<p> Maintaining intraspecific variation is important for populations&rsquo; long-term success and is increasingly being recognized as an important conservation goal. Populations in anthropogenically fragmented habitats may lose variation rapidly via genetic drift, particularly in small fragments with a high ratio of edge to interior habitat. We studied the population and ecological genetic effects of habitat fragmentation on both a foundation plant, <i>Spartina patens,</i> and a dependent herbivore, <i>Tumidagena minuta,</i> using a naturally fragmented, salt marsh model system. We employed microsatellite marker analyses to estimate various measures of genetic variation, including allelic richness and heterozygosity, and to estimate the strength of genetic drift using estimates of effective population size (Ne). To achieve this, we developed a new program to estimate Ne and developed new markers for <i>S. patens</i> from genome sequence data. We found lower <i>S. patens</i> genetic variation and lower <i>T. minuta </i> Ne near the <i>S. alterniflora</i> edges, indicating that <i> T. minuta</i> experience stronger genetic drift near edges. These findings reinforce the importance of habitat patch shape in influencing populations. </p>

For a sexually reproducing species, the two major decisions facing all individuals are when and with whom to reproduce. When scaled to the population level, the outcome from all individual decisions determines reproductive variance, and age-class contribution to population growth rate. Both of these attributes determine a population's effective size (Ne), which is directly correlated with its fitness, persistence probability, and adaptability. The questions of when and with whom to reproduce, and their subsequent effects on Ne and age-at-maturity were assessed for wild brook trout (Salvelinus fontinalis) populations. Mating pairs were significantly size-assortative, with individual length accounting for 37% of the variation. This pattern of size assortative mate choice resulted in a reproductive strategy closer to monogamy than polygamy. Of all reproducing adults (n=157), 80% (n=126) produced only one full-sibling family, and only 6% (n=9) contributed to more than two full-sibling families. The number of families and offspring contributed increased with length for both males and females. Comparison of the effective population size estimate to the adult census size (Nc) estimate returned an Ne:Nc ratio of 0.49 averaged over both populations. This value is nearly five times greater than the average reported across 165 (0.14) and 102 (0.10) different species. Age-at-maturity ranged from 0 to 2 years, with the proportion of age-0 and age-1 individuals maturing in a given year dependent upon growth opportunities determined primarily by environmental conditions. Mature fish were significantly larger than immature fish within an age-class, however, survival rates of mature and immature fish were similar. Furthermore, parental length did not influence offspring survival. These data suggest that the cost of early maturation is instead manifested through a reduction in egg number for females, and a reduced ability to acquire mates for males, both determined by an individual's size. Indeed, fecundity predicted by mean length of immature and mature fish within an age-class would result in mature fish producing an average of 38% (age-0) and 33% (age-1) more eggs than immature fish. These findings are discussed in the context of population persistence given the trend of increasing habitat fragmentation and looming climate change.

<p> Pine species (genus <i>Pinus</i>) have been introduced across the Southern Hemisphere for forestry and several species have invaded surrounding ecosystems. Pine introduction across biogeographic regions sets up an ideal natural experiment to test underlying theories and assumptions of invasion biology. We studied the factors determining patterns of <i> Pinus contorta</i> invasion across nine sites in both the native and introduced ranges to understand how the invasion drivers change across sites and invasion stages. We found that propagule pressure is the most important factor in explaining invasion density in young invasions, but that biotic factors play an important role at later invasion stages. Additionally, we found higher invasion densities in the introduced than native range which may be explained by faster growth and earlier and more prolific reproduction in the introduced range. </p><p> We examined the impacts of ^{P. contorta} invasions on plant biodiversity across sites and found that species richness and native plant cover decline with increasing ^{P. contorta} cover across sites in both the native and introduced range. There were more significant changes in species composition and individual species cover at grassland and shrubland sites in the introduced range than in the native range or a native forest site in the introduced range. </p><p> Finally, there is concern that invasive pines, which are fire adapted, will alter fire regimes in a way that promotes a new fire-prone state further increasing their success over native plants. We examined the potential for ^{P. contorta} to form a positive feedback with fire by quantifying fuel loads and fire effects across an invasive gradient. We also examined ^{P. contorta} and native plant recovery following fire across an invasion density gradient. We found that fuel loads and simulated soil heating increased with older ^{P. contorta} invasions. Following fire, ^{P. contorta} dominated communities only when the pre-fire density was high. Therefore, we expect that a positive feedback between ^{P. contorta} invasion and fire will form only above an invasion threshold. Our invasion-fire simulation model suggested that fire in older invasions will increase invasion rates, but that fires in young invasions will not affect the invasion rate.</p>

<p>We propose to establish a free-living, fresh water flatworm species from the superphylum Lophotrochozoa, Schmidtea mediterranea, to be a genetic model system. S. mediterranea has been vigorously investigated as a powerful system to study adult stem cells and organ regeneration. Its sexual biotype has also been established as a system to understand the inductive mode of germ cell formation that is broadly shared by a lot of species including mammals. However, little is known about the sexual reproduction and genetics in this organism, which limited the availability of genetic approaches. As the sexual planarian is found scattered but with relative abundance in Sardinia, its natural history also presents us the opportunity to study inbreeding?s effect on genetic variability and species survival. Therefore, to study sexual reproduction and genetic inheritance in S. mediterranea will provide us unique opportunities to understand whole body regeneration, inductive germ cell formation, and inbreeding. In this dissertation, progresses in the establishment of the foundation for genetic analysis in S. mediterranea were presented. Though a simultaneous hermaphrodite, the anatomical and genotyping studies concluded that S. mediterranea cross-fertilize. One worm (line S2) was inbred for 10 generations by taking one progeny from each generation and crossing this individual to its regenerated clones. Whole genome sequencing of four different generations in this inbreeding pedigree revealed ~300Mb of the genome maintained their heterozygosity. Further sequencing analysis of the male and female gametes found these regions had low recombination rates, and maintained as two haplotypes (J-/V- haplotypes). Failure of gametes of the same haplotype to form progeny is unlikely due to embryonic lethality as the arrested embryos were significantly less than hatchlings. Additional analysis of two lines (D5D/D5I) with 90% of these regions homozygous as the J-haplotype suggested failure in fertilization between gametes of the same haplotype. Hence, we propose that haplotype incompatibility is the driving mechanisms to maintain genome heterozygosity in the planarian genome. Understanding of the genetic strategies in S. mediterranea will help the development of genetic approaches to study regeneration and germ cell specification. Our findings also suggest S. mediterranea can be a model system to study the evolution of sex and gamete incompatibility.

<p> This project aims to develop a panel of sequence capture baits to use for SNP genotyping for pedigree analysis in Wood Ducks (<i>Aix sponsa </i>) as well as for general population genetic analysis within species in the family Anatidae. SbfI RAD libraries were prepared with samples comprising five duck species (N = 96). Sequenced libraries were aligned to the Mallard (<i>Anas platyrhynchos</i>) reference genome and screened for 120bp regions proximal to the SbfI cutsite that contained SNPs conserved collectively in each species. A series of screenings identified regions which were used to produce 2,508 custom sequence capture baits. These baits were tested in novel individuals from the same species used to design the baits as well as novel species representing different taxonomic ingroup and outgroup levels within Aves. These baits delineate species at various taxonomic scales, even above the taxonomic level that was originally targeted and will prove useful for analyses of population and comparative genetics for species of Anatidae and perhaps more broadly.</p><p>

<p> The federally threatened Delta Smelt has been cultured in a conservation hatchery since 2008 in response to significant declines in the wild. The refuge relies on accurate, efficacious, and repeatable molecular techniques to help maintain the population's overall genetic diversity and minimize inbreeding. We have created a panel of single nucleotide polymorphisms (SNPs) to support broodstock pedigree reconstruction and improve upon current genetic management with microsatellites. Properly implemented, a SNP panel is a more powerful, repeatable, and higher-throughput method. Its use will streamline the management of the captive Delta Smelt population, which is performed in near real-time throughout the spawning season (February - May). For the SNP discovery, we sequenced 27 broodstock samples from the 2012 spawn using restriction site associated DNA sequencing (RAD-seq). We then created a linkage map by genotyping three single pair crosses at 2317 newly discovered loci with RAD-seq. We successfully mapped 1123 loci and identified 26 linkage groups. Fluidigm SNPtype genotyping assays were developed for 104 mapped loci selected for minor allele frequency (>20%), neutrality (Hardy-Weinberg equilibrium), and marker location. Candidates for the genotyping panel were evaluated on a 96x96 Integrated Fluidic Circuit and tested for marker accuracy and ability to accurately assign parentage. When applied in conjunction with mating records, we found that a panel of 24 independent SNPs successfully assigned 100% of tested offspring if all samples were genotyped at a minimum of 18 loci.</p>

The analysis of the colonization and development of communities on islands, or the Theory of Island Biogeography, predicts an initial increase of species upon newly exposed islands. However, as the extent of species invasion increases, species extinction also increases. Eventually, an equilibrium is reached where species recruitment is balanced by species extinction. To investigate whether genetic change within clonal plant populations parallels community development upon islands, this study investigated genetic diversity in different-aged populations of Ammophila breviligulata. Results from previous studies of Ammophila breviligulata have yielded conflicting conclusions. Laing found sexual reproduction to be infrequent in mature populations of A. breviligulata, and, therefore, suggested that genetic diversity must decrease as A. breviligulata populations age. In three different aged populations of A. breviligulata, Carlson, using isozymes, found that the number of genotypes per population increased with increasing population age. Using RAPDs, I determined genetic diversity in four young (between two and six years) and four old populations (greater than one-hundred years) of A. breviligulata. Young populations contained an intermediate number of genets, while old populations varied in clonal diversity. Populations of A. breviligulata examined in this study were founded by a diversity of propagules. However, sexual reproduction and vegetative immigration may be limited in some older populations, and thus the lack of continual recruitment in A. breviligulata populations may cause departures from the assumptions of the island colonization model. Alternatively, sporadic sexual reproduction may occur in some older populations, and clonal diversity could thus be maintained or increased over time, as was found in one population of this study. The variance in the number of genets within old A. breviligulata populations indicates that genetic diversity in different aged populations is not correlated with predicted community changes on islands. RAPDs may be useful in identifying genets in natural populations, since similar patterns of clonal diversity were detected within populations by both RAPDs and isozymes, although RAPDs detected a somewhat greater number of genets. Somatic mutation within genets may possibly be detected by RAPDs and isozymes.

Much work on sex ratios in dioecious plants has involved the genus Silene. The classic literature indicates that female-biased sex ratios result from excess pollen because pollen tubes from female-determining pollen reach the ovary more quickly, on average, than pollen tubes from male-determining pollen. I proposed the "weak male hypothesis" to account for female-biased ratios from limited amounts of pollen. This hypothesis assumes that male-determining pollen either germinates at a lower rate or experiences greater pollen tube attrition than female-determining pollen. To test this hypothesis, limited numbers of pollen grains were placed at one of three positions along the style. According to the hypothesis, if male-determining pollen is handicapped in germination, seed set and progeny sex ratios, which should all be female biased, should not be affected by where on the style the pollen is placed. If handicapping occurs during pollen tube growth, seed set should decrease and sex ratios should become increasingly female biased as the distance traveled by the pollen tubes increases. Seed set exhibited a nonsignificant decrease as style distance increased; none of the sex ratios was female biased. Therefore, the weak male hypothesis is rejected. In another experiment, pollen from individual anthers was separated into nonoverlapping small and large size classes. Sex ratios resulting from the two size classes did not differ, indicating that there is no sex-related bimodality for pollen size. In two other experiments, excess pollen was placed at one of two positions on the style. Of 48 resulting sex ratios, only six deviated significantly from 1:1; of these six, three were female biased and three were male biased. Style position had a significant effect in one experiment (progeny from distant pollinations contained excess males), but not the other. Sex ratios were not affected by either parent in these experiments. The data indicate that female-biased sex ratios do not necessarily result from excess pollen. Therefore, gametophytic competition cannot be assumed to explain the preponderance of females in natural populations. Reasons for the differences between my results and results of early experiments are discussed.

This study uses habitats that have been naturally fragmented throughout the Holocene to examine the effects of habitat fragmentation on a much longer time scale. To investigate the long-term effects of habitat fragmentation on population genetic structure of Carex bigelowii, Diapensia lapponica , and Minuartia groenlandica, isozyme variation in fragmented patches of alpine tundra was compared to variation in sites from continuous alpine tundra. The questions posed by this study include: Is genetic variation reduced in fragmented habitat? Does gene flow occur between habitat fragments? What is the effect of fragment size on genetic variation? Have populations from fragments diverged more than populations separated by a similar distance in continuous habitat? Some of the results agree with the predictions of population genetic theory, and some do not. Dipensia lapponica and C. bigelowii have significantly less genetic variation in fragmented habitat. Contrary to theoretical predictions, M. groenlandica has significantly more genetic variation in fragmented habitat. Gene flow between populations of D. lapponica and C. bigelowii in fragmented habitat appears to be absent or reduced compared to unfragmented habitat. Gene flow between populations of M. groenlandica does not seem to have been affected by the scale of habitat fragmentation in this study. Correlation of genetic variation with fragment size is positive for C. bigelowii, not significant for D. lapponica and negative for M. groenlandica. Contrary to theoretical predictions, populations of M. groenlandica have significantly more genetic variation in small habitat patches than in large ones. Populations of D. lapponica and C. bigelowii have diverged more in fragmented habitat than in unfragmented habitat, possibly as a result of genetic drift. Minuartia groenlandica populations have not diverged more in fragmented than in unfragmented habitat. Diapensia lapponica, C. bigelowii, and M. groenlandica have virtually identical distributions in the northeast, and must have migrated into the region contemporaneously (on a geologic time scale) from southern refugia, yet have strikingly different patterns of genetic variation. This observation should serve as a cautionary note in attempts to infer past migration patterns from current patterns of genetic variation. (Abstract shortened by UMI.)

The olive fruit fly, Bactrocera oleae, (Rossi) (Diptera:Tephritidae), is a key pest of olive crops. The sterile insect technique (SIT) is an environmentally benign and species-specific method of pest control, aiming to reduce the reproductive potential of a wild population through the mass-release of sterile insects. Previous olive fly SIT trials, involving the release of gamma-ray sterilised mixed-sex populations, achieved limited success. Key problems included altered diurnal mating rhythms of the laboratory-reared insects, leading to assortative mating between released and wild populations, and low competitiveness of the radiation sterilised mass-reared flies. Consequently, the production of competitive, male-only release cohorts is seen as essential. The RIDL (Release of Insects carrying a Dominant Lethal) system is a transgene-based derivative of SIT, one version of which involves the mass release of insects carrying a female specific lethal transgene (fsRIDL). This thesis describes: 1) the development of fsRIDL olive fly strains and the molecular analysis of transgene insertion and function; 2) the analysis of strain life-history parameters; 3) studies into sexual selection and mating compatibility; 4) a caged proof-of-principle population suppression trial; and, 5) selection dynamics on the fsRIDL trait in caged populations. Olive fly fsRIDL strains were developed with full female-lethal penetrance and repressibility. The lead strain displayed similar life-history and sexual competitiveness traits to those of the wild-type strain from which they were derived. In addition, transgenic males showed photoperiod compatibility and strong sexual competitiveness with field-collected wild olive flies. The feasibility of the fsRIDL approach was demonstrated when repeated male releases caused eradication of caged olive fly populations. Although needing field confirmation, these results suggest that fsRIDL olive fly strains may help to mitigate key problems experienced in previous olive fly SIT trials, and could help form the basis of a renewed effort towards olive fly SIT control.