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Data for this study were age-adjusted linear scores on all cows scored between 1980 and 1993. Lifetime production information on these cows and their herdmates was used to calculate Relative Net Income adjusted for opportunity cost (RNIOC) for the 2,249,835 cows with an 84 month herdlife opportunity. The effect of inbreeding was analyzed using both a fixed and animal model, with little difference in results. Inbreeding depressed RNIOC by $12.69 in a fluid market and $11.53 in a manufacturing market per 1% increase in inbreeding. Addition of somatic cell information in the profit function had little effect. Heritabilities of profit functions were .16 and .14 for a fluid and manufacturing market, respectively. Animal model estimates of inbreeding depression were +.16 days, -6.7 days and -5.1 days for age at first freshening (AFF), days of productive life (DPL) and days in milk (TDIM), respectively. Inbreeding decreased first lactation mature equivalent milk, fat, and protein by 23.7 kg, .85 kg, and .76 kg, respectively and lifetime milk, fat, and protein production by 176.9 kg, 6.4 kg, 5.6 kg, respectively per 1% increase in inbreeding. Inbreeding had little effect on conformation traits. Effects of inbreeding were cumulative, exacting a larger effect on lifetime profit functions than on individual traits, when expressed as a percent of additive standard deviation. This study gives evidence that though not alarming, inbreeding has a deleterious effect on the lifetime performance of dairy cattle. / Master of Science

As environmental change continues and increases, understanding how species will respond to change and how these responses may affect populations will be important for conserving and managing species. Red-cockaded Woodpeckers (Picoides borealis) are well-studied and provide an ideal system in which to examine ecological and evolutionary questions related to life histories because monitoring them accurately is relatively easy, their behavior is well-described and structured. In this study, I examined the following questions using long-term data (1980-2013) from two study sites in North Carolina: 1) what traits contribute most to lifetime fitness, 2) how have traits changed over time and how is climate change influencing life history, and 3) to what extent are traits that contribute to fitness and that are changing over time heritable in this species. I found that a multitude of factors contribute to different aspects of fitness, including: parental age and hatch date affecting survival to year one and probability of attaining breeding status; and lay date, clutch size, age at first reproduction, and variance in clutch size affecting lifetime fitness. I also found that many traits were changing over time including lay date, clutch size, partial brood loss, and survival to year one. These traits were strongly influenced by local climate variables at each study site, but it is not clear that climate has changed over time at the study sites to account for all the observed changes in life history traits. Habitat improvement has also played a role as evidenced by increased fledgling production in terms of raw numbers (without accounting for covariates). I also found that lay date, clutch size, and partial brood loss had low heritabilities after accounting for other random and fixed effects. These results indicate that Red-cockaded Woodpeckers at these two study sites are shifting traits successfully in response to changing conditions, and that these changes are in the direction that increases aspects of fitness. These shifts indicate that individuals are plastic with respect to these traits, but most of the variance in traits was related to external habitat-associated factors rather than additive genetic variance or environmental × genotype interactions. / Ph. D.

The goals of captive breeding programs for endangered species include preserving genetic diversity and avoiding inbreeding. Typically this is accomplished by minimizing population mean kinship; however, this approach becomes less effective when errors in the pedigree exist and may result in inbreeding depression, or reduced survival. Here, both pedigree- and DNA-based methods were used to assess inbreeding depression in the critically endangered Attwater’s prairie-chicken (Tympanuchus cupido attwateri). Less variation in the pedigree-based inbreeding coefficients and parental relatedness values were observed compared to DNA-based measures suggesting that errors exist in the pedigree. Further, chicks identified with high parental DNA-based relatedness exhibited decreased survival at both 14- and 50-days post-hatch. A similar pattern was observed in later life stages (> 50 days post-hatch) with birds released to the wild; however, the pattern varied depending on the time post-release. While DNA-based inbreeding coefficient was positively correlated with mortality to one month post-release, an opposite pattern was observed at nine months suggesting purging of deleterious alleles. I also investigated whether immunocompetence, or the ability to produce a normal immune response, was correlated with survival; however, no significant correlation was observed suggesting that inbreeding was a more important factor influencing survival. Pairing individuals for breeding by minimizing DNA-based parental relatedness values resulted in a significant increase in chick survival. This study highlights the importance of using DNA-based methods to avoid inbreeding depression when errors exist in the pedigree.

Endogamy levels are usually estimated using genealogical or molecular markers data. By means of both type of data from a traditional Brazilian tri-hybrid quilombo population aggregate (located at the Ribeira River Valley in the State of São Paulo), the aim of this work, using different methods, was to obtain reliable estimates of its average inbreeding coefficient, as well as to establish pertinent demographic inferences. The results we obtained are presented in three chapters. The first one, represented by the offprint of a published paper, deals with the estimation of the inbreeding coefficient using both a complete genealogical and comprehensive molecular information. F values were estimated for each community using all available pedigree information and averaging the inbreeding coefficients from all individuals represented in the genealogies. Molecular f values were estimated from the analysis of 30 highly heterogenous sets of molecular markers (14 biallelic SNPs and 16 multiallelic microsatellites), genotyped in different groups of individuals from the population. The second chapter (a research paper already published), presents a simplified method to estimate the variance of the inbreeding coefficient. The simple approximations we provided can be applied to a locus with any number of alleles, producing estimates fully validated by computer simulations. The last chapter is a manuscript yet to be published that deals with inbreeding and demographic inferences, obtained from the information of hundreds of thousands of biallelic SNP markers. A new manner to obtain estimates of Wright\'s fixation index f is presented, consisting in the use of the joint information of two sets of markers (one complete and another excluding markers in patent linkage disequilibrium). Quilombo demographic inferences were obtained by means of ROHs analyses, which were adapted to cope with a highly admixed population with a complex foundation history / Os níveis de endogamia de uma população são comumente estimados por meio do coeficiente de endocruzamento, que pode ser obtido de dados genealógicos (F) ou dados provenientes da análise de marcadores moleculares (f). O objetivo do trabalho foi obter estimativas confiáveis do coeficiente de endocruzamento populacional, bem como realizar inferências demográficas, usando dados de um agregado populacional quilombola miscigenado com ancestralidade complexa tri-híbrida, localizado no Vale do Rio Ribeira, na região sul do estado de São Paulo. No trabalho é apresentado em três capítulos. No primeiro (um trabalho já publicado), estimamos o coeficiente de endocruzamento usando dados genealógicos e moleculares. As estimativas genealógicas de F foram obtidas para cada comunidade por meio da média dos coeficientes individuais de todos os indivíduos representados nas genealogias da população. Os valores de f foram estimados por meio dos dados de 30 marcadores moleculares altamente heterogêneos (14 SNPs e 16 microssatélites), genotipados em diferentes grupos de indivíduos com diferentes finalidades. O segundo capítulo, representado por um trabalho também já publicado, apresenta um método simples para estimar a variância do coeficiente de endocruzamento f. As aproximações obtidas, validadas devidamente por simulações em computador, podem ser aplicadas a lóci multialélicos, produzindo estimativas que não diferem significativamente de outras aproximações complicadas descritas na literatura. O último capítulo (um manuscrito a ser submetido para publicação) apresenta inferências a respeito dos processos de endogamia e demografia no isolado quilombola, utilizando a informação de centenas de milhares de marcadores moleculares bialélicos. É apresentada uma nova maneira de se estimar o índice de fixação f de Wright, usando a informação combinada de dois conjuntos de marcadores (o conjunto completo de marcadores e um outro contendo apenas marcadores não ligados significativamente entre si). Também foram feitas inferências sobre a história demográfica do isolado por meio do estudo das regiões genômicas em homozigose (ROHs), uma contribuição inédita e importante do trabalho, adaptada à análise de um isolado populacional altamente miscigenado com contribuição tri-híbrida e uma história de fundação complexa

Inbreeding can have profound negative effects on individuals by reducing fertility and viability. In populations, inbreeding depression can reduce growth rates and increases extinction risk. The aims of this thesis are to investigate inbreeding depression in male guppies (Poecilia reticulata) and to study the evolution of mechanisms for inbreeding avoidance in females, using guppies from a feral population in Queensland, Australia. Male guppies are highly polymorphic in their sexual ornamentation, indeed they show one of the most extreme polymorphisms observed in nature. Female guppies exhibit complex mate choice based on preferences for ornamentation, as well as social context. I aim is to examine how these factors of inbreeding avoidance alter sexual selection. In male guppies I found strong inbreeding depression in male sperm numbers, which is amplified under semi-natural compared to laboratory conditions (Chapter 2). Moreover, inbreeding depression results in low fertility under sperm competition: an experiment using artificial insemination techniques reveals that highly inbred males are heavily disadvantaged in gaining paternity (Chapter 3). On population level, inbreeding depression is manifest in reduced growth rates, predominantly in the early stages of inbreeding (Chapter 4). Population growth at inbreeding coefficients f=0.375-0.59 did not seem to lead to inbreeding depression, whereas lower levels of inbreeding reduced population growth. Although the growth rates in inbred populations appear normal, severe inbreeding depression is uncovered after outbred immigrants are added. Specifically, male immigrants are most efficient in short-term genetic rescue, probably due to insemination of large numbers of females whereas females are limited in the number of eggs they can produce (Chapter 4). Male ornamental traits show significant inbreeding depression in semi-natural conditions only (Chapters 2 & 3). Inbreeding avoidance mechanisms seem to have evolved in females: they prefer courtship displays of non-inbred males (Chapter 2), unfamiliar males (Chapter 5) and males with rare patterns (Chapter 6). This preference might increase the mating success of immigrants, and may have evolved to facilitate the avoidance of inbreeding. Together with context-independent preferences for ornament combinations (Chapter 6), it also offers an explanation for the maintenance of polymorphism in this species.

Inbreeding can have profound negative effects on individuals by reducing fertility and viability. In populations, inbreeding depression can reduce growth rates and increases extinction risk. The aims of this thesis are to investigate inbreeding depression in male guppies (Poecilia reticulata) and to study the evolution of mechanisms for inbreeding avoidance in females, using guppies from a feral population in Queensland, Australia. Male guppies are highly polymorphic in their sexual ornamentation, indeed they show one of the most extreme polymorphisms observed in nature. Female guppies exhibit complex mate choice based on preferences for ornamentation, as well as social context. I aim is to examine how these factors of inbreeding avoidance alter sexual selection. In male guppies I found strong inbreeding depression in male sperm numbers, which is amplified under semi-natural compared to laboratory conditions (Chapter 2). Moreover, inbreeding depression results in low fertility under sperm competition: an experiment using artificial insemination techniques reveals that highly inbred males are heavily disadvantaged in gaining paternity (Chapter 3). On population level, inbreeding depression is manifest in reduced growth rates, predominantly in the early stages of inbreeding (Chapter 4). Population growth at inbreeding coefficients f=0.375-0.59 did not seem to lead to inbreeding depression, whereas lower levels of inbreeding reduced population growth. Although the growth rates in inbred populations appear normal, severe inbreeding depression is uncovered after outbred immigrants are added. Specifically, male immigrants are most efficient in short-term genetic rescue, probably due to insemination of large numbers of females whereas females are limited in the number of eggs they can produce (Chapter 4). Male ornamental traits show significant inbreeding depression in semi-natural conditions only (Chapters 2 & 3). Inbreeding avoidance mechanisms seem to have evolved in females: they prefer courtship displays of non-inbred males (Chapter 2), unfamiliar males (Chapter 5) and males with rare patterns (Chapter 6). This preference might increase the mating success of immigrants, and may have evolved to facilitate the avoidance of inbreeding. Together with context-independent preferences for ornament combinations (Chapter 6), it also offers an explanation for the maintenance of polymorphism in this species.

Inbreeding can have profound negative effects on individuals by reducing fertility and viability. In populations, inbreeding depression can reduce growth rates and increases extinction risk. The aims of this thesis are to investigate inbreeding depression in male guppies (Poecilia reticulata) and to study the evolution of mechanisms for inbreeding avoidance in females, using guppies from a feral population in Queensland, Australia. Male guppies are highly polymorphic in their sexual ornamentation, indeed they show one of the most extreme polymorphisms observed in nature. Female guppies exhibit complex mate choice based on preferences for ornamentation, as well as social context. I aim is to examine how these factors of inbreeding avoidance alter sexual selection. In male guppies I found strong inbreeding depression in male sperm numbers, which is amplified under semi-natural compared to laboratory conditions (Chapter 2). Moreover, inbreeding depression results in low fertility under sperm competition: an experiment using artificial insemination techniques reveals that highly inbred males are heavily disadvantaged in gaining paternity (Chapter 3). On population level, inbreeding depression is manifest in reduced growth rates, predominantly in the early stages of inbreeding (Chapter 4). Population growth at inbreeding coefficients f=0.375-0.59 did not seem to lead to inbreeding depression, whereas lower levels of inbreeding reduced population growth. Although the growth rates in inbred populations appear normal, severe inbreeding depression is uncovered after outbred immigrants are added. Specifically, male immigrants are most efficient in short-term genetic rescue, probably due to insemination of large numbers of females whereas females are limited in the number of eggs they can produce (Chapter 4). Male ornamental traits show significant inbreeding depression in semi-natural conditions only (Chapters 2 & 3). Inbreeding avoidance mechanisms seem to have evolved in females: they prefer courtship displays of non-inbred males (Chapter 2), unfamiliar males (Chapter 5) and males with rare patterns (Chapter 6). This preference might increase the mating success of immigrants, and may have evolved to facilitate the avoidance of inbreeding. Together with context-independent preferences for ornament combinations (Chapter 6), it also offers an explanation for the maintenance of polymorphism in this species.

Inbreeding can have profound negative effects on individuals by reducing fertility and viability. In populations, inbreeding depression can reduce growth rates and increases extinction risk. The aims of this thesis are to investigate inbreeding depression in male guppies (Poecilia reticulata) and to study the evolution of mechanisms for inbreeding avoidance in females, using guppies from a feral population in Queensland, Australia. Male guppies are highly polymorphic in their sexual ornamentation, indeed they show one of the most extreme polymorphisms observed in nature. Female guppies exhibit complex mate choice based on preferences for ornamentation, as well as social context. I aim is to examine how these factors of inbreeding avoidance alter sexual selection. In male guppies I found strong inbreeding depression in male sperm numbers, which is amplified under semi-natural compared to laboratory conditions (Chapter 2). Moreover, inbreeding depression results in low fertility under sperm competition: an experiment using artificial insemination techniques reveals that highly inbred males are heavily disadvantaged in gaining paternity (Chapter 3). On population level, inbreeding depression is manifest in reduced growth rates, predominantly in the early stages of inbreeding (Chapter 4). Population growth at inbreeding coefficients f=0.375-0.59 did not seem to lead to inbreeding depression, whereas lower levels of inbreeding reduced population growth. Although the growth rates in inbred populations appear normal, severe inbreeding depression is uncovered after outbred immigrants are added. Specifically, male immigrants are most efficient in short-term genetic rescue, probably due to insemination of large numbers of females whereas females are limited in the number of eggs they can produce (Chapter 4). Male ornamental traits show significant inbreeding depression in semi-natural conditions only (Chapters 2 & 3). Inbreeding avoidance mechanisms seem to have evolved in females: they prefer courtship displays of non-inbred males (Chapter 2), unfamiliar males (Chapter 5) and males with rare patterns (Chapter 6). This preference might increase the mating success of immigrants, and may have evolved to facilitate the avoidance of inbreeding. Together with context-independent preferences for ornament combinations (Chapter 6), it also offers an explanation for the maintenance of polymorphism in this species.

Inbreeding can have profound negative effects on individuals by reducing fertility and viability. In populations, inbreeding depression can reduce growth rates and increases extinction risk. The aims of this thesis are to investigate inbreeding depression in male guppies (Poecilia reticulata) and to study the evolution of mechanisms for inbreeding avoidance in females, using guppies from a feral population in Queensland, Australia. Male guppies are highly polymorphic in their sexual ornamentation, indeed they show one of the most extreme polymorphisms observed in nature. Female guppies exhibit complex mate choice based on preferences for ornamentation, as well as social context. I aim is to examine how these factors of inbreeding avoidance alter sexual selection. In male guppies I found strong inbreeding depression in male sperm numbers, which is amplified under semi-natural compared to laboratory conditions (Chapter 2). Moreover, inbreeding depression results in low fertility under sperm competition: an experiment using artificial insemination techniques reveals that highly inbred males are heavily disadvantaged in gaining paternity (Chapter 3). On population level, inbreeding depression is manifest in reduced growth rates, predominantly in the early stages of inbreeding (Chapter 4). Population growth at inbreeding coefficients f=0.375-0.59 did not seem to lead to inbreeding depression, whereas lower levels of inbreeding reduced population growth. Although the growth rates in inbred populations appear normal, severe inbreeding depression is uncovered after outbred immigrants are added. Specifically, male immigrants are most efficient in short-term genetic rescue, probably due to insemination of large numbers of females whereas females are limited in the number of eggs they can produce (Chapter 4). Male ornamental traits show significant inbreeding depression in semi-natural conditions only (Chapters 2 & 3). Inbreeding avoidance mechanisms seem to have evolved in females: they prefer courtship displays of non-inbred males (Chapter 2), unfamiliar males (Chapter 5) and males with rare patterns (Chapter 6). This preference might increase the mating success of immigrants, and may have evolved to facilitate the avoidance of inbreeding. Together with context-independent preferences for ornament combinations (Chapter 6), it also offers an explanation for the maintenance of polymorphism in this species.