Esta tese está dividida em três partes: I Filogenética Básica, II Filogenia de Pilocarpinae e III Novidades Taxonômicas em Esenbeckiinae. Parte I Filogenética Básica - fornece uma rápida revisão de alguns dos métodos básicos atualmente em uso na filogenética, envolvendo aspectos teóricos e operacionais, assim como algumas de suas possíveis implicações. O Capítulo 1 discute dois conceitos importantes (grupo e caráter) e interrelacionados, mostra como pode ser construído um modelo estocástico para o tratamento de caractres, enfatizando sua adequação e demonstranto como homologia e, por conseqüência grupos, podem ser adequadamente tratados sob ótica probabilística. O Capítulo 2 apresenta os métodos de construção e otimização de árvores uzando máxima verossimilhnaça e análise bayesiana. Parte II Filogenia de Pilocarpinae - apresenta a filogenia de Pilocarpinae baseada em dados moleculares (espaçadores ITS1, ITS2 e gene 5.8 S do DNA nuclear e espaçador trnG-S do DNA platidial) e a filogenia de Pilocarpus Vahl baseada em dados moleculares (mesmas regiões usadas anteriormente) e morfológicos. O Capítulo 3 apresenta a filogenia em nível genérico da subtribo Pilocarpinae e de gêneros relacionados (Helietta e Balfourodendron ), mostrando que, exceto Esenbeckia , os gêneros tradicionalmente reconhecidos (Metrodorea , Pilocarpus e Raulinoa - monoespecífico) emergem como monofiléticos (embora a subtribo não) e que Balfourodendron e Helietta (ambos da subtribo Pteleinae) possuem relações mais estreitas com parte dos gêneros de Pilocarpinae do que com o gênero-tipo de sua própria subtribo (Pteleinae) e reúnem-se (junto com Esenbeckia , Metrodorea e Raulinoa ) em um clado caracterizado pela presença de inflorescências ramificadas, para o qual foi criada uma subtribo, ficando Pilocarpinae monogenérica; além disso, este capítulo apresenta um protocolo para detecção de burn-in em análises filogenéticas bayesia- nas usando métodos já bem estabelecidos em estudos de convergência de MCMC. Por sua vez, o Capítulo 4 apresenta a filogenia das espécies de Pilocarpus baseada em dados morfológicos e moleculares; essa filogenia, associada a simulações computacionais, é utiliza como base para traçar hipóteses evolutivas sobre os padrões foliares e de estivação da corola no gênero, mostrando como os estados desses caracteres se comportam nas árvores obtidas e quão apropriado é utilizar os diferentes estados como sinapomorfias/homoplasias usando o método MCMC como base e contrastando com o mapeamento com parcimônia, deixando claro que sina- pomorfia/homplasia é mais adequadamente tratada como uma questão de probabilidade. Parte III Novidades Taxonômicas em Esenbeckiinae representa um reflexo das atividades de campo e de análise de material de herbário. No Capítulo 5 é apresentada uma redescrição de E. cowanii Kaastra, espécie anteriormente conhecida apenas da Guiana Francesa e apenas pelo material tipo, cuja morfologia floral era desconhecida e foi encontrada nos Estados do Acre, Mato Grosso, Pará e Rondônia durante as expedições de campo que fiz para a Amazônia; além disso, é proposto um epítipo para o táxon. O Capítulo 6 apresenta a descrição de uma nova espécie de Esenbeckia (embora ainda sem diagnose latina), coletada nos estados do Acre e Rondônia e caracterizada pela posse de brácteas persistentes. / This dissertation is composed of three major parts: I Basic Phylogenetics, II Phylogeny of Pilocarpinae, and III Taxonomic Novelties in Esenbecki- inae. Part I Basic Phylogenetics - provides a mini-review of some basic methods currently used in phylogenetics, covering theroretical and operational issues, and some of their implications as well. In the Chapter 1 I discuss two major concepts in phylogenetics, namely groups and characters, demonstrate how to build an evolutionary model and emphasize the importance of models in phylogenetics. As an outcome, the meanings of character evolution and groups are reviewed and improved under a probabilistic view. Chapter 2 presents an introduction to the very basic methods of tree construction and optimization using maximum likelihood and bayesian methods. Part II Phylogenetics of Pilocarpinae - presents a phylogeny of Pilocarpinae based on molecular data (internal trancribed spacers ITS1, ITS2, gene 5.8 S - from the nuclear DNA , and spacer trnG-S - from the plastidial DNA), and a phylogeny of Pilocarpus based on morphological and molecular (same DNA regions used before) evidence. Chapter 3 presents a generic-level phylogeny of the Pilocarpinae and allied genera (Balfourodendron and Helietta), which supports the monophyly of the traditionally recognized genera (Metrodorea and Pilocarpus , Raulinoa - monospecific), except Esenbeckia (which is included in a polytomy), whe- reas the subtribe itself is not monophyletic; it is also shown that Balfourodendron and Helietta (both from subtribe Pteleinae) are more closely related to some genera of Pilocarpinae than to the type genus of their own subtribe (Pteleinae), and emerge (together with Esenbeckia , Metrodorea , and Raulinoa ) nested within a clade that has multi-axis inflorescences, for which I created a new subtribe, leaving the Pilocarpinae monogeneric; moreover, this Chapter presents a new2 protocol to be used in MCMC diagnosis in phylogenetic studies. In the Chapter 4 , in turn, the phylo- geny of Pilocarpus is investigated based on morphological and molecular data; that phylogeny, combined to computer simulations, is then used to propose evolutionary hypotheses of leaf blade and corolla aestivation patterns, and show how appropriate the use of character states as synapomorphy/homoplasy can be using the MCMC method; additionally the MCMC and parsimony character mapping procedures are compared, and it is shown that synapomorphy/homoplasy is just a matter of probability. Part III Taxonomic Novelties in Esenbeckiinae is clearly a direct result of my field expeditions to the Amazon, and herbarium work. In the Chapter 5 I present a re-description and epitypification of E. cowanii Kaastra, previously known only from the type locality (and by the type specimens) and whose floral morphology was unknown, which I collected in Acre, Mato Grosso, Pará, and Rondônia States during my collecting trips in the Amazon; further, given the poor type material, I propose an epitype for the species. In the Chapter 6 I describe a new species of Esenbeckia (still without latin diagnose), which I collected in Acre and Rondonia states, whose diagnostic feature is the presence of persistent bracts.

Ixodes ricinus is the most important human-biting tick in Europe and the principal vector of Lyme borreliosis. In addition, this hard tick species transmits a large number of microbial pathogens that are of importance to animal and human health. Little is known about the diversity and genetic population structure of I. ricinus across Europe. Genetic diversity of these tick populations may have implications on disease transmission. I. ricinus primers were designed for a number of mitochondrial genes and a Multilocus Sequence Typing-like Scheme (MLST) was devised. This was termed mitochondrial MLST (mtMLST). MLST has so far mainly been used for typing microbes, and the development of a MLST scheme for an arthropod vector is novel. Understanding the geographic structure of I. ricinus populations, in combination with studies regarding the migration of tick-borne microbial infections, e.g. Lyme borreliosis, is likely to illuminate important processes in the evolution and spread of tick-borne diseases.

A família Bougainvilliidae é um grupo de hidrozoários \"Anthoathecata\" \"Filifera\" pouco conhecido. Nesse estudo, diversos aspectos da biologia do grupo e de táxons relacionados a ele foram analisados e discutidos. Nossas análises incluem: uma revisão bibliográfica dos táxons de Bougainvilliidae, a partir de um embasamento histórico e geográfico sobre seu conhecimento atual; uma síntese sobre sua estrutura exoesquelética, abrangendo informações de outros medusozoários fósseis e atuais; análises histológicas e microestruturais de pólipos de diversos grupos de Medusozoa; e um estudo integrado da evolução de Bougainvilliidae, considerando-se dados moleculares e morfológicos. Os resultados desvendaram gêneros e espécies válidos, padrões possíveis de distribuição latitudinal para pólipos e medusas de Bougainvilliidae, assim como a universalidade e evolução do exoesqueleto como fonte de informação para compreender padrões de diversificação dentro de Bougainvilliidae e em relação a outros Medusozoa. Além disso, os resultados evidenciam a variação na síntese, estrutura e função do exoesqueleto dentre os medusozoários, apontando que a esqueletogênese retrocede ao Ediacarano, sendo que o exoesqueleto axial córneo (complexo quitina-proteico) predomina nos pólipos atuais e atua como uma estrutura de suporte e proteção, entre outras funções. O exoesqueleto apresenta maior variação e complexidade estrutural entre os pólipos de Hydroidolina, grupo para o qual foi descrito um novo tipo de exoesqueleto bicamada, que é encontrado na maioria dos Bougainvilliidae. Resultados das análises filogenéticas identificam a \"Bougainvilliidae\" e \"Bougainvillia\" como táxons não-monofiléticos, e demonstram que o grupo monofilético Pseudothecata taxon novum inclui os gêneros classicamente assumidos em \"Bougainvilliidae\" (exceto Dicoryne), entre outras famílias de \"Anthoathecata\". Neste estudo, ampliamos o nosso entendimento sobre a natureza química e física do exoesqueleto em Medusozoa, estrutura com um valor subestimado na taxonomia do grupo. Concluímos que estudar a \"síntese molecular\", \"matriz molecular\" e \"expressão morfológica\" do exoesqueleto é essencial para inferências evolutivas e ecológicas, as quais podem ser intrinsecamente correlacionadas com outras áreas biológicas, tais como biologia de conservação e filogeografia / The family Bougainvillidae is a poorly known group of hydrozoans \"Anthoathecata\" \"Filifera\". In this study, several aspects of the biology of this group and other related taxa are analyzed and discussed. Our analyzes include: a bibliographic revision of the taxa comprising the Bougainvilliidae, based on its current historical and geographical knowledge; a synthesis regarding its exoskeletal structure, including information on other extinct and extant medusozoans; histological and microstructural analyzes of polyps of several groups of Medusozoa; and an integrated study on the evolution of the Bougainvilliidae, considering molecular and morphological data. The results validated several genera and species and possible latitudinal distributional patterns for polyps and medusae of Bougainvilliidae, as well as the universality and evolution of the exoskeleton as a source of information to understand its role in the diversification patterns in Bougainvilliidae and with relation to other Medusozoa. Additionally, the results reveal the existence of variation on the synthesis, structure and function of the exoskeleton among the Medusozoa, showing that the exoskeletogenesis dates back to the Ediacaran, since the corneus exoskeleton (chitin-protein complex) predominates today in current polyps and acts as a supporting structure and protection, among other functions. The skeleton has higher variation and structural complexity among polyps of Hydroidolina, taxon from which we described a new type of bilayer exoskeleton, which is found in most of the species of Bougainvilliidae. Results of phylogenetic analyzes identificate \"Bougainvilliidae\" and \"Bougainvillia\" as non-monophyletic taxa, and showed that the monophyletic group Pseudothecata taxon novum includes the classical genera usually inserted in the \"Bougainvilliidae\" (excluding Dicoryne), and other families of \"Anthoathecata\". In this study, we increased our understanding of the chemical and physical nature of the exoeskeleton of Medusozoa, a structure whith an underestimate role in the taxonomy of the group. We concluded that the study of the \"molecular synthesis\", the \"molecular matrix\" and the \"morphological expression\" of the exoskeleton is necessary for evolutionary and ecological inferences, which are intrinsically related to other biological areas, such as conservation biology and phylogeography

Toll-like receptor 4 (TLR4) is an important vertebrate innate immune receptor. TLR4 recognizes both endogenous and exogenous danger signals to trigger an NF-kB dependent inflammatory response. While exogenous danger signal recognition is an essential part of pathogen response by the innate immune system, endogenous danger signal recognition by TLR4 can lead to chronic and pathological inflammation. Understanding the differences in recognition of these two types of danger signals would allow for independent modulation of pathogen and host triggered inflammatory response through TLR4. Here, we examine the evolution of activation of TLR4 by two agonists, pathogen-derived lipopolysaccharide and host-produced S100A9. We show that these two types of signals evolved earlier than previously thought. We identified TLR4 cofactors MD-2 and CD14 in amphibians and fish, and validated that zebrafish TLR4 can recognize LPS. By contrast, we find that S100 activation evolved in the ancestor of amniotes. We identified an ortholog of S100A9 in birds and reptiles capable of activating TLR4. Using comparative immunology, we found that the requirements for LPS and S100A9 activation are different. In addition to our evolutionary studies, we used molecular approaches to probe if zinc binding to S100A9 is necessary for TLR4 activation. We found that activation of TLR4 by S100A9 occurs even in the absence of zinc. Finally, we describe how our evolutionary approach led to mechanistic hypotheses regarding TLR4 activation by both LPS and S100A9. This has led to ongoing projects in the Harms lab. This dissertation includes previously published and unpublished co-authored material. / 2021-04-30

Within bioinformatics, phylogenetics is the study of the evolutionary relationships between different species and organisms. The genetic revolution has caused an explosion in the amount of raw genomic information that is available to scientists for study. While there has been an explosion in available data, analysis methods have lagged behind. A key task in phylogenetics is identifying homology clusters. Current methods rely on using heuristics based on pairwise sequence comparison to identify homology clusters. We propose the Orthology Group Cleaner (the OGCleaner) as a method to evaluate cluster level verification of putative homology clusters in order to create higher quality phylogenetic tree reconstruction.

Borealosuchus Brochu 1997 was erected for a group of Late Cretaceous through early Eocene eusuchian crocodyliform species formerly assigned to Leidyosuchus Lambe 1907. Borealosuchus wilsoni was originally described by Mook (1959) based solely on a dorsoventrally crushed skull from the early Eocene (Wasatchian) Green River Formation of Wyoming, and assigned to Leidyosuchus. Later analyses referred specimens from the late Paleocene and middle Miocene to the species (Brochu, 1997). In phylogenetic analyses, Borealosuchus has been retrieved as either a basal crocodylian (e.g., Salisbury and Willis, 1996; Brochu, 1997; Wu et al., 2001; Buscalioni et al., 2011; Brochu et al., 2012; Narváez et al., 2016) or a close crocodylian outgroup (e.g. Benton and Clark, 1988; Pol et al., 2009; Turner and Pritchard, 2015). More exact phylogenetic placement of Borealosuchus remains unclear. Borealosuchus wilsoni is stratigraphically the youngest species of Borealosuchus, and one of the most completely known, and as such, it figures prominently in ongoing debates over the phylogenetic relationships and origin of crown group Crocodylia. Given its long stratigraphic range in the literature, the question of whether specimens currently referred to B. wilsoni all pertain to a single species is open. This study focuses on a more thorough description of the skeletal morphology of Eocene Borealosuchus, and a revision of the taxonomy of this assemblage, including the conspecific nature of Wasatchian Borealosuchus wilsoni and middle Eocene (Bridgerian) fossils referred to Borealosuchus wilsoni, including material of Diplocynodon stuckeri Mook 1960. A phylogenetic re-assessment of B. wilsoni will hopefully provide further resolution within Borealosuchus and among other closely related taxa. Specimens were coded with a matrix of 190 morphological characters and subjected to phylogenetic analysis. The diversity of Borealosuchus during the Eocene has been underestimated and specimens from the Bridgerian are diagnosable and distinct from those of the preceding Wasatchian stage. A new species will be erected to contain this material. The erection of a new species of Eocene Borealosuchus renders the holotype of D. stuckeri non-diagnostic at the species level, and a new holotype USNM 12990 is designated for Bridgerian Borealosuchus. Some specimens assigned to Brachyuranochampsa eversolei and Crocodylus affinis may also be referable to Borealosuchus. The addition of new material to Borealosuchus increases the diversity of this group during the Eocene.

This project seeks to explore, name, and describe some of the earliest known members of Alligatoroidea. Explorations of Bottosaurus harlani and Deinosuchus reveal that early in their evolutionary history alligatoroids had attained bauplans that are highly divergent from the ancestral condition in both body size and morphology. Bottosaurus harlani preserves aspects of the skull table – including constricted supratemporal fenestrae, a linear frontoparietal suture, and a large trapezoidal dorsal supraoccipital exposure – that are similar to those of caimans. Optimal trees from phylogenetic analysis recover B. harlani in three different positions; as a sister either to the modern dwarf caimans (Paleosuchus), or either living species of Paleosuchus. That a substantial stratigraphic gap separates B. harlani from both species of Paleosuchus, which first appears in the Miocene, along with low character and nodal support raises questions about this relationship. However, should the relationships recovered here be true, Bottosaurus harlani would be the oldest known caiman. The taxon indicates that morphologies common to modern caimans date to the earliest record of the clade. In addition to the enigmatic B. harlani, the Campanian giant Deinosuchus was re-evaluated as part of this project. Recent consensus has been that the three named species of Deinosuchus (D. hatcheri, D. riograndensis, and D. rugosus) represent a single, widely ranging species. Newly-collected material from the Big Bend region of western Texas and increased sampling of the lineage from throughout North America allowed for a review of species-level systematics of Deinosuchus and helped refine its phylogenetic placement among crocodylians. Deinosuchus from western and eastern North America can be consistently differentiated and represent different species. As a result of the lack of diagnostic characters in the very incomplete holotype specimen, the name Deinosuchus is restricted to D. hatcheri. To encompass specimens formerly included in Deinosuchus a new genus, Deinosuchoides, is erected. In addition to naming a new genus, the holotype specimen for Deinosuchus rugosus is determined to be undiagnostic to species level and is therefore a nomen dubium. A new species, Deinosuchoides schwimmeri, is erected upon a cranial specimen from Mississippi. The snout of Deinosuchoides is very long and wide. Almost invariably, crocodylian snouts are either long or wide, but not both. In addition to the unusually long and wide snout, the skull table of this taxon bears hallmarks found in species of other long-snouted taxa such as Tomistoma and Gavialis. To explore the variability of the crocodylian skull table a morphometric analysis was conducted with the inclusion of fossil taxa. As the skull table is robust and likely to be recovered in the paleontological record this element was an ideal fit for a morphometric study. In addition to establishing the morphospace occupation of fossil taxa, the morphometric analysis found considerable overlap in morphospace between Alligatoroidea and Crocodyloidea – the overlap between these groups may be the product of shared ancestry. Additionally, similarities exist in the ecologies of these groups as evidenced by shared snout shape categories. This project finds association between skull table shape and snout length. As such, plotting isolated skull tables in morphospace, may indicate snout length and thus ecology of fossil taxa. When landmarks representing the supratemporal fenestrae are included in the analysis Gavialoidea is broadly separated from the other groups in morphospace. It has been long hypothesized that the size of the supratemporal fenestrae reflect the length of the snout as a result of jaw musculature attaching to their medial margins. However, this relationship is not as straightforward as previously hypothesized; the snouts of the crocodyloids Tomistoma and Euthecodon may exceed the length of the snout in gavialoids but their supratemporal fenestrae are proportionally smaller. This study suggests that a phylogenetic constraint on the size of the supratemporal fenestrae may be present in crocodyloids. In addition to exploring morphospace occupation, allometric trajectories of all extant taxa with available ontogenetic sequences were explored. The smallest extant taxa (O. tetraspis, P. palpebrosus, and P. trigonatus) demonstrate allometric trajectories that plot alongside the juveniles of the other taxa in this analysis. This may suggest that the small sizes of the skull tables in these species were achieved through paedomorphosis, or the maintenance of juvenile morphologies into adulthood.

Goniopholididae is a distinctive and common clade of crocodyliforms known from the Jurasic and Cretaceous of Europe, Asia, and North America. Their position within Neosuchia makes them makes them very important to the study of crocodyliform evolution, but unfortunately their phylogenetic status is ambiguous. This study describes the osteology of two North American fossil taxa: Amphicotylus stovalli, a previously under-represented goniopholidid from the Jurassic Morrison Formation of Oklahoma, and new material of Denazinosuchus kirtlandicus from the Cretaceous Kirtland Formation of New Mexico. A phylogenetic dataset is then constructed including a full sampling of Jurassic North American forms and incorporating new new goniopholidid taxa not previously treated in a phylogenetic context. The affinity of North American and European members of Goniopholis is assessed as are the taxonomic status of putitive goniopholidids Vetisuchus and Denazinosuchus. Goniopholididae is monophyletic, and North American goniopholidids form a nested clade united by a distinctive palate morphology. Furthermore, all Morrison Formation goniopholidids are further nested in the North American clade. North American "Goniopholis" are generically distinct from European forms, and should be ascribed to Amphicotylus. Amphicotylus gilmorei is a junior synonym of A. lucasii. Denazinosuchus and Vectisuchus are not constituents of Goniopholididae, and instead are more closely related to pholidosaurs and thalattosuchians.

Cave organisms are classic examples of regressive evolution, as many disparate taxa have evolved similar convergent phenotypes in subterranean environments. While recent phylogeographic and population genetic analyses have greatly improved our understanding of the evolutionary and biogeographic history of cave organisms, many questions remain unanswered or poorly investigated. I investigated several evolutionary and biogeographic questions in a model system for regressive evolution and studies of ecological and evolutionary mechanisms, amblyopsid cavefishes. In chapter I, I used recently developed methods to delimit species boundaries and relationships in a widely distributed cavefish, Typhlichthys. I show that species diversity in Typhlichthys is currently underestimated and that the view of a single, widely distributed species is not valid. Rather, several morphologically cryptic lineages comprise the diversity in this clade. In chapter II, I examined regressive evolution and potential re-evolution of an eyed, surface form in amblyopsid cavefishes. Whether evolution is truly irreversible, known as Dollo’s Law, has become a question of increasing interest, as several recent studies have made claims that complex structures can be recovered after loss. Phylogenetic and ancestral character state analyses of amblyopsid cavefishes are consistent with re-evolution of eyes and pigmentation and recolonization of surface habitats in the surface-dweller Forbesichthys, providing an opportunity to rigorously discriminate between re-evolution and parallel evolution of cave phenotypes. Despite strong support for re-evolution and contradiction of Dollo’s Law, eye histological evidence and analyses of molecular evolution in the eye gene rhodopsin are consistent with Dollo’s Law supporting at least three independent subterranean colonizations and eye degeneration. Phylogenetic reconstructions of character evolution can occasionally produce strongly supported yet misleading results. In chapter III, I examined the biogeography and speciation of Typhlichthys. Phylogenetic and divergence time analyses support monophyly of Typhlichthys with the majority of cladogenic events occurring in the late Pliocene to Pleistocene, implicating climate change as the primary mechanism driving diversification. Biogeographical analyses, examination of molecular variation in rhodopsin, and structuring of genetic variation with hydrological boundaries, support multiple colonization events by a broadly distributed surface ancestor that subsequently went extinct rather than a single colonization event followed by subterranean dispersal and vicariance.

The Nygmiini is a tussock moth tribe which is redominantly distributed in most regions of the Old World. It was established in order to accommodate several genera that were previously associated with the polyphyletic genus Euproctis Hübner, 1819, which was erected upon the western European Euproctis chrysorrhoea (Linnaeus, 1758)(=Phalaena chrysorrhoea) and has included 682 valid specific names since the early 19th century. The caterpillars of Nygmiini are fairly polyphagous on various woody plant families, and thus many of them are considered as pests with significant importance. They are also known for having importance in public health due to the strong allergic reaction caused by the urticating setae. Although the tribe Nygmiini as well as the core genus Euproctis has such importance in various aspects, it¡¦s monophyletic status and phylogenetic relationships have never been tested using modern phylogenetic methods. I therefore sampled 175 lymantriid species representing most of the potential members of Nygmiini plus one arctiid species as the outgroup taxon to reconstruct the phylogeny of this tribe based on morphological characters from all development stages. The results suggest that the tribe Orgyiini forms a monophyletic clade with the Nygmiini, while neither the Nygmiini sensu Holloway nor the genus Euproctis sensu auctorum is monophyletic, and thus the taxonomic boundary of the tribe should be redefined in accordance to the hypothesis proposed by the present study. On the other hand, larval characters become the major source of the synapomorphies of the Nygmiini. The adult wing patterns which are used to taxonomic identification, however, are highly convergent among genera and thus these characters are not supposed to be informative in systematic research.