A delimitação de espécies é um aspecto de fundamental importância dentro da Biologia Evolutiva, bem como para a conservação da biodiversidade. No entanto, delimitar espécies com base em morfologia é extremamente complicado, especialmente em grupos que tiveram uma radiação recente e que apresentam pouca descontinuidade morfológica entre os táxons, como a tribo Andropogoneae (Poaceae). A presente tese utiliza sequências de DNA, como genes nucleares de cópia-única (low-copy nuclear loci) e sequenciamento completo do plastoma, para resolver a circunscrição de complexos de espécies em Andropogoneae, particularmente dos gêneros Saccharum e Eriochrysis, bem como para investigar o posicionamento filogenético dos mesmos em relação aos demais gêneros da tribo. Aspectos filogenéticos, taxonômicos e nomenclaturais foram investigados. Do ponto de vista nomenclatural, foi possível esclarecer que Andropogoneae Dumortier é o nome correto para a tribo, e não Sacchareae Martinov, como recentemente sugerido por diversos autores. As análises filogenéticas realizadas corroboram a hipótese de uma diversificação inicial rápida em Andropogoneae e a não monofilia da subtribo Saccharinae. A origem alopoliploide do gênero Saccharum foi demonstrada a partir de evidências de genes nucleares. Saccharum s.l. é polifilético e Tripidium deve ser reconhecido como um gênero distinto. As análises filogenéticas também foram capazes de resolver a circunscrição interna de Saccharum s.l., confirmando a ocorrência de três espécies nativas na América do Sul: S. angustifolium, S. asperum e S. villosum. A ocorrência de híbridos naturais entre S. villosum e S. angustifolium foi documentada. As análises filogenéticas de Eriochrysis confirmaram a monofilia do gênero e resolveram a circunscrição de suas espécies: E. villosa é um táxon distinto de E. cayennensis, bem como E. laxa é uma espécie distinta de E. warmingiana. Híbridos naturais entre E. laxa e E. villosa também foram documentados. Eriochrysis villosa é citada pela primeira vez para o Uruguai e E. laxa para o estado do Rio Grande do Sul. A presente tese demonstrou a eficiência dos genes nucleares de cópia única na delimitação de espécies e gêneros da tribo Andropogoneae, mesmo na presença de poliploidia, evolução reticulada e radiação recente. O sequenciamento completo do plastoma também se mostrou uma ferramenta extremamente promissora para inferências filogenéticas em Andropogoneae. / Species delimitation is a vital issue concerning evolutionary biology and conservation of biodiversity. However, delimiting species based on morphology is a difficult task especially in plant groups with an evolutionary history involving rapid radiation and little morphological discontinuity between taxa, as the tribe Andropogoneae (Poaceae). The present thesis uses DNA sequences, such as low-copy nuclear genes and complete plastome sequencing, to resolve the taxonomic circumscriptions of species complexes in Andropogoneae, particularly from genera Saccharum and Eriochrysis, and to investigate their phylogenetic affinities to other genera of the tribe. Phylogenetic, taxonomic, and nomenclatural aspects were investigated. We clarified that Andropogoneae Dumortier is the correct name for the tribe, rather than Sacchareae Martinov, as recently suggested by several authors. The present phylogenetic analyses support the hypothesis of an initial rapid diversification in Andropogoneae and the non-monophyly of subtribe Saccharinae. The allopolyploid origin of Saccharum was demonstrated using evidence from nuclear genes. Saccharum s.l. is polyphyletic and Tripidium should be recognized as a distinct genus. The phylogenetic analyses were also able to define the circumscriptions of the species of Saccharum s.l., confirming the occurrence of three native species in South America: S. angustifolium, S. asperum and S. villosum. The occurrence of natural hybrids between S. villosum and S. angustifolium was documented. The phylogenetic analyses of Eriochrysis confirmed the monophyly of the genus and resolved the circumscriptions of its species: E. villosa is distinct from E. cayennensis, and E. laxa is distinct from E. warmingiana. Natural hybrids between E. laxa and E. villosa were also documented. Eriochrysis villosa is reported here for the first time for Uruguay and E. laxa for the State of Rio Grande do Sul. The present thesis has demonstrated the efficiency of low-copy nuclear genes in the delimitation of species and genera from tribe Andropogoneae, even in presence of polyploidy, reticulate evolution and recent radiation. The complete plastome sequencing is also a promising tool for phylogenetic inferences in Andropogoneae.

A delimitação de espécies é um aspecto de fundamental importância dentro da Biologia Evolutiva, bem como para a conservação da biodiversidade. No entanto, delimitar espécies com base em morfologia é extremamente complicado, especialmente em grupos que tiveram uma radiação recente e que apresentam pouca descontinuidade morfológica entre os táxons, como a tribo Andropogoneae (Poaceae). A presente tese utiliza sequências de DNA, como genes nucleares de cópia-única (low-copy nuclear loci) e sequenciamento completo do plastoma, para resolver a circunscrição de complexos de espécies em Andropogoneae, particularmente dos gêneros Saccharum e Eriochrysis, bem como para investigar o posicionamento filogenético dos mesmos em relação aos demais gêneros da tribo. Aspectos filogenéticos, taxonômicos e nomenclaturais foram investigados. Do ponto de vista nomenclatural, foi possível esclarecer que Andropogoneae Dumortier é o nome correto para a tribo, e não Sacchareae Martinov, como recentemente sugerido por diversos autores. As análises filogenéticas realizadas corroboram a hipótese de uma diversificação inicial rápida em Andropogoneae e a não monofilia da subtribo Saccharinae. A origem alopoliploide do gênero Saccharum foi demonstrada a partir de evidências de genes nucleares. Saccharum s.l. é polifilético e Tripidium deve ser reconhecido como um gênero distinto. As análises filogenéticas também foram capazes de resolver a circunscrição interna de Saccharum s.l., confirmando a ocorrência de três espécies nativas na América do Sul: S. angustifolium, S. asperum e S. villosum. A ocorrência de híbridos naturais entre S. villosum e S. angustifolium foi documentada. As análises filogenéticas de Eriochrysis confirmaram a monofilia do gênero e resolveram a circunscrição de suas espécies: E. villosa é um táxon distinto de E. cayennensis, bem como E. laxa é uma espécie distinta de E. warmingiana. Híbridos naturais entre E. laxa e E. villosa também foram documentados. Eriochrysis villosa é citada pela primeira vez para o Uruguai e E. laxa para o estado do Rio Grande do Sul. A presente tese demonstrou a eficiência dos genes nucleares de cópia única na delimitação de espécies e gêneros da tribo Andropogoneae, mesmo na presença de poliploidia, evolução reticulada e radiação recente. O sequenciamento completo do plastoma também se mostrou uma ferramenta extremamente promissora para inferências filogenéticas em Andropogoneae. / Species delimitation is a vital issue concerning evolutionary biology and conservation of biodiversity. However, delimiting species based on morphology is a difficult task especially in plant groups with an evolutionary history involving rapid radiation and little morphological discontinuity between taxa, as the tribe Andropogoneae (Poaceae). The present thesis uses DNA sequences, such as low-copy nuclear genes and complete plastome sequencing, to resolve the taxonomic circumscriptions of species complexes in Andropogoneae, particularly from genera Saccharum and Eriochrysis, and to investigate their phylogenetic affinities to other genera of the tribe. Phylogenetic, taxonomic, and nomenclatural aspects were investigated. We clarified that Andropogoneae Dumortier is the correct name for the tribe, rather than Sacchareae Martinov, as recently suggested by several authors. The present phylogenetic analyses support the hypothesis of an initial rapid diversification in Andropogoneae and the non-monophyly of subtribe Saccharinae. The allopolyploid origin of Saccharum was demonstrated using evidence from nuclear genes. Saccharum s.l. is polyphyletic and Tripidium should be recognized as a distinct genus. The phylogenetic analyses were also able to define the circumscriptions of the species of Saccharum s.l., confirming the occurrence of three native species in South America: S. angustifolium, S. asperum and S. villosum. The occurrence of natural hybrids between S. villosum and S. angustifolium was documented. The phylogenetic analyses of Eriochrysis confirmed the monophyly of the genus and resolved the circumscriptions of its species: E. villosa is distinct from E. cayennensis, and E. laxa is distinct from E. warmingiana. Natural hybrids between E. laxa and E. villosa were also documented. Eriochrysis villosa is reported here for the first time for Uruguay and E. laxa for the State of Rio Grande do Sul. The present thesis has demonstrated the efficiency of low-copy nuclear genes in the delimitation of species and genera from tribe Andropogoneae, even in presence of polyploidy, reticulate evolution and recent radiation. The complete plastome sequencing is also a promising tool for phylogenetic inferences in Andropogoneae.

A delimitação de espécies é um aspecto de fundamental importância dentro da Biologia Evolutiva, bem como para a conservação da biodiversidade. No entanto, delimitar espécies com base em morfologia é extremamente complicado, especialmente em grupos que tiveram uma radiação recente e que apresentam pouca descontinuidade morfológica entre os táxons, como a tribo Andropogoneae (Poaceae). A presente tese utiliza sequências de DNA, como genes nucleares de cópia-única (low-copy nuclear loci) e sequenciamento completo do plastoma, para resolver a circunscrição de complexos de espécies em Andropogoneae, particularmente dos gêneros Saccharum e Eriochrysis, bem como para investigar o posicionamento filogenético dos mesmos em relação aos demais gêneros da tribo. Aspectos filogenéticos, taxonômicos e nomenclaturais foram investigados. Do ponto de vista nomenclatural, foi possível esclarecer que Andropogoneae Dumortier é o nome correto para a tribo, e não Sacchareae Martinov, como recentemente sugerido por diversos autores. As análises filogenéticas realizadas corroboram a hipótese de uma diversificação inicial rápida em Andropogoneae e a não monofilia da subtribo Saccharinae. A origem alopoliploide do gênero Saccharum foi demonstrada a partir de evidências de genes nucleares. Saccharum s.l. é polifilético e Tripidium deve ser reconhecido como um gênero distinto. As análises filogenéticas também foram capazes de resolver a circunscrição interna de Saccharum s.l., confirmando a ocorrência de três espécies nativas na América do Sul: S. angustifolium, S. asperum e S. villosum. A ocorrência de híbridos naturais entre S. villosum e S. angustifolium foi documentada. As análises filogenéticas de Eriochrysis confirmaram a monofilia do gênero e resolveram a circunscrição de suas espécies: E. villosa é um táxon distinto de E. cayennensis, bem como E. laxa é uma espécie distinta de E. warmingiana. Híbridos naturais entre E. laxa e E. villosa também foram documentados. Eriochrysis villosa é citada pela primeira vez para o Uruguai e E. laxa para o estado do Rio Grande do Sul. A presente tese demonstrou a eficiência dos genes nucleares de cópia única na delimitação de espécies e gêneros da tribo Andropogoneae, mesmo na presença de poliploidia, evolução reticulada e radiação recente. O sequenciamento completo do plastoma também se mostrou uma ferramenta extremamente promissora para inferências filogenéticas em Andropogoneae. / Species delimitation is a vital issue concerning evolutionary biology and conservation of biodiversity. However, delimiting species based on morphology is a difficult task especially in plant groups with an evolutionary history involving rapid radiation and little morphological discontinuity between taxa, as the tribe Andropogoneae (Poaceae). The present thesis uses DNA sequences, such as low-copy nuclear genes and complete plastome sequencing, to resolve the taxonomic circumscriptions of species complexes in Andropogoneae, particularly from genera Saccharum and Eriochrysis, and to investigate their phylogenetic affinities to other genera of the tribe. Phylogenetic, taxonomic, and nomenclatural aspects were investigated. We clarified that Andropogoneae Dumortier is the correct name for the tribe, rather than Sacchareae Martinov, as recently suggested by several authors. The present phylogenetic analyses support the hypothesis of an initial rapid diversification in Andropogoneae and the non-monophyly of subtribe Saccharinae. The allopolyploid origin of Saccharum was demonstrated using evidence from nuclear genes. Saccharum s.l. is polyphyletic and Tripidium should be recognized as a distinct genus. The phylogenetic analyses were also able to define the circumscriptions of the species of Saccharum s.l., confirming the occurrence of three native species in South America: S. angustifolium, S. asperum and S. villosum. The occurrence of natural hybrids between S. villosum and S. angustifolium was documented. The phylogenetic analyses of Eriochrysis confirmed the monophyly of the genus and resolved the circumscriptions of its species: E. villosa is distinct from E. cayennensis, and E. laxa is distinct from E. warmingiana. Natural hybrids between E. laxa and E. villosa were also documented. Eriochrysis villosa is reported here for the first time for Uruguay and E. laxa for the State of Rio Grande do Sul. The present thesis has demonstrated the efficiency of low-copy nuclear genes in the delimitation of species and genera from tribe Andropogoneae, even in presence of polyploidy, reticulate evolution and recent radiation. The complete plastome sequencing is also a promising tool for phylogenetic inferences in Andropogoneae.

Thesis (PhD)--Stellenbosch University, 2012. / ENGLISH ABSTRACT: Potato virus Y (PVY) is responsible for considerable yield losses in the South African potato industry. The incidence of this virus has greatly increased over the past 20 years. In previous studies nonrecombinant strains of PVY, PVY N and PVY O, were detected in South African potatoes. In a recent study the occurrence of non-recombinant strains of PVY in South African potatoes was shown to have decreased while infection by more virulent recombinant strains, PVY NTN and PVY N-W, had increased dramatically. Infection of potato plants with PVY may cause stunted growth and mosaic or necrotic leaf symptoms which in turn can lead to a significant reduction in yield. Highly virulent recombinant PVY isolates as well as some of the non-recombinant strains may cause potato tuber necrotic ringspot disease (PTNRD) which may result in losses of 10% to total crop failure. For this reason investigation of infection by local recombinant isolates on local cultivars was important. To this end a representative number of isolates were selected for whole genome sequencing based on the relative occurrence of the various isolates in South Africa. A number of these sequenced isolates were subsequently used to infect local cultivars of potato in order to investigate the influence of genetic variation within the viral genome on symptom expression. In this study 27 South African isolates of PVY were sequenced through overlapping RT-PCR fragments. Seven of these isolates, six PVY NTN and one PVY N-W, were used to mechanically infect four local cultivars of potatoes under greenhouse conditions. The infected plants were monitored to establish the rate of systemic spread using a highly sensitive qRT-PCR and resulting tubers were visually screened for PTNRD. Highly variable recombinant isolates appear to be less virulent than the more conserved recombinant isolates possibly indicating molecular determinants for pathogenicity. For this reason the amino acid sequences of the South African isolates were compared to those of international isolates and scrutinized for variation and substitutions. Some South African isolates displayed amino acid substitutions unique to the specific isolate, making them unlike those found internationally. Substitution rates throughout the amino acid sequences differed greatly, with some isolates displaying hardly any changes whilst others varied a great deal from overseas isolates. Certain regions, many of which had specific functions, were more conserved than others. This study further investigated the recombination events within the PVY genome using reticulate phylogenetic analysis, molecular dating and network construction techniques. Unlike existing approaches, the one described in this study neither assumes an underlying strictly bifurcating species tree nor assumes prior knowledge of processes underlying deviations between individual gene trees. Through the use of the resulting robust time calibrated phylogeny, the patterns of diversification and recombination in PVY may be placed in the historical context of human cultivation of potatoes. Through the use of these techniques the study aimed to test whether diversification of the major strains of PVY and recombination between them occurred within the time frame of the domestication and modern cultivation of potatoes. From these analyses it can be deduced that recombinant strains of PVY were imported into South Africa. / AFRIKAANSE OPSOMMING: Aartappel virus Y (PVY) is verantwoordelik vir aansienlike opbrengs verliese in die Suid-Afrikaanse aartappelbedryf. Die voorkoms van die virus het grootliks toegeneem oor die afgelope 20 jaar. In vorige studies is nie-rekombinante rasse van PVY, PVY N en PVY O, gedokumenteer in Suid-Afrikaanse aartappels. 'n Onlangse studie het gevind dat die voorkoms van nie-rekombinante rasse van PVY in Suid- Afrikaanse aartappels aansienlik gedaal het terwyl infeksie deur virulente rekombinante rasse, PVY NTN en PVY N-W, dramaties toegeneem het. Infeksie van aartappelplante met PVY kan vertraagde groei en mosaïek- of nekrotiese blaarsimptome veroorsaak wat kan lei tot aansienlike vermindering in opbrengs. Hoogs virulente rekombinante PVY isolate, sowel as sommige nie-rekombinante rasse, kan aartappel nekrotiese ring simptome (PTNRD) veroorsaak wat verliese van 10% tot totale misoes tot gevolg kan hê. Om hierdie rede was die ondersoek van infeksie deur plaaslike rekombinante isolate op plaaslike kultivare belangrik. Vir hierdie doel is 'n verteenwoordigende aantal isolate gekies, gebaseer op die relatiewe voorkoms daarvan in Suid-Afrika, vir heelgenoom-volgordebepaling. Van die isolate is vervolgens gebruik om plaaslike kultivare te besmet ten einde die invloed van genetiese variasie binne die virale genoom op simptoom uitdrukking te ondersoek. In hierdie studie is 27 heelgenoomvolgordes van Suid-Afrikaanse PVY isolate bepaal deur oorvleuelende RT-PCR fragmente. Sewe van hierdie isolate, ses PVY NTN en een PVY N-W, is gebruik om vier plaaslike aartappel kultivare, gegroei onder kweekhuis kondisies, meganies te infekteer. Die geïnfekteerde plante is gemonitor om die tempo van sistemiese verspreiding vas te stel deur middel van 'n hoogs sensitiewe qRTPCR en knolle is visueel inspekteer vir PTNRD. Hoogs variante rekombinante isolate blyk om minder virulent te wees as die meer bewaarde rekombinante isolate wat dui op molekulêre determinante van patogenisiteit. Om hierdie rede is die aminosuurvolgordes van die Suid-Afrikaanse isolate vergelyk met die van internasionale isolate en ondersoek vir variasie en substitusies. Sommige Suid-Afrikaanse isolate vertoon aminosuur substitusies wat uniek is tot die spesifieke isolaat en maak hul dus anders as internasionale isolate. Die aantal aminosuursubstitusies in die volgordes verskil grootliks. In vergelyking met internasionale isolate toon sommige isolate skaars enige veranderinge terwyl ander ‘n aantal verskille toon. Sekere gebiede, waarvan baie spesifieke funksies het, was meer gekonserveerd as ander. Hierdie studie ondersoek ook rekombinasie gebeure binne die PVY genoom deur retikulêre filogenetiese analise, molekulêre datering en netwerk konstruksie tegnieke. In teenstelling met bestaande benaderinge, aanvaar die tegniek wat hier beskryf word nie ‘n streng bifurkeerende filogenie, wat onderliggende verdeel, of enige voorafgaande kennis van die prosesse onderliggend aan afwykings tussen individuele filogenieë nie. ‘n Robuuste, tyd gekalibreer filogenie kan diversifikasie patrone en rekombinasie van PVY plaas in die historiese konteks van menslike verbouing van aartappels. Deur gebruik te maak van hierdie tegnieke poog die studie om te toets of diversifikasie en rekombinasie van PVY rasse plaasgevind het binne die tydsbestek van die inburgering en moderne verbouing van aartappels. Van hierdie ontledinge word afgelei dat rekombinante rasse van PVY wat in Suid-Afrika voorkom, ingevoer is.

<p>DNA sequences from the <i>rps16</i> intron and the <i>psbE-petL</i> spacer from the chloroplast genome, the ribosomal nuclear ITS region, and introns from the low copy nuclear genes <i>RPA2</i>, <i>RPB2</i>, <i>RPD2a</i> and <i>RPD2b</i>, are in different combinations used to infer phylogenetic relationships in <i>Sileneae</i> (<i>Caryophyllaceae</i>). Used in concert, the biparentally inherited nuclear regions are useful to distinguish between paralogy due to allopolyploidy and single gene duplications, respectively, because the latter are not expected to give rise to repeated phylogenetic patterns in potentially unlinked sequence regions. In addition, the sequences resolve previously poorly known relationships in the tribe <i>Sileneae</i>. Several independent losses and incomplete concerted evolution are inferred between the two <i>RPD2</i> paralogues in a subgroup of <i>Silene</i>.</p><p>An allopolyploid origin is suggested for the tetraploid <i>S. aegaea</i>, with the maternal ancestor from the diploid <i>S. pentelica</i> lineage, and the paternal contributor from the diploid <i>S. sedoides</i> lineage.</p><p><i>Silene involucrata</i> originated as an allotetraploid with the diploid lineage of Arctic <i>S. uralensis</i> as cytoplasmic donor and the diploid Siberian/Northeast Asian <i>S. ajanensis</i> lineage as pollen donor. A subsequent allopolyploidization with the <i>S. ajanensis</i> lineage as pollen donor and the tetraploid <i>S. involucrata</i> lineage as cytoplasmic donor resulted in the hexaploid lineage of <i>S. sorensenis sensu lato</i>.</p><p>A monophyletic origin of the North American polyploids is rejected. One lineage consists of tetraploid <i>S. menziesii</i> and its diploid allies. A separate lineage leads to a clade consisting of both diploid and polyploid Arctic, European and Asian taxa in addition to the majority of the North American polyploids. The tetraploid <i>S. californica</i> and the hexaploid <i>S. hookeri</i> are derived from separate allopolyploidization events between these two lineages.</p>

The focus for the first part of the thesis is on the systematics of species belonging to Silene subgenus Silene. Phylogenetic relationships are inferred from DNA sequences from both the plastid (the rps16 intron) and the nuclear (ITS, intron of the RPB2 gene) genomes. Silene section Rigidulae is shown to be non-monophyletic in its previous circumscription, but instead consisting of six separate clades, each correlated to the geographical distribution of the included species. The taxonomic consequences for each clade are discussed. One of the clades is recognized as a new section and described as Silene sect. Arenosae sect. nov. The morphological descriptions of the species are formalized using a novel implementation of the Prometheus Description Model. Two proposals are included in the thesis, one to reject the name Silene polyphylla L., which is a senior synonym to S. portensis L. Silene linearis Decne. is proposed for conservation against the rarely used S. linearis Sweet. Silene antirrhina, a weedy American annual, is strongly supported as sister to the Hawaiian endemic species of Silene, suggesting an American origin for these. Two of the endemics have evolved woodiness after introduction to Hawaii. In the second part of the thesis we use four nuclear DNA regions, (introns from RPA2, RPB2, RPD2a, RPD2b), and the chloroplast psbE-petG spacer. A framework is developed to evaluate different phylogenetic explanations for conflicting gene trees, where divergence times are used to discriminate among inter- and intralineage processes. The incongruences observed regarding the relationships among the three major lineages of Heliosperma are best explained by homoploid hybridization. The pattern regarding the origin of Heliosperma itself is more complicated and is likely to include several reticulate events. Two lineages have probably been involved in the origin of Heliosperma, one leading to Viscaria and Atocion and the other to Eudianthe and/or Petrocoptis.

In this thesis relationships and the occurrence of reticulate evolutionary events in the club moss genus Diphasiastrum are investigated. Diphasiastrum is initially established as a monophyletic group within Lycopodiaceae using non recombinant chloroplast sequence data. Support is obtained for eight distinct parental lineages in Diphasiastrum, and relationships among the putative parent taxa in the hypothesized hybrid complexes; D. alpinum, D. complanatum, D. digitatum, D. multispicatum, D. sitchense, D. tristachyum and D. veitchii are presented. Feulgen DNA image densitometry data and sequence data obtained from three nuclear regions, RPB2, LEAFY and LAMB4, were used to infer the origins of three different taxa confirmed to be allopolyploid; D. zanclophyllum from South Africa, D. wightianum from Malaysia and an undescribed taxon from China. The two Asian polyploids have originated from two different hybrid combinations, D. multispicatum x D. veitchii and D. tristachyum x D. veitchii. Diphasiastrum zanclophyllum originates from a cross between D. digitatum and an unidentified diploid taxon. The occurrence of three homoploid hybrid combinations commonly recognized in Europe, D. alpinum x D. complanatum, D. alpinum x D. tristachyum and D. complanatum x D. tristachyum, are verified using the same three nuclear regions. Two of the three hybrid combinations are also shown to have originated from reciprocal crosses. Admixture analyses performed on an extended, dataset similarly identified predominately F1 hybrids and backcrosses. The observations and common recognition of hybrid species in the included populations are hence most likely due to frequent observations of neohybrids in hybrid zones. Reticulate patterns are, however, prominent in the presented dataset. Hence future studies addressing evolutionary and ecological questions in Diphasiastrum should emphasize the impact of gene flow between parent lineages rather than speciation as the result of hybridization.

DNA sequences from the rps16 intron and the psbE-petL spacer from the chloroplast genome, the ribosomal nuclear ITS region, and introns from the low copy nuclear genes RPA2, RPB2, RPD2a and RPD2b, are in different combinations used to infer phylogenetic relationships in Sileneae (Caryophyllaceae). Used in concert, the biparentally inherited nuclear regions are useful to distinguish between paralogy due to allopolyploidy and single gene duplications, respectively, because the latter are not expected to give rise to repeated phylogenetic patterns in potentially unlinked sequence regions. In addition, the sequences resolve previously poorly known relationships in the tribe Sileneae. Several independent losses and incomplete concerted evolution are inferred between the two RPD2 paralogues in a subgroup of Silene. An allopolyploid origin is suggested for the tetraploid S. aegaea, with the maternal ancestor from the diploid S. pentelica lineage, and the paternal contributor from the diploid S. sedoides lineage. Silene involucrata originated as an allotetraploid with the diploid lineage of Arctic S. uralensis as cytoplasmic donor and the diploid Siberian/Northeast Asian S. ajanensis lineage as pollen donor. A subsequent allopolyploidization with the S. ajanensis lineage as pollen donor and the tetraploid S. involucrata lineage as cytoplasmic donor resulted in the hexaploid lineage of S. sorensenis sensu lato. A monophyletic origin of the North American polyploids is rejected. One lineage consists of tetraploid S. menziesii and its diploid allies. A separate lineage leads to a clade consisting of both diploid and polyploid Arctic, European and Asian taxa in addition to the majority of the North American polyploids. The tetraploid S. californica and the hexaploid S. hookeri are derived from separate allopolyploidization events between these two lineages.

[pt] Consideramos o problema de contar e classificar coberturas por dominós de toros quadriculados. O problema de contagem para retângulos foi estudado por Kasteleyn e usamos muitas de suas ideias. Coberturas por dominós de regiões planares podem ser representadas por funções altura; para um toro dado por um reticulado L, estas funções exibem L-quasiperiodicidade aritmética. As constantes aditivas determinam o fluxo da cobertura, que pode ser interpretado como um vetor no reticulado dual (2L) asterisco. Damos uma caracterização dos valores de fluxo efetivamente realizados e de como coberturas correspondentes se comportam. Também consideramos coberturas por dominós do reticulado quadrado infinito; coberturas de toros podem ser vistas como um caso particular destas. Descrevemos a construção e uso de matrizes de Kasteleyn no problema de contagem, e como elas podem ser aplicadas para contar coberturas com valores de fluxo prescritos. Finalmente, estudamos a distribuição limite do número de coberturas com um dado valor de fluxo quando o reticulado L sofre uma dilatação uniforme. / [en] We consider the problem of counting and classifying domino tilings of a quadriculated torus. The counting problem for rectangles was studied by Kasteleyn and we use many of his ideas. Domino tilings of planar regions can be represented by height functions; for a torus given by a lattice L, these functions exhibit arithmetic L-quasiperiodicity. The additive constants determine the flux of the tiling, which can be interpreted as a vector in the dual lattice (2L) asterisk. We give a characterization of the actual flux values, and of how corresponding tilings behave. We also consider domino tilings of the infinite square lattice; tilings of tori can be seen as a particular case of those. We describe the construction and usage of Kasteleyn matrices in the counting problem, and how they can be applied to count tilings with prescribed flux values. Finally, we study the limit distribution of the number of tilings with a given flux value as a uniform scaling dilates the lattice L.

[pt] Uma Rede Organizacional Virtual é uma organização de cooperação interorganizacional, com uso intenso de Tecnologia de Informação e Comunicação, típica do ambiente globalizado. Nesta dissertação, busca-se caracterizar esse padrão de rede e propor instrumentos para seu gerenciamento. O termo Redes Organizacionais Virtuais é introduzido, a partir da caracterização e da classificação das Redes de Cooperação e das Organizações Virtuais. Propõe- se a Metodologia de Reticulação para o planejamento e formação dessas redes e explicita-se a necessidade de instrumentos de coordenação, controle e avaliação para assegurar o seu melhor desempenho. Com essa fundamentação, analisa-se a Rede de Projeto e Desenvolvimento de Turbinas a Gás - RTG, determinando-se suas características e propondo-se metodologias de planejamento, coordenação e controle para sua administração. Recomenda-se, ainda, a implementação de um sistema de informações como instrumento reticulador. / [en] A Virtual Organizational Network is an inter-organizational cooperation organization, based in Communication and Information Technology, typical of the global environment. The objective of this dissertation is to characterize this network and propose appropriate management tools for its adequate functioning. The term Virtual Organizational Network is introduced based on the characteristics and taxonomy of Cooperation Networks and Virtual Organizations. To form, consolidate and plan this network, the Reticulation Methodology is proposed. The necessity of coordination, governance and performance evaluation tools for these networks is made explicit. This constitutes the basis for the analysis of the Gas Turbine Development and Project Network- RTG. Its characteristics are identified and methodologies for its planning, coordination and governance are proposed, as well as an Information System, as instrument for reticulation.