Paddlefish (Polyodon spathula) is a commercially and recreationally important species, with a native range that extends over 22 US states. This is a large, long-lived, highly mobile riverine species that has been negatively impacted by habitat fragmentation, historic overharvest, and hatchery supplementation. Dams are the primary cause of habitat fragmentation, blocking migration routes, flooding spawning grounds, and isolating populations. A common management action to mitigate the impacts of habitat fragmentation and maintain harvestable populations is hatchery propagation and stocking. Reduction in stock size, isolation of populations, and stocking can all negatively impact the genetic integrity of Paddlefish. I evaluated the impacts of isolation and hatchery supplementation on the effective population size (Ne) of Paddlefish as well as the range-wide genetic structure of Paddlefish.

Malaria is a deadly disease that causes nearly one million deaths each year. Understanding the demographic history of the malaria parasite Plasmodium falciparum and the genetic basis of its adaptations to antimalarial treatments and the human immune system is important for developing methods to control and eradicate malaria. To study the long-term demographic history and recent effective size of the population in order to identify genes under selection more efficiently and predict the effectiveness of selection, in Chapter 2 we sequenced the complete genomes of 25 cultured P. falciparum isolates from Senegal. In addition, in Chapter 3 we estimated temporal allele frequencies in 24 loci among 528 strains from the same population across six years. Based on genetic diversity of the genome sequences, we estimate the long-term effective population size to be approximately 100,000, and a major population expansion of the parasite population approximately 20,000-40,000 years ago. Based on temporal changes in allele frequencies, however, the recent effective size is estimated to be less than 100 from 2007-2011. The discrepancy may reflect recent aggressive efforts to control malaria in Senegal or migration between populations.

The critically endangered Kemp's ridley sea turtle experienced a dramatic decline in population size (demographic bottleneck) between 1947 and 1987 from 160,000 mature individuals to less than 5000. Demographic bottlenecks can cause genetic bottlenecks where significant losses of genetic diversity occur through genetic drift. The loss of genetic diversity can lower fitness through the random loss of adaptive alleles and through an increase in the expression of deleterious alleles. Molecular genetic studies on endangered species require collecting tissue using non-invasive or minimally invasive techniques. Such sampling techniques are well developed for birds and mammals, but not for sea turtles. The first objective was to explore the relative success of several minimally invasive tissue-sampling methods as source of DNA from Kemp's ridley sea turtles. Tissue sampling techniques included; blood, cheek swabs, cloacal swabs, carapace scrapings, and a minimally invasive tissue biopsy of the hind flipper. Single copy nuclear DNA loci were PCR amplified with turtle-specific primers. Blood tissue provided the best DNA extractions. Additionally, archival plasma samples are shown to be good sources of DNA. However, when dealing with hatchlings or very small individuals in field situations, the tissue biopsy of the hind flipper is the preferred method. This study's main focus was to evaluate whether the Kemp's ridley sea turtle sustained a measurable loss of genetic variation resulting from the demographic bottleneck. To achieve this goal, three alternative approaches were used to detect a reduction in Kemp's ridley's effective population size (Ne) from microsatellite data. These approaches were 1) Temporal change in allele frequencies, 2)An excess of heterozygotes in progeny, and 3)A mean ratio (M) of the number of alleles (k) to the range of allele size (r). DNA samples were obtained from Kemp's ridleys caught in the wild. PCR was used to amplify eight microsatellite loci and allele frequencies were determined. Data from only four microsatellites could be used. Although the reduced number of loci was a limiting factor in this study, the results of all three approaches suggest that Kemp's ridley sustained a measurable loss of genetic variation due to the demographic bottleneck.

Population structure in five African beef cattle breeds in South Africa was investigated, to assess the effect of animal recording in management of genetic diversity and genetic improvement. Pedigree records of 247,173 Afrikaner, 57,561 Boran, 198,557 Drakensberger, 256,692 Nguni and 55,309 Tuli breed were analysed using the online POPREP software system. Pedigree completeness over six generations varied with the lowest completeness in the Boran and the highest in the Afrikaner.The average generation interval ranged between 6.0 to 6.4 years. The rates of inbreeding per year were 0.03%, 0.04%, 0.06%, 0.07% and 0.08% in Boran, Nguni, Afrikaner, Drakensberger and Tuli respectively. Effective population sizes were 89, 107, 122, 191 and 364 in Tuli, Afrikaner, Drakensberger, Nguni and Boran respectively. Inbreeding and effective population size for the Boran was not a true reflection due to poor pedigree recording. These results indicate that none of the breeds are in critical limits of endangerment. Breeding values were regressed on birth year of each breed for weight traits; Kleiber ratio and scrotal circumference from 1986 to 2012. Genetic trends were stable for birth weights except the Afrikaner and Tuli. Genetic progress has been made in weaning and post weaning weights for all the breeds except for limited progress in the Nguni. Kleiber ratio and scrotal circumference in all measured breeds have shown good progress. The results of this study confirmed that recording of pedigree and performance records are effective in maintenance of genetic diversity and genetic improvement through selection based on EBVs of recorded traits. / Dissertation (MScAgric)--University of Pretoria, 2014. / tm2015 / Animal and Wildlife Sciences / MScAgric / Unrestricted

The objectives of this study were to: (1) quantify levels of genetic intermixing in remnant Illinois eastern woodrat populations augmented with Ozark woodrats, and (2) assess genetic health and population viability in remnant and reintroduced woodrat populations. This dissertation is arranged into 3 chapters. DNA extractions, microsatellite genotyping, and mtDNA haplotype sequencing were conducted for individuals from the western Shawnee National Forest (WSNF) (i.e., LaRue Pine Hills [LPH], Fountain Bluff, Horseshoe Bluff), eastern Arkansas (AR), southern Missouri (MO), and 5 locations in the eastern Shawnee National Forest (ESNF), Illinois. Genetic data provided a strong signal in STRUCTURE which confirmed MO, AR, and LPH were genetically distinct populations prior to the genetic augmentation at LPH. Following augmentation, eastern woodrats in ESNF and WSNF have experienced admixture with introduced populations, increased allelic richness, decreased inbreeding, and increased effective population size, while genetic swamping was not observed. Haplotypes from both introduced populations were observed after augmentation at LPH but neither were detected in adjacent remnant populations. Reintroduced populations in the ESNF are acting as a single population and descendants consist of primarily AR and MO individuals. Admixture was apparent in all ESNF populations and haplotypes from all source populations persisted. Effective population size was largest at Garden of the Gods but all 5 populations had similar allelic richness and heterozygosity. In the ESNF, migration is not supported between study populations and additional habitat management may be needed. Future population monitoring of the ESNF population should focus efforts in the 3 central populations which are likely source populations. Future eastern woodrat management efforts should focus on (1) connectivity between ESNF populations and (2) connectivity in the WSNF amongst remnant populations and between remnant and reintroduced populations in the central Shawnee National Forest. I recommend the establishment of migration corridors by decreasing canopy cover in the forested matrix and the establishment of artificial rock outcrops in the form of boulder piles along migration corridors. My study indicates that genetic augmentations can be a beneficial management action in isolated eastern woodrat populations having experienced loss in gene flow, while reintroductions can benefit woodrats in areas believed to have experienced local extirpation. I also recommend identifying genetic structure of source populations for genetic augmentations and reintroductions beforehand to confirm multiple source populations, genetic variation, and introduction of multiple alleles. As rodents often have short lifespans and individual reintroductions may fail to establish, genetic augmentations and reintroductions should include the relocation of multiple individuals over time via soft release.

Study of the genetic relationships and evolutionary histories of pupfish populations (Cyprinodontidae: Cyprinodon spp.) from the remnant aquatic habitats of Death Valley was approached by exploring the genetic structure and divergence within and among populations using mitochondrial and nuclear DNA markers. The findings of these studies illustrate the influences of population size and isolation time in the divergence of small, fragmented populations largely via genetic drift. The information revealed in this study has implications for assessing priorities in the conservation of the unique evolutionary heritage among populations of the Death Valley pupfishes. A new retrotransposable element family was identified and characterized. This family of genetic elements was uncovered during a search of the pupfish genome for transposable elements to be used as molecular markers for population analyses. The description of this element family, named "Swimmer 1" (SW1), provides new insights into the evolution of long interspersed nuclear elements (LINEs) in vertebrates. Therefore, a full characterization of the SW1 element family was undertaken in the Japanese medaka (Oryzias latipes) as well as in the pupfish genome. The Japanese medaka is a model organism widely used for genetic and developmental biology studies. / Ph. D.

Barriers to fish movement can cause aquatic habitat fragmentation by reducing the amount of available habitat. The primary goal of my research was to investigate applications of population genetic analysis tools as indicators of barrier effects on brook trout populations in fragmented subwatersheds. In chapter1, I tested the hypothesis that brook trout population genetic differentiation (FST) above and below barriers will differ in relation to barrier height and gradient. I also tested the hypothesis that average gene diversity per locus (H) and the numbers of alleles (A) differed between samples below and above each barrier. There was no significant difference in average number of alleles (A) or average gene diversity per locus (H) between the above- and below-barrier samples, but linear regression identified a statistically significant relationship between barrier height and FST values. Unrooted neighbor-joining consensus trees of Cavalli-Sforza and Edwards (1967) chord distances provided evidence of genetic differentiation between samples of resident brook trout above and below natural barriers. Additionally, average total allelic diversity (A), average gene diversity per locus (H), average number of private alleles per locus per sample, and total alleles per sample differed between Level III Ecoregions. In chapter 2 I tested the hypothesis that the presence of a barrier, total habitat potentially isolated above a barrier (km), road density, and percent forest cover within a subwatershed (USGS 6th-level Hydrologic Units) were significant habitat fragmentation factors affecting the effective population size (Ne) of brook trout in the Blue Ridge Level III Ecoregion. Multivariable linear regression indicated that total habitat above the barrier (km) and road density were significant variables retained in the model to predict Ne. In chapter 3, the objective of the study was to infer relationships between barriers and family structure in brook trout populations. Maximum likelihood analysis of pairwise kinship relationships between above- and below-barrier individuals indicated the presence of parent-offspring relationships between above- and below-barrier individuals at six sites in the Blue Ridge Level III Ecoregion and five sites in the Northern Lakes and Forests Level III Ecoregion, which indicated movement of individuals between the above- and below-barrier locations. / Ph. D.

Gilthead seabream (Sparus aurata) is one of the most important species of intensively reared fish in the Mediterranean region. Its short history of domestication, along with the need to develop markets, new products and efficiency in the production process, has resulted in an increased interest in the potential genetic improvement of this species. Little work has so far been directed at establishing the procedures for selective breeding in gilthead seabream at a commercial level, although genetic parameters calculated in other studies have indicated that there is a large potential for improvement in certain traits. Selective breeding of commercial gilthead seabream populations is constrained by aspects of the biology that complicate the production of genetic groups and the maintenance of same-age offspring populations. The aim of this thesis was to develop a protocol for the selective breeding of gilthead seabream, specifically to serve a commercial hatchery and on-growing unit in Cyprus, where the fieldwork was carried out. The hatchery broodstock was monitored over a three-year period to identify the rate of sex reversal in introduced fish and to quantify the sex ratio of the stock over time. The analysis of the egg production records was used to evaluate the success of photoperiod manipulation in each group. Size variation in the larval and juvenile stages is a common problem in the rearing of gilthead seabream, leading to cannibalism and labour-intensive sorting operations. Studies on larval populations, from first feeding through to metamorphosis, indicated the origin of size variation was the differences in early feeding ability. The size advantages could be maintained throughout the larval period. During the juvenile stage of the farm production system, a method to standardise the size sorting of populations by grading was developed in order to counter environmental effects of separating groups of fish. Using this method, grading would be suitable to form the first stage of a selection programme for growth rate. The potential gain of selection for growth rate during the on-growing stage was very high, using a simulated criterion and previous estimates of heritability. Other possible quality traits for selection were also examined and quantified in the hatchery populations. Existing and specifically developed microsatellite markers were used for the assignment of offspring to parents from mass spawning of the hatchery broodstock. The effective population size of single spawning events were found to be low and determined by a high variation in contribution to mass spawning. Contribution was found to be significantly linked to body size, which led to the formation of a replacement policy for the broodstock to maximise spawning performance. Survival of individual families through the larval period was also examined. Based on the results of the experimental work, a two-stage selection programme was designed, along with the presentation of specific procedures for each stage of the production system. This project makes recommendations on various strategies that can increase the effective population size within a selection programme and these are discussed as part of the genetic management of hatchery populations. Significant progress has also been made in the use of genetic markers in monitoring the rate of inbreeding and contribution of individual broodfish, which are considered essential in this species.

<p>Although the practice of releasing fish into the wild is common in the management and conservation of fish populations, the success of release programmes and the potential harmful genetic and ecological effects that may follow are rarely considered. This thesis focuses on genetic and ecological consequences of fish releases, exemplified by supportive breeding of brown trout (<i>Salmo trutta</i>) and translocation of European eel (<i>Anguilla anguilla</i>). Specific questions addressed include: What is the relative performance of hatchery produced fish released to support wild populations, and do released hatchery fish contribute to the natural productivity? What is the variation in reproductive success in the wild, and how does it affect the genetic consequences of a supportive breeding programme? Is there a spatial genetic structure in the European eel that must be considered in the management of this rapidly declining species?</p><p>Experiments conducted under natural and near-natural conditions in the River Dalälven, Sweden, suggest that hatchery produced trout can reproduce in the wild. In fact, when the pronounced variation between individual breeders was accounted for, there were no detectable differences between hatchery produced and wild born trout in reproductive success or offspring survival. These results were supported by molecular genetic data suggesting a pronounced gene flow from hatchery to wild trout in the river. Hatchery reared trout were, however, found to exhibit reduced survival rates immediately following release into the wild, an effect that was most likely due to phenotypic responses to the hatchery environment during ontogeny and a lack of experience of the wild.</p><p>In sharp contrast to recently published studies, the present genetic analyses of European eels sampled across the whole distribution range suggest no spatial genetic structure but a subtle temporal genetic heterogeneity within sampled locations. These results emphasise the need to consider temporal replication when assessing population structure of marine species.</p><p>The results obtained have general implications for the management and conservation of fish populations. First, supportive breeding of threatened salmonid populations might be successful, not only for boosting the census size and thereby reducing the short-term probability of extinction, but also for reducing the risks of inbreeding depression and loss of adaptive potential in future generations. However, the results also highlight the need to restore the natural productivity of a population under supportive breeding to avoid a potential reduction in fitness due to hatchery selection. Further, the lack of a detectable spatial genetic structure in the European eel suggests that the management strategy of translocating juvenile eels from locations were they are overabundant to other suitable freshwater habitats does not necessarily have to include genetic considerations with respect to the geographical origin of the translocated eels.</p>

Although the practice of releasing fish into the wild is common in the management and conservation of fish populations, the success of release programmes and the potential harmful genetic and ecological effects that may follow are rarely considered. This thesis focuses on genetic and ecological consequences of fish releases, exemplified by supportive breeding of brown trout (Salmo trutta) and translocation of European eel (Anguilla anguilla). Specific questions addressed include: What is the relative performance of hatchery produced fish released to support wild populations, and do released hatchery fish contribute to the natural productivity? What is the variation in reproductive success in the wild, and how does it affect the genetic consequences of a supportive breeding programme? Is there a spatial genetic structure in the European eel that must be considered in the management of this rapidly declining species? Experiments conducted under natural and near-natural conditions in the River Dalälven, Sweden, suggest that hatchery produced trout can reproduce in the wild. In fact, when the pronounced variation between individual breeders was accounted for, there were no detectable differences between hatchery produced and wild born trout in reproductive success or offspring survival. These results were supported by molecular genetic data suggesting a pronounced gene flow from hatchery to wild trout in the river. Hatchery reared trout were, however, found to exhibit reduced survival rates immediately following release into the wild, an effect that was most likely due to phenotypic responses to the hatchery environment during ontogeny and a lack of experience of the wild. In sharp contrast to recently published studies, the present genetic analyses of European eels sampled across the whole distribution range suggest no spatial genetic structure but a subtle temporal genetic heterogeneity within sampled locations. These results emphasise the need to consider temporal replication when assessing population structure of marine species. The results obtained have general implications for the management and conservation of fish populations. First, supportive breeding of threatened salmonid populations might be successful, not only for boosting the census size and thereby reducing the short-term probability of extinction, but also for reducing the risks of inbreeding depression and loss of adaptive potential in future generations. However, the results also highlight the need to restore the natural productivity of a population under supportive breeding to avoid a potential reduction in fitness due to hatchery selection. Further, the lack of a detectable spatial genetic structure in the European eel suggests that the management strategy of translocating juvenile eels from locations were they are overabundant to other suitable freshwater habitats does not necessarily have to include genetic considerations with respect to the geographical origin of the translocated eels.