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.

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.

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.

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.

Les rongeurs caviomorphes constituent l’un des groupes de mammifères placentaires les plus diversifiés d’Amérique du Sud. Malgré la grande diversité actuelle et néogène du groupe, les premières phases de l’histoire évolutive des caviomorphes n’étaient documentées que par quelques localités à l’échelle de tout le continent sud-américain. Les recherches paléontologiques récentes menées en Amazonie péruvienne ont permis la découverte de 18 localités éocènes et oligocènes, livrant de nombreux restes dentaires de caviomorphes inédits. L’étude de ces fossiles a conduit à la description et à la comparaison de 52 taxons distincts, dont 11 nouveaux genres et 17 nouvelles espèces. Ce travail révèle une riche diversité alpha-taxonomique des caviomorphes en Amazonie péruvienne à la fin de l’Éocène moyen, mais surtout à l’Oligocène inférieur et à l’Oligocène supérieur, trois fenêtres temporelles jusqu’alors très peu documentées dans les régions de basses latitudes du continent sud-américain. Les localités étudiées de la fin de l’Éocène moyen livrent les plus anciens caviomorphes connus à ce jour. Dans ces localités, la faible diversité taxinomique, associée à une faible disparité morphologique, incluant des taxons caractérisés par des traits dentaires plésiomorphes, rappelant les formes hystricognathes sub-contemporaines de l’Ancien Monde. Cela suggère un intervalle de temps court entre l’arrivée en Amérique du Sud des hystricognathes pionniers et l’émergence des espèces étudiées. Les assemblages de caviomorphes des localités plus récentes montrent une disparité plus importante et livrent des représentants des éréthizontoïdes, octodontoïdes et chinchilloïdes. L’analyse approfondie du matériel d’étude et sa comparaison avec des spécimens provenant d’autres gisements sud-américains ont permis une meilleure compréhension de l’homologie et de l’évolution des structures dentaires chez les caviomorphes. Une analyse cladistique de grande ampleur, incluant un grand nombre de familles des quatre super-familles (i.e., Cavioidea, Erethizontoidea, Chinchilloidea et Octodontoidea) a été réalisée. Elle a permis pour la première fois la reconnaissance de groupes basaux des caviomorphes. Les régions de basses latitudes du continent sud-américain paraissent être le centre d’origine des caviomorphes et le lieu d’une première diversification basale du groupe à la fin de l’Éocène moyen. Les quatre super-familles émergeraient au cours de l’Éocène supérieur–Oligocène inférieur, illustrant ainsi une deuxième radiation majeure du groupe au cours du Paléogène. Durant cette période, les caviomorphes se seraient dispersés aux moyennes et hautes latitudes. L’origine géographique des super-familles reste quelque peu ambiguë, excepté pour les chinchilloïdes qui émergeraient dans les régions de basses latitudes. Nos résultats mettent également en évidence l’existence d’une troisième radiation autour de la limite Oligocène–Miocène. Cette troisième phase correspondrait à la diversification des chinchilloïdes, octodontoïdes, et éréthizontinés basaux et à l’émergence du groupe couronne des caviidés, des octodontoïdes et très probablement des chinchilloïdes. Ces trois événements de diversifications majeures au cours du Paléogène sont concomitants avec des évènements climatiques globaux et des périodes intenses de surrection andine. / Caviomorph rodents represent one of the most successful groups of placental mammals from South America. Despite their high modern and Neogene diversity, their early evolutionary history has long remained obscure. Recent paleontological investigations in Peruvian Amazonia allowed for the discovery of 18 Eocene and Oligocene localities yielding many new fossils of caviomorphs (mainly isolated teeth). Fifty-two taxa, including 11 new genera and 17 new species, are described here. This study reveals a rich alpha-taxonomic diversity of caviomorphs in Peruvian Amazonia during the late Middle Eocene, Early Oligocene and Late Oligocene. These three periods were until now poorly documented in the low-latitudes of South America. The late Middle Eocene localities yield the earliest representatives of the group. In these localities, the low taxonomical diversity, associated with a low morphological disparity including taxa that harbor very primitive dental features, reminiscent to those observed in coeval Old World hystricognaths, suggest that a short time range of caviomorph evolutionary history had undergone in South America prior the emergence of these rodents. The most recent caviomorph assemblages show a higher disparity and yield representatives of erethizontoids, octodontoids and chinchilloids. The exhaustive analysis of the material and its comparison with specimens from other South American localities further our understanding regarding the homology and the evolution of dentary structures in caviomorphs. A cladistic assessment with a comprehensive taxonomic sampling including most families of the four superfamilies (i.e., Cavioidea, Erethizontoidea, Chinchilloidea, and Octodontoidea) was undertaken. For the first time, several stem Caviomorpha were recognized. Low latitudes of South America are thus viewed as the cradle and the first diversity hotspot of early caviomorphs. A second radiation would have occurred during the Late Eocene–Early Oligocene and would correspond to the emergence of the four superfamilies. At this time, caviomorphs would disperse towards the middle and high latitudes. The geographic origin of modern superfamilies remains somewhat ambiguous, except for chinchilloids which would emerge in low-latitude regions. A third radiation would have also occurred, around the Oligocene–Miocene transition, corresponding to the more recent diversification of stem Chinchilloidea, Octodontoidea, Erethizontoidea and the emergence of crown Erethizontinae, Caviidae, Octodontoidea, and probably Chinchilloidea. It is noteworthy that these three Paleogene diversification phases were contemporaneous with global climatic events and intense Andean uplift events.

The eight southern African King Cricket genera, namely Bochus, Borborothis, Henicus, Libanasa, Libanasidus, Nasidius, Onosandridus, and Onosandrus are redescribed from type and museum material and a key to the genera is provided. Additionally, the status of Libanasidus impicta is investigated and species characteristics confirmed. A key to the two Libanasidus species is also provided. No morphological support for these eight southern African anostostomatid genera was attained with cladistic analysis, despite the incorporation of taxonomically important characters. High levels of homoplasy and possible incorrect species placement, resulting in character ambiguity within genera, renders many of the diagnostic characters of this group ineffective for resolving generic relationships. Genetic data based on the large ribosomal subunit (16S) did provide phylogenetic resolution between six of the genera with good bootstrap support. This confirmed speculation by previous authors as to the ancestral nature of Bochus and Borborothis to other genera within the Anostostomatini tribe, as well as the placement of Libanasa within a separate tribe, the Lutosini. The recent merge of the genus Platysiagon with Libanasa is also provisionally supported. Close association was obtained between Libanasidus and Nasidius with Onosandrus being more related to Bochus and Borborothis, supported by the lack of sexual dimorphism in Onosandrus and Borborothis. The phylogenetic position of the genera Henicus and Onosandridus remains unresolved. It is suggested that the designation of the eight anostostomatid genera in southern Africa are valid, but that species placement within these genera need to be revised to resolve character conflict. Focusing on the genetic and morphometric structuring within the famous Parktown Prawn, Libanasidus vittatus from southern Africa consistently suggests two main population assemblages. These correspond to a large North-South ranging population including individuals west of the prominent escarpment, and a smaller population including individuals from the eastern side of the escarpment. COI sequence data recovers two clades representing these two populations with good bootstrap support in likelihood, parsimony, Bayesian and distance analyses. Genetic divergence between the two clades averaged 3.3%, while population parameters estimated using maximum likelihood methods show low migration rates corresponding to less that one female migration per generation. A priori morphometric analyses including PCA&clustering methods show no biologically meaningful variation, suggesting that the two clades recovered represent cryptic sibling species. Inferring a molecular clock of 2% divergence per million years used for sister taxa, signifies isolation of the eastern population at 1.65 mya. A posteriori morphometric analyses confirmed the genetic results, based on 11 size-related measurements. This study provides a starting point for further work on the taxonomy, behaviour and ecology of these fascinating insects. Cytogenetics, multiple genetic loci and geometric morphometrics will provide useful insight into the taxonomic status of the 51 anostostomatid species in southern Africa and is promoted for further studies. / Dissertation (MSc Entomology)--University of Pretoria, 2006. / Zoology and Entomology / unrestricted

Thesis (MSc)--University of Stellenbosch, 2006. / ENGLISH ABSTRACT: Erica is a genus of about 860 species world wide, with 700 of these found in South Africa’s southwestern and southern Cape, making it by far the most speciose genus in the Cape Floristic Region. This poses a particular challenge in the construction of a molecular phylogeny of the genus. The choice of suitably variable gene regions is a crucial decision on which the successful phylogenetic reconstruction of this important genus is critically dependent. The aim of this project was therefore to determine which DNA regions, both chloroplast and nuclear, would be sufficiently variable to give adequate informative characters that may be useful at the species level phylogenetic reconstruction. A subset of 30 species, representing the range of morphological diversity and pollinator preference within Erica, was selected for study. For each of these species the variability in eight chloroplast regions (trnL-F, matK, trnS-G, rps12- rpl20, psbAtrnH, trnC-D, rps4-trnT and trnT-L) and the nuclear ITS region was investigated. The psbA-trnH, trnC-D, rps4-trnT and trnT-L chloroplast regions were found to be problematic to amplify and to possess too few Parsimony Informative Characters to be of use in phylogenetic reconstruction. Four of the chloroplast regions, trnS-G, trnL-F, matK and rpS12-rpL20 and the nuclear ITS region could be amplified and sequenced with success. The ITS region was found to be reasonably variable, with the chloroplast genes showing less variability. The DNA extraction method employed showed itself to be of critical importance in the success of the study. Two DNA extraction protocols, both modified from the original Doyle and Doyle (1987) method, were tested. The one included double the amount of β-mercaptoethanol and Polyvinylpyrrolidone (PVP) and the other included an extended phenol: chloroform: isoamylalcohol step. These variables, together with the effectiveness of these methods on fresh vs. silica dried plant samples, were investigated to determine which of the two would yield high quantities and qualities of DNA and result in the best method for the extraction of DNA from Erica species. / AFRIKAANSE OPSOMMING: Erica is ‘n genus van omtrent 860 spesies wêreldwyd, met 700 van hierdie spesies aanwesig in die suidwes en suid Kaap van Suid Afrika, wat dit by verre die mees spesieryke genus in die Kaapse Floristiese Streek maak. Dit stel ’n besondere uitdaging in die konstruksie van ’n molekulêre filogenie van die genus. Die keuse van geskikte variërende geen-areas is ‘n belangrike besluit waarvan die suksesvolle filogenetiese rekonstruksie van hierdie belangrike genus krities afhanklik sal wees. Die doel van hierdie projek was dus om te bepaal watter DNS areas, buide chloroplas en kern, genoegsaam varieer om voldoende informatiewe kenmerke te lewer om bruikbaar te wees in ’n spesie-vlak molekulêre rekonstruksie. ’n Subgroep van 30 spesies, wat die reeks van morfologiese diversiteit en bestuiwer voorkeure in Erica verteenwoordig, is dus vir die studie geselekteer. Vir elk van hierdie spesies is die variasie in agt chloroplast areas (trnL-F, matK, trnS-G, rps12- rpl20, psbA-trnH, trnC-D, rps4-trnT en trnT-L) en die kern ITS area ondersoek. Dit was problematies om die psbA-trnH, trnC-D, rps4-trnT en trnT-L chloroplast areas te amplifiseer, en daar is gevind dat hulle te min Parsimonie Informatiewe Kenmerke besig om bruikbaar te wees in filogenetiese rekonstruksie. Vier van die chloroplas areas, trnS-G, trnL-F, matK en rpS12-rpL20 en die kern ITS kon suksesvol geamplifiseer word en die basisvolgordes kon suksesvol bepaal word. Daar is gevind dat die ITS area redelik variërend is, terwyl chloroplas areas minder variasie getoon het. Die DNS ekstraksie metode wat gebruik is het die kritiese belang van die ekstraksie metode in die sukses van die studie bewys. Twee DNS protokolle, beide gemodifiseer van die oorspronklike Doyle en Doyle (1987) metode, is getoets. Die een het dubbel die hoeveelheid β-mercaptoetanol en Polyvinylpyrrolidone (PVP) bevat, en die het ’n uitgebruide fenol: chloroform: isoamylalkohol stap ingesluit. Hierdie veranderlikes, saam met die effektiwiteit van hierdie metodes op vars teenoor silika-gedroogde plant monsters, is ondersoek om vas te stel watter een van die twee die hoogste kwaliteit en kwantiteit DNS sou lewer en dus sal lei tot die beste DNS ekstraksie metode vir Erica spesies.

Molecular phylogenetic analyses of subtribe Senecioninae, based on combining sequenced ITS and trnL-F fragments from specimens collected in the field with sequences collected from GenBank, suggest the subtribe is monophyletic, as is Senecio s.str. (including Robinsonia), and suggest an expanded monophyletic section Senecio. Many Senecio species should be removed from the genus, as they are only distantly related to it, emphasising the para- or polyphyletic nature of Senecio as it is currently circumscribed. Area optimisation suggests southern Africa as a possible geographical origin for the genus and section. Harvey’s (1865) sectional classification of South African Senecio species (the only attempt to date to impose infrageneric groupings on these taxa), was tested for monophyly which, however, was not seen in the sections tested. A number of southern African species from Harvey’s sections are suggested for inclusion in an expanded section Senecio. A clade suggested as basal to sect. Senecio, consisting of Senecio engleranus and Senecio flavus, was found to be only distantly related to the section. Resolution of the two species within the clade was not evident; a comparative study was therefore made employing RAPDs, morphometrics and breeding experiments. The two proved to be distinct entities, both genetically and morphologically, although they remain interfertile, suggesting that intrinsic postzygotic barriers between them are weak, and that hybridisation – not found in the wild - is mainly prevented by prezygotic barriers. F1 hybrids created between the two were seen to have intermediate morphologies and RAPD profiles. A single F1 individual self-pollinated to produce a vigorous F2 generation, allowing preliminary surveys of pollen number, pollen fertility and pappus type. Pappus type is seen to be under the control of allelic variations in a single major gene, while pollen numbers and pollen fertility are seen to be under more complex genetic control.

The advent of new technology enhance the speed and reduce the cost for sequencing biological data. Making biological sense of this genomic data is a big challenge to the algorithm design as well as the high performance computing society. There are many problems in Bioinformatics, such as how new functional genes arise, why genes are organized into chromosomes, how species are connected through the evolutionary tree of life, or why arrangements are subject to change. Phylogenetic analyses have become essential to research on the evolutionary tree of life. It can help us to track the history of species and the relationship between different genes or genomes through millions of years. One of the fundamentals for phylogenetic construction is the computation of distances between genomes. Since there are much more complicated combinatoric patterns in rearrangement events, the distance computation is still a hot topic as much belongs to mathematics as to biology. For the distance computation with input of two genomes containing unequal gene contents (with insertions/deletions and duplications) the problem is especially hard. In this thesis, we will discuss about our contributions to the distance estimation for unequal gene order data. The problem of finding the median of three genomes is the key process in building the most parsimonious phylogenetic trees from genome rearrangement data. For genomes with unequal contents, to the best of our knowledge, there is no algorithm that can help to find the median. In this thesis, we make our contributions to the median computation in two aspects. 1) Algorithm engineering aspect, we harness the power of streaming graph analytics methods to implement an exact DCJ median algorithm which run as fast as the heuristic algorithm and can help construct a better phylogenetic tree. 2) Algorithmic aspect, we theoretically formulate the problem of finding median with input of genomes having unequal gene content, which leads to the design and implementation of an efficient Lin-Kernighan heuristic based median algorithm. Inferring phylogenies (evolutionary history) of a set of given species is the ultimate goal when the distance and median model are chosen. For more than a decade, biologists and computer scientists have studied how to infer phylogenies by the measurement of genome rearrangement events using gene order data. While evolution is not an inherently parsimonious process, maximum parsimony (MP) phylogenetic analysis has been supported by widely applied to the phylogeny inference to study the evolutionary patterns of genome rearrangements. There are generally two problems with the MP phylogenetic arose by genome rearrangement: One is, given a set of modern genomes, how to compute the topologies of the according phylogenetic tree; Another is, given the topology of a model tree, how to infer the gene orders of the ancestor species. To assemble a MP phylogenetic tree constructor, there are multiple NP hard problems involved, unfortunately, they organized as one problem on top of other problems. Which means, to solve a NP hard problem, we need to solve multiple NP hard sub-problems. For phylogenetic tree construction with the input of unequal content genomes, there are three layers of NP hard problems. In this thesis, we will mainly discuss about our contributions to the design and implementation of the software package DCJUC (Phylogeny Inference using DCJ model to cope with Unequal Content Genomes), that can help to achieve both of these two goals. Aside from the biological problems, another issue we need to concern is about the use of the power of parallel computing to assist accelerating algorithms to handle huge data sets, such as the high resolution gene order data. For one thing, all of the method to tackle with phylogenetic problems are based on branch and bound algorithms, which are quite irregular and unfriendly to parallel computing. To parallelize these algorithms, we need to properly enhance the efficiency for localized memory access and load balance methods to make sure that each thread can put their potentials into full play. For the other, there is a revolution taking place in computing with the availability of commodity graphical processors such as Nvidia GPU and with many-core CPUs such as Cray-XMT, or Intel Xeon Phi Coprocessor with 60 cores. These architectures provide a new way for us to achieve high performance at much lower cost. However, code running on these machines are not so easily programmed, and scientific computing is hard to tune well on them. We try to explore the potentials of these architectures to help us accelerate branch and bound based phylogenetic algorithms.

Orientador: Maria do Carmo Estanislau do Amaral / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-10T06:25:59Z (GMT). No. of bitstreams: 1 Koehler_Samantha_D.pdf: 6443365 bytes, checksum: 6a01c884fb24c1fbf015cf1b2ab4e212 (MD5) Previous issue date: 2007 / Resumo: Não informado / Abstract: Not informed. / Doutorado / Biologia Vegetal / Mestre em Biologia Vegetal