The limits of mean-field heterozygosity estimates under spatial extension in simulated plant populations

Computational models of evolutionary processes are increasingly required to incorporate multiple and diverse sources of data. A popular feature to include in population genetics models is spatial extension, which reflects more accurately natural populations than does a mean field approach. However, such models necessarily violate the mean field assumptions of classical population genetics, as do natural populations in the real world. Recently, it has been questioned whether classical approaches are truly applicable to the real world. Individual based models (IBM) are a powerful and versatile approach to achieve integration in models. In this study an IBM was used to examine how populations of plants deviate from classical expectations under spatial extension. Populations of plants that used three different mating strategies were placed in a range of arena sizes giving crowded to sparse occupation densities. Using a measure of population density, the pollen communication distance (Pcd), the deviation exhibited by outbreeding populations differed from classical mean field expectations by less than 5% when Pcd was less than 1, and over this threshold value the deviation significantly increased. Populations with an intermediate mating strategy did not have such a threshold and deviated directly with increasing isolation between individuals. Populations with a selfing strategy were influenced more by the mating strategy than by increased isolation. In all cases pollen dispersal was more influential than seed dispersal. The IBM model showed that mean field calculations can be reasonably applied to natural outbreeding plant populations that occur at a density in which individuals are less than the average pollen dispersal distance from their neighbors

Genomics methodologies to access autozygosity and inbreeding in dairy cattle

Orientador: Dr. Rodrigo de Almeida TeixeiraCoorientador: Dr. Roberto CarvalheiroTese (doutorado) - Universidade Federal do Paraná, Setor de Ciências Agrárias, Programa de Pós-Graduação em Zootecnia. Defesa : Curitiba, 22/02/2019Inclui referênciasResumo: Para alcançar a demanda crescente de produtos de origem animal a cadeia de produção de leite tem mudado constantemente nos últimos 20 anos. Por exemplo, o melhoramento genético de bovinos de leite tem aumentado o ganho genético de inúmeras características de qualidade e produtividade. Porém, o intenso uso de um pequeno número de reprodutores e a inseminação artificial nos programas de melhoramento genético tem aumentado também o nível de endogamia dessas populações. Altos índices de endogamia têm sido relacionados com a redução no desempenho produtivo e reprodutivo. Atualmente, em bovinos da raça Holandesa, é praticamente impossível encontrar animais sem algum nível de endogamia. O interesse em estimar coeficientes de endogamia com informação genômica apareceu com o advento da tecnologia de genotipagem utilizando milhares de marcadores. Por exemplo, tem sido aplicada em bovinos de leite a estimativa de endogamia através das corridas de homozigose (ROH). Portanto, o objetivo deste estudo foi avaliar o efeito da seleção com o acasalamento preferencial positivo sobre a depressão endogâmica em diferentes populações simuladas de bovinos leiteiros, diferentes em desequilíbrio de ligação (LD). Além disso, esta tese avaliou o uso de dados genômicos simulados para investigar muitos aspectos e cenários de endogamia e autozigose em populações de bovinos de leite. Portanto, o objetivo também foi em avaliar a habilidade do método da janela de SNPs e do método de SNPs consecutivos para determinação de ROH e o seu acesso à autozigosidade e ao coeficiente de endogamia genômica em populações simuladas de bovinos taurinos e indianos. A avaliação foi aplicada em populações simuladas de bovinos leiteiros diferentes em níveis de desequilíbrio de ligação (LD). Utilizando o software QMSim, as populações foram simuladas pelo processo forward-in-time. Os parâmetros foram escolhidos para gerar populações com características similares às raças leiteiras taurinas e zebuínas. Foram simulados 93 QTLs relacionados à produção de leite, e aleatoriamente distribuídos em 29 autossomos de Bos taurus. Para criar alto e baixo desequilíbrio de ligação foi realizado um afunilamento na população histórica, 1.020 ou 2.020 gerações foram simuladas iniciando com um tamanho efetivo de 1.000 e terminando com 200 animais no final do ciclo. Para fundar 20 gerações em 5 cenários diferentes para cada nível de desequilíbrio de ligação, as populações foram simuladas com diferentes sistemas de acasalamento e critérios de seleção. A seleção foi feita baseada nos valores genéticos estimados pelo método BLUP ou pelo valor genético verdadeiro estimado com o efeito dos QTLs. A média de endogamia de cada geração foi estimada pelo próprio QMSim e associado com o nível de depressão endogâmica para produção de leite encontrado na literatura. Da última geração da população histórica, para gerar o genótipo para a seleção, foram aleatoriamente selecionados 50.000 marcadores da população (MAF ? 0,02), estes dados imitam os painéis utilizados comumente para genotipar bovinos. As corridas de homozigose foram obtidas por duas diferentes metodologias do pacote detecRUNS do programa R para 1.000 animais nas gerações 1, 5, 10, 15 e 20. O primeiro, o método das janelas consecutivas de SNPs, escaneia cada SNP ao longo do genótipo de cada animal para a detecção de segmentos em homozigose de acordo com um tamanho de corridas de homozigose e um número mínimo de SNPs em homozigose. O segundo, o método consecutivo, não utiliza as janelas para evitar a determinação de falsos ROH, menores que a janela. O coeficiente de endogamia baseado nas corridas de homozigose (FROH) é definido como a proporção de corridas de homozigose em relação ao genoma total do indivíduo. Os níveis mais altos de endogamia foram obtidos nos cenários com acasalamento preferencial positivo, e variaram de 0,2 a 0,36 na vigésima geração de seleção. O uso intenso de um pequeno número de touros em vinte gerações de seleção poderia causar perda entre 6,98 e 7,20% na produção de leite nos piores cenários. Em geral, para os cenários imitando o acasalamento dirigido, e minimizando a endogamia, o aumento no nível médio de endogamia de ~3% e ~8% diminui ~0,6 e ~1,8% a produção de leite aos 305 dias respectivamente. A seleção intensa para uma característica pode incrementar rapidamente os níveis do coeficiente de endogamia para valores críticos em populações com baixo e alto desequilíbrio de ligação inicial. Sistemas de acasalamento dirigido podem ser aplicados para a manutenção de baixos níveis de endogamia e consequentemente controlar a depressão endogâmica. Em geral, o maior número de corridas de homozigose nas gerações de 1 a 20 estão na classe com comprimento variando entre 1-2 Mb. A porcentagem de corridas de homozigose diminuíram com o passar das gerações para a classe 1-2 Mb de comprimento. No entanto, a porcentagem de corridas de homozigose aumentou da primeira para a vigésima geração na classe > 8 Mb nas diferentes populações e metodologias utilizadas para a detecção de ROH. A média do comprimento de ROH na classe 1-2 Mb é maior para populações taurinas comparadas às populações indianas. No entanto, para a classe > 8 Mb, a população indiana geralmente possui um média maior no comprimento da corrida de homozigose. O coeficiente de endogamia baseado no pedigree (FPED) aumentou ao longo das 20 gerações simuladas para as populações taurinas e indianas. Porém, os coeficientes de endogamia genômicos baseados nas corridas de homozigose (FROH), detectados pelas diferentes metodologias, são diferentes entre as populações taurinas e indianas. Estes resultados sugerem que FROH calculado a partir das corridas de homozigose, obtidas em ambas metodologias, é capaz de acessar a autozigosidade muito antiga. A detecção de corridas de homozigose, pelo método das janelas ou dos SNPs consecutivos, são metodologias importantes para acessar endogamia recente ou mais antiga. A estimativa de endogamia genômica baseada nas corridas de homozigose é capaz de demonstrar eventos evolutivos que diferenciam algumas raças de bovinos. Palavras-chave: Holandesa, Ligação, Desequilíbrio, QMSim, Simulação, Seleção, ROH, Homozigosidade, SNP.Abstract: To achieve the livestock products demand, the milk productive chain has been changed constantly over the last 20 years. For instance, dairy cattle's breeding has been improving many milk quality and productivity traits. But, the heavy use of a small number of sires and the artificial insemination practice on breeding programs has been increasing the dairy cattle inbreeding. Besides that, these high levels have been related to reduced fitness and reproductive performance. In Holstein dairy cattle it is almost impossible to find individuals without some level of inbreeding. The interest to estimate inbreeding coefficients with genomic information appears with the advent of high throughput genotyping technologies. For instance, was applied in dairy cattle the estimation of inbreeding coefficient with runs of homozygosity (ROH). Therefore, the aim of this study was to evaluate the effect of selection with assortative positive mating on inbreeding depression considering simulated dairy cattle populations distinguished by linkage disequilibrium (LD). In addition, this thesis evaluated the use of genomic simulated data to investigate many aspects and scenarios of inbreeding and autozygosity under dairy cattle populations. Thus, also the aim of was to evaluate the ability of sliding and consecutive ROH approach to detect and express autozygosity and genomic inbreeding coefficient (FROH) in taurine and indicine simulated populations with twenty generations of assortative positive mating. The evaluation was applied in dairy cattle populations distinguished by linkage disequilibrium (LD). Using the QMSim software, the populations were simulated based on forward-in-time process. The parameters were chosen to try and generate a population with similar characteristics of taurine and indicine dairy cattle. Were simulated 93 milk yield QTLs randomly distributed on 29 autosomal chromosomes of Bos taurus. To create a high and low level of initial linkage disequilibrium were made a bottleneck in the historical population, 1,020 or 2,020 generations were simulated starting from an effective population of 1,000 to 200 animals at the end of the cycle. To found 20 generations of five different scenarios for each level of LD, the populations were simulated with a different mating system and selection criteria. The selection was based on breeding values estimated with BLUP method or, the true breeding value estimated with the effect of QTLs. Each generation inbreeding mean was estimated by QMSim and associated with the level of inbreeding depression of milk yield found in the literature. From the last generation of the historical population, to generate genotypic data for the selection, the individuals were randomly selected with a total of 50,000 markers (MAF ? 0.02), these data mimicked the commonly SNP panel used to genotype cattle. The runs of homozygosity were obtained by two different methodologies in the detectRUNS package of R software for 1,000 individuals of generations 1, 5, 10, 15, and 20. At first, the sliding window method scans along everyone's genotype, at each SNP marker position, for detection of homozygous segments with a specified length or number of homozygous SNPs. At second, the consecutive method does not use the sliding windows to avoid the introduction of artificial ROH that are shorter than the window. Inbreeding coefficient based on ROH (FROH) is a genomic portion of individual autozygosity and defined it as the proportion of the autosomal genome lying in ROH of certain minimal length relative to the overall genome in interest. The highest inbreeding levels, varying from 0.2 to 0.36, in the twentieth generation were obtained for positive assortative mating systems. The intense use of a few numbers of sires in twenty generations of selection may cause a loss between 6.98 and 7.20% on milk yield in the worst scenarios. In general, for minimizing inbreeding scenarios, the average level inbreeding increasing of ~3 and ~8% in the twenty generations of selection decreases ~0.6 and ~1.8% the milk yield at 305 days respectively. The intensive selection for one trait could rapidly increase the average inbreeding coefficient on critical levels in populations with high and low initial LD. Non-random mating systems must be applied to control inbreeding levels and consequently inbreeding depression. In general, the class of 1-2 Mb length size has the highest number of ROH across all evaluations on generations 1, 5, 10 and 20. The percentage of ROH class 1-2 Mb decreases from generation 1 to 20. Nevertheless, the percentage of ROH class >8 increase across the twenty generations of selection in the distinguished populations and ROH detection methodologies. The mean ROH length in the class 1-2 Mb is higher for taurine than to indicine simulated population. Otherwise, for the class >8 Mb the indicine generally has higher mean ROH length. The inbreeding coefficient level based on pedigree (FPED) increases across the twenty simulated generations for taurine and indicine populations. But, genomic inbreeding coefficients based on ROH detected by sliding approach (FROHs) and ROH detected with the consecutive approach (FROHc) are different among these two populations. These results suggest that FROH from both methods to access ROH can detect ancient and recent autozygosity. Genomic inbreeding estimates based on ROH segments can represent and evolutionary events which distinguish some breeds. Key-words: Holstein, Linkage, Disequilibrium, QMSim, Simulation, Selection, ROH, homozygosity, SNP

Evaluation of genetic improvement programmes using multiple ovulation and embryo transfer in dairy cattle

SIGLEAvailable from British Library Document Supply Centre- DSC:D94937 / BLDSC - British Library Document Supply CentreGBUnited Kingdo

Population Response to Climate Change: Wintering Strategy has Carryover Effects on the Timing of Nest Initiation and Mate Choice in a Partial Migrant, the American Kestrel (\u3cem\u3eFalco sparverius\u3c/em\u3e)

The ability of a population to respond to climate change will depend on phenotypic plasticity, adaptation, or both. Bird populations have already responded to warming temperatures by shifting their distributions, adjusting migration distance and timing, and breeding earlier. A population of American kestrels (Falco sparverius) in southwestern Idaho has advanced its nesting by approximately 30 days, on average, in the last 30 years and this has been correlated with changes in winter climate. The mechanisms allowing for this shift, however, are not clearly understood. I investigated if assortative mating of wintering kestrels and non-wintering kestrels is accompanying to this shift by monitoring kestrels in the winter and breeding seasons from 2010-2013. I asked if 1) wintering kestrels nest earlier than non-wintering kestrels, 2) wintering kestrels tend to mate with wintering kestrels and non-wintering kestrels mate with non-wintering kestrels, and 3) early breeding kestrels are genetically differentiated from late breeding kestrels. Results indicate that wintering kestrels nest earlier than non-wintering kestrels but this effect varies across years. Wintering strategy of females significantly predicted the wintering strategy of its mate which provides evidence for assortative mating. Analysis of 6 polymorphic microsatellite loci, however, gave no evidence of genetic differentiation or genetic structure between early and late breeding kestrels. This could be because there is still mixing between the groups despite differences in phenology, or the assortative mating pattern has arisen too recently to have resulted in genetic differentiation. Overall, this study documents that there are carryover effects of wintering strategy on the timing of nest initiation and mate pairing in American kestrels. It provides evidence for assortative mating of kestrels by wintering strategy, but this assortative mating has not lead to genetic divergence in kestrels of southwestern Idaho at this time

The effects of SNP-density and sample size on G-REML estimates of genetic and genic variance

EM-AB

Heterostyly: speciation within a species

Almost all organisms in nature show nonrandom mating to different degrees. Two extreme results of nonrandom mating are speciation and sexual differentiation. Heterostyly is a form of sexual differentiation considered to have evolved to resolve conflicts between male and female functions of hermaphrodite flowers. Our study examines necessary and sufficient conditions for establishment of heterostyly using a configuration individual-based model. Previous models assume invasion of a mutant phenotype into a population with monomorphic wild phenotype. In contrast, our model demonstrates that heterostyly can be established from a population with continuous phenotypic variation, a proposition that requires simpler assumptions than the previous hypotheses. Results of our simulation show that genetic linkage between stigma and anther heights is essential for establishment of heterostyly. Dominance effects on the genes for stamen or stigma heights are not necessary, but they promote evolution of heterostyly. Probability of evolution of heterostyly also depends on the functional relationship between stigma–anther distance and strength of sexual interference, and the distance and probability of pollen deposition success. Parallelity and difference between speciation and sexual differentiation are also discussed

Mate choice and the evolution of female promiscuity in a socially monogamous species

Chapter 1: Male zebra fiches have limited ability to identify high-fecundity females Abstract: In species with bi-parental care and lifetime monogamy, the fecundity of a male’s partner can be a major component of his fitness, but it is unclear whether males can assess female fecundity before breeding. We carried out an experiment in which we measured variation in female fecundity (repeatability 39%, 213 females) in a captive zebra finch population, and tested whether males preferred unfamiliar females of high fecundity (approximately top 10% of the population; 30 eggs laid on average) over those of low fecundity (bottom 10%; 6 eggs). We first tested whether naïve human observers could identify the high-fecundity female when confronted with duos of high and low fecundity. Humans guessed correctly in 58% of the cases (95% CI 50%-66%) indicating that differences in female condition were not highly obvious to humans. Zebra finch males preferred the high-fecundity female in 59% of choice tests that lasted 20 min (CI 52%-66%). When extending such choice tests over several days, male “success” in associating with the high-fecundity female was still modest (61% correct choices, CI 44%-76%). Overall, male zebra finches seem to have only limited abilities to identify the better mate when faced with a choice between extremes in terms of female fecundity. We found no male preference for heavier females. We speculate that such a preference may not have evolved because, in contrast to many ectothermic species, predicting fecundity from female weight is not sufficiently accurate (r2 = 0.04) for the benefits to outweigh the costs of increased male-male competition for heavy females. Chapter 2:No mutual mate choice for quality in zebra finches: time to question a widely-held assumption Abstract: Studies of mate choice typically assume that individuals will prefer high quality mates and select them based on condition-dependent indicator traits. In species where both sexes invest substantially in parental care, mutual mate choice is expected to result in assortative mating for quality. When assortment is not perfect, the lower quality pair members are expected to compensate by increased parental investment in order to secure their partner (positive differential allocation). This framework has been assumed to hold for monogamous model species like the zebra finch (Taeniopygia guttata), but little positive evidence has emerged, maybe because of the difficulty of defining individual quality. By combining multiple measures of causes (inbreeding, early nutrition) and consequences (ornaments, displays, fitness components) of variation in quality into a single principal component, we here show that quality variation can be quantified successfully and it indeed predicts individual pairing success, presumably because it reflects an individual’s vigor or ability to invest in reproduction. Yet, despite high statistical power, we found no evidence for either assortative mating or for positive differential allocation. We suggest that zebra finch ornaments and displays are not sufficiently reliable for choosy individuals to obtain benefits from being selective about such traits that are greater than the costs of competition for the putative best partner. We call for unbiased quantification of preference strength and signal honesty and avoidance of selective reporting of significant results. Chapter 3: Irreproducible text-book ‘knowledge’: the effects of color bands on zebra finch fitness Abstract: Many fields of science – including behavioral ecology – currently experience a heated debate about the extent to which publication bias against null-findings results in a misrepresentative scientific literature. Here, we show a case of an extreme mismatch between strong positive support for an effect in the literature and a failure to detect this effect across multiple attempts at replication. For decades, researchers working with birds have individually marked their study species with colored leg bands. For the zebra finch Taeniopygia guttata, a model organism in behavioral ecology, many studies over the past 35 years have reported effects of bands of certain colors on male or female attractiveness and further on behavior, physiology, life-history and fitness. Only 8 out of 39 publications presented exclusively null-findings. Here, we analyze the results of eight experiments in which we quantified the fitness of a total of 730 color-banded individuals from four captive populations (two domesticated and two recently wild-derived). This sample size exceeds the combined sample size of all 23 publications that clearly support the “color-band effect” hypothesis. We found that band color explains no variance in either male or female fitness. We also found no heterogeneity in color-band effects, arguing against both context- and population-specificity. Analysis of unpublished data from three other laboratories strengthens the generality of our null finding. Finally, a meta-analysis of previously published results is indicative of selective reporting and suggests that the effect size approaches zero when sample size is large. We argue that our field – and science in general – would benefit from more effective means to counter confirmation bias and publication bias. Chapter 4: Scrutinizing assortative mating in birds Abstract: Pair bonds often form between individuals that resemble one another. Such assortative mating appears to be widespread not only in humans but also throughout the animal kingdom. Yet it remains usually unclear whether assortative mating arises primarily from mate choice (‘like attracts like’), from spatial or temporal separation, or from observer, reporting, publication and search bias. Here, we reveal how compelling meta-analytical evidence for size-assortative mating in birds (r = 0.201 ± 0.022 SE, 58 species, 15,971 pairs) vanishes gradually with increased control of confounding factors. Specifically, the effect size decreased to half when we estimated assortative mating from unpublished data (free of reporting and publication bias) of nine long-term field studies (r = 0.106 ± 0.048 SE, eight species, 16,611 pairs) and assortative mating nearly disappeared (to around r = 0.018) when both partners were measured by independent observers or separate in space and time. Finally, we found no evidence for assortative mating in a direct experimental test for mutual mate choice in captive populations of zebra finches (r = -0.003 ± 0.141 SE, 1,414 pairs). These results highlight the importance of unpublished data in generating unbiased meta-analytical conclusions, and suggest that the apparent ubiquity of assortative mating reported in the literature is overestimated and may typically not be driven by mate choice. Chapter 5: Genetic constraints of female promiscuity: male corollary or independent trajectory? Abstract: The question of why females of many socially monogamous species engage in copulations outside the social pair bond has intrigued behavioral ecologists for many decades, especially because the benefits of such promiscuous behavior often do not seem to outweigh the costs. Hence, models of genetic constraint have been proposed, where female promiscuity emerges as a genetic corollary of alleles that are either beneficial for male extra-pair mating success (intersexual pleiotropy hypothesis) or beneficial for female fecundity (intrasexual pleiotropy hypothesis). In a first empirical test using captive zebra finches we had found support for the former hypothesis, suggesting that artificial selection on male sex drive could alter female extra-pair mating behavior as a genetic corollary. Here, we directly follow up on this suggestion and re-examine both hypotheses after establishing selection lines for male sex drive. After testing for intersexual pleiotropy with much increased statistical power, we now have to revise our previous conclusions, because the new data does not confirm the idea that male and female promiscuity are genetically homologous traits. However, we find some support for the idea that female promiscuity is genetically correlated with female fecundity, calling for more empirical tests of the intrasexual pleiotropy hypothesis. We also find that female extra-pair mating behavior is strongly context dependent, rendering genetic studies difficult and suggesting that social network analyses might shed more light on when and why females mate outside the pair bond

Mate Selection for Joint Control of Response and Inbreeding in Closed Pig Breeding Herds

Simple mate selection procedures for the joint control of response to selection and inbreeding were evaluated in a dynamic pig breeding population using stochastic simulation. The simulated populations modelled a closed breeding herd of moderate size (approx. 270 sows), characterised by overlapping generations and continuous cycles of performance testing and selection. Two studies were conducted: 1) where selection was for a single trait under three different heritabilities (ST), and; 2) where selection was for an aggregate genotype under three different breeding objectives (MT). Trait heritabilities for ST studies were 0.1, 0.35 and 0.6, and breeding objectives for MT studies defined general purpose (GP), terminal sire (TS) and maternal (MAT) selection lines

Portfolio theory, utility theory and mate selection

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