Genetic algorithms have a lot of properties that makes it a good choice when one needs to solve very complicated problems. The performance of genetic algorithms is affected by the parameters that are used. Optimization of the parameters for the genetic algorithm is one of the most popular research fields of genetic algorithms. One of the reasons for this is because of the complicated relation between the parameters and factors such as the complexity of the problem. This thesis describes what happens when time constraints are added to this problem. One of the most important parameters is population size and we have found by testing a well known set of optimization benchmark problems that the optimal population size is not the same when time constraints were involved. / Genetiska algoritmer har många egenskaper som gör dem till ett bra val när man ska lösa väldigt komplicerade problem. Prestandan för genetiska algoritmer påverkas av de parametrar som används. Optimering av parametrarna för genetiska algoritmer är ett av de mest populära forskningsområdena för genetiska algoritmer. En av anledningarna till detta är den komplexa relationen mellan parametrarna och faktorer så som komplexiteten av problemet. Detta arbete beskriver vad som händer när tidsfaktorn läggs till detta problem. En av de viktigaste parametrarna är populationsstorlek och vi har sett genom att testa en grupp med väl testade optimiseringsproblem att optimal populationsstorlek inte är samma när tidsfaktorn är inblandat.

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. 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. 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.

A research report submitted to the Faculty of Science, in partial fulfilment of the requirements for the degree of Master of Science in Environmental Science, University of the Witwatersrand, Johannesburg, 2015. / Wildlife conservation and management requires an in-depth understanding of the demographics and dynamics of the population concerned to enable sound management decisions. Yet it is often very challenging to obtain reliable information of cryptic and highly migratory species. I used photo identification and capture-recapture methods to study the population of nyala, a highly secretive species, in the Umkhuzi game reserve. The nyala species is individually identifiable by the mark pattern on their body. Photographs used for this project were taken at a waterhole in Umkhuzi game reserve between June 23rd and 01 July 2014, representing nine sampling occasions. Identification of individuals was achieved with a computer-assisted technique using open source pattern identification software called Wild-ID version 1.0.1. A total of 652 photographs were taken at the sampling site and from these pictures wild-ID identified 372 distinct animals. An encounter history for each individual during the nine sampling occasions was also produced using Wild-ID. The encounter histories of all individuals were entered into Program MARK. I used the closed population models in Program MARK to obtain population estimates. Program MARK indicated that Mh was the most appropriate model to fit this data as indicated by the AICc ranking. Mh showed population estimates as follows: adult males: 111.90 ± 16.07, adult females: 298.01 ± 36.66; young adult males: 21.33 ±19.34; juvenile males: 37.15 ±16.84; yearling males: 37.73 ±8.51; yearling females: 96.48 ±22.75 and juvenile unidentified: 69.03. ±28.96 Closure test performed to ascertain demographic and geographic closure during the sampling period showed a χ2= 21.74, p= 0.08, df = 14, for the Stanley & Burnham test and a p and z-values of 0.06 and -1.51 respectively for the Otis et al test. These results shows marginal violation of population closure, nevertheless closed population models were used to estimate population abundance due to the fact the violations are marginal and the sampling period iii was very short, nine days. The study revealed that there is as much as twice the number of females compared to males.

No description available.

Biodiversity is a complex concept encapsulating the variation that occurs within and among levels of biological organization. It is positively linked to ecosystem persistence, adaptability, and function. Biodiversity loss, driven by global change and human activities, is one of the most prominent threats to ecosystems. Characterizing the variation of and processes driving biodiversity is a critical step in understanding the causes, consequences, and magnitude of biodiversity loss. However, characterizing biodiversity comprehensively requires understanding multiple dimensions, or types, of diversity, such as genetic, taxonomic, phylogenetic, and life history diversity, that encompass both ecological and evolutionary processes varying across space and time. In this dissertation, I investigate spatial and temporal variation in frog and toad (order Anura) biodiversity to understand the effects of how diversity is measured on biodiversity characterization and the underlying processes driving biodiversity. In my first chapter, I examined the spatial and temporal variation of genetic diversity and other population genetic metrics to understand the effects of multi-year sampling on population genetic inference in an anuran metapopulation (Arizona treefrog, Hyla (Dryophytes) wrightorum). I found that a single sample year captures global, but not local, population genetic dynamics, as there is considerable temporal variation in genetic metrics within individual populations. In my second chapter, I developed a tool to improve the characterization of anuran life history diversity using species traits. Traits are the measurable attributes of species, and a suite of species traits is used to distinguish ecological strategies found among species. I collated trait data from 411 primary and secondary sources for 106 anuran species found in the United States to develop an anuran traits database for use in conservation, management, and research. In my third chapter, I investigated spatial variation within and among taxonomic, phylogenetic, and life history anuran diversity in the United States and examined the abiotic relationships behind observed patterns. To do this, I developed species distribution models at a 1 km2 resolution for the majority of the native US anurans. I identified relationships among diversity metrics for improved, comprehensive biodiversity characterization and potential ecological and evolutionary processes underlying biodiversity. Spatial variation in multidimensional relationships highlights regional needs for multiple metrics of diversity to comprehensively characterize biodiversity. This spatial variation is driven by temperature, elevation, and water availability, likely related to the biological limits for anurans. Collectively, these chapters highlight the considerable variation that exists within and among species of a broad and diverse biological. Furthermore, these chapters call attention to the importance of measuring multiple biodiversity dimensions for effective conservation in a rapidly changing world. / Doctor of Philosophy / Biodiversity loss, from global change and human activities, is one of the biggest threats to the Earth's ecosystems. Biodiversity is the similarities and differences in organismal characteristics, such as their genetics, evolutionary history, and ecology. Biodiversity is often linked to how well an ecosystem will persist and adapt to global change. To understand the causes and consequences of biodiversity loss, it is important to first measure diversity and what shapes it. However, there are many types of diversity and ways to measure them, such as the number of species in a system, or species richness, the span of evolutionary lineages in a system, or phylogenetic diversity, the number of roles species fill in a system, or life history diversity, and the genetic relationships within individuals and populations, or genetic diversity. In this dissertation, I investigate how our understanding of biodiversity is affected by the ways it can be measured and the relationship among those metrics. To do this, I studied diversity in three ways for frogs and toads of the United States. First, I investigated whether sampling across multiple years is necessary to adequately characterize genetic diversity in a frog species (Arizona treefrog: Hyla (Dryophytes) wrightorum) with populations that fluctuate in size over time. Here, I found that multiple sample years are necessary to capture the genetic variation within individual populations over time, but unnecessary to capture the average genetic variation among all populations over space and time. Second, I developed a tool to improve our ability to measure anuran life history diversity using traits. Traits are measurable attributes of species, and multiple species traits can be used to define the role of a species in an ecosystem. I collected trait data from 411 sources for 106 frog and toad species found in the United States to develop a traits database for use in conservation, management, and research. Third, I investigated the similarities in multiple diversity metrics across the United States using species richness, phylogenetic diversity, and life history diversity. Species richness is highest in the eastern US, phylogenetic diversity is highest in the western US, and life history diversity is clustered around eastern US mountains. These regional relationships among metrics coincided with regional water availability, temperature, and elevation. These results collectively call attention to changes over space and time in frog and toad diversity and how the relationships within and among diversity types relate to our understanding of frog and toad biodiversity. Considering how, where, and when to measure biodiversity can lead to more effect biodiversity conservation in a rapidly changing world.

In a single capture-recapture problem, two new Wilson methods for interval estimation of population size are derived. Classical Chapman interval, Wilson and Wilson-cc intervals are examined and compared in terms of their expected interval width and exact coverage properties in two models. The new approach performs better than the Chapman in each model. Bayesian analysis also gives a different way to estimate population size.

Body size is important in determining the outcome of competition and predator-prey interactions. Size structure of a population (i.e. relative proportion of large and small conspecifics) may be particularly important in organisms with prolonged breeding periods and rapid growth where populations may have multiple cohorts at different stages of development competing for one resource. Both the consumptive and nonconsumptive effects of predators can also be size-dependent and can alter competitive interactions. Here we study the importance of size structure in the Neotropical leaf-breeding tree frog, Agalychnis callidryas. This species is a prolonged breeder such that multiple overlapping cohorts of differing sizes are common. Specifically, we examine size-specific intraspecific competition between A. callidryas tadpoles and then explore how predation affects these interactions. To determine the strength of inter-cohort competition, we manipulated the density and relative proportion of large and hatchling tadpoles in a response surface design and quantified growth. We then observed the effect of a dragonfly larvae predator (Anax amazili) on tadpole growth and survival at different size-structured treatments. Large tadpoles were greater per individual competitors while hatchlings were greater per gram competitors. When predators were added, dragonflies reduced survival and growth of hatchlings substantially, but had no effect on large tadpoles. Further, dragonflies reduced hatchling growth more when other hatchlings were present. The predator effect on hatchling growth was 23% larger than the effect of competition with large tadpoles, such that the importance of size structure for A. callidryas may be mediated more through predation than intercohort competition.

Through series of experiments this work compares effects of different types of genetic algorithms on evolution of a neural network that is used to control a robot. Genetic algorithms using binary and real coded individuals, algorithms using basic and advanced mutations and crossovers and algorithms using fixed and variable population size are compared on three tasks of evoltionary robotics. The goal is to determine wether usage of advanced genetic algorithms leads to faster convergence or to better solution than usage of basic genetic algorithm. Experiments are performed in an easily extendable simulator developed for purposes of this work.

In this dissertation, I report new information that is necessary for future mating system studies in a little studied species, the marbled salamander (Ambystoma opacum). I studied female mating behavior, sexual selection, and the consequences of polyandry for individual females and salamander populations. I also compared the performance of several statistical approaches for analyzing genetic mating system data. The first chapter summarizes the characteristics of several novel microsatellite DNA loci as well as cross-amplified loci for marbled salamanders and mole salamanders that may be used for future studies. In the second chapter, I report estimates of sire number for 13 marbled salamander clutches based on microsatellite data from 32 hatchlings per clutch. Females mated with as many as three different males as indicated by conservative techniques. Less than half of females mated with multiple males. Based on comparative analyses, I recommend the parental reconstruction approach with the computer program GERUD for assessing multiple paternity. The third chapter describes an experiment designed to study sexual selection. As expected, in breeding mesocosms, the potential for sexual selection was much higher for males than for females. Size was unrelated to variance in male reproductive fitness. Only opportunity for selection and Morisita’s index conformed to theoretical expectations of the relationship between operational sex ratio and the potential for sexual selection among males. Because opportunity for selection has intuitive links to formal sexual selection theory, I recommend its continued use. In the fourth chapter, I compared polyandrous and monandrous females to explore the potential fitness consequences of multimale mating. No fitness measure at the egg or hatchling stage (clutch size, hatching success, hatchling size, etc.) differed between the two types of clutches. Size of metamorphs was not different, but polyandrous clutches had significantly higher survival to metamorphosis. In the fifth chapter, I analyzed effects of increased polyandry and male availability on genetic diversity, effective population size (Ne), and fitness of experimental populations. Although no analyses were significant, some effects were moderate to high in size. Ne was higher when estimated from hatchlings than with metamorphs.

O presente estudo teve como objetivo avaliar a estrutura populacional, estimar parâmetros (coeficientes de herdabilidade e correlações) e determinar as tendências genéticas e fenotípicas de características de crescimento e adaptação em bovinos da raça Nelore, linhagem Lemgruber. O banco de dados utilizado nas análises constituiu-se de 39.290 animais no arquivo de pedigree e de 24.353 animais no arquivo de produção. Os parâmetros populacionais foram obtidos por meio dos softwares POPREP (GROENEVELD et al., 2009) e ENDOG v 3.2 (GUTIÉRREZ e GOYACHE, 2005). As estatísticas descritivas e os parâmetros genéticos para cada característica estudada foram estimadas por meio de quatro análises hepta-característica utilizando o programa VCE-6 (KOVAC & GROENEVELD, 2003) sob modelo animal completo. As tendências genéticas e fenotípicas foram obtidas pela regressão dos valores genéticos e fenotípicos respectivamente sobre o ano de nascimento dos animais e os coeficientes da regressão foram estimados por meio do método de quadrados mínimos. Apesar da endogamia média do rebanho ser considerada moderada verificou-se alta porcentagem de indivíduos endogâmicos e reduzido tamanho efetivo populacional. Além disso, o incremento contínuo de endogamia ao longo dos anos demonstra a necessidade de intervenção na seleção dos indivíduos para reprodução, de modo que, problemas futuros possam ser evitados. Os coeficientes de herdabilidade direta foram estimados em 0,24, 0,31, 0,31, 0,21, 0,19, 0,30, 0,41, 0,19 e 0,17 respectivamente para peso ao nascimento (PN), peso aos 120 dias de idade (P120), peso à desmama (PD), peso ao ano (PES12), ganho de peso pós desmama, de 205 aos 550 dias (GP345), ganho de peso na prova à pasto da ABCZ, em 224 dias (GP224), perímetro escrotal (PE), temperamento (TEMP), e repelência (REP) e indicam que a variabilidade genética aditiva existente é suficiente para a obtenção do ganho genético em resposta à seleção desde que sejam realizados ajustes, tanto nas estratégias de seleção adotadas para a obtenção de maiores ganhos nos valores genéticos, como também nos fatores ambientais que possam possibilitar ao máximo, a expressão do potencial genético dos animais. / The present study had as objective to evaluate the population structure, to estimate parameters (coefficients of heritability and correlation) and to determine the phenotypic and genetic trends for growth and adaptability traits in Nellore cattle, Lemgruber line. The database used in the analysis consisted of 39,290 animals in the pedigree and 24,353 animals in the production file. The population parameters were obtained from the software POPREP (Groeneveld et al., 2009) and ENDOG v 3.2 (Gutierrez and GOYACHE, 2005). The descriptive statistics and genetic parameters for each characteristic studied were estimated by four seven-traits analysis using the program VCE-6 (Kovac & GROENEVELD, 2003) which uses the animal model. The phenotypic and genetic trends were obtained by means of phenotypic and genetic values respectively on the year of birth of the animals and the regression coefficients were estimated by the method of least squares. Although the average inbreeding of the herd being considered moderate, there was high percentage of inbred individuals and small effective population size. Furthermore, the continuous increase in inbreeding over the years demonstrates the need for intervention in the selection of individuals for reproduction, so that future problems can be avoided. Direct heritability coefficients were estimated as 0.24, 0.31, 0.31, 0.21, 0.19, 0.30, 0.41, 0.19 and 0.17 respectively for birth weight (PN), weight 120 days of age (P120), weaning weight (PD), weight at 12 months of age (PES12), weight gain after weaning from 205 to 550 days (GP345), weight gain during the pasture test of ABCZ in 224 days (GP224), scrotal circumference (PE), docility (TEMP) and repellency (REP) and indicate that the additive genetic variability is sufficient to obtain genetic gain in response to selection as far as adjustments in selection strategies are adopted to achieve larger gains in breeding values, and environmental factors that may allow the expression of the genetic potential of the animals.