Tettigoniidae (katydids) has more than 7200 species and is the largest family within the insect order Orthoptera. Their unique biology including leaf-like crypsis, acoustic signaling, and courtship rituals garners much of their academic attention. However, the taxonomy of katydids is chaotic and previous to these studies, little work had been done to decipher the phylogenetic relationships within this family. Without a robust phylogenetic framework, questions regarding the evolution of katydid disguises including the leaf-like crypsis cannot be addressed. This dissertation contains three chapters. Chapter 1 provides the first phylogenetic hypothesis focusing on Tettigoniidae. In this chapter we show a character thought to be taxonomically informative, the thoracic auditory spiracle, is homoplasious within Tettigoniidae. We provide evidence that the leaf-like wings of katydids have been derived independently in multiple lineages. Additionally, in Chapter 1 the problematic taxonomy within Tettigoniidae, particularly the lack of monophyly in many of the larger and widespread subfamilies, is addressed. Chapter 2 contains a more in depth look into the evolution of crypsis. Leaf-like wings are common throughout Tettigoniidae, but the definition of leaf-like has varied by author. In this second chapter we provide a ratio method for differentiating between leaf-like and non leaf-like wings. Our ratio method was then verified using geometric morphometics. We found at least 15 independent derivations of leaf-like wings in Tettigoniidae. Furthermore we found that throughout Tettigoniidae the leaf-like wings are not a driver of speciation and selection may favor a shift away from the leaf-like wings. Within the cosmopolitan Phaneropterinae, the trend differs, as there is no significant difference between the speciation and transition rates of the leaf-like and non leaf-like lineages. Chapter 3 presents the largest and most comprehensive phylogeny for Tettigoniidae to date and provides a hypothesis for origins and biogeographic dispersal of katydids. Characters that define subfamilies are similar due to similar selective pressures and are not taxonomically informative. As a result, many of the larger and widespread subfamilies, particularly those with species in similar but geographically distant habitats, are paraphyletic. In this chapter we also provide temporary names to define the two large clades containing the bulk of Tettigoniidae diversity (tettigonioid clade and phaneropteroid clade) in addition to smaller subfamily groups to simplify discussion of katydid relationships until a higher-level taxonomic revision is completed.

I highlight two squamate lineages endemic to Southeast Asia, the Asian water monitors (Varanus salvator Complex) and the Angle-headed lizards (Agamidae: Gonocephalus), and elucidate their systematic affinities and historical biogeography. My results represent novel phylogenetic inferences, with biogeographic histories and diversification events corresponding to major climatic fluctuations over the past 30 million years. Additionally, I solidify the taxonomy and systematics of the Varanus salvator Complex, and enumerate more than a dozen Gonocephalus lineages as candidate species in need of taxonomic scrutiny. Lastly, I investigate contemporary and historical patterns of dispersal throughout Sundaland, and between Sundaland and the Philippines.

Alligatorines are a diverse clade of crocodylians whose history spans the entire Cenozoic. They are suited to answer a variety of questions with far‐reaching impacts due to their physiology and preservation potential, and have been the subject of several phylogenetic, biogeographic, and diversity analyses. However, prior phylogenetic analyses had poor resolution and several putative alligatorines have never been included, while other analyses would be more informative and accurate if viewed through the context of evolutionary history. Here, I analyze the phylogenetics, taxonomy, biogeography, ecomorphology, and diversity dynamics of alligatorines. An almost fully resolved phylogenetic hypothesis returns two major clades within Alligatorinae and includes several putative alligatorines not previously analyzed. The clade originated in North America and dispersed to Europe and Asia three to five times via at least three different corridors at high latitudes when climate—and potentially salinity—were favorable, likely including the recently discovered subaerial Lomonosov Ridge. The modern American alligator is a dietary generalist, but evolved from a durophagous specialist, contrary to the intuitive reasoning of the “Law of the Unspecialized”. It was able to do so by entering the generalist niche vacated by basal crocodyloids following their extirpation from mid‐latitude North America. Alligatorine diversity only weakly tracks climate change and does not track the rock record excepting swampy environments. Alligatorine diversity correlates with climate change. Climate change correlates with rocks, though in a more complicated pattern. Some diversity metrics correlate with some aspects of the rock record, but predominantly do not. There is more support for the common‐cause hypothesis than for rock record bias driving apparent alligatorine diversity. Overall, alligator evolution exhibits a pattern of being more diverse taxonomically and morphologically when the climate is warmer, and dispersing during the warmest and wettest of those times.

In 2011, several wild North American bumble bee pollinator species were reported to have declined by up to 96% in relative abundance in comparison to historic estimates, and one species was speculated to be extinct. None of these species have yet been documented to have recovered from these declines and additional species are now suggested to be at risk. Imperiled species in particular show increased specificity to narrow climatic envelopes, as opposed to putatively stable species. My dissertation describes patterns of population genetic diversity, structure, and gene flow pathways associated with climate variation and historical biogeography of bumble bees distributed in western North America. The results of my dissertation research suggests that (1) historic climate variability predicts contemporary patterns of population genetic structure and divergence in an economically important species, (2) color variability in bumble bees is likely associated with lineage diversification and phylogeography, (3) bumble bee community structure across evolutionary time is likely driven by Müllerian mimicry at narrow spatial scales, and (4) bumble bees inhabiting specialized ecological niches are associated with high levels of genetic fixation at regional spatial scales in the Pacific Northwest. The results of my research directly contribute to current efforts to effectively manage, conserve, and advocate for wild bumble bee pollinators in the context of global change.

Blow flies (Diptera: Calliphoridae) are among the most dominant and conspicuous insects in the decomposition process. They are important in forensic entomology to determine time of death and, in certain situations, cause of death or relocation of a body. Insects are now included as standard operating procedures in crime scene investigations in many countries, however, this is not standard procedure in the Caribbean area due to lack of knowledge of insects involved in cadaveric decomposition. Successful application of forensic entomology depends on solid underlying data. Our main goal is to advance the knowledge of Calliphoridae in the Caribbean to enable forensic entomology studies. We performed a mega-transect across the Caribbean and extensively collected flies attracted to rotten meat baits during five years from 2011 to 2015. Overall we collected 61,332 flies of which 34,650 were Calliphoridae. We sampled 16 of the 18 species of forensically important Caribbean Calliphoridae and three continental species. We determine the diversity and distribution of Calliphoridae in the Caribbean. We also present a thorough DNA barcode dataset, covering the geographic range of most species in the region. Finally we established phylogenetic relationships among Calliphoridae species and test biogeographical hypotheses, and patterns of diversification and endemism in the Caribbean. In sum, this is the most comprehensive study of the family Calliphoridae from the Caribbean that will open the door for future research on forensic entomology in the region.

The human population is rapidly urbanizing. While this will undoubtedly present challenges for humans it will also place pressure on birds in these areas. To better manage these spaces in a manner that promotes avian biodiversity, we must first come to understand how human development affects the distribution and abundance of bird species and guilds within cities and if patterns observed previously in large cities can be extended to smaller ones. Breeding birds were surveyed along a gradient of increasing urbanization in Iowa City, Iowa, during the summers of 2014 and 2015. Study areas included a forested park, recreational park, low density residential area, medium density residential area, high density/mixed-use area, and urban core. Birds were censused a total of four times at each site using variable circular plot counts. Landscape characteristics were measured using a high resolution land cover dataset and tree canopy model. Regression models were developed to investigate relationships between the bird community and land cover characteristics. Bird species richness, diversity, and evenness all decreased with increasing urbanization, while biomass and the number of individuals peaked in the urban core. The community shifted from non-native, resident, granivorous, multi-brooding building nesters in highly developed areas to native, migrant, invertivorous, single-brooding, tree and tree cavity nesters at the least developed sites. Regression models indicated varied relationships among landscape characteristics and species richness and community prevalence of functional guilds. Native, migratory, invertivorous, tree cavity-nesting, and single-brooding species showed negative relationships to variables measuring the built environment, while non-native, resident, granivorous, building nesting, and multi-brooding species showed positive relationships to these measures. Overall, the response of avian functional guilds to varying levels of urban intensity in Iowa City were remarkably similar to the results of previous studies. This suggests that much of what has been learned previously concerning avian responses to human development can be extended to planning and implementing conservation strategies in smaller cities.

The alpine treeline ecotone is primarily caused by climate at continental and regional scales, but at finer scales exhibits increasing complexity and linkages with abiotic factors. In order to better understand the dynamics and geographic properties of treeline, a three-pronged study was conducted. The study's first objective investigated what factors account for local treeline variation by comparing a climate-based predictive surface with actual treeline elevation. After finding that a mean growing season temperature of 10.27°C was the strongest predictor of treeline at continental scales, statistical analyses attempted to model the differences between predicted and actual treeline elevation based on local climatic and geomorphological controls. Site elevation and latitude were found to correlate most strongly. Roughness also exerted positive influences, as well as precipitation when coupled with certain terrain factors. The second objective explored the distribution of treeline carbon at site scales by analyzing field data gathered in August 2009 in Glacier National Park, Montana. This confirmed the expected relationship of upright trees containing the highest biomass density, tundra the lowest, and krummholz in the middle. A high degree of dead organic matter was discovered, which may have important implications for treeline as a carbon source or sink when considering treeline's slow decomposition rates, and how these will change under climate warming. An additional analysis investigated the potential for relative biomass gain with future treeline advance, based on site and regional differences in slope and environmental lapse rates. The third objective asked what the potential for change in treeline biomass is across the western United States is by using freeze-thaw days as a proposed indicator. This potential importance is based on existing knowledge of the facilitating relationships between solifluction, surface geomorphology, and seedling establishment and survival. Freeze-thaw days were found to be highly variable, but correlated most strongly with elevation, suggesting increased temperature variability at higher elevations. The concluding chapter synthesizes the findings and maps potential biomass gain and freeze-thaw days together to highlight treeline sites and regions with the greatest potential for advance in a warming climate.

Spider wasps are solitary parasitoids that use one spider to lay a single egg. Even though their behavior seems homogeneous, the features pertaining to nesting and hunting behavior are diverse for different species. There are approximately 5,000 described species, in 120 genera, but there are probably many undescribed species. The systematics of Pompilidae has been studied in recent years, but only morphological data have been used for this purpose. Because of the morphological homogeneity of spider wasps, molecular data may prove promising for understanding the systematics of the group. Furthermore, dated molecular phylogenies calibrated with fossil data may allow studying the historical biogeography and evolution of the group. I used the nuclear molecular markers elongation factor–1 α F2 copy (EF1), long–wavelength rhodopsin (LWRh), wingless (Wg), RNA polymerase II (Pol2), the D2–D3 regions of the 28S ribosomal RNA (28S), and the mitochondrial Cytochrome C Oxidase I (COI) in a Bayesian and Maximum Likelihood framework, to reconstruct the phylogenies of four main Pompilidae groups: the subfamily Pompilinae, the tribe Aporini, the genus Psorthaspis, and the genus Drepanaporus. I also studied the fossil Pompilidae, and used those results to produce time-calibrated phylogenies of Pompilinae, Aporini, and Psorthaspis. Molecular phylogenetic results support the utility of the use of molecular markers for species delimitation and sex-associations in Pompilidae. In addition, the use of dated phylogenies supports the correlation of host use with diversification rate-shifts, the coevolution of mimicry between pompilids and velvet ants, and various biogeographical hypotheses never tested before for spider wasps.

No presente trabalho nós investigamos a história filogeográfica de dois passeriformes: Dendrocincla turdina (Dendrocolaptidae) e Drymophila squamata (Thamnophilidae). As duas espécies são endêmicas de baixadas da Mata Atlântica e boa parte de suas distribuições é coincidente, mas D. turdina chega a altitudes maiores e D. squamata ocorre em uma região disjunta no nordeste onde D. turdina não ocorre. Foram analisadas a estrutura genética das duas espécies e suas histórias demográficas, também foram feitas inferências sobre os processos históricos que poderiam ter contribuído para a diversidade genética que observamos hoje. Para D. turdina foram utilizados sete microssatélites, um marcador mitocondrial e um íntron. Enquanto para D. squamata foram utilizados um marcador mitocondrial e dois íntrons. O primeiro capítulo da Tese aborda os dados de D. turdina, que mostraram ausência de estrutura geográfica e evidências de expansão populacional. A utilização de microssatélites reforçou a possibilidade de ser uma população única, uma vez que, dada a alta taxa de mutação desses marcadores, em geral é possível detectar divergências recentes. A expansão demográfica foi evidenciada e datada a partir do último máximo glacial (UMG) baseado no marcador mitocondrial e no íntron. A computação Bayesiana aproximada (ABC) foi utilizada para testar esse cenário de população única com expansão populacional baseado nos nove marcadores. Os parâmetros estimados foram congruentes com os resultados das outras análises. Parece ter ocorrido um gargalo genético seguido por aumento do tamanho populacional, sendo que no UMG o tamanho efetivo populacional era duas ordens de grandeza menor do que o atual. No segundo capítulo da Tese analisamos a espécie D. squamata, para a qual foram encontradas quatro linhagens mitocondriais separadas geograficamente. Sendo que as linhagens Sul, Centro e Norte parecem ter se divergido durante o Pleistoceno médio, enquanto o grupo Nordeste, composto pela população disjunta, parece ter se diversificado há mais tempo, cerca de 1,1 milhão de anos atrás. Para os clados Sul e Norte foram identificadas expansões demográficas no UMG. Tanto eventos geotectônicos quanto oscilações climáticas do Quaternário podem ter atuado no processo de diversificação; enquanto os rios podem ter contribuído para a manutenção dessas divergências, ao menos entre os clados Norte e Centro. Os grupos genéticos encontrados no presente estudo não condizem com a distribuição geográfica descrita para as subespécies descritas de D. squamata, isso indica a necessidade de uma revisão taxonômica. A divergência do clado Nordeste parece ser bastante antiga e essa linhagem ocorre em uma área reduzida e impactada da mata Atlântica, além de geograficamente isolada das maior área de distribuição do táxon. Isso indica que o clado Nordeste merece atenção quanto à sua conservação. A presente Tese contribuiu com o melhor entendimento da distribuição da diversidade genética das espécies aqui estudadas e da história da biodiversidade da mata Atlântica, trazendo informações sobre dois táxons com histórias filogeográficas diferentes, embora possivelmente moldadas por processos semelhantes. / Here we present the phylogeographic history of two Passerine birds: Dendrocincla turdina (Dendrocolaptidae) and Drymophila squamata (Thamnophilidae). Both are endemic species of the Atlantic Forest lowlands and their occurrence overlaps along most of their geographic distribution, but D. turdina reaches higher altitudes and D. squamata has in a disjunct population in the northeast, where D. turdina does not occur. The genetic structure and the demographic history of both species was studied, and inferences about potential historical processes that could have influenced their genetic diversity pattern were made. For D. turdina we used seven microsatellites and sequences of one mitochondrial (mtDNA) gene and one intron. For D. squamata sequences of one mtDNA gene and two introns were obtained. The first chapter shows that D. turdina does not present population genetic structure but has evidences of population expansion. Microsatellite analyses also show absence of structure and given their high mutation rates, this indicates that there is no evidence of any recent divergences. Results based on mtDNA and intron sequences showed that the demographic expansion started during the last glacial maximum (LGM). Approximate bayesian computation (ABC) was used to test this scenario of a unique population with expansion based on nine molecular markers. The results were congruent with those from other analyses. It seems that a bottleneck was followed by an increase of population size, and at the LGM the population effective size was two orders of magnitude lower than nowadays. The second chapter presents data on D. squamata. Four mitochondrial lineages that are geographically separated were observed. Lineages South, Center, and North seem to have diverged in the middle of the Pleistocene and the Northeast lineage, that grouped the disjunct population, seems to have diverged around 1.1 million years ago. Clades South and North presented evidences of demographic expansions during the LGM. Both geotectonic and climatic oscillations from the Quaternay could have beeen involved in the diversification process; while rivers may helped to maintain the lineages differentiated, at least clades North and Center. The geographic distribution of these lineages did not match the one described for D. squamata subspecies. Thus, indicating that a taxonomic revision is needed. The divergence of the Northeast lineage seems to be old and it occurs in a reduced and deforested area, besides it is geographically isolated from the main distribution of the species. This highlights that the conservation of the Northeast lineage should be granted major attention. This thesis contributed with data on two avian species with distinct phylogeographic histories that could have been shaped by similar processes that occurred in the Atlantic forest.

Since the mid 19th century, the biogeography of island South-East Asia has been the subject of much study. Early researchers explained many of the species distribution patterns by the rise and fall of sea levels and land. This and the work of other researchers culminated in a theory that emphasized the role of Pleistocene sea level low stands in species evolution. With the advent of newly developed molecular techniques, however, it became clear that many species divergence events had taken place before the Pleistocene and a biogeographical theory focusing on Pleistocene sea level changes was inadequate. In this research, I have developed a new biogeographic model that explains present-day distribution patterns and evolutionary relationships between species. I use this new model to explain 10 ‘mammalian riddles’, i.e. evolutionary or distribution patterns in selected mammal species groups that could not be explained with the existing theories. I developed the new model by analyzing the geological literature for this region, and by mapping palaeogeographical and palaeoenvironmental changes for the last 20 million years. In addition I compiled information on the palaeontological record for the region and on divergence times between taxa using a molecular clock assumption. These phylogenetic data were compared with the palaeomaps to assess whether particular divergence events could be correlated with certain palaeogeographical or palaeoenvironmental changes. The combination of these two information sources has resulted in a much-improved understanding of mammalian evolution in island SE Asia. Using this model it is now possible to relate important palaeoenvironmental events, such as the Late Miocene cooling, an Early–Middle Pliocene highstand, or the emergence and submergence of a land bridge between the Malay Peninsula and Java to evolutionary changes in species. I test the accuracy of the new model by analysing the relationships within several mammal groups using craniometric and molecular analysis. The observed relationships and deduced timing of divergence between taxa could in many cases be explained by the model, which indicates that it is relatively accurate. In addition, with the new model I have been able to find solutions to most mammalian riddles, although these results require further testing. Overall, I therefore believe I have made a significant contribution to the biogeographical understanding of island SE Asia.