Thesis (Ph.D)--Biology, Georgia Institute of Technology, 2009. / Committee Chair: Dr. Soojin Yi; Committee Member: Dr. Eric Vigoda; Committee Member: Dr. James Thomas; Committee Member: Dr. John McDonald; Committee Member: Dr. Kirill Lobachev; Committee Member: Dr. Michael Goodisman. Part of the SMARTech Electronic Thesis and Dissertation Collection.

Thesis (M.S.)--New England College of Optometry, 2009. / Includes bibliographical references (p. 41-45).

Thesis (M.S.)--Brigham Young University. Dept. of Physiology and Developmental Biology, 2008. / Includes bibliographical references (p. 38-40).

Thesis (Ph. D.)--University of Chicago, Dept. of Biochemistry and Molecular Biology, June 2003. / Includes bibliographical references. Also available on the Internet.

Thesis (M.S.)--Rochester Institute of Technology, 2007. / Typescript. Includes bibliographical references (leaves 66-67).

This study involves two village chicken populations sampled from Horro and Jarso regions of Western and Eastern Ethiopia respectively. This study maps the phenomic and genomic landscape of the two chicken populations using morphological markers and a high density (600K) SNP array. Although the two chicken populations tend to display nondescript morphological characteristics, they show a subtle variation except for rare morph variants that have been in most instances scored on Jarso chickens. Morphological analysis uncovers a vast array of intrapopulation variation. Genetic diversity and population structure analyses assign the two chicken populations to two distinct genepools representing their population of origin. A high intrapopulation genetic diversity is uncovered, which shows a broad genetic base (high genetic diversity) of the two chicken populations. We hypothesized that a clearly evident genetic divergence observed between the two chicken populations may be attributed to difference in demographic history, origin (routes of introduction to Africa), breeding history of the two chicken populations and demographic structure of subsistence farmers. Absence of gene flow owing to their distant geographic location and ecological variation may have also contributed to this divergence. A population structure analysis performed on a random subset of the two Ethiopian chicken populations along with village chickens sampled from other African countries, Asia and Latin America, commercial populations and the junglefowl species reveals a unique genetic structure of Ethiopian chickens, which implicates the need for further study on the genetic landscape of the latter. To infer the extent of inbreeding we performed a run of homozygosity analysis (ROH). Our analysis indicates that ROH is more intense in Jarso than Horro chickens and in macrochromosomes than microchromosomes. The extensive ROH mapped in some chickens implicates the need to restructure the existing traditional breeding practice of subsistence farmers. Our analysis confirms the commonness of ROH in genic regions. For the first time, we detect twenty three putative uniparental disomy in twenty two Ethiopian village chickens. Signature of selection analysis detects divergently selected genomic regions in the two chicken populations indicating a considerable divergent selection imposed on the two populations. Genes involving in melanogenesis pathway are among those subjected to a divergent selection. However, some overlapping regions were also mapped in the two chicken populations implicating the ubiquitous impact of natural selection on genes regulating vital biological processes. A genome-wide association study performed on pigmentation (earlobe, plumage and shank) traits and variants of crest, comb and a lightly feathered shank maps a number of putative loci that may underlie variations in these traits. Our GWAS analysis on pigmentation traits produced a long list of loci than that have been known to involve in the genetic control of pigmentation in the chicken, with most of these have been mapped in the mouse. We also refined further the causative variants underlying a lightly feathered shank mutation. Our GWAS analysis map a number of putative novel loci that may underlie the genetic control of the traits analysed and this has laid a foundation for subsequent work that would involve targeted sequencing and a candidate gene approach. This study is the first of its kind in Africa that uses a large number of samples and a high density SNP array to unlock phenomic and genomic landscape of the true type village chickens.

The study was aimed to obtain basic information about the distribution of intestinal parasites of mammals and birds in Svalbard. Faeces of different species were used to detect intestinal parasites. All samples were collected during two seasons and examined by microscopic methods and molecular diagnostic was used for detection of microsporidia, cryptosporidia, coccidia and giardiae.

Here I investigate, using autosomal whole-genome sequence data, the signature of positive selection and/or introgression in the indigenous domestic village chickens from three countries (Ethiopia, Saudi Arabia, Sri Lanka), three fancy birds, three junglefowl species (red junglefowl Gallus gallus, grey junglefowl G. sonneratii, Ceylon Junglefowl G. lafayettii) and the Javan red junglefowl G. g. bankiva. All the new sequencing data were obtained from Illumina HiSeq 2000/2500 DNA sequencers with an individual bird depth of genome coverage ranging from 10 X to 30 X. The analyses in this thesis have been completed using the reference genome Galgal 4.0. For the detection of signatures of positive selection, this analysis excluded the three fancy birds and the grey junglefowl due to small sample size. Using the pool heterozygosity and SweeD composite likelihood selection signature methods, I identified two candidate selected regions shared between all the three indigenous domestic village chicken populations and the red junglefowl (chapter 2). These regions contain genes that are associated with the development of the central nervous system and adaptation to hypoxic environments. Five candidate regions were shared among the three indigenous village chicken populations, and they represent candidate domestication regions. Unique regions in each domestic chicken population were also identified. Functional genes have not been assigned to most of these regions but in those where the genes have been annotated, the gene function may be related to production and reproductive traits as well as adaptation to cold/hot temperatures and hypoxia. In chapter 3, I analysed only the Ceylon and green junglefowl whole genome sequences for the detection of candidate signatures of positive selection using both the pool heterozygosity and Tajima’s D. In both species, I identified candidate selected regions that contained genes which may be linked to adaptation to different environmental challenges e.g disease resistance, stress, thermoregulation and hypoxia. In the genome of green junglefowl, candidate selected regions associated with skeletal formation and ovarian follicle development were significantly detected. In chapter 4, I identified introgressed candidate regions from the grey and Ceylon junglefowls in domestic chicken (including the three indigenous chicken populations and fancy birds) using the ABBA – BABA four taxon method. Our result shows that, domestic chickens shared 75.8% of their genome with the red junglefowl, 4% with the grey junglefowl and 1.1% with the Ceylon junglefowl. I observed introgression in both directions, namely from the grey/Ceylon junglefowls into domestic chickens and vice versa. While from the grey junglefowl, introgression was present in all the domestic chicken populations as well as interestingly in the red junglefowl, for the Ceylon junglefowl, introgression was more restricted to the domestic chicken from Sri Lanka. From the ABBA – BABA analysis between the grey junglefowl and the domestic chicken, I also identified a single candidate introgressed region from the green junglefowl G. varius in two domestic birds from Sri Lanka. Future study should therefore consider investigating the genome-wide analysis of introgression from the green junglefowl into the domestic chicken. In chapter 5, I ended our introgression study by investigating if a distantly related subspecies of red junglefowl, the Javan red junglefowl Gallus gallus bankiva, has contributed to the gene pool of the domestic chicken. Alongside the three indigenous domestic chicken populations, I included the genome sequences of three domestic chickens sampled from the Java island of Indonesia. Our result shows a significant 10.6% genome admixture between the domestic chicken and the Javan red junglefowl. Overall, our results indicate that the genetic make-up of the domestic chicken is rather complex with multiple species and subspecies influences. These introgression events have contributed to the genetic diversity of these domesticates. Our results also support the geographic difference of introgression and indicate that these introgression events may have contributed to the adaptive traits of the domestic chicken. However, this requires further investigation.

Made available in DSpace on 2016-01-13T13:27:04Z (GMT). No. of bitstreams: 0 Previous issue date: 2015-04-17. Added 1 bitstream(s) on 2016-01-13T13:32:23Z : No. of bitstreams: 1 000855485.pdf: 7534024 bytes, checksum: 3199f68c4c86807d828a2b5a85013760 (MD5) / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Amphisbaenia é um importante grupo de amniotas reptilianos, providos de corpo cilíndrico e alongado, usualmente desprovidos de membros, com a exceção da Família Bipedidae, que apresentam os anteriores desenvolvidos. Esta anatomia facilita a vida fossorial. São alocados aos Squamata, por possuírem hemipênis, dente para romper e sair do ovo, cloaca transversal e tegumento coberto de escamas. Por assemelharem-se a lacertílios e ofídios, seu posicionamento filogenético tem sido amplamente discutido e sua ancestralidade é ainda controversa. São limitados às regiões subtropicais e tropicais, constituindo importante informação para abordagens paleoecológicas e paleobiogeográficas. Confeccionam profundos túneis compactando o solo, o que implica em grandes modificações morfológicas, tais como crânio robusto, formado por placas ósseas rígidas, e ligações interdigitais na região frontal, podendo ser sobrepostas, o que lhes confere maior resistência contra impactos na escavação. Sua anatomia é bastante convergente com aquela dos fósseis de lacertiformes mesozóicos, demonstrando um provável ancestral em comum com estes diápsidos. Um espécimen de Cryptolacerta, oriundo da Alemanha, compartilha características com Amphisbaenia. Entretanto sua filogenia ainda é incerta. De todo modo, junto com Sineoamphisbaena, pode indicar características convergentes entre lagartos laurasianos, possivelmente com aqueles que originaram Amphisbaenia. Os fósseis de anfisbênios são geograficamente restritos, predominantemente encontrados nos Estados Unidos, em quantidade relativamente escassa. A maior parte está relacionada à Família Rhineuridae, que poderia ser considerada primitiva. No entanto Bipedidae, um grupo recente, também é considerado como primitivo, devido à presença de cintura escapular e membros anteriores. Entretanto não há registros fósseis seguros, pois até então não foram encontrados restos fossilizados.. / Amphisbaenia is an important group of reptilian amniotes, provided with cylindrical and elongated body, usually limbless, with the exception of the Family Bipedidae, which presents limbs. This anatomy facilitates fossorial life. They are allocated to Squamata, by having hemipenis, tooth to break the egg, cross cloacal vent and integument covered with scales. Resembling lacertilians and snakes, their phylogenetic position has been widely discussed and their ancestry is still controversial. They are limited to subtropical and tropical regions, providing important paleoecological and paleobiogeographical informations to the group. They cave deep tunnels, compacting soil, which implies major morphological changes, such as robust skull bones, with rigid plates, and strong osteological connections in the frontal region, with superimposed bones, giving them greater resistance to impacts during excavation. Their anatomy is quite convergent with Mesozoic lacertiform fossils, showing a probable common ancestor with these diapsids. A specimen of VIII Cryptolacerta, from Germany, shares features with Amphisbaenia. However its phylogeny is still uncertain. But Sineoamphisbaena may indicate convergent features between Laurasian lizards, possibly with those originated Amphisbaenia. The fossil records are geographically restricted, predominantly from USA, in relatively small quantity. Most are related to the Family Rhineuridae, which could be considered primitive. However the Family Bipedidae, a recent group, is classified also as primitive, due to the presence of shoulder girdle and forelimbs. But Bipedidae does not present fossils, because until now there are not fossilized remains assigned to them. Morphological convergence occurs in Rhineuridae, detailed in phylogenetic analyses, placing it as a apomorphic group. Anyway it is clear that the origin of Amphisbaenia remains obscure. There are not well preserved fossil materials before beginning of Eocene

Orientador: Reinaldo José Bertini / Banca: Maria Eliana Carvalho Navega Gonçalves / Banca: Silvia Regina Gobbo Rodrigues / Resumo: Amphisbaenia é um importante grupo de amniotas reptilianos, providos de corpo cilíndrico e alongado, usualmente desprovidos de membros, com a exceção da Família Bipedidae, que apresentam os anteriores desenvolvidos. Esta anatomia facilita a vida fossorial. São alocados aos Squamata, por possuírem hemipênis, dente para romper e sair do ovo, cloaca transversal e tegumento coberto de escamas. Por assemelharem-se a lacertílios e ofídios, seu posicionamento filogenético tem sido amplamente discutido e sua ancestralidade é ainda controversa. São limitados às regiões subtropicais e tropicais, constituindo importante informação para abordagens paleoecológicas e paleobiogeográficas. Confeccionam profundos túneis compactando o solo, o que implica em grandes modificações morfológicas, tais como crânio robusto, formado por placas ósseas rígidas, e ligações interdigitais na região frontal, podendo ser sobrepostas, o que lhes confere maior resistência contra impactos na escavação. Sua anatomia é bastante convergente com aquela dos fósseis de lacertiformes mesozóicos, demonstrando um provável ancestral em comum com estes diápsidos. Um espécimen de Cryptolacerta, oriundo da Alemanha, compartilha características com Amphisbaenia. Entretanto sua filogenia ainda é incerta. De todo modo, junto com Sineoamphisbaena, pode indicar características convergentes entre "lagartos" laurasianos, possivelmente com aqueles que originaram Amphisbaenia. Os fósseis de anfisbênios são geograficamente restritos, predominantemente encontrados nos Estados Unidos, em quantidade relativamente escassa. A maior parte está relacionada à Família Rhineuridae, que poderia ser considerada primitiva. No entanto Bipedidae, um grupo recente, também é considerado como primitivo, devido à presença de cintura escapular e membros anteriores. Entretanto não há registros fósseis seguros, pois até então não foram encontrados restos fossilizados.. / Abstract: Amphisbaenia is an important group of reptilian amniotes, provided with cylindrical and elongated body, usually limbless, with the exception of the Family Bipedidae, which presents limbs. This anatomy facilitates fossorial life. They are allocated to Squamata, by having hemipenis, tooth to break the egg, cross cloacal vent and integument covered with scales. Resembling lacertilians and snakes, their phylogenetic position has been widely discussed and their ancestry is still controversial. They are limited to subtropical and tropical regions, providing important paleoecological and paleobiogeographical informations to the group. They cave deep tunnels, compacting soil, which implies major morphological changes, such as robust skull bones, with rigid plates, and strong osteological connections in the frontal region, with superimposed bones, giving them greater resistance to impacts during excavation. Their anatomy is quite convergent with Mesozoic lacertiform fossils, showing a probable common ancestor with these diapsids. A specimen of VIII Cryptolacerta, from Germany, shares features with Amphisbaenia. However its phylogeny is still uncertain. But Sineoamphisbaena may indicate convergent features between Laurasian "lizards", possibly with those originated Amphisbaenia. The fossil records are geographically restricted, predominantly from USA, in relatively small quantity. Most are related to the Family Rhineuridae, which could be considered primitive. However the Family Bipedidae, a recent group, is classified also as primitive, due to the presence of shoulder girdle and forelimbs. But Bipedidae does not present fossils, because until now there are not fossilized remains assigned to them. Morphological convergence occurs in Rhineuridae, detailed in phylogenetic analyses, placing it as a apomorphic group. Anyway it is clear that the origin of Amphisbaenia remains obscure. There are not well preserved fossil materials before beginning of Eocene / Mestre