<p>U&nbsp; radu&nbsp; je&nbsp; izvr&scaron;en&nbsp; integrativno-taksonomski&nbsp; pristup analize&nbsp; kompleksa&nbsp; vrsta&nbsp; <em>Merodon</em>&nbsp; <em>avidus&nbsp; </em>(Diptera: Syrphidae),&nbsp; na&nbsp; geografski&nbsp; i&nbsp; vemenski&nbsp; obimnom materijalu.&nbsp; U&nbsp; okviru&nbsp; genetičke&nbsp; karakterizacije&nbsp; kriptičnih vrsta&nbsp; navedenog&nbsp; kompleksa,&nbsp; bazirane&nbsp; na&nbsp; 3&#39;&nbsp; i&nbsp; 5&#39;<br />fragmentima&nbsp; mitohondrijalnog&nbsp; COI&nbsp; gena,&nbsp; određeni&nbsp; su parametri&nbsp; genetičke&nbsp; varijabilnosti&nbsp; i&nbsp; utvrđeni&nbsp; jedinstveni&nbsp; i deljeni&nbsp; haplotipovi&nbsp; u&nbsp; okviru&nbsp; i&nbsp; između&nbsp; pretpostavljenih vrsta.&nbsp; Rezultati&nbsp; genetičke&nbsp; varijabilnosti&nbsp; COI&nbsp; DNK&nbsp; sekvenci pokazali&nbsp; su&nbsp; da&nbsp; jedinke&nbsp; sa&nbsp; ostrva&nbsp; Krf&nbsp; i&nbsp; Evia&nbsp; i&nbsp; poluostrva Peloponez,&nbsp; preliminarno&nbsp; identifikovane&nbsp; kao M. moenium, predstavljaju&nbsp; novu,&nbsp; endemsku&nbsp; vrstu&nbsp; proučavanog<br />kompleksa.&nbsp; Dijagnostički&nbsp; enzimski&nbsp; lokusi&nbsp; pokazali&nbsp; su&nbsp; da M.&nbsp; avidus&nbsp; i&nbsp; M.&nbsp; moenium&nbsp; predstavljaju&nbsp; sestrinske&nbsp; vrste, koje&nbsp; su&nbsp; se,&nbsp; u&nbsp; okviru&nbsp; kompleksa&nbsp; vrsta&nbsp;<em> M.&nbsp; avidus,&nbsp; </em>poslednje razdvojile.&nbsp; Zaključeno&nbsp; je&nbsp; da&nbsp; se&nbsp; kompleks&nbsp; vrsta&nbsp; M.&nbsp; avidus sastoji od 5 vrsta: <em>M. avidus, M. moenium, M. megavidus, M.&nbsp; ibericus&nbsp; i&nbsp; M.&nbsp; aff.&nbsp; moenium</em>.&nbsp; U&nbsp; nastavku,&nbsp; oslanjajući&nbsp; se na&nbsp; moderne&nbsp; tehnike&nbsp; ve&scaron;tačke&nbsp; inteligencije,&nbsp; izvr&scaron;eno&nbsp; je modelovanje&nbsp; distribucije&nbsp; vrsta&nbsp; i&nbsp; poređenje&nbsp; sličnosti utvrđenih&nbsp; ekolo&scaron;kih&nbsp; ni&scaron;a.&nbsp; U&nbsp; poslednjem&nbsp; segmentu istraživanja,&nbsp; prednosti&nbsp; ve&scaron;tačke&nbsp; inteligencije&nbsp; iskori&scaron;ćene su&nbsp; u&nbsp; modelovanju&nbsp; sistema&nbsp; za&nbsp; determinaciju&nbsp; jedinki sestrinskih vrsta u uzorku, na osnovu adekvatne varijable.Ovo&nbsp; istraživanje&nbsp; doprinelo&nbsp; je&nbsp; karakterizaciji&nbsp; biodiverziteta osolikih&nbsp; muva,&nbsp; rasvetljavanju&nbsp; taksonomskog&nbsp; statusa&nbsp; vrsta i&nbsp; kreiranju&nbsp; smernica&nbsp; za&nbsp; definisanje&nbsp; budućih konzervacionih&nbsp; programa&nbsp; za&scaron;tite&nbsp; biodiverziteta&nbsp; vrsta <em>Merodon avidus </em>kompleksa.</p> / <p>During this research, an integrative-taxonomic&nbsp; analysis of M. avidus species complex was performed. The study was based on geographically and temporally extensive material. Genetic characterisation of cryptic species, based on 5&rsquo; and 3&rsquo; regions of COI gene, defined parameters of genetic variability. Shared and unique haplotypes between and within of cryptic species were detected. The results of genetic variability analysis based on COI gene showed that specimens from the islands Corfu, Evia and half-island Peloponnese, which were preliminarily identified as M. moenium, represent a new, endemic species of the selected complex. Diagnostic enzyme loci showed that M. avidus and M. moenium represent sibling species, which were the last one who separated within M. avidus complex. According to current information, it was concluded that M. avidus complex consists of 5 species: M. avidus, M. moenium, M. megavidus, M. ibericus and M. aff. moenium. In the next&nbsp; chapter, relying on modern techniques of artificial&nbsp; intelligence, the species distribution modelling and the comparison of ecological niches were performed. In the last part of the research, the advantages of artificial intelligence were used in order to model a system that was able to determinate one of two sibling species, based on appropriate predictor. This research has generally contributed to a characterization of hoverfly diversity and helped resolving a taxonomic status of species in one of the most challenging groups in Syrphidae family. Genetic differentiation data represent directions for defining future conservation strategies for biodiversity protection of defined cryptic species of Merodon avidus complex</p>

Nemertodermatida is a group of microscopic marine worm-like animals that live as part of the marine meiofauna in sandy or muddy sediments; one species lives commensally in a holothurian. These benthic worms were thought to disperse passively with ocean currents, resulting in little speciation and thus wide or even cosmopolitan distributions. Individuals occur in low abundance and have few light microscopically available characters, which altogether may explain why only eight species had been described between the discovery of the taxon in 1930 and this thesis. We used molecular methods to address the diversity and phylogeny of this group for the first time. In a study of two nominal species with samples from all around the world, a high degree of cryptic speciation was discovered and several new species described. Diagnoses were based on molecular data complemented by morphological characters, where available. Given the patchy geographical record it can be assumed that the majority of the biodiversity of Nemertodermatida is yet to be described. A phylogenetic study including all but three known species revealed a deep divergence between the two families of Nemertodermatida but non-monophyly of the taxon was rejected by an Approximately Unbiased test. Confocal laser scanning microscopic studies of several species show that the pattern of the body-wall musculature and the nervous system are specific for different genera. The muscular system of all species consists of a basic orthogonal grid with specific diagonal musculature and specialized muscles associated with body openings. The mouth appears to be transient feature in Nemertodermatida, developing only after hatching and being reduced again in mature worms. The nervous system is highly variable with very different ground patterns between the genera, such as an epidermal net, a centralized neuropile or a commissural brain. / <p>At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 3: Manuscript. Paper 4. Manuscript.</p>

Τα ισόποδα αποτελούν τα πιο ποικίλα σε δομή και τα πλουσιότερα σε είδη Καρκινοειδή της υπέρταξης των Περακαρίδων. Πρόκειται για κοινούς κατοίκους όλων σχεδόν των οικοσυστημάτων. Η οικογένεια Sphaeromatidae (Latreille, 1825) ανήκει στην υπόταξη Flabellifera (μια από τις 10 υποτάξεις των ισοπόδων). Δύο εκπρόσωποι της οικογένειας αυτής είναι τα είδη Sphaeroma serratum (Fabricius, 1787) και Lekanesphaera hookeri (Leach, 1814), που είναι κοσμοπολιτικά, εντοπίζονται σε πολλές περιοχές της Ελλάδας και αποτέλεσαν τα πειραματόζωα στην παρούσα μελέτη. Οι φυλογενετικές μελέτες στον ελλαδικό χώρο περιορίζονται κυρίως στη μελέτη ειδών χερσαίων ισοπόδων, κυρίως λόγω των πολλών ενδημικών ειδών. Ωστόσο εντοπίζονται και άλλα είδη, τα οποία διαβιούν τόσο στη θάλασσα όσο και σε περιοχές με γλυκά και υφάλμυρα νερά, τα οποία δεν έχουν μελετηθεί ακόμη, αν και θα μπορούσαν να δώσουν απαντήσεις σε ερωτήματα σχετικά με τους μηχανισμούς απομόνωσης των πληθυσμών αλλά και την οικολογία, καθώς και την παλαιογεωγραφία της περιοχής. Η παρούσα εργασία αποτελεί την πρώτη απόπειρα μελέτης των φυλογενετικών σχέσεων των δύο αυτών ειδών τόσο στον ελλαδικό όσο και στον ευρωπαϊκό χώρο γενικότερα. Ο σκοπός της παρούσας εργασίας ήταν ο προσδιορισμός της γενετικής δομής και των φυλογενετικών σχέσεων ειδών της οικογένειας Sphaeromatidae. Για τη μελέτη χρησιμοποιήθηκαν μοριακοί δείκτες από 18 πληθυσμούς του είδους Sphaeroma serratum και 2 πληθυσμούς του είδους Lekanesphaera hookeri (ως εξωομάδα). Η πειραματική προσέγγιση περιελάμβανε τον πολλαπλασιασμό αλληλουχιών των μιτοχονδριακών γονιδιακών τόπων 16S rDNA και COI (δείκτες που χρησιμοποιούνται ευρέως για μελέτες σε επίπεδο πληθυσμών και ειδών) με τη μέθοδο της PCR, τον προσδιορισμό των αλληλουχιών αυτών και, ακολούθως, τη στατιστική και φυλογενετική τους ανάλυση με τις μεθόδους της Σύνδεσης Γειτόνων (Neighbor Joining), της Μέγιστης Φειδωλότητας (Maximum Parsimony) και της Μπεϊεσιανής Συμπερασματολογίας (Bayesian Inference). Το τελικό μήκος των αλληλουχιών μετά την επεξεργασία ήταν 396 θέσεις για το γενετικό τόπο 16S και 500 θέσεις για το γενετικό τόπο COI. Τα δεδομένα από τους δύο γενετικούς τόπους ήταν δυνατό να συνδυαστούν, επομένως πραγματοποιήθηκε τόσο ανεξάρτητη όσο και συνδυασμένη ανάλυση. Τα αποτελέσματα που προέκυψαν από τη χρήση των μιτοχονδριακών μοριακών δεικτών και την εφαρμογή των φυλογενετικών μεθόδων που προαναφέρθηκαν, τόσο όσον αφορά τις νουκλεοτιδικές αποκλίσεις όσο και τα φυλογενετικά δέντρα που προέκυψαν, επιβεβαιώνουν τη μεγάλη γενετική διαφοροποίηση μεταξύ των δύο ειδών και αναγνωρίζουν επίσης μεγάλη γενετική διαφοροποίηση μεταξύ των πληθυσμών του είδους Sphaeroma serratum. Η διαφοροποίηση αυτή δεν ακολουθεί κάποιο σαφές γεωγραφικό πρότυπο, ωστόσο φαίνεται να συνδέεται με τα διαφορετικά επίπεδα αλατότητας που παρατηρούνται στις διάφορες περιοχές συλλογής. Οδηγούμαστε συνεπώς στην υπόθεση ότι είναι πιθανή η ύπαρξη κρυπτικών ειδών μέσα στους πληθυσμούς του είδους. / Isopods, the most diverse in form and the most species-rich crustaceans of the superorder Peracarida, have successfully settled all possible habitats. The family Sphaeromatidae (Latreille, 1825) is classified in the suborder Flabellifera (one of the 10 suborders of isopods). Two representatives of this family are the species Sphaeroma serratum (Fabricius, 1787) and Lekanesphaera hookeri (Leach, 1814). They are both cosmopolitan species and have colonized widely the Greek marine shorelines and lagoons. The phylogenetic relations studies in Greece regard only terrestrial isopods, due to the large variety of endemic species. However, there are also non terrestrial species that haven’t been studied yet. This type of studies could give answers to questions about the isolation mechanisms of the populations, about ecological factors and the palaeogeography of Greece. The present study is the first attempt to resolve the phylogenetic relations of the two species mentioned above, in Greece and generally in Europe. In order to resolve those relations, we used two mitochondrial markers (16S rDNA and COI) from 18 populations of Sphaeroma serratum and 2 populations of Lekanesphaera hookeri (outgroup). Our experimental approach included PCR amplification, sequencing and computational statistic and phylogenetic analyses using Neighbor Joining, Maximum Parsimony and Bayesian Inference methods. Regardless of the method used, the results verify the great genetic divergence between the two species and also indicate great divergence among the populations of Sphaeroma serratum. Divergence patterns do not show any clear geographic structure, although they seam to be related somehow with the different salinity levels observed in the sampling regions, implicating the existence of cryptic species.

Submitted by FERNANDA CRERES ROSA null (fer_creres@hotmail.com) on 2016-04-04T19:15:40Z No. of bitstreams: 1 Fernanda Rosa - Dissertação Mestrado.pdf: 2522596 bytes, checksum: e6a718a620bc5e59e8744c6971a6c1c1 (MD5) / Approved for entry into archive by Ana Paula Grisoto (grisotoana@reitoria.unesp.br) on 2016-04-06T14:43:55Z (GMT) No. of bitstreams: 1 rosa_fc_me_assis.pdf: 2522596 bytes, checksum: e6a718a620bc5e59e8744c6971a6c1c1 (MD5) / Made available in DSpace on 2016-04-06T14:43:55Z (GMT). No. of bitstreams: 1 rosa_fc_me_assis.pdf: 2522596 bytes, checksum: e6a718a620bc5e59e8744c6971a6c1c1 (MD5) Previous issue date: 2016-02-26 / Chrysaora é um dos gêneros mais ricos de espécies dentro da subclasse Discomedusae Haeckel, 1880. Na América do Sul existem duas espécies do gênero Chrysaora, Chrysaora lactea (Eschscholtz, 1829) e Chrysaora plocamia (Lesson 1830). A cifomedusa C. lactea é uma das mais comuns e amplamente distribuídas medusas de Scyphozoa na costa. A distribuição dessa espécie é contínua desde o Golfo do México até a costa norte da Argentina (Morandini e Marques 2010). Já a espécie C. plocamia apresenta um incomum padrão de distribuição, ocorrendo em ambos os lados do sul da América do Sul; região oriental do Pacífico Sul (Peru, Chile) e oeste do Atlântico Sul (Argentina), sofrendo forte influência das correntes oceânicas. Assim, o objetivo principal do projeto foi realizar um levantamento da distribuição do gênero Chrysaora na América do Sul. Adicionalmente buscou-se confirmar a ocorrência da espécie C. plocamia no litoral do Uruguai, analisar a estrutura morfológica e molecular das populaçõesde C. lactea distribuídas ao longo do Atlântico Sul Ocidental e comparar os indivíduos entre as diferentes regiões. Foram realizadas análises morfológicas e morfométricas, o estudo da composição dos nematocistos através das medidas e análises estatísticas, além de análises moleculares, através da avaliação do marcador molecular mitocondrial (16S) dos indivíduos da espécie C. lactea e C. plocamia, de diferentes localidades. Os resultados apontam que a distribuição da espécie C. lactea é continua desde o Uruguai até o norte do Brasil e que possivelmente não há incidência de espécies crípticas nessa região analisada. Já a espécie C. plocamia está associada às águas frias neríticas do Atlântico e Pacífico, notando-se a presença dessa espécie também na região do Uruguai. / Chrysaora is one of the richest genera within the subclass Discomedusae Haeckel, 1880. In South America, there are two species of the genus Chrysaora, Chrysaora lactea (Eschscholtz, 1829) and Chrysaora plocamia (Lesson 1830). The scyphomedusa C. lactea is one of the most common and widely distributed Scyphozoa jellyfish on the coast. The distribution of this species is continuous from the Gulf of Mexico to the north coast of Argentina (Morandini e Marques 2010). C. plocamia has an unusual distribution pattern, occurring on both sides of southern South America, eastern South Pacific (Peru, Chile) and western South Atlantic (Argentina). The objective of this study was to promote a survey of the distribution of the genus Chrysaora in South America. Additionally, we confirmed the occurrence of C. plocamia in Uruguay coast, analyzed the morphological and molecular structureof C. lactea distributed over Western South Atlantic comparing individuals between different regions, especially looking for the incidence of cryptic species. Morphological and morphometric analyzes were performed, as well as the study of the composition of nematocysts by measurements and statistical analysis, in addition to molecular analysis by evaluating the mitochondrial molecular markers 16S of individuals of C. lactea and C. plocamia from different locations. The results showed that the distribution of the species C. lactea is continuous from the Uruguay to the Northern Brasil and there was no incidence of cryptic species. Also, C. plocamia is associated with cold inshore waters of the Atlantic and Pacific, noting the presence of this species also in Uruguay.

Estudo da termitofauna (Insecta, Isoptera) da região do alto Rio Madeira, Rondônia. Na região conhecida como alto Rio Madeira, no município de Porto Velho, Rondônia, estão sendo criadas as Usinas Hidrelétricas (UHEs) de Santo Antônio e Jirau. As construções das represas das UHEs estão inundando grandes porções de floresta ao longo das duas margens do rio Madeira. Desta forma o conhecimento da biota local, especialmente de sua distribuição no espaço, é extremamente importante, ainda mais porque o alinhamento dos rios Amazonas-Madeira-Mamoré separa a região Neotropical em duas áreas de endemismo para diversos grupos de animais. Essa tese tem por objetivo apresentar os resultados gerais obtidos ao longo de três anos de monitoramento de cupins nas áreas de influência da UHE de Jirau e dois anos nas áreas de influência da UHE de Santo Antônio, assim como desenvolver um estudo de comunidades e análise da distribuição espacial dos cupins presentes nas áreas de influência da UHE de Jirau (Capítulo 1). Outro objetivo é o estudo da estrutura genética das populações de Heterotermes tenuis (Rhinotermitidae) ao longo das áreas de influência das duas UHEs, visando investigar a existência de fluxo gênico entre as populações de cada margem do Rio Madeira (Capítulo 2). Foram amostrados doze módulos, sete na margem esquerda do rio e cinco na margem direita. Cada um era compostos por transectos de 3 ou 4 km e parcelas perpendiculares a cada 1km, e as amostragens foram realizadas em subparcelas de 5x2m dentro das parcelas. Durante um total de 20 campanhas foram investigadas 1121 subparcelas, totalizando 7875 amostras de cupins e pelo menos 169 espécies. Esse é provavelmente o trabalho com maior esforço amostral já empregado e também o que registrou o maior número de espécies de cupins até hoje. Para o estudo de comunidades, foram aleatorizadas 20 subparcelas nos seis módulos da UHE de Jirau, sendo cinco subparcelas dentro das parcelas marcadas nas seguintes distâncias em relação à margem do rio: P1 - 50 m, P2 - 1 km, P3 - 2 km e P4 - 3 km. A composição de cupins não está relacionada com o lado do rio. O estimador que mais se aproximou do provável número real de espécies foi o Jackknife 2. Como resultado das análises de diversidade beta utilizando a composição de espécies de cupins houve um agrupamento dos módulos com o mesmo tipo de solo, sugerindo que algumas espécies de cupins estejam distribuídas de acordo com esta variável. Em relação à distância para o rio, a parcela mais próxima do rio foi a mais singular, tanto em relação à composição de espécies quanto à riqueza e abundância, sendo que existem espécies restritas à P1 e outras praticamente ausentes nessas parcelas. Das dez variáveis ambientais analisadas, a riqueza de cupins se mostrou correlacionada com a altitude, concentração de argila e silte no solo e estratificação vegetal entre 1 e 5 m. Para o estudo da estrutura genética das populações de H. tenuis foram utilizadas 84 sequências dessa espécie dos 12 módulos de monitoramento, seis de colônias do Cerrado e três do GenBank (de Manaus, Guiana Francesa, e Equador), além de uma de H. longiceps como grupo externo. Nas análises iniciais, foi encontrada uma forte estruturação genética entre as sequências: todas as análises filogenéticas (máxima parcimônia, máxima verossimilhança e inferência bayesiana), assim como a rede de haplótipos, formaram dois grupos consistentes, mas sem qualquer relação espacial. A partir disso, passou-se a trabalhar com a hipótese de que há duas espécies crípticas (chamadas Ht. A e Ht. B). Desta forma, todas as análises para testar se o Rio Madeira funcionava como barreira biogeográfica foram testadas separadamente para cada uma das supostas duas espécies crípticas, entretanto, não foi constatada qualquer influência do rio como barreira ao fluxo gênico entre as populações de cada margem. / The Santo Antônio and Jirau hydroelectrics plants (HP) are being built in the Madeira River region, in Porto Velho, RO, Brazil. The HPs will flood large portions of native forest, and thus knowledge of the local biota and its distribution in space is extremely important for the formulation of management plans for creation of protected areas. This region in particular is unique, since the alignment of Amazonas-Madeira-Mamoré Rivers divides the Neotropical region into two areas of endemism for a diversity of taxa. The main objective of this thesis was to monitor termites for three years in areas near the Jirau HP and two years in areas near the Santo Antônio HP. As well as conduct a community level study and analyze the spatial distributions of termites from the areas influenced by Jirau HP (Chapter 1); and investigate the population genetic structure of Heterotermes tenuis (Rhinotermitidae), for the two areas influenced by the HPs, to test whether there is genetic flow between the populations on either bank of the Madeira River (Chapter 2). Twelve modules were marked, seven on the left bank of the river and five on the right bank. Each module was composed of 3 or 4 km transects and perpendicular parcels every 1 km. The sampling was conducted in sub parcels of 5 x 2 m inside each main parcels. During 20 expeditions, 1121 subparcels were investigated and a total of 7875 samples were collected and identified to 169 species. This study incorporates greater sampling effort than already employed by other published studies to date and also registered the highest number of termites species of any similar study. For the community study, 20 subparcels were randomized in the six modules of the Jirau HP, with five subparcels marked in relation to distance from the river margin (P1 - 50 m, P2 - 1 km, P3 - 2 km, and P4 - 3 km). The termite species composition was not related to side of the river bank. The richness estimator Jackknife 2 was the best estimator of the real number of species diversity. The beta diversity analysis with termite species composition clustered for modules with the same soil type, suggesting that some termite species may be distributed according to the soil type. Parcels closest to the river were the most unique, both in terms of termite species composition and abundance patterns, with some species restricted to the P1 and others absent. Of the ten environmental variables measured, termite species richness was correlated with altitude, clay and silt concentration in the soil, and vegetation stratification between 1 and 5 m, among. For the study of the genetic structure of Heterotermes tenuis, 84 sequences of this species were used from the 12 monitoring modules, six from colonies from the Cerrado (Brazilian Savanna), three from GeneBank (from Manaus, French Guiana and Ecuador), and one of H. longiceps as outgroup. In the initial analysis, relatively strong genetic structure within the samples was found: all phylogenetic analysis (maximum parsimony and likelihood, and Bayesian inference), and haplotype networks, consistently clustered two groups of haplotypes, but without any spatial relationships. Thus was assumed that there were two cryptic species (here called Ht. A and Ht. B), and all the analysis to test whether the Madeira River was a biogeographic barrier were conducted separately for each putative species. However, it was not possible to detect any influence of the river to genetic flow between the populations from either side of the river.

L’oïdium est une des maladies les plus communes sur chêne en Europe. Cette maladie a été signalée à partir du début du 20ème siècle. Toutefois, peu de données sont disponibles sur l’identité de l’agent causal et de son interaction avec l’hôte. L’objectif de cette étude est d’améliorer les connaissances sur ce pathosystème : (1) caractériser son agent causal avec un marqueur moléculaire (ADN ribosomal) et étudier la distribution spatiale des différentes lignées ; (2) étudier l’adaptation locale du parasite à son hôte ; (3) explorer le déterminisme génétique de la résistance de l’hôte. L’étude de l’ADN ribosomal (ITS=Internal transcribed region et IGS= Intergenic spacer) a mis en évidence l’existence de quatre haplotypes, dont trois seulement avaient été associés à des agents d’oïdium sur chêne en Europe. Erysiphe alphitoïdes, classiquement considéré comme responsable de l’épidémie du XXème siècle est bien l’espèce prépondérante (environ 80% des détections), E. hypophylla et Phyllactinia sp étant détectés à fréquence beaucoup plus faible. Un résultat inattendu est la détection d’une quatrième séquence, présentant 100% d’homologie avec celle de plusieurs agents d’oïdium d’arbres tropicaux et avec Erysiphe quercicola, très récemment décrit sur chêne en Asie et Australie mais jusqu’alors inconnu en Europe. L’ITS de E. quercicola est détecté dans toutes les régions de France, à une fréquence non négligeable (de l’ordre de 15% en moyenne). On le trouve dans les mêmes parcelles et parfois sur les mêmes arbres, voire dans les mêmes lésions que E. alphitoides. La mise au point d’une méthode d’inoculation artificielle a permis d’étudier de façon quantitative l’interaction chêne-oïdium. Une expérimentation d’inoculations réciproques montre que les souches d’oïdium sont plus performantes sur les descendants des arbres dont elles ont été isolées que sur ceux d’autres arbres, suggèrant une adaptation trans- générationnelle. Des inoculations artificielles, complétées par des observations en conditions naturelles, ont également permis de démontrer un déterminisme génétique de la résistance des chênes, avec l’identification de plusieurs QTL. Certains de ces QTL co-localisent avec des QTL de phénologie, en accord avec l’importance de la résistance ontogénique des chênes à l’oïdium. L’ensemble de l’étude amène à reconsidérer l’oïdium du chêne comme un probable complexe d’espèces cryptiques, dont l’histoire de l’invasion et la co-existence en Europe restent à préciser. Les résultats acquis sur l’héritabilité de la résistance et l’adaptation locale du parasite constituent une première étape dans la compréhension des interactions démo-génétiques entre hôte et parasite dans ce pathosystème. / Powdery mildew is the most common disease on oaks in Europe where it was first recorded at the beginning of the 20th century. Yet, little is known about the identity of the causal agent and his interaction with its host. The objective of this study was: (1) to characterize the species responsible of oak powdery mildew with a molecular marker (ribosomal DNA); to study the spatial distribution of these different lineages and (2) to study local adaptation of the parasite to its host (3) to explore the genetic determinism of host resistance. The study of the ITS (internal transcribed region) and IGS (intergenic spacer) diversity revealed the existence of four haplotypes, only three had been already associated with oak powdery mildew in Europe. Erysiphe alphitoïdes, for a long time considered as sole responsible for the epidemic of the XXth century, was the predominant species (~ 80% of detections), E. hypophylla and Phyllactinia sp. were detected at lower frequencies. An unexpected result is the detection of a fourth sequence which show 100% homology with ITS sequences of several powdery mildew agents of tropical trees and Erysiphe quercicola, recently described on oak in Asia and Australia but previously unknown in Europe. E. quercicola ITS was detected in all French regions, at a significant frequency (~ 15%). The study showed that E. alphitoides was often found in association with different ITS types in the same region, the same tree, and even in the same lesion. The development of an artificial inoculation method allowed the quantitative evaluation of the oak-powdery mildew interaction. A reciprocal inoculation experiment showed that powdery mildew strains were more efficient on their mother tress and their descendants than on the other trees, suggesting a trans-generational adaptation. Artificial inoculations, supplemented by observations in natural conditions, have also demonstrated a genetic determination of resistance of oak trees, with the identification of several QTL. Some of these QTL co-localize with QTL controlling phenology, in agreement with the importance of oaks ontogenic resistance to powdery mildew. The entire study leads to reconsider oak powdery mildew as a probable complex of cryptic species; the invasion history and the co-existence in Europe are still to be determined. The results achieved on the heritability of resistance and localization of the parasite are a first step in understanding the demo-genetic interactions between host and parasite in this pathosystem.

This study is part of the Swedish Taxonomy Initiative (STI) - one of the most ambitious all taxa biodiversity inventories in the world. One of the pillars in STI is to support taxonomic research on the most neglected taxonomic groups with the aim to lift the level of knowledge of biodiversity in the country. There is still a lot to be discovered, especially in the microscopic world, and this includes mites. Many aspects of mite biology and diversity are poorly known, such as species richness, abundance, distribution, lifestyle and behavior of species. Mites inhabits all sorts of aquatic, terrestrial, arboreal and parasitic habitats, nevertheless even in well-studied systems mites are often overlooked. Despite being among the smallest of arthropods, they are of medical and economical importance and may be very abundant in the ecosystems they inhabit. This thesis focuses on Parasitengona (Acariformes: Prostigmata), one of the most diverse taxa among the arachnids. It includes the aquatic Hydrachnidia (water mites) and the terrestrial Trombidia (e.g. velvet mites, chiggers). A unifying characteristic of Parasitengona is their complex life cycle of active and inactive stages, parasitic larvae and predatory deutonymphs and adults. They typically parasitize and prey on arthropods, except the chiggers which have vertebrates as hosts. The aim of this thesis is to shed light on the phylogeny and taxonomy of Parasitengona with emphasis on the Swedish fauna. To achieve this, mites were collected from different localities throughout the country between the years 2007-2016. Water mites were sampled with a hand net. Larvae of terrestrial Parasitengona were collected with sweeping nets and sorted out from malaise trap samples from the Swedish Malaise Trap Project. To collect the adults Berlese-Tullgren extractor and pitfall traps were used as well as hand collecting and sifting with litter reducer. The material collected abroad was kindly provided through collaboration.  Methods used in the papers included morphometrics, multivariate analyses, experimental rearing, DNA extraction and sequencing, Bayesian phylogenetic analyses and molecular species delimitation. In paper I and II, we combine molecular species delimitation models and morphological data to resolve taxonomical issues. This integrative taxonomic approach of combining data resulted in Piona dispersa Sokolow, 1926 as a valid species and redescriptions, new synonyms and neotypes provided for Erythraeus phalangoides (De Geer, 1778),  E. cinereus (Dugès, 1834) and E. regalis (C.L. Koch, 1837). Based on the new inventories we produce an updated and annotated checklist of 105 terrestrial Parasitengona species for Fennoscandia in paper III, and use metadata to increase the knowledge on distribution, habitat preferences, life stages and abundance. Out of these, 20 species are new findings for the region and five are potential new species for science. In paper IV, we provide a molecular phylogeny of Parasitengona based on the genes 18S, 28S and COI for 80 taxa with a sampling focus on the terrestrial lineages. Based on the results we offer a revised higher-level classification of the group. In particular the analyses supported Tanaupodoidea Thor, 1935 as a separate superfamily, but Trombiculoidea Ewing, 1929 was not monophyletic and was synonymized, along with Chyzerioidea Womersley, 1954, with Trombidioidea Leach, 1815. / <p>At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 3: Manuscript. Paper 4: Manuscript.</p><p> </p>

The delineation of desmid species was traditionally based on purely morphological features. However, a frequent misinterpretation of morphological variability in desmids has led in the past to extensive taxonomical confusion within this important group of green algae which complicates the interpretation of their biodiversity in freshwater ecology, biogeography and biomonitoring. Consequently, I focused in this thesis predominantly on a previously neglected issue, the application of polyphasic approaches in the species-level taxonomy of desmids. In the most studies, a combination of both traditional morphological and modern molecular phylogenetic and geometric morphometric methods has been used to evaluate the taxonomy of selected desmid species, particularly representatives of the morphologically complex genera Micrasterias and Xanthidium. In two papers, I used the combination of traditional morphological and autecological data to clear up the taxonomy of several morphologically less prominent desmid taxa. Generally, the results of the thesis demonstrated that the way we recently see the diversity and distribution of desmids should be thoroughly changed. The real species diversity is mostly distinctly finer than that estimated by classical morphological taxonomy, often corresponds to varieties of...

A especiação de isolados clínicos de Aspergillus ganhou relevância nos últimos anos devido à descrição de espécies crípticas resistentes aos derivados azólicos. A identificação morfológica convencional não é capaz de discriminar as espécies de Aspergillus e o sequenciamento de DNA é uma técnica pouco adaptada a laboratórios clínicos. A espectrometria de massas por ionização/dessorção a laser auxiliada por matriz tempo-devoo (EM MALDI-TOF) é uma metodologia emergente que vem sendo explorada com intuito de fornecer identificação rápida e acurada de microrganismos, incluindo os fungos filamentosos de importância clínica. Entretanto, há poucos estudos avaliando a plataforma VITEK MS® para a identificação de espécies de Aspergillus. O presente estudo teve como objetivo fornecer dados adicionais sobre a performance dos sistemas do VITEK MS® e suas bibliotecas de espectros de referências (ER) In Vitro Diagnostics (IVD) e Research Use Only (RUO) para identificar as espécies de Aspergillus de relevância clínica. Uma biblioteca de ER in-house também foi construída e avaliada. Um total de 106 organismos foram avaliados por EM, incluindo 47 cepas provenientes das coleções de fungos do Westerdijk Fungal Biodiversity Institute (Holanda) e do LEMIUNIFESP, seis isolados ambientais (IMT-USP) e 53 isolados cínicos do HC-FMUSP. Foram utilizados dois protocolos de extração proteica, um recomendado pelo fabricante e outro empregando meio de cultura líquido para os isolados/cepas com baixa esporulação. Trinta e cinco organismos foram selecionadas para construir os ERs, e os 71 restantes foram usados para avaliação de desempenho das bibliotecas IVD, RUO e RUO+in-house. Entre os 71 organismos analisados, 91,5%, 84,5% e 100% tiveram identificação correta de gênero pelos bibliotecas IVD, RUO e RUO+in-house, respectivamente. Enquanto para identificação de espécie, as bibliotecas IVD, RUO e RUO+in-house mostraram 83,1%, 77,4% e 90,1% de identificações de espécie, respectivamente. Para as 16 espécies crípticas de Aspergillus analisadas, a identificação foi correta em 31,2%, 18,7% e 62,5%, pelos sistemas IVD, RUO e RUO+in-house, respectivamente. Entre as espécies crípticas resistentes aos derivados azólicos, o sistema IVD forneceu identificação correta para as espécies Aspergillus lentulus, Aspergillus calidoustus e Aspergillus sydowii. Entretanto, Aspergillus fumigatiaffinis e Neosartorya pseudofischeri foram erroneamente identificadas como Aspergillus fumigatus pelo sistema IVD. A biblioteca in-house demonstrou melhor performance, mas espécies filogeneticamente próximas como A. fumigatiaffinis e A. lentulus tiveram identificações cruzadas. Concluímos que o VITEK® MS demonstrou boa performance para a identificação das espécies de Aspergillus, porém para algumas espécies crípticas, há necessidade de melhoria das bibliotecas de espectro de referência comercializadas. Algumas espécies crípticas filogeneticamente relacionadas apresentaram espectros similares e são de difícil diferenciação por EM MALDI, mesmo com a construção de uma biblioteca de ER in-house com vários representantes de cada espécie / Aspergillus spp. identification has become more relevant in clinical practice since azoleresistant cryptic species have emerged in the last years. Conventional morphologic identification is not able to discriminate Aspergillus species and DNA sequencing is not feasible for clinical laboratories. Matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) is an emergent technology that has been explored to provide fast and accurate identification of microorganisms, including clinically relevant molds. However, only a few studies have explored the platform VITEK MS® for the identification of Aspergillus species. The present study aimed to provide additional data regarding the performance of the In Vitro Diagnostics (IVD) and Research Use Only (RUO) systems for the identification of Aspergillus species, including azoleresistant ones, and also to construct and to evaluate an in-house reference spectrum library. A total of 106 organisms were evaluated by MS, including 47 Aspergillus strains (Westerdijk Fungal Biodiversity Institute and LEMI-UNIFESP collections), six environmental (IMT-USP) and 53 clinical isolates (HC-FMUSP). Two protein extraction protocols were used, one recommended by the manufacturer and another with liquid broth for the organisms with poor sporulation. Thirty-five organisms were selected to construct the in-house reference spectrum library and the remaining 71 were used for the performance evaluation. Correct genus identification was provided in 91.5%, 84.5% and 100% by the IVD, RUO, and RUO+in-house reference spectrum libraries, respectively. Correct species identification was provided in 83.1%, 77.4% and 90.1% by the IVD, RUO, and RUO+in-house reference spectrum libraries, respectively. Among the 16 Aspergillus cryptic species, correct identification was provided in 31.5%, 18.7% and 62.5% by the IVD, RUO, and RUO+in-house reference spectrum libraries, respectively. Among the azole-resistant cryptic species, the IVD system provided correct identification for Aspergillus lentulus, Aspergillus calidoustus and Aspergillus sydowii. However, Aspergillus fumigatiaffinis and Neosartorya pseudofischeri were misidentified as Aspergillus fumigatus by the IVD system. The in-house library had better performance for the identification of Aspergillus cryptic species, but closely related taxa may be difficult to have correct differentiation by MALDI-TOF MS. In conclusion, VITEK® MS showed good performance for the identification of Aspergillus species and some azoleresistant species. However, a more robust reference spectrum library including more representatives of azole-resistant cryptic species may be necessary to achieve better identification performance of closely related taxa

Enquanto muitas espécies de mosquitos são conhecidas por sua importância epidemiológica, a capacidade vetorial de algumas ainda não é clara. A identificação taxonômica, bem como a sexagem dos espécimes de Culicidae são essenciais para qualquer estudo ou ação, entretanto muitas vezes caracteres-chave estão danificados ou são restritos a uma fase de vida do animal. Em espécies crípticas, a identificação dos espécimes também pode ser prejudicada, o que dificulta, sobretudo, a compreensão da atividade vetorial em mosquitos. A morfometria geométrica alar, uma técnica barata e precisa para identificação de sutis dissimilaridades morfológicas, pode contribuir para a resolução destes tipos de problemas. O grupo de pesquisa MosquitoLab aplica esta técnica há mais de 10 anos e acumulou milhares imagens de asas com seus respectivos metadados. Estas informações, se organizadas como banco de dados relacional, podem permitir a sistematização do uso, consulta e armazenamento dos dados, além de viabilizar novos estudos e servir também como base para aplicações de identificação automática de mosquitos. Portanto, os objetivos deste trabalho foram avaliar a utilidade da morfometria geométrica alar para a resolução de dois problemas biológicos: dimorfismo sexual e espécies crípticas, e desenvolver um protótipo de plataforma para armazenamento de dados biológicos relacionados à morfometria de asa, por meio de um banco de dados relacional e um sistema web nomeado WingBank. Com base na técnica de morfometria geométrica alar, dois estudos de caso foram realizados: a) avaliação do dimorfismo sexual de 10 espécies de mosquitos de interesse médico e, b) diferenciação morfológica alar de Anopheles strodei s.s. e Anopheles arthuri s.l. com base em dois diferentes conjuntos de pontos anatômicos. Para construção do protótipo do WingBank uma equipe multidisciplinar realizou levantamento de requisitos, modelagem e criação do banco de dados relacional, e implementação de uma plataforma web. Os resultados referentes ao dimorfismo sexual alar apresentaram significativa diferenciação entre os sexos e padrões específicos de forma alar em todas as espécies estudadas. Os pontos anatômicos alares mais variáveis foram os das regiões proximal e distal das veias mediana e radial. Fêmeas apresentaram asas significativamente mais largas e curtas do que os machos. Diferenciação morfológica alar entre as espécies crípticas avaliadas foi observada em ambos os conjuntos de dados (18 e 22 pontos), sendo que no conjunto de 22 pontos com alometria, foi mais evidente. Os pontos anatômicos mais variáveis nas análises com os conjuntos de 18 e 22 pontos foram 1, 2 e 17, e 1, 2, 19, respectivamente. Finalmente, o protótipo WingBank foi implementado com dados referentes a 77 espécies pertencentes a 15 gêneros de Culicidae. Ao todo foram catalogados 13.287 registros de asas, dos quais 2.138 já estão disponibilizados a partir do presente trabalho, para uso de terceiros. Globalmente, este é o maior banco de dados de asas de Culicidae de que temos conhecimento. / While many species of mosquitoes are known for their epidemiological importance, the vector capacity of some is still unclear. Taxonomic identification and sexing of Culicidae specimens are essential for any study or action; however, often key characters are damaged or restricted to a stage of life of the animal. In cryptic species, the identification of specimens can also be damaged, which makes it difficult to understand the vector activity in mosquitoes. Geometric morphometry, an cheap and precise technique for identifying subtle morphological dissimilarities, may contribute to the resolution of these types of problems. The MosquitoLab research group has applied this technique for more than 10 years and has accumulated thousands of wing images with their metadata. This information, if organized as a relational database, may allow the systematization of the use, consultation and storage of the data, besides making possible new studies and lso serve as a basis for applications of automatic identification of mosquitoes. Therefore, the aims of this work were to evaluate the usefulness of the geometric morphometry to solve two biological problems: sexual dimorphism and cryptic species, and to develop a prototype of plataform for the storage of biological data related to wing morphometry, by means of a relational database and a web system named \"WingBank\". Based on the technique of wing geometric morphometry, two case studies were carried out: a) evaluation of the sexual dimorphism of 10 species of mosquitoes of medical importance and b) wing morphological differentiation of Anopheles strodei s.s. and Anopheles arthuri s.l. based on two different sets of landmarks. In order to build the WingBank prototype a multidisciplinary team performed requirements survey, modeling and creation of the relational database, and implemented a web platform. The results regarding wing sexual dimorphism showed significant differentiation between the sexes and specific patterns of wing shape in all species studied. The most variable landmarks were those of the proximal and distal regions of the medial and radial veins. Females showed slightly and significantly wider and shorter wings than males. Wing morphological differentiation between An. strodei s.s. and An. arthuri s.l. was observed in both sets of data (18 and 22 landmarks), but in the set of 22 with allometry, it was more evident. The most variable landmarks in the analyzes with the sets of 18 and 22 landmarks were 1, 2 and 17, and 1, 2, 19, respectively. Finally, the WingBank prototype was implemented with data referring to 77 species belonging to 15 genera of Culicidae. In all, 13,287 wing records were cataloged, of which 2,138 are from the present work, already available for use by third parties. Globally, as far as we know, this is the largest database of Culicidae wings.