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Submitted by Ana Cristina Herrera Rios (anacristinah@gmail.com) on 2018-09-06T21:12:03Z No. of bitstreams: 1 Herrera_a_ma_jabo.pdf: 1549720 bytes, checksum: cc3a9f221086386bf628813bbc967443 (MD5) / Approved for entry into archive by Neli Silvia Pereira null (nelisps@fcav.unesp.br) on 2018-09-10T16:57:12Z (GMT) No. of bitstreams: 1 herrerarios_ac_dr_jabo.pdf: 1549720 bytes, checksum: cc3a9f221086386bf628813bbc967443 (MD5) / Made available in DSpace on 2018-09-10T16:57:12Z (GMT). No. of bitstreams: 1 herrerarios_ac_dr_jabo.pdf: 1549720 bytes, checksum: cc3a9f221086386bf628813bbc967443 (MD5) Previous issue date: 2018-07-30 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / O uso intensivo de biotecnologias reprodutivas tem feito com que se eleve a taxa de nascimento de progênies com maior grau de parentesco (maior taxa de nascimento de meio-irmãos e irmãos completos). Assim, o conhecimento sobre o coeficiente da endogamia média do rebanho torna-se relevante para a eficiência do sistema de produção. Com o advento da genômica, o coeficiente de endogamia (F) pode ser estimado com base na informação de milhares de marcadores do tipo polimorfismos de base única (SNPs), espalhados por todo o genoma. No presente estudo, informações de 3.785 animais da raça Nelore (1,760 machos e 2,025 fêmeas) genotipados para 777.962 SNPs do BovineHD BeadChip (Illumina Inc., San Diego, CA, USA) foram utilizadas com o objetivo de avaliar a taxa de endogamia em rebanhos comerciais da raça Nelore, bem como investigar o seu efeito (depressão endogâmica) sobre a expressão fenotípica de características reprodutivas (idade ao primeiro parto (IPP), ocorrência de prenhez precoce (OPP) e reconcepcão de novilhas (REC)). A estimativa do valor de F, bem como da depressão endogâmica, foi feita utilizando diferentes metodologias: (i) matriz de parentesco genômica com frequências alélicas obtidas da população base (FG); (ii) matriz de parentesco genômica com frequências alélicas fixadas em 0,5 (FGRM); (iii) com base no excesso de SNPs em homozigose (FSNP); e (iv) corrida de homosigose (FROH). Os resultados da corrida de homosigose também foram utilizados para identificar os padrões (tamanho e distribuição) dos segmentos ROH na raça Nelore bem como para identificar ilhas de homosigose (segmentos ROH compartilhados por mais de 50% da população). Foram identificados 210.636 segmentos ROH distribuídos nos 29 autossomos e cinco ilhas de homozigose localizadas nos cromossomos 5, 7, 12, 21 e 26, nas quais 43 genes foram identificados. Alguns destes genes (INHBE, INHBC, STAT6, FGF8 e DPCD) foram previamente associados com caracteristicas reproductivas, de crescimento, resposta inmume e adaptabilidade em bovinos. As médias para o coeficiente de endogamia calculado com base nas diferentes abordagens foram: -0,0006 (FG), 0,4376 (FGRM), 0,5500 (FSNP) e 0,0590 (FROH). As correlações foram ente baixas FG-FSNP (-0,28), FG-FGRM (-0,20), FG-FROH (0,21), a moderadas FROH-FSNP (0,68), FROH-FGRM (0,72) e fortemente alta para FSNP-FGRM (0,99). O valor médio de F variou de acordo com a metodologia utilizada. O valor extremamente alto do FSNP denota que este método tende a superestimar as taxas de endogamia. Independentemente do método utilizado para obter os valores de F, foi verificado que o aumento de 1% no coeficiente de endogamia médio do rebanho influenciou desfavoravelmente a média das características reprodutivas avaliadas. / The intensive use of reproductive biotechnologies has increased the birth rate of progenies with high degree of relationships (higher birth rate of half- and full-sibs). Thus, the control of herd inbreeding becomes relevant for the efficiency of the production system. With genomics, the inbreeding coefficient can be estimated using thousands of single nucleotide polymorphisms (SNPs), spread throughout the genome. In the present study, information of 3,785 Nelore animals (1,760 males and 2,025 females) genotyped with 777,962 SNP markers of BovineHD BeadChip (Illumina Inc., San Diego, CA, USA) was used with the objective of evaluating the inbreeding rates of Nelore commercial herds, as well as to investigate the effects of inbreeding (inbreeding depression) on the phenotypic expression of reproductive traits (age at first calving (AFC), heifer early pregnancy (EP), and heifer rebreeding (HR)). The inbreeding coefficient (F) and inbreeding depression were estimated based on (i) genomic relationship matrix considering allele frequencies estimated from the base population (FG); (ii) genomic relationship matrix considering allele frequencies fixed at 0.5 (FGRM); (iii) excess of homozygous SNPs (FSNP); and (iv) runs of homozygosity (FROH). The runs of homozygosity results were also used to identify the pattern (size and distribution) of ROH segments as well as to identify ROH islands (ROH segments shared by more than 50% of the population). In total, there were identified 210,636 ROH segments and five ROH Islands located on the chromosomes 5, 7, 12, 21 and 26, in which 43 annotated genes were identified. Some of these genes (INHBE, INHBC, STAT6, FGF8 and DPCD) were previously associated with reproduction and growth traits, inmume response and adaptability in cattle. The average inbreeding calculated based on different approaches were -0.0006 (FG), 0.4376 (FGRM), 0.5500 (FSNP) e 0.0590 (FROH). These correlations ranged from low FG-FSNP (-0.28), FG-FGRM (-0.20), FG-FROH (0.21), to moderated FROH-FSNP (0.68), FROH-FGRM (0.72) and extremely high FSNP-FGRM (0.99). The average population inbreeding coefficient ranged according to the method used. The extremely high value of FSNP indicates that this approach tend to overestimate the inbreeding rates. Independently of the method used to obtain the F values, it was verified that the increase of 1% in the average herd inbreeding unfavorably influenced the mean value of the evaluated reproductive traits. / FAPESP#2009/16118-5

<p>An unresolved problem in evolutionary biology is the nature of forces that maintain standing variation for quantitative traits. In this study we take advantage of newly developed genomic resources to understand how variation is maintained for flower size and fitness components in a natural population of annual Mimulus guttatus in the Oregon Cascades. Extensive inbreeding depression has been documented in this population for fertility and viability (Willis 1999 a,b), while previous biometric experiments have demonstrated that some of the floral variation in this site is due to common alleles perhaps maintained by balancing selection (Kelly and Willis 2001, Kelly 2003). Detailed comparison of the genetic architecture of these two categories of traits can clarify the relative contributions of mutation versus selection in maintaining trait variation within populations as well as the relevance of standing variation for trait diversification. </p><p>We present here the results from a large scale effort to dissect variation for flower size and a suite of genetically correlated traits. In 3 independent F2 mapping populations we mapped QTLs for floral morphology (flower width and length, pistil length, and stamen length), flowering time, and leaf size. We also mapped segregation distortion loci and QTLs for fertility components (pollen viability and seed set) that exhibit inbreeding depression. We compare the genetic architecture of these two sets of traits and find clear differences. Morphological traits and flowering time are polygenic and QTLs are generally additive. In contrast, deleterious QTLs associated with segregation distortion or fertility are partially recessive and include major QTLs. There is also little co-localization between morphological/flowering time and fertility QTLs. The analysis suggests that the genetic basis of segregating variation in morphology is fundamentally different from traits exhibiting inbreeding depression. Further, there is considerable variation in the extant of pleiotropy exhibited by QTLs for morphological traits as well as flowering time and we report that epistasis contributes to the standing variation for these traits. The analysis suggests that the standing variation is relevant for trait diversification and that the variation in floral allometry, plant form, and life history observed in the guttatus species complex could have readily evolved from the standing variation.</p> / Dissertation

Yes / In many species, the offspring of related parents suffer reduced reproductive success, a phenomenon known as inbreeding depression. In humans, the importance of this effect has remained unclear, partly because reproduction between close relatives is both rare and frequently associated with confounding social factors. Here, using genomic inbreeding coefficients (FROH) for >1.4 million individuals, we show that FROH is significantly associated (p < 0.0005) with apparently deleterious changes in 32 out of 100 traits analysed. These changes are associated with runs of homozygosity (ROH), but not with common variant homozygosity, suggesting that genetic variants associated with inbreeding depression are predominantly rare. The effect on fertility is striking: FROH equivalent to the offspring of first cousins is associated with a 55% decrease [95% CI 44–66%] in the odds of having children. Finally, the effects of FROH are confirmed within full-sibling pairs, where the variation in FROH is independent of all environmental confounding.

It is generally accepted that populations which experience severe bottlenecks have a reduction in fitness. One of the most frequently reported fitness costs is increased hatching failure in bottlenecked populations of birds. The mechanism responsible for increased hatching failure is unknown. Research on other animals suggest that reduced population numbers cause unavoidable inbreeding that in turn leads to abnormalities in the gametes. In this thesis I examine some of the possible causes for increased hatching failure in severely bottlenecked populations of introduced birds in New Zealand. I look at three traits identified as a cause for infertility or hatching failure previously and determine whether there is a link with the size of a population s bottleneck. It is possible that reduced numbers of sperm reaching the site of fertilisation is a primary cause of hatching failure. I examined the perivitelline membrane of various species of introduced birds and counted the total number of sperm present to compare to how many would be expected in non-bottlenecked species. Although there was no relationship between the size of the bottleneck and the number of sperm present, all species had lower than expected sperm counts. In many species of mammals, a reduction in the quality of sperm is attributed to inbreeding depression bought about by genetic bottlenecks. I next compared the level of sperm abnormalities, variation in midpiece size sperm, and sperm motility with the size of the bottleneck each species passed through when introduced to New Zealand. There was no significant correlation between either the variation in midpiece size or sperm motility with bottleneck size. However, there was a trend for species that passed through more severe bottlenecks to have a slightly higher level of midpiece size and lower motility. Finally, I examined whether there was a link between abnormalities in the eggshell and the size of the respective bottleneck. There was no significant change in eggshell thickness or any change in the number of pores associated bottleneck size. However, there was a decreased number of round pores in severely bottlenecked species, although the consequences of this are unknown. My findings do not directly link a single cause for increased hatching failure in bottlenecked species of birds, but they do highlight the need for monitoring of reproductive traits in endangered species that have experienced a population bottleneck.

O monitoramento da endogamia é fundamental para o estabelecimento de um programa de melhoramento animal. Os coeficientes de endogamia foram estimados a partir de segmentos de homozigose (FROH), matriz de parentesco genômico com frequências alélicas derivadas dos dados (FGRM), frequências alélicas ajustadas a 0,5 (FGRM05), excesso de homozigose (FHOM) e informação de pedigree (FPED) em bovinos Nelore e ovelhas Santa Inês. Os dados genotípicos para a população Nelore foram obtidos de 2.569 animais utilizando um painel de 725,293 polimorfismos de nucleotídeo único e um pedigree composto por 15.846 indivíduos. Para a população de ovinos Santa Inês, 576 animais foram genotipados para 47.033 polimorfismos de nucleotídeo único, juntamente com dados de pedigree de 32.266 indivíduos. Picos notáveis nos cromossomos 7, 12 e 21 dos bovinos e no cromossomo 16 das ovelhas, representavam ilhas de ROH (&gt; 47%), destacando regiões possivelmente afetadas pela pressão seletiva. Os valores médios para FPED, FROH, FGRM e FGRM05 foram 0,005, 0,058, -0,007 e 0,40, respectivamente no caso do Nelore, enquanto valores medias de 0,32, 0,049, 0,015, 0,287 e 0,015 para FPED, FROH, FGRM, FGRM05 e FHOM, respectivamente no caso das ovelhas. Esses coeficientes de endogamia foram associados negativamente com peso ao nascer, peso à desmama, ganho de peso pós-desmame, escore de muscularidade, precocidade, conformação e circunferência escrotal em bovinos Nelore e para todas as características analisadas em Santa Inês. Também foi encontrada uma correlação negativa entre depressão endogâmica e estimativas de variâncias genômicas de dominância variando de -0,35 a -0,98 para Nelore e -0,89 a -0,91 para ovinos Santa Inês. Nós afirmamos que as descobertas relatadas podem ser usadas para manter a diversidade genética em bovinos Nelore e ovelhas Santa Inês sob uma perspectiva genômica. / Monitoring inbreeding is critical for establishing a sustainable breeding program. Inbreeding coefficients were estimated from runs of homozygosity (FROH), genomic relationship matrices coupled with allele frequencies derived from data (FGRM), allele frequencies set to 0.5 (FGRM05), excess of homozygosity (FHOM), and pedigree information (FPED) from Nellore cattle and Santa Ines populations. Genotypic data for the Nellore population were obtained from 2,803 animals using a panel of 725, 293 single-nucleotide polymorphisms and a pedigree consisting of 15,846 individuals. For the Santa Ines sheep population 576 animals were genotyped for 47,033 single-nucleotide polymorphisms along with pedigree data of 32,266 individuals. In cattle noticeable peaks on chromosome 7, 12, and 21, and in sheep on chromosome 16, represented hotspots of autozygosity (&gt; 47%), highlighting putative regions affected by selective pressure. The mean values for FPED, FROH, FGRM, and FGRM05 were 0.005, 0.058, -0.007, and 0.40, respectively for Nellore, while for Santa Ines were 0.32, 0.049, 0.015, 0.287 and 0.015 for FPED, FROH, FGRM, FGRM05 and FHOM, respectively. These inbreeding coefficients were negatively associated with birth weight, weaning weight, post-weaning weight gain, muscularity score, finishing score, conformation score, and scrotal circumference on Nellore and for all traits analyzed on Santa Ines. Also, a negative correlation was found between inbreeding depression and estimates of dominance genomic variances ranging from -0.35 to -0.98 for Nellore and -0.89 to -0.91 for Santa Ines sheep. We contend that the findings reported here can be used to maintain genetic diversity in Nellore cattle and Santa Ines sheep from a genomic perspective.

Je m’intéresse à l’écologie évolutive et en particulier à l’évolution des systèmes de reproduction, à l’adaptation et aux interactions de ces deux processus. En effet, les modèles théoriques ainsi qu’un certain nombre d’observations en populations naturelles soulignent que le système de reproduction devrait avoir un effet majeur sur les processus évolutifs et démographiques en populations naturelles. Lors de ma thèse, j’aborde ces thèmes sous divers angles à partir d’une Brassicacée tolérante et hyper-accumulatrice aux métaux lourds, Noccaea caerulescens, et à partir de modèles théoriques. Dans un premier temps, je m’intéresse à la variation du système de reproduction en populations naturelles. Comment s’organisent les flux de gènes entre populations ou sous-populations, et entre individus d’une même population ? Je me suis particulièrement intéressée à l’influence de la pollution des sols sur le taux d’autofécondation chez N. caerulescens, aux flux de gènes entre populations vivant dans les mines et populations vivant sur des sols non contaminés, et à la structure à l’intérieur des populations. Afin de mieux comprendre les facteurs influençant le système de reproduction, j’ai ensuite testé l’effet de la densité en plantes sur le taux d’autofécondations en populations naturelles. Dans un second temps, je teste les interactions existant entre adaptation à des milieux potentiellement très toxiques et système de reproduction. Plus spécifiquement, je teste si la dépression de consanguinité dépend du niveau de stress que subissent les populations, en interaction avec l’histoire des pressions de sélection qu’on subies les populations par le passé. Enfin, à l’aide de simulations, j’étudie comment la variation interannuelle du système de reproduction peut influencer la probabilité d’adaptation de populations faisant face à un changement environnemental. / During my PhD, I focused on the evolution of mating system, adaptation and the mutual influences of both processes. I have been studying different aspects of this interaction using a hypertolerant, hyperaccumulator plant species, Noccaea caerulescens. This species grows on former mines and non-contaminated soils in Europe and in particularly in the Cévennes, and it is an excellent model to study the interaction of local adaptation in a heterogeneous environment and mating system. Firstly, I finely characterized N. caerulescens mating system in natural population, and see how metal pollution affects the variation of mating system in the Cévennes region. I showed that contrary to a couple of classical results (Antonovics 1968), in this system, metallicolous populations have lower self-fertilization rates than nonmetallicolous populations (article submitted). I then tested our best potential factor potentially explaining the variation of mating system in natural populations: plant density. In two different measures, with two different methods, density seems to have no or only a weak effect on self-fertilization rates in Noccaea caerulescens (article in prep). In a second project, I test the interaction between inbreeding depression, stress and the history of adaptation to a given environment using Noccaea caerulescens. Inbreeding depression is known to vary with environment and, sometimes, stress. Both experimental data (Long et al 2013) and theoretical models (Ronce et al 2009) stress the importance of the effect of the history of selection and adaptation in populations on the magnitude of inbreeding depression. Since we have populations of Noccaea caerulescens that are adapted to different levels of pollution, since different levels of pollution impose differential stress on the two ecotypes (strong polution is not good for nonmetallicolous plants) and since the species is self-compatible, this seems like an excellent system to test predictions on the interaction of inbreeding depression and mating system.

O monitoramento da endogamia é fundamental para o estabelecimento de um programa de melhoramento animal. Os coeficientes de endogamia foram estimados a partir de segmentos de homozigose (FROH), matriz de parentesco genômico com frequências alélicas derivadas dos dados (FGRM), frequências alélicas ajustadas a 0,5 (FGRM05), excesso de homozigose (FHOM) e informação de pedigree (FPED) em bovinos Nelore e ovelhas Santa Inês. Os dados genotípicos para a população Nelore foram obtidos de 2.569 animais utilizando um painel de 725,293 polimorfismos de nucleotídeo único e um pedigree composto por 15.846 indivíduos. Para a população de ovinos Santa Inês, 576 animais foram genotipados para 47.033 polimorfismos de nucleotídeo único, juntamente com dados de pedigree de 32.266 indivíduos. Picos notáveis nos cromossomos 7, 12 e 21 dos bovinos e no cromossomo 16 das ovelhas, representavam ilhas de ROH (&gt; 47%), destacando regiões possivelmente afetadas pela pressão seletiva. Os valores médios para FPED, FROH, FGRM e FGRM05 foram 0,005, 0,058, -0,007 e 0,40, respectivamente no caso do Nelore, enquanto valores medias de 0,32, 0,049, 0,015, 0,287 e 0,015 para FPED, FROH, FGRM, FGRM05 e FHOM, respectivamente no caso das ovelhas. Esses coeficientes de endogamia foram associados negativamente com peso ao nascer, peso à desmama, ganho de peso pós-desmame, escore de muscularidade, precocidade, conformação e circunferência escrotal em bovinos Nelore e para todas as características analisadas em Santa Inês. Também foi encontrada uma correlação negativa entre depressão endogâmica e estimativas de variâncias genômicas de dominância variando de -0,35 a -0,98 para Nelore e -0,89 a -0,91 para ovinos Santa Inês. Nós afirmamos que as descobertas relatadas podem ser usadas para manter a diversidade genética em bovinos Nelore e ovelhas Santa Inês sob uma perspectiva genômica. / Monitoring inbreeding is critical for establishing a sustainable breeding program. Inbreeding coefficients were estimated from runs of homozygosity (FROH), genomic relationship matrices coupled with allele frequencies derived from data (FGRM), allele frequencies set to 0.5 (FGRM05), excess of homozygosity (FHOM), and pedigree information (FPED) from Nellore cattle and Santa Ines populations. Genotypic data for the Nellore population were obtained from 2,803 animals using a panel of 725, 293 single-nucleotide polymorphisms and a pedigree consisting of 15,846 individuals. For the Santa Ines sheep population 576 animals were genotyped for 47,033 single-nucleotide polymorphisms along with pedigree data of 32,266 individuals. In cattle noticeable peaks on chromosome 7, 12, and 21, and in sheep on chromosome 16, represented hotspots of autozygosity (&gt; 47%), highlighting putative regions affected by selective pressure. The mean values for FPED, FROH, FGRM, and FGRM05 were 0.005, 0.058, -0.007, and 0.40, respectively for Nellore, while for Santa Ines were 0.32, 0.049, 0.015, 0.287 and 0.015 for FPED, FROH, FGRM, FGRM05 and FHOM, respectively. These inbreeding coefficients were negatively associated with birth weight, weaning weight, post-weaning weight gain, muscularity score, finishing score, conformation score, and scrotal circumference on Nellore and for all traits analyzed on Santa Ines. Also, a negative correlation was found between inbreeding depression and estimates of dominance genomic variances ranging from -0.35 to -0.98 for Nellore and -0.89 to -0.91 for Santa Ines sheep. We contend that the findings reported here can be used to maintain genetic diversity in Nellore cattle and Santa Ines sheep from a genomic perspective.

Pollinator visitation patterns should affect pollination success and mating patterns in flowering species. In the orchid family, about one third of the species do not provide any reward for their pollinators. Pollination by deceit is typically associated with low fruit set but may increase the chance of cross-pollination since the pollinator should soon leave the individual plant when there is no reward in the flowers. This may be beneficial if self-fertilisation results in inbreeding depression. I studied the mating patterns of one rewarding and one deceptive orchid in two closely related genera by tracking the fate of stained pollinia. I also conducted controlled crosses to estimate inbreeding depression. The results show that the deceptive orchid Dactylorhiza lapponica has lower pollination success, but higher cross-pollination rate (ca. 90%) than the nectariferous orchid Gymnadenia conopsea (ca. 18% cross-pollination). The results further suggest that in G. conopsea, nocturnal visitors mediate higher geitonogamous pollination rate (ca. 100%) than diurnal visitors (ca. 60%). In both study species, fruits produced from cross-pollination were heavier than fruits produced from selfing. Inbreeding depression for fruit mass did not differ significantly between the two species (δ = 0.21 in D. lapponica and δ = 0.29 in G. conopsea). These data support the hypothesis that pollination by deceit can enhance cross-pollination. A literature study including several rewarding and non-rewarding orchid species indicated lower geitonogamy in the deceptive orchids, but the difference was not statistically significant.

Although the process by which fertilization occurs in bryozoans is well described, the ability to self-fertilize and the subsequent ecological consequences are poorly understood. Culturing experiments were conducted examining the effects of selfing on offspring survival and reproduction in the simultaneous hermaphrodite Bugula stolonifera collected from Eel Pond, Woods Hole, MA. Results from these experiments document significant decreases in survival and fecundity of selfed offspring, compared to outcrossed controls, suggesting that these animals are not routinely self-fertilizing in Eel Pond. How these arborescent colonies minimize selfing remains unclear, but it is hypothesized that conspecific aggregations could serve to minimize the chances that a colony utilizes its own sperm for fertilization. The genetic composition of these aggregations was investigated using a newly developed microsatellite library. As larvae routinely metamorphose on conspecific colonies, the possibility that larvae select or avoid their maternal colony was also investigated. Analyses of genetic structure document homogeneity throughout these aggregations on extremely small spatial scales, suggesting high amounts of larval dispersal within aggregations. When combined with results from parentage-exclusion and kinship analyses, these results indicate that a colony's nearest neighbors are not composed of siblings, potentially minimizing inbreeding. Molecular analyses were then used to determine if the high larval dispersal within aggregations resulted in high mixing between aggregations. Sites within Eel Pond separated by 100-300 m were routinely sampled from 2009 to 2011, and analyses were conducted to investigate potential inter- and intra-annual genotypic differentiation within and between aggregations. Results document that although low levels of mixing could result in increased homogeneity between some aggregations, barriers to genetic exchange prevent mixing between most sites. Further, inter-annual comparisons within sites document that significant differentiation can occur between reproductive seasons. Hence, any potential homogeneity achieved between sites during one reproductive season will likely be lost by the beginning of the next reproductive season. Additionally, while sampling in Eel Pond in 2010, I document the first occurrence from the western Atlantic Ocean of another aggregating arborescent bryozoan, Tricellaria inopinata. The growth and reproductive biology of these animals was monitored throughout 2011; results suggest that this introduction is likely to persist.