FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W2890690735> ?p ?o ?g. }

• W2890690735 abstract "This thesis examined if signals of selection are present in the bottlenecked and reintroduced populations of the Alpine ibex (Capra ibex). By utilizing single nucleotide polymorphism (SNP) data, I identified weak signals of purifying selection and positive selection. Furthermore, I quantified the detection accuracy achievable for studies using genetic outliers or associations among allele frequencies and environmental variables to detect positive selection after a bottleneck. Additionally, I discussed the biases present in a high-throughput sequencing dataset due to batch effects that can arise in long-term studies where sequencing data is added incrementally. Finally, in this thesis I discussed the importance of considering genetics when planning the reintroduction of a species. Population bottlenecks can have profound and long-lasting genetic consequences. Due to their reduced effective population size, bottlenecked species experience strong genetic drift, loss of genetic variation, and increased inbreeding. They are therefore at risk of maladaptation and extinction. Despite these risks examples of thriving bottlenecked populations are known. Outside of conservation biology, population bottlenecks are important evolutionary forces because they can affect the rate and direction of adaptation. As a result, identifying examples of selection after a bottleneck is of importance to evolutionary and conservation biology. In this thesis, I utilised genome-wide SNP data for 27 populations of Alpine ibex, including the remnant population in the Gran Paradiso National Park. This data was generated with restriction site associated DNA sequencing (RADseq). RADseq is a high-throughput sequencing method that sequences genomic DNA around a restriction enzyme site. I identified over 6000 SNPs in the Alpine ibex genome. With this data, I identified putative signals of purifying selection by comparing exonic SNPs, which are likely under selection, with intronic SNPs and SNPs in intergenic regions, that are expected to be largely neutral. Furthermore I examined the ratio of non-synonymous to synonymous sites. The heterozygosity of exonic SNPs was significantly below that of introns and of intergenic SNPs. In addition, the ratio of non-synonymous to synonymous sites was below one. While this suggests purifyingii selection, due to marker and test limitations, these results are not conclusive and the presence of purifying selection should be viewed with caution. I then searched for signals of positive selection by scanning for large differences in allele frequencies among populations and for correlations between allele frequencies and an environmental variable. The high rates of genetic drift in bottlenecked populations can create false signals of positive selection when using such methods. Therefore, I used a population genetic (forward-time) simulation approach that followed Alpine ibex demography, to generate a simulated set of SNPs including neutral loci and loci that were under selection. I then used these loci to quantify the accuracy of three selection detection methods. To this end, I examined the number of false positive neutral SNPs identified by each method, as well as the number of true positive and false negative simulated selected SNPs. I found that a true discovery rate of over 70% can be achieved by combining three selection detection methods to identify “triple positive” SNPs, and an environmental correlation detection approach. When I applied the selection detection methods to the Alpine ibex empirical RADseq dataset no triple positive SNPs were identified by the triple positive environmental correlation approach. Thus there are no SNPs I confidently identified as under selection, though weak candidates were found by the lower accuracy methods (30- 50% true discovery rate) that may be suitable for further examination. High-throughput sequencing is maturing and an increasing number of studies have used data obtained over time or generated by different investigators. In this thesis, I also discuss the biases and errors, so-called ‘batch effects’, that can be introduced into a study if subsets of data differ in how they were obtained and contain different technical artefacts. I present a case study in the Alpine ibex where batch effects lead to a misleading biological conclusion. Finally in an additional co-authored publication, the importance of considering the long-term genetics of a population during a reintroduction was presented and discussed." @default.
• W2890690735 created "2018-09-27" @default.
• W2890690735 creator A5016014733 @default.
• W2890690735 date "2018-01-01" @default.
• W2890690735 modified "2023-09-26" @default.
• W2890690735 title "Population genomics of the Alpine ibex (Capra ibex)" @default.
• W2890690735 doi "https://doi.org/10.5167/uzh-146764" @default.
• W2890690735 hasPublicationYear "2018" @default.
• W2890690735 type Work @default.
• W2890690735 sameAs 2890690735 @default.
• W2890690735 citedByCount "0" @default.
• W2890690735 crossrefType "dissertation" @default.
• W2890690735 hasAuthorship W2890690735A5016014733 @default.
• W2890690735 hasConcept C104317684 @default.
• W2890690735 hasConcept C105076106 @default.
• W2890690735 hasConcept C119857082 @default.
• W2890690735 hasConcept C141231307 @default.
• W2890690735 hasConcept C144024400 @default.
• W2890690735 hasConcept C149923435 @default.
• W2890690735 hasConcept C180754005 @default.
• W2890690735 hasConcept C189206191 @default.
• W2890690735 hasConcept C2779040068 @default.
• W2890690735 hasConcept C2908647359 @default.
• W2890690735 hasConcept C3641667 @default.
• W2890690735 hasConcept C41008148 @default.
• W2890690735 hasConcept C54355233 @default.
• W2890690735 hasConcept C61320498 @default.
• W2890690735 hasConcept C68873052 @default.
• W2890690735 hasConcept C78458016 @default.
• W2890690735 hasConcept C80990810 @default.
• W2890690735 hasConcept C81917197 @default.
• W2890690735 hasConcept C85721925 @default.
• W2890690735 hasConcept C86803240 @default.
• W2890690735 hasConceptScore W2890690735C104317684 @default.
• W2890690735 hasConceptScore W2890690735C105076106 @default.
• W2890690735 hasConceptScore W2890690735C119857082 @default.
• W2890690735 hasConceptScore W2890690735C141231307 @default.
• W2890690735 hasConceptScore W2890690735C144024400 @default.
• W2890690735 hasConceptScore W2890690735C149923435 @default.
• W2890690735 hasConceptScore W2890690735C180754005 @default.
• W2890690735 hasConceptScore W2890690735C189206191 @default.
• W2890690735 hasConceptScore W2890690735C2779040068 @default.
• W2890690735 hasConceptScore W2890690735C2908647359 @default.
• W2890690735 hasConceptScore W2890690735C3641667 @default.
• W2890690735 hasConceptScore W2890690735C41008148 @default.
• W2890690735 hasConceptScore W2890690735C54355233 @default.
• W2890690735 hasConceptScore W2890690735C61320498 @default.
• W2890690735 hasConceptScore W2890690735C68873052 @default.
• W2890690735 hasConceptScore W2890690735C78458016 @default.
• W2890690735 hasConceptScore W2890690735C80990810 @default.
• W2890690735 hasConceptScore W2890690735C81917197 @default.
• W2890690735 hasConceptScore W2890690735C85721925 @default.
• W2890690735 hasConceptScore W2890690735C86803240 @default.
• W2890690735 hasLocation W28906907351 @default.
• W2890690735 hasOpenAccess W2890690735 @default.
• W2890690735 hasPrimaryLocation W28906907351 @default.
• W2890690735 hasRelatedWork W1875950308 @default.
• W2890690735 hasRelatedWork W2002682901 @default.
• W2890690735 hasRelatedWork W2021810789 @default.
• W2890690735 hasRelatedWork W2025253353 @default.
• W2890690735 hasRelatedWork W2097103181 @default.
• W2890690735 hasRelatedWork W2123720538 @default.
• W2890690735 hasRelatedWork W2134275486 @default.
• W2890690735 hasRelatedWork W2156169823 @default.
• W2890690735 hasRelatedWork W2168912878 @default.
• W2890690735 hasRelatedWork W2172440179 @default.
• W2890690735 hasRelatedWork W2345405914 @default.
• W2890690735 hasRelatedWork W2767062083 @default.
• W2890690735 hasRelatedWork W2905495423 @default.
• W2890690735 hasRelatedWork W2916815356 @default.
• W2890690735 hasRelatedWork W2952641079 @default.
• W2890690735 hasRelatedWork W2967589030 @default.
• W2890690735 hasRelatedWork W3009075383 @default.
• W2890690735 hasRelatedWork W3018233365 @default.
• W2890690735 hasRelatedWork W3123660041 @default.
• W2890690735 hasRelatedWork W3128972156 @default.
• W2890690735 isParatext "false" @default.
• W2890690735 isRetracted "false" @default.
• W2890690735 magId "2890690735" @default.
• W2890690735 workType "dissertation" @default.