The species–area relationship (SAR) has been applied to predict species richness declines as area is converted to human-dominated land covers.In many areas of the world, however, many species persist in human-dominated areas, including threatened species. Because SARs are decelerating nonlinear, small extents of natural habitat can be converted to human use with little expected loss of associated species, but with the addition of more species that are associated with human land uses. Decelerating SARs suggest that, as area is converted to human-dominated forms, more species will be added to the rare habitat than are lost from the common one. This should lead to a peaked relationship between richness and natural area. I found that the effect of natural area on avian richness across Ontario was consistent with the sum of SARs for natural habitat species and human-dominated habitat species, suggesting that almost half the natural area can be converted to human-dominated forms before richness declines. However, I found that this spatial relationship did not remain consistent through time: bird richness increased when natural cover was removed (up to 4%), irrespective of its original extent. The inclusion of metapopulation processes in predictive models of species presence improves predictions of diversity change through time dramatically. Variability in site occupancy was common among bird species evaluated in this study, likely resulting from local extinction-colonization dynamics. Likelihood of species presence declined when few neighbouring sites were previously occupied by the species. Site occupancy was also less likely when little suitable habitat was present. Consistent with expectations that larger habitats are easier targets for colonists, habitat area was more important for more isolated sites. Accounting for the effect of metapopulation dynamics on site occupancy predicted change in richness better than land cover change and increased the strength of the regional richness–natural area relationship to levels observed for continental richness–environment relationships suggesting that these metapopulation processes “scale up” to modify regional species richness patterns making them more difficult to predict. It is the existence of absences in otherwise suitable habitat within species’ ranges that appears to weaken regional richness–environment relationships.

Diss. (sammanfattning) Uppsala : Sveriges lantbruksuniv., 2008. / Härtill 4 uppsatser.

Thesis (M. Phil.)--University of Hong Kong, 2009. / Includes bibliographical references (leaves 78-89) Also available in print.

Thesis (M. Phil.)--University of Hong Kong, 2009. / Includes bibliographical references (leaves 78-89) Also available online.

Jumping is one of the common methods that flight capable birds use to initiate the take-off phase. Flapping-wing robots that can achieve jumping take-off similar to birds will be significantly valuable since they can reduce the workload of the wing in producing the instantaneous power required for take-off and enables remote operations as well. This thesis progresses the state of the art in leg based jumping systems for flapping-wing robots through a contribution to the fundamental understanding of jumping dynamics and the development of experimentally validated simulation tools. Three reference leg postures are identified from video analysis of a rook take-off: stand, crouch and extended. Birds often use different kinematic patterns for the leg flexion (stand to crouch) and extension (crouch to extended) phases. This is made possible by their multi degree of freedom (Dof) leg structure and complex, multi actuated muscle systems. As an alternative strategy, a conceptual design of a singly actuated jumping leg is proposed where a multi Dof segmented leg is linked to a single actuator. The structure is based on the avian leg and foot anatomy. The study identifies that a dynamically unstable jumping take-off using a tilt and jump approach enables a singly actuated robotic leg to achieve jumping performance similar to birds. A combination of analytical, numerical and physical modelling approaches is used in this study. A generic analytical jumping model is used to establish fundamental understanding of jumping dynamics. The study shows that the take-off dynamics of a jumping system can be idealised as an inelastic collision between the dynamic and static rigid bodies of the system. This provides a simpler way to understand jumping dynamics in general. A physical prismatic jumping model is fabricated principally for validation purposes. A motion capture system is used to quantitatively analyse the jumping kinematics of the model. The take-off velocities predicted through analytical and numerical models agree closely with the experimental data. A multi-segmented numerical simulation model is then developed based on the proposed singly actuated jumping leg design. In the same way an analytical model is developed. It is found that the singly actuated design concept with the assumption of massless segments greatly reduced the complexity of the multi-segmented analytical model. The proposed analytical approach and simulation tool are demonstrated by designing a multi-segmented jumping leg for an example robotic bird. The transparency of the approach enables the designer to understand how design parameters such as take-off weight, actuation properties, leg postures and sizes of the segments affect the take-off velocity. Numerical simulation analysis confirms that jumping performance similar to birds is achieved in the proposed singly actuated jumping legs with the integration of tilt and jump method. For the presented case study, the use of the dynamic tilting method improves the minimum achievable take-off angle from 73° to 12° with respect to the horizontal axis.

Heavily-selected livestock production traits rarely come without compromise; altered physiology arising from intensive selection often gives rise to concern of a welfare trade-off. A particularly clear example of welfare challenge caused by genetic selection in chickens is the ‘broiler-breeder paradox’, wherein breeding populations of broiler-type birds selected for fast growth are feed-restricted in order to reduce growth and maintain reproductive viability at sexual maturity. In order to better-inform management and breeding strategies for alleviating reproductive problems resulting from genetic selection for growth, it is essential to develop a better understanding of the physiological processes underpinning growth. Whereas the molecular mechanisms governing energy balance in mammals have been relatively welldescribed, analogous avian systems have not received as much research attention and remain somewhat poorly understood. The broad aim of this doctoral project was to contribute to understanding of avian energy balance, particularly in the context of selection for high growth. Using an advanced broiler-layer intercross chicken line (AIL), high- and low-growth haplotypes at the locus encoding the cholecystokinin A receptor (CCKAR), underlying the most significant QTL for growth in chickens, were characterised. Of over 300 variations detected, a select panel spaced across the CCKAR locus were tested for prediction of bodyweight in a diverse cohort of chicken populations. One intronic SNP was found to be significant (p < 0.05) and proximal to transcription factor binding sites. The effect of this locus on gross bodyweight remained significant into the 20th AIL generation (~20% at 10wk, p < 0.05). In this otherwise effectively genetically homogeneous population, several specific physiological traits were predicted by CCKAR haplotype alone, yielding some clues as to the significance of perturbed cholecystokinin (CCK) signalling in broiler strains. While birds with high-growth CCKAR haplotype (HG) did not appear to consume more, feed conversion efficiency (FCE) was improved, at least for males, compared to low-growth (LG) (p < 0.05). Visceral organ anatomies were morphologically disparate, with HG individuals exhibiting ~1/3 less gallbladder mass (p < 0.01), and ~10% shorter GI tract (p < 0.01) and metatarsal bone (p < 0.05). Further gaps in knowledge of the expression of peripheral satiety hormones in chicken are addressed in this thesis. Tissue distributions for expression of CCK, gastrin, pancreatic polypeptide (PPY) and peptide YY (PYY), were mapped and their respective dynamic responses to nutritive state examined. CCK was found to be most highly expressed in the brain, whereas PYY, PPY and gastrin were far more abundant in distinct regions of the periphery. Interestingly, peripheral CCK was not responsive to short-term (< 10h) satiety in experimental populations where PYY and gastrin were. PYY expression was found to be greatest in the pancreas and consistently upregulated within hours after feeding (p < 0.01), whereas gastrin expression was confined to the gastric antrum and paradoxically highest in fasting birds (p < 0.01). PPY expression is strictly limited to the pancreas and appears dependent on longerterm energy state. These results highlight similarities and differences to mammalian systems; notably, the avian pancreas seems to fulfil an exceptional role as a site of signal integration, perhaps unsurprising considering its disproportionate size compared to mammals. Indeed, pancreatic PYY appears to act as a primary peripheral short-term satiety hormone in birds. This body of work contributes to the understanding of avian energy balance and growth. An invaluable foundation for future research is formed by the identification of the major locations of production, and basic nutrient-responsive trends, for several peripheral avian hormones. Information on the growth role of CCKAR is consolidated and expanded upon, demonstrating a clear genetic contribution to maintenance organ morphology and overall growth. Such knowledge can be used to reliably assess and advise on selection and management of chickens to stem welfare concerns without compromising production. Comparisons between avian and other vertebrate endocrine systems make for interesting insight into the adaptive role of energy homeostatic mechanisms in divergent evolution of mammals and non-mammalian vertebrates. In some aspects, birds might better represent the ancestral phenotype from which each vertebrate clade arose.

L’utilisation intensive des antibiotiques a conduit à l’émergence inquiétante de souches bactériennes multi-résistantes, notamment chez les salmonelles et les colibacilles responsables de maladies infectieuses préoccupantes en santé publique et vétérinaire. Les peptides de défense de l’hôte (HDP) constituent les effecteurs antimicrobiens essentiels de l’immunité innée des animaux. La principale famille d’HDPs chez les oiseaux sont les défensines aviaires, dont deux membres (AvBD2 et AvBD7) isolés de la moelle osseuse du poulet présentent un large spectre antibactérien et constituent ainsi des molécules candidates alternatives aux antibiotiques. Pour démontrer l’intérêt thérapeutique de l’AvBD2 et de l’AvBD7, nous avons (1) prouvé leur efficacité antibactérienne in vitro contre des souches cliniques multirésistantes, (2) montré leur stabilité structurale et fonctionnelle face aux protéases digestives majeures, (3) mis en évidence un nouvel effet antimicrobien dans les macrophages infectés, et finalement (4) prouvé le concept thérapeutique en réduisant la mortalité et la charge bactérienne après injection d’AvBD7 dans un modèle de salmonellose systémique létale chez la souris. / Large-scale use of antibiotics has leaded to the emergence of multi drug resistant bacterial strains, particularly in the genus Salmonella and Escherichia coli responsible for infectious diseases outbreaks. This constitutes a major veterinary and public health concern. Host defense peptides (HDPs) represent major effector molecules of the animal’s innate immune system. In birds, the main family of HDPs is composed of avian defensins whose two members (AvBD2 and AvBD7) isolated from chicken bone marrow exhibit large spectrum antibacterial activity. Thus, they both constitute potential candidate molecules as alternative to antibiotics. To demonstrate the therapeutic interest of AvBD2 and AvBD7, we have (1) proved their antibacterial efficiency in vitro towards clinical and multi drug resistant bacterial strains, (2) shown their functional and structural stability when facing major digestive proteases, (3) identified a novel antibacterial effect in infected macrophages, and finally (4) proved the therapeutic concept by reducing mortality and bacterial load after AvBD7 injection in a murine model of lethal salmonellosis.

Neste trabalho foi estuda a interação da E. coli patogênica aviária (APEC), agente etiológico da colibacilose aviária, e células não fagocitárias. A APEC é uma ExPEC (E. coli extra-intestinais), grupo que também inclui a UPEC (E. coli uropatogênica) e a NMEC (E. coli de meningite neonatal). Foi analisado o comportamento de 8 cepas APEC - MT78, IMT2470, A2363, UEL31, UEL13, UEL17, IMT5155, UEL29 - frente a duas linhagens de células não-fagocitárias, fibroblastos aviários CEC-32 e células endoteliais humanas EAhy926. Foi realizada a genotipagem de 33 genes associados à virulência, verificou-se capacidade de associação (adesão e invasão), de invasão e de multiplicação intracelular, de citotoxicidade e de ativação das caspases 3/7 das cepas após infecção de fibroblastos aviários. Foi observado que enquanto todas as cepas foram capazes de aderir aos fibroblastos aviários, somente a cepa MT78 foi capaz de invadí-los em níveis comparáveis à bactéria invasiva Salmonella Typhymurium SL1344. As cepas APEC não induziram ativação de capases 3/7, nem foram citotóxicas aos fibroblastos. Uma vez que a cepa invasiva, MT78, e a não invasiva, IMT2470, apresentam genótipos de virulência muito similares, foi realizado o estudo da expressão por RT-PCR dos genes de virulência da bactéria crescida com e sem fibroblastos aviários, por 3 h. Os resultados mostraram a expressão de adesinas, sideróforos e protectinas/estruturas de resistência ao soro para ambas as cepas na ausência e presença de fibroblastos. A análise da expressão dos genes fimH, ompA, ibeA e gimB pela técnica RT-qPCR revelou a repressão do gene fimH na MT78, mas indução do mesmo na IMT2470. Já as invasinas, gimB e ibeA, estavam induzidas em MT78 e reprimidas em IMT2470, enquanto o gene ompA estava sendo expresso em ambas as cepas. A expressão das invasinas gimB e ibeA explica em parte o fenótipo invasivo da MT78. No presente estudo também foi analisado o comportamento das 8 cepas APEC em relação ao perfil de associação, invasão e multiplicação intracelular ao infectarem células EAhy926. As cepas não mostraram capacidade de invadir as células mas apresentaram um nível de associação muito superior ao dos fibroblastos aviários (até 14 vezes superior para algumas cepas). Este trabalho mostrou que o ensaio in vitro com CEC-32 é um modelo adequado para o estudo da interação celular entre APEC e células eucarióticas e agregou mais conhecimento sobre o patotipo. / In this work the interaction between avian pathogenic E. coli (APEC), the etiological agent of avian colibacillosis, and non-phagocytic cells was studied. APEC is an ExPEC (extraintestinal E. coli), a group that also includes UPEC (uropathogenic E. coli) and NMEC (E. coli neonatal meningitis). We analysed the behavior of 8 APEC strains - MT78, IMT2470, A2363, UEL31, UEL13, UEL17, IMT5155, UEL29 - against two non-phagocytic cell lines, avian fibroblasts (CEC-32) and human endothelial cells (Eahy926). Strains were genotyped for 33 virulence associated genes, and investigated the association capacity (adhesion and invasion), the invasion ability, intracellular multiplication, cytotoxicity and activation of caspases 3/7 of the strains after infecting avian fibroblasts. While all strains were able to adhere to avian fibroblasts, only the strain MT78 was able to invade them at levels comparable to the invasive bacterium Salmonella Typhymurium SL1344. APEC strains could not induce activation of caspases 3/7, nor were cytotoxic to fibroblasts. Since the invasive MT78 and the non-invasive IMT2470 strains presented very similar virulence genotypes, the expression of virulence genes of the bacteria grown in the absence and presence of avian fibroblasts by 3 h was analysed by RT-PCR. Results showed the expression of adhesins, siderophores and protectins/serum resistance structures for both strains in the two culture conditions, with and without fibroblasts. Analysis of the expression of fimH, ompA, ibeA and gimB by RT-qPCR revealed the repression of fimH in MT78, but the induction in IMT2470. In relation to ibeA and gimB invasins, they were induced in MT78 but repressed in IMT2470, while the ompA gene was expressed in both strains. The expression of invasins partly explains the invasive phenotype of MT78. It was also analysed the behaviour of the strains in relation to the association profile, invasion and intracellular multiplication when infecting EAhy926 human endothelial cells. The strains showed no ability to invade endothelial cells but showed a high level of association (up to 14 times higher than for fibroblasts cells for some strains). This study showed that the CEC-32 in vitro model is suitable for the study of cellular interaction between APEC and eukaryotic cells, and added more knowledge about the pathotype.

North American populations of grassland birds have been declining consistently for the past several decades. Grassland birds respond to multiple scales which encompass a spectrum of habitat variables, and the habitat scale of importance may depend on the response of interest. For practitioners, having knowledge of the effect of scale is useful because conservation efforts can be focused at the most appropriate scale. However, previous multi-scale studies of grassland birds and other taxa have rarely incorporated on-the-ground habitat management while simultaneously investigating site-specific species turnover dynamics (Chapter 1) and daily nest survival (Chapter 2). Also, habitat management-related studies often suffer when not accounting for inherent variation between fields, field landscapes, and study year; thus, to disentangle specific effects of management, it is important to account for this variation by using these factors as random effects within mixed-effects models (Chapter 3). Understanding multi-scale habitat relationships affecting site turnover, also known as dynamic occupancy, and daily nest survival rate (nest survival or DSR), as well as how multiple avian responses vary with grassland management would further benefit conservation decision making for focal species. I investigated dynamic occupancy and nest survival of both obligate and facultative grassland species relative to multi-scale habitat factors on private lands (Conservation Reserve Program) in northwest Illinois during 2011-2014. I also conducted a separate analysis focusing on how multiple avian responses, ranging from species presence/absence (P/A) to species-specific nest survival, are influenced by non-fire grassland management treatments. For dynamic occupancy, a combination of ≥2 scales always outperformed single-scale models for all species. Three of 7 species responded to either cumulative habitat management (proportion of field managed over the study period) or yearly management (33% of field managed before a particular breeding season) regardless of dominant grass type. Of the 48 covariates appearing in top models across species for both dynamic and single-season occupancy, microhabitat covariates (42%) were represented most often, followed by patch-scale (33%) and landscape-scale (25%) factors. Covariates with the most consistent effects and the greatest frequencies appearing in competitive (∆AIC ≤ 4) dynamic and single-season occupancy models included landscape forest cover (n = 10), surrounding patch grassland cover (n = 7), and field size (n = 6). In general, increasing levels of forest cover adjoining fields had consistently negative effects on occupancy, colonization, and persistence across species, while grassland surrounding fields and field size had positive effects on these responses. Microhabitat covariates better explained colonization and extinction across the focal species. Of the 22 habitat covariates in top colonization and extinction models, microhabitat variables were represented 50% of the time, compared to 32% and 18% representation for patch-scale and landscape-scale covariates, respectively. I recommend that wildlife biologists utilize habitat management techniques to ensure grassland birds have different successional stages within their range of preferences. My results suggest that grassland disturbance, while influencing turnover dynamics of different species, may be less influential within smaller fields and landscapes dominated by forest cover. I analyzed the daily nest survival rate for 2 species (red-winged blackbirds and dickcissels) and 2 groups of nesting communities (ground and above-ground nesters). Temporal variables such as Julian date and stage of nest were significant predictors of nest survival for red-wings (50.58 ∆AICc = best temporal model) and dickcissels (2.28 ∆AICc = best temporal model) in addition to habitat covariates. In 3 of 4 analyses ≥2 habitat scales were better predictors of nest survival over one scale. For ground nesters the patch scale was be best predictor of nest survival. However, the best model for ground nesters did not have overwhelming support compared to the random model (1.43 ∆AICc). The ground-nesting community appeared to suffer decreased nest survival with increasing proportion of surrounding grassland. The blackbird top model included nest- and landscape-scale covariates, and top models for dickcissels and the above-ground nesting community included the nest- and patch-scale covariates. Blackbirds had a significant increase in nest survival when nests were placed in areas with higher vegetation density and height (greater visual obstruction). Comparatively, the predictive ability of habitat covariates was not as strong for the other 3 analyses; however, notable patterns include dickcissel nest survival decreasing with increasing nest distance to edge and above-ground nests had increased nest survival with increasing patch perimeter-area-ratio. My results suggest different species are responding to different scales, but finer-scale habitat covariates generally help predict nest survival over course-scale habitat features, such as landscape covariates. Songbird nest survival maybe more influenced by fine-scale habitat characteristics such as nesting cover and field vegetation complexity and density, which can deter nest predators and reduce their search efficiency. In a way, this is positive news for practitioners working in grasslands patches located in less than ideal patch or landscape configurations, suggesting more effort could be focused on improving conditions for colonization and persistence of focal species (Chapter 1). By focusing management on dynamic occupancy responses, increasing potential nesting habitat and territory quality for focal species will likely follow. When investigating multiple avian responses to management, within a consistent mixed-effect modeling framework, it appeared that avian survey related responses were best supported, having consistently larger ∆AICc values for top models, when compared to nesting-related data. One explanation of this relative difference could be attributed sample size difference between analyses. Focusing on the effects of management, this analysis accounted for inherent variation across fields, year, and potentially field landscape, as random effects within all models. As suggested from Chapter 2, and despite a large sample of nests, explanation of DSR across all species and focal species showed little improvement with management covariates. Brome fields cumulatively managed with spray or spray/seed treatments (Chapter 1) appeared to respond most and likely explained general positive effects for red-winged blackbird and dickcissel abundance; however, this was at a cost to species abundance for bobolink (Dolichonyx oryzivorus), Henslow’s sparrow (Ammodramus henslowii), eastern meadowlark (Sturnella magna), field sparrow (Spizella pusilla), and northern bobwhites (Colinus virginianus), due to the release of tall forbs within the seed bank after spraying brome dominated fields. Dramatic vegetation responses in sprayed brome fields likely led to an overall decrease in obligate-grassland bird richness and conservation value on brome field types that were cumulatively management over the course of the study. These results suggest the importance of non-native brome CRP fields for certain grassland-obligate bird species, while also revealing the apparent decoupling of nest survival and other avian responses measured commonly. I suggest managers and researchers pay closer attention to variables affecting nesting abundance/density in grassland systems when possible and recognize the potential importance of non-native grasses for grassland-obligate birds in some regions.

Entre os problemas cirúrgicos das aves, as fraturas são os de maior prevalência. Em virtude das variações no tamanho, peso, anatomia óssea peculiar, alta incidência de fraturas complicadas e às diferentes demandas funcionais entre espécies e indivíduos, não foi possível estabelecer ainda um método ideal de osteossíntese para os ossos longos das aves. Por isso, diversos estudos têm sido realizados buscando um método adequado para as diferentes necessidades desses animais. Microplacas de titânio comumente utilizadas em cirurgias maxilofaciais de humanos foram empregadas recentemente na osteossíntese de aves, porém com poucos resultados disponíveis. O objetivo do presente estudo foi avaliar a utilização das microplacas de titânio no tratamento de fraturas experimentais de tibiotarso em pombos domésticos (Columba livia). Foram utilizadas 30 aves, adultas, machos e fêmeas, com 7 meses de idade, pesando entre 400 a 500 gramas, oriundas do Biotério Central da Universidade Federal de Santa Catarina (UFSC). Os animais foram separados aleatoriamente em 3 grupos de dez animais, sendo que no grupo 1 foi utilizado uma microplaca de titânio com 6 furos e espaçador central, no grupo 2 com 8 furos sem espaçador central e no grupo 3 com 8 furos com espaçador central. Após avaliação clínica, as aves foram submetidas a osteotomia médio-diafisária no tibiotarso direito para colocação das diferentes configurações de microplaca de titânio, sendo fixadas com microparafusos de titânio com 7mm de comprimento. Os animais foram avaliados clinica e radiograficamente até os 90 dias de pós-operatório. Após esse período, foi realizada eutanásia em 2 animais de cada grupo. Em todos animais foi observado a consolidação óssea, no grupo 1 o tempo médio e o desvio padrão foram 32,9±9,9; no grupo 2 30,8±6,7 e no grupo 3 26,6±6,4 dias, não havendo diferença estatística entre os grupos. O envergamento do implante foi a complicação mais frequente. A configuração da microplaca resultou em diferença estatística significativa em relação a deambulação e ao grau de envergamento nos diferentes grupos. Sendo que no grupo 3 houve maior precocidade no apoio do membro e menor grau de envergamento em relação aos outros grupos. Histologicamente foi verificado formação de calo ósseo em todos animais e presença de tecido ósseo ao redor da microplaca e microparafusos. Apesar das complicações observadas as microplacas de titânio são uma opção para osteossíntese de tibiotarso em aves de médio porte. / Among the surgical problems in birds, the fractures are the most prevalent. Due to variations in size, weight, peculiar bone anatomy, high incidence of complicated fractures and the functional demands of different species and individuals, is not possible yet to establish an ideal method for osteosynthesis of long bones in birds. Therefore, several studies have been conducted looking for a suitable method for the different needs of these animals. Titanium microplates commonly used in human maxillofacial surgery have been recently employed in osteosynthesis of birds, but with few results available. The aim of this study was to evaluate the use of titanium microplates in the treatment of tibiotarsus fractures in pigeons (Columba livia) 30 birds were used, adult males and females, with 7 months old, weighing from 400 to 500 that came from the Animal Center Facility of the Federal University of Santa Catarina (UFSC). The animals were divided into 3 groups with ten animals each. In group 1 a titanium microplate with 6 holes and a central spacer were used; in group 2 a titanium microplate with 8 holes without a spacer in the center; in group 3 a titanium microplate with 8 holes with central spacer. After clinical evaluation, the birds were submitted to mid-diaphyseal osteotomy in the right bone for placement of different configurations of the titanium plate, and fixed with titanium microscrews 7mm long. The animals were evaluated clinically and radiographically until 90 days postoperatively. After this period, euthanasia was performed in 2 animals from each group. In all animals was observed bone healing and in group 1 the mean and standard deviation were 32.9 ± 9.9, in group 2 30.8 ± 6.7 in group 3 26.6 ± 6.4 days, not having statistical difference in healing time between groups. The bending of the implant was the most common complication. The configuration of the plate resulted in a statistically significant difference in relation to walking and the degree of bending in different groups. Moreover, in group 3 there was higher precocity in the member suppor and a lower degree of bending in relation to other groups. Histologically it was verified the formation of the callus in all animals and the presence of bone tissue around the plate and microscrews. Despite the complications of titanium microplates, they are an option for osteosynthesis of tibiotarsus in birds of medium size.