Thesis (Ph.D.)--Murdoch University, 2005. / Thesis submitted to the Division of Health Sciences. CD-ROM contains appendix. Bibliography: leaves 104-120.

Thesis (Master)--İzmir Institute of Technology, İzmir, 2005. / Includes bibliographical references (leaves. 111-115).

Thesis (M. Sc.)--University of Canterbury, 2009. / Typescript (photocopy). Includes bibliographical references (leaves 128-130) and index. Also available via the World Wide Web.

Thesis (M.S.)--Baylor University, 2006. / Includes bibliographical references (p. 58-64).

Even today, many genes are without any known homolog. These "orphans" are found in all species, from Viruses to Prokaryotes and Eukaryotes. For a portion of these genes, we might simply not have enough data to find homologs yet. Some of them are imported from taxonomically distant organisms via lateral transfer; others have homologs, but mutated beyond the point of recognition. However, a sizeable fraction of orphan genes is unambiguously created via "de novo" mechanisms. The study of such novel genes can contribute to our understanding of the emergence of functional novelty and the adaptation of species to new ecological niches. In this work, we first survey the field of orphan studies, and illustrate some of the common issues. Next, we analyze some of the intrinsic properties of orphans proteins, including secondary structure elements and Intrinsic Structural Disorder; specifically, we observe that in young proteins the relationship between these properties and the G+C content of their coding sequence is stronger than in older proteins. We then tackle some of the methodological problems often found in orphan studies. We find that using evolutionarily close species, and sensitive, state-of-the art homology recognition methods is instrumental to the identification of a set of orphans enriched in de novo created ones. Finally, we compare how intrinsic disorder is distributed in bacteria versus eukaryota. Eukaryotic proteins are longer and more disordered; the difference is to be attributed primarily to eukaryotic-specific domains and linker regions. In these sections of the proteins, a higher frequency of the disorder-promoting amino acid Serine can be observed in Eukaryotes. / <p>At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 3: Submitted. Paper 4: Manuscript.</p>

Understanding our evolutionary history as a species has since long been one of the most attracting and controversial themes of the scientific investigation. From its geographical position, outstanding fossil record and richness of human diversity, the Horn of Africa and, particularly, the Ethiopian region offers an unmatched opportunity to investigate our origins from a genetic perspective. To carry out a genome-wide survey of this region, 13 out of the estimated 80 extant Ethiopian populations were typed on an Illumina Omni 1M SNP array. The results showed a good concordance between genetic and linguistic stratification and, overall, a complex population structure placing the Ethiopians in between North and Sub Saharan Africans, due to the recent non African gene flow which was dated at around 3000 years ago. Furthermore the SNP array data unveiled putative traces of the out of Africa migrations as well as, in two of the typed populations, signatures of genetic adaptation to high altitude. To obtain an unbiased, high resolution representation of the Ethiopian genetic landscape, 25 individuals from each of five populations were newly collected and sequenced on an Illumina HiSeq platform. These populations were chosen, from among the ones typed on the SNP array, to represent the main components of Ethiopian genetic diversity. Of the 25 samples per population, 24 were sequenced at low depth to generate a broad list of genetic variants, while one sample from each was sequenced at high depth to provide a higher resolution list of variants peculiar to each analysed population. The 125 Ethiopian genomes thus sequenced, while overall consistent with the genotyping results, described the Ethiopian populations in a less biased way than the SNP array data. Furthermore estimation of past effective population size fluctuations from the individual genomes unveiled a unique pattern in the ancestry of the Ethiopian populations in the early stages of human evolution. These results provide a data resource which can be used in future analyses.

Following their dispersal out of Africa, humans colonised all continents of the world save one, Antarctica. Whilst Europe was initially peopled soon after this exodus, paleoclimatic, archaeological, and historical evidence suggest that successive waves and migrations of people have contributed to the population resident in Europe today. I therefore examined the impact of past events on the European population through the analysis of DNA sampled both from contemporary Europeans, and from worldwide populations pertinent to its history. I genotyped and analysed data from the Y chromosomes of over 2,000 haplogroup R-M269 European men from over 30 different populations and, in combination with comparable datasets gathered from the literature, show that there it is not possible to assign a date to the origin of this lineage in Europe, and thus that any conclusion as to the ancient or recent spread of this lineage in Europe is unfounded. I also show that commonly used Y chromosome lineage dating techniques based on STR variation are biased by the markers used and conclusions based on such dates should be viewed with a large amount of caution. I next use genome-wide SNP data from 1,550 individuals from 95 worldwide populations to explore the population structure of Europe and present an analysis of the detailed structure of Europe in a novel analytical framework using ChromoPainter and fineSTRUCTURE. Admixture analysis based this data reveals distinct genomic inputs to peripheral European populations, from North Africa, Sub-Saharan Africa, the Middle East, and East Asia, and provides dates for this admixture within the last 1,000 years that correspond to the emergence and decline of empires and kingdoms in these regions of Europe. This novel analysis highlights the importance of recent historical events on European population structure, but also suggests a degree of ancient structure across European populations. Taken together, these analyses demonstrate the substantial effects of both ancient and recent migrations and mixture on the contemporary genetic structure of Europe.

Carbohydrate Active Enzyme family 6 (CA6) glycosyltransferases (GTs) are type II transmembrane proteins localized in the Golgi apparatus. CA6 GTs have a GT-A fold, a type of structure that resembles the Rossman fold and catalyze the transfer either galactose (Gal) or N-acetylgalactosamine (GalNAc) from the UDP nucleotide sugar to an non-reducing terminal Gal or GalNAc on an acceptor via an a-1,3 linkage. In this reaction, the anomeric configuration of the sugar moiety of the donor is retained in the product. CA6 GTs includes the histo-blood group A and B GTs, a-galactosyltransferase (a3GT), Forssman glycolipid synthase (FS), isogloboside 3 synthase (iGb3) in mammals. a3GT and its products (a-Gal epitode) are present in most mammals but are absent in humans and old world primates because of inactivating mutations. The absence of a3GT and its products results in the production of anti-a-Gal epitope natural antibodies in these species. / Up to date, the catalytic mechanisms of the CA6 GTs are not well understood. Based on previous structural and mutagenesis studies of bovine aB3GT, we investigated active site residues (His315, Asp316, Ser318, His319, and Lys359) that are highly conserved among CA6 GTs. We have also investigated the role of the C-terminal region by progressive C-terminal truncations. Findings from these studies clarify the functional roles of these residues in structure, catalysis, and specificity in these enzymes and have implications for their catalytic mechanisms. GTs are useful tools in synthesis of glycans for various applications in science and medicine. Methods for the large scale production of pure glycans are continuously being developed. We created a limited randomized combinatorial library based on knowledge of structural information and sequence analysis of the enzyme and its mammalian homologues. / Two GalNAc-specific variants were identified from the library and one Glc-specific variant was identified by site-direct mutagenesis. The glycosyltransferase activities of these variants are expected to be improved by further screens of libraries which are designed using the variants as templates. The mammalian CA6 GTs that have been characterized to date are metal-independent and require the divalent cation, Mn2+ for activity. In some recently-discovered bacterial CA6 GTs, the DXD sequence that is present in eukaryotic GTs is replaced by NXN. We cloned and expressed one of these proteins from Bacteroides ovatus, a bacterium that has been linked with inflammatory bowel disease. Functional characterization shows it is a metal-independent monomeric GT that efficiently catalyzes the synthesis of oligosaccharides similar to human blood group A glycan. / Mutational studies indicated that despite the lack of a metal cofactor there are similarities in structure-function relationships between the bacterial and vertebrate family 6 GTs. / by Percy Tumbale. / Thesis (Ph.D.)--Florida Atlantic University, 2009. / Includes bibliography. / Electronic reproduction. Boca Raton, Fla., 2009. Mode of access: World Wide Web.

Hybrid zones are regions where genetically differentiated forms come together and exchange genes through hybrid offspring. The study of characters gradually changing across such zones (clines) can give insight into evolutionary processes, providing exceptionally sensitive estimates of the intensity of selection, and allowing the detection of loci that might be involved in reproductive isolation and speciation. The Alpine grasshopper Podisma pedestris has a hybrid zone in Southern France where two populations meet. They differ in their sex chromosome system, and strong selection against hybrids is observed. These distinct populations likely have split and re-joined several times during the Quaternary glacial cycles. A model explaining the selection observed against hybrids postulates hundreds of loci of small effect spread over two differentiated genomes meeting in secondary contact. Yet, over 50 years of study to-date non have been discovered. However, so far the study of P. pedestris has not made use of high-throughput sequencing data which provides an unprecedented resolution of molecular markers. I am aiming to close the gap with this thesis. I assemble the grasshopper's mitochondrial genome sequence and infer what proportion of its genome is made up by mitochondrial inserts (Numts). Using transcriptome data from two individuals, I then go on to fit demographic models, finding the populations split approximately 400 000 years ago and that the current-day population sizes are considerably smaller than the ancestral one. The final data chapter explores the genetic architecture of the hybrid zone using data from a targeted sequence capture of hundreds of loci covering some 10 000 polymorphic sites. Only two loci under selection are identified, which is surprising given the power of the analysis. Both loci are located on the X chromosome and are subject to weak selection (0.3% and 0.03%). This shows the power of hybrid zone analysis to infer targets of selection. The results are discussed in light of a theoretical chapter on the 'inexorable spread' phenomenon and lead to the proposal for further research into the causes of the reproductive isolation observed between the grasshopper populations.

Selection in spatially heterogeneous environments is a convenient explanation for the high levels of genetic variation observed in natural populations. Indeed, theoretical studies predict that spatial heterogeneity leads to higher levels of variation in a variety of selection models. These models, however, have assumed quite restrictive parameters (e.g., two alleles, fixed gene flow and specific selection schemes). Therefore, the effect on spatial heterogeneity is still poorly understood for a wider range of parameters (e.g., multiple alleles, different levels of gene flow and more general selection schemes). We have relaxed some of the assumptions that have limited the previous models and studied the effect of spatial heterogeneity using simple single-locus viability selection models. First, we investigate the rarity of the parts of fitness space maintaining variation for multiple alleles and different levels of gene flow by randomly sampling that space using a "fitness space" approach. The volume of fitness space maintaining variation is always larger in a spatial model compared to a single-population model regardless of gene flow. Moreover, this volume is relatively larger for higher numbers of alleles, indicating that spatial heterogeneity is more efficient maintaining higher levels of variation. Second, we investigate the ease with which a more natural process of recurrent mutation and selection evolves to the particular area of fitness space maintaining variation using a "construction" approach. Depending on the amount of gene flow, the construction approach leads to both higher and lower levels of variation compared to a single-population model. Thus, spatial heterogeneity can both constrain and promote the ease with which a natural process of mutation and selection evolves to maintain variation. Also, the construction approach results in variation being maintained in a more stable subset of the volume of fitness space than the volume that resulted from the fitness space approach. Third, we investigate the effect of higher and lower levels of spatial environmental heterogeneity using the construction approach. The different levels of heterogeneity and gene flow interact to influence the amount of variation that is eventually maintained and this interaction effect is especially strong for intermediate levels of gene flow. More heterogeneous environments can maintain higher levels of variation, but selection in these environments also results in a higher level of migration load, lowering the final amount of adaptation that is achieved by the simulated evolutionary process. Finally, we investigate effect of genetic drift and finite populations using the construction approach. Interestingly, two different effects emerge for smaller and larger populations; in smaller populations genetic drift lowers the amount of variation as expected, whereas, more surprisingly, genetic drift increases the amount of variation in larger populations. Overall, spatial heterogeneity has profound effects on the outcome of selection, resulting in elevated levels of genetic variation for a wide variety of parameters.