No description available.

L'introgression est un processus fréquent et qui a d'importantes conséquences évolutives. L'objectif de ce travail était de tester un modèle neutre d'introgression chez des épicéas du Plateau tibétain et des régions voisines. Le travail a permis de mettre en évidence que la direction de l'introgression pouvait être prédite par la dynamique passée des populations d'arbres, et que l'importance de cette introgression était inversement proportionnelle à l'intensité des échanges génétiques au sein de l'espèce invasive, grâce à la comparaison de la structure génétique basée sur des marqueurs chloroplastiques (à hérédité paternelle) et mitochondriaux (à hérédité maternelle). / Introgression is a widespread phenomenon with potentially profound evolutionaryconsequences. Recently, significant progress in our understanding of introgression hasbeen made with the development of a neutral model. This model predicts that, whenone species invades an area already occupied by a related species, introgression ofneutral genes takes place mainly from the local species towards the invading ones. Inaddition, following a contact between two hybridizing species, the model predicts thatintrogression should be particularly frequent for genome components experiencinglittle gene flow. However, to date, there was no empirical example available, in whichone species expanded into the range of a closely related one and two markers withcontrasted rates of gene flow had been studied for both species. Only in such a casecould the two predictions outlined above be tested simultaneously. In addition, basedon these two predictions, species delimitation should be more efficient when usingmolecular markers experiencing high rates of gene flow. The present thesis was designed to test the hypotheses of this model. The biologicalmodel used was conifers, a group in which introgression and hybridization arecommon because of incomplete reproductive isolation. The species investigatedbelong to the genus Picea (spruce). We focused on two species complexes,represented by monographic clades in a phylogenetic study using the chloroplast genematK. All species studied occur in the Qinghai-Tibetan Plateau (QTP) and adjacenthighlands. The phylogeography of these species complexes was reconstructed usingorganelle markers (mitochondrial DNA, mtDNA and chloroplast DNA, cpDNA). Inconifers, mtDNA and cpDNA have contrasted modes of inheritance. The former ismaternally inherited, transmitted by seeds experiencing little gene flow while thelatter is paternally inherited, transmitted by both pollen and seeds experiencing highlevels of gene flow. Therefore, uniparentally inherited mtDNA and cpDNA markersexperience different rates of gene flow in such a group, providing an ideal model to test the relationship between rates of gene flow, introgression and species delimitation.Two mtDNA fragments (nad1intron b/c; nad5 intron1) and three cpDNA fragments(ndhK-C；trnL-trnF；trnS-trnG) were sequenced for nine species belonging to thePicea asperata and P. likiangensis species complex.(1) Nine mtDNA and nine cpDNA haplotypes were detected in 459 individualsfrom 46 natural populations in five species of P. asperata complex. As found in mostconifer species studied so far, low variation is present in the two mtDNA intronsalong with a high level of differentiation among populations (GST = 0.90). In contrast,higher variation and lower differentiation among populations was found at cpDNAmarkers (GST = 0.56). The cpDNA, although far from being fully diagnostic, is morespecies-specific than mtDNA: four groups of populations were identified usingcpDNA markers, all of them related to species or groups of species, whereas formtDNA, geographical variation prevails over species differentiation. A literaturereview shows that mtDNA variants are often shared among related conifer species,whereas cpDNA variants are more species-specific. Hence, increased intraspecificgene flow appears to decrease differentiation within species but not among species.[...]

Parmi les lignées des Caesalpinioideae (dans la famille des Leguminosae), l’un des groupes importants au sein duquel les relations phylogénétiques demeurent nébuleuses est le « groupe Caesalpinia », un clade de plus de 205 espèces, réparties présentement entre 14 à 21 genres. La complexité taxonomique du groupe Caesalpinia provient du fait qu’on n’arrive pas à résoudre les questions de délimitations génériques de Caesalpinia sensu lato (s.l.), un regroupement de 150 espèces qui sont provisoirement classées en huit genres. Afin d’arriver à une classification générique stable, des analyses phylogénétiques de cinq loci chloroplastiques et de la région nucléaire ITS ont été effectuées sur une matrice comportant un échantillonnage taxonomique du groupe sans précédent (~84% des espèces du groupe) et couvrant la quasi-totalité de la variation morphologique et géographique du groupe Caesalpinia. Ces analyses ont permis de déterminer que plusieurs genres du groupe Caesalpinia, tels que présentement définis, sont polyphylétiques ou paraphylétiques. Nous considérons que 26 clades bien résolus représentent des genres, et une nouvelle classification générique du groupe Caesalpinia est proposée : elle inclut une clé des genres, une description des 26 genres et des espèces acceptées au sein de ces groupes. Cette nouvelle classification maintient l’inclusion de douze genres (Balsamocarpon, Cordeauxia, Guilandina, Haematoxylum, Hoffmanseggia, Lophocarpinia, Mezoneuron, Pomaria, Pterolobium, Stenodrepanum, Stuhlmannia, Zuccagnia) et en abolit deux (Stahlia et Poincianella). Elle propose aussi de réinstaurer deux genres (Biancaea et Denisophytum), de reconnaître cinq nouveaux genres (Arquita, Gelrebia, Hererolandia, Hultholia et Paubrasilia), et d’amender la description de sept genres (Caesalpinia, Cenostigma, Coulteria, Erythrostemon, Libidibia, Moullava, Tara). Les résultats indiquent qu’il y aurait possiblement aussi une 27e lignée qui correspondrait au genre Ticanto, mais un échantillonage taxonomique plus important serait nécéssaire pour éclaircir ce problème. Les espèces du groupe Caesalpinia ont une répartition pantropicale qui correspond presque parfaitement aux aires du biome succulent, mais se retrouvent aussi dans les déserts, les prairies, les savanes et les forêts tropicales humides. À l’échelle planétaire, le biome succulent consiste en une série d’habitats arides ou semi-arides hautement fragmentés et caractérisés par l’absence de feu, et abrite souvent des espèces végétales grasses, comme les Cactacées dans les néo-tropiques et les Euphorbiacées en Afrique. L’histoire biogéographique du groupe Caesalpinia a été reconstruite afin de mieux comprendre l’évolution de la flore au sein de ce biome succulent. Ce portrait biogéographique a été obtenu grâce à des analyses de datations moléculaires et des changements de taux de diversification, à une reconstruction des aires ancestrales utilisant le modèle de dispersion-extinction-cladogenèse, et à la reconstruction de l’évolution des biomes et du port des plantes sur la phylogénie du groupe Caesalpinia. Ces analyses démontrent que les disjonctions trans-continentales entre espèces sœurs qui appartiennent au même biome sont plus fréquentes que le nombre total de changements de biomes à travers la phylogénie, suggérant qu’il y a une forte conservation de niches, et qu’il est plus facile de bouger que de changer et d’évoluer au sein d’un biome différent. Par ailleurs, contrairement à nos hypothèses initiales, aucun changement de taux de diversification n’est détecté dans la phylogénie, même lorsque les espèces évoluent dans des biomes différents ou qu’il y a changement de port de la plante, et qu’elle se transforme, par exemple, en liane ou herbacée. Nous suggérons que même lorsqu’ils habitent des biomes très différents, tels que les savanes ou les forêts tropicales humides, les membres du groupe Caesalpinia se retrouvent néanmoins dans des conditions écologiques locales qui rappellent celles du biome succulent. Finalement, bien que la diversité des espèces du biome succulent ne se compare pas à celle retrouvée dans les forêts tropicales humides, ce milieu se distingue par un haut taux d’espèces endémiques, réparties dans des aires disjointes. Cette diversité spécifique est probablement sous-estimée et mérite d’être évaluée attentivement, comme en témoigne la découverte de plusieurs nouvelles espèces d’arbres et arbustes de légumineuses dans la dernière décennie. Le dernier objectif de cette thèse consiste à examiner les limites au niveau spécifique du complexe C. trichocarpa, un arbuste des Andes ayant une population disjointe au Pérou qui représente potentiellement une nouvelle espèce. Des analyses morphologiques et moléculaires sur les populations présentes à travers les Andes permettent de conclure que les populations au Pérou représentent une nouvelle espèce, qui est génétiquement distincte et comporte des caractéristiques morphologiques subtiles permettant de la distinguer des populations retrouvées en Argentine et en Bolivie. Nous décrivons cette nouvelle espèce, Arquita grandiflora, dans le cadre d’une révision taxonomique du genre Arquita, un clade de cinq espèces retrouvées exclusivement dans les vallées andines. / Amongst the lineages of the Caesalpinioideae (in the family Leguminosae), one of the largest groups where phylogenetic relationships remains unclear is the Caesalpinia Group, a clade of ca. 200 species, currently considered to comprise between 14 and 21 genera. The taxonomic complexity of the Caesalpinia Group stems from persisting doubts on the generic delimitations within Caesalpinia sensu lato, a group of 150 species that are provisionally classified into eight genera. In order to establish a stable generic classification, phylogenetic analyses of five chloroplastic loci and the nuclear ribosomal ITS locus were carried out on a matrix containing an unprecedented taxonomic sampling of the Caesalpinia Group (~84% of species of this group included), with virtually all of the morphological variation and geographic distribution represented. These analyses allowed us to determine that several genera of the Caesalpinia Group, as currently defined, are polyphyletic or paraphyletic. We consider that there are 26 well-resolved clades that represent distinct genera, and a new generic classification system is proposed, which includes a key to genera, the description of the 26 genera and all species accepted within these groups. A total of twelve previously accepted genera are maintained in this classification (Balsamocarpon, Cordeauxia, Guilandina, Haematoxylum, Hoffmanseggia, Lophocarpinia, Mezoneuron, Pomaria, Pterolobium, Stenodrepanum, Stuhlmannia, and Zuccagnia), whereas two genea are abolished (Stahlia and Poincianella). In addition, two genera are re-instated (Biancaea and Denisophytum), five new genera are described, (Arquita, Gelrebia, Hererolandia, Hultholia and Paubrasilia), and the description of seven genera are emended (Caesalpinia, Cenostigma, Coulteria, Erythrostemon, Libidibia, Moullava, Tara). Our results also indicate that there could possible be a 27th lineage corresponding to the genus Ticanto, but an increased taxonomic sampling is needed to adequately address this issue. The Caesalpinia Group has a pantropical distribution that corresponds almost perfectly to the geographical distribution of the Succulent Biome, but are also found in deserts, grassland prairies, savannahs, and tropical rainforests. On a planetary scale, the Succulent Biome consists of a series of semi-arid to arid habitats that are highly fragmented, and which are characterised by the absence of fire, such as deserts and dry forests. This biome often harbours succulent plant taxa, such as the Cactaceae in the Neotropics and the Euphorbiaceae in Africa. The biogeographical history of the Caesalpinia Group was reconstructed in order to gain insight into the evolution of the flora within this Succulent biome. This biogeographical portrait of this group was reconstructed using molecular dating analysis, diversification rate shifts tests, the reconstruction of ancestral areas using the dispersal-extinction-cladogenesis model (DEC), as well as through ancestral character reconstruction of the biomes and habits. These analyses demonstrate that intercontinental disjunctions between sister species belonging to the same biome are more frequent than the total number of biome shifts across the phylogeny, suggesting that there is a strong conservation of niches, and that it is easier to move than to switch to and evolve in a different biome. Furthermore, contrary to our initial hypothesis, no changes in diversification rates were detected in our phylogenies, even when species switched biomes or evolved a different plant habit, e.g. becoming lianas or herbaceous perennials. We suggest that even when members of the Caesalpinia Group inhabit different biomes, such as savannahs or tropical rainforests, they are still tracking local ecological conditions that are typical of the Succulent biome. Finally, while total plant species diversity in the Succulent Biome does not compare to the diversity found in tropical rainforests, this biome distinguishes itself by a high number of endemic species, distributed in disjunct patches across the world. This species diversity is probably under-estimated and needs to be carefully re-evaluated, as shown in several recent descriptions of new tree and shrub species from the Succulent biome, all published in the last decade. The last objective of this thesis is to examine the species limits in Caesalpinia trichocarpa, a shrub from the Andes that has a disjunct population in Peru, which potentially represents a new species. Morphological and molecular analyses of populations occurring across the Andes, including Bolivia and Argentina, allow us to conclude that the populations in Peru represent a new species, which is genetically distinct and has subtle morphological characteristics that allow it to be distinguished from populations found in Argentina and Bolivia. We describe this news species, Arquita grandiflora, in a taxonomic revision of the genus Arquita, a clade of five species found exclusively in Andean valleys.

Os camarões do gênero Atya Leach, 1816 são os maiores camarões da família Atyidae, sendo que as 13 espécies reconhecidas estão distribuídas em rios e riachos das regiões tropicais e subtropicais da América (vertentes atlântica e pacífica) e oeste da África. O primeiro relato de uma Atya ocorreu no séc. XVII e, desde então, novas espécies foram descritas e descrições prévias revisadas, produzindo um histórico de instabilidade e reclassificações. Embora ao longo do séc. XX revisões taxonômicas tenham estabilizado a sistemática do gênero, a variabilidade morfológica e distribuição geográfica trans-ístmica da espécie A. innocous gerou questionamentos. Além disso, mais recentemente trabalhos de filogenia molecular da família Atyidae que incluíram representantes de Atya suscitaram questões em relação à sistemática do gênero (possível não monofilia) e de algumas espécies como A. gabonensis, A. margaritacea e A. scabra. Visto que o uso de marcadores moleculares nunca foi empregado para a delimitação das espécies de Atya e que seu uso de forma complementar à morfologia poderia aperfeiçoar a sistemática do gênero, o objetivo do presente estudo foi avaliar por meio de dados moleculares as hipóteses taxonômicas das espécies A. gabonensis, A. innocous, A. margaritacea e A. scabra. Sequências dos genes mitocondriais 16S e Citocromo Oxidase I e gene nuclear Histona 3 foram geradas por meio de protocolos de extração e sequenciamento de DNA a partir do tecido de espécimes obtidos em empréstimos/doações. Potenciais espécies evidenciadas pelas análises de similaridade nucleotídicas (distâncias genéticas), compartilhamento de caracteres em um contexto evolutivo (reconstruções filogenéticas), Automatic Barcode Gap Discovery, Poisson Tree Processes e Generalized Mixed Yule Coalescence foram confrontadas com as hipóteses taxonômicas específicas atuais. A avaliação sistemática com dados moleculares aqui realizada, adicionalmente às informações morfológicas existentes na literatura sustentaram A. gabonensis como uma espécie de distribuição anfi-atlântica, mas não corroborou a hipótese de A. innocous como uma espécie trans-ístmica. Assim, o uso do nome A. innocous para as populações do Mar do Caribe e A. tenella para aquelas restritas ao Pacífico é sugerido. A espécie A. margaritacea, distribuída ao longo da costa pacífica da América foi considerada uma espécie válida e distinta de A. scabra, amplamente distribuída na vertente atlântica da América do Sul, África e Mar do Caribe. Contudo, é discutida a possibilidade de uma espécie críptica restrita no Golfo do México existir. Adicionalmente, o conhecimento existente e pertinente para futuros estudos de sistemática e taxonomia sobre os camarões do gênero Atya foram sumarizados e são apresentados. / The genus Atya Leach, 1816 shrimps are the largest of the Atyidae family, and the 13 acknowledge species are geographically distributed in rivers and stream in the tropical and subtropical regions of America (Atlantic and Pacific drainages) and West Africa. The first registry of an Atya was in the XVII century and since then new species were described and previous description revised in an eventful taxonomic historic. Although throughout the XX century taxonomic revisions stabilized the genus systematics, the morphological variability and the trans-isthmic geographic distribution of A. innocous caused questioning. Moreover, molecular phylogenetic studies that included Atya representatives raised doubt on the genus systematics (possibly non-monophyletism) and some species A. gabonensis A. margaritacea and A. scabra hypothesis. As molecular markers have never been used concerning Atya species delimitation complementary to the morphology and it could improve the genus systematics, the goal of this study was to evaluate with molecular markers the taxonomic hypothesis of the species A. gabonensis, A. innocous, A. margaritacea e A. scabra. Sequences of the mitochondrial genes 16S and Cytochrome Oxidase I and nuclear gene Histone 3 were generated by means of DNA extraction and sequence protocols from specimens obtained in loans/donations. Putative species evidenced by the analysis of nucleotide similarity (genetic distances), character sharing (phylogenetic reconstitutions), Automatic Barcode Gap Discovery, Poisson Tree Processes and Generalized Mixed Yule Coalescence were compared to the prevailing taxonomic hypothesis. The systematic evaluation with the molecular data of this study, in addition with the morphological information in the literature sustain A. gabonensis as an amphi-atlantic distributed species, but do not corroborated A. innocous hypothesis as an trans-isthmian species. In this sense, the use of A. innocous stricto sensu for the Caribbeans Sea populations and A. tenella to that restricted to the pacific drainage of America is suggested. Atya margaritacea, distributed along the pacific drainage of America, is considered a valid species distinct from A. scabra, widespread distributed in the Atlantic drainage of America and Africa, besides Caribbean Sea. However, the possibility of a cryptic species in the Gulf of Mexico population is discussed. Aditionally, the relevant knowledge to future systematic and taxonomy studies about the shrimps of the genus Atya were summarized and are shown.

Delimitar espécies e reconstruir a história evolutiva em complexos de espécies pode demandar grandes esforços uma vez que grupos taxonomicamente problemáticos são muitas vezes consequência de eventos de especiação recente ou de rápida especiação. O complexo \'Cattleya coccinea\', da família Orchidaceae, é composto por orquídeas com alto valor ornamental, epifíticas e rupícolas de porte pequeno. Apesar de estarem descritas com caracteres morfológicos diagnósticos claros que permitem sua identificação, a delimitação das espécies atualmente reconhecidas é problemática. Portanto, os objetivos dessa pesquisa foram revisar a delimitação de espécies do complexo e a relação entre as espécies, além de avaliar a diversidade e estrutura genética, aliadas às análises filogeográficas para testar a ocorrência de eventos demográficos históricos. Para responder tais questões foram utilizadas regiões de sequência de cpDNA e nrDNA, 11 locos microssatélites, além de inferência bayesiana e modelo coalescente somadas às estatísticas tradicionais como metodologia. Os resultados suportam o monofiletismo para o clado para as regiões de cpDNA concatenadas. Indicam também quatro grandes eventos de reticulação das espécies do clado C. coccinea com outras espécies do gênero Cattleya. Adicionalmente, suportam o reconhecimento de sete diferentes espécies para o clado C. coccinea, composto por duas principais linhagens evolutivas mais ao norte da região Sudeste: C. brevipedunculata predominante da Serra do Espinhaço e C. wittigiana do norte da Serra do Mar. E cinco espécies distribuídas ao longo da Serra do Mar e Serra da Mantiqueira (C. coccinea, C. mantiqueirae, e mais três espécies correspondentes às populações de DMES; SJPSP e CSRS/JOSC/PMPR. As análises de diversidade mostraram de moderados a altos níveis de diversidade genética e apontam que as espécies C. coccinea e C. brevipedunculata apresentam os maiores níveis de diversidade comparadas a outras espécies do clado. A estruturação genética entre populações dentro de espécies mostrou variação entre níveis baixos a altos. A análise de atribuição de indivíduos a partir de inferência bayesiana mostrou a formação de oito grupos geneticamente distintos. A análise de taxa de dispersão de fluxo gênico pólen x semente mostrou que a dispersão via pólen é aproximadamente oito vezes mais eficiente que a dispersão via sementes somente para C. coccinea. Além disso, a rede de haplótipos indicou que as espécies raramente compartilham haplótipos e que C. coccinea e C. brevipedunculata apresentam maior diversidade com eventos de expansão. A análise de estimativa de tempo de divergência demonstrou que C. brevipedunculata e C. wittigiana provavelmente se originaram entre o Plioceno e o Pleistoceno. As outras espécies do clado se diversificaram no Pleistoceno. Eventos de expansão populacional foram observados para todas as espécies em eras glaciais do Pleistoceno. Por se tratarem de espécies ameaçadas, esse estudo recomenda a conservação \"in situ\" como também a conservação \"ex situ\" de todas as espécies do clado, com atenção especial às duas espécies do Espírito Santo: C. wittigiana e a espécie da localidade DMES, além da espécie da localidade SJPSP em São Paulo. / Species delimitation and reconstruction of the evolutionary history of species complexes may require great efforts since taxonomically problematic groups are often a result of recent speciation events or rapid speciation. The \'Cattleya coccinea\' complex, of the orchid family, consists of epiphytic and small rupicolous orchids with high ornamental value. Despite being described with clear diagnostic morphological characters that allow their identification, delimitation of the currently recognized species is problematic. Therefore, the objectives of this study were to review the species delimitation of the complex and the relationship between species, and to evaluate the genetic diversity and structure, combined with phylogeographic analyzes to test the occurrence of historical demographic events. To answer such questions, cpDNA and nrDNA sequence regions, 11 microsatellite loci, and Bayesian inference and coalescent model were used, combined with traditional statistics and methodology. The results support the monophyly for the clade for concatenated cpDNA regions. They also indicate four major reticulation events of C. coccinea species clade with other species of the genus Cattleya. Additionally, results support the recognition of seven different species for C. coccinea clade, composed of two main evolutionary lineages further north in the Southeast: C. brevipedunculata predominant in the Serra do Espinhaço and C. wittigiana from northern Serra do Mar. And five species distributed along the Serra do Mar and Serra da Mantiqueira (C. coccinea, C. mantiqueirae, and three other species of the populations DMES; SJPSP and CSRS/JOSC/PMPR. The diversity analyzes showed moderate to high levels of genetic diversity and point out that the species C. coccinea and C. brevipedunculata have the highest levels of diversity compared to other species of the clade. The genetic structure of populations within species showed variation from low to high. Assigning individuals analysis from Bayesian inference showed the formation of eight genetically distinct groups. The dispersal rate analysis of pollen x seed gene flow showed that dispersal through pollen is approximately eight times more efficient than the dispersal through seeds only for C. coccinea. Furthermore, the haplotype network indicated that the species rarely share haplotypes and that C.coccinea and C. brevipedunculata present greater diversity with expansion events. The divergence time estimation analysis showed that C. brevipedunculata and C. wittigiana probably originated between the Pliocene and the Pleistocene. The other clade species have diversified in the Pleistocene. Population expansion events were observed for all species in the Pleistocene ice ages. Because they are endangered species, this study recommends the \"in situ\" conservation as well as \"ex situ\" conservation for all species of clade, with special attention for two species of Espírito Santo: C. wittigiana and the species of DMES locality, in addition to the species of SJPSP location in São Paulo.

Orientador: Célio Fernando Baptista Haddad / Resumo: Thoropa Cope, 1865 (Anura: Cycloramphidae) é um gênero de rãs endêmicas do domínio Mata Atlântica e de ecótonos associados. Possui atualmente seis espécies (T. miliaris, T. petropolitana, T. taophora, T. lutzi, T. megatympanum e T. saxatilis), divididas em dois grupos morfológicos: grupo petropolitana (T. petropolitana e T. lutzi) e grupo miliaris (T. miliaris, T. taophora, T. megatympanum e T. saxatilis). Todas as espécies se reproduzem e se desenvolvem em rochas molhadas de água doce, encontradas em afloramentos rochosos, cachoeiras e riachos. Um estudo recente sobre a filogenia molecular mostrou que T. miliaris é parafilética a T. taophora, e que T. taophora, T. megatympanum e T. saxatilis são monofiléticas com alto suporte (Sabbag et al. 2018). Esse estudo também encontrou diversos clados dentro de cada uma das espécies, especialmente em T. miliaris. Porém, não foi possível estudarem molecularmente as espécies do grupo petropolitana porque existe apenas uma amostra de DNA disponível para o grupo. No presente trabalho, estudamos aspectos genéticos e morfológicos das seis espécies do gênero a fim de investigar a diversidade molecular previamente encontrada, a parafilia de T. miliaris e as características morfológicas das espécies que coincidam com a diversidade genética conhecida. Encontramos que os clados conhecidos de T. miliaris são linhagens evoluindo separadamente e que os clados conhecidos de T. taophora fazem parte de uma linhagem única. Thoropa miliaris e T. taophor... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Thoropa Cope, 1865 (Anura: Cycloramphidae) is a frog genus endemic to theAtlantic forest domain and associated ecotones. It comprises six species (T. miliaris, T. petropolitana, T. taophora, T. lutzi, T. megatympanum and T. saxatilis), divided in two morphological groups: petropolitana group (T. petropolitana and T. lutzi) and miliaris group (T. miliaris, T. taophora, T. megatympanum and T. saxatilis). All the species reproduce and develop in freshwater wet rocks that can be found in rock outcrops, waterfalls and streams. A recent study on molecular phylogeny has shown that T. miliaris is paraphyletic in respect to T. taophora and that T. taophora, T. megatympanum and T. saxatilis are monophyletic with high support. This study also found many clades inside each of those species, especially within T. miliaris. Nevertheless, it was not possible to study molecular aspects of the petropolitana group because there is only one DNA sample available for the group. In this work, we studied genetic and morphological aspects of all six species of the genus in order to investigate the molecular diversity found previously, the paraphyly found for T. miliaris, and the species morphological characteristics that coincide with the known genetic diversity. We found that the known clades of T. miliaris are separately evolving lineages and that the clades of T. taophora are part of a whole lineage. Thoropa miliaris and T. taophora are reciprocally monophyletic. We also found that the diversifica... (Complete abstract click electronic access below) / Doutor

Species identifications have been historically difficult in the economically important spruce budworm (Choristoneura fumiferana) pest complex. Morphological, ecological, behavioural, and genetic characters have been studied to try to understand the taxonomy of this group, but diagnostic character states differ in frequency rather than being complete replacements between each species. I developed a morphology-based character system that focuses on forewing colour components (Chapter 2), as well as eight simple sequence repeats (SSRs, also referred to as microsatellite markers) (Chapter 3). I tested these along with a 470 bp region of COI mitochondrial DNA (mtDNA) (Chapter 2, 4) to determine their congruence with putative species that were identified by adaptive traits (larval host plant, length of larval diapause, larval and adult morphology, pheromone attraction, distribution). The morphometrics system was effective for identification of the five species tested, with only slight overlap between C. fumiferana and C. biennis. MtDNA distinguished C. fumiferana and C. pinus pinus, but the remaining species shared haplotypes. SSRs distinguished four species (C. fumiferana, C. pinus pinus, C. retiniana, C. lambertiana) but the remaining four species that were included in this survey (Chapter 4) remained mixed within two populations. There was evidence for hybridization between several species pairs. I also conducted a detailed study (Chapter 5) in Cypress Hills, an isolated remnant coniferous forest in western Canada, where identifying individuals from the Choristoneura fumiferana complex has been impossible due to the unusual ecogeographic characteristics of the area. I integrated data on behaviour, ecology, morphology, mtDNA, and SSRs, comparing Cypress Hills populations to those from other regions of North America to determine which species they resembled most. I delimited at least three populations, resembling C. fumiferana, C. occidentalis and C. lambertiana. Adult flight phenology, along with pheromone attraction, were identified as major isolating mechanisms between these populations. My studies highlighted the importance of integrative taxonomy for understanding species boundaries. Their patterns of differentiation suggest that spruce budworm species have recently diverged via natural selection in spite of some gene flow. Overall, this work is intended to contribute to more accurate identification of specimens and a better understanding of the evolutionary processes that drive speciation. / Systematics and Evolution

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Orientador: Fernando Fernandes Mendonça / Resumo: A atividade pesqueira desempenha um importante papel ambiental e socioeconômico, pois é fonte de renda e alimento para milhões de pessoas no mundo. Entretanto, falhas em sua gestão e lacunas nos dados biológicos para muitas espécies, tem resultado na sobreexplotação de seus estoques, o que pode impactar diversos ecossistemas marinhos. Neste contexto, os peixes-de-bico, grupo formado pelas famílias Xiphiidae e Istiophoridae, são considerados valiosos recursos pesqueiros, porém ainda não há consenso sobre o número e a validade das espécies da família Istiophoridae e também há incertezas sobre a avaliação atual de seus estoques. Sendo assim, o objetivo deste estudo é o de delimitar as espécies da família Istiophoridae e os estoques genéticos do agulhão-vela Istiophorus platypterus no Oceano Atlântico utilizando marcadores moleculares mitocondriais. Entre os resultados dos testes de delimitação de espécies, o número variou entre 6 e 12 táxons possíveis, dependendo do teste aplicado. Em relação a delimitação dos estoques genéticos de I. platypterus no Atlântico, assumindo-se apenas uma espécie no gênero Istiophorus, nossos resultados apontam a existência de alta diversidade genética, componde um único estoque genético no Atlântico (ΦST=0,01121, p=0,02438), apresentando um alto fluxo gênico. Porém, pela análise da rede de haplótipos e da inferência bayesiana observa-se a existência de diferentes linhagens mitocondriais simpátricas, que divergiram durante o Mioceno Superior e foram ... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Fishing activity plays an important environmental and socio-economic role, as it is a source of income and food for millions of people worldwide. Although, shortcomings in management and gaps in biological data for many species resulted in the overexploitation of their stocks, which may impact several marine ecosystems. In this context, billfishes, a group compounded by the Xiphiidae and Istiophoridae families, are considered valuable fish resources, but there is still no consensus on the number and validity of the species of Istiophoridae family and there are also uncertainties about the current fisheries stocks assessments. Thus, the main objectives of this study are to delimit the species of the Istiophoridae family and the genetic stocks of the sailfish, Istiophorus platypterus, in the Atlantic Ocean using mitochondrial molecular markers. Among the species delimitation tests results, the number ranged from 6 to 12 possible taxa depending on the test applied. In order to determine the genetic stock of I. platypterus in the Atlantic Ocean, assuming only one species in the genus Istiophorus, our results point to the existence of high genetic diversity, comprising a single genetic stock in the Atlantic (ΦST = 0.01121, p = 0.02438), presenting a high gene flow. However, the analysis of the network of haplotypes and Bayesian inference shows the existence of different sympatric mitochondrial lines, which diverged during the Upper Miocene and were re-approximated, interrupting th... (Complete abstract click electronic access below) / Doutor