Passive acoustic monitoring (PAM) is a valuable tool in wildlife research, offering non-invasive and cost-effective means to collect acoustic data. However, the processing of PAM recordings can be time-consuming, prompting the use of acoustic indices to expedite analysis. Acoustic indices are numerical values that characterize biological information in sound recordings based on an environment’s acoustic characteristics. While acoustic indices have been correlated with species richness across ecological contexts, their reliability diminishes in areas with heightened vehicular noise. However, it is unclear if index biases caused by vehicular noise are consistent across all traffic levels, and which acoustic indices are most biologically informative in these human-developed contexts. I assessed the direct impact of vehicular noise on nine acoustic indices through controlled manipulation of vehicular noise within 598 computer-generated bird assemblage soundscapes. Using the bird assemblage soundscapes, I also investigated the effects of three high-pass filter treatments (482 Hz, 1 KHz, and 2 KHz) on these acoustic indices under different levels of traffic noise interference. These filtering effects were also assessed within empirical PAM recordings taken from 147 sites in southern Illinois from May into mid-July of 2022 and 220 sites across the state during late-April to mid-July of 2023. Results indicate that proximity to roads and vehicular traffic significantly affect index values, albeit to varying degrees. Four indices – Bioacoustic Index, Acoustic Complexity Index, Acoustic Diversity Index, and Acoustic Evenness Index – exhibited greater resilience to vehicular noise and may be better suited for urban environments. Notably, the Acoustic Diversity Index, Acoustic Evenness Index, and the Number of Frequency Peaks also displayed consistent species richness estimations regardless of vehicular noise level. While filtering had variable interactive effects with vehicular noise, no consistent benefits of filtering were observed across all indices. Nevertheless, the Acoustic Complexity Index, Acoustic Richness Index, and CityBioNet displayed minimal biases when high-pass filters were applied, and CityBioNet demonstrated particularly high correlations with species richness. These findings underscore the importance of understanding index behavior under anthropogenic noise and different filtering methodologies. My findings serve to inform acoustic index implementation within acoustic monitoring efforts, thus expanding access and reliability of these methodologies within human-developed environments.

My thesis focuses on different ranch management practices and the effects they may have on bird communities in northern Texas. Specifically, I address the potential differences between ranches enrolled in the Audubon Conservation Ranching program versus ranches that are not enrolled. Each research chapter is meant to be an individual publication. Chapter 2 compares and contrasts two different ways to survey bird communities in prairie systems. Chapter 3 compares ranch management techniques, prairie health indicators, and bird communities. This study aims to observe any mechanistic drivers of rangeland health that may elicit a positive bird assemblage response.

Peregrine falcon subspecies taxonomy is widely debated due to uncertainty in their evolutionary history and unresolved phylogenetic reconstruction using both morphological and molecular data. Previous genetic work has shown limited support for subspecies taxonomy largely as a result of molecular markers used, potential contemporary gene flow, incomplete lineage sorting, and ancestral polymorphisms. With the advent of next-generation sequencing, the cost of generating large amounts of sequence data has dropped significantly, making whole genome re-sequencing (WGR) studies of non-model organisms more tangible. In this study, WGR methods have been utilized to investigate the phylogenetic relationships among all 20 currently recognized peregrine falcon subspecies. By generating whole-genome data for all 20 subspecies, subspecies specific diagnostic SNPs have been identified to aid in subspecies delimitation. Results of this study broadly support current subspecies, however, reveal that further study is needed to investigate regional relationships among subspecies in Asia, Australia, and western North America. With these results, conservation efforts can be further supported by allowing for accurate delimitation of local subspecies and subspecies boundaries.

published_or_final_version / Public Management / Master / Master of Public Administration

Made available in DSpace on 2014-06-11T19:27:57Z (GMT). No. of bitstreams: 0 Previous issue date: 2007-02-26Bitstream added on 2014-06-13T19:57:05Z : No. of bitstreams: 1 okino_ch_me_jabo.pdf: 1181305 bytes, checksum: cf91a5205aface873e536d06ccd0eb78 (MD5) / Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / A bronquite infecciosa das galinhas (BIG) é uma doença infecciosa que está amplamente disseminada entre as criações avícolas brasileiras e é uma das enfermidades virais que mais têm causado perdas econômicas na atualidade. Portanto, a rápida detecção e identificação do agente causal são imprescindíveis para que medidas eficazes de controle sejam prontamente tomadas. Para tanto, é necessário que os métodos de diagnóstico empregados sejam sensíveis, específicos, rápidos e também de baixo custo. Nesse contexto, a técnica de RTPCR em tempo real abordada no presente estudo permitiu a amplificação de duas regiões de hipervariabilidade do gene S1 de 17 estirpes diferentes do vírus da BIG (VBI), que foram testadas, mas não foi capaz de amplificar nenhum dos RNAvírus heterólogos analisados (vírus da doença de Newcastle, pneumovírus aviário e vírus da doença de Gumboro). Com essa mesma técnica foi possível fazer a diferenciação em grupos geneticamente distintos, de estirpes do VBI através de análises das curvas de dissociação de fragmentos amplificados a partir das regiões de hipervariabilidade gênica I e II do gene S1. A RT-PCR em tempo real desenvolvida apresentou maior sensibilidade na detecção do VBI em amostras teciduais, quando comparada à técnica padrão de Isolamento Viral em ovos embrionados de galinha... / The avian infectious bronchitis virus (IBV) is an infectious disease widely spread in Brazilian commercial poultries where causes significant economical losses. Rapid and accurate diagnosis of the IBV strain involved in a field outbreak is necessary to establish an effective control of this disease. The real-time RT-PCR performed in this study to amplify two hypervariable regions of S1 gene, was able to detect 17 IBV strains, e.g., nine reference strains (including Massachussets, Connecticut, JMK, SE 17 and Iowa serotypes) and eight Brazilian field isolates, whilst non-related avian viral pathogens such as Newcastle disease virus, Avian Pneumovirus and Gumboro disease virus were not detected. The differentiation between IBV strains was accomplished using the melting curve analysis of the amplified fragments corresponding to the hypervariable regions I and II of S1 gene. The real-time RT-PCR developed here showed a higher rate of IBV detection in tissue samples of experimentally infected chickens, when compared to the goldstandard technique of Viral Isolation in embryonated chicken eggs, and the same rate of detection was found for the conventional RT-PCR... (Complete abstract, click electronic access below)

Cette thèse évalue le risque d’émergence d’un pathogène via l’avifaune sauvage dans une région indemne en combinant deux approches :(1) L’étude de pathogènes partageant des caractéristiques éco-épidémiologiques communes avec le pathogène émergeant ;et (2) L’utilisation de données écologiques disponibles dans la région indemne.<p>\ / Doctorat en Sciences agronomiques et ingénierie biologique / info:eu-repo/semantics/nonPublished

Avian pathogenic Escherichia coli (APEC) is a bacterium that is responsible for colibacillosis in birds. However, information about broiler breeder APEC isolates is limited, but the data is critical due to the transfer of this bacteria down the production pyramid to progenies resulting in high mortality. Therefore, we evaluated the phenotypic virulence characteristics of 28 isolates using embryo lethality and day-old chick challenge assays. Also, the in vitro adhesion and invasion potential of selected nine isolates were identified. Results showed more than 1/3rd of the isolates were highly virulent and the virulence increased as the number of virulence-associated genes increased. High adhesion and invasion rates were observed among the isolates. Overall, the study helped us to evaluate the virulence characteristics of APEC from broiler breeders. However, future studies based on whole genome approach would help to identify the specific targets which can be used to develop effective interventions.

Highly pathogenic (HP) avian influenza viruses (AIVs) are naturally restricted to H5 and H7 subtypes with a polybasic cleavage site (CS) in hemagglutinin (HA) and any AIV with an intravenous pathogenicity index (IVPI) ≥ 1.2. Although only a few non-H5/H7 viruses fulfill the criteria of HPAIV; it remains unclear why these viruses did not spread in domestic birds. In 2012, a unique H4N2 virus with a polybasic CS 322PEKRRTR/G329 was isolated from quails in California which, however, was avirulent in chickens. This is the only known non-H5/H7 virus with four basic amino acids in the HACS. Here, we investigated the virulence of this virus in chickens after expansion of the polybasic CS by substitution of T327R (322PEKRRRR/G329) or T327K (322PEKRRKR/G329) with or without reassortment with HPAIV H5N1 and H7N7. The impact of single mutations or reassortment on virus fitness in vitro and in vivo was studied. Efficient cell culture replication of T327R/K carrying H4N2 viruses increased by treatment with trypsin, particularly in MDCK cells, and reassortment with HPAIV H5N1. Replication, virus excretion and bird-to-bird transmission of H4N2 was remarkably compromised by the CS mutations, but restored after reassortment with HPAIV H5N1, although not with HPAIV H7N7. Viruses carrying the H4-HA with or without R327 or K327 mutations and the other seven gene segments from HPAIV H5N1 exhibited high virulence and efficient transmission in chickens. Together, increasing the number of basic amino acids in the H4N2 HACS was detrimental for viral fitness particularly in vivo but compensated by reassortment with HPAIV H5N1. This may explain the absence of non-H5/H7 HPAIV in poultry.

Highly pathogenic (HP) avian influenza viruses (AIVs) are naturally restricted to H5 and H7 subtypes with a polybasic cleavage site (CS) in hemagglutinin (HA) and any AIV with an intravenous pathogenicity index (IVPI) 1.2. Although only a few non-H5/H7 viruses fulfill the criteria of HPAIV; it remains unclear why these viruses did not spread in domestic birds. In 2012, a unique H4N2 virus with a polybasic CS 322PEKRRTR/G329 was isolated from quails in California which, however, was avirulent in chickens. This is the only known non-H5/H7 virus with four basic amino acids in the HACS. Here, we investigated the virulence of this virus in chickens after expansion of the polybasic CS by substitution of T327R (322PEKRRRR/G329) or T327K (322PEKRRKR/G329) with or without reassortment with HPAIV H5N1 and H7N7. The impact of single mutations or reassortment on virus fitness in vitro and in vivo was studied. Ecient cell culture replication of T327R/K carrying H4N2 viruses increased by treatment with trypsin, particularly in MDCK cells, and reassortment with HPAIV H5N1. Replication, virus excretion and bird-to-bird transmission of H4N2 was remarkably compromised by the CS mutations, but restored after reassortment with HPAIV H5N1, although not with HPAIV H7N7. Viruses carrying the H4-HA with or without R327 or K327 mutations and the other seven gene segments from HPAIV H5N1 exhibited high virulence and ecient transmission in chickens. Together, increasing the number of basic amino acids in the H4N2 HACS was detrimental for viral fitness particularly in vivo but compensated by reassortment with HPAIV H5N1. This may explain the absence of non-H5/H7 HPAIV in poultry.

Recent global climate change is influencing the behaviour and ecology of species worldwide. Birds are typical systems to study in this context, as they are often migratory and thus subjected to a variety of environmental effects. This thesis employs the use of long-term ringing records, field observations, historical maps and historical volunteer observations with the aim of describing behavioural and ecological responses of birds to the current environmental change. An investigation into the spring arrival, reproduction and autumn departure in willow warblers (Phylloscopus trochilus) breeding at a southern study site in Sweden (65°N 18°E) showed that all three phenological events had advanced in parallel. Thus birds arrive earlier, start breeding earlier and leave Sweden earlier, with the breeding period staying the same in length. By teasing apart the migratory responses of different individuals, it became clear that particularly early arriving males and early departing juveniles had advanced migration. However, willow warblers migrating past a northern study site in Sweden (65°N 23°E) displayed no change in autumn departure. When migration in the two regionally separate populations were analyzed in relation to climatic variables, the results indicated that foremost a combined effect of growing season onset and the North Atlantic Oscillation influenced migratory timing, and only in individuals that had advanced migration. As growing season onset had advanced at both regions, but only elicited migratory change in southern willow warblers, it is proposed that intra-specific difference between populations prepare them differently to climate change. Willow warblers breeding at northern latitudes were also displaying absence of an otherwise common behaviour of the species: philopatry. It is suggested that the climate induced change in onset of the growing season, coupled with an increase in available territories, could have enabled a southern influx of dispersal-prone birds adopting a less philopatric breeding behaviour. Availability of territories was also studied in southern Sweden, in relation to 100 years of land use change and future climate change effects on forestry. The mass-conversion of grazed forest into coniferous sylvicultures that has occurred in Sweden 1900-2013 was shown to have negatively affected territory availability for willow warblers. The second most common bird species in Sweden, the chaffinch (Fringilla coelebs), was however shown to be largely unaffected. In a future scenario where rising temperatures will increase growth rates of trees, harvest rotation will be faster and both sylvicultures and logged areas will increase in coverage, favouring both species. Thus commonness in terms of landscape and species occurrence has altered historically and is dynamically linked. Historic perspectives were also applied to observations of spring arrival of 14 migratory bird species. A relative comparison of two data sets, collected over 140 years, revealed that short-distance migrants have changed their spring arrival more than long-distance migrants in southern Sweden. In conclusion, the results of this thesis provide insights into climate change effects on avian behaviour and ecology, document unique observations and contribute with a great spectrum of knowledge, from exact details on responses by individual birds, through long-term changes in populations to historical perspectives on shifts in entire landscapes / <p>At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 2: Manuscript. Paper 3: Manuscript. Paper 4: Manuscript.</p>