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Signs of inversions in the willow warbler genome

Sigeman, Hanna (2016) BION01 20152
Degree Projects in Biology
Abstract
Inversions have the capacity to maintain genetic differentiation between hybridizing populations, which makes them highly interesting targets for understanding the processes of early speciation. In-versions can generate “islands of differentiation”, genomic peaks of heightened divergence, by lower-ing recombination in heterozygotes. Two genetically similar and hybridizing subspecies of the willow warbler (Phylloscopus trochilus) have been found to differ by three islands of differentiation, which in this study was searched for signatures of inversions. A newly assembled willow warbler reference ge-nome was synteny mapped, structural variation detection was done on resequencing data from both subspecies and Long-Range PCR experiments aiming... (More)
Inversions have the capacity to maintain genetic differentiation between hybridizing populations, which makes them highly interesting targets for understanding the processes of early speciation. In-versions can generate “islands of differentiation”, genomic peaks of heightened divergence, by lower-ing recombination in heterozygotes. Two genetically similar and hybridizing subspecies of the willow warbler (Phylloscopus trochilus) have been found to differ by three islands of differentiation, which in this study was searched for signatures of inversions. A newly assembled willow warbler reference ge-nome was synteny mapped, structural variation detection was done on resequencing data from both subspecies and Long-Range PCR experiments aiming at sequencing across inversion breakpoints was attempted. Several signatures of inversions were found, including subspecies specific structural variation within these islands and repeat elements near the putative inversion breakpoints. (Less)
Popular Abstract
Inversions – Creators of Biodiversity

Ever since the theory of evolution was put forward, biologists have tried to understand how new species form. One of the remaining mysteries relate to how speciation involving still hybridizing groups can progress. In this master project, I have been searching for a form of mutations called inversions, which can maintain genetic differentiation in diverging species and might be a key feature in understanding speciation with hybridization.

Inversions are created when a chromosome segment breaks off from the rest of the chromosome and flip around before being reinserted in the same place from where they detached. They can form during cell division and be either small or span many millions of base... (More)
Inversions – Creators of Biodiversity

Ever since the theory of evolution was put forward, biologists have tried to understand how new species form. One of the remaining mysteries relate to how speciation involving still hybridizing groups can progress. In this master project, I have been searching for a form of mutations called inversions, which can maintain genetic differentiation in diverging species and might be a key feature in understanding speciation with hybridization.

Inversions are created when a chromosome segment breaks off from the rest of the chromosome and flip around before being reinserted in the same place from where they detached. They can form during cell division and be either small or span many millions of base pairs. Inversions that capture several locally adapted genes can quickly rise in frequency within a population, and selection would act upon these inversions to keep them intact when recombining within individuals with only one copy of the inversion. With time, these inverted regions could evolve and become increasingly differentiated from the non-inverted state and even develop genes involved in reproductive isolation.

The willow warbler is a small songbird common throughout Europe and Asia. Two willow warbler subspecies live and breed in Sweden, one mainly in the north and one mainly in the South. The subspecies are genetically very similar and often hybridize when they meet. The only genetic differentiation between these subspecies is restricted to three regions on separate chromosomes. I have been using bioinformatics to analyse these regions and look for signs that the differences are being maintained by inversions in one of the subspecies.

How do you find inversions?
Inversions are most commonly found by analysing next-generation sequencing data, which are large data files filled with genetic code. Possible inversions can be found with programs that analyse patterns and differences within these files. But inversions are hard to detect since they are often found in complex regions of the genome.

By analysing differences between the northern and southern subspecies, and also by comparing the genetic data from the willow warbler to other bird species, I found signatures indicating the presence of inversions for at least two of these regions. Among my results were additional evidence that the willow warblers only differ within the three chromosomal regions. I also found repetitive DNA near the outermost regions of the differentiated regions, which is a signature of inversion breakpoints. But in order to know for sure that we have inversions in the willow warbler genome additional research is needed, preferentially including additional sequencing of willow warbler DNA.




Advisor: Max Lundberg, Staffan Bensch
Master´s Degree Project 45 credits in Biology, 2015
Department of Biology, Lund University (Less)
Please use this url to cite or link to this publication:
author
Sigeman, Hanna
supervisor
organization
course
BION01 20152
year
type
H2 - Master's Degree (Two Years)
subject
language
English
id
8871055
date added to LUP
2016-04-15 09:06:39
date last changed
2016-04-15 09:06:39
@misc{8871055,
  abstract     = {Inversions have the capacity to maintain genetic differentiation between hybridizing populations, which makes them highly interesting targets for understanding the processes of early speciation. In-versions can generate “islands of differentiation”, genomic peaks of heightened divergence, by lower-ing recombination in heterozygotes. Two genetically similar and hybridizing subspecies of the willow warbler (Phylloscopus trochilus) have been found to differ by three islands of differentiation, which in this study was searched for signatures of inversions. A newly assembled willow warbler reference ge-nome was synteny mapped, structural variation detection was done on resequencing data from both subspecies and Long-Range PCR experiments aiming at sequencing across inversion breakpoints was attempted. Several signatures of inversions were found, including subspecies specific structural variation within these islands and repeat elements near the putative inversion breakpoints.},
  author       = {Sigeman, Hanna},
  language     = {eng},
  note         = {Student Paper},
  title        = {Signs of inversions in the willow warbler genome},
  year         = {2016},
}