Doctor of Philosophy / Division of Biology / Mark C. Ungerer / Nuclear genome size varies immensely across flowering plants, spanning nearly 2400-fold. The causes and consequences of this vast amount of variation have intrigued biologists since it became clear that nuclear DNA amount did not reflect organismal complexity (the so-called C-value paradox). In my dissertation I utilize wild sunflower species in the genus Helianthus to examine the role of transposable elements (TEs), and in particular, long terminal repeat (LTR) retrotransposons, in generating genome size variation and whether variation in genome size influences aspects of plant growth and development across multiple organizational levels. The genus Helianthus provides an excellent system for studying these questions given four-fold variation in nuclear DNA content among diploid species and well-resolved phylogenetic relationships. Utilizing short-read Illumina data and sequence information from a diverse panel of Helianthus annuus (common sunflower) full-length LTR retrotransposons, I found that nuclear genome size in Helianthus species is positively correlated with repetitive DNA, and LTR retrotransposon subtypes generally show similar patterns in genomic abundance across taxa. Helianthus species with the largest genomes, however, exhibit large-scale amplification of a small number of LTR retrotransposon subtypes. Measuring aspects of plant growth and development at cell-, organ- and whole plant-levels in a panel of diploid Helianthus species that vary 4-fold in nuclear genome size, I found that genome size is negatively correlated with cell production rate, but that this negative correlation does not persist at higher organizational levels. Taken together, these results provide insights into the mechanisms contributing to genome size evolution in plants and the organizational level at which genome size may impact growth patterns and developmental rates. Genome expansion in wild sunflowers is influenced most significantly by amplification of a small number of TEs and not necessarily by a greater diversity of TEs. Genome size is strongly negatively correlated with cell production rate but this relationship weakens at higher organizational levels, such as that of organ and whole-plant development.

A species threshold was used to assign unidentified Hymenoptera into DNA barcode Operational Taxa (DbOT) for both an assessment of species richness in rose gall communities and as part of a broad scale survey of genome size diversity. The species threshold of 2.2% was calculated from minimum interspecific divergence of DNA barcode (COI, mtDNA) and internal transcribed spacer region 1 (ITS1, rDNA) sequences from both identified and unidentified Hymenoptera associated with rose galls induced by Diplolepis (Cynipidae). Analysis of both DNA barcodes and ITS1 sequences suggested that several described species of Diplolepis (Cynipidae), Periclistus (Cynipidae), and Torymus (Torymidae) require re-examination to define species boundaries. It was also determined that the total number of DbOTs is higher than previous estimates of species richness of Hymenoptera associated with rose galls induced by Diplolepis. Additionally, genome size estimations were determined for 51 DbOTs from all eight families of Hymenoptera associated with rose galls induced by Diplolepis, five of which did not have any previous genome size estimates. A subsequent large-scale survey of Hymenoptera enabled by the use of the DbOT approach produced genome size estimations for 309 DbOTs from 36 families in 13 superfamilies. It was shown that Hymenoptera do not have smaller genome sizes than other holometabolous orders, and that a parasitoid lifestyle does not appear to constrain genome size. The suggested positive relationship between genome size and development time was investigated by comparing mean genome size of taxa with known or apparent differences in development rate. It was concluded that statistical comparisons between taxa that are grouped in broad categories would be unlikely to detect significant differences in mean genome size because the range of biological features within such categories is highly variable. However, comparisons between interacting groups with narrowly defined development strategies determined that mean genome size was statistically smaller in taxa that obtained resources within a narrow window of opportunity. This result suggests that rapid development in relation to competitors may be important in species of Hymenoptera with higher mortality risk.

The DNA content of blood cell nuclei of 15 species of cranes was determined by Feulgen-DNA cytophotometry. Genome sizes agree with values reported elsewhere for several crane species analyzed by flow cytometry. Males have more DNA per cell than females in several species. A karyotype where 2n = 80 is reported for a male greater sandhill crane.

Variation in nuclear DNA content within some eukaryotic species is well documented, but causes and consequences of such variation remain unclear. Here we report genome size of an estuarine and salt-marsh calanoid copepod, Eurytemora affinis, which has recently invaded inland freshwater habitats independently and repeatedly in North America, Europe, and Asia. Adults and embryos of E. affinis from the St. Lawrence River drainage were examined for somatic cell DNA content and the presence or absence of embryonic chromatin diminution, using Feulgen-DNA cytophotometry to determine a diploid or 2C genome size of 0.6-0.7 pg DNA/cell. The majority of somatic cell nuclei, however, have twice this DNA content (1.3 pg/nucleus) in all of the adults examined and possibly represent a population of cells arrested at the G2 stage of the cell cycle or associated with some degree of endopolyploidy. Both suggestions contradict assumptions that DNA replication does not occur in adult tissues during the determinate growth characteristic of copepods. Absence of germ cell nuclei with markedly elevated DNA values, commonly found for species of cyclopoid copepods that show chromatin diminution, indicates that E. affinis lacks this trait. The small genome size and presumed absence of chromatin diminution increase the potential utility of E. affinis as a model for genomic studies on mechanisms of adaptation during freshwater invasions.

Genome size in plants varies greatly; in angiosperms this variability can make a 2400- fold difference. This is why the subject of many studies is the attempt to explain these differences in various contexts. One of these is the phylogenetic viewpoint, which studies the relationships between genome size and different taxonomic groups. Many studies have been published so far which explore the plants of the temperate zone; there are however very few studies investigating genome size in tropical plants. For this reason, the subject of this thesis is the analysis of genome size in the pantropical family Costaceae Nakai. This family presently includes seven genera: Monocostus K.Schum., Dimerocostus Kuntze, Costus L., Paracostus C.D.Specht, Chamaecostus C.D.Specht & D.W.Stev, Hellenia Retz. and Tapeinochilos Miq., counting altogether about 300 species. The family is sister to the family Zingiberaceae, which has been notably better explored due to its economic importance. One of the aims of this thesis was a partial revision of the phylogeny published by Specht (2006). Molecular methods were used to analyse the phylogenetic relationships; these methods included classical sequencing of the trnL-F region and next-generation sequencing, where probes designed in advance were used to obtain the targeted genes....

Genome size (GS) is a fundamental trait influencing cellular, developmental and ecological parameters, and varies c. 2400- fold in angiosperms. This astonishing range has the potential to influence a plant's nutrient demands, since nucleic acids are amongst the most phosphate and nitrogen demanding cellular biomolecules, and hence its ability to grow and compete in environments where macronutrients are limited. Angiosperm GS are strongly skewed towards small genomes, despite the prevalence of polyploidy in the ancestry of most if not all angiosperm lineages. This thesis examines the hypothesis that large genome sizes are costly to build and maintain and that angiosperm species with large GS are constrained by nitrogen and phosphate limitation. It untangles the interactions between GS, polyploidy and competition in plant communities, and examines how herbivory and GS play a role in plant productivity, measured as above-ground biomass. The hypothesis that large GS are costly was approached by analysing: 1) plant communities growing under different macronutrient conditions at the Park Grass Experiment (Rothamsted, UK); 2) plant communities under different conditions of macronutrient limitation and insect, mollusc, and rabbit herbivory at Nash's Field in Silwood Park (UK); and, 3) Ellenberg's indicator values which represent the realised niche of a species in terms light, water, and soil fertility. Support for the hypothesis was found in all experiments. The range of analyses show that angiosperm plants with large genomes (e.g. 1C-value > 5 pg) are indeed under greater macronutrient limitation in comparison to plants with small genomes, and that it is polyploid plants with large GS which are the most competitive when macronutrient resources are plentiful. In terms of herbivory, the key finding is a highly significant negative association between GS and rabbit herbivory. A species' realised niche for soil fertility was found to show a positive association with its GS. Overall the thesis shows that angiosperm GS plays a central role in plant community composition and responses to macronutrient conditions, and potentially on higher ecosystem processes through associations at different trophic levels.

It has long been evident that genome size is not an accurate measure of organismal complexity. This paradox was “solved” with the discovery of nonfunctional and selfish DNA in the 1970s. However, emerging from this explanation was an enigma of complexity. Neither neutral nor adaptive models can account for all genome size variation across the tree of life. An organism with intraspecific variation is needed to investigate the functional role of genome size differences. Here I use different populations of the seed beetle, Callosobruchus maculatus, with a known intraspecific genome size variation of ~4%. It has previously been shown that a larger genome is associated with higher scores in fitness-related traits for this species. In this study, genome size is regressed with phenotypic plasticity along three different environmental gradients. Genome size did not correlate with plasticity in mass and development time along environmental gradients of temperature and host types. However, the results show that larger genomes are consistent with higher canalization of fitness under different food regimes. This further supports the idea that natural selection acts on genome size variation in this species.

In parasites, there are several examples of changes in genome size linked to a parasitic lifestyle—with some species having greatly reduced or expanded genome sizes relative to free-living non-parasitic relatives. What is unknown is whether there is correlated evolution between genome size and host specialization, and whether there is a generalizable framework in predicting genome size evolution in parasites using their genetic architecture and host use ecology. Here, I tested whether genome size of 96 eukaryotic parasites across a wide variety of taxa correlates with host specialization, quantified by the number and phylogenetic relatedness of host species they parasitize. I did not find that genome size and host specialization shared a correlated phylogenetic history; however, I did find that ectoparasites tended to have larger genomes then endoparasites, and that parasitic fungi had more host species then either animal or protozoan parasites. Although no clear trends in the evolution of genomes and host specificity were observed among parasites, my study was significantly limited by gaps in both genome size and host range availability. Future research should seek to address these gaps, as well as improve taxonomic coverage of data, so that trends in the evolution of parasite genome architecture could be adequately tested and delineated.

No description available.

Embryonic chromatin diminution, the selective excision of large amounts of heterochromatic DNA from presomatic cell lineages, provides an example of an unusually large augmentation of the germline genome and raises questions regarding the source of the increased amount of DNA and its relevance to the biology of the organism. DNA levels in adult germ cell nuclei of the copepod Cyclops kolensis were determined by DNA-Feulgen cytophotometry and compared with those of somatic nuclei of adults and both pre- and postdiminuted embryos from the same mothers. Almost 75 pg DNA/nucleus is excised by diminution, resulting in the return of each generation to the approximately 1 pg DNA/nucleus level found for adult soma. To account for the increase in DNA levels of germ cells observed here, we propose alternative hypotheses to the original model of chromatin diminution: (1) repetitive endocycles or (2) proliferation of genetic elements. Specific tests for these hypotheses using next-generation sequencing and quantitative cytophotometry, as well as the functional significance of germ cell DNA augmentation to the copepod, are discussed.