Os caranguejos de água doce estão alocados em cinco famílias e apenas duas tem ocorrência para o Brasil: Pseudothelphusidae e Trichodactylidae. Trichodactylus , gênero-tipo da família Trichodactylidae e alocado em Trichodactylinae, foi descrito por Latreille, 1828 para acomodar uma única espécie, T. fluviatilis. Baseado na hipótese de que Trichodactylus não é um grupo monofilético foi realizada uma extensiva amostragem morfológica e molecular. A Inferência filogenética com dois genes mitocondriais (16S rRNA e COI) e um nuclear (Histona 3) mostrou claramente que Trichodactylus não é monofilético. Foram encontradas três grandes linhagens em ambas as análises (Inferência Bayesiana e Máxima Verossimilhança), sendo T. quinquedentatus mais proximamente relacionado com espécies de Avotrichodactylus. O tempo de divergência entre essas linhagens foi estimado em 38 a 53 Ma. Nesse estudo, dez novas espécies pertencentes ao complexo Trichodactylus foram descritas. Adicionalmente, uma espécie e um gênero revalidado. Nesse estudo, portanto, a subfamília Trichodactylinae é composta pelos seguintes gêneros: Avotrichodactylus , Mikrotrichodactylus , Rodriguezia e Trichodactylus . Além disso, a designação de neótipo para T. fluviatilis é de fundamental importância, uma vez que, a série tipo foi perdida. O uso em conjunto e comparativo de diferentes ferramentas, tais como a molecular e morfológica, permitiu reconhecer que a biodiversidade de caranguejos de água doce no Brasil ainda está subestimada / The freshwater crabs are allocated in five families and only two of them have occurrence for Brazil: Pseudothelphusidae and Trichodactylidae. Trichodactylus , the genus-type of the family Trichodactylidae and allocated in Trichodactylinae, was described by Latreille, 1828 to accommodate a single species, T. fluviatilis. Based on the hypothesis that Trichodactylus is not a monophyletic group we realized an extensive morphological and molecular sampling. Phylogenetic inference based on two mitochondrial (16S rRNA e COI) and one nuclear (Histone 3) genes clearly indicated that Trichodactylus is not monophyletic. Were found three great lineages in both analysis (Bayesian Inference and Maximum Likelihood), being T. quinquedentatus more closely related to species of Avotrichodactylus . The time of divergence between these lineages was estimated at 38 to 53 Ma. In this study, nine new species belonging to the T. fluviatilis complex were described. Additionally, one species and one genus were revalidated. Therefore, in this study, the subfamily Trichodactylinae is composed by the following genus: Avotrichodactylus , Mikrotrichodactylus , Rodriguezia e Trichodactylus . Furthermore, we show that the designation of a neotype for T. fluviatilis is strongly needed, since that its type series has been lost. The joint and comparative use of different tools, such as molecular and morphological, allowed us to recognize that the biodiversity of freshwater crabs in Brazil is still very underestimated

Swede midge, Contarinia nasturtii Kieffer (Diptera: Cecidomyiidae), is an invasive pest causing marketable losses on Brassica crops in the Northeastern United States and throughout southern Canada. Heading brassicas, like cauliflower and broccoli, are particularly susceptible because larvae feed concealed inside meristematic tissues of the plant, where head formation occurs. Our work details the development of a sustainable, affordable pest management tactic for swede midge – plant derived repellents. First, it was necessary to establish both a damage and marketability threshold for swede midge, so we developed a technique to manipulate larval density of swede midge on cauliflower, We asked: (1) What is the swede midge damage threshold? (2) How many swede midge larvae can render cauliflower crowns unmarketable? and (3) Does the age of cauliflower at infestation influence the severity of damage? We found that even a single larva causes mild twisting and scarring rendering cauliflower unmarketable 52% of the time, with more larvae causing more severe damage and additional losses, regardless of cauliflower age at infestation. Repellency is an important management approach to consider for swede midge. Since the host range of specialist insects appears constrained by plant phylogeny, we hypothesized that odors from less phylogenetically related plants would be more repellent to swede midge. To test our hypothesis, we performed no-choice and choice biological assays, asking: (1) How do essential oils from different plant species influence midge densities on broccoli? (2) What is the relationship between phylogenetic distance of non-host odors and larval densities on broccoli? Biological assays identified multiple essential oils that reduced larval densities, and phylogenetic analyses showed that less related plants were more effective. In addition to the biological assays, we tested 15 essential oils for their ability to repel gravid females from broccoli tissue in y-tube olfactometer assays. While most of the essential oils reduced the frequency at which females chose host plant meristems, wintergreen, thyme, lemongrass, eucalyptus lemon, garlic, cinnamon, and star anise were most effective. Additionally, we used chemical fingerprints (physical/chemical properties) from PubChem to compare the essential oil volatile compounds and develop an index for their similarity. We found that physicochemical similarity was predictive of repellency. Finally, for repellency to be an effective, long-term strategy, it was important to consider how and whether the repellent response of midges changes over time or previous experience. In our final chapter, we performed electroantennography trials testing how previous experience with garlic or eucalyptus lemon odor for one or 10 s influences the neurophysiological response of swede midge to host (broccoli) or non-host (garlic or eucalyptus lemon) odors. We asked: (1) Does previous experience with garlic or eucalyptus lemon influence the physiological response of swede midge to host or non-host odors? (2) Does the time of previous exposure to non-host odors influence their physiological response to host or non-host odors? Our findings show that swede midge, after 10 s of exposure to either repellent, was more responsive to repellents than host compounds, suggesting that the effectiveness of repellents will not diminish over time.

ABSTRACT The success of land plants can be attributed to the evolution of beneficial associations between plant roots and soil microbes. Root-microbe mutualisms extend the range of plant nutrient acquisition delivered through the hyphal network of mycorrhiza, an ancient and widespread plant symbiosis, or by the more recent adaptive innovation of nitrogen-fixing nodule symbioses. A plant’s genetic toolkit governs its selection of beneficial symbionts and the developmental extent of these intimate interactions. However, the evolutionary origins and function for only a few symbiotic signaling components have been explored. The central aim of this dissertation is to resolve the evolutionary events that contributed two, novel genetic components for establishing root symbioses, NPF1B and NPF1C. The Medicago truncatula (Mt) LATD/NIP/NPF1.7C transporter functions in root and nodule meristems and is a member of the large NPF1 gene subfamily. Here, I propose that LATD/NIP’s role in establishing nitrogen-fixing symbioses is derived from the ancient mycorrhizal signaling pathway. I used a comparative phylogenomic approach to investigate the evolutionary origins of the NPF1 gene across flowering plants and then asked whether diversifying or purifying selection forces influenced NPF1 gene retention. I postulated that such gene retention correlates with the adaptive traits of mycorrhizal or nitrogen-fixing root nodule symbiosis; to test this I measured trait correlation within my dataset. I found that the NPF1 phylogeny is comprised of five well-supported angiosperm clades, A, B, C, D1 and D2, that arose by successive duplications and have unequal gene retention. NPF1B is present as a single copy gene or lost entirely, while the other major NPF1 clades expanded to multiple genes within angiosperms. The NPF1A, B and C genes are under strong purifying selection while the NPF1D genes display positive, diversifying selection. My data revealed a statistically significant correlation of NPF1A, B, C, and D2, but not NPF1D1, gene retention with the ability of a species to form mycorrhizal associations. Additionally, the retention of the NPF1B, C, D1, D2, but not NPF1A, genes within a species is statistically correlated with its ability to form nitrogen-fixing symbiosis. Supporting this correlation, NPF1B genes are expressed in plant root tissues with and without mycorrhizal fungi yet available datasets failed to detect NPF1B expression in nodule tissues whereas the NPF1C genes are expressed in both symbiotic and non-symbiotic plant root tissues. In support of functional conservation, expression of legume LATD/NIP cDNAs from Cicer arietinum (Ca) and Lotus japonicus (Lj) restored, in part, the root and nodule defects of the Mtlatd mutant and resulted in the formation of peculiar hybrid lateral root-nodule structures while, in wild-type M. truncatula, significantly augmented root development. In L. japonicus, the disruption of LATD/NIP alters the number of lateral roots and nodules My thesis data support the hypothesis for an ancestral NPF1 gene function in establishing mycorrhizal associations in angiosperms and, consequent to the monocot-eudicot divergence, co-opted this function for accommodating nitrogen-fixing symbioses in eudicots. Successive duplications then yielded the NPF1B and NPF1C genes that, by neofunctionalization and natural selection, further refined their roles in root organogenesis and symbiosis; a prerequisite for the evolution of nodule organs.

The aim of this thesis is to use phylogenetic analyses of mitochondrial DNA to investigate the biogeography and evolutionary relationships within the freshwater shrimp family Atyidae in Australia at a nested series of scales, both geographic and systematic. At the largest scale, the relationships between Australian and Indo-West Pacific species were inferred using the two most common atyid genera in Australia, Caridina and Paratya. Most atyids are hypothesised to have colonised Australia from Southeast Asia, but Paratya may be a Gondwanan relict given its distribution. Australian Paratya all form a strong clade, with a sister relationship to species from Tasman Sea islands. Molecular clock estimates place all of the splits within Paratya after the break-up of Gondwana, with Australia being colonised once 3½-8½ million years ago. This transoceanic dispersal is conjectured to have taken place through oceanic currents because of the amphidromous life cycle of some taxa of Paratya. Caridina has a very different biogeographic history in Australia, as numerous Australian species have close evolutionary relationships with non-Australian taxa from locations throughout the region. This implies many colonisations to or from Australia over a long period, and thus highlights the surprising adeptness of freshwater shrimp in dispersal across ocean barriers and the unity of much of the region's freshwater biota. A number of potential species radiations within Australia were also identified. This agrees with patterns detected for a large number of Australian freshwater taxa, and implies a vicariant explanation due to the development of colder, dryer climates. The systematic relationships of the remaining two Australian surface genera (Caridinides, Australatya) and two subterranean genera (Parisia, Pycnisia) were also investigated. Australatya forms a strong clade with Pacific 'Atya-like' genera, and Caridinides falls within a clade containing Australian Caridina. The hypogean genera, Parisia and Pycnisia, form a strong clade in all analyses, implying an Australian subterranean speciation. The possibility of a relationship between Parisia/Pycnisia and some Australian Caridina species may have implications for the monophyly of the highly disjunct genus Parisia, as it may descend from local Caridina species and represent convergent morphologies. The common and speciose genus Caridina was used as a model taxon for analyses within Australia. At the medium scale, molecular taxonomic techniques were used to uncover cryptic species within a problematic east Australian species complex. At least five species were detected. Phylogeographic and population genetic analyses were carried out on each of these five cryptic species, which diverged from each other in the late Miocene/Pliocene. There were very large differences between the species in the scales of overall geographic distribution, intraspecific divergence and population structure. These were characterised as either: 1) species with large ranges, low intraspecific divergence, limited phylogeographic structuring (Caridina sp. D); 2) species with large ranges, high intraspecific divergence, a high level of phylogeographic structuring (sp. B); 3) species with a limited range, low intraspecific divergence, no phylogeographic structuring (sp. E); or 4) species with limited ranges, high intraspecific divergences, a high level of phylogeographic structuring (sp. A & C). These patterns reflect a combination of large-scale factors, such as landscape structure and climate change, and small-scale factors, such as species-specific tolerances to local conditions and differing dispersal capabilities. Life history variation (egg size) between species may be correlated with different dispersal abilities. Species with the smallest eggs have the least intraspecific divergence and largest distribution, while those with the biggest eggs have the most divergence and smallest distribution, with medium-sized egg species in between. At the smallest phylogeographic scale, C. sp. C from the sand dune islands of Moreton Bay in southeastern Queensland was further analysed. Two different lineages (C1, C2) were found which diverged from each other during the late Miocene/Pliocene and so are older than the current landscape in which they are found. Small-scale phylogeographic analyses within C1, C2 and a sympatric fish identified divergences dating to the Pleistocene (about 100-300 thousand years ago). This implies that ice age sea-level changes may have structured these populations, although there is little observable influence of the last glacial maximum (about 18 thousand years ago). This study has highlighted a number of taxonomic anomalies within the Atyidae. The detection of many cryptic species implies that biodiversity within freshwater invertebrates is higher than currently appreciated. The evolutionary and biogeographic relationships of Australian atyids have proved complex, with many taxa having their own individual histories. At the large Indo-Pacific scale, dispersal is most evident, but within Australia, both vicariance and dispersal have been responsible for structuring all taxa at every scale.

octor of Philosophy(PhD) / Molecular Evolution is the key to explain the divergence of species and the origin of life on earth. The main task in the study of molecular evolution is the reconstruction of evolutionary trees from sequences data of the current species. This thesis introduces a novel algorithm for inferring evolutionary trees from genetic data using quartet-based approach. The new method recursively merges sub-trees based on a global statistical provided by the global quartet weight matrix. The quarte weights can be computed using several methods. Since the quartet weights computation is the most expensive procedure in this approach, the new method enables the parallel inference of large evolutionary trees. Several techniques developed to deal with quartets inaccuracies. In addition, the new method we developed is flexible in such a way that can combine morphological and molecular phylogenetic analyses to yield more accurate trees. Also, we introduce the concept of critical point where more than one possible merges are possible for the same sub-tree. The critical point concept can provide information about the relationships between species in more details and show how close they are. This enables us to detect other reasonable trees. We evaluated the algorithm on both synthetic and real data sets. Experimental results showed that the new method achieved significantly better accuracy in comparison with existing methods.

<p>alpha-actinin is a ubiquitous protein found in most eukaryotic organisms. The ability to form dimers allows alpha-actinin to cross-link actin in different structures. In muscle cells alpha-actinin is found at the Z-disk of sarcomeres. In non-muscle cells alpha-actinin is found in zonula adherens or focal adhesion sites where it can bind actin to the plasma membrane.</p><p>alpha-actinin is the shortest member of the spectrin superfamily of proteins which also includes spectrin, dystrophin and utrophin. Several hypotheses suggest that alpha-actinin is the ancestor of this superfamily.</p><p>The structure of alpha-actinin in higher organisms has been well characterized consisting of three main domains: an N-terminal actin-binding domain with two calponin homology domains, a central rod domain with four spectrin repeats and a C-terminal calcium-binding domain. Data mining of genomes from diverse organisms has made possible the discovery of new and atypical alpha-actinin isoforms that have not been characterized yet.</p><p>Invertebrates contain a single alpha-actinin isoform, whereas most of the vertebrates contain four. These four isoforms can be broadly classified in two groups, muscle isoforms and non-muscle isoforms. Muscle isoforms bind actin in a calcium independent manner whereas non-muscle isoforms bind actin in a calcium-dependent manner.</p><p>Some of the protozoa and fungi isoforms are atypical in that they contain fewer spectrin repeats in the rod domain. We have purified and characterized two ancestral alpha-actinins from the parasite Entamoeba histolytica. Our results show that despite the shorter rod domain they conserve the most important functions of modern alpha-actinin such as actin-bundling formation and calcium-binding regulation. Therefore it is suggested that they are genuine alpha-actinins.</p><p>The phylogenetic tree of alpha-actinin shows that the four different alpha-actinin isoforms appeared after the vertebrate-invertebrate split as a result of two rounds of genome duplication. The atypical alpha-actinin isoforms are placed as the most divergent isoforms suggesting that they are ancestral isoforms. We also propose that the most ancestral alpha-actinin contained a single repeat in its rod domain. After a first intragene duplication alpha-actinin with two spectrin repeats were created and a second intragene duplication gave rise to modern alpha-actinins with four spectrin repeats.</p>

<p>This dissertation is primarily focused on the <i>Buellia</i> species with pluriseptate spores, often referred to the section or genus <i>Diplotomma</i>, and secondarily on the Physciaceae. An ultrastructural study at family level gives new information on spore characters. Variations in the composition and structure of the spore wall layers and septa are described.</p><p>A phylogenetic analysis of the Physciaceae, based on morphological and chemical characters, is presented. In the resulting trees the species with pluriseptate spores appear in a poorly resolved clade together with other crustose species with 1-septate spores. A subsequent analysis, excluding foliose and fruticose species, shows that the species with pluriseptate spores do not form a monophyletic group, and that only a few are grouped together with the type species of <i>Diplotomma</i>. Due to low resolution, poor branch support, and uncertainty concerning the typification of <i>Buellia</i> all species treated are retained in <i>Buellia</i>.</p><p>Altogether 35 species with pluriseptate spores are treated, including ten new to science, viz. <i>B. aeruginosa</i>, <i>B. morsina</i>, <i>B. muriformis</i>, <i>B. oidaliella</i>, <i>B. pallido-marginata</i>, <i>B. romoletia</i>, <i>B. rubroreagens</i>, <i>B. terricola</i>, <i>B. tombadorensis</i>, and <i>B. tri-septata</i>. Historical outlines are presented, and information on life strategy, morphology, chemistry, ecology, and distribution is given. All species are similar and macroscopically not easily distinguished, having crustose thalli and blackish apothecia, but there is a great variation in microscopic characters, secondary chemistry, substrate preferences, habitat ecology, and distribution range. Several names are typified and many synonyms are listed. References are given to all species referred to <i>Diplotomma</i> in literature.</p>

I investigated the paired sternum V glands in thirty-eight trichopteran families and all lepidopteran families possessing the gland or associated structures. Using my morphological data and literature data on sternum V gland secretions, I examined phylogenetic trends in morphology and gland products and reconstructed ancestral states. I investigated correlations between gland products, between morphological traits and between chemistry and morphology. The gland is present in twenty-five trichopteran families. It is generally present in Annulipalpia, except Dipseudopsidae, and in Spicipalpia. It is widespread in Plenitentoria, but is often absent in Brevitentoria, especially in males. In Lepidoptera, I present the first report on the reduced, but functional glands in Neopseustidae and Nepticulidae. The gland is typically an invagination from sternum V with a duct leading to a reservoir surrounded by secretory tissue. An opening muscle inserts just inside the opening. I found two non-homologous opening-muscle types, one in Lepidoptera and some Trichoptera, another in the remaining Trichoptera. Muscle fibres often surround the reservoir, sometimes also the secretory tissue. Exceptions are found in Psychomyiidae (no opening muscle), female Philopotamidae (fenestra with separate glandular complex), Agathiphagidae (several unique features), Neopseustidae and Nepticulidae (gland present without gland opening). Using variations in gland structure, I identified phylogenetically useful characters from the superorder to the species level. The fenestrae in female Philopotamidae, Eriocraniidae, Neopseustidae and Nepticulidae are perforated, and perforated patches are present in female Psychomyiidae. The perforated patches are associated with a reservoir, secretory tissue and a distinctive sunburst musculature in both Trichoptera and Lepidoptera. The probable ancestral gland compounds are heptan-2-ol, 4-hepten-2-one, 4-hepten-2-ol, nonan-2-one, 6- nonen-2-one and 6-nonen-2-ol, making pheromone production a plausible ancestral function. The most widespread gland compounds are heptan-2-one, heptan-2-ol, nonan-2-one and nonan-2-ol, but these are absent from Apataniidae + Limnephilidae, which instead produce methylated 3-ketones and -ols, unique within Trichoptera. These compounds all probably function as pheromones. Both large and small glands in females can function in sex pheromone production, while large glands in male Hydropsyche (Hydropsychidae) are likely linked to male aggregation pheromone production. Relative sizes of regular gland reservoirs and fenestral gland reservoirs in female philopotamids suggest a complementary function. / Systematics and Evolution

Background: Mitochondrial genomes are a valuable source of data for analysing phylogenetic relationships. Besides sequence information, mitochondrial gene order may add phylogenetically useful information, too. Sipuncula are unsegmented marine worms, traditionally placed in their own phylum. Recent molecular and morphological findings suggest a close affinity to the segmented Annelida. Results: The first complete mitochondrial genome of a member of Sipuncula, Sipunculus nudus, is presented. All 37 genes characteristic for metazoan mtDNA were detected and are encoded on the same strand. The mitochondrial gene order (protein-coding and ribosomal RNA genes) resembles that of annelids, but shows several derivations so far found only in Sipuncula. Sequence based phylogenetic analysis of mitochondrial protein-coding genes results in significant bootstrap support for Annelida sensu lato, combining Annelida together with Sipuncula, Echiura, Pogonophora and Myzostomida. Conclusion: The mitochondrial sequence data support a close relationship of Annelida and Sipuncula. Also the most parsimonious explanation of changes in gene order favours a derivation from the annelid gene order. These results complement findings from recent phylogenetic analyses of nuclear encoded genes as well as a report of a segmental neural patterning in Sipuncula.

<p>Lignocellulosic biomass represents an important renewable resource for biofuels production. Lignocellulosic biomass is comprised of cellulose, hemicellulose and lignin. Lignocellulosics are highly recalcitrant to enzymatic degradation and due to its complex nature a range of enzymes are required to synergistically hydrolyse biomass. Many microorganisms are capable of producing these enzymes as part of their hemicellulolytic hydrolysis system(s). The aim of this study was the characterisation of a thermophilic actinobacterial isolate (ORS10), capable of producing hemicellulosic enzymes, and the cloning and characterization of a hemicellulosic enzyme produced by the isolate. Phylogenetic analyses clustered ORS10 with species of the genus Streptomyces. BLAST analysis revealed that ORS10 was most closely related to Streptomyces achromogenes (99% identity). A small-insert genomic library was constructed and a putative acetylxylan esterase (AXEase) gene, axe10, was identified. The enzyme, Axe10, has moderate similarity to &alpha / /&beta / hydrolase proteins, and contains an esterase/lipase superfamily conserved domain and a typical AXEase catalytic triad. The axe10 gene was sub-cloned into an expression vector [pET21a(+)] and a 28.7 kDa protein with demonstrated AXE activity was purified from E. coli Rosetta (DE3) pLysS. Axe10 displayed optimum activity at 37oC and pH 7.0. Despite being derived from a thermophilic Streptomyces species Axe10 was not thermostable. However, given the relative novelty of Axe10, further characterisation and assessment of this enzyme is warranted.</p>