Bell Family Bible, Family Record, 1853-1897

The Family Record page from the Bell Family Bible providing information on the births of Bell ancestors. Relatives of the Bell family include former American slaves who later settled in Canada. This Bible was in the possession of the Rick Bell Family of St. Catharines, Ontario.

Bell Family Bible, Marriages, Tyrell - Gains, 1849

The Marriages page from the Bell Family Bible listing the marriage of Lewis Tyrell to Jane Gains on Aug. 31, 1849 at Culpepper Court House, Virginia. This Bible was in the possession of the Richard Bell Family of St. Catharines, Ontario. Ancestors of the Bell family include former American slaves who settled in Canada.

The Slomans: Albert, Josie, Shirley and Bert, 1942

A black and white snapshot of Albert and Josie Sloman, with Shirley and Bert Sloman. The date recorded on the back of the photograph is May 24, 1942, possibly the Victoria Day weekend. The location appears to be the Oakes Garden Theatre in Niagara Falls. This photograph was in the possession of the Rick Bell family, of St. Catharines, whose ancestors include former Black slaves from the United States.

Photograph of Mildred Sloman [n.d.]

Mildred Sloman is pictured with three unidentified gentlemen in this undated photograph, believed to be taken in London, Ontario. This black and white snapshot was in the possession of the Rick Bell family, whose ancestors include Black slaves from the United States.

Photograph of Josephine Sloman [n.d.]

Josephine Sloman pictured in this undated photograph taken in Niagara Falls. Josephine (Ellen Butler) Sloman was born in 1891 in London, Ontario. This small photo was among the family memorabilia in the possession of Rick Bell, of St. Catharines, whose ancestors include former Black slaves from the United States.

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.