A sistemática de Cnidaria Anthozoa foi revisada inúmeras vezes e por vários autores, sendo que os Ceriantharia sempre foram avaliados através de dados clássicos e muito pretéritos. O clado Ceriantharia, uma ordem dentre Hexacorallia, apresenta muitos caracteres dúbios e que poderiam colocar os animais em várias posições sistemáticas dentre Cnidaria. Ainda, as revisões de Ceriantharia são sempre derivadas de análises das mesmas espécies, principalmente do Mar Mediterrâneo. O presente trabalho tem como enfoque a discussão dos caracteres taxonômicos (morfológicos e moleculares) de Ceriantharia, sua posição sistemática, levantamento taxonômico de áreas no Oceano Atlântico praticamente inexploradas para o grupo e aspectos da biologia das espécies encontradas. Os resultados apontam para uma nova posição sistemática de Ceriantharia, levando o grupo à base de Anthozoa e como um ramo independente. A utilização de dados moleculares evidenciou o vigor do emprego de DNA barcoding na zoologia comparada de Ceriantharia. Aspectos de especiação e de revisão sistemática resultaram pelas análises moleculares. Ao mesmo tempo, os dados morfológicos são extremamente confusos e muito do que foi utilizado como caractere de delimitação de espécies pela tradição de se assumir homologias com Actiniaria é, aparentemente, inconsistente. O ciclo de vida de Isarachnanthus noturnus foi verificado, sendo que o seu estágio jovem, planctônico, e de dispersão é de longa duração. Dados sobre regeneração em pólipos também foi verificada e com a constatação de mecanismos divergentes entre as espécies. / The Cnidaria Anthozoa systematics was revised several times by a number of authors, and the Ceriantharia always evaluated using very classical and ancient data. The Ceriantharia clade, an Hexacorallia order, has many dubious characters that could place the animals in various systematic positions within Cnidaria. Also, the Ceriantharia reviews are always derived from analysis of the same species, mainly from the Mediterranean Sea. This work focuses on the discussion of taxonomic characters (morphological and molecular) of Ceriantharia, the systematic position, taxonomic survey of virtually unexplored Atlantic Ocean areas for the group and the biology of the observed species. The results suggest a new systematic position of Ceriantharia placing the group at the basis of Anthozoa and as an independent branch. The molecular data comparison showed the force of DNA barcoding use in Ceriantharia comparative zoology. The molecular data allowed the discussion of several aspects of speciation and systematics. At the same time, the morphological data are extremely confusing and much of it was used as delimiting species character by the tradition of assuming homologies with Actiniaria is, apparently, inconsistent. The life cycle of Isarachnanthus noturnus was observed, and the young, planktonic and dispersal stage is long-lived. Data on regeneration of polyps was also verified with the observation that mechanisms differ between species.

Orientador: Maria do Carmo Estanislau do Amaral / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-25T17:58:32Z (GMT). No. of bitstreams: 1 Coelho_RubensLuizGayoso_D.pdf: 16483435 bytes, checksum: 9f9fa2f59adeb6ee576f1bdd24e451b0 (MD5) Previous issue date: 2014 / Resumo: A família Sapindaceae apresenta cerca de 141 gêneros e aproximadamente 1900 espécies sendo representada no Brasil por 24 gêneros e cerca de 400 espécies. O presente trabalho foi realizado através de consultas bibliográficas, atividades de campo, consulta aos acervos dos principais herbários, além dos resultados obtidos através das análises moleculares filogenéticas e da metodologia de barcoding e refere-se a um estudo sistemático e filogenético das espécies neotropicais de Allophylus L. (Sapindaceae) que conta com espécies arbustivas ou arbóreas, distribuídas em todas as regiões tropicais do mundo alcançando algumas áreas temperadas. Desta forma, o trabalho conta com descrições das espécies, ilustrações, chave de identificação, mapas de distribuição geográfica, comentários, fotografias das espécies quando obtidas, análise filogenética utilizando-se os marcadores ITS e trnL-F e finalmente o teste da metodologia de barcoding aplicada às espécies neotropicais do gênero e outros integrantes da família. As análises filogenéticas apresentam evidencias de monofiletismo do gênero e sua relação com Thouinia, como gênero irmão, e integrantes da tribo Paullinieae. Em seguida, as essas análises foram importantes para a tomada de decisão em relação ao número de espécies e finalmente para o teste da metodologia de barcoding que se mostrou funcional entre as espécies do gênero. O gênero Allophylus é representado na região neotropical por 43 espécies sendo a região amazônica apresentando a maior diversidade no número de espécies (25 spp.). Além disso, são apresentados 33 novos sinônimos e 10 novas lectotipificações para o gênero. / Abstract: Sapindaceae presents 141 genera and approximately 1900 species being represented in Brazil by 24 genera and around 400 species. This work has been carried out through bibliographic research, field activities, consult of the main herbarium collections, as well as the results obtained through phylogenetic molecular analysis and the testing of barcoding methodology and refers to a systematic and phylogenetic study of neotropical Allophylus L. (Sapindaceae) that counts with shrubby or arboreous species distributed in all tropical regions of world reaching some temperate areas. Thus the work counts with the description of the species, illustrations, an identification key, maps of geographical distribution, taxonomic comments, photographs of the species when it was possible to obtain, a phylogenetic analysis using the ITS and trnL-F markers and finally to test the barcoding methodology applied to the neotropical species of the genus. The phylogenetic analysis confirmed the monophyly of the genus and its sister-group relation with Thouinia and part of the Paullinieae tribe related with both genera. Then, the analysis were important to make a decision on the number of species and finally to the test of the barcoding methodology among the species of the genus. Allophylus is represented in the neotropical region by 43 species being the Amazon region presenting the greatest diversity in species number (25 spp.). Furthermore, 33 new synonyms and 10 new lectotypifications are presented to the genus / Doutorado / Biologia Vegetal / Doutor em Biologia Vegetal

Abstract Species are the fundamental units of biological diversity, but their identification and delimitation is often difficult. The difficulties are pronounced in diverse taxa such as insects. DNA barcodes, short standardized segments of the genome, have recently become a popular tool for identifying specimens to species, and are increasingly used as one of the sources of information for species delimitation. In this thesis, I studied the utility of DNA barcodes in species identification and delimitation in beetles (Coleoptera). Beetles are one of the most diverse animal groups, with nearly 400 000 known species. The Nordic beetle fauna is among the most thoroughly studied on the planet, providing excellent conditions for these studies. I also approached barcode sequences from a new angle, exploring amino acid variation and its connections to life history in a sample of the entire animal kingdom. I also studied variation and evolution at the amino acid level in large-scale samples of beetles and moths & butterflies (Lepidoptera). DNA barcodes proved to be a feasible tool for identifying species of Nordic beetles: depending on the criteria for successful identification, 95-98% of specimens could be identified to the species level based on DNA barcodes. Regardless of the delimitation method used, approximately 90% of the currently accepted species were perfectly recovered based on barcode data, and simple rules for forming consensus between delimitations improved the fit between species and barcode clusters even further. Several species that were split into two or more sequence clusters apparently include species new to science that have been previously overlooked. This conclusion is supported by preliminary morphological analysis. The study on amino acid variation revealed both a general pattern of structural conservation throughout the animal kingdom, and some interesting amino acid substitutions with potential to affect enzymatic function. Amino acid variation was more extensive in Coleoptera than in Lepidoptera, potentially due to differences in selection pressure and patterns of molecular evolution in the barcode region between the two orders. / Tiivistelmä Laji on luonnon monimuotoisuuden perusyksikkö, mutta lajien tunnistaminen ja rajaaminen on usein vaikeaa. Vaikeudet korostuvat erityisesti hyvin monimuotoisissa eliöryhmissä kuten hyönteisissä. DNA-viivakoodit ovat lyhyitä standardoituja DNA-sekvenssejä, joiden käyttö lajien tunnistamisessa sekä yhtenä tiedon lähteenä lajien rajaamisessa on viime aikoina yleistynyt nopeasti. Tutkin väitöskirjatyössäni DNA-viivakoodien soveltuvuutta lajinmääritykseen ja lajien rajaamiseen kovakuoriaisilla. Kovakuoriaiset ovat yksi maailman lajirikkaimmista eliöryhmistä: lajeja on kuvattu lähes 400000. Pohjois-Euroopan lajisto tunnetaan koko maailman mittakaavassa poikkeuksellisen hyvin, mikä tarjoaa erinomaiset edellytykset tutkia DNA-viivakoodeihin liittyviä kysymyksiä kuoriaisilla. Tutkin DNA-viivakoodeja myös kokonaan uudesta näkökulmasta, selvittäen aminohappotason muuntelua koko eläinkunnan kattavassa otoksessa, sekä laajalla perhos- ja kuoriaisaineistolla. DNA-viivakoodit osoittautuivat erinomaiseksi työkaluksi lajinmääritykseen: riippuen onnistuneen määrityksen kriteereistä 95–98 % kuoriaislajeista voitiin tunnistaa luotettavasti viivakoodien perusteella. Käytetystä menetelmästä riippumatta noin 90 % nykykäsityksen mukaisista lajeista voitiin rajata viivakoodien perusteella oikein, ja soveltamalla yksinkertaisia konsensus-sääntöjä yhteensopivuus lajien ja viivakoodiklustereiden välillä kasvoi entisestään. Useat kuoriaislajit, jotka jakautuivat kahteen tai useampaan viivakoodiklusteriin, sisältävät alustavien morfologisten tutkimusten perusteella aiemmin huomaamatta jääneitä uusia lajeja. Aminohappo- ja proteiinitason tutkimus osoitti, että viivakoodijakson koodaaman proteiinin rakenne on yleisesti ottaen konservoitunut kautta eläinkunnan. Havaitsin kuitenkin myös useita kiinnostavia aminohappo-muutoksia, jotka saattavat vaikuttaa entsyymitoimintaan. Aminohapposekvenssi muuntelee kuoriaisilla paljon enemmän kuin perhosilla, mahdollisesti johtuen taksonien välisistä eroista molekyylievoluutiossa ja viivakoodisekvenssiin kohdistuvassa valintapaineessa.

Lytopylus is species-rich genus of Agathidinae (Hymenoptera: Braconidae: Agathidinae), but limited information of the genus has been published. Morphological, molecular, and ecological data were compared to resolve the species limits of Lytopylus reared from caterpillars collected the Area de Conservación Guanacaste (ACG) in Costa Rica. Molecular data were initially used to hypothesize species limits, and morphological and host use data were employed to make a final decision when molecular data was indecisive, e.g., when the genetic difference between species was slight. Thirty-two new species are described with image plates of each species. Phylogenetic analyses of the barcode region of the cytochrome c oxidase subunit I (COI) mitochondrial gene was conducted using Neighbor-Joining (NJ) and the Maximum likelihood (ML) analysis. A concatenated COI+28S dataset was analyzed by ML analysis to elucidate evolutionary patterns in ecological characters.

The aim of this work is a literature review on the topic of the mitochondrial genome and DNA barcoding, building a dataset of mitochondrial sequences from GenBank database and creatione of a software function for extraction of individual genes that are present in the mitochondrial genome. This function was developed in Matlab. DNA barcoding is a method that uses short DNA sequence of mitochondrial genome for identification of species. There is no comprehensive work examining the appropriateness of different mitochondrial genes. This aim investigates the potential of other mitochondrial genes and evaluate their effectiveness for DNA barcoding and calculation of intra-and interspecific variability.

There are two predominant sources of taxonomically useful morphological variability in the diverse tardigrade family Echiniscidae: the internal structure and surface sculpture of the cuticular plates covering the dorsum (sculpturing) and the arrangement and morphology of the trunk appendages (chaetotaxy). However, since the appendages often exhibit intraspecific variation (they can be reduced or can develop asymmetrically), sculpturing has been considered more stable at the species level and descriptions of new echiniscid species based solely on morphology are still being published. Here, we present a case study in which a detailed analysis of the morphology and multiple genetic markers of several species of the genus Viridiscus shows that cuticular sculpture may also exhibit considerable intraspecific variation and lead to false taxonomic conclusions. In a population collected from the eastern Nearctic, in the type locality of the recently described species V. miraviridis, individuals with transitional morphotypes between those reported for V. viridissimus and V. miraviridis were found. Importantly, all morphotypes within the viridissimus-miraviridis spectrum were grouped in a single monospecific clade according to rapidly evolving markers (ITS-1, ITS-2 and COI). Given the morphological and genetic evidence, we establish V. miraviridis as a junior synonym of V. viridissimus. This study explicitly demonstrates that a lack of DNA data associated with morphological descriptions of new taxa jeopardizes the efforts to unclutter tardigrade systematics. Additionally, V. perviridis and V. viridissimus are reported from Lâm Đồng Province in southern Vietnam, which considerably broadens their known geographic ranges.

No description available.

No description available.

Many species have evolved to live in groups. Gregarious behavior was believed to be adaptive for whole-population survival and predator evasion until selfish-herd theory was introduced. It proposed that individuals congregate not as a method of protection for the entire population, but instead to better the individual's chance of survival, thereby using the group to benefit itself (i.e., "selfishness"). Selfish behavior is a common part of mutualisms, which are complex, dynamic interactions that often change with biotic or abiotic circumstance. Here, I investigate potential selfish behavior within the mixed-species spawning aggregations hosted by bluehead chub (Nocomis leptocephalus). I hypothesized that the host benefits more directly from the aggregation it supports than previous research suggests – specifically, by using nest associates to decrease its own risk of predation (creating a selfish-herd) and simultaneously forcing associate embryos into marginal nest locations while locating its own embryo in the safer locations within the nest (creating an "embryonic selfish-herd"). In Chapter 1, I investigated the adult spawning aggregation for possible selfishness by monitoring the chub's spatial location within the aggregation and vigilance behavior under varying associate abundances. I found that the host occupied the central location within the aggregation and was less vigilant when associate abundance was high. In Chapter 2, I examined the "embryonic herd" contained within Nocomis nests for possible embryonic selfishness orchestrated by the chub host, leading to increased embryonic survival for chub young and elevated fitness for chub parents. I found that deeper nest sections support higher embryonic survival than shallower sections, and that chub embryo make up a disproportionate percentage of embryos found in those deeper sections. I also conducted a preliminary study investigating embryo-predation by host on associate embryo which produced evidence for embryo-predation by both host and two associates on each other's offspring. Cohesively, my results support the identification of the host as a selfish participant and confirm the presence of both an adult and embryonic selfish-herd in this mutualism. This is the first study to demonstrate selfish behavior on the part of the host in this system and the first to prove the existence of an embryonic selfish-herd. / Master of Science / A fish has three goals: to survive, to grow, and to reproduce. Mutualisms – when all participants experience a net benefit from interacting – arise when two or more species rely on each other to meet these objectives. In many mutualisms, however, not all participants benefit equally. Selfish-herd theory identifies those that maximize their own benefit while minimizing or negating any cost as "selfish" individuals. I examined the mutualistic mixed-species spawning aggregations hosted by a freshwater minnow, bluehead chub (Nocomis leptocephalus), for possible selfish behavior. I found that bluehead chubs disproportionately benefit from the aggregations they host and use the aggregation to improve their own survival, improve their offspring's survival, and obtain food (by eating others' offspring). Thus, I identify bluehead chub as a selfish participant and provide evidence for the existence of two selfish herds in this mutualism – one among the adult fishes and one among their young – both orchestrated by and benefiting the bluehead chub. This study is the first to identify the bluehead chub as such and rewrites our previous understanding of this mutualism, which largely denied bluehead chub as a direct beneficiary. This work contributes to the global discussion of mutualisms by attesting the complexity of these relationships and offers support for re-examination of the classification of many known interspecific interactions, such as those cursorily termed nest parasitisms.

Mon travail de thèse porte sur l'identification d'un arbre médicinal africain par le DNA barcoding et l'étude de composés à activité anti-VIH de cet arbre. Une première analyse de la séquence du marqueur ITS2 déterminée à partir d'ADN extrait de copeaux de bois a suggéré que la plante pourrait appartenir au genre Cassia ou au genre apparenté Senna. En analysant la séquence de ce marqueur ITS2 et aussi celle du trnHpsbA spacer d'une cinquantaine d'espèces des genres Cassia et Senna j'ai pu identifier la plante comme étant Cassia abbreviata. L'alignement de ces séquences m'a permis d'identifier, pour les deux marqueurs,des structures particulières spécifiques aux espèces du genre Cassia, permettant donc de les différencier des espèces du genre Senna. J'ai utilisé ces alignements pour effectuer une étude phylogenetique qui illustre que,pour les deux marqueurs, les Cassia forment en effet un clade bien séparé du clade des Senna qui peut être divisé en plusieurs sous-clades. Dans un deuxième temps j'ai étudié les effets anti-VIH de l'extrait alcoolique ainsi que de 57 composés purifiés obtenus au laboratoire. L'extrait brut ainsi qu'un des composés purifiés, le piceatannol, ont montré un grand spectre d’activités antivirales pour le VIH et le virus de l’herpès. Ils inhibent,à un stade précoce, l'infection par le VIH de lignées cellulaires de référence et d'isolats cliniques, ceci indépendamment de l'utilisation du co-récepteur (IC50: 10.47-40.77 μg/ml, CC50>1000 μg/ml; IC50: 8.04-47.46 μM, CC50>300 μM, respectivement). Ni l'un ni l'autre n'a d'effet sur CD4 et CCR5/CXCR4. L'extrait brut,mais pas le piceatannol, bloque l'interaction CD4-gp120, suggérant que l'extrait brut cible gp120 alors que le piceatannol agit comme un inhibiteur non-spécifique d'attachement du virus. Aussi, dans un modèle in vitro de tract génital femelle, le piceatannol inhibe l'infection de cellules cibles TZM-Bl par le VIH et n'active pas les cellules PBMCs, suggérant qu'il pourrait être un bon candidat comme microbicide. D'autres composés à activité anti-VIH dans l'extrait comportent l'acide oléanolique, l'acide palmitique, la taxifoline, ainsi que troiscomposés dont la structure est en train d'être élucidée. / My thesis project deals with the identification, by DNA barcoding, of an African medicinal plant and the study of anti-HIV compounds from this plant. A first analysis of the ITS2 marker sequence determined from DNA extracted from the wood suggested that the plant could belong to the Cassia or the related Senna genus. A further analysis of ITS2 as well as of trnH-psbA spacer sequences from about 50 species of the two genera allowed me to identify the plant as Cassia abbreviata. The sequence alignments, which reveal unique features present in the Cassia but not the Senna sequences, were used to construct phylogenetic trees showing the clear separation of the species of the Cassia and the Senna genus. The two markers therefore allow a quick discrimination between the species of the Cassia and the Senna genus and appear to be excellent barcode markers for identification of these species. Following the identification of the plant I have tested the crude ethanol extract as well as 57 purified compounds from the plant for an anti-HIV activity. The extract, as well as one of the compounds, namely piceatannol, showed a broad spectrum of antiviral activities for HIV and HSV. They inhibited HIV-1 infection at the early stage against various reference strains and resistant clinical isolates independent of the co-receptor usage (IC50: 10.47-40.77 μg/ml, CC50>1000 μg/ml; IC50: 8.04-47.46 μM,CC50>300 μM, respectively). Neither the crude extract nor piceatannol had an effect on CD4 and CCR5/CXCR4. The crude extract blocked CD4-gp120 interaction while piceatannol did not, indicating that CE may target gp120 and piceatannol may act as a non-specific viral attachment inhibitor. Moreover, piceatannol inhibited HIV infection of TZM-Bl target cells in an in vitro female genital tract model and did not activate PBMCs, suggesting that it may represent a good candidate as microbicide. Other anti-HIV compounds found in Cassia abbreviata include oleanolic acid, palmitic acid, taxifolin and three other compounds the structure of which is presently being elucidated.