The seed storage globulins found among virtually all spermatophytes comprise a multi-gene family of proteins with ancient evolutionary origins. The two main groups of storage globulins include the legumins (11S) and vicilins (7S), both of which play a main role in protein deposition and storage in the seed endosperm. Composed of two cupin domains (bicupin), these proteins have been recently noted not only for their close structural relationships among the two subfamilies (7S and 11S) but also for their similarity to other proteins such as germin-like proteins (GLP's), bacterial oxalate decarboxylases, and other cupin containing proteins. Previous studies have investigated the evolutionary relationships among the legumin and vicilin groups, as well as their presumed evolutionary link to other cupin containing proteins; however these have each come short of any comprehensive resolved evolutionary history of the globulin family. This study focuses first on resolving the relationships among the cupin super-family in relation to the storage globulins, as well as the GLP's, which have been postulated to be the single domain ancestors of the bicupin storage globulins. Nucleotide coding sequences for both N-terminus and C-terminus cupin domains of the storage globulins, including conserved non-cupin domain helical repeats and inter-domain spacers were aligned to a comparably sized set of single cupin coding sequences (CDS). The phylogenetic relationships among the two globulin domains as well as the single cupin genes were elucidated using Bayesian inference of tree likelihoods. Further phylogenetic analysis was performed on the complete CDS's for all storage globulin sequences in the study, using an appropriate out-group of similar overall domain architecture determined by the overall topology of the cupin super-family. This globulin muti-gene tree was used, along with an alignment corresponding to structurally resolved portions of the mature globulin peptides, to perform an analysis of patterns of selection among the various lineages of cupin-containing globulins. The results of these analyses provide evidence for a common origin of all cupin containing genes. The GLP and storage globulin domains do not appear to be immediate ancestors of one another, but are grouped with the fungal spherulins as well, suggesting that the single cupin genes which gave rise to these groups had already diverged prior to the rise of land plants. The storage globulin gene tree provides evidence supporting the notion that true legumins and vicilins were recruited as seed storage proteins independent of one another, after their divergence. This is evidenced by the fact that they comprise two separate groups each with basal non-storage 11S/7S-like proteins. Additional insight into the differentiating selection pressures provides a clearer picture of how similar suites of physicochemical properties came under selection after the recruitment of the 11S and 7S families as seed specific proteins. Regions under strong destabilizing selection correspond to regions known to be of importance in the overall structure of storage globulins. Strong destabilizing selection at the pore of the globulin subunit suggests that this region may have undergone more functional diversification than previously thought to have occurred among the legumins and vicilins.

As a primary factor in human evolution, natural selection is an important component of genetic research. Studies of lactase persistence suggest that positive selection has played a powerful role in the adaptation to a lifelong consumption of fresh milk. Using multiple research studies of lactase persistence and suspected corresponding single nucleotide genetic polymorphisms, this study combines data sources to determine whether evidence exists for natural selection of a specific cytosine-to-thymine genetic mutation located 13,910 base pairs (T-13910) upstream from the lactase gene. This polymorphism has potential to be a causal element for lactase persistence, and data suggest that natural selection has played a role in the rising frequency and distribution of this allele, if only in some regions. European and neighboring regions appear to have the highest frequencies with little or no frequency in Asia, Africa and Indonesia; however the presence of lactase persistence in those areas suggests convergent evolution may be occurring on a phenotypic level. To examine this possibility several other identified polymorphisms in the same region as the T-13910 will be included in this study

Small bacterial genomes are believed to be evolutionarily derived from larger genomes through massive loss of genes and are usually associated with symbiotic or pathogenic lifestyles. It is therefore intriguing that a similar phenomenon of genome reduction has been reported within a group of free-living phototrophic marine cyanobacteria Prochlorococcus. Here I have investigated the roles of natural selection and mutation rate in the process of Prochlorococcus genome size reduction. Using a data set of complete cyanobacterial genomes including 12 Prochlorococcus and a sister group of 5 marine Synechococcus, I first reconstructed the steps leading to Prochlorococcus genome reduction in a phylogenetic context. The result reveals that small genome sizes within Prochlorococcus were largely determined by massive gene loss shortly after the split of Prochlorococcus and Synechococcus (a process we refer to as early genome reduction). A maximum likelihood approach was then used to estimate changes in both selection effect and mutation rate in the evolutionary history of Prochlorococcus. I also examined the effect of selection and functional importance of a subset of ancestor-derived genes those are lost in Prochlorococcus but are still retained in the genomes of its sister Synechococcus group. It appears that purifying selection was strongest when a large number of small effect genes were deleted from nearly all functional categories. And during this period, mutation rate also accelerated. Based on these results, I propose that shortly after Prochlorococcus diverged from its common ancestor with marine Synechococcus, its population size increased quickly and thus the efficacy of selection became very high. Due to limited nutrients and relatively constant environment, selection favored a streamlined genome for maximum economies in material and energy, causing subsequent reduction in genome size and possibly also contributing to the observed higher mutation rate.

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<p>Repetitive elements, including tandem repeats and transposable elements (TE), are genetic features of all plant and animal genomes. Despite their abundance and the phylogenetic breadth of host genomes, factors that control the genome-wide distribution of repetitive elements are not well understood. Here we have evaluated the correlation between various genomic predictor variables such as gene expression level, distance from genes, and GC content, with the presence of TEs and non-TE repeats in two kilobase windows of the complete genome sequence of the Western Clawed Frog (<em>Silurana tropicalis</em>). We found that the distributions of different classes of TEs and repeats have distinct correlations with these predictor variables, including a generally strong negative correlation with proximity to exons and GC content. We also found that DNA transposons, but not retrotransposons, are preferentially inserted or preferentially retained near germline-expressed genes. Retrotransposons and simple repeats are found more often in or near conserved regions than expected by chance. These results offer insights into various models that have been proposed to account for heterogeneity in the genomic distribution of repetitive elements, most notably for the “gene disruption model” which posits that TE insertion and repeat presence near or in genes imposes costs to host fitness. In general, multiple lines of evidence suggests that the nature of natural selection on TE and other repetitive element evolution in this frog appears to be similar to that acting on TE and other repetitive elements in the human genome. This is possibly related to the similar size and level of complexity of the genomes of both of these species.</p> / Master of Science (MSc)

yes / The aim of this paper is to examine the notion of social mechanisms by comparison with the notions of evolutionary and physical mechanisms. It is argued that social mechanisms are based on trends, and not lawlike regularities, so that social mechanisms are different from mechanisms in the natural sciences. Taking as an example of social causation the abolition of the slave trade, the paper argues that social mechanisms should be incorporated in Weber’s wider notion of adequate causation in order to achieve their explanatory purpose.

Argues that, without the publication of Charles Darwin's "Origin of Species," Bram Stoker's novel "Dracula" and Oscar Wilde's novel "The Picture of Dorian Gray" would not have been written with their distinct style and themes, as evolution clashes with degeneration and female power (and the sexuality derived from that power) clashes with the new science. Stoker and Wilde combine the science of the late 19th century with the characters of their imaginations. Natural and sexual selection plays a part in these characters' core development. The mixture of sexuality, science and power in these two novels all combine to formulate what is known as Victorian sexology.

Reconstructing the origins and evolutionary journey of humans is a central piece of biology. Complementary to archeology, population genetics studying genetic variation among individuals in extant populations has made considerable progress in understanding the evolution of our species. Particularly, studies in indigenous humans provide valuable insights on the prehistory of humans because their life history closely resembles that of our ancestors. Despite these efforts, it can be difficult to disentangle population genetic inferences because of the interplay among evolutionary forces, including mutation, recombination, selection, and demographic processes. To date, few studies have adopted a comprehensive framework to jointly account for these confounding effects. The shortage of such an approach inspired this dissertation work, which centered on the development of model-based analysis and demonstrated its importance in population genetic inferences. Indigenous African Pygmy hunter-gatherers have been long studied because of interest in their short stature, foraging subsistence strategy in rainforests, and long-term socio-economic relationship with nearby farmers. I proposed detailed demographic models using genomes from seven Western African Pygmies and nine Western African farmers (Appendix A). Statistical evidence was shown for a much deeper divergence than previously thought and for asymmetric migrations with a larger contribution from the farmers to Pygmies. The model-based analyses revealed significant adaption signals in the Pygmies for genes involved in muscle development, bone synthesis, immunity, reproduction, etc. I also showed that the proposed model-based approach is robust to the confounding effects of evolutionary forces (Appendix A). Contrary to the low-latitude African homeland of humans, the indigenous Siberians are long-term survivors inhabiting one of the coldest places on Earth. Leveraging whole exome sequencing data from two Siberian populations, I presented demographic models for these North Asian dwellers that include divergence, isolation, and gene flow (Appendix B). The best-fit models suggested a closer genetic affinity of these Siberians to East Asians than to Europeans. Using the model-based framework, seven NCBI BioSystems gene sets showed significance for polygenic selection in these Siberians. Interestingly, many of these candidate gene sets are heavily related to diet, indicating possible adaptations to special dietary requirements in these populations in cold, resource-limited environments. Finally, I moved beyond studying the history of extant humans to explore the origins of our species in Africa (Appendix C). Specifically, with statistical analyses using genomes only from extant Africans, I rejected the null model of no archaic admixture in Africa and in turn gave the first whole-genome evidence for interbreeding among human species in Africa. Using extensive simulation analyses under various archaic admixture models, the results suggest recurrent admixture between the ancestors of archaic and modern Africans, with evidence that at least one such event occurred in the last 30,000 years in Africa.