Title from linking web page (University of Missouri--St. Louis, viewed February 16, 2010). Includes bibliographical references.

Thesis--University of Hawaii. / Includes bibliography.

Inbreeding depression affects captive populations and those that have been recently impacted by anthropogenic disturbance. However, the evolutionary importance of inbreeding depression in natural populations is not well understood. This study focuses on a naturally small population of Cyclura carinata, the Turks and Caicos Rock Iguana, that has likely been stable for hundreds of generations. Genotypic data at 13 polymorphic microsatellite loci, along with fitness proxies, were collected from 188 individuals across three age classes. Multi-locus heterozygosity is strongly predictive of age class (p < 0.03), and is significantly lower in hatchlings than in juveniles or adults. Estimates for intensity of selection favoring heterozygosity range from 0.498-0.627, indicating that this proportion of individuals fail to survive due to inbreeding depression. The heterozygosityitness correlation among adults is significant (p < 0.01), suggesting outbred individuals have higher reproduction success. Hence, the lifetime influence of inbreeding on fitness is extremely high.

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Dispersal is a critical life-history component; it determines gene flow and has profound effects on population structure, demography, social systems, and population viability. To add to our knowledge of dispersal and, in particular, our understanding of the relationship between dispersal and inbreeding, I studied three aspects of the biology of the red-cockaded woodpecker: dispersal of breeding females; the costs, benefits, and frequency of inbreeding; and the effect of inbreeding on natal dispersal. Dispersal of breeding female red-cockaded woodpeckers is strongly associated with inbreeding avoidance and mate choice, weakly associated with site choice, and not found to be associated with social constraints. Estimates of mortality for non-dispersing and dispersing breeding females were 24 and 59 percent per year, respectively-rare evidence of the cost of breeding dispersal. Significant costs of close inbreeding were found. Closely related pairs (kinship coefficient greater than 0.1) had lower hatching success as well as lower survival and recruitment of fledglings than unrelated pairs. Moderately related pairs (kinship coefficient between 0 and 0.1) and moderately inbred individuals had increased hatching success, but did not produce more young. Despite documented costs of close inbreeding and a predictable spatial distribution of closely related males near the natal territory, female fledglings disperse a median of only two territories and a modal distance of one territory. Natal dispersal of females is affected by closely related males on the natal site but unaffected by closely related males or moderately related males that are off the natal site. / Master of Science

Call number: LD2668 .T4 1963 B37 / Master of Science

Inbreeding results in increased levels of homozygosity for deleterious recessive alleles, leading to increased incidence of monogenic disease in inbred families. It has also been suggested that inbreeding increases the risk of diseases such as cancer and heart disease, implying a role for the combined effects of many recessive alleles distributed across the genome. A better understanding of the links between inbreeding, homozygosity and disease is therefore of interest to those concerned with understanding the genetic architecture of complex disease. A homozygous genotype is defined as autozygous if both alleles originate from the same ancestor. Quantifying inbreeding involves quantifying autozygosity. A new, observational method of quantifying autozygosity using genomic data is developed here. Based on runs of homozygosity (ROH), this approach has a sound theoretical basis in the biological processes involved in inbreeding. It is also backed by strong empirical evidence, correlating strongly with pedigree-derived estimates of inbreeding and discriminating well between populations with different demographic histories. ROH are a signature of autozygosity, but not necessarily autozygosity of recent origin. Short ROH are shown to be abundant in demonstrably outbred individuals and it is suggested that this is a source of individual genetic variation which merits investigation as a disease risk factor, although denser genotype scans than those used in the present study are required for the reliable detection of very short ROH. In the absence of such dense scans, it is suggested that ROH longer than 1 or 1.5 Mb be used to estimate the effects of inbreeding on disease or quantitative physiological traits (QT), and that a simple measure of homozygosity be used to investigate overall recessive effects. Evidence for recessive effects on 13 QT important in cardiovascular and metabolic disease was investigated in 5 European isolate populations, characterised by heightened levels of inbreeding. A significant decrease in height was associated both with increased homozygosity and (to a lesser extent) with increased ROH longer than 5 Mb (i.e. inbreeding) estimated using a 300,000 SNP panel. No evidence was found for recessive effects on any of the other QTs. Evidence for recessive effects on colorectal cancer risk were investigated in two outbred case control samples typed with a 500,000 SNP panel. Cases were significantly more homozygous and had more of their genome in short ROH than did controls. Cases were significantly more homozygous than controls even when inbred individuals were removed from the sample. There was also some evidence of an inbreeding effect, with inbred subjects having slightly significantly higher odds of colorectal cancer than outbred subjects. This study provides evidence of recessive effects on a common, complex disease in outbred populations and on height in both inbred and outbred populations and shows that such effects are not solely attributable to increased levels of homozygosity resulting from recent inbreeding. Individual variation among outbred individuals in the proportion of the genome that is homozygous may be important in disease risk. The development of denser genotype scans will facilitate better enumeration of short ROH in outbred individuals so that these can be properly enumerated and investigated as a disease risk factor.

Thesis (MSc)--Stellenbosch University, 2015. / ENGLISH ABSTRACT: The effects of acute inbreeding on growth performance, yield and occurrence of deformity traits were studied in experimental full-sibling inbred populations of Mozambique tilapia Oreochromis mossambicus at three levels of inbreeding coefficients, namely F = 0.000, F = 0.250 and F = 0.375. The base population with F = 0.000 was established through the crossing of two geographically separated and genetically unrelated farm stocks. At each generation, the inbreeding depression indicated by body weight (BW), standard length (SL), specific growth rate (SGR) and yield were highly significant, but no linear relationship was found between level of inbreeding and inbreeding depression. Both condition factor (K) and the number of observed deformities appears not to be significantly affected by inbreeding at all three levels. Over all, the average inbreeding depression at F = 0.250 and F = 0.375 respectively was found to be 46.5 percent and 46.6 percent for body weight (BW); 18.2 percent and 18.0 percent for standard length (SL); 21.8 percent and 20.3 percent for specific growth rate (SGR) and 5.752 percent and 8.940 percent for flesh yield. The outbred Control group differed significantly (P<0.05) from the six inbred family groups in terms of body weight (BW), standard length (SL), specific growth rate (SGR) and yield at all levels of inbreeding studied (F = 0.000, F = 0.250 and F = 0.375). Average inbreeding depression for body weight (BW) amongst the six inbred families ranged from 39.6 to 54.2 percent at F = 0.250 (in Gen 2) and 45.6 to 47.3 percent at F = 0.375 (in Gen 3). The inbreeding depression coefficient for body weight (BW) per 10% increase in F, amongst the six inbred families, ranged from 15.9 to 21.7 percent at F = 0.250 and from 12.2 to 12.6 percent at F = 0.375. Average inbreeding depression for standard length (SL) amongst the six inbred families ranged from 14.0 to 22.3 percent at F = 0.250 and from 17.2 to 18.4 percent at F = 0.375. The inbreeding depression coefficient for standard length (SL) amongst the six inbred families ranged from 5.6 to 8.9 percent at F = 0.250 and from 4.6 to 4.9 percent at F = 0.375. Average inbreeding depression for specific growth rate (SGR) amongst the six inbred families ranged from 17.9 to 27.9 percent at F = 0.250 and from 16.7 to 27.2 percent at F = 0.375. The inbreeding depression coefficient amongst the six inbred families ranged from 7.2 to 11.2 percent at F = 0.250 and from 4.5 to 7.3 percent at F = 0.375. Average inbreeding depression for yield amongst the six inbred families ranged from 0.4 to 7.7 percent at F = 0.250 and from 8.5 to 10.2 percent at F = 0.375. The inbreeding depression coefficient for yield amongst the six inbred families ranged between 0.2 and 3.1 percent at F = 0.250 and from 2.3 to 2.7 percent at F = 0.375. The condition factor (K) of the six inbred families showed no significant differences to the Control (P > 0.05) at all levels of inbreeding with K-values ranging from 1.42 to 2.85. The occurrence of morphological deformities in all seven family groups including the Control showed no noticeable trend, with a random, nonlinear occurrence of fluctuating asymmetry observed at different inbreeding levels in O. mossambicus. This study demonstrates that inbreeding has a significant negative effect on the production traits of Oreochromis mossambicus, especially growth. Results from this study emphasize the need to create awareness amongst small scale farmers of the importance of preventing uncontrolled inbreeding in production systems, as well as to monitor inbreeding levels during the process of dissemination of improved fish strains to small scale fish growers in developing countries, including Africa. / AFRIKAANSE OPSOMMING: Die gevolge van akute inteling op die groei prestasie, opbrengs en voorkoms van misvorming eienskappe bestudeer in eksperimentele full-broer ingeteelde bevolkings van Mosambiek tilapia Oreochromis mossambicus op drie vlakke van inteling koëffisiënte, naamlik F = 0,000, F = 0,250 en F = 0,375. Die basis bevolking F = 0,000 gestig deur die kruising van twee geografies geskei en geneties onverwant plaas aandele. Op elke generasie, die inteling depressie aangedui deur die liggaam gewig (BW), standaard lengte (SL), spesifieke groeitempo (SGR) en opbrengs was hoogs betekenisvol, maar geen lineêre verband is gevind tussen vlak van inteling en inteling depressie. Beide toestand faktor (K) en die aantal waargeneem deformiteite verskyn om nie beduidend beïnvloed deur inteling op al drie vlakke. Oor alles is, die gemiddelde inteling depressie by F = 0,250 en F = 0,375 onderskeidelik gevind om 46,5 persent en 46,6 persent vir die liggaam gewig (BW) wees; 18,2 persent en 18,0 persent vir standaard lengte (SL); 21,8 persent en 20,3 persent vir spesifieke groeitempo (SGR) en 5,752 persent en 8,940 persent vir vlees opbrengs. Die outbred beheer betekenisvol verskil (P <0,05) van die ses ingeteelde familie groepe in terme van die liggaam gewig (BW), standaard lengte (SL), spesifieke groeitempo (SGR) en opbrengs op alle vlakke van inteling bestudeer (F = 0,000 , F = 0,250 en F = 0,375). Gemiddeld inteling depressie vir die liggaam gewig (BW) onder die ses ingeteelde families gewissel 39,6-54,2 persent by F = 0,250 (in Gen 2) en 45,6-47,3 persent by F = 0,375 (in Gen 3). Die inteling depressie koëffisiënt vir die liggaam gewig (BW) per 10% toename in F, onder die ses ingeteelde families, het gewissel 15,9-21,7 persent by F = 0,250 en 12,2-12,6 persent by F = 0,375. Gemiddeld inteling depressie vir standaard lengte (SL) onder die ses ingeteelde families gewissel 14,0-22,3 persent by F = 0,250 en 17,2-18,4 persent by F = 0,375. Die inteling depressie koëffisiënt vir standaard lengte (SL) onder die ses ingeteelde families gewissel 5,6-8,9 persent by F = 0,250 en 4,6-4,9 persent by F = 0,375. Gemiddeld inteling depressie vir spesifieke groeitempo (SGR) onder die ses ingeteelde families gewissel 17,9-27,9 persent by F = 0,250 en 16,7-27,2 persent by F = 0,375. Die inteling depressie koëffisiënt onder die ses ingeteelde families gewissel 7,2-11,2 persent by F = 0,250 en 4,5-7,3 persent by F = 0,375. Gemiddeld inteling depressie vir opbrengs onder die ses ingeteelde families het gewissel van 0,4-7,7 persent by F = 0,250 en 8,5-10,2 persent by F = 0,375. Die inteling depressie koëffisiënt vir opbrengs onder die ses ingeteelde families gewissel tussen 0,2 en 3,1 persent by F = 0,250 en 2,3-2,7 persent by F = 0,375. Die toestand faktor (K) van die ses ingeteelde families het geen betekenisvolle verskille op die Beheer (P> 0,05) op alle vlakke van inteling met K-waardes wissel 1,42-2,85. Die voorkoms van morfologiese afwykings in al sewe familie groepe, insluitend die beheer het geen merkbare neiging, met 'n ewekansige, nie-lineêre voorkoms van wisselende asimmetrie waargeneem op verskillende vlakke in inteling O. mossambicus. Hierdie studie toon dat inteling het 'n beduidende negatiewe uitwerking op die produksie-eienskappe van Oreochromis mossambicus, veral groei. Resultate van hierdie studie beklemtoon die noodsaaklikheid om bewustheid onder kleinboere van die belangrikheid van die voorkoming van onbeheerde inteling in die produksie stelsels, sowel as om te monitor inteling vlakke tydens die proses van verspreiding van verbeterde vis stamme klein skaal vis produsente in ontwikkelende lande te skep, insluitend Afrika.

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