Please read the Summary in the section 00front of this document / Thesis (PhD)--University of Pretoria, 2005. / Genetics / Unrestricted

Orientador: Prof. Dr. Charles Morphy Dias dos Santos / Dissertação (mestrado) - Universidade Federal do ABC, Programa de Pós-Graduação em Evolução e Diversidade, Santo André, 2018. / A família Athericidae (Diptera, Brachycera) foi criada e posicionada como o grupo irmão da família Tabanidae por Stuckenberg (1973), incluindo vários gêneros anteriormente associados a Rhagionidae. Ainda não há estudo formal que discuta as relações filogenéticas entre as espécies de Athericidae. Portanto, as relações entre os gêneros permanecem incertas. Além disso, a recente descoberta de espécies fósseis previamente atribuídas à família traz à tona a importância de um correto posicionamento filogenético desse grupo. O objetivo deste projeto foi contribuir para o conhecimento taxonômico e filogenético da família, especialmente para a região neotropical, e também resolver as questões de posicionamento das espécies fósseis em relação à Athericidae. Este estudo possui grande relevância no sentido de reconstruir as relações entre as espécies da família, bem como fornecer informações filogenéticas que podem ser úteis para entender mais profundamente a evolução do grupo. / The family Athericidae (Diptera, Brachycera) was erected and positioned as the sistergroup of the family Tabanidae by Stuckenberg (1973), including several genera previously associated with Rhagionidae. There is still no formal study discussing the phylogenetic relationships among the species of Athericidae. Hence, the position of most athericid genera remains unclear. Besides that, the recent discovery of fossil species previously assigned to the family brings to light the importance of a correct phylogenetic positioning of this group. The aim of this project was to contribute to the taxonomic and phylogenetic knowledge of the family, especially to the neotropical region, and also to solve the issues of positioning of the fossil species in relation to Athericidae. This study has great relevance in the reconstruction of the relationships among the species of the family, as well as to provide phylogenetic information that can be useful to understand more deeply the evolution of the group.

Thesis (Ph.D. (Zoology)) --University of Limpopo, 2021 / The present study was conducted to evaluate the morphological and molecular characterisation of species of Dactylogyrus parasitising Enteromius spp. from the Limpopo River System, South Africa. In addition, the study was intended to establish host-parasite associations from this system. A total of 95 host specimens were collected from eight localities between 2015 and 2016 within the Limpopo River System. Fish hosts were collected using gill nets, seine nets, fyke nets, and an electric shocker. From these, three host species were identified, E. afrohamiltoni, E. unitaeniatus, and E. trimaculatus where after monogenean parasites were retrieved from the gills using stereo microscopes. Morphometric analysis of the haptoral hard parts and male copulatory organs were studied for species identification, supported by nuclear ribosomal DNA sequences of the partial 18S rDNA region and the entire ITS-1 and partial 5.8S rDNA region, and the partial 28S rDNA region. Examination of E. afrohamiltoni revealed the presence of D. afrohamiltonii which is the first record of a monogenean parasite from this host. In addition, E. unitaeniatus revealed the presence of two species of Dactylogyrus: D. letabaensis and D. limpopoensis which are the first record of monogenean parasites from this host. The remaining Dactylogyrus species were retrieved from E. trimaculatus, namely, D. afrolongicornis, D. allolongionchus, and D. myersi. Enteromius trimaculatus harboured five of the species retrieved. The two species, D. afrolongicornis and D. allolongionchus were the most abundant from six of the eight localities studied, followed by D. myersi abundant in five of the eight localities. Dactylogyrus afrohamiltonii was considered a strict specialist, while the remaining species were considered to be intermediate specialists. Forty-one sequences of the partial 18S rDNA and the entire ITS-1 and partial 5.8S rDNA region and 19 sequences of the partial 28S rDNA region of Dactylogyrus species, including Pseudodactylogyrus anguillae were included to reconstruct the phylogenetic relationships. Based on this, molecular analysis of D. afrolongicornis from Enteromius hosts were recorded for the first time for the combined 18S rDNA and the entire ITS-1 and partial 5.8S rDNA region. The analysis revealed several groupings of Dactylogyrus species inferred largely from European cyprinoids and corresponded to host specificity. From the partial 28S rDNA, three clades were revealed linked to their biogeographical regions. Phylogenetic analysis from the 28S rDNA suggests that D. aspili from E. macrops and D. afrolongicornis are closely related. / National Research Foundation (NRF) and DST Innovation Scholarship and the Vlaamse Interuniversitaire RaadUniversity Development Corporation (VLIR-UOS)

Alligator mississippiensis is only distantly related to the other extant alligator (A. sinensis), with much closer relatives known from the geologic past of North America. While A. mississippiensis is well known from the early Pleistocene and later, no Alligator was known from the middle and late Pliocene until the discovery of Haile 7C and 7G late Pliocene (~2 Ma) sites from Florida. These specimens were analyzed using a diagnostic character matrix along with systematic analyses of the results. This research upholds A. mefferdi as a valid taxon, and the utility of the species in fossil identification is further established. The Haile material cannot be placed within either of the aforementioned taxa, and a new species description is planned in a later publication. Furthermore, the systematic analysis used in this research suggests that the line leading to A. sinensis diverged before the earliest known Alligator. An Eocene dispersal of the genus into Asia is plausible.

Bombyliidae é uma das maiores famílias de Diptera com mais de 4822 espécies descritas ao redor do mundo, divididas em 16 subfamílias e 18 tribos. A tribo Exoprosopini dividem-se em 11 gêneros, dos quais Exoprosopa e Ligyra tem distribuição cosmopolita. O gênero Ligyra Newman s.l. objeto deste estudo, possui 109 espécies, das quais 20 têm sido descritas no Novo Mundo. Uma revisão taxonômica das espécies neárticas e neotropicais de Ligyra é feita no presente estudo, incluindo redescrições e registros fotográficos das mesmas. Após a revisão taxonômica, quatro espécies foram sinonimizadas (L. fenestella syn. nov. e L. maracaensis syn. nov. são consideradas sinônimos júnior de Gen. nov. harpyia; L. guerinii syn. nov. foi considerado sinônimo júnior de Gen. nov. latreilli; L. klugii syn. nov. foi considerado sinônimo júnior de Gen. nov. proserpina e a subespécie Ligyra cerberus trifigurata foi considerada sinônimo júnior de Gen. nov. cerberus). Uma chave para identificação destas espécies, baseada em caracteres morfológicos diagnósticos, de fácil observação, também é apresentada. Além da revisão taxonômica uma análise cladística de Ligyra no Novo Mundo foi feita a fim de testar se essas espécies, que atualmente estão incluídas no gênero, pertencem, de fato, a este grupo ou se precisam ser realocadas em algum outro gênero de Exoprosopini ou ainda em um novo gênero. Para tal, neste estudo foi utilizada uma matriz de caracteres morfológicos disponível em literatura, que já vem sendo utilizada para inferir a filogenia dos Exoprosopini. A análise cladística contou com 92 táxons terminais e 207 caracteres morfológicos obtendo-se como resultado, após análise com algoritmos de novas tecnologias a partir do software TNT, 12 árvores mais parcimoniosas cujo consenso estrito possui L=3089, CI: 15 e RI: 49. Os resultados apontam que Ligyra s.l. forma um grupo monofilético composto pelos gêneros: Ligyra s. str. (spp. Australianas), Euligyra (spp. Afrotropicais) e Gênero novo (spp. do Novo Mundo). As espécies de Ligyra s.l. no Novo Mundo foram realocadas em um gênero novo suportado por uma sinapomorfia e quatro homoplasias. / Bombyliidae is one of the largest families of Diptera with more than 4800 species, known worldwide, divided in 16 subfamilies and 18 tribes. The tribe Exoprosopini is divided into 11 genera, of which Exoprosopa Macquart and Ligyra Newman has cosmopolitan distribution. The genus Ligyra s.l., main subject of this study, has 109 species, of which 20 were described to the New World. A taxonomic review of the Nearctic and Neotropical species of Ligyra is implemented in this study, including redescription and photographic records of them. After the taxonomic review, four species were synonymized (L. fenestella syn. nov.and L. maracaensis syn. nov. are considered junior synonym of Gen. nov. harpyia; L. guerinii syn. nov. is considered junior synonym of Gen. nov. latreilli; L. klugii syn. nov .is considered junior synonym of Gen. nov. proserpina and the subspecies Ligyra Cerberus trifigurata is considered junior synonym of Gen. nov. cerberus). An identification key for these species, based on morphological diagnostic characters, easily seen, is also presented. Besides the taxonomic revision a cladistics analysis of the New Worlds Ligyra is implemented in order to test whether these species, which are currently included in the genus, belong, in fact, to this group or if they need to be relocated at some other genus of Exoprosopini or even to a new genus. For this purpose, we used a matrix of morphological characters available in the literature, which is already being used to infer the phylogeny of Exoprosopini. The cladistic analysis included 92 terminal taxa and 207 morphological characters. After analysis with algorithms of new technologies from the software TNT, 12 more parsimonious trees, whose strict consensus has L = 3089, CI 15 and RI: 49, are obtained. The results show that Ligyra s.l. constitutes a monophyletic group composed by the following genera: Ligyra s. str. (Australian spp.), Euligyra (Afrotropical spp.) and New Genus (New World spp.). The species of Ligyra s.l. in the New World are relocated into a new genus, which monophyly is supported by one synapomorphy and four homoplasies.

A tribo Asphondyliini, pertencente à família Cecidomyiidae, conta com 521 espécies divididas em 44 gêneros com distribuição cosmopolita. Os Asphondyliini estão inseridos na subfamília Cecidomyiinae, que é a maior subfamília em número de espécies, 5100, e se encontra dividida em quatro supertribos: Brachineuridi, Stromatosematidi, Cecidomyiidi e Lasiopteridi. As larvas de Cecidomyiinae possuem hábito micetófago, predador e galhador, sendo que este último aparece nas supertribos Cecidomyiidi e Lasiopteridi. Os galhadores são os organismos indutores responsáveis por malformações de porções dos tecidos ou órgãos das plantas, conhecidas como galhas. A relação entre os insetos galhadores e suas plantas hospedeiras é de alta especificidade e devido a isso, para as espécies descritas, é possível identificá-las pelo seu tipo de galha induzida no hospedeiro. O gênero Bruggmanniella Tavares, 1909, possui 11 espécies com distribuição majoritária na região Neotropical (oito espécies) e representantes descritos para as regiões Neártica (uma espécie) e Oriental (duas espécies). Neste trabalho foi realizada a primeira análise cladística para compreensão da relação de parentesco entre as espécies de Bruggmanniela, a descrição de uma espécie nova do Estado de São Paulo, Brasil, além da atualização da chave de identificação das espécies de Bruggmanniella. Na análise cladística foram levantados 56 caracteres morfológicos para 26 táxons terminais. Entre esses, 15 pertencem ao grupo-externo e 11 ao interno. A análise utilizando busca heurística de pesos iguais resultou em uma única árvore mais parcimoniosa com comprimento igual a 148 passos (IC=0.443 e IR=0.565) e a de busca por pesagem implícita também gerou uma única árvore com 149 passos (IC=0.440 e IR=0.561). O gênero Bruggmanniella tem sua monofilia suportada principalmente pela ausência do espessamento da margem cefálica da pupa. B. byrsonimae ainda possue posicionamento incerto por falta de conhecimenro do estágio larval. As duas espécies orientais descritas originalmente em Bruggmanniella, B. actinodaphnes e B. cinnamomi, posicionaram-se no ramo do grupo-irmão Pseudasphondylia, ensejando a proposição de duas novas combinações: P. actinodaphnes comb. nov e P. cinnamomi comb. nov. Apresentamos ainda, uma discussão acerca da distribuição geográfica das espécies de Bruggmanniella e Pseudasphondylia e a ocupação dos hospedeiros. / The tribe Asphondyliini, belonging to the family Cecidomyiidae, has 521 species divided into 44 genera with cosmopolitan distribution. The Asphondyliini are included in the subfamily Cecidomyiinae, which is the largest subfamily in number of species, 5100, and is divided into four supertribes: Brachineuridi, Stromatosematidi, Cecidomyiidi and Lasiopteridi. The larvae of Cecidomyiinae have mycethophagous, predatory and galling habit, the latter appearing in the supertribes Cecidomyiidi and Lasiopteridi. Gallers are the inducing organisms responsible for malformations of portions of the tissues or organs of plants, known as gall. The relation between the galling insects and their host plants is of high specificity and due to this, for the described species, it is possible to identify them by their type of host-induced gall. Bruggmanniella Tavares, 1909 has 11 species with major distribution in the Neotropical region (eight species) and representatives described for the regions Neartica (one species) and Oriental (two species). In this work, the first cladistic analysis was carried out to understand the kinship relationship between the Bruggmanniela species, the description of a new species from São Paulo State, Brazil. Bruggmanniela species identification key was also updated. In the cladistic analysis, 56 morphological characters were collected for 26 terminal taxa. Of these, 15 belong to the external group and 11 to the internal group. The analysis using heuristic search of equal weights resulted in a single more parsimonious tree with length equal to 148 steps (IC = 0.443 and IR = 0.565) and the search for implicit weighing also generated a single tree with 149 steps (CI = 0.440 and IR = 0.561). The genus Bruggmanniella has its monophyly supported mainly by the absence of thickening of the cephalic margin of the pupa. B. byrsonimae still has uncertain position due to lack of larval stage. The two eastern species originally described in Bruggmanniella, B. actinodaphnes and B. cinnamomi, were placed in the branch of the sister-group Pseudasphondylia, indicating two new combinations: P. actinodaphnes comb. nov and P. cinnamomi comb. nov. We also argue the geographical distribution of Bruggmanniella and Pseudaphondylia species and the occupation of the hosts.

Os opiliões são um bom modelo para o estudo da biogeografia histórica, especialmente na Mata Atlântica, onde existe a maior diversidade de espécies do grupo no mundo. A presente tese foi dividida em três capítulos: o primeiro objetiva a delimitação de áreas de endemismo para a Mata Atlântica, usando a ocorrência de espécies de Gonyleptidae; o segundo objetiva encontrar um padrão geral de relação histórica entre essas áreas de endemismo que explique a diversificação no bioma, usando as filogenias de sete subfamílias de Gonyleptidae; o terceiro é a revisão sistemática da subfamília Hernandariinae. Foram delimitadas 12 áreas de endemismo para a Mata Atlântica, usando a ocorrência de 109 espécies. Foram usados os métodos numéricos PAE (Análise de Parcimônia de Endemicidade) e NDM, e desenvolvidos seis Critérios Combinados para a avaliação e delimitação das áreas. Para procurar por um padrão geral histórico de relação entre essas áreas, foram usados os métodos de biogeografia cladística para construção de cladogramas gerais de áreas. As 12 áreas de endemismo se relacionam historicamente formando três blocos principais na Mata Atlântica, com a separação do componente norte (Pernambuco e Bahia) inicialmente e posterior separação do componente central (Rio de Janeiro e São Paulo) do componente sul (sul de São Paulo, Paraná e Santa Catarina). São discutidos os principais eventos históricos geológicos, climáticos e biológicos que determinaram essas divisões e a diversificação da fauna de opiliões no bioma. A subfamília Hernandariinae, após a presente revisão, é composto por 23 espécies em 6 gêneros. Nova classificação é proposta baseada em uma análise cladística usando 67 caracteres morfológicos. Quatro novas combinações foram propostas: Hernandaria armatifrons, H. una, Acrogonyleptes granulatus e A. pectinifemur. Três revalidações de espécies são propostas: A. granulatus, A. pectinifemur e A. spinifrons. Oito espécies novas são propostas: quatro de Hernandaria, duas de Acrogonyleptes e duas de Pseudotrogulus. Seis sinonímias são propostas: Proweyhia e Metaxundarava = Hernandaria, Apembolephaenus calcaratus = H. armatifrons, Paraproweyhia = Acrogonyleptes, Paraproweyhia curitibae = A. exochus, e Melloleitaniana curitibae = A. spinifrons. Ariaeus é transferido para Gonyleptinae. / Harvestmen are a good model to historical biogeography studies, especially in Atlantic Rain Forest of Brazil, where harbors the greatest species diversity of the group in the world. This thesis was divided in three chapters: the first one aimed to delimit areas of endemism for Atlantic Forest, using the occurrence of species of Gonyleptidae; the second one aimed to search for a general pattern of historical relationships among areas of endemism that explain the diversification of bioma, using phylogenies of seven Gonyleptidae subfamilies; the third one reviewed the subfamily Hernandariinae. Twelve areas of endemism were delimited for Atlantic Forest, using the occurrence of 109 species. Numerical methods PAE (Parsimony Analysis of Endemicity) and NDM were employed. Six Combined Criteria for evaluation and delimitation of areas were proposed. Methods of Cladistic Biogeography was used for constructing general cladograms of areas, which represent the general historic pattern. The 12 areas of endemism historically relate among them, forming three main components in Atlantic Forest, with separation of a northern component (Pernambuco and Bahia) firstly and a second separation of central component (Rio de Janeiro and São Paulo) from a southern component (south of São Paulo, Paraná, and Santa Catarina). The main geological, climatical and biological events which determined those divisions and the diversification of harvestmen in the Atlantic Forest were discussed. The subfamily Hernandariinae, after this review, is composed by 23 species in 6 genera. A new classification is presented based on an cladistic analysis, using 67 morphological characters. Four new combinations are proposed: Hernandaria armatifrons, H. una, Acrogonyleptes granulatus, and A. pectinifemur. Three species are revalidated: A. granulatus, A. pectinifemur, and A. spinifrons. Eight new species are proposed: four of Hernandaria, two of Acrogonyleptes, and two of Pseudotrogulus. Six synonimies are proposed: Proweyhia and Metaxundarava = Hernandaria, Apembolephaenus calcaratus = H. armatifrons, Paraproweyhia = Acrogonyleptes, Paraproweyhia curitibae = A. exochus, and Melloleitaniana curitibae = A. spinifrons. Ariaeus is transferred to Gonyleptinae.

O gênero Mallodeta Butler, exclusivamente neotropical, contava, no início deste estudo, com seis espécies: M. clavata (Walker) (espécie-tipo), M. sortita (Walker), M. consors (Walker), M. sanguipuncta Druce, M. cubana Gaede e M. simplex Rothschild. Estas espécies, mais Phoenicoprocta parthenii (Fabricius), outrora também considerada integrante daquele gênero, foram estudadas quanto às suas relações filogenéticas. A hipótese de monofiletismo de Mallodeta não foi corroborada, sendo as espécies historicamente associadas ao gênero doravante consideradas pertencentes a três clados: (i) Mallodeta, composto unicamente por sua espécie-tipo; (ii) Rezia Kirby gen. reval., composto por R. sortita comb. nov., R. consors comb. nov. e R. sanguipuncta, além de R. cardinale (Hampson), R. erythrarchos (Walker) comb. nov., R. cruenta (Perty) comb. nov. e R. hanga (Herrich-Schäffer) comb. nov., previamente tratadas em Cosmosoma Hübner; (iii) Antilleana gen. nov., composto por A. parthenii comb. nov., A. jamaicensis (Schaus) comb. nov., A. capistrata (Fabricius) comb. nov. e A. carminata (Hampson) comb. nov., todas anteriormente alocadas em Phoenicoprocta Druce. Dentre as conclusões taxonômicas, M. simplex foi tratada como sin. nov. de M. clavata, Glaucopis (Erruca) deyrolii Walker, 1854 sin. nov. de Rezia sortita, Laemocharis ignicolor Ménétriés sin. nov. de Rezia erythrarchos e M. cubana sin. nov. de A. capistrata. Todas as espécies tratadas no presente estudo foram redescritas, ilustradas e tiveram sua distribuição geográfica elucidada. / At the beginning of this study the genus Mallodeta Butler, exclusively neotropical, comprised six species: M. clavata (Walker) (type species), M. sortita (Walker), M. consors (Walker), M. sanguipuncta Druce, M. cubana Gaede and M. simplex Rothschild. These species besides Phoenicoprocta parthenii (Fabricius), formerly considered part of Mallodeta, had their phylogenetic relationships elucidated. The monophyly of Mallodeta was not corroborated, and the species historicaly associated to it should be considered, from now on, belonging to three different clades: (i) Mallodeta, composed exclusively by its type species; (ii) Rezia Kirby rev. gen, comprising R. sortita n. comb., R. consors n. comb. and R. sanguipuncta, plus R. cardinale (Hampson), R. erythrarchos (Walker) n. comb., R. cruenta (Perty) n. comb. and R. hanga (Herrich-Schäffer) n. comb., previously treated in the genus Cosmosoma Hübner; (iii) Antilleana n. gen., comprised by A. parthenii n. comb., A. jamaicensis (Schaus) n. comb., A. capistrata (Fabricius) n. comb. and A. carminata (Hampson) n. comb., formerly treated in Phoenicoprocta Druce. Among taxonomic conclusions we discovered M. simplex to be a n. syn. of M. clavata, Glaucopis (Erruca) deyrolii Walker, 1854 n. syn of Rezia sortita, Laemocharis ignicolor Ménétriés n. syn of Rezia erythrarchos and M. cubana n. syn. of A. capistrata. All species studied were redescribed, illustrated and had their geographical distribution elucidated.

Crinoids are the most primitive living members of the Phylum Echinodermata. Though still present in reduced numbers today, crinoids were the dominant echinoderms from the Ordovician to the Permian. The crinoid body plan consists of three major regions, the column, the calyx, and the arms. Each region serves important functions in crinoids. The column raises the rest of the body into the water column for more efficient feeding. The calyx contains the visceral mass and mouth. Arms extend out from the top of the calyx to trap microorgansisms and suspended organic particles in the water column. A re-evaluation of these functional units is undertaken to understand the importance of various structures and to obtain discrete characters for use in a cladistic analysis. The relationship of crinoid crown groups has been an active area of research for the past couple of decades. With each proposed phylogenetic relationship, a new interpretation of thecal plate homology has been proposed. Here each study is re-examined in the light of new data. A review of functional morphology indicates a dual-reference system to be the most supported interpretation of plate homology. The two reference points in this system are the stem-cup and the cup-arm junctions, at the top and bottom of the calyx. The difference between a two-circlet and three-circlet crinoid is the presence or absence of the middle (basal) circlet. A new cladistic analysis is presented, with the topology of trees obtained giving support for the retention of Paleozoic crinoid stem and crown groups. Crinoids appear abruptly in the fossil record. Questions pertaining to origins and ancestral stock abound. A biogeography study is employed to look at the distribution of crinoids from the Early to Middle Ordovician. Locality information, combined with an understanding of the movement of major plates, paleoclimate data, an understanding of larval distribution, and a review of similar studies carried out on different taxa, gives insight into possible radiation and dispersal patterns of crinoids from the first half of the Ordovician. / text

I evaluate the methods of cladistic parsimony and maximum likelihood in phylogenetic systematics by their affinity to Popper‘s degree of corroboration. My work analyzes an important recent exchange between the proponents of the two methods. Until this exchange, only advocates of cladistic parsimony have claimed a basis for their method on epistemological grounds through corroboration. Advocates of maximum likelihood, on the other hand, have based the rational justification for their method largely on statistical grounds. In Part One I outline corroboration in terms of content, severity of test and explanatory power. In Part Two I introduce the two methods. In Part Three I analyze three important debates. The first involves the appropriate probability interpretation for phylogenetics. The second is about severity of test. The third concerns explanatory power. In Part Four I conclude that corroboration can decide none of these debates, and therefore cannot decide the debate between cladistic parsimony and maximum likelihood.