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.

Hypervariable, nuclear-encoded microsatellites were used to (i) estimate genetic effective size (Ne) of red drum spawning over a two-week period in nine brood tanks at a TPWD hatchery; (ii) estimate heritability of early-larval growth and of growth rate and cold tolerance of juveniles; and (iii) test Mendelian segregation and independent assortment of 31 nuclear-encoded microsatellites. Assuming all tanks contributed equally to an offspring population, the maximum (expected) and observed Ne over the nine brood tanks was 43.2 and 27.0, respectively. The estimate of Ne based on observed variation in family size was 19.4. Simulations indicated that over a limited time period the simplest approach to maximizing Ne for a release population would be to utilize equal numbers of progeny from each brood tank. A family (genetic) effect was found to contribute significantly to the variance in early larval growth, juvenile growth rate, and cold tolerance. Estimates of narrow-sense heritability for these three traits were 0.07 +- 0.03, 0.52 +- 0.21 and 0.20 +- 0.10 (two growth intervals measured), and 0.30 +- 0.11, respectively, under the genetic models employed. The relatively low estimate of heritability for early larval growth suggests that genetic improvement for this trait likely would be slow. The heritability estimates for juvenile growth rate and cold tolerance, alternatively, suggest that genetic selection for these traits could be effective. Segregation at all 31 microsatellites fit Mendelian expectations for autosomal loci; a null allele was inferred at two of the microsatellites. Results from pairwise tests of independent assortment demonstrated that 20 of the 31 microsatellites could be placed into seven linkage groups. Additional linkage groups inferred from a prior study increased the number of inferred linkage groups in red drum to nine, with a range of two - five (avg. = 2.78) microsatellites in each linkage group. The remaining 11 microsatellites tested in this study assorted independently from all other microsatellites, suggesting the possibility of 11 additional linkage groups.

Includes vita. / Title from PDF of title page. / Document formatted into pages; contains 241 pages. / Thesis (Ph.D.)--University of South Florida, 2003. / Includes bibliographical references. / Text (Electronic thesis) in PDF format. / ABSTRACT: Genetic changes likely occur in wild fish populations as a consequence of interactions with cultured fish, but to what extent do those changes threaten the maintenance of natural genetic diversity and population viability? Following a review and categorization of numerous processes suspected of being agents of post-release genetic change in recipient wild populations (Chapter 1), I focus on risks relating to the magnitude and duration of releases -- but with a twist. That is, I assume that the mean fitness of released, cultured individuals does not differ from that of the recipient natural population. Throughout, attention is devoted to potential post-release changes in inbreeding (NeI) and variance (NeV) effective population sizes -- indicators of expected rates of population-level change in inbreeding and drift variance, respectively. The reductive effect that large-scale releases exert on NeI in recipient populations can be significant. / ABSTRACT: The effect is shown to be a threshold process (Chapter 2) and thus suggestive of an approach for determining risk-adverse stocking (or release) rates. This approach is utilized in Chapter 3, which describes genetic recommendations for an incipient marine stocking program. Several discordant contemporary NeI models are examined mathematically and by computer simulation (Chapter 4). I show that certain published results pertaining to the effect of multiple paternity on NeI are erroneous; a general model is described which accounts for inbreeding and relatedness in and among parents. That model is utilized in an empirical study of gene correlation in a hatchery cohort (Chapter 5). Propagation-related causes of reductions in NeI are also investigated in this cohort. / ABSTRACT: Finally, extending mutational meltdown theory to accommodate fluctuating population sizes and recessive selective effects, I show that when large reductions in NeV occur (such as those that accompany admixtures of cultured and wild fish), the expected time to population inviability is significantly reduced (Chapter 6). Although a more comprehensive theoretical approach is needed, a precautionary inference may be drawn -- aquaculture-induced reductions in Ne, even though they may be transient, can lead to adverse genetic impacts. Avoidance of Ne-reductions cannot be accomplished, in a practical sense, without considering the stocking or release rates of cultured fish. / System requirements: World Wide Web browser and PDF reader. / Mode of access: World Wide Web.

Population Genetics has led to countless numbers of fruitful studies of evolution, due to its abilities for prediction and description of the most important evolutionary processes such as mutation, genetic drift and selection. The field is still growing today, with new methods and models being developed to answer questions of evolutionary relevance and to lift the veil on the past of all life forms. In this thesis, I present a modest contribution to the growth of population genetics. I investigate different questions related to the dynamics of populations, with particular focus on studying human evolution. I derive an upper bound and a lower bound for FST, a classical measure of population differentiation, as functions of the homozygosity in each of the two studied populations, and apply the result to discuss observed differentiation levels between human populations. I introduce a new criterion, the Gain of Informativeness for Assignment, to help us decide whether two genetic markers should be combined into a haplotype marker and improve the assignment of individuals to a panel of reference populations. Applying the method on SNP data for French, German and Swiss individuals, I show how haplotypes can lead to better assignment results when they are supervised by GIA. I also derive the population size over time as a function of the densities of cumulative coalescent times, show the robustness of this result to the number of loci as well as the sample size, and together with a simple algorithm of gene-genealogy inference, apply the method on low recombining regions of the human genome for four worldwide populations. I recover previously observed population size shapes, as well as uncover an early divergence of the Yoruba population from the non-African populations, suggesting ancient population structure on the African continent prior to the Out-of-Africa event. Finally, I present a case study of human adaptation to an arsenic-rich environment.

The Jollyville Plateau Salamander (JPS), Eurycea tonkawae, is a species of salamander endemic to Texas, the United States. It is a candidate for protection under the Endangered Species Act. This report assesses the JPS population abundances at Lanier Spring, Long Hollow Creek at Wheless Spring, and Ribelin Spring in Austin using a mark-recapture method. The maximum likelihood estimation method was used to obtain the population size estimates under two models, the M₀ model and the M[subscript t] model. The M₀ model assumes that every animal has the same capture probability in the population for each sampling period while the M[subscript t] model allows capture probabilities to vary by time. Simulations were performed by using an MCMC algorithm based on the M₀ model. Between 2007 and 2009, the population size estimates for JPS (>16mm snout-vent length, (SVL)) at Lanier Spring varied between 86 and 554 under the M₀ model, between 80 and 549 under the M[subscript t] model, and between 76 and 564 using MCMC simulations. During 2007 monitoring periods, the population size estimates for JPS (>16mm SVL) at Ribelin Spring varied between 105 and 236 under the M₀ model, between 104 and 196 under the M[subscript t] model, and between 105 and 265 using MCMC simulations. During 2007 and 2008 monitoring periods, the population size estimates for JPS (>16mm SVL) at Wheless Spring varied between 368 and 1087 under the M₀ model, between 339 and 1075 under the M[subscript t] model, and between 411 and 1098 using MCMC simulations. Different estimation methods yielded consistent estimates. No clear population trends were detected due to the big fluctuations in estimates in this study. / text

French Polynesia relies solely on the collection of wild Pinctada margaritifera spat for pearl oyster culture. This was developed to help protect the wild populations from overexploitation, but it is feared that massive spat collection could lead to erosion of genetic diversity both in farmed and wild stocks. Wild and farmed collections of P. margaritifera from four atolls in French Polynesia were genotyped at eight microsatellite loci to determine whether there was a loss of genetic diversity from the wild to adjacent farmed aggregations. The average allelic richness for wild samples was not significantly different from that seen for farmed samples, but there was a significant effect of atoll and locus. Pair-wise genetic differentiation (FST) was not significant between adjacent wild and farmed collections or across atolls. Overall there was no evidence for a loss of genetic variability in farmed oysters. Both farmed and wild individuals analyzed here were adults and could have originated from multiple spawning events in time and space. This could have masked genetic processes linked to recruitment happening at a finer scale. P. margaritifera demonstrates high recruitment variability, but the number of parents contributing to a successful cohort of juveniles recruited on collectors is unknown. Low effective number of breeders and variable recruitment are assumed to be responsible for the genetic patchiness that has been observed at a small spatial scale for this species and this could lead to a loss of genetic diversity in both the farmed and wild stocks. The genetic diversity and family make-up of three groups of 1.5 year old oysters were assessed using 13 microsatellite markers. These individuals were harvested on collectors in three closely located sites of the Takapoto atoll. Higher recruitment density and higher allelic richness was observed in one zone compared to the other two. Significant genetic differentiation was also observed at a small spatial scale. Pair-wise FST estimates between collectors within zone were not significant, but were generally significant across zones. Estimates of effective population size and number of families present for these individuals were larger than expected and suggested that the numbers of parents contributing to the recruits on these collector lines were not limited. Similar results were obtained when assessing monthly cohorts of recruits collected in Takapoto over 5 months with 11 microsatellites. Levels of allelic richness were not significantly different among monthly cohorts, and were comparable to the levels observed in the adult samples above. Small but significant temporal genetic differentiation was observed between the monthly cohorts. Again, there was no evidence for low effective population size or for significant family structuring and it did not appear that a limited number of parents produced these temporal cohorts. Patchy genetic structure was observed, but recruitment on collectors does not seem to be driven by a limited number of successful parents. It does not appear that the current pearl culture practices are negatively impacting the local farmed and wild stocks of P. margaritifera in French Polynesia by reducing their levels of genetic diversity.

I describe temporal changes in the genetic composition of a small anadromous Atlantic salmon (Salmo salar) population from South Newfoundland, an area where salmon populations are considered as Threatened (COSEWIC 2010). I examined the genetic variability (13 microsatellite loci) in 869 out-migrating smolt and post-spawning kelt samples, collected from 1985 to 2011 for a total of 22 annual collections and a 30 year span of assigned cohorts. I estimated the annual effective number of breeders (Nb) and the generational effective population size (Ne) through genetic methods and demographically using the anadromous sex ratio. Comparisons between genetic and demographic estimates show that the anadromous spawners inadequately explain the observed Ne estimates, suggesting that mature male parr are significantly increasing Nb and Ne over the study period. Spawning as parr appears to be a viable and important strategy in the near absence of anadromous males.

Sous l'effet de la pêche, de nombreuses espèces de raies des eaux européennes ont décliné au cours du 20ème siècle. La conservation de ces espèces est un objectif majeur quant à la gestion des ressources marines. La raie bouclée (Raja clavata) est l'espèce de raie la plus répandue d'Atlantique Nord-Est. Sa gestion, basée sur un quota non spécifique, repose principalement sur les observations scientifiques et professionnelles et non sur des méthodes d'évaluations d'abondance. Les objectifs de cette thèse consistent ainsi à comparer les méthodes d'évaluations d'abondances disponibles pour cette espèce et à les appliquer aux données disponiblesDeux grands axes sont creusés : l'utilisation de méthodes basées sur la démographie de l'espèce et de méthodes basées sur la génétique. / During the 20th century, several skates and rays species in European waters declined because of fishing. Conservation of these species is a major objective of the management of marine resources. The thornback ray (Raja clavata) is the most widespread species of the North-Est Atlantic. Its management is based on a nonspecific quota and lay on observations only as no stock assessment is available.Thus this thesis aims to compare the available stock assessments methods for this species and to apply them to empiric data. Two types of methods are investigated: methods based on population demography and methods based on population genetics.

abstract: Urban scaling analysis has introduced a new scientific paradigm to the study of cities. With it, the notions of <italic>size</italic>, <italic>heterogeneity</italic> and <italic>structure</italic> have taken a leading role. These notions are assumed to be behind the causes for why cities differ from one another, sometimes wildly. However, the mechanisms by which size, heterogeneity and structure shape the general statistical patterns that describe urban economic output are still unclear. Given the rapid rate of urbanization around the globe, we need precise and formal mathematical understandings of these matters. In this context, I perform in this dissertation probabilistic, distributional and computational explorations of (i) how the broadness, or narrowness, of the distribution of individual productivities within cities determines what and how we measure urban systemic output, (ii) how urban scaling may be expressed as a statistical statement when urban metrics display strong stochasticity, (iii) how the processes of aggregation constrain the variability of total urban output, and (iv) how the structure of urban skills diversification within cities induces a multiplicative process in the production of urban output. / Dissertation/Thesis / Doctoral Dissertation Applied Mathematics for the Life and Social Sciences 2014

The presented thesis deals with habitat requirements, population size and survival of the Spotted Fritillary (Melitaea didyma) in national nature reserve The Mohelno Serpentinite steppe. The estimated population size is about two thousands of individuals, and the individuals frequently migrate between habitat patches. The optimal habitat structure is characterized by grassy pasture steppe with occurrence of larval host plant and abundant nectar plants for adults. The most frequent male behaviour is searching for females, while the females spend most time by nectaring. Caterpillars were found on two species of family Scrophulariaceae.