Magister Scientiae (Biodiversity and Conservation Biology) / The spread of invasive species is one of the greatest threats to global biodiversity. Alien plant invasions also have serious economic impact in terms of the delivery of ecosystem goods and services. Studies of biological invasions in southern Africa have tended to overlook grasses (family Poaceae), although there are many naturalised species in the region. Only a few of these, all perennials, have been officially categorised as invasive in South Africa, but in the winter rainfall region of the Western Cape, grass invasion especially by Mediterranean European annuals have also been noted. These grasses can be difficult to identify. DNA barcoding has been suggested as an alternative method of identifying grasses in the hope of facilitating identification of existing invaders and preventing future invasions. In this study a list of all known naturalised grasses in South Africa was compiled, and a DNA barcoding reference database was assembled for these naturalised grass species as well as for native southern African grass species. The two official markers for plant DNA barcoding (rbcLa + matK) were used in barcoding and phylogenetic analyses, both individually and in combination. The barcoding data was assessed for identification efficacy using three distance-based metrics and one tree-based metric in the R package SPIDER, both including and excluding singleton data. This study lists 128 naturalised grass species and subspecies found in South Africa. In the DNA barcoding analyses, matK was found to perform better as a single barcode than rbcLa, with identification success rates of up to 84% for matK and 76% for rbcLa, using the most successful metric which was the Nearest Neighbour criterion for both of these markers in the data sets without singletons. The combined rbcLa + matK data set performed better than either of the two individual markers, with identification success rates of up to 91% in the data without singletons, with the most successful metric again being the Nearest Neighbour criterion. The combined rbcLa + matK data would therefore be the recommended DNA barcode for southern African grasses of the three data sets tested, based on the results of this study. Phylogenetic trees were constructed with the DNA barcoding data using Bayesian Inference (BI) and Maximum Parsimony (MP) to assess the usefulness of the data in phylogenetic studies and to confirm the efficacy of this grass DNA barcoding data when using tree-based methods of identification. Both the matK and combined datasets resolved all of the grass tribes represented in this study as monophyletic, but the rbcLa data did not.

Submitted by Automa??o e Estat?stica (sst@bczm.ufrn.br) on 2017-07-17T13:30:06Z No. of bitstreams: 1 FrancoiseDantasDeLima_TESE.pdf: 8585044 bytes, checksum: 0ae8905bac9e200a95b966507fc7aa0e (MD5) / Approved for entry into archive by Arlan Eloi Leite Silva (eloihistoriador@yahoo.com.br) on 2017-07-19T15:09:29Z (GMT) No. of bitstreams: 1 FrancoiseDantasDeLima_TESE.pdf: 8585044 bytes, checksum: 0ae8905bac9e200a95b966507fc7aa0e (MD5) / Made available in DSpace on 2017-07-19T15:09:29Z (GMT). No. of bitstreams: 1 FrancoiseDantasDeLima_TESE.pdf: 8585044 bytes, checksum: 0ae8905bac9e200a95b966507fc7aa0e (MD5) Previous issue date: 2017-04-07 / Coordena??o de Aperfei?oamento de Pessoal de N?vel Superior (CAPES) / A abordagem integrativa aplicada ? conserva??o de uma esp?cie ? essencial para a compreens?o dos fatores que contribuem para a diversifica??o de popula??es, processos de especia??o e identifica??o de padr?es ecol?gicos. Para tra?ar um panorama de conserva??o para Octopus insularis, foi adotada uma abordagem integrativa que envolve elementos da filogenia, filogeografia, Barcoding, modelagem do nicho clim?tico e gen?tica da paisagem. O presente estudo foi realizado em 15 localidades da costa oeste e ilhas oce?nicas do Atl?ntico Tropical. Foi identificado um aumento da ?rea de distribui??o de O. insularis para o mar do Caribe, o qual confirma o alto potencial da esp?cie para dominar ambientes de ?guas quentes e rasas. Al?m disso, verificou-se problemas com a identifica??o incorreta das esp?cies que comp?em os estoques pesqueiros dessa regi?o e do Golfo do M?xico, o que pode amea?ar a esp?cie end?mica O. maya. Atrav?s do enfoque filogen?tico com infer?ncia biogeogr?fica, foi poss?vel identificar o Caribe como poss?vel centro de origem do O. insularis, a qual divergiu de outras do g?nero ap?s o soerguimento do Istmo do Panam?. Tr?s clados contendo esp?cies transistimianas confirmam a import?ncia desse evento geol?gico no processo de especia??o em oct?podes. A influ?ncia dos processos clim?ticos subsequentes nas popula??es de O. insularis foi analisada atrav?s da modelagem do nicho em cinco cen?rios temporais. A an?lise revelou expans?o do nicho de O. insularis, em dire??o a regi?es temperadas nos cen?rios de aquecimento global. J? a filogeografia, estrutura??o populacional mostrou quatro popula??es/estoques bem delimitados geneticamente, devido ao regime da Corrente Sul Equatorial e montes submersos. Tais resultados corroboram a hip?tese do isolamento por Resist?ncia. Os resultados do presente estudo permitiram uma vis?o hol?stica dos fatores gen?ticos, ecol?gicos e oceanogr?ficos que influenciam a esp?cie O. insularis e auxiliaram a tra?ar um atual panorama de conserva??o e regulamenta??o da esp?cie, bem como sugerir futuras medidas de manejo para e esp?cie. / The integrative approach applied to species conservation is essential to understand the factors that contribute to population diversification, speciation processes and identification of ecological patterns. To propose a panorama for the conservation of Octopus insularis, a wide distributed species in the Tropical Atlantic, an integrative approach involving phylogeny, phylogeography, Barcoding, climatic niche modeling and landscape genetics was adopted. The present study was performed in 15 localities of the Tropical Atlantic west coast and oceanic islands. It was identified a northward increase in the O. insularis distribution area towards the Caribbean Sea, which confirms high potential of this species to dominate warm and shallow waters. Furthermore, misidentification of the species that compose fisheries stocks in the Gulf of Mexico was detected, which may threaten the endemic species O. maya. By using phylogeny approach with biogeographic interference, it was possible to identify Caribbean Sea as an origin area of O. insularis, which diverged from others congeners after the uplift of Isthmus of Panama. Tree clades formed by transisthmian species confirmed the importance of this geological event on speciation processes in octopod. The influence of the historical e future climate changes on distribution and expansion of O. insularis populations was analyzed by ecological niche modeling in five temporal scenarios. The analysis revealed a climatic niche expansion of O. insularis towards temperate regions on global warming scenarios. Whereas, phylogeography and population structure showed four populations/stocks well delimited, mainly due to South Equatorial Current and seamounts. These results corroborate the Isolation by Distance hypothesis. The present results allowed a holistic view, including genetic, ecology and oceanographic factors, which influences O. insularis life history. Those findings can help to build an actual panorama of species conservation and regulation, as well, to suggest future management measures to attenuate possible consequence of global climatic changes.

abstract: An understanding of diet habits is crucial in implementing proper management strategies for wildlife. Diet analysis, however, remains a challenge for ruminant species. Microhistological analysis, the method most often employed in herbivore diet studies, is tedious and time consuming. In addition, it requires considerable training and an extensive reference plant collection. The development of DNA barcoding (species identification using a standardized DNA sequence) and the availability of recent DNA sequencing techniques offer new possibilities in diet analysis for ungulates. Using fecal material collected from controlled feeding trials on pygmy goats, (Capra hicus), novel DNA barcoding technology using the P6-loop of the chloroplast trnL (UAA) intron was compared with the traditional microhistological technique. At its current stage of technological development, this study demonstrated that DNA barcoding did not enhance the ability to detect plant species in herbivore diets. A higher mean species composition was reported with microhistological analysis (79%) as compared to DNA barcoding (50%). Microhistological analysis consistently reported a higher species presence by forage class. For affect positive species identification, microhistology estimated an average of 89% correct detection in control diets, while DNA barcoding estimated 50% correct detection of species. It was hypothesized that a number of factors, including variation in chloroplast content in feed species and the effect of rumen bacteria on degradation of DNA, influenced the ability to detect plant species in herbivore diets and concluded that while DNA barcoding opens up new possibilities in the study of plant-herbivore interactions, further studies are needed to standardize techniques and for DNA bar-coding in this context. / Dissertation/Thesis / M.S. Applied Biological Sciences 2012

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.

Le multiplexage optique basé sur des nanoparticules offre de nombreux avantages pour la biodétection et l'imagerie à multiparamètres. Toutefois, les modifications apportées à un paramètre entraînent également la modification d’autres paramètres. Par conséquent, la couleur, la durée de vie ou l’intensité ne peuvent pas être utilisées, respectivement, comme paramètre indépendant. Cette thèse peut être divisée en deux aspects. Le premier concerne le développement d'un multiplexage à une seule nanoparticule avec un temps résolu, basé sur le transfert d'énergie par résonance de type Förster (FRET) des complexes de lanthanides aux points quantiques (QD) et ensuite aux colorants fluorescents. Une investigation systématique de toutes les différentes combinaisons avec une large gamme de donneurs et d'accepteurs sur le QD est présentée, et les résultats expérimentaux sont comparés à la modélisation théorique. Le résultat ne contribue pas seulement à une compréhension complète de ces voies de transfert d'énergie compliquée entre multi donneurs / accepteurs sur des nanoparticules, mais offre également la possibilité d'utiliser les modèles pour développer de nouvelles stratégies permettant de préparer le QD avec une couleur, une durée de vie et une intensité réglables de manière indépendante. Le deuxième aspect porte sur le mécanisme de transfert d'énergie du Tb à la nanoparticule d'or (AuNP). Le transfert d'énergie par nanosurface (NSET) s'est révélé être un mécanisme opérationnel pour l'extinction des PL par les AuNP, une information importante pour le développement, la caractérisation et l'application de nanobiocapteurs basés sur l'extinction des PL par les AuNP. / Optical multiplexing based on nanoparticles provides many advantages for multiparameter biosensing and imaging. However, the changes in one parameter also lead to changing of other parameters, and thus, color, lifetime, or intensity could not be used as an independent parameter, respectively. This thesis can be divided into two aspects. The first one focuses on developing time-resolved single-nanoparticle multiplexing based on Förster resonance energy transfer (FRET) from lanthanide complexes to quantum dot (QD) to fluorescent dyes. Systematical investigation of all different combinations with a broad range of numbers of donors and acceptors on QD are presented, and the experimental results are compared with theoretical modelling. The result do not only contribute to a full understanding of such complicated multi donor-acceptor energy transfer pathways on nanoparticles but also open the opportunity to use the models for developing new strategies to achieve the QD with independent tunable color, lifetime and intensity. The second aspect focuses on the energy transfer mechanism from Tb to gold nanoparticle (AuNP). Nanosurface energy transfer (NSET) proved to be an operational mechanism in PL quenching by AuNPs, which is important information for the development, characterization, and application of nanobiosensors based on PL quenching by AuNPs.

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.