HUMAN GENOME VARIATIONS AND EVOLUTION WITH A FOCUS ON THE ANALYSIS OF TRANSPOSABLE ELEMENTS

Genome sequence varies in numerous ways among individuals although the gross architecture is fixed for all humans. Retrotransposons create one of the most abundant structural variants in the human genome and are divided in many families, with certain members in some families, e.g., L1, Alu, SVA, and HERV-K, remaining active for transposition. Along with other types of genomic variants, retrotransponson-derived variants contribute to the whole spectrum of genome variants in humans. With the advancement of sequencing techniques, many human genomes are being sequenced at the individual level, fueling the comparative research on these variants among individuals. In this thesis, the evolution and functional impact of structural variations is examined primarily focusing on retrotransposons in the context of human evolution. The thesis comprises of three different studies on the topics that are presented in three data chapters. First, the recent evolution of all human specific AluYb members, representing the second most active subfamily of Alus, was tracked to identify their source/master copy using a novel approach. All human-specific AluYb elements from the reference genome were extracted, aligned with one another to construct clusters of similar copies and each cluster was analyzed to generate the evolutionary relationship between the members of the cluster. The approach resulted in identification of one major driver copy of all human specific Yb8 and the source copy of the Yb9 lineage. Three new subfamilies within the AluYb family – Yb8a1, Yb10 and Yb11 were also identified, with Yb11 being the youngest and most polymorphic. Second, an attempt to construct a relation between transposable elements (TEs) and tandem repeats (TRs) was made at a genome-wide scale for the first time. Upon sequence comparison, positional cross-checking and other relevant analyses, it was observed that over 20% of all TRs are derived from TEs. This result established the first connection between these two types of repetitive elements, and extends our appreciation for the impact of TEs on genomes. Furthermore, only 6% of these TE-derived TRs follow the already postulated initiation and expansion mechanisms, suggesting that the others are likely to follow a yet-unidentified mechanism. Third, by taking a combination of multiple computational approaches involving all types of genetic variations published so far including transposable elements, the first whole genome sequence of the most recent common ancestor of all modern human populations that diverged into different populations around 125,000-100,000 years ago was constructed. The study shows that the current reference genome sequence is 8.89 million base pairs larger than our common ancestor’s genome, contributed by a whole spectrum of genetic mechanisms. The use of this ancestral reference genome to facilitate the analysis of personal genomes was demonstrated using an example genome and more insightful recent evolutionary analyses involving the Neanderthal genome. The three data chapters presented in this thesis conclude that the tandem repeats and transposable elements are not two entirely distinctly isolated elements as over 20% TRs are actually derived from TEs. Certain subfamilies of TEs themselves are still evolving with the generation of newer subfamilies. The evolutionary analyses of all TEs along with other genomic variants helped to construct the genome sequence of the most recent common ancestor to all modern human populations which provides a better alternative to human reference genome and can be a useful resource for the study of personal genomics, population genetics, human and primate evolution.

Microstructural and geochemical investigation of North American lower-middle Paleozoic trilobites and recent arthropods

Trilobites ¥tere collected from Ordovician and Devonian formations of Ontario} New York} Ohio} Oklahoma} and Indiana. Diversity was generally low} but 19..?telllS and Ph..~tY>ps ¥tere the most abundant species from the Ordovician and Devonian} respectively. Recent marine arthropods ¥tere collected from the Atlantic shore of the middle Florida Keys} and from the Pacific and lagoonal waters at Cape Beale} B. C. Fresh-water arthropods were collected along the shore of the Severn River in northcentral Ontario. Cuticles ¥tere analyzed for major} minor and trace elements, 180 and 13C isotopes, as ¥tell as examined by scanning electron micr?scope to identify original and diagenetic fabrics. Examination of trilobite cuticles by scanning electron microscope revealed several microstructures consistent with those observed in Recent arthropods. Microstructures} such as setae and tegumental gland duct openings} in like sized Lim/IllS and Isoteline trilobites may indicate common ancestral origins for these organisms, or simply parallel cuticle evolutions. The dendritic microstructure, originally' thought to be a diagenetic indicator, was found in Recent specimens and therefore its presence in trilobites may be suggestive of the delicate nature of diagenesis in trilobites. The absence of other primary microstructures in trilobites may indicate alteration, taxonomic control} or that there is some inherent feature of S EM examination which may' not allow detection of some features} while others are apparently visit·le onl~1 under SH.·1. The region of the cuticle sampled for examination is also a major influence in detecting pristine microstructures, as not all areas of trilobite and Recent arthropod cuticles will have microstructures identifiable in a SEM study. Subtleties in the process of alteration, however} ma~·· leave pristine microstructures in cuticles that are partial~/ silicified or do 10m itized, and degree and type of alteration may vary stratigraphically and longitudinally within a unit. The presence of fused matrices, angular calcite rhombs, and pyrite in the cuticle are thought to be indicative of altered cuticles, although pyritization may not affect the entire cuticle. t-~atural processes in Recent arthropods, such as molting, lead to variations in cuticle chemistries, and are thought to reflect the area of concentration of the elements during calcification. The level of sodium in Recent arthropods was found to be higher than that in trilobites, but highly mobile when sUbjected to the actions of VY'€'athering. Less saline water produced lovy'€'r magnesium and higher calcium values in Recent specimens .. and metal variations in pristine Ordovician trilobite cuticle appears to follow the constraints outlined for Recent arthropods, of regulation due to the chemislry of the surrounding medium. In diagenetic analysis, sodium, strontium and magnesium proved most beneficial in separating altered from least altered trilobites. Using this criterion, specimens from shale show the least amount of geochemical alteration, and have an original mineralogy of 1.7 - 2.4 mole % MgC03 (8000 t(> 9500 ppm magnesium) for both /s>..?/e/11S lJA'i.riff!11S and PseIAit'11J17ites I..itmirpin..itl/~ and 2.8 - 3.3 mole % MgC03 (5000 to 7000 ppm magnesium) for Ph.i{).?PS This is Slightly lower than the mineralogy of Recent marine arthropods (4.43 - 12.1 mole % MgC03), and slightly higher than that of fresh-water crayfish (0.96 - 1.82 mole % MgC03). Geochemically pristine trilobites were also found to possess primary microstructures. Stable isotope values and trends support the assertion that marine-meteoriclburial fluids were responsible for the alteration observed in a number of the trilobite specimens. The results of this stUdy suggest that fossil material has to be evaluated separately along taxonomic and lithological lines to arrive at sensible diagenetic and e nvironmenta I interpretations.