Population genomics in Drosophila melanogaster: a bioinformatics approach

dc.contributor
Universitat Autònoma de Barcelona. Departament de Genètica i de Microbiologia
dc.contributor.author
Hervás Fernàndez, Sergi
dc.date.accessioned
2019-02-22T06:41:43Z
dc.date.available
2019-02-22T06:41:43Z
dc.date.issued
2018-11-30
dc.identifier.isbn
9788449084140
en_US
dc.identifier.uri
http://hdl.handle.net/10803/665851
dc.description.abstract
High-throughput sequencing technologies are allowing the description of genome-wide variation patterns for an ever-growing number of organisms. However, we still lack a thorough comprehension of the relative amount of different types of genetic variation, their phenotypic effects, and the detection and quantification of distinct selection regimes acting on genomes. The recent compilation of more than one thousand of worldwide wild-derived Drosophila melanogaster genome sequences reassembled using a standardized pipeline (Drosophila Genome Nexus, DGN, Lack et al. 2015, 2016) provides a unique resource to test molecular population genetics hypotheses, and ultimately understand the evolutionary dynamics of genetic variation in the populations. Besides, the increasing amount of genomic data available requires the continuous development and optimization of bioinformatics tools able to handle and analyze such information. Thus, the development and implementation of new biologically-oriented software addressing several steps from data acquisition, filtering, processing, display or analysis to the final reporting step is a constantly growing need, especially in fields dealing with large data sets, such as population genomics. This thesis is conceived as a comprehensive bioinformatics and population genomics project. It is centered in the development and application of bioinformatics tools for the analysis and visualization of nucleotide variation patterns and the detection of selective events in the genome of D. melanogaster, using the DGN data. The main goal is accomplished in three sequential steps: (i) capture the evolutionary properties of the analyzed sequences (i.e., create a catalog of population genetics metrics) and implement a tool for the graphical display of such information; (ii) develop a statistical package for the computation of the diverse selection regimes acting on genomes (positive and purifying selection), and finally (iii) perform an initial population genomics analysis in D. melanogaster using the previously developed tools. The common approach applied to process the data, starting at the assembly of genome sequences and ending up at the estimates of population genetics metrics, allows performing, for the first time, a comprehensive comparison and interpretation of results using samples from five continents. Overall, this work provides a global overview of the nucleotide variation and adaptation patterns along the genome, and a general assessment of the relative impact of the major genomic determinants of genetic variation, in Drosophila meta-populations with different geographical origin.
en_US
dc.format.extent
252 p.
en_US
dc.format.mimetype
application/pdf
dc.language.iso
eng
en_US
dc.publisher
Universitat Autònoma de Barcelona
dc.rights.license
L'accés als continguts d'aquesta tesi queda condicionat a l'acceptació de les condicions d'ús establertes per la següent llicència Creative Commons: http://creativecommons.org/licenses/by-nc-nd/4.0/
dc.rights.uri
http://creativecommons.org/licenses/by-nc-nd/4.0/
*
dc.source
TDX (Tesis Doctorals en Xarxa)
dc.subject
Genòmica
en_US
dc.subject
Genómica
en_US
dc.subject
Genomics
en_US
dc.subject
Bioinformàtica
en_US
dc.subject
Bioinformática
en_US
dc.subject
Bioinformatics
en_US
dc.subject
Evolució
en_US
dc.subject
Evolución
en_US
dc.subject
Evolution
en_US
dc.subject.other
Ciències Experimentals57
en_US
dc.title
Population genomics in Drosophila melanogaster: a bioinformatics approach
en_US
dc.type
info:eu-repo/semantics/doctoralThesis
dc.type
info:eu-repo/semantics/publishedVersion
dc.subject.udc
575
en_US
dc.contributor.authoremail
sergi.hervas@uab.cat
en_US
dc.contributor.director
Barbadilla Prados, Antonio
dc.contributor.director
Casillas Viladerrams, Sònia
dc.embargo.terms
cap
en_US
dc.rights.accessLevel
info:eu-repo/semantics/openAccess


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