Deserticolous birds inhabit an environment characterised by high ambient temperatures and low rainfall that has low primary productivity. The combination of these factors may lead to the evolution of adaptations that minimise food and water requirements. One physiological adaptation that has been found in many deserticolous birds is the reduction of basal metabolic rate (BMR). I measured metabolic rate in the laboratory using four species of African lovebirds (Agapornis) , and four species of Australian grass parakeets (one Neopsephotus and three Neophema), all similar in body mass. Tests for differences between groups were carried out using both conventional and phylogenetically independent methods. The BMRs of the lovebird and grass parakeet species were not statistically correlated with habitat type. These results confirm the findings of previous studies on the effect of desert conditions on the BMR of parrots. I also found no significant differences in BMR between the species assemblages from different continents. The lack of significant differences in BMR between deserticolous and nondeserticolous parrots supports the idea that birds are "ex-adapted" to living in desert environments. I suggest that the results may have been affected by phenotypic plasticity in BMR, as recent evidence has shown that the scaling exponent of BMR differs between captive-raised and wild-caught birds. To elucidate the effect of origin (captive-raised vs. wild-caught) on the BMR of birds used in this study a large scale analysis of bird BMR data was undertaken. BMR and body mass data for 242 species of birds were obtained from the literature, this study, and unpublished data from various sources. A phylogeny was constructed using molecular and morphological phylogenies from the literature, and analysed using conventional and phylogenetically independent methods. The conventional analysis found significant differences in the scaling exponents of BMR of captive-raised and wild-caught birds. However the phylogenetically independent method showed non-significant differences between these two groups. Conventional analysis of differences between parrots and all other birds yielded significant differences between these two groups, with parrots having significantly higher BMRs than other birds. Again the phylogenetically independent analysis found non-significant differences between these VII two groups. A test of homogeneity of variance between these two groups found significant differences between the variances ofthe two groups, probably due to disparity in sample size and range of body sizes. The conventional and phylogenetically independent tests for differences between captive-raised and wild-caught parrots yielded non-significant results, suggesting that the parrots are not subject to the phenotypic adjustments postulated for all other birds. The lack of significant differences between captive-raised and wild-caught parrots suggests that the analyses of differing habitat type for African and Australian parrots is indeed valid. / Thesis (M.Sc.)-University of KwaZulu-Natal, Pietermaritzburg, 2006.

The circovirus Beak and feather disease virus (BFDV) causes psittacine beak and feather disease (PBFD) that is characterised by a chronic disease process associated with feather abnormalities, beak deformities and eventual death in various species of birds in the order Psittaciformes. This disease is seen in captive and wild psittacine species in Australia and several other countries and is a significant threat to the survival of some endangered psittacine species. This thesis reports on genetic studies that have furthered the understanding of the diversity of BFDV present within Australia. These studies have optimised methods of detecting BFDV. They have also resulted in the production of an immunogenic and antigenic recombinant BFDV Capsid protein that could lead to alternate methods of producing viral antigen for serological tests and the development of a BFDV vaccine. To assess the optimal method of the detection of BFDV infection, feather and blood samples were submitted by referring veterinarians throughout Australia from psittacine birds tentatively diagnosed with PBFD or with a history of being in contact with PBFD-affected birds. These samples were examined by 3 procedures commonly used to detect BFDV infection: a polymerase chain reaction (PCR) assay and haemagglutination (HA) for the detection of virus, and haemagglutination inhibition (HI) tests for the detection of virus antibody in response to infection. Of the samples examined from 623 psittacine birds, the prevalence of BFDV DNA in feather samples detected by PCR was 18.85%. There was a strong correlation between PCR and HA testing of feather samples, although possible false-positive and false-negative PCR and HA results were obtained in some samples. Of the 143 birds that were PCR feather-positive only 2 had detectable HI antibody and these birds were also HA feather-negative, which suggests that they were developing immunity to recent infection. All birds with HI antibody were feather HA negative. Despite the rare occurrence of PBFD in cockatiels (Nymphicus hollandicus), 2 of the 13 samples collected from this species were PCR and HA positive indicating that this species can be infected with BFDV. Three studies were undertaken to further our understanding of the genetics of BFDV in Australian avifauna: sequence analysis of the BFDV detected in a grey cockatiel (Nymphicus hollandicus), a species normally considered resistant to infection with BFDV; analysis of the genome of BFDV present in lorikeets (Trichoglossus sp.) in Australia; and analysis of the genome of BFDV detected in endangered swift parrots (Lathamus discolor). Sequence analysis of the entire genome of the cockatiel BFDV isolate revealed that it clustered phylogenetically with 2 other viruses, one from a sulphur crested cockatoo (SCC1-AUS) and one from a Major Mitchell cockatoo (MMC-AUS), which suggests that this isolate from the grey cockatiel was not a cockatiel-specific biotype. Phylogenetic analysis of the ORF V1 of BFDV detected in 7 lorikeets demonstrated these 7 isolates clustered phylogenetically with other BFDV isolates obtained from Loriidae species elsewhere in the world and confirmed the presence of a loriid-specific genotype. Phylogenetic analysis of the sequence data generated from ORF V1 of virus detected in 2 endangered swift parrots provided evidence they were also infected with BFDV genotypes derived from other species of birds, one isolate clustering with viruses from a Loriidae genotype and the other with isolates derived from species of Cacatuidae and Psittacidae. As part of this research, a baculovirus expression system was successfully developed for the production of recombinant BFDV Capsid protein. Inoculation of this protein into chickens resulted in the development of HI antibody, which demonstrated its immunogenicity. When used as an antigen in HI tests it detected antibody in virus-infected birds, which demonstrated its antigenicity. This protein offers potential application as an antigen for the development of serological tests and as an immunogen for incorporation into vaccines for control of PBFD.

Murdoch University (Ph.D.)--Murdoch University, 2008. / Contains three published journal articles at back of thesis. Thesis submitted to the Faculty of Health Sciences. Includes bibliographical references (leaves 196-231)

Diss. vet.-med. Univ. Bern, 2004.

Title from title page of PDF (University of Missouri--St. Louis, viewed March 8, 2010). Includes bibliographical references.

O complexo sul americano de Amazona aestiva/Amazona ochrocephala possui ampla distribuição geográfica, compreendendo desde o nordeste brasileiro até o norte da Argentina e do norte da América do Sul até a Bacia Amazônica, respectivamente. Estudos de filogenia e filogeografia indicam que esses táxons não são reciprocamente monofiléticos. Contudo, esses trabalhos foram baseados apenas no DNA mitocondrial. Assim, o presente estudo teve como objetivo realizar uma análise de filogeografia multilocos do complexo A. aestiva/A. ochrocephala da América do Sul. Foram utilizados os locos mitocondriais COI (512 pb) e ND2 (524 pb) de 189 e 146 indivíduos, respectivamente; os locos nucleares autossômicos AMZ-02 (525 pb), AMZ-10 (524 pb) e AMZ-12 (524 pb) de 132, 133 e 132 indivíduos, respectivamente; e um íntron de um gene ligado ao cromossomo Z (PLAA, 473 pb) de 132 indivíduos. A estrutura genética mitocondrial indicou a presença de quatro linhagens que, apesar de incluírem indivíduos das duas espécies, cada linhagem é majoritariamente composta de indivíduos de uma das espécies. Ou seja, nossos dados mostraram maior tendência a separar os indivíduos das duas espécies do que os estudos prévios, mas ainda sem congruência total com a taxonomia vigente. Duas amostras novas se agruparam na linhagem do norte da América do Sul, ampliando sua distribuição e mostrando incongruência com a atual classificação das subespécies de A. ochrocephala. A distribuição geográfica das linhagens possui concordância com diferentes domínios, sugerindo que pressões seletivas dos ambientes podem ter contribuído para sua diversificação. Adicionalmente, os ciclos glaciais durante o Pleistoceno podem ter alguma relação com mudanças no tamanho populacional das linhagens. A estrutura baseada no loco ligado ao cromossomo Z mostrou boa congruência com a atual taxonomia de espécies. O compartilhamento de haplótipos principalmente nas áreas de maior proximidade entre A. aestiva e A. ochrocephala pode ser um indicativo de introgressão. As incongruências entre genética e plumagem encontrados no presente trabalho ressaltam a necessidade de mais estudos para melhor entender as relações dentro desse complexo de espécies. Sob o ponto de vista da conservação, as linhagens mitocondriais podem ser consideradas como Unidades de Manejo distintas. De um modo geral, o presente estudo contribuiu com mais informações sobre o complexo sul americano de A. aestiva/A. ochrocephala e mostra a importância da utilização de mais amostras e marcadores em estudos evolutivos para uma investigação de padrões filogeográficos e histórias evolutivas de maneira mais ampla / The South American Amazona aestiva/Amazona ochrocephala complex has a broad distribution, ranging from northeast Brazil to the north of Argentina and from the north of South America to the Amazon Basin, respectively. Phylogenetic and phylogeographic studies have shown that these taxa are not reciprocally monophyletic. However, these studies were based only on mitochondrial DNA. Therefore, in the present study we performed a phylogeographic analysis of South American A. aestiva/A. ochrocephala using a multilocus approach. Our database included mitochondrial DNA sequences of COI (512 bp) and ND2 (524 bp) from 189 and 146 individuals, respectively; autosomal nuclear sequences of AMZ-02 (525 bp), AMZ-10 (524 bp) and AMZ-12 (524 bp) from 132, 133 and 132 individuals, respectively; and one intron of a Z chromosome-linked gene (PLAA, 473 bp) from 132 individuals. Mitochondrial data recovered four South American lineages. Even though each lineage groups individuals from both species, the majority of individuals from each lineage belongs to one of the species. Thus, our data showed a clearer tendency to separate individuals from each species than previous studies, but still did not fully agree with current taxonomy. Two new samples clustered in the northern South America lineage, expanding its distribution and revealing incongruence between genetic data and current taxonomy of subspecies of A. ochrocephala. The geographic distribution of lineages matched that of different biomes, suggesting that selective environmental pressures may have contributed to their diversification. Additionally, climatic oscillations during the Pleistocene could have influenced demographic changes of these lineages. The genetic structure based on the Z-linked locus fairly agrees with species taxonomy. The overlap of different mitochondrial lineages mostly occured where the geographic distributions of A. aestiva and A. ochrocephala were closer, suggesting that haplotype sharing could be caused by introgression. The lack of agreement between genetic and plumage data indicated that more studies are needed to solve this question. Regarding conservation, mitochondrial lineages could be considered as distinct Management Units. In sum, the present study contributed to improve the knowledge about the South American A. aestiva/A. ochrocephala complex and highlights the importance of using more samples and markers in evolutionary studies

A pré-medicação apesar de ser freqüentemente utilizada nos mamíferos, é raramente utilizada nas espécies aviárias. O objetivo deste estudo foi avaliar o efeito da pré-medicação na indução e anestesia com sevofluorano em papagaios. Foram utilizados trinta e seis animais adultos oriundos do Parque ecológico do Tietê. Os animais foram randomicamente distribuídos em três grupos: grupo I (n = 12), tratado com NaCl 0,9% como placebo, grupo II (n = 12), com cetamina 10 mg.Kg-1 e grupo III (n = 12), com cetamina 10 mg.Kg-1 e diazepam 0,5 mg.Kg-1, por via intramuscular. Quinze minutos após a pré-medicação, a indução foi realizada por meio de máscara facial conectada a um circuito sem reinalação, usando 4,5% de sevofluorano em 100% de oxigênio, com um fluxo de 1,5L. Tanto os efeitos cardiovasculares e respiratórios, bem como, a qualidade da pré-medicação, indução e recuperação da anestesia foram avaliadas. A Dose anestésica mínima obtida neste estudo foi de 2.4 ± 0.37%, 1.7 ± 0.39%, e 1.3 ± 0.32% para os grupos I, II e III respectivamente. Foi concluído que a cetamina isolada ou cetamina/diazepam diminuem consideravelmente a dose anestésica mínima em papagaios. A cetamina isolada ou em associação, promoveu uma boa qualidade de sedação, permitindo uma melhor indução da anestesia quando comparada a indução com o agente inalatório. Tanto a cetamina isolada quanto a associação, mostraram-se seguras, não alterando as funções cardiovasculares, a oxigenação ou ventilação, podendo ser utilizados com sucesso nesta espécie. Além disto, a anestesia com o sevofluorano foi considerada segura para esta espécie em todos os protocolos estudados. / Although pre-medication is commonly used in mammals, it is rarely used in avian species. The aim of this study was to evaluate the effect of pre-medication in the induction and anesthesia with sevoflurane in parrots. Thirty-six adults animals were utilized from Tietê ecologic park. The animals were randomically distributed in three groups: group I (n = 12), was pre-medicated with NaCl0.9% as a placebo, group II (n = 12), with ketamine 10 mg.kg-1 and group III (n = 12), with ketamine 10mg.kg-1 and diazepam 0.5mg.kg-1, intramuscularly. Fifteen minutes after pre-medication, the induction was accomplished with a facial mask connected to a non rebreathing circuit using 4.5% of sevoflurane in 100% oxygen with a flow rate of 1.5L. The cardiovascular and respiratory effects were evaluated as well as the quality of pre-medication, induction and recovery of anesthesia. The minimal anesthetic concentration obtained at this study was 2.4 ± 0.37%, 1.7 ± 0.39%, and 1.3 ± 0.32% for group I, II and III respectively. It was concluded that ketamine alone or ketamine/diazepam consider decreased the DAM of sevofluorano in parrots. ketamine alone or in association, promoted a good quality of sedation allowing better induction of anesthesia when compared with the induction with inhalant agent. Even ketamine alone or the association were considered a safe procedure, not changing cardiovascular, oxygenation and ventilation and could be successfully used in this specie. Furthermore, the anesthesia with sevoflurane was considered safe to this specie in all protocols.

O presente trabalho foi organizado em cinco capítulos. No primeiro é apresentada uma breve revisão da bibliografia relacionada ao DNA barcode, apontando as aplicações e os limites desse marcador. Os resultados obtidos são apresentados nos três capítulos subsequentes. O segundo capítulo teve como objetivo avaliar o potencial do método de DNA barcoding na distinção de 783 amostras de 228 espécies diferentes de aves neotropicais de 16 ordens baseado na diferença dos valores de divergências intra- e interespecíficas. O DNA barcode permitiu a diagnose da maioria das espécies tanto utilizando os valores de distância quanto os agrupamentos nas árvores de Neighbor-joining (NJ), mostrando ser um marcador muito útil na identificação rápida de aves neotropicais. Além disso, verificamos que ele gera informações que podem ser relevantes a estudos biogeográficos. Foram identificadas espécies proximamente relacionadas que não puderam ser identificadas seguindo essa metodologia, todas pertencentes aos psitaciformes. Assim, o objetivo do capítulo seguinte foi investigar se há caracteres diagnósticos no coxI de pares de espécies irmãs de psitacídeos neotropicais (gêneros Amazona, Ara, Aratinga, Brotogeris e Graydidascalus) e de grupos que não puderam ser identificados nas análises anteriores devido a baixas distâncias interespecíficas ou por não formarem clados reciprocamente monofiléticos nas árvores de NJ (espécies dos gêneros Amazona, Aratinga, Myiopsitta, Pionites, Pyrrhura e Rhynchopsitta). As espécies irmãs apresentaram de quatro a 39 sítios diagnósticos puros e as espécies proximamente relacionadas apresentaram de um a 11 sítios diagnósticos. Apenas as espécies Rhynchopsitta pachyrhyncha e R. terrisi e as espécies Amazona aestiva e A. ochrochephala, não apresentaram caracteres diagnósticos exclusivos e, portanto não puderam ser identificadas. Os resultados mostraram que é possível identificar grande parte das espécies proximamente relacionadas desse grupo de aves utilizando caracteres diagnósticos do DNA barcode. O penúltimo capítulo teve como objetivo identificar espécies de embriões de aves apreendidos do tráfico internacional de animais, utilizando o DNA barcode. Das 58 amostras totais, 93% foram identificadas, sendo três amostras de Ara ararauna, duas de Triclaria malachitacea e 49 de Alipiopsitta xanthops. As quatro amostras restantes (7%) foram identificadas como Amazona aestiva e/ou Amazona ochrochephala. Essas espécies formam um complexo já descrito em alguns trabalhos de filogenia molecular, o que inviabiliza qualquer sistema de identificação de espécies ao nível molecular. O DNA barcoding parece ser eficaz na correta identificação de espécies de aves e é especialmente útil em casos nos quais dados morfológicos não são acessíveis, como o presente exemplo. Por fim são descritas as principais conclusões de cada capítulo. / The present study was organized in five chapters. The first one is a brief review of the literature on DNA barcode, pointing out its applications and limits. The results are presented in the three subsequent chapters. The second chapter aimed to evaluate the potential of the DNA barcoding method in the distinction of 783 samples of 228 different Neotropical birds species from 16 orders, based on the difference of values of intra- and interspecific distances. DNA barcode was able to diagnose most of the species using distance values and Neighbor-joining (NJ) trees. Thus, it is a useful tool for rapid identification of Neotropical birds and it can provide information that may be relevant to biogeography studies. Some closely related species, all psitaciformes, could not be identified. Thus, the following chapter attempted to identify diagnostic characters in the DNA barcode sequences of sister species pairs of Neotropical parrots (genera Amazona, Ara, Aratinga, Brotogeris and Graydidascalus) and groups of species that could not be identified due to low interspecific distances or lack of monophyly in NJ trees (species of the genera Amazona, Aratinga, Myiopsitta, Pionites, Pyrrhura, Rhynchopsitta). The pairs of sister species had four to 39 pure diagnostic sites and closely related species had one to 11 diagnostic sites. Only the pair of species Rhynchopsitta pachyrhyncha and R. terrisi, and Amazona aestiva and A. ochrochephala did not have exclusive characters and therefore could not be identified with this method. The results showed that it is possible to identify the majority of the closely related species of this avian group using DNA barcode characters. The next chapter intended to identify the species of bird embryos apprehended from the illegal animal trade using DNA barcodes. From the total of 58 samples, 93% were identified as: three Ara ararauna, two Triclaria malachitacea and 49 Alipiopsitta xanthops. The four remaining samples (7%) were identified as Amazona aestiva and/or A. ochrochephala. These species form a complex that was already suggested in previous molecular phylogeny studies. Thus, it seems to be impossible to distinguish them based on molecular markers. DNA barcoding seems to be efficient in the identification of species of birds and is especially useful in cases where morphological data is not accessible, as the present example. Finally the main conclusions are described in the last chapter.

Conflict between psittacines (birds within the parrot family) and agriculture is a growing, unstudied threat to psittacine conservation throughout the Caribbean. The intensification of conflict as an apparent outcome of successful conservation interventions is of particular concern on the island of Dominica. Here, conflict between the island's globally threatened parrots and citrus farmers is a potential roadblock to advancing the gains of threatened species recovery programs. This dissertation provides empirical data on the extent and severity of the losses experienced by farmers due to parrots, and the degree to which the resulting conflict has provoked a parrot conservation backlash. This dissertation analyzes the causes of citrus fruit loss including the role of parrot frugivory in these losses and the predictors of parrot frugivory at multiple scales. It also highlights parrot frugivory as a source of a poorly understood commensal relationship with small passerine birds and suggests that the role of psittacines as top-down modifiers of canopy community dynamics is underappreciated. Using social science research methods I illustrate the importance of investigating the meanings and value-oriented attitudes that stakeholders hold towards parrots. I show that it is possible for popular conservation tools such as the flagship concept to inadvertently marginalize other closely related species within a local culture, and that this may be particularly important when human-wildlife conflicts are present. Finally the dissertation illustrates that, overall, crop loss attributed to parrots on Dominica has become a surrogate issue and focal point within a much larger public dispute about the state of agriculture and the security of farmers on Dominica. The findings therefore illustrate the inherent complexity of conflicts involving wild animals and underscore that efforts to understand and mitigate such conflicts in a traditional reductionist manner as purely wildlife-crop loss issues may be misguided. I therefore advocate that multidisciplinary systems perspectives are essential for both the study and management of this and similar conflicts.

O presente trabalho foi organizado em cinco capítulos. No primeiro é apresentada uma breve revisão da bibliografia relacionada ao DNA barcode, apontando as aplicações e os limites desse marcador. Os resultados obtidos são apresentados nos três capítulos subsequentes. O segundo capítulo teve como objetivo avaliar o potencial do método de DNA barcoding na distinção de 783 amostras de 228 espécies diferentes de aves neotropicais de 16 ordens baseado na diferença dos valores de divergências intra- e interespecíficas. O DNA barcode permitiu a diagnose da maioria das espécies tanto utilizando os valores de distância quanto os agrupamentos nas árvores de Neighbor-joining (NJ), mostrando ser um marcador muito útil na identificação rápida de aves neotropicais. Além disso, verificamos que ele gera informações que podem ser relevantes a estudos biogeográficos. Foram identificadas espécies proximamente relacionadas que não puderam ser identificadas seguindo essa metodologia, todas pertencentes aos psitaciformes. Assim, o objetivo do capítulo seguinte foi investigar se há caracteres diagnósticos no coxI de pares de espécies irmãs de psitacídeos neotropicais (gêneros Amazona, Ara, Aratinga, Brotogeris e Graydidascalus) e de grupos que não puderam ser identificados nas análises anteriores devido a baixas distâncias interespecíficas ou por não formarem clados reciprocamente monofiléticos nas árvores de NJ (espécies dos gêneros Amazona, Aratinga, Myiopsitta, Pionites, Pyrrhura e Rhynchopsitta). As espécies irmãs apresentaram de quatro a 39 sítios diagnósticos puros e as espécies proximamente relacionadas apresentaram de um a 11 sítios diagnósticos. Apenas as espécies Rhynchopsitta pachyrhyncha e R. terrisi e as espécies Amazona aestiva e A. ochrochephala, não apresentaram caracteres diagnósticos exclusivos e, portanto não puderam ser identificadas. Os resultados mostraram que é possível identificar grande parte das espécies proximamente relacionadas desse grupo de aves utilizando caracteres diagnósticos do DNA barcode. O penúltimo capítulo teve como objetivo identificar espécies de embriões de aves apreendidos do tráfico internacional de animais, utilizando o DNA barcode. Das 58 amostras totais, 93% foram identificadas, sendo três amostras de Ara ararauna, duas de Triclaria malachitacea e 49 de Alipiopsitta xanthops. As quatro amostras restantes (7%) foram identificadas como Amazona aestiva e/ou Amazona ochrochephala. Essas espécies formam um complexo já descrito em alguns trabalhos de filogenia molecular, o que inviabiliza qualquer sistema de identificação de espécies ao nível molecular. O DNA barcoding parece ser eficaz na correta identificação de espécies de aves e é especialmente útil em casos nos quais dados morfológicos não são acessíveis, como o presente exemplo. Por fim são descritas as principais conclusões de cada capítulo. / The present study was organized in five chapters. The first one is a brief review of the literature on DNA barcode, pointing out its applications and limits. The results are presented in the three subsequent chapters. The second chapter aimed to evaluate the potential of the DNA barcoding method in the distinction of 783 samples of 228 different Neotropical birds species from 16 orders, based on the difference of values of intra- and interspecific distances. DNA barcode was able to diagnose most of the species using distance values and Neighbor-joining (NJ) trees. Thus, it is a useful tool for rapid identification of Neotropical birds and it can provide information that may be relevant to biogeography studies. Some closely related species, all psitaciformes, could not be identified. Thus, the following chapter attempted to identify diagnostic characters in the DNA barcode sequences of sister species pairs of Neotropical parrots (genera Amazona, Ara, Aratinga, Brotogeris and Graydidascalus) and groups of species that could not be identified due to low interspecific distances or lack of monophyly in NJ trees (species of the genera Amazona, Aratinga, Myiopsitta, Pionites, Pyrrhura, Rhynchopsitta). The pairs of sister species had four to 39 pure diagnostic sites and closely related species had one to 11 diagnostic sites. Only the pair of species Rhynchopsitta pachyrhyncha and R. terrisi, and Amazona aestiva and A. ochrochephala did not have exclusive characters and therefore could not be identified with this method. The results showed that it is possible to identify the majority of the closely related species of this avian group using DNA barcode characters. The next chapter intended to identify the species of bird embryos apprehended from the illegal animal trade using DNA barcodes. From the total of 58 samples, 93% were identified as: three Ara ararauna, two Triclaria malachitacea and 49 Alipiopsitta xanthops. The four remaining samples (7%) were identified as Amazona aestiva and/or A. ochrochephala. These species form a complex that was already suggested in previous molecular phylogeny studies. Thus, it seems to be impossible to distinguish them based on molecular markers. DNA barcoding seems to be efficient in the identification of species of birds and is especially useful in cases where morphological data is not accessible, as the present example. Finally the main conclusions are described in the last chapter.