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Mensen zijn van nature nieuwsgierig naar hun verleden, afkomst en oorsprong. Het is dan ook niet verwonderlijk dat heel wat mensen zich bezig houden met het reconstrueren van hun stamboom Sinds enkele jaren heeft genealogie ook de aandacht gekregen van de moleculaire biologie, die aan de hand van het Y-chromosoom de genetica achter de stambomen kan bestuderen. Het Y-chromosoom is het geslachtsdeterminerende chromosoom en wordt net als de familienaam grotendeels onveranderd doorgegeven van vader op zoon. Maar soms ontstaan er op het Y-chromosoom toch spontane mutaties. Zo is het mogelijk op basis van de snellere mutaties (‘Short Tandem Repeats’ of Y-STRs) familiale lijnen te achterhalen. Deze studie vergelijkt 46 Y-STRs tussen ver verwante mannelijke naamgenoten die een gemeenschappelijke voorvader delen in vaderlijke lijn, ook wel genealogische koppels genoemd. De focus van deze studie ligt op de graad van buitenechtelijkheid. Indien er tussen de Y-chromosomen van de naamgenoten een verschil is van meer dan 7 op de 46 geanalyseerde Y-STRs, is er geen dichte genetische verwantschap mogelijk door een onderbreking in hun vaderlijke lijn. De man is nooit 100% zeker van zijn biologisch vaderschap. Zo is het mogelijk dat de vrouw ervoor kiest om met iemand anders te paren dan haar sociale partner, hier spreekt men van het zoeken naar een extra paar vaderschap (EPP). EPP kan worden verklaard aan de hand van de ‘Life History’ theorie, waarbij de keuze van vreemdgaan bij de vrouw afhankelijk is van de afweging tussen het risico van het verlaten van haar sociale partner en het voordeel dat haar kind wordt verwekt door een man met betere genen. De gemiddelde EPP graad in de hedendaagse Westerse bevolkingsgroepen ligt tussen één en drie procent per generatie. In dit onderzoek werd aan de hand van 334 genealogische koppels uit de Lage Landen onderzocht of er subtiele verschillen in EPP graad kunnen worden geobserveerd in tijd en ruimte. Bij de onderzoeksvraag naar de temporele differentiatie werd een hogere EPP graad gevonden bij de hedendaagse bevolking in vergelijking met de verleden bevolking. De hogere huidige EPP graad kan een gevolg zijn van de opkomst van mobiliteit na de industriële revolutie, of de verstedelijking door de bevolkingsgroei. Hierbij komen vrouwen met meer mannen in contact dan vroeger. Deze man-vrouw interactie kan leiden tot wantrouwen of jaloezie, die op haar beurt kan zorgen voor instabiliteit binnen het huwelijk. Bij de onderzoeksvraag naar de spatiale differentiatie werd gevonden dat ook de bevolkingsdichtheid de EPP graad kan beïnvloeden. Hierbij werd een significant lagere EPP graad gevonden bij genealogische koppels uit kleinschalige dorpen in vergelijking met de druk bezette steden. Een mogelijke verklaring voor deze resultaten kan onder andere liggen bij de hogere sociale controle en lage anonimiteit of bij de hogere invloed van de kerk. Algemeen kan er uit dit onderzoek worden geconcludeerd dat verstedelijking zowel in tijd en ruimte een invloed heeft gehad op de graad van buitenechtelijkheid bij de mens.
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In the past decade next-generation sequencing (NGS) technologies have revolutionized the fields of molecular biology, genetics and genomics by enabling cost-effective and quick generation of DNA sequence data with exquisite accuracy and resolution. The technical strategy of the NGS technology is straightforward: the sequencing throughput is boosted by miniaturizing the sequencing chemical reactions such that millions of those reactions can take place. The amount of data produced by the NGS technologies has been truly astonishing: about every seven months this produced data is doubled and it is expected that their sequencing capacities will continue to grow very rapidly over the next ten years. This allows for answering several new research questions while new kinds of experiments can be performed as the NGS technology is used creatively to sequence the genome, transcriptome and their interactions with the proteome. Investigations that were, for most, unreachable luxuries just a few years ago are now being increasingly enabled, at a rapid pace.Two different applications that use the current advantages of NGS in biology and which were the main focus of my PhD thesis, are the enlarging of the human Y chromosomal phylogeny and the detection of genomic imprinting in social insects. Publically available NGS data are used to validate and improve the existing human Y chromosomal phylogeny which represents the evolutionary relationship among the studied human Y chromosomes. The human genome can be sequenced with NGS in a time- and cost-efficient manner and therefore, more and more human genomes will become publically available in the coming years. By using Y chromosomal NGS data, a more detailed genealogical history of the evolutionary change of the Y chromosome can be reconstructed. We created two software packages, AMY-tree and PENNY, to deal with NGS data to improve the phylogeny. AMY-tree is created to determine the Y chromosomal lineage of a sample while also detecting Y-SNP recurrent mutations and wrongly reported Y-SNP conversions and reporting Y-SNPs which are not yet reported in scientific publications. As there are still many false positive SNP calls in NGS data, PENNY was developed to deal in silico with the huge number of newly reported Y-SNPs before adding them to the phylogeny. Both programs are validated based on a dataset of DNA samples sequenced on different NGS platforms and with different sequencing depths. This resulted in a new Y chromosomal phylogeny, however, the practical use of this phylogeny is becoming increasingly complex and therefore, also a minimalized version of the Y phylogeny has been constructed.The second application developed during my PhD project, is the use of NGS in a complex experimental design to find genomic imprinting in bumblebee Bombus terrestris. Genomic imprinting is the epigenetic phenomenon whereby alleles are expressed based on their inheritance from one specific parent and since it only effects a small amount of genes, it definitely benefits from the use of NGS technologies. NGS makes it possible to determine the genetic variation in the parents first before the transcriptome of the offspring is sequenced to find the parent-of-origin specific gene expression. Without NGS finding new imprinted genes is almost unfeasible as only targeted genes can be tested. A large number of samples is required to distinguish parent-of-origin effects from other effects specific for the family, lineage and individual and the falling cost of NGS technologies make it possible to study imprinting in a genome-wide manner in this social bumble bee. Our extensive experiment was designed such that parent-of-origin effects on gene expression could be discriminated from other effects and this resulted in the detection of 93 genes with a parent-of-origin bias which all expressed the patrigene more than the matrigene. The found number of imprinted genes accords with the percentages found in other species, however, no known imprinted genes or functions found. As the experimental design is complex it was crucial that all technical requirements regarding the NGS were fulfilled to successfully detect parent-of-origin gene expression. Our results do not support David Haig's kin conflict theory as an adaptive basis of genomic imprinting in bees. Instead, both our results from bumblebees and a recently published study on genomic imprinting in the honeybee show that genomic imprinting is used to tune and reduce the phenotypic variance at specific loci.For decades it was laborious to get an adequate amount of DNA and RNA data but with the upswing in NGS technologies the challenges have been shifted onto the interpretation of the huge amounts of data that can be generated shown by the complexity to detect genomic imprinting in B. terrestris. Furthermore, the efforts that make it possible to answer research questions are also challenges resulting from the increasing use of NGS methods as shown by updating the human Y chromosomal phylogeny. By updating the phylogeny the discrimination power of samples increases such that other fields using this Y chromosomal phylogeny can answer their research questions more accurately.
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Commercially reared bumblebees are important pollinators of agricultural crops. Biobest Group NV was the first company to commercially rear bumblebees for pollination purposes and constantly aims to optimize the pollination services that are provided by their bumblebee colonies. One potential threat to the bumblebees’ pollination capacity is drifting, which is the behavior whereby an individual leaves its natal colony and enters a conspecific foreign one. This can lead to a broad range of negative consequences for the drifter’s natal colony, as well as for the host colony, and the grower or farmer who is using the bumblebee colonies for pollination purposes. For example, some colonies experience a reduction in the number of workers due to workers drifting out of the colony, which can negatively impact the colony’s survival chances and pollination capacity. Moreover, drifting can cause horizontal disease and parasite transfer between colonies. Drifting can be an accidental behavior, meaning that a worker unintentionally enters a foreign colony due to orientation errors. Therefore, the amount of drift is considerably higher in artificial settings, such as greenhouses, where unnaturally high densities of colonies are present and which lack visual cues to aid in orientation, than in wild colonies. However, more recent studies found that some drifters lay eggs in foreign colonies, and that drifters produce significantly more male offspring than native bees from the host colony, indicating that drifting might be not a purely accidental behavior. The aim of this master thesis study was to investigate whether proximal visual cues (hive figures) can reduce the amount of drifting of commercial Bombus terrestris colonies, and to get more insights into the drivers of bumblebee drifting: is it an accidental behavior resulting from orientation errors, or do workers drift intentionally? To investigate this, B. terrestris workers were individually marked using numbered tags in a colony-specific color and the presence of drifters inside the colonies was determined by performing observations inside the colonies. The amount of drift was then compared between a control treatment where no hive figures were present, and two figure treatments. Moreover, to gain more insights into the drivers of bumblebee drift, natives (i.e., workers who never drifted) and drifters were dissected. The ovarian development was then compared between natives and drifters to evaluate whether they differ in the probability of being egg layers. We found that the use of geometric figures can lower the amount of drifting, which indicates that drifting has an important accidental aspect. However, we also found that resident drifters had a higher probability of having stage IV ovaries and more mature eggs inside their ovaries compared to natives, indicating that drifting was most likely not a purely accidental behavior and that at least some residents may have drifted intentionally to reproduce in foreign colonies. The results thus showed that drifting of commercial bumblebees is likely not a purely accidental or purely intentional phenomenon, but rather a combination of both. Our study thus shows that hive figures can be used to reduce the amount of drift of commercial bumblebees. More research is needed regarding the effects of drifting on the colonies’ pollination capacities to assess whether the use of hive figures will be economically interesting.
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