Analysis of genome-wide patterns of differentiation in the chiffchaff (Phylloscopus collybita spp.)
Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
Unraveling the genetic basis of reproductive isolation is significant for the understanding of the speciation process. Hybrid zones, the regions where two species co-occur and produce hybrids, offer excellent natural environments where the initiation and establishment of genetic barriers to gene flow between two incipient species can be studied. The chiffchaff species system with its natural hybrid zone is a great model system in this regard. This study aims at quantifying the genetic differentiation between European (Phylloscopus collybita abietinus) and Siberian (P. c. tristis) chiffchaff species and identifying genes of potential significance for reproductive isolation by identification of highly differentiated genomic regions between these two subspecies. A reference-assisted consensus assembly for chiffchaff was generated using collared flycatcher as the reference and then population re-sequencing analyses including calculation of population genetic summary statistics were carried out for both allopatric and sympatric samples of both subspecies. The average genetic differentiation between allopatric populations of abietinus and tristis was found to be moderate (FST = 0.220), higher than between subspecies sampled in the sympatric zone (FST = 0.107). The genetic differentiation on the Z chromosome was found to be higher (FST = 0.31) than the differentiation on the autosomes (FST = 0.21). Eight distinct peaks of divergence were detected where genomes of the subspecies were highly differentiated in a limited genetic region. These regions contained around 26 genes, of which the most interesting have functions related to sensory perception of sound, learning and pigmentation. In addition, the nucleotide diversity was also found to be lower in all those high FST peak regions than the surrounding genomic regions. High fixation index values, low nucleotide diversity and identification of genes important for reproductive isolation on the same peak of divergence indicate that these regions in the genome of chiffchaff species are, or have been, under the influence of selection. The results have implications for understanding the genetic basis of local adaptation and reproductive isolation in chiffchaff in particular and for the understanding of speciation and adaptation processes in general.
Place, publisher, year, edition, pages
2016. , 31 p.
Speciation, genomics, population genetics
Bioinformatics (Computational Biology)
IdentifiersURN: urn:nbn:se:uu:diva-306203OAI: oai:DiVA.org:uu-306203DiVA: diva2:1040912
Master Programme in Bioinformatics