The aim of this study was to provide deeper insights in passerine phylogenetic relationships using new molecular markers. The monophyly of the largest avian order Passeriformes (~59% of all living birds) and the division into its suborders suboscines and oscines are well established. Phylogenetic relationships within the group have been extremely puzzling, as most of the evolutionary lineages originated through rapid radiation. Numerous studies have hypothesised conflicting passerine phylogenies and have repeatedly stimulated further research with new markers. In the present study, I used three different approaches to contribute to the ongoing phylogenetic debate in Passeriformes. I investigated the recently introduced gene ZENK for its phylogenetic utility for passerine systematics in combination and comparison to three already established nuclear markers. My phylogenetic analyses of a comprehensive data set yielded highly resolved, consistent and strongly supported trees. I was able to show the high utility of ZENK for elucidating phylogenetic relationships within Passeriformes. For the second and third approach, I used chicken repeat 1 (CR1) retrotransposons as phylogenetic markers. I presented two specific CR1 insertions as apomorphic characters, whose presence/absence pattern significantly contributed to the resolution of a particular phylogenetic uncertainty, namely the position of the rockfowl species Picathartes spp. in the passerine tree. Based on my results, I suggest a closer relationship of these birds to crows, ravens, jays, and allies. For the third approach, I showed that CR1 sequences contain phylogenetic signal and investigated their applicability in more detail. In this context, I screened for CR1 elements in different passerine birds, used sequences of several loci to construct phylogenetic trees, and evaluated their reliability. I was able to corroborate existing hypotheses and provide strong evidence for some new hypotheses, e.g. I suggest a revision of the taxa Corvidae and Corvinae as vireos are closer related to crows, ravens, and allies. The subdivision of the Passerida into three superfamilies, Sylvioidea, Passeroidea, and Muscicapoidea was strongly supported. I found evidence for a split within Sylvioidea into two clades, one consisting of tits and the other comprising warblers, bulbuls, laughingthrushes, whitethroats, and allies. Whereas Passeridae appear to be paraphyletic, monophyly of weavers and estrild finches as a separate clade was strongly supported. The sister taxon relationships of dippers and the thrushes/flycatcher/chat assemblage was corroborated and I suggest a closer relationship of waxwings and kinglets to wrens, tree-creepers, and nuthatches. / Das Ziel dieser Arbeit war es, mittels neuer molekularer Marker zusätzliche Informationen über die phylogenetischen Verwandtschaftsverhältnisse der Sperlingsvögel (Passeriformes) zu erhalten. Die Monophylie der Passeriformes, der größten Vogelgruppe (~59% aller lebenden Arten), sowie ihrer Unterteilung in Suboscines und Oscines sind gut belegt. Die phylogenetischen Verwandtschaftsverhältnisse innerhalb dieser Gruppen sind jedoch seit jeher sehr schwer zu entschlüsseln, da sich die meisten Linien durch eine schnelle Radiation entwickelten. Zahlreiche Studien haben verschiedene Hypothesen zur Phylogenie der Sperlingsvögel aufgestellt und damit die Suche nach neuen Markern initiiert. In meiner Untersuchung habe ich drei verschiedene Ansätze benutzt, um zur Klärung der Phylogenie beizutragen. Ich untersuchte das kürzlich als Marker eingeführte ZENK-Gen im Hinblick auf seinen Nutzen in der Systematik der Sperlingsvögel in Kombination und im Vergleich zu drei bereits etablierten nukleären Markern. Meine phylogenetischen Analysen eines umfassenden Datensatzes ergaben hoch aufgelöste, konsistente und stark unterstütze Stammbäume, so dass ich den hohen Nutzwert des ZENK-Gens für die Klärung phylogenetischer Verwandtschaftsverhältnisse der Passeriformes zeigen konnte. Für den zweiten und dritten Ansatz habe ich Chicken Repeat 1 (CR1) Retrotransposons als phylogenetische Marker benutzt. Anhand zweier spezifischer CR1 Insertionen als apomorphe Merkmale und deren Insertionsmuster in verschiedenen Sperlingsvögeln konnte ich die phylogenetische Position der afrikanischen Felshüpfer, Picathartes spp., klären. Aufgrund meiner Ergebnisse schließe ich auf eine engere Verwandtschaft der Felshüpfer zu den Rabenvögeln. Durch meinen dritten Ansatz konnte ich nachweisen, dass CR1-Sequenzen phylogenetische Informationen enthalten, und untersuchte detailliert deren Anwendung als Marker. Dafür habe ich in verschiedenen Sperlingsvögeln nach CR1 Elementen gesucht und mit einigen dieser Sequenzen Stammbäume berechnet, um die Verlässlichkeit der Marker zu überprüfen. Durch meine Untersuchungen konnte ich existierende Hypothesen stützen und zusätzlich starke Hinweise auf neue Hypothesen finden. Beispielsweise schlage ich eine Revision der Taxa Corvidae und Corvinae vor, da Vireos eng mit den Rabenvögeln verwandt sind. Die Unterteilung der Passerida in die drei Unterfamilien Sylvioidea, Passeroidea und Muscicapoidea konnte deutlich bestätigt werden. Ich habe Hinweise auf eine Trennung der Sylvioidea in zwei taxonomische Gruppen erhalten, einer bestehend aus Meisen und Verwandten und der andere aus Grasmücken, Bülbüls, Häherlingen, Brillenvögeln und Verwandten. Während die Passeridae paraphyletisch sind, wurde die Monophylie der Weber und Astrilden als ein eigenes Taxon unterstützt. Das Schwestergruppenverhältnis zwischen Wasseramseln und dem Drossel/Fliegenschnäpper/Schmätzer-Taxon wurde ebenfalls bestätigt. Außerdem habe ich Hinweise auf eine nähere Verwandtschaft zwischen Seidenschwänzen und Goldhähnchen zu Zaunkönigen, Baumläufern und Kleibern gefunden.

Thesis PlanA (M.S.)--University of Wisconsin--Stout, 2006. / Includes bibliographical references.

Orientador: Edir Nepomuceno da Silva / Tese (doutorado) - Universidade Estadual de Campinas, Faculdade de Engenharia de Alimentos / Made available in DSpace on 2018-08-05T13:16:01Z (GMT). No. of bitstreams: 1 Pinto_AndreaTroller_D.pdf: 1260936 bytes, checksum: df21a83a56a9b358c3745669a0ae4ab3 (MD5) Previous issue date: 2005 / Resumo: A salmonelose humana é epidêmica no mundo todo. O consumo de ovos in natura crus ou parcialmente cozidos está associado a esta ocorrência, principalmente quando possuem defeitos de casca e são submetidos a estocagem inadequada. Os trabalhos com contaminação experimental de ovos de galinha geralmente utilizam grandes inóculos e a imersão de ovos em culturas bacterianas puras. Este trabalho teve como objetivo utilizar metodologia de contaminação de ovos com casca íntegra ou com defeitos que se aproximam da realidade operacional de granjas e entrepostos de ovos a fim de avaliar alguns riscos de contaminação por Salmonella Enteritidis (SE) e Escherichia coli em ovos de consumo, a partir da simulação de condições reais como contaminação pós lavagem, lavagem manual, oscilação de temperatura em ovos submetidos a diferentes condições de armazenagem, bem como verificar indicadores de perda de qualidade como a perda de peso e mudanças de pH. Também foi verificado o comportamento destes dois microrganismos em albúmen e gema de ovos de galinha submetidos a duas temperaturas de armazenagem. Os microrganismos estudados tem sua viabilidade diminuida na superfície de ovos com casca íntegra ou com defeitos quando os mesmos são submetidos a temperatura de 30°C, enquanto que a 8°C eles permanecem viáveis na casca. A temperatura de 30°C é responsável pela tendência maior de invasão dos microrganismos no conteúdo interno de ovos de galinha. Foi possível verificar, também, que há uma maior perda de peso em ovos armazenados a 30°C, independentemente da qualidade da casca. O pH de albúmen e gema aumentou ao longo do tempo, independentemente da forma de armazenagem, entretanto a velocidade de alteração do pH do albúmen foi maior na temperatura mais alta / Abstract: Human salmonelosis is epidemic all over the world. Food containing raw and partially coocked eggs is associated with this occurrence. Mainly when they have shell defects and/or are submitted to inadequate storage. The researches with experimental hem eggs contamination use big innocua and dipping eggs into bacterial cultures. This research had as objective, by using egg shell contamination methodology, evaluate some risks of contamination by Salmonella Enteritidis (SE) and Escherichia coli in consumption eggs. It was done by simulation of real operacional system, in an egg grading plant, like post-washing and post-manual washing contamination, oscillation of storage temperature; and by submitting eggs under different temperatures, as well as verifying loss of quality as the loss of weight and changes of pH. Also, the behavior SE and E. coli was verified in albumen and yolk that were submitted by 8° and 30°C. The results were that SE and E. coli decresase their viability on the egg surface, in intact and in imperfect shells, when the eggs were stored by 30°C, while that 8°C they remain viable on the surface. By 30°C, the bacteria can penetrate more easily in the egg contens. It was possible to verify that thre are a bigger loss of weight in the eggs stored at 30°C, independently of the shell quality. The pH of the albumen and the yolk increased, independently of the storage temperature, however the speed of alteration of pH of albumen it was bigger in the highest temperature / Doutorado / Doutor em Tecnologia de Alimentos

The phenotypic characteristics, level of production, management system and contribution of the local chickens to household studied in the north central Namibia. The study involved both qualitative and quantitative methods to gather the data. The questionnaire was used for survey while phenotypic characteristics and egg production forms were used to collect the actual data. The findings revealed that farmers in the study area regarded chicken production as their primary source of domestic animal protein, with the domestic fowl being the most widely kept poultry species. Other uses are participation in socio-cultural ceremonies, selling for money and gifts. The average number of eggs per clutch ranged from 10 to 15. The hatchability ranged between 50% and 60%). Phenotypic characteristics measures revealed the absence of pure white plumage colour that can be associated with the introduction of White Leghorn to the flock. Generally, normal feather cover was the main feather morphology of local chicken populations in north central Namibia. However, features like crested heads, naked necked, frizzling, and feathered shanks occurred sporadically among local chickens in the study area. Fifty-seven percentages of chickens in the surveyed region had single comb, while 29.6% and 13.8% had rose and pea combs respectively. The most frequent shank colour was black followed by yellow, whitish, orange, and reddish shank. The wing span had positive correlation with body weight and chest circumference at (r = 0.994). Other researchers discover the strong correlation of chest circumference with length shank at (r = 0.827). The current study attained the mean body weight of 1.7 to 2.1 kg of both sexes combined which falls within the range of 1.6 to 2.18 kg reported by (Alabi et al. 2012). In conclusion, the current study revealed large variation of phenotypical characteristics with poor correlation to their productivity due to lack of record keeping although production forms were made available to the farmers. The part of productivity according to their identified phenotypic characteristics is not accepted nor rejected due to poor records, but recommended for further study with training on record keeping by farmers / College of Agriculture and Environmental Sciences / M. Sc. (Agriculture)

The Attwater’s prairie-chicken (Tympanuchus cupido attwateri; APC) is a species of grouse native to Texas coastal prairies and is on the critically endangered species list as a result of habitat destruction and overhunting. All of the current populations were captively bred and released into the wild. Survivorship for released APCs is very low, and individuals seldom survive to reproduce in the wild. One factor contributing to this may be an alteration in the gut microbiota as a result of captivity. Factors potentially influencing the gut microbial composition in captivity include antibiotic therapy, stress, and a predominantly commercially formulated diet. Recent studies have begun to shed light on the importance of the host microbial endosymbionts. Antibiotic administration, stress, diet, age, genotype and other factors have been shown to influence microbial populations in the gastrointestinal tracts of many different vertebrates. Sequencing of 16S rRNA gene amplicons on the Ion Torrent™ platform was used in this study to identify groups of bacteria in the cloacas as a surrogate for the gut microbiota in the APC. Antibiotic-treated and untreated birds, wild-hatched and captive-bred birds, and individuals sampled before and after release to the wild were examined. Significant differences were found between wild-hatched and captive raised birds both pre- and post release. In addition, there was extensive variation among the populations at the lower taxonomic ranks between individuals for each group of APCs. Principal coordinate analysis based on the weighted UniFrac distance metric further exhibited some clustering of individuals by treatment. These data suggest that captive breeding may have long-term effects on the cloacal microbiota of APCs with unknown consequences to their long-term health and survivorship.

Day old Dekalb XL-link pullets were randomly assigned to eight dietary treatments of 100 birds each. The percent crude protein (CP) with the respective weeks fed in parentheses for each treatment (T) was as follows: T1. control 18(0-6), 15(6-14) and 12(14-20); T2. 18(0-1), 12(1-8), 15(8-14) and 18(14-20); T3. 18(0-1), 12(1-10), 15(10-16) and 18(16-20); T4. 18(0-1), 12(1-12), 15(12-16) and 18(16-20); T5. 16(0-1), 12(1-10), 15(10-16) and 18 ( 16- 20 ); T6 . 16 ( 0-1 ) , 12 ( 1-12 ) , 15 ( 12 -16 ) and 18 ( 16- 2 0); T7. 20(0-1), 12(1-10), 15(10-16) and 18(16-20); and T8. 20(0-1), 12(1-12), 15(12-16) and 18(16-20). All diets were fed ad lib. The control pullets were heavier for most of the 20-week growing period. Skeletal growth was highly correlated with body weight, however body size was not different at 20 weeks. Cumulative feed intake of the control fed birds was significantly greater than five of the reverse protein fed birds. Feed conversion and protein intake suggested a potential economic advantage in reverse protein feeding. At 20 weeks of age, 576 pullets were transferred to laying cages and fed a common diet. No differences in body weight were seen at 28 weeks of age. Livability was not affected by dietary treatment. Hen-day and hen-housed figures showed significant treatment effects during the first 28-day period only. No significant differences were seen in egg weight, % egg size, egg mass, egg specific gravity, shell deformation, Haugh units or any feed trait. Reverse protein feeding appeared to offer promise as a method of restricting growth in egg-type pullets. The significance of effects on egg production traits may have been masked by small sample size. / M.S.

To identify antigens unique to live Pasteurella multocida P1059, 10 week old specific pathogen-free (SPF) chickens were vaccinated three times with one of the following: viable cells from P. multocida P1059, 3865, 3866, or cells from formalin-killed strain PI059 or formalin-killed strain P1059 that were opsonized with antiserum directed against killed strain PI059 prior to immunization. Vaccinated birds were challenged with 1.5 x 10⁷ CFU of live strain P1059. Eight, 71, 86, and 50% of the birds that received live strains P1059, 3865, 3866 and killed strain P1059 (respectively), exhibited clinical signs of fowl cholera. Antisera directed against live strain PI059 recognized 23 proteins ranging from 14- to 92-kilodaltons (kDa); 20 of which were adsorbed by strain 3865. The molecular masses of the three remaining proteins were 25-, 30- and 43-kDa. A genomic library of strain P1059 was constructed using the plasmid vector pUC-19 and screened with antisera against live strain P1059; 12 out of 4,100 clones were recognized. The inserts of the plasmids from these clones ranged from 0.48- to 6.S-kilobases (kb) in length. Five of the 12 clones expressed proteins with molecular masses of 34-, 37-, 42-, 46- and 55-kDa. Escherichia coli CSR603(pOP43- 2G) and CSR603(pOP33-SF) expressed proteins recognized by antisera directed against live strain P1059. E. coli CSR603(pOP43-2G) expressed an epitope(s) which was recognized by antisera directed against strains 3865 and 3866. Conditions for transformation were optimized and attempts were made to create a shuttle vector in order to establish a cloning system for gene expression in P. multocida. The highest efficiency of transformation (1.25 x 10⁷ CFU/μg DNA) was obtained when 7.6 x 10¹⁰ cells of P. multocida R473 were electroporated at 12.5 kV cm⁻¹ for 10 ms with 5 ng of the plasmid, p VM109. Of the six strains tested, representing serogroups A, B, D and E, all were transformed successfully. Vectors including pBR322, pUC19, pJFF224-NX and pSP329 were unable to transform P. multocida. To create a shuttle vector for gene expression in P. multocida, a Pasteurella plasmid (pLAR-1) was cloned in both orientations into the BamH I site of pBR322. These plasmids, pLRBR-21 and pLRBR-67, had a transformation efficiency of 4.5 to 8 x 10⁴ CFU/μg of DNA in strain R473. Chromosomal DNA containing the Brucella abortus copper-zinc superoxide dismutase gene was cloned into the Cla I site of pLRBR-21. The 1.8-kb fragment encoding a 42-kDa Pasteurella protein was cloned into an additional unique site (Nru 1) of pLRBR-21 to determine if this plasmid was a viable shuttle vector for gene expression in P. multocida. / Ph. D.

Typescript (photocopy). / Digitized by Kansas Correctional Industries

Call number: LD2668 .T4 1956 G53 / Master of Science

Many phenotypes are controlled by factors which include the genes, the environment, interactions between genes and interaction between the genotypes and the environment. Great strides have been made to understand how these various factors affect traits of agricultural, medical and environmental importance. The chicken is regarded as a model organism whose study would not only assist efforts towards increased agricultural productivity but also provide insight into the genetic determination of traits with potential application in understanding human health and disease. Detection of genomic regions or loci responsible for controlling quantitative traits (QTL) in poultry has focussed mainly on growth and production traits with limited information on reproductive traits. Most of the reported results have used additive-dominance models which are easy to implement because they ignore epistatic gene action despite indications that it may be important for traits with low heritability and high heterosis. The thesis presents results on the detection of loci and genetic mechanisms involved in sexual maturity traits through modelling both additive-dominance gene actions and epistasis. The study was conducted on an F2 broiler x White Leghorn layer cross for QTL detection for age, weight, abdominal fat, ovary weight, oviduct weight, comb weight, number of ovarian yellow follicles, a score for the persistence of the right oviduct and bone density. In addition, body weight QTL at 3, 6, 12, 24, 48 and 72 weeks of age, QTL for growth rate between the successive ages and QTL for the parameters of the growth curve were also detected. Most of the QTL for traits at sexual maturity acted additively. A few of the QTL explained a modest proportion of the phenotypic variation with most of the QTL explaining a small component of the cumulative proportion of the variation explained by the QTL. Body weight QTL were critical in determining the attainment of puberty. The broiler allele had positive effects on weight at first egg and negative effects on age at first egg. Most QTL affecting weight at first egg overlapped with QTL for age at first egg and for early growth rate (6-9 weeks) suggesting that growth rate QTL are intimately related to the onset of puberty. Specific QTL for early and adult growth were detected but most QTL had varying influence on growth throughout life. Chromosome 4 harboured most of QTL for the assessed traits which explained the highest proportion of the phenotypic variation in the traits confirming its critical role in influencing traits of economic importance. There was no evidence for epistasis for almost all the studied traits. Evidence for role of epistasis was significant for ovary weight and suggestive for both growth rate and abdominal fat.