger preferential co-expression in the basal ganglia, a structure of known importance in this disorder.

The work presented in this thesis investigates whether primitive pallial brain circuits such as those found in teleost fish may also encode complex information such as spatial memory despite its circuitry being “simpler” than those found in species with much larger brains such as primates and rodents. Previous behavioral studies have already shown that most teleost fish are capable of spatially orienting themselves and remembering past food locations. Behavioral studies combined with selective brain lesions and related anatomical studies have identified a hippocampal-like region in the fish’s pallium; however, it is unknown whether the neurons located in this structure can also perform cortical-like computations as those found in the mammalian hippocampus. Consequently, this thesis will first present an anatomical characterization of the intrinsic circuitry of this hippocampal-like structure, followed by an in vitro electrophysiological characterization of its constituent neurons. Surprisingly, we have found that this hippocampal-like structure possesses many features reminiscent of the mammalian cortex, including recurrent local connectivity as well as a laminar/columnar-like organization. Furthermore, we have also identified many biophysical properties which would describe these hippocampal-like neurons as sparse coders, including a prominent after-hyperpolarizing potential and an adapting spike threshold with slow recovery. Since this particular dynamic spike threshold mechanism has not been thoroughly characterized in the mammalian hippocampus, we have further investigated the dynamic threshold in the major rodent hippocampal cell types. We have found that only a subset of excitatory neurons displayed this dynamic spike threshold on the time scale that was observed in teleost pallial cells, which allowed us to discuss its potential role in encoding spatial information in both species. Nevertheless, the fact that this teleost hippocampal homologue possesses characteristics that are both akin to the cortex and hippocampus suggest that it may perform computations that, in a mammalian brain, would require both structures and makes this ancestral structure a very interesting candidate to study the mechanism(s) underlying spatial memory.

<p>Changing environmental conditions may present substantial challenges to organisms experiencing them. In animals, the fastest way to respond to these changes is often by altering behavior. This ability, called behavioral flexibility, varies among species and can be studied on several levels. First, the extent of behavioral flexibility exhibited by a species can be determined by observation of that species' behavior, either in nature or in experimental settings. Second, because the central nervous system is the substrate determining behavior, neuroanatomy can be studied as the proximate cause of behavioral flexibility. Finally, the ultimate causation can be examined by studying ecological factors that favor the evolution of behavioral flexibility. In this dissertation, I investigate behavioral flexibility across all three levels by examining the relationship between habitat structure, the size of different structures within the brain and total brain size, and behavioral flexibility in six closely-related species of Puerto Rican <italic>Anolis</italic> lizards. <italic>Anolis</italic> lizards provide an excellent taxon for this study as certain species, including those used here, are classified as belonging to different ecomorphs and are morphologically and behaviorally specialized to distinct structural habitat types.</p><p>In order to determine the presence of behavioral flexibility in <italic>Anolis</italic>, I first presented <italic>Anolis evermanni</italic> with a series of tasks requiring motor learning and a single instance of reversal learning. <italic>Anolis evermanni</italic> demonstrated high levels of behavioral flexibility in both tasks.</p><p>To address the pattern of brain evolution in the <italic>Anolis</italic> brain, I used a histological approach to measure the volume of the whole brain, telencephalon, dorsal cortex, dorsomedial cortex, medial cortex, dorsal ventricular ridge, cerebellum, and medulla in six closely-related species of Puerto Rican <italic>Anolis</italic> lizards belonging to three ecomorphs. These data were analyzed to determine the relative contribution of concerted and mosaic brain evolution to <italic>Anolis</italic> brain evolution. The cerebellum showed a trend toward mosaic evolution while the remaining brain structures matched the predictions of concerted brain evolution. </p><p>I then examined the relationship between the complexity of structural habitat occupied by each species and brain size in order to determine if complex habitats are associated with relatively large brains. I measured brain volume using histological methods and directly measured habitat complexity in all six species. Using Principal Component Analysis, I condensed the measures of habitat structure to a single variable and corrected it for the scale of each lizard species' movement, calling the resulting measurement relevant habitat complexity. I tested the relationship between relative volume of the telencephalon, dorsal cortex, dorsomedial cortex, and whole brain against both relative habitat complexity and ecomorph classification. There was no relationship between the relative volume of any brain structure examined and either relevant habitat complexity or ecomorph. However, relevant habitat complexities for each species did not completely match their ecomorph classifications. </p><p>Finally, I tested the levels of behavioral flexibility of three species of <italic>Anolis</italic>, <italic>A. evermanni</italic>, <italic>A. pulchellus</italic>, and <italic>A. cristatellus</italic>, belonging to three distinct ecomorphs, by presenting them with tasks requiring motor and reversal learning. <italic>Anolis evermanni</italic> performed well in both tasks, while <italic>A. pulchellus</italic> required more trials to learn the motor task. Only a single <italic>Anolis cristatellus</italic> was able to perform either task. <italic>Anolis evermanni</italic> displayed lower levels of neophobia than the other species, which may be related to its superior performance.</p><p>In combination, this research suggests that <italic>Anolis</italic> of different ecomorphs display different levels of behavioral flexibility. At the proximate level, this difference in behavioral flexibility cannot be explained by changes in the relative size of the total brain or brain structures associated with cognitive abilities in other taxa. At the ultimate level, the size of the brain and several constituent structures cannot be predicted by habitat complexity. However, behavioral flexibility in certain tasks may be favored by utilization of complex habitats. Flexibility in different tasks is not correlated, rendering broad comparisons to a habitat complexity problematic.</p> / Dissertation

Many passerine birds, particularly corvids, are known to express complex cognitive skills comparable to those observed in primates. In order to examine how these similarities are reflected at the cellular level, I counted neurons and nonneuronal cells in passerine brains using the isotropic fractionator method. I show that, in these birds, neuronal numbers scale almost isometrically with telencephalic size, i.e., the average neuron size shows little increase and neuronal density decreases minimally as brains get larger. Neuronal densities in the passerine telencephalon exceed those observed in the primate cerebral cortex by a factor of 3-6. As a result, the number of telencephalic neurons in the Common Raven (Corvus corax) equals those observed in the cerebral cortex of small monkeys. The cerebellum features similar scaling rules. However, because the relative size of the cerebellum is smaller than in mammalian brains, cerebellar neurons make a much smaller proportion of total brain neurons than in mammals. In contrast to the little variation in neuronal densities in telencephalon and cerebellum, the density of neurons rapidly decreases with increasing structure size in the diencephalon, optic tectum and brain stem. For all examined brain structures, the densities of nonneuronal cells remain constant...

Galliform birds (Galliformes) make up together with anseriform birds (Anseriformes) the clade Galloanserae, the sister group of Neoaves and the most basal clade of Neognathae. However, to date no quantitative data on cellular composition of their brains have been available. Here, I used the isotropic fractionator to determine numbers of neurons and non-neuronal cells in specific brain regions of 15 species of galliform birds. I find that cellular scaling rules for galliforms differ starkly from those for songbirds and parrots. When compared to these crown avian lineages, galliform birds feature lower degree of encephalization, a proportionally smaller telencephalon, small telencephalic and dominant cerebellar neuronal fractions, generally lower neuronal densities and larger glia/neuron ratios. Consequently, their brains and especially their forebrains harbor much smaller absolute numbers of neurons than those of equivalently sized songbird and parrots, the fact that undoubtedly constrains cognitive abilities of galliforms. However, this not to say that galliform birds are "bird brains" with low numbers of neurons and a limited ability to learn. Because they have high neuronal densities, their relatively small brains contain about equal numbers of neurons as brains of equivalently sized rodents and...

Recent comparative studies have shown that bird brains, although small, have a high processing capacity. The brains of parrots and songbirds have higher neuronal densities than brains of mammals; especially large parrots and corvids compete with or even outnumber primates by the number of telencephalic neurons. However, the processing capacity of the avian brain appears to differ significantly between various phylogenetic lineages. Basal groups such as galliform birds have much lower absolute numbers of neurons and lower neuronal densities than songbirds and parrots. In this Master thesis, I used the isotropic fractionator to determine numbers of neurons and non-neural cells in specific brain regions in 19 species of hornbills (Bucerotiformes), woodpeckers (Piciformes) and coraciiform birds (Coraciiformes). The brains of hornbills and woodpeckers (but not coraciiform birds) have numbers of neurons comparable to that of songbirds and parrots and significantly more neurons than equivalently sized brains of pigeons (Columbiformes) and galliform birds (Galliformes). In the crown groups, we can observe similar trends such as a higher degree of encephalization, a proportionally larger telencephalon and increasing percentage of telencephalic neurons. On the contrary, in pigeons and galliform birds, we can...

In this thesis I apply new sequencing technologies and analytical methods derived from genomics and computer science to the neuroanatomy of gene expression. The first project explores characteristics of gene expression across adult neocortical layers in a representative mammal – the mouse. Amongst the thousands of genes and transcripts differentially expressed across layers, I found common functional characteristics of genes that define certain layers, candidate cases of isoform switching, and over a thousand apparent long intergenic non-coding RNA transcripts. The second project compares patterns of gene expression in the structurally diverged adult derivatives of the pallium in mice and chickens. Overall, gene expression levels were moderately correlated between the two species. While expression patterns of ‘marker’ genes were only poorly conserved in these regions, there nevertheless was significant conservation of cross-species marker genes for homologous structures, cell types and functionally analogous regions. Many aspects of these data from both projects can now be easily browsed and searched from custom-built web interfaces. In addition to generating unprecedented genome-wide resources for the neuroscience community to explore the functional and structural dimensions of gene expression amongst different pallial regions in mammals and birds, this work also provides new insights into the widespread evolutionary shuffling of adult marker gene expression.