Phylogenetic diversity (PD) is a measure of species biodiversity quantified by how much of an evolutionary tree is spanned by a subset of species. In this thesis, we study optimization problems that aim to find species sets with maximum PD in different scenarios, and examine random extinction models under various assumptions to predict the PD of species that will still be present in the future. Optimizing PD with Dependencies is a combinatorial optimization problem in which species form an ecological network. Here, we are interested in selecting species sets of a given size that are ecologically viable and that maximize PD. The NP-hardness of this problem is proved and it is established which special cases of the problem are computationally easy and which are computationally hard. It is also shown that it is NP-complete to decide whether the feasible solution obtained by the greedy algorithm is optimal. We formulate the optimization problem as an integer linear program and find exact solutions to the largest food web currently in the empirical literature. In addition, we give a generalization of PD that can be used for example when we do not know the true evolutionary history. Based on this measure, an optimization problem is formulated. We discuss the complexity and the approximability properties of this problem. In the generalized field of bullets model (g-FOB), species are assumed to become extinct with possibly different probabilities, and extinction events are independent. We show that under this model the distribution of future phylogenetic diversity converges to a normal distribution as the number of species grows. When extinction probabilities are influenced by some binary character on the tree, the state-based field of bullets model (s-FOB) represents a more realistic picture. We compare the expected loss of PD under this model to that under the associated g-FOB model and find that the former is always greater than or equal to the latter. It is natural to further generalize the s-FOB model to allow more than one binary character to affect the extinction probabilities. The expected future PD obtained for the resulting trait-dependent field of bullets model (t-FOB) is compared to that for the associated g-FOB model and our previous result is generalized.

Significant phylogenetic codivergence between plant or animal hosts (H) and their symbionts or parasites (P) indicate the importance of their interactions on evolutionary time scales. However, valid and realistic methods to test for codivergence are not fully developed. One of the systems where possible codivergence has been of interest involves the large subfamily of temperate grasses (Pooideae) and their endophytic fungi (epichloae). Here we introduce the MRCALink (most-recent-common-ancestor link) method and use it to investigate the possibility of grass-epichloё codivergence. MRCALink applied to ultrametric H and P trees identifies all corresponding nodes for pairwise comparisons of MRCA ages. The result is compared to the space of random H and Ptree pairs estimated by a Monte Carlo method. Compared to tree reconciliation the method is less dependent on tree topologies (which often can be misleading), and it crucially improves on phylogeny-independent methods such as ParaFit or the Mantel test by eliminating an extreme (but previously unrecognized) distortion of node-pair sampling. Analysis of 26 grass species-epichloё species symbioses did not reject random association of H and P MRCA ages. However, when five obvious host jumps were removed the analysis significantly rejected random association and supported grass-endophyte codivergence. Interestingly, early cladogenesis events in the Pooideae corresponded to early cladogenesis events in epichloae, suggesting concomitant origins of this grass subfamily and its remarkable group of symbionts.

A central theme in phylogenetics is the reconstruction and analysis of evolutionary trees from a given set of data. To determine the optimal search methods for the reconstruction of trees, it is crucial to understand the size and structure of neighbourhoods of trees under tree rearrangement operations. The diameter and size of the immediate neighbourhood of a tree has been well-studied, however little is known about the number of trees at distance two, three or (more generally) k from a given tree. In this thesis we explore previous results on the size of these neighbourhoods under common tree rearrangement operations (NNI, SPR and TBR). We obtain new results concerning the number of trees at distance k from a given tree under the Robinson-Foulds (RF) metric and the Nearest Neighbour Interchange (NNI) operation, and the number of trees at distance two from a given tree under the Subtree Prune and Regraft (SPR) operation. We also obtain an exact count for the number of pairs of binary phylogenetic trees that share a first RF or NNI neighbour.

Climate change has been invoked to explain patterns of speciation, extinction and biogeographic change over time, however it can be a difficult hypothesis to test empirically. One area of particular interest is climate change in the African Neogene, linked with the origin of hominins. A perfect model clade to test these hypotheses is the papionin monkeys, a diverse group (both extinct and extant), represented by an excellent fossil record. I describe new fossil papionin specimens from Coopers Cave, South Africa, and redescribe and discuss some previously known fossil material. This rich data set provides a necessary deep-time perspective, and, in conjunction with independently generated data, can be used to test hypotheses related to climatic and geological events (such as increasing late Pleistocene aridity and persistence of forest refugia) that may be directly linked to patterns of speciation and biogeographic distribution in the fossil record and in living species. Testing these hypotheses requires a robust phylogenetic hypothesis. I collected morphological character data for a species-level phylogenetic analysis of the papionin clade in order to reconstruct the phylogeny of the group. My analysis found that the living species Theropithecus gelada is nested within extinct theropiths, and is primitive relative to the Pleistocene taxa Theropithecus darti, T. oswaldi and T. leakeyi. Also falling within the theropith lineage are the early Pliocene taxon Pliopapio, the South African taxa Dinopithecus and Gorgopithecus, and two species whose relationships were uncertain until my analysis. “Papio” quadratirostris and “Papio” baringensis are nested within the theropiths, and should be referred to the genus Theropithecus. Biogeographic analysis demonstrates that papionin monkeys share a similar pattern with other Neogene African mammals; they first disperse out of Africa during the mid-Miocene, return to Africa by the late Miocene and undergo a series of vicariant speciation events and range restriction to central Africa, but disperse out into eastern and southern Africa by the Pleistocene. These speciation and dispersal events are tightly correlated with global climatic and tectonic changes.

Anseriformes, or waterfowl, are related to Galliformes (chickens and kin), together forming the most basal sister of Neoaves. The order is generally considered to comprise four families: Presbyornithidae (Late Cretaceous - Eocene); Anseranatidae (Paleocene-present); Anhimidae (Oligocene-present); Anatidae (Oligocene-present), but the giant Tertiary flightless taxa Dromornithidae (Australia), Gastornithidae (Eurasia) and Diatrymidae (North America) have also been referred to the order. Australasia presently has a unique waterfowl fauna characterized by low species diversity but high phylogenetic diversity: the Magpie Goose Anseranas (the sole surviving anseranatid), several monotypic endemic anatid genera of uncertain relationships (Cape Barren Goose Cereopsis, Freckled Duck Stictonetta, Pinkeared Duck Malacorhynchus and Musk Duck Biziura), several relatively primitive taxa (the aforementioned plus whistling ducks Dendrocygna and Blue-billed Duck Oxyura). The evolutionary history of this fauna has, until now, not been examined via the fossil record. In this thesis, the literature for the global fossil record of Anseranatidae and Anatidae is reviewed. The Neogene (Oligocene-Pliocene) fossil record of Anseriformes, exclusive of dromornithids, is studied from both New Zealand and Australia. For New Zealand, all materials derive from the St Bathans Fauna, Early Miocene (19-16 Ma), Otago. Herein, the first description of this fauna is provided, with four anatid genera (Manuherikia, Dunstanetta, Matanas and Miotadorna) established for five species, with a sixth taxon reported (Chapter 2). The phylogenetic affinities of Manuherikia, Dunstanetta and Miotadorna are examined using parsimony analysis of morphological data (133 characters) in Chapter 3. Miotadorna is a shelduck related to tadornines, perhaps sister to Tadorna, and Manuherikia and Dunstanetta are oxyurines related to the Stictonetta, Malacorhynchus, Oxyura and Biziura). A further species of Manuherikia and the existence of definite anserines, probably related to Cereopsis, are described in Chapter 4. The fossil record of Australian anseriforms is described in Chapters 5-8. The Oligo- Miocene record derives principally from the Etadunna and Namba Formations (26-24 Ma) in the Lake Eyre and Frome Basins, respectively, in South Australia. Four taxa are described, with all occurring both in the Namba and Etadunna Formations: a single genus, Pinpanetta, is established for three species and another, Australotadorna, for a tadornine. Phylogenetic analyses (parsimony and Bayesian) of a dataset (150 characters, 61 taxa) show Pinpanetta is an oxyurine and confirm the previously found oxyurine affinity of Manuherikia and Dunstanetta. A monophyletic clade with moderate support is found for an expanded Oxyurinae that has Stictonetta basal, followed successively by Mionetta (Oligo- Miocene of Europe), Malacorhynchus, Pinpanetta, Manuherikia, Dunstanetta, Oxyura and Nomonyx, Biziura and Thalassornis. This same analysis finds anserines the most basal group in Anatidae, so changing position with Dendrocygna, considered by recent authors to be the most basal anatid. A new genus and species of anseranatid is described from a Faunal Zone A (System A, Late Oligocene) deposit at Riversleigh, northwestern Queensland (Chapter 6). This first pre-Pliocene record of the family in Australia is of equivalent age to the youngest European fossil anseranatid, Anserpica from France, but younger than the Eocene Anatalavis of England. Only one of three other waterfowl bones known from Riversleigh deposits is identifiable and is referred to a species of Pinpanetta found in the Etadunna Formation. Mid-Late Miocene deposits containing waterfowl are restricted in Australia to just the Waite Formation (c. 8 Ma) at Alcoota in the Northern Territory. Three bones indicate an undetermined tadornine and an undetermined anatid, different from any known species. The Pliocene record of anseriforms in South Australia is described from the Tirari Formation (Kanunka and Toolapinna Faunas) (Chapter 7). Nine modern species (Anseranas semipalmata, Cereopsis novaehollandiae, Cygnus atratus, Tadorna tadornoides, Biziura lobata, Oxyura australis, Anas cf A. castanea, A. cf A. gracilis and Aythya australis) are represented. A single extinct species, Tirarinetta kanunka, is described and referred to Oxyurinae. From the Parilla Sands, Late Pliocene, at Bookmark Cliffs on the Murray River, a single humerus is described (Chapter 8) and referred to Tadorna cf. T. tadornoides. A total of 11 anatid taxa is described from latest Oligocene-Early Miocene deposits in Australasia, which considerably adds to the global record of seven species previously reported for this period. Considering also the anseranatids, the Late Oligocene – Early Miocene fauna of Australia is thus established as having equivalent diversity to that from similar-aged deposits in Europe, but by the late Early Miocene, the New Zealand fauna was more diverse than any other Oligo-Miocene fauna known. The more limited samples available, compared to those from New Zealand, probably explain the lack of a similar diversity being revealed for Australia from this period. In both Australia and New Zealand, the Oligo-Miocene faunas are dominated by oxyurine taxa, as were those in Europe. The presence of a tadornine in Australia in the latest Oligocene and another in New Zealand in the Early Miocene precede the appearance of this subfamily in the Northern Hemisphere by 10 Ma, implying a southern origin for this group. The Late Oligocene presence of Mionetta in Europe and of Pinpanetta in Australia, and their referral to Oxyurinae, establishes a minimum age for the origin of this subfamily in the latest Oligocene. The establishment of a fauna comprised of modern species by the Pliocene indicates substantial faunal turnover probably in the Late Miocene. This turnover is due in part to immigration of taxa (Cygnus, Anas, Aythya) and in situ evolution (all endemic genera), as occurred in other Australian vertebrates (rodents, snakes, bats). Thus faunal composition in Australia appears to have been more affected by attainment of some threshold in proximity to Asia being breached by the northward continental drift of Australia, than by aridification, which has been ongoing since the Middle Miocene. / http://proxy.library.adelaide.edu.au/login?url= http://library.adelaide.edu.au/cgi-bin/Pwebrecon.cgi?BBID=1339803 / Thesis (Ph.D.) - University of Adelaide, School of Earth and Environmental Sciences, 2008

Anseriformes, or waterfowl, are related to Galliformes (chickens and kin), together forming the most basal sister of Neoaves. The order is generally considered to comprise four families: Presbyornithidae (Late Cretaceous - Eocene); Anseranatidae (Paleocene-present); Anhimidae (Oligocene-present); Anatidae (Oligocene-present), but the giant Tertiary flightless taxa Dromornithidae (Australia), Gastornithidae (Eurasia) and Diatrymidae (North America) have also been referred to the order. Australasia presently has a unique waterfowl fauna characterized by low species diversity but high phylogenetic diversity: the Magpie Goose Anseranas (the sole surviving anseranatid), several monotypic endemic anatid genera of uncertain relationships (Cape Barren Goose Cereopsis, Freckled Duck Stictonetta, Pinkeared Duck Malacorhynchus and Musk Duck Biziura), several relatively primitive taxa (the aforementioned plus whistling ducks Dendrocygna and Blue-billed Duck Oxyura). The evolutionary history of this fauna has, until now, not been examined via the fossil record. In this thesis, the literature for the global fossil record of Anseranatidae and Anatidae is reviewed. The Neogene (Oligocene-Pliocene) fossil record of Anseriformes, exclusive of dromornithids, is studied from both New Zealand and Australia. For New Zealand, all materials derive from the St Bathans Fauna, Early Miocene (19-16 Ma), Otago. Herein, the first description of this fauna is provided, with four anatid genera (Manuherikia, Dunstanetta, Matanas and Miotadorna) established for five species, with a sixth taxon reported (Chapter 2). The phylogenetic affinities of Manuherikia, Dunstanetta and Miotadorna are examined using parsimony analysis of morphological data (133 characters) in Chapter 3. Miotadorna is a shelduck related to tadornines, perhaps sister to Tadorna, and Manuherikia and Dunstanetta are oxyurines related to the Stictonetta, Malacorhynchus, Oxyura and Biziura). A further species of Manuherikia and the existence of definite anserines, probably related to Cereopsis, are described in Chapter 4. The fossil record of Australian anseriforms is described in Chapters 5-8. The Oligo- Miocene record derives principally from the Etadunna and Namba Formations (26-24 Ma) in the Lake Eyre and Frome Basins, respectively, in South Australia. Four taxa are described, with all occurring both in the Namba and Etadunna Formations: a single genus, Pinpanetta, is established for three species and another, Australotadorna, for a tadornine. Phylogenetic analyses (parsimony and Bayesian) of a dataset (150 characters, 61 taxa) show Pinpanetta is an oxyurine and confirm the previously found oxyurine affinity of Manuherikia and Dunstanetta. A monophyletic clade with moderate support is found for an expanded Oxyurinae that has Stictonetta basal, followed successively by Mionetta (Oligo- Miocene of Europe), Malacorhynchus, Pinpanetta, Manuherikia, Dunstanetta, Oxyura and Nomonyx, Biziura and Thalassornis. This same analysis finds anserines the most basal group in Anatidae, so changing position with Dendrocygna, considered by recent authors to be the most basal anatid. A new genus and species of anseranatid is described from a Faunal Zone A (System A, Late Oligocene) deposit at Riversleigh, northwestern Queensland (Chapter 6). This first pre-Pliocene record of the family in Australia is of equivalent age to the youngest European fossil anseranatid, Anserpica from France, but younger than the Eocene Anatalavis of England. Only one of three other waterfowl bones known from Riversleigh deposits is identifiable and is referred to a species of Pinpanetta found in the Etadunna Formation. Mid-Late Miocene deposits containing waterfowl are restricted in Australia to just the Waite Formation (c. 8 Ma) at Alcoota in the Northern Territory. Three bones indicate an undetermined tadornine and an undetermined anatid, different from any known species. The Pliocene record of anseriforms in South Australia is described from the Tirari Formation (Kanunka and Toolapinna Faunas) (Chapter 7). Nine modern species (Anseranas semipalmata, Cereopsis novaehollandiae, Cygnus atratus, Tadorna tadornoides, Biziura lobata, Oxyura australis, Anas cf A. castanea, A. cf A. gracilis and Aythya australis) are represented. A single extinct species, Tirarinetta kanunka, is described and referred to Oxyurinae. From the Parilla Sands, Late Pliocene, at Bookmark Cliffs on the Murray River, a single humerus is described (Chapter 8) and referred to Tadorna cf. T. tadornoides. A total of 11 anatid taxa is described from latest Oligocene-Early Miocene deposits in Australasia, which considerably adds to the global record of seven species previously reported for this period. Considering also the anseranatids, the Late Oligocene – Early Miocene fauna of Australia is thus established as having equivalent diversity to that from similar-aged deposits in Europe, but by the late Early Miocene, the New Zealand fauna was more diverse than any other Oligo-Miocene fauna known. The more limited samples available, compared to those from New Zealand, probably explain the lack of a similar diversity being revealed for Australia from this period. In both Australia and New Zealand, the Oligo-Miocene faunas are dominated by oxyurine taxa, as were those in Europe. The presence of a tadornine in Australia in the latest Oligocene and another in New Zealand in the Early Miocene precede the appearance of this subfamily in the Northern Hemisphere by 10 Ma, implying a southern origin for this group. The Late Oligocene presence of Mionetta in Europe and of Pinpanetta in Australia, and their referral to Oxyurinae, establishes a minimum age for the origin of this subfamily in the latest Oligocene. The establishment of a fauna comprised of modern species by the Pliocene indicates substantial faunal turnover probably in the Late Miocene. This turnover is due in part to immigration of taxa (Cygnus, Anas, Aythya) and in situ evolution (all endemic genera), as occurred in other Australian vertebrates (rodents, snakes, bats). Thus faunal composition in Australia appears to have been more affected by attainment of some threshold in proximity to Asia being breached by the northward continental drift of Australia, than by aridification, which has been ongoing since the Middle Miocene. / http://proxy.library.adelaide.edu.au/login?url= http://library.adelaide.edu.au/cgi-bin/Pwebrecon.cgi?BBID=1339803 / Thesis (Ph.D.) - University of Adelaide, School of Earth and Environmental Sciences, 2008

Os padrões de associação entre epífitos e forófitos não podem ser considerados espécie-específicos, mas as árvores que os epífitos colonizam também não são um conjunto aleatório das espécies forofíticas de um determinado local. Ao invés disso, parece haver uma preferência de certos epífitos por diferentes forófitos. No entanto, se conhece pouco sobre os fatores que determinam essa preferência. Nosso objetivo nesse trabalho é avaliar como os atributos funcionais e a filogenia dos epífitos vasculares influenciam na associação dos epífitos com os forófitos em uma Floresta Ombrófila Mista no sul do Brasil. Para isso nós (1) investigamos padrões de associação positiva e negativa entre grupos funcionais de epífitos e grupos de forófitos e como a diversidade e os atributos funcionais dos epífitos variavam em função do tamanho do forófito e (2) inferimos sobre a existência de sinal filogenético no uso de árvores hospedeiras pelos epífitos, procuramos por estrutura filogenética nas comunidades epifíticas e investigamos diferenças de composição filogenética de epífitos vasculares em diferentes clados de forófitos. Foram amostrados 70 forófitos compreendendo 15 espécies pertencentes a diversos clados e com arquiteturas e características variadas. A amostragem compreendeu 31 espécies epifíticas com os principais clados sendo Polypodiaceae, Bromeliaceae e Orchidaceae. A associação de grupos de epífitos vasculares com diferentes grupos de forófitos sugere que as características dos forófitos proporcionam ambientes contrastantes e que diferentes valores de atributos são necessários para colonizar esses ambientes. Mais especificamente espécies epifíticas com menor área específica foliar (SLA) parecem predominar em árvores maiores e maior SLA em árvores menores. Encontramos sinal filogenético na utilização dos forófitos, sugerindo que a conservação das interações com os forófitos deve ter sido importante ao longo da evolução dos epífitos. A tendência a agrupamento filogenético nas comunidades epifíticas sugere a influência de filtros ambientais representados pelas diferentes características dos forófitos estruturando as assembleias de epífitos. Clados mais basais de forófitos apresentaram composição filogenética distinta devido, sobretudo, a presença de diferentes clados de monilófitos epifíticos nessas árvores. Angiospermas epifíticas ocorreram principalmente em forófitos pertencente as eurosídeas. A preferência de epífitos por forófitos parece ser influenciada pelo surgimento de novidades morfológicas e ecofisiológicas em alguns clados, enquanto outros mantiveram o seu nicho ancestral. A composição florística das florestas quando da origem dos clados epifíticos também parece influenciar a associação entre epífitos e forófitos. Ao utilizar informações sobre os atributos e filogenia das espécies de epífitos vasculares nós podemos melhor compreender os mecanismos ecológicos e históricos que influenciam os padrões de associação entre epífitos e forófitos. / It has been shown that patterns of association between epiphytes and phorophytes can not be considered species-specific, although the trees that epiphytes colonize are not a random subset of phorophyte species in a particular location. Instead, there seems to be a preference of some epiphytes for different phorophytic species. However, little is known about the factors determining this choice. Our objective in this study is to assess how functional attributes and phylogeny of vascular epiphytes influence the association of epiphytes with the phorophytes in an Araucaria Forest in Southern Brazil. For that we (1) investigated the positive and negative association patterns between functional groups of epiphytes and groups of phorophytes and how functional diversity and functional traits of epiphytes varied with host tree size and (2) inferred about the existence of phylogenetic signal on the host trees use by epiphytes, looked for phylogenetic structure in the epiphytic communities and investigated differences in the phylogenetic composition of vascular epiphytes in different phorophyte clades. We used a sample of 70 phorophytes comprising 15 species and belonging to different clades and with different architectures and traits. The sample comprised 31 epiphytic species, the major clades being Polypodiaceae, Bromeliaceae and Orchidaceae. The combination of vascular epiphyte groups with different groups of 15 phorophytes suggests that phorophyte traits provide contrasting environments and that different trait values are needed to colonize these environments. More specifically, epiphytic species with lower specific leaf area (SLA) seem to predominate on larger trees and with higher SLA values on smaller trees. We found phylogenetic signal on the host tree use, suggesting that conservatism of the interactions with phorophytes must have been important throughout the evolution of epiphytes. The tendency to phylogenetic clustering in the epiphytic communities suggests the influence of environmental filters represented by phorophyte traits structuring epiphyte assemblages. More basal clades of phorophytes showed different phylogenetic composition mainly due to the presence of different epiphytic monilophyte clades on these trees. Epiphytic angiosperms occurred mainly on those trees belonging to eurosids. The preference of epiphytes for phorophytes seems to be influenced by morphological and ecophysiological novelties in some lineages, while other clades kept their ancestral niche. The floristic composition of forests at the origins of epiphytic lineages also appears to influence the association between epiphytes and phorophytes. By using information about the traits and phylogeny of species of vascular epiphytes we can better understand the ecological and historical mechanisms that influence the patterns of association between epiphytes and phorophytes.

Tumour development has long been recognised as an evolutionary process during which cells accumulate mutations and evolve into a mix of genetically distinct cell subpopulations. The resulting genetic intra-tumour heterogeneity poses a major challenge to cancer therapy, as it increases the chance of drug resistance. To study tumour evolution in more detail, reliable approaches to infer the life histories of tumours are needed. This dissertation focuses on computational methods for inferring trees of tumour evolution from single-cell and multi-sample sequencing data. Recent advances in single-cell sequencing technologies have promised to reveal tumour heterogeneity at a much higher resolution, but single-cell sequencing data is inherently noisy, making it unsuitable for analysis with classic phylogenetic methods. The first part of the dissertation describes OncoNEM, a novel probabilistic method to infer clonal lineage trees from noisy single nucleotide variants of single cells. Simulation studies are used to validate the method and to compare its performance to that of other methods. Finally, OncoNEM is applied in two case studies. In the second part of the dissertation, a comprehensive collection of existing multi-sample approaches is used to infer the phylogenies of metastatic breast cancers from ten patients. In particular, shallow whole-genome, whole exome and targeted deep sequencing data are analysed. The inference methods comprise copy number and point mutation based approaches, as well as a method that utilises a combination of the two. To improve the copy number based inference, a novel allele-specific multi-sample segmentation algorithm is presented. The results are compared across methods and data types to assess the reliability of the different methods. In summary, this thesis presents substantial methodological advances to understand tumour evolution from genomic profiles of single cells or related bulk samples.

Os padrões de associação entre epífitos e forófitos não podem ser considerados espécie-específicos, mas as árvores que os epífitos colonizam também não são um conjunto aleatório das espécies forofíticas de um determinado local. Ao invés disso, parece haver uma preferência de certos epífitos por diferentes forófitos. No entanto, se conhece pouco sobre os fatores que determinam essa preferência. Nosso objetivo nesse trabalho é avaliar como os atributos funcionais e a filogenia dos epífitos vasculares influenciam na associação dos epífitos com os forófitos em uma Floresta Ombrófila Mista no sul do Brasil. Para isso nós (1) investigamos padrões de associação positiva e negativa entre grupos funcionais de epífitos e grupos de forófitos e como a diversidade e os atributos funcionais dos epífitos variavam em função do tamanho do forófito e (2) inferimos sobre a existência de sinal filogenético no uso de árvores hospedeiras pelos epífitos, procuramos por estrutura filogenética nas comunidades epifíticas e investigamos diferenças de composição filogenética de epífitos vasculares em diferentes clados de forófitos. Foram amostrados 70 forófitos compreendendo 15 espécies pertencentes a diversos clados e com arquiteturas e características variadas. A amostragem compreendeu 31 espécies epifíticas com os principais clados sendo Polypodiaceae, Bromeliaceae e Orchidaceae. A associação de grupos de epífitos vasculares com diferentes grupos de forófitos sugere que as características dos forófitos proporcionam ambientes contrastantes e que diferentes valores de atributos são necessários para colonizar esses ambientes. Mais especificamente espécies epifíticas com menor área específica foliar (SLA) parecem predominar em árvores maiores e maior SLA em árvores menores. Encontramos sinal filogenético na utilização dos forófitos, sugerindo que a conservação das interações com os forófitos deve ter sido importante ao longo da evolução dos epífitos. A tendência a agrupamento filogenético nas comunidades epifíticas sugere a influência de filtros ambientais representados pelas diferentes características dos forófitos estruturando as assembleias de epífitos. Clados mais basais de forófitos apresentaram composição filogenética distinta devido, sobretudo, a presença de diferentes clados de monilófitos epifíticos nessas árvores. Angiospermas epifíticas ocorreram principalmente em forófitos pertencente as eurosídeas. A preferência de epífitos por forófitos parece ser influenciada pelo surgimento de novidades morfológicas e ecofisiológicas em alguns clados, enquanto outros mantiveram o seu nicho ancestral. A composição florística das florestas quando da origem dos clados epifíticos também parece influenciar a associação entre epífitos e forófitos. Ao utilizar informações sobre os atributos e filogenia das espécies de epífitos vasculares nós podemos melhor compreender os mecanismos ecológicos e históricos que influenciam os padrões de associação entre epífitos e forófitos. / It has been shown that patterns of association between epiphytes and phorophytes can not be considered species-specific, although the trees that epiphytes colonize are not a random subset of phorophyte species in a particular location. Instead, there seems to be a preference of some epiphytes for different phorophytic species. However, little is known about the factors determining this choice. Our objective in this study is to assess how functional attributes and phylogeny of vascular epiphytes influence the association of epiphytes with the phorophytes in an Araucaria Forest in Southern Brazil. For that we (1) investigated the positive and negative association patterns between functional groups of epiphytes and groups of phorophytes and how functional diversity and functional traits of epiphytes varied with host tree size and (2) inferred about the existence of phylogenetic signal on the host trees use by epiphytes, looked for phylogenetic structure in the epiphytic communities and investigated differences in the phylogenetic composition of vascular epiphytes in different phorophyte clades. We used a sample of 70 phorophytes comprising 15 species and belonging to different clades and with different architectures and traits. The sample comprised 31 epiphytic species, the major clades being Polypodiaceae, Bromeliaceae and Orchidaceae. The combination of vascular epiphyte groups with different groups of 15 phorophytes suggests that phorophyte traits provide contrasting environments and that different trait values are needed to colonize these environments. More specifically, epiphytic species with lower specific leaf area (SLA) seem to predominate on larger trees and with higher SLA values on smaller trees. We found phylogenetic signal on the host tree use, suggesting that conservatism of the interactions with phorophytes must have been important throughout the evolution of epiphytes. The tendency to phylogenetic clustering in the epiphytic communities suggests the influence of environmental filters represented by phorophyte traits structuring epiphyte assemblages. More basal clades of phorophytes showed different phylogenetic composition mainly due to the presence of different epiphytic monilophyte clades on these trees. Epiphytic angiosperms occurred mainly on those trees belonging to eurosids. The preference of epiphytes for phorophytes seems to be influenced by morphological and ecophysiological novelties in some lineages, while other clades kept their ancestral niche. The floristic composition of forests at the origins of epiphytic lineages also appears to influence the association between epiphytes and phorophytes. By using information about the traits and phylogeny of species of vascular epiphytes we can better understand the ecological and historical mechanisms that influence the patterns of association between epiphytes and phorophytes.

Made available in DSpace on 2014-06-11T19:26:13Z (GMT). No. of bitstreams: 0 Previous issue date: 2007-08-31Bitstream added on 2014-06-13T19:13:14Z : No. of bitstreams: 1 pinheiro_aep_me_rcla.pdf: 11299460 bytes, checksum: 40e26adee463ede931292878bcb40a3d (MD5) / Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) / O presente trabalho aborda a Sistemática Filogenética da Infra-Ordem Sebecosuchia, visando um melhor entendimento sobre a história evolutiva do grupo e igualmente contribuindo para sua Taxonomia. Levantaram-se informações sobre os táxons que constituem o referido grupo enfoque, sendo estas de caráteres paleobiológico, geológico e biocronológico. Além dos espécimens sebecossuquianos bem documentados, estão incluídos materiais inéditos como Forma Itaboraí e Forma Tiupampa, e materiais que apesar de não representarem novos táxons, contribuem com dados adicionais na compreensão de tais espécies, como Stratiotosuchus maxhechti. Também estão incluídos táxons que não são usualmente utilizados neste tipo de investigação, pela falta de informações devido à fragmentação dos espécimens, como é o caso de Ilchunaia parca e Forma Sebecus Itaboraí. Estes táxons, apesar de não poderem revelar informações sólidas, servem para uma prévia aproximação e vislumbre sobre Sistemática, enquanto materiais mais completos não são encontrados. As análises filogenéticas foram realizadas valendo-se de 46 táxons crocodilomorfianos e 241 caracteres. Os caracteres são referentes a crânio, mandíbula e dentição, regiões anatômicas que respondem mais prontamente as pressões seletivas, refletindo com mais fidelidade as transformações sofridas pelas linhagens. Além do que, com exceção de alguns espécimens de poucas espécies, a maioria dos materiais sebecossuquianos é constituída por fragmentos provenientes destas regiões. Os resultados, extraídos de análises cladísticas heurísticas, semi-exaustivas e exaustivas, permitiram entre outros aspectos: 1 - constatação de merofiletismo para Sebecosuquia, que seria válido como clado com a inclusão de peirossauromorfos e eussuquianos no referido grupo... / The present study approaches the Phylogenetic Systematic of the Infra-Order Sebecosuchia, seeking a better knowledge about its evolutive history and even helping Taxonomy. Taxon information, Paleobiology, Geology and Biocronology were gain up to the refered group. Besides well documented sebecosuchian specimens, are added some unplublished materials, like Forma Itaboraí and Forma Tiupampa. Some materials, despite not being new taxons, contributes with complementary data, increasing the comprehension of refered species like Stratiotosuchus maxhechti. Further taxons, not often available in cladistic contributions, were included. This unusual employment is due ton the lack of informations on fragmentary materials. It occurs with Ilchunaia parca and Forma Sebecus Itaboraí for example, both despite do not have much solid data, they are usefull to previous systematic approach, while new more complete materials are not find. The phyilogenetic analisys were made including 46 crocodylomorphian taxa, and 241 characters. These characters are refered to skull, jaw and teeth, which answer selective pressures, reflecting the changes suffered by the lineages. Moreover, with some exceptions, most of the sebecosuchians is constituted by fragments from those anatomies. The cladistic results, heuristic, semi-exhaustive, and exhaustive, allowed the main conclusions. 1 - Sebecosuchia is a merophyletic group, only being valid with addition of peirosauromorphs and eusuchians; 2 - Baurusuchidae is a well supported family, crossing Cretaceous-Paleogene limit by inclusion of two taxa, Forma Tiupampa and Iberosuchus, ranging until Eocene of the Iberic region; 3 - the informal name Sebecoidea is employed to keep the genera Sebecus, Bretesuchus, Ayllusuchus and Bergisuchus, showing relationships to trematochampsids and eusuchians lineages; 4 - Forma Itaboraí is confirmed as a morphotype belonging to the Family Bretesuchidae.