Submitted by HELSI MARIA ISIDRO CRISTOBAL null (helmar2009@live.com.mx) on 2017-10-25T12:25:09Z No. of bitstreams: 1 Dissertação_Helsi_final.pdf: 975344 bytes, checksum: bb2e31aa42ebcacbcd49b7790b75ac33 (MD5) / Approved for entry into archive by Monique Sasaki (sayumi_sasaki@hotmail.com) on 2017-10-31T15:36:17Z (GMT) No. of bitstreams: 1 cristobal_hmi_me_jabo.pdf: 975344 bytes, checksum: bb2e31aa42ebcacbcd49b7790b75ac33 (MD5) / Made available in DSpace on 2017-10-31T15:36:17Z (GMT). No. of bitstreams: 1 cristobal_hmi_me_jabo.pdf: 975344 bytes, checksum: bb2e31aa42ebcacbcd49b7790b75ac33 (MD5) Previous issue date: 2017-09-26 / Consejo Nacional de Ciencia y Tecnología (CONACYT) / Os programas de melhoramento em espécies aquícolas apresentam, no geral, um número restrito de famílias e um pequeno tamanho efetivo populacional, levando ao acasalamento de animais aparentados e, consequentemente, ao aumento da endogamia. Por sua vez, maiores níveis de endogamia tendem a ocasionar queda no desempenho dos animais causada pela depressão endogâmica. O objetivo deste estudo foi estimar os níveis de endogamia e depressão endogâmica sobre as características de peso à despesca, comprimento à despesca e resistência a Piscirickettsia salmonis em uma população de salmão coho. A resistência a Piscirickettsia salmonis foi definida como o dia da morte de cada peixe após desafio conduzido em dois anos, com média de 42 dias em 2012 e 14 dias no ano de 2014. Foi utilizado um banco de dados composto por 53.504 observações, provenientes de nove gerações e 930 famílias. A estimação dos componentes de variância e endogamia foram obtidas utilizando o programa computacional AIREMLF90 e os valores de depressão endogâmica foram estimados a partir de um modelo animal. Os valores observados para o coeficiente de endogamia foram crescentes ao longo das gerações, com uma taxa média máxima de 8,75% no ano de 2014. A depressão endogâmica afetou em maior nível as características de peso à despesca e dia de morte, com redução de 6,4 e 9,2% no desempenho dos animais, respectivamente, para o nível máximo de endogamia observado (30%). Os resultados indicam a necessidade de uso de estratégias mais efetivas de controle da endogamia para a manutenção do progresso genético do programa de melhoramento de salmão coho. / Aquaculture breeding programs present, in general, low number of families and reduced effective population size, resulting in mating of related animals and, consequently, increased level of inbreeding. High inbreeding coefficient may negatively impact the animals’ performance due to inbreeding depression. The objective of this study was to estimate inbreeding coefficient and inbreeding depression on growth traits and resistance against Piscirickettsia salmonis in a coho salmon population. Resistance against P. salmonis was defined as days to death of each fish after being challenged in two different years, with an average of 42 days in 2012 and 14 days in 2014. Data of 53,504 animals from 930 families was analyzed. Variance components were estimated using the software AIREMLF90, and inbreeding depression was estimated under an animal model. An increasing rate of inbreeding was observed, attaining an average of 8.75% in 2014. Inbreeding depression was more pronounced for harvest weight (PD) and days to death (DM), in comparison with harvest length. At the highest observed inbreeding level (30%), the estimated reduction caused by inbreeding depression was equal to 6,4% for PD and 9,2% for DM. The results indicate the necessity to control inbreeding more effectively for the studied coho salmon population, to guarantee genetic progress in the long term. / CONACYT: 579741/410470

Orientador: Ricardo da Fonseca / Resumo: As raças ovinas deslanadas são parte do patrimônio genético do Brasil, formado por animais adaptados ao semiárido nordestino e com potencial de produção de carne e pele. No entanto tratam-se de raças de recente formação, ainda com poucos programas de melhoramento genético, e consequentemente, carente de estudos da estrutura populacional, variabilidade genética, endogamia e grau de conservação. Diante disso este trabalho teve dois objetivos: 1) analisar a variabilidade genética da raça Santa Inês no Brasil com base em informações de pedigree utilizando registros de animais da raça Santa Inês, provenientes da Associação Sergipana de Criadores de Caprinos e Ovinos (ASCCO) criados na Região Nordeste do Brasil e 2) avaliar a estrutura genética e variabilidade genética do núcleo de conservação da Embrapa Caprinos e Ovinos, localizada na cidade de Sobral, região do norte do estado do Ceará, controlado pelo Sistema de Gerenciamento de rebanho (SGR) dentro do dentro do programa de melhoramento genético de caprinos e ovinos de corte – GENECOC®. O arquivo de pedigree da raça Santa Inês (ASCCO) continha 29080 animais e os arquivos de dados genealógicos pertencentes ao GENECOC 904 indivíduos da raça Santa Inês, 972 indivíduos da raça Somalis e 1372 indivíduos da raça Morada Nova. Para a primeira análise dos animais Santa Inês a média da integridade do pedigree nas últimas quatro gerações foi maior que 50% e o número de gerações completas equivalente foi igual a 4,89. O valor do coeficient... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: The wooless sheep breeds are part of the genetic heritage of Brazil, formed by animals highly adapted to semi-arid Northeast and high capacity of production of meat and skin. However it is of recent formation breeds, still few breeding programs, and consequently lacking in studies of population structure, genetic variability, inbreeding and degree of conservation. Therefore this study had two objectives: 1) to analyze the genetic variability of Santa Ines in Brazil based on pedigree information using animal records Santa Ines, from the Goat Breeders of Sergipana Association and Sheep (ASCCO) created in Northeast of Brazil and 2) evaluate the genetic structure and genetic variability conservation nucleus of Embrapa goats and sheep, located in Sobral, northern region of the state of Ceará, compiled by Management System for Livestock, part of the within the Breeding Program of Goats and sheep - GENECOC® . Santa Inês breed pedigree file (ASCCO) contained 29080 animals and genealogical data files belonging to GENECOC 904 individuals Santa Ines, 972 individuals of Somalis breed and 1372 individuals of Morada Nova breed. For the first analysis of animal Santa Inês the average pedigree integrity in the last four generations was greater than 50% and the number of full generations equivalent was equal to 4.89. The value of endogamic coefficient (F) was 0.32% and the obtained relationship coefficient was 3.1%. The generation interval was 5.75 years. For the results of the parameters bas... (Complete abstract click electronic access below) / Mestre

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Inbreeding occurs when relatives mate and have offspring. Inbreeding depression is hypothesized to have influenced the evolution of mating systems and behavioural mechanisms of inbreeding avoidance in the animal kingdom. Inbreeding in the wild is difficult to measure, as in order to build a pedigree allowing us to identify matings between relatives, the identity of as many as possible members of a population needs to be known. For a long time, the main source of knowledge about inbreeding depression was based on laboratory and agricultural studies, which did not reflect the array of environmental pressures wild populations have to cope with. In consequence, the deleterious consequences of inbreeding have often been underestimated. This is problematic because accurate estimates of the effect size of inbreeding depression are needed to study the strength of selection on inbreeding avoidance mechanisms, and are also of importance to conservation genetics. The aim of this thesis was to use pedigree data to infer the occurrence and effects of inbreeding using over forty years of breeding events of the great tit Parus major from Wytham Woods, Oxfordshire. The effects of inbreeding on fitness were investigated across a life-history continuum, and across environments. I found that close inbreeding (f=0.25) resulted in pronounced inbreeding depression, which acted independently on hatching success, fledging success, and recruitment success, and reduced the number of fledged grand-offspring by 55%. My results therefore suggest that estimates of fitness costs of inbreeding must focus on the entire life cycle. I also show that the variation in the strength of inbreeding depression varies across environments, particularly so the more the environmental variable considered is linked to fitness. These results emphasise the need of using relevant environmental contrasts when investigating inbreeding by environment interactions. I further asked whether individuals involved in matings with relatives differed relative to individuals mating with unrelated partners. I did not find any evidence for clear predictors of inbreeding, and I show that inbreeding depression in our population is entirely independent of any tendency for low quality parental genotypes, or phenotypes, to inbreed. Neither did I find any evidence for active inbreeding avoidance: great tits did not mate less often with kin than expected based on several scenarios of random mating, nor did I find increased rates of extra-pair paternity among birds breeding with relatives. In fact, I observed quite the contrary, as birds mating with kin exhibited a higher than average rate of close inbreeding relative to all scenarios of random mating investigated, showed lower rates of extra-pair paternity and divorce than birds mated to unrelated partners. I hypothesise that cases of occasional inbreeding in this population may result from mis-imprinting or a related process whereby some birds develop particularly strong bonds that are at odds with all predictions of avoiding inbreeding. Finally, I asked to what extent natal dispersal, a behaviour that is often hypothesized to play an important role in avoiding inbreeding, indeed reduces the likelihood of inbreeding. I found that male and female individuals breeding with a relative dispersed over several-fold shorter distances than those outbreeding. This led to a 3.4 fold increase (2.3-5, 95% CI) in the likelihood of close inbreeding relative to the population average when individuals dispersed less than 200m. This thesis demonstrates that inbreeding has deleterious effects on a wild population of birds, occurring throughout an individual’s life, and is of varying strength across environments. My findings strongly support the theory that natal dispersal should be considered as a mechanism of prime importance for inbreeding avoidance.

O objetivo geral deste trabalho foi avaliar aspectos fenotípicos e genéticos de características de crescimento, temperamento e repelência em bovinos da raça Nelore. As características analisadas neste trabalho foram peso ao nascer (PN, N=13.374), peso a desmama (PD, N=19.835), peso ao sobreano (P18M, N=15.291), ganho de peso da desmama ao sobreano (GP345, N=12.873), ganho de peso da desmama ao sobreano diferenciado (GP345DIF, N=12.873), temperamento (TEMP, N=13.253) e repelência (REP, N=1.859). O arquivo de pedigree foi constituído por 30.233 animais. Os componentes de variância, (co)variância, parâmetros genéticos, bem como as predições dos valores genéticos foram estimados por máxima verossimilhança restrita (REML). As estimativas de herdabilidade observadas para PN, PD, P198M, GP345, GP345DIF, TEMP e REP foram 0,22, 0,34, 0,34, 0,12, 0,12, 0,15 e 0,18, respectivamente. As estimativas de correlação genéticas verificadas foram 0,50 (PD e PN), 0,96 (PD e P18M), 0,49 (PD e GP345), 0,55 (PD e GP345DIF), 0,41 (PD e TEMP) e 0,20(PD e REP). As tendências fenotípicas para as características avaliadas foram todas negativas (P<0,01), a exceção de PD (P>0,05). As tendências genéticas para as características avaliadas foram todas positivas (P<0,01), a exceção de REP (P<0,01) que apresentou tendência negativa. As taxas de endogamia individual, paterna e materna apresentaram comportamento crescente (P<0,01) ao longo do período de estudo. Foram verificados efeitos significativos dos coeficientes de endogamia individuais sobre todas as características avaliadas, a exceção de TEMP. Os coeficientes de endogamia paternos influenciaram significativamente as características P18M, GP345 e GP345DIF. Por outro lado, a endogamia materna influenciou significativamente as características PD, GP345 e GP345DIF. / The general aim of this study was evaluated phenotypic and genetic aspects to growth traits, temperament and resistance in Nelore beef cattle. The traits analyzed in this study were birth weight (BW, N=13,374), weaning weight (WW, N=19,835), weight to over year (W18M, N=15,291), weight gain from weaning to over year (WG345, N=12,873), differentiated weight gain from weaning to over year (WG345DIF, N=12,873), temperament (TEMP, N=13,253) e resistance (RES, N=1,859). The pedigree information was composed by 30,233 animals. Variance and (co)variance components, genetic parameters, as well as predict breeding values were estimated using restricted maximum likelihood analyses (REML). Heritability estimates for BW, WW, W18M, WG345, WG345DIF, TEMP and RES were 0.22, 0.34, 0.34, 0.12, 0.12, 0.15 e 0.18, respectively. The genetics correlations verified were 0.50 (WW and BW), 0.96 (WW and W18M), 0.49 (WW and WG345), 0.55 (WW and WG345DIF), 0.41 (WW and TEMP) and 0.20 (WW and RES). All phenotypic trends to the evaluated traits were negatives (P<0.01), except for WW (P>0.05). All genetic trends to the evaluated traits were positives (P<0.01), except for RES (P<0.01) which presented negative trend. The individual, paternal and maternal inbreeding rates showed increasing behavior (P<0.01) along the study period. Were verified significant effects of individual inbreeding coefficients in all evaluated traits, except for TEMP. The paternal inbreeding coefficients affected significantly the W18M, WG345, WG345DIF traits. Even so, the maternal inbreeding coefficients affected significantly the WW, WG345, WG345DIF traits.

Diss. (sammanfattning) Umeå : Sveriges lantbruksuniv. / Härtill 4 uppsatser.

O objetivo geral deste trabalho foi avaliar aspectos fenotípicos e genéticos de características de crescimento, temperamento e repelência em bovinos da raça Nelore. As características analisadas neste trabalho foram peso ao nascer (PN, N=13.374), peso a desmama (PD, N=19.835), peso ao sobreano (P18M, N=15.291), ganho de peso da desmama ao sobreano (GP345, N=12.873), ganho de peso da desmama ao sobreano diferenciado (GP345DIF, N=12.873), temperamento (TEMP, N=13.253) e repelência (REP, N=1.859). O arquivo de pedigree foi constituído por 30.233 animais. Os componentes de variância, (co)variância, parâmetros genéticos, bem como as predições dos valores genéticos foram estimados por máxima verossimilhança restrita (REML). As estimativas de herdabilidade observadas para PN, PD, P198M, GP345, GP345DIF, TEMP e REP foram 0,22, 0,34, 0,34, 0,12, 0,12, 0,15 e 0,18, respectivamente. As estimativas de correlação genéticas verificadas foram 0,50 (PD e PN), 0,96 (PD e P18M), 0,49 (PD e GP345), 0,55 (PD e GP345DIF), 0,41 (PD e TEMP) e 0,20(PD e REP). As tendências fenotípicas para as características avaliadas foram todas negativas (P<0,01), a exceção de PD (P>0,05). As tendências genéticas para as características avaliadas foram todas positivas (P<0,01), a exceção de REP (P<0,01) que apresentou tendência negativa. As taxas de endogamia individual, paterna e materna apresentaram comportamento crescente (P<0,01) ao longo do período de estudo. Foram verificados efeitos significativos dos coeficientes de endogamia individuais sobre todas as características avaliadas, a exceção de TEMP. Os coeficientes de endogamia paternos influenciaram significativamente as características P18M, GP345 e GP345DIF. Por outro lado, a endogamia materna influenciou significativamente as características PD, GP345 e GP345DIF. / The general aim of this study was evaluated phenotypic and genetic aspects to growth traits, temperament and resistance in Nelore beef cattle. The traits analyzed in this study were birth weight (BW, N=13,374), weaning weight (WW, N=19,835), weight to over year (W18M, N=15,291), weight gain from weaning to over year (WG345, N=12,873), differentiated weight gain from weaning to over year (WG345DIF, N=12,873), temperament (TEMP, N=13,253) e resistance (RES, N=1,859). The pedigree information was composed by 30,233 animals. Variance and (co)variance components, genetic parameters, as well as predict breeding values were estimated using restricted maximum likelihood analyses (REML). Heritability estimates for BW, WW, W18M, WG345, WG345DIF, TEMP and RES were 0.22, 0.34, 0.34, 0.12, 0.12, 0.15 e 0.18, respectively. The genetics correlations verified were 0.50 (WW and BW), 0.96 (WW and W18M), 0.49 (WW and WG345), 0.55 (WW and WG345DIF), 0.41 (WW and TEMP) and 0.20 (WW and RES). All phenotypic trends to the evaluated traits were negatives (P<0.01), except for WW (P>0.05). All genetic trends to the evaluated traits were positives (P<0.01), except for RES (P<0.01) which presented negative trend. The individual, paternal and maternal inbreeding rates showed increasing behavior (P<0.01) along the study period. Were verified significant effects of individual inbreeding coefficients in all evaluated traits, except for TEMP. The paternal inbreeding coefficients affected significantly the W18M, WG345, WG345DIF traits. Even so, the maternal inbreeding coefficients affected significantly the WW, WG345, WG345DIF traits.

Insular fauna face disproportionate risks of extinction owing to direct human perturbation and intrinsic factors that are enhanced at small population sizes. Currently, our understanding of the processes that promote long-term persistence of naturally small populations and the cryptic processes that may contribute to accelerating their decline is limited by lack of empirical investigations across the range of natural conditions. Implementing effective protections for rare and understudied taxa requires the identification and examination of factors that limit recruitment at critical life stages. Predicting population health outcomes of future perturbations further necessitates an understanding a taxon’s behavioral ecology. Finally, cryptic threats to viability, such as inbreeding depression, must be investigated with an appreciation for taxon-specific life history, as these attributes can alter the context in which severe fitness reductions are expressed. In this project I enlist integrative and cross-disciplinary approaches to study the behavioral ecology and conservation genetics of a critically endangered West Indian Rock Iguana, Cyclura nubila caymanensis, on Little Cayman Island. I demonstrate how coastal communal nesting areas, a critical limiting resource on the island, serve a diverse population demographic and contribute to significantly enhanced nesting outcomes. These data emphasize the importance of expanding protections for major sites, as aggregative nesting appears to be perpetuated by both habitat suitability and adaptive fitness benefits. I next evaluate the possibility of evolved inbreeding avoidance strategies, including natal dispersal, non-assortative mate choice, and genetic bet-hedging. I conclude that the contribution of pre-reproductive dispersal to inbreeding avoidance likely outweighs that of active mate choice. Importantly, observed patterns of siring success imply constrained female choice and sexual conflict over genetic mating outcomes – a pattern that may extend to many territorial, male-driven mating systems and therefore should be an important consideration in genetic management. Finally, I investigate age-dependent inbreeding effects and the degree to which inbreeding depression may limit recruitment to the breeding population. I fail to reveal significant correlations of multi-locus heterozygosity with hatchling fitness; however, negative effects of parental inbreeding on fecundity and hatching success imply fitness consequences of inbreeding depression could be felt at other life stages.

Divergence in the face of gene flow is perhaps the most wildly disputed subject among researchers through time. The debate is an old one and we find its origin as far back as the era of Darwin. The theories dealing with sympatric and parapatric speciation, its processes and ecological conditions, are numerous and the empirical data supporting the ideas is constantly growing. However, the reach of a consensus almost seem as distant as ever. Two fundamental prerequisites can be identified for the evolution of divergence with gene flow, the act of disruptive selection, and the development of assortative mating. A set of models in which speciation with gene flow seem particularly likely is when a shift occurs in host preference in phytophagous insects and mating takes place on the host. In the work behind this thesis, the role of assortative mating in the initial stages of sympatric and parapatric speciation has been studied, as has the interaction between assortative mating and inbreeding and how it effects speciation in small sympatric populations, an aspect not much attended to earlier in the literature. My results show that assortative mating based on resource preference, can evolve rapidly upon secondary contact, and even in parapatric populations with a migration rate of 8% (13-15 individuals) per generation. However for assortative mating to be maintained selection against hybrids is needed. My results also suggests that small inbred populations have a hard time coping with strong assortative mating an as a consequence tend to relax their mating preferences to avoid inbreeding depression. Based on these results, I advocate for the importance of considering not only assortative mating in itself, but also the joint effects of assortative mating and inbreeding when dealing with theories of speciation with gene flow.