A major recent trend in systematics is the re-integration of morphological data into total evidence analysis. To date, few studies have explored the effects of incorporating morphological and molecular data into total evidence analyses; however, those that have done so have found that even a comparatively small phenomic dataset can have disproportionately large impacts on results. Given the demonstrated importance of morphological characters in testing the phylogenetic relationships, herein I provide a case in point for the exploration of the effects of incorporating morphological evidence as an independent source of phylogenetic evidence, and an important framework to test hypotheses supported by molecular evidence, in the superfamily Brachycephaloidea. In this study, 338 amphibian species are included, of which 318 species correspond to the superfamily Brachycephaloidea. All known genera within the superfamily were sampled. The complete dataset included 13,686 molecular characters (mitochondrial and nuclear markers) and 185 morphological characters, which were analyzed together. In addition, I performed additional analyses modifying the complete datasets to evaluate the effects of character and taxon sampling. As results, I found that the superfamily Brachycephaloidea does not represent a monophyletic as previously thought. Likewise, the phylogeny resulting from this analysis showed several taxa to be nonmonophyletic: Brachycephalidae and Craugastoridae as well as genera Craugastor, Psychrophynella, and Pristimantis. From the detailed examination of the impact of both character and taxon sampling on the phylogenetic relationships of the superfamily Brachycephaloidea, I found that the inclusion of a comparatively small phenomic dataset (185 character) as well as the inclusion of two key taxa (Atopophrynus syntomopus and Dischidodactylus duidensis) had disproportionately large impacts on the tree topology. Finally, I provide a new taxonomy for this group. In this, I recognize five families, of which three are morphologically diagnosable (Eleutherodactylidae, Hypodactylidae, and Strabomantidae) whereas the other two are diagnosable solely with molecular evidence (Ceuthomantidae and Craugastoridae). Likewise, 12 out of 26 genera included are morphologically diagnosable. / Uma grande tendência em estudos de sistemática filogenética é a reintegração de dados morfológicos em análises de evidência total. Até o momento, poucos estudos exploraram os efeitos da incorporação de dados morfológicos conjuntamente com dados moleculares em análises de evidência total. No entanto, aqueles que o fizeram concluíram que mesmo uma pequena base de dados fenômicos pode ter grandes e desproporcionais impactos nos resultados. Dada a demonstrada importância de caracteres morfológicos em testes de relacionamentos filogenéticos, aqui apresento um caso de exploração dos efeitos da incorporação de evidência morfológica como uma fonte independente de evidência filogenética e como importante \"framework\" para testar hipóteses suportadas por evidência molecular na superfamília Brachycephaloidea. Nesse estudo, 338 espécies de anfíbios foram incluídas, das quais 318 correspondem a espécies da superfamília Brachycephaloidea. Todos os gêneros conhecidos da superfamília foram amostrados. A base de dados completa inclui 13.686 caracteres moleculares (marcadores mitocondriais e nucleares) e 185 caracteres morfológicos, que foram analisados conjuntamente. Ademais, realizei análises adicionais modificando as bases de dados para avaliar os efeitos de amostragem de caracteres e táxons. Como resultado, encontrei que a superfamília Brachycephaloidea não é monofilética, como anteriormente considerada. Da mesma forma, a filogenia resultante da análise de evidência total mostrou que vários outros táxons também não são monofiléticos: as famílias Brachycephalidae e Craugastoridae, assim como os gêneros Craugastor, Psychrophrynella e Pristimantis. Através do exame detalhado do impacto de diferentes amostragens de caracteres e táxons sobre as relações filogenética na superfamília Brachycephaloidea, encontrei que a inclusão de dois táxons chaves (Atopophrynus syntomopus e Dischidodactylus duidensis) tiveram grandes e desproporcionais impactos na topologia das árvores. Finalmente, eu apresento uma nova taxonomia para as rãs de desenvolvimento direto, reconhecendo cinco famílias, das quais três são morfologicamente diagnosticáveis (Eleutherodactylidae, Hypodactylidae e Strabomantidae), enquanto as outras duas são diagnosticáveis apenas com evidência molecular (Ceuthomantidae e Craugastoridae). Da mesma forma, 12 dos 26 gêneros inclusos são morfologicamente diagnosticáveis.

The subfamily Phryninae (Arachnida: Amblypygi) has not been recently revised, which causes many difficulties for species identification. Thus far, no phylogenetic hypothesis has been proposed for this subfamily. The nomenclature of diagnostic characters is not uniform, and most illustrations are poorly detailed. We reviewed the subfamily Phryninae, redescribed all known species, and described six new species. We proposed a unified nomenclature for teeth of chelicerae and pedipalpal spines. We performed a phylogenetic analysis using total evidence and direct optimization in the program POY. We built a morphological matrix of 92 terminals and 174 characters, and a molecular matrix with 1557 pb (markers COl, 12s and 16s). Both sets of information were analyzed separately to understand their influence over the total evidence analysis. The results of the three analyses were different: the morphological analysis did not recover the subfamily Phryninae as monophyletic, this analysis produced 90 equally parsimonious topologies, however, the strict concensus tree had good resolution. The molecular analysis did not recover the family Phrynidae as monophyletic, but Phryninae was recovered. Total evidence analysis allowed for obtain just one more parsimonious hypothesis which included all species of Phrynidae, and resolved the politomies obtained with the analysis using morphology only, in this hypothesis Phrynidae and its subfamilies are monophyletic. ln all results, the genera of Phryninae were polyphyletic. We selected the tree of total evidence analysis to build a new taxonomic proposal, we decided to keep Acanthophrynus, Phrynus, and Paraphrynus and to create five new genera: Caicedophrynus gen. nov., Cronopiophrynus gen. nov., Gabophrynus gen. nov., Gentiloprynus gen. nov., Girondophrynus gen. novo Accordingly, we proposed 44 nomenclatural changes. Our results showed that the diversity of this group could be greater, therefore, we highlight that populational and phylogeographic studies of Phryninae are important / A subfamília Phryninae (Arachnida: Amblypygi) não possui uma revisão recente. Isso traz muitas dificuldades na identificação das espécies. Nenhuma hipótese filogenética para a subfamília foi proposta. A nomenclatura dos caracteres diagnósticos não é uniforme e a maioria das ilustrações não é suficientemente detalhada. Aqui, nós revisamos a subfamília Phryninae, redescrevemos as espécies conhecidas e seis espécies novas, e propomos uma nomenclatura uniforme para os dentes das quelíceras e espinhos dos pedipalpos. Nós realizamos uma análise filogenética usando evidência total e otimização direta no programa POY. Construímos uma matriz morfológica de 92 terminais e 174 caracteres, e uma matriz molecular usando 1557 pb (marcadores COI, l2S e 16S). Os dois conjuntos de informação foram analisados separadamente para perceber a influência de cada um deles na análise de evidência total. Os resultados das três análises foram diferentes. A análise morfológica não recuperou a subfamília Phryninae como monofilética, resultando em 90 topologias igualmente parcimoniosas, Porém, a árvore de consenso estrito teve uma boa resolução. A análise molecular recuperou Phryninae como monofilética, embora não tenha recuperado a família Phrynidae. A análise de evidência total permitiu obter uma única hipótese mais parcimoniosa a qual inclui todas as espécies de Phrynidae, e permitiu resolver as politomias obtidas na análise morfológica. Nesta hipótese, tanto Phrynidae como suas subfamílias se mantiveram monofiléticas. Em todos os resultados, os gêneros de Phryninae são polifiléticos. A árvore da análise de evidência total foi selecionada para elaborar uma nova proposta taxonômica. Mantivemos os gêneros Acanthophrynus, Phrynus e Paraphrynus e criamos cinco gêneros novos: Caicedophrynus gen. nov., Cronopiophrynus gen. nov., Gabophrynus gen. nov., Gentilophrynus gen. nov., e Girondophrynus gen. novo Propusemos 44 mudanças nomenclaturais, Nossos resultados sugerem que a diversidade do grupo é maior do que a conhecida. Isso nos faz considerar importante análises populacionais e filogeográficas em Phryninae

The subfamily Phryninae (Arachnida: Amblypygi) has not been recently revised, which causes many difficulties for species identification. Thus far, no phylogenetic hypothesis has been proposed for this subfamily. The nomenclature of diagnostic characters is not uniform, and most illustrations are poorly detailed. We reviewed the subfamily Phryninae, redescribed all known species, and described six new species. We proposed a unified nomenclature for teeth of chelicerae and pedipalpal spines. We performed a phylogenetic analysis using total evidence and direct optimization in the program POY. We built a morphological matrix of 92 terminals and 174 characters, and a molecular matrix with 1557 pb (markers COl, 12s and 16s). Both sets of information were analyzed separately to understand their influence over the total evidence analysis. The results of the three analyses were different: the morphological analysis did not recover the subfamily Phryninae as monophyletic, this analysis produced 90 equally parsimonious topologies, however, the strict concensus tree had good resolution. The molecular analysis did not recover the family Phrynidae as monophyletic, but Phryninae was recovered. Total evidence analysis allowed for obtain just one more parsimonious hypothesis which included all species of Phrynidae, and resolved the politomies obtained with the analysis using morphology only, in this hypothesis Phrynidae and its subfamilies are monophyletic. ln all results, the genera of Phryninae were polyphyletic. We selected the tree of total evidence analysis to build a new taxonomic proposal, we decided to keep Acanthophrynus, Phrynus, and Paraphrynus and to create five new genera: Caicedophrynus gen. nov., Cronopiophrynus gen. nov., Gabophrynus gen. nov., Gentiloprynus gen. nov., Girondophrynus gen. novo Accordingly, we proposed 44 nomenclatural changes. Our results showed that the diversity of this group could be greater, therefore, we highlight that populational and phylogeographic studies of Phryninae are important / A subfamília Phryninae (Arachnida: Amblypygi) não possui uma revisão recente. Isso traz muitas dificuldades na identificação das espécies. Nenhuma hipótese filogenética para a subfamília foi proposta. A nomenclatura dos caracteres diagnósticos não é uniforme e a maioria das ilustrações não é suficientemente detalhada. Aqui, nós revisamos a subfamília Phryninae, redescrevemos as espécies conhecidas e seis espécies novas, e propomos uma nomenclatura uniforme para os dentes das quelíceras e espinhos dos pedipalpos. Nós realizamos uma análise filogenética usando evidência total e otimização direta no programa POY. Construímos uma matriz morfológica de 92 terminais e 174 caracteres, e uma matriz molecular usando 1557 pb (marcadores COI, l2S e 16S). Os dois conjuntos de informação foram analisados separadamente para perceber a influência de cada um deles na análise de evidência total. Os resultados das três análises foram diferentes. A análise morfológica não recuperou a subfamília Phryninae como monofilética, resultando em 90 topologias igualmente parcimoniosas, Porém, a árvore de consenso estrito teve uma boa resolução. A análise molecular recuperou Phryninae como monofilética, embora não tenha recuperado a família Phrynidae. A análise de evidência total permitiu obter uma única hipótese mais parcimoniosa a qual inclui todas as espécies de Phrynidae, e permitiu resolver as politomias obtidas na análise morfológica. Nesta hipótese, tanto Phrynidae como suas subfamílias se mantiveram monofiléticas. Em todos os resultados, os gêneros de Phryninae são polifiléticos. A árvore da análise de evidência total foi selecionada para elaborar uma nova proposta taxonômica. Mantivemos os gêneros Acanthophrynus, Phrynus e Paraphrynus e criamos cinco gêneros novos: Caicedophrynus gen. nov., Cronopiophrynus gen. nov., Gabophrynus gen. nov., Gentilophrynus gen. nov., e Girondophrynus gen. novo Propusemos 44 mudanças nomenclaturais, Nossos resultados sugerem que a diversidade do grupo é maior do que a conhecida. Isso nos faz considerar importante análises populacionais e filogeográficas em Phryninae

Chapter 1. The family Pteronarcyidae (Plecoptera) is a highly studied group of stoneflies and very important to a wide variety of aquatic studies. Several phylogenies have been proposed for this group recent decades, however there is little congruence between the various topologies. The present study revises the phylogeny of the group by combining molecular data from mitochondrial cytochrome oxidase subunit II, ribosomal subunit 12S, ribosomal subunit 16S, and nuclear loci ribosomal subinit 18S and Histone H3, with published morphological data in a parsimony-based total evidence analysis. The analysis produced a well-supported phylogeny with novel relationships within the genus Pteronarcys. Maximum Likelihood and Bayesian analyses produced topologies congruent with parsimony analysis. Character mapping revealed several homoplasious morphological characters that were previously thought to be homologous. Chapter 2. Phylogeographic studies in aquatic insects provide valuable insights into mechanisms that shape the genetic structure of aquatic communities. Yet studies that include broad geographic areas are uncommon for this group. We conducted a broad scale phylogeographic analysis of P. badia across western North America. In order to allow us to generate a larger mitochondrial data set, we used 454 seqeuncing to reconstruct the complete mitochondrial genome in the early stages of the project. Our analysis reveals what appears to be a complex history of isolation and multiple invasions among some lineages. The study provides evidence of multiple glacial refugia and suggests that historical climactic isolations have been important mechanisms in determining genetic structure of insects in western North America. Our ability to generate a large mitochondrial data set through mitochondrial genome reconstruction greatly improved nodal support of our mitochondrial gene tree, and allowed us to make stronger inference of relationships between lineages and timing of divergence events.

Cybercrime and related malicious activity in our increasingly digital world has become more prevalent and sophisticated, evading traditional security mechanisms. Digital forensics has been proposed to help investigate, understand and eventually mitigate such attacks. The practice of digital forensics, however, is still fraught with various challenges. Some of the most prominent of these challenges include the increasing amounts of data and the diversity of digital evidence sources appearing in digital investigations. Mobile devices and cloud infrastructures are an interesting specimen, as they inherently exhibit these challenging circumstances and are becoming more prevalent in digital investigations today. Additionally they embody further characteristics such as large volumes of data from multiple sources, dynamic sharing of resources, limited individual device capabilities and the presence of sensitive data. These combined set of circumstances make digital investigations in mobile and cloud environments particularly challenging. This is not aided by the fact that digital forensics today still involves manual, time consuming tasks within the processes of identifying evidence, performing evidence acquisition and correlating multiple diverse sources of evidence in the analysis phase. Furthermore, industry standard tools developed are largely evidence-oriented, have limited support for evidence integration and only automate certain precursory tasks, such as indexing and text searching. In this study, efficiency, in the form of reducing the time and human labour effort expended, is sought after in digital investigations in highly networked environments through the automation of certain activities in the digital forensic process. To this end requirements are outlined and an architecture designed for an automated system that performs digital forensics in highly networked mobile and cloud environments. Part of the remote evidence acquisition activity of this architecture is built and tested on several mobile devices in terms of speed and reliability. A method for integrating multiple diverse evidence sources in an automated manner, supporting correlation and automated reasoning is developed and tested. Finally the proposed architecture is reviewed and enhancements proposed in order to further automate the architecture by introducing decentralization particularly within the storage and processing functionality. This decentralization also improves machine to machine communication supporting several digital investigation processes enabled by the architecture through harnessing the properties of various peer-to-peer overlays. Remote evidence acquisition helps to improve the efficiency (time and effort involved) in digital investigations by removing the need for proximity to the evidence. Experiments show that a single TCP connection client-server paradigm does not offer the required scalability and reliability for remote evidence acquisition and that a multi-TCP connection paradigm is required. The automated integration, correlation and reasoning on multiple diverse evidence sources demonstrated in the experiments improves speed and reduces the human effort needed in the analysis phase by removing the need for time-consuming manual correlation. Finally, informed by published scientific literature, the proposed enhancements for further decentralizing the Live Evidence Information Aggregator (LEIA) architecture offer a platform for increased machine-to-machine communication thereby enabling automation and reducing the need for manual human intervention.

Indiana University-Purdue University Indianapolis (IUPUI) / The aim of this study was to use multivariate statistical techniques to: (1) determine the reproducibility of fiber evidence analyzed by MSP, (2) determine whether XRF is an appropriate technique for forensic tape analysis, and (3) determine if DART/MS is an appropriate technique for forensic tape analysis. This was achieved by employing several multivariate statistical techniques including agglomerative hierarchical clustering, principal component analysis, discriminant analysis, and analysis of variance. First, twelve dyed textile fibers were analyzed by UV-Visible MSP. This analysis included an inter-laboratory study, external validations, differing preprocessing techniques, and color coordinates. The inter-laboratory study showed no statistically significant difference between the different instruments. The external validations had overall acceptable results. Using first derivatives as a preprocessing technique and color coordinates to define color did not result in any additional information. Next, the tape backings of thirty-three brands were analyzed by XRF. After chemometric analysis it was concluded that the 3M tapes with black adhesive can be classified by brand except for Super 33+ (Cold Weather) and Super 88. The colorless adhesive tapes were separated into two large groups which were correlated with the presence of aluminosilicate filler. Overall, no additional discrimination was seen by using XRF compared to the traditional instrumentation for tape analysis previously published. Lastly, the backings of eighty-nine brands of tape were analyzed by DART/MS. The analysis of the black adhesive tapes showed that again discrimination between brands is possible except for Super 33+ and Super 88. However, now Tartan and Temflex have become indistinguishable. The colorless adhesive tapes again were more or less indistinguishable from one another with the exception of Tuff Hand Tool, Qualpack, and a roll of 3M Tartan, which were found to be unique. It cannot be determined if additional discrimination was achieved with DART/MS because the multivariate statistical techniques have not been applied to the other instrumental techniques used during tape analysis.