The South Pacific is a region of incredible biological, cultural and linguistic diversity, reflecting its early settlement by human populations. It has been a region of interest to scholars because of this diversity, as well as its unique geography and settlement history. Current evidence suggests there was an initial settlement of Near Oceania during the Pleistocene by Papuan-speaking foragers, followed by a later Holocene settlement of Remote Oceania by Oceanic-speaking agriculturalists. Previous studies of human biological variation have been used to illuminate the migration history of and population relationships within Oceania. In this study, I analyzed Y-chromosome (NRY) diversity in 842 unrelated males to more fully characterize the phylogeography of paternal genetic lineages in this region, using a large number of regionally informative markers on an intensive sample set from Northern Island Melanesia. This approach facilitated an analysis of NRY haplogroup distributions, an evaluation of the ancestral paternal genetic contribution to the region, and a comparison of regional NRY diversity with that observed at different genetic loci (e.g., mtDNA). This project is part of a collaborative effort by faculty and graduate students from the Temple University Department of Anthropology that focused on characterizing biological variation and genetic structure in Melanesia, and better resolving the phylogeographic specificity of Northern Island Melanesia. Overall, this study generated a higher resolution view of NRY haplogroup variation than detected in previous studies through the use of newly defined and very informative SNP markers. It also showed that there is a very small ancestral East Asian paternal contribution to this area, and a rather large proportion of older Melanesian NRY lineages present there. In addition, this study observed extraordinary NRY diversity within Northern Island Melanesia, as well as genetic structure influenced more by geography than linguistic variation. This structure and diversity was essentially equivalent to that noted for mtDNA data for this region. Finally, this study helped to resolve questions about the placement of the 50f2/c deletion within the larger NRY tree. Overall, this work has refined our understanding of the migration and demographic history of Northern Island Melanesia. / Anthropology

Most vertebrates have separate sexes, and sex-specific traits that are regulated by genes with sex-biased expression patterns. In many species with genetic sex determination system, genetic recombination is suppressed in genomic regions linked to the master regulator of sex determination – the gene or set of linked loci that orchestrate sexual differentiation. Natural selection may favour alleles with sex-specific effects - including those with sexually antagonistic (SA) fitness effects (e.g., beneficial to females but harmful to males) – to become fixed in or be translocated to these non-recombining regions of sex chromosomes, because sex-specific or sex-biased modes of inheritance can resolve genomic conflict associated with SA. Sexually antagonism may also be resolve by sex-biased gene expression, and in theory these two mechanism (sex-linkage and sex-biased gene expression) could operate synergistically. However, there are relatively few empirical studies that test whether genes with sex biased expression patterns are indeed more abundant on sex chromosomes – and especially on newly evolved sex chromosomes. We explored this question with an African frog species Xenopus borealis, whose sex chromosome evolved within the last 25 million years (my) and have a large (~50Mbp) region of suppressed recombination, making it a young sex chromosome system compared to many other intensively studied systems, such as the sex chromosomes of mammals. We tested the possibility that a higher proportion of genes with sex-biased expression would be located on the sex-linked region of the sex chromosome of this species. By examining gene expression in adult liver and gonad and also tadpole gonad/mesenephros at two developmental stages, we found that the sex-linked region of these sex chromosome do have a higher proportion of sex biased genes compared to the non-sex-linked region of the same sex chromosomes, compared to (i) a homeologous genomic region in the tetraploid genome of X. borealis, and also (ii) the autosomes of this species. We did not observe the same pattern in a closely related frog species, Xenopus laevis, which has sex chromosome that are not homologous to those of X. borealis and, unlike X. borealis, lacks a large region of suppressed recombination on its sex chromosome. Using Brownian Motion model, we found as well that expression divergence evolution of genes in the sex-linked region of X. borealis is faster compared to its non-sex-linked homeologs (within X. borealis), and also compared to orthologous regions that are also non-sex-linked. One possible explanation for these observations is that natural selection favoured an expansion of recombination suppression (via unknown mechanisms) on chromosome such that polymorphic regulatory regions became linked (or unlinked) to the sex determining locus in such a way to resolve SA. Alternatively, it is possible that these sex-biased expression pattern evolved rapidly after recombination suppression. / Thesis / Master of Science (MSc) / Sexual selection favours the evolution of distinctive traits in each sex in order to optimize the reproductive success of each one. However, because most of the genome is shared between the sexes, sexual selection may result in genomic conflict when mutations are beneficial to one sex but harmful to the other; this conflict is known as sexual antagonism. Genomic conflict associated with alleles with sexually antagonistic (SA) fitness effects can be resolved via the origin of sex-biased expression patterns and this may be catalyzed by genetic linkage to a sex-determining locus on a sex chromosome. Consequently, one might predict there to be an enrichment of genes with sex-biased expression patterns on the sex chromosome as compared to the autosomes. We tested this expectation in an African frog species Xenopus borealis, which has a relatively young sex chromosomes and a large region of recombination suppression on the female-specific W-chromosome. We found enrichment of sex-biased genes on the nonrecombining region of the sex chromosomes of this species in adult liver and gonad tissue and also tadpole mesenephros/gonads at two developmental stages. Additionally, we found that expression divergence of genes in the non-recombining region have a faster rate of evolution as compared to the rate of expression divergence of genes in other genomic regions. One possible explanation for these observations is that natural selection favours an expansion of recombination suppression (via unknown mechanisms) on sex chromosome such that polymorphic regulatory region become linked (or unlinked) to the sex determining locus in such a way as to resolve SA.

Mémoire numérisé par la Direction des bibliothèques de l'Université de Montréal.

The correct number of chromosomes is important for the maintenance of healthy cells and organisms. Maintenance of a correct chromosome number depends on the accurate distribution of chromosomes to the daughter cells during cell division, and errors in chromosome segregation result in abnormal chromosome numbers, or aneuploidy. Aneuploidy is typically associated with deleterious effects on organismal and cellular fitness; however, aneuploidy has also been associated with enhanced cellular growth in certain contexts, such as cancer. Another type of deviation from the normal chromosome number can occur when entire sets of chromosomes are added to the normal (diploid) chromosome number, resulting in polyploidy. Whereas polyploidy is found in certain normal tissues and organisms, tetraploidy (four sets of chromosomes) is associated with a number of precancerous lesions and is believed to promote aneuploidy and tumorigenesis. While it is clear that chromosome mis-segregation causes aneuploidy, the effect of aneuploidy on chromosome segregation is less clear. Similarly, it is unclear whether and how tetraploidy may affect chromosome segregation. The work described here shows that aneuploidy can cause chromosome mis-segregation and induces chromosome-specific phenotypic effects. In contrast, tetraploidy does not per se induce chromosome mis-segregation, but enables the accumulation of aneuploidy thanks to a "genetic buffer" effect that allows tetraploid cells to tolerate aneuploidy better than diploid cells. / Ph. D.

No description available.

This dissertation unravels intricate biological dynamics in three distinct biological systems as the following. These studies combine mathematical models with experimental data to enhance our understanding of these complex processes. 1. Bipolar Spindle Assembly: Mitosis relies on the formation of a bipolar mitotic spindle, which ensures an even distribution of duplicated chromosomes to daughter cells. We address the issue of how the spindle can robustly recover bipolarity from the irregular forms caused by centrosome defects/perturbations. By developing a biophysical model based on experimental data, we uncover the mechanisms that guide the separation and/or clustering of centrosomes. Our model identifies key biophysical factors that play a critical role in achieving robust spindle bipolarization, when centrosomes initially organize a monopolar or multipolar spindle. These factors encompass force fluctuations between centrosomes, balance between repulsive and attractive inter-centrosomal forces, centrosome exclusion from the cell center, proper cell size and geometry, and limitation of the centrosome number. 2. Chromosome Oscillation: During mitotic metaphase, chromosomes align at the spindle equator in preparation for segregation, and form the metaphase plate. However, these chromosomes are not static; they exhibit continuous oscillations around the spindle equator. Notably, either increasing or decreasing centromeric stiffness in PtK1 cells can lead to prolonged metaphase chromosome oscillations. To understand this biphasic relationship, we employ a force-balance model to reveal how oscillation arises in the spindle, and how the amplitude and period of chromosome oscillations depend on the biological properties of spindle components, including centromeric stiffness. 3. Pattern Formation in Bacterial-Phage Systems: The coexistence of bacteriophages (phages) and their host bacteria is essential for maintaining microbial communities. In resource-limited environments, mobile bacteria actively move toward nutrient-rich areas, while phages, lacking mobility, infect these motile bacterial hosts and disperse spatially through them. We utilize a combination of experimental methods and mathematical modeling to explore the coexistence and co-propagation of lytic phages and their mobile host bacteria. Our mathematical model highlights the role of local nutrient depletion in shaping a sector-shaped lysis pattern in the 2D phage-bacteria system. Our model further shows that this pattern, characterized by straight radial boundaries, is a distinctive indicator of extended coexistence and co-propagation of bacteria and phages. Such patterns rely on a delicate balance among the intrinsic biological characteristics of phages and bacteria, which have likely arisen from the coevolution of cognate pairs of phages and bacteria. / Doctor of Philosophy / Mathematical modeling is a powerful tool for studying intricate biological dynamics, as modeling can provide a comprehensive and coherent picture about the system of interest that facilitates our understanding, and can provide ways to probe the system that are otherwise impossible through experiments. This dissertation includes three studies of biological dynamics using mathematical modeling: 1. Bipolar Spindle Assembly: Mitotic spindle is a bipolar subcellular structure that self-assembles during cell division. The spindle ensures an even distribution of duplicated chromosomes into two daughter cells. Certain perturbations can cause the spindle to assemble abnormally with one pole or more than two poles, which would cause the daughter cells to inherit incorrect number of chromosomes and die from the error. However, the cell is surprisingly good at correcting these spindle abnormalities and recovering the bipolar spindle. Here we build a model to explore how the cell achieves such recoveries and preferentially form a bipolar spindle to rescue itself. 2. Chromosome Oscillation: In mitotic metaphase, chromosomes are aligned at the spindle equator before they segregate. Interestingly, unlike the cartoon images in textbooks, the aligned chromosomes often move rhythmically around the spindle equator. We used a mathematical model to unravel how the chromosome oscillation arises and how it depends on the biological properties of the spindle components, such as stiffness of the centromere, the structure that connects the two halves of duplicated chromosomes. 3. Pattern Formation in Bacterial-Phage System: Phages are viruses that hijack their host bacteria for proliferation and spreading. In this study we developed a mathematical model to elucidate a common lysis pattern that forms when expanding host bacterial colony encounters phages. Interestingly, our model revealed that such a lysis pattern is a telltale sign that the bacterium-phage pair have achieved a delicate balance between each other and are capable of spreading together over a long period of time.

DNA replication initiates at a precise location on the bacterial chromosome, the origin of replication (oriC). This work has localized the origin of DNA replication on the Sinorhizobium meliloti chromosome to a region spanning the hemE gene. A genetic dissection of the locus revealed that a much larger fragment of DNA (1802 bp) is required for a functional oriC than that of the other characterized alpha-proteobacterial chromosome origin from Caulobacter crescentus. Site-directed mutations of predicted DnaA binding sites has identified several essential elements for replication of the plasmid borne oriC. Mutations in these DnaA boxes also reduce transcription of hemE and thus it is likely that transcription of hemE and replication of the S. meliloti chromosome are coupled. The ColEl plasmid pUCP30T can autonomously replicate when the S. meliloti oriC is cloned into the suicide vector (pTH838) and can be efficiently mobilized out of S. meliloti into E. coli. The pTH838 oriC plasmid when transferred into S. meliloti results in both small and large colonies and both of these transconjugant classes take longer to form than the S. meliloti recA::Tn5 recipient. We attributed this phenotype to the very low copy number of the pTH838 plasmid which was determined to be 0.053 - 0.135 copies per chromosome. The DnaA protein responsible for replication initiation in many bacteria has been purified and used in electrophoretic mobility shift assays. The DnaA protein interacts specifically with sequences in the hemE - Y02793 intergenic region and upstream of the repA2 gene on the pSymA megaplasmid. The DnaA protein has also been implicated as a link between DNA replication and cell division in S. meliloti as overexpression of DnaA in both E. coli and S. meliloti results in filamentation. / Thesis / Master of Science (MSc)

Resistant and susceptible field strains of the German cockroach were compared for possible chromosome aberrations. Resistant strain females produced significantly higher numbers of aberrant oothecae ( >5 unhatched eggs ) than the susceptible strains. Chromosome aberrations found in the susceptible strains were attachments (autosome-autosome, autosome-x) and fragments that did not reappear in outcrosses. Attachments (autosome-autosome, autosome-x), fragments, three translocation configurations that did not reappear in outcrosses and two reciprocal translocation heterozygotes occurred in the resistant strains. These two translocations have been tentatively identified as T(12:8)/12:8 from the Bowl strain and T(11:6)/11:6 from the K851 strain. T(12:8)/12:8 exhibits random disjunction at metaphase I. There were no differences related to susceptible vs. resistant strains in the frequency of chromosome aberrations from the aberrant oothecae. There was no evidence, except in the K851 strain, to support a relationship between egg arrest and chromosome aberrations, or the hypothesis that chromosome aberrations result from the selective pressure of insecticides. It is suggested by this study that translocations are the most common type of “floating” polymorphism in the German cockroach. The first occurrence of three known phenotypic mutants, bent bristle, yellow body, and pallid eye, and one new phenotypic mutant, colorless eye, in field strains are reported by this study. / Master of Science

Yes / The mammalian X and Y chromosomes originated from a pair of ordinary autosomes. Over the past ~180 million years, the X and Y have become highly differentiated and now only recombine with each other within a short pseudoautosomal region. While the X chromosome broadly preserved its gene content, the Y chromosome lost ~92% of the genes it once shared with the X chromosome. PRSSLY is a Y-linked gene identified in only a few mammalian species that was thought to be acquired, not ancestral. However, PRSSLY's presence in widely divergent species-bull and mouse-led us to further investigate its evolutionary history. We discovered that PRSSLY is broadly conserved across eutherians and has ancient origins. PRSSLY homologs are found in syntenic regions on the X chromosome in marsupials and on autosomes in more distant animals, including lizards, indicating that PRSSLY was present on the ancestral autosomes but was lost from the X and retained on the Y in eutherian mammals. We found that across eutheria, PRSSLY's expression is testis-specific, and, in mouse, it is most robustly expressed in post-meiotic germ cells. The closest paralog to PRSSLY is the autosomal gene PRSS55, which is expressed exclusively in testes, involved in sperm differentiation and migration, and essential for male fertility in mice. Outside of eutheria, in species where PRSSLY orthologs are not Y-linked, we find expression in a broader range of somatic tissues, suggesting that PRSSLY has adopted a germ-cell-specific function in eutherians. Finally, we generated Prssly mutant mice and found that they are fully fertile but produce offspring with a modest female-biased sex ratio compared to controls. PRSSLY appears to be the first example of a gene that derives from the mammalian ancestral sex chromosomes that was lost from the X and retained on the Y. Although the function of PRSSLY remains to be determined, it may influence the sex ratio by promoting the survival or propagation of Y-bearing sperm. / The group of D.C.P. is supported by the Howard Hughes Medical Institute, the Whitehead Institute, and philanthropic gifts from Brit and Alexander d’Arbeloff, Authur W. and Carol Tobin Brill, and Charles Ellis.

In an attempt to significantly increase the discriminatory potential of Y-STR systems available to the forensic community, two Y-STR multiplex systems have been developed and validated. The two systems were developed to supplement the recommended nine "minimal haplotype loci," used extensively throughout the European forensic community. In accordance with multiplex development requirements, attempts were made to construct highly discriminatory multiplex systems with an increased number of Y-STR loci contained therein, while seeking to ensure a high degree of sensitivity (1-3 ng of template DNA) and specificity (no artifact production due to confounding female DNA). Two Y-STR multiplex systems, Multiplex ill (MPIII) and Multiplex IV (MPIV), have been developed. They allow for the co-amplification of nine and twenty-one novel Y-STR loci, respectively. Both multiplexes performed well over a wide range of primer, magnesium, and DNA polymerase concentrations. A number of performance checks were employed to characterize the system including sensitivity, specificity, discriminatory capacity and non-probative casework studies. Full male profiles can be obtained with as little as 50 pg of te􀀫plate DNA with Multiplex ill and Multiplex IV, and both systems exhibited a lack of significant female DNA derived artifacts when tested with female DNA alone or in a male/female DNA admixture. Cervicovaginal samples taken up to 48 hours after intercourse resulted in full haplotype determination with both multiplexes. These results demonstrate the potential usefulness of Multiplex III and Multiplex IV for forensic casework.