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Evolution of sex chromosomes in Sylvioidea songbirds

Sigeman, Hanna LU (2021)
Abstract
Sex chromosomes were discovered more than 100 years ago. They have been studied intensely from a theoretical perspective since then, giving rise to a large body of testable predictions about their evolution from autosomes. A common feature of sex chromosomes is recombination suppression between the sex chromosome copies (X and Y in male heterogametic systems, or Z and W in female heterogametic systems). Without recombination, the sex-limited chromosome (Y or W) is expected to degenerate through the accumulation of deleterious mutations and repeat elements. Over long evolutionary time scales, this degeneration may leave the Y/W chromosomes short and almost completely devoid of functional genes.

Using genome sequencing technology,... (More)
Sex chromosomes were discovered more than 100 years ago. They have been studied intensely from a theoretical perspective since then, giving rise to a large body of testable predictions about their evolution from autosomes. A common feature of sex chromosomes is recombination suppression between the sex chromosome copies (X and Y in male heterogametic systems, or Z and W in female heterogametic systems). Without recombination, the sex-limited chromosome (Y or W) is expected to degenerate through the accumulation of deleterious mutations and repeat elements. Over long evolutionary time scales, this degeneration may leave the Y/W chromosomes short and almost completely devoid of functional genes.

Using genome sequencing technology, we can now study the full DNA sequence of sex chromosomes. The analysis of sequence data from a wide range of taxonomic groups has revealed that sex chromosomes are more dynamic and variable than previously believed. Several aspects of sex chromosome evolution, however, remain poorly understood, especially relating to the early stages of evolution from autosomes. This is partly because some hypotheses are challenging to test, but also because most well-studied sex chromosome systems are evolutionarily old and biased towards XY systems.

In this thesis, I study the evolution of sex chromosomes across Sylvioidea songbirds using genomic data and bioinformatic methodology. All members of this superfamily have a shared “neo-sex chromosome”: a fusion between an autosome (chromosome 4A) and the existing sex chromosomes. The sex chromosomes of birds (ZW) formed in a common ancestor more than 100 million years ago. Since then, the W chromosome has undergone severe degradation and shortening, obscuring almost all traces of their early evolution. Additions of new genetic material through autosome-sex chromosome fusions, however, allow us to study the early stages of sex chromosome evolution.

I developed a computational pipeline aimed at discovering and visualizing sex chromosomes. I applied this pipeline to genomic data from species belonging to 13 different Sylvioidea families, and found that four additional autosome-sex chromosome fusions have occurred in different lineages within the group (involving chromosomes 3, 4, 5 and 8). These different fused regions have intermediate to extremely low W degeneration levels, with dosage sensitive and evolutionarily constrained genes being retained to a higher degree than other genes. I also studied the structure of these neo-sex chromosomes, how female gene expression changes in response to W degeneration and how recombination suppression extends along newly added sex chromosome regions. The work in this thesis shows that Sylvioidea songbirds are an ideal system for testing theory relating to sex chromosome evolution, and that bird sex chromosomes are more variable than previously believed. (Less)
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author
supervisor
opponent
  • Professor Sunnucks, Paul, Monash University, Australia
organization
publishing date
type
Thesis
publication status
published
subject
keywords
Sex chromosome, neo-sex chromosome, Birds, vertebrates, Genomics, Bioinformatics
pages
228 pages
publisher
Lund University (Media-Tryck)
defense location
Blå hallen, Ekologihuset, Biologiska institutionen, Lund. Join via zoom:https://lu-se.zoom.us/j/63900299557
defense date
2021-04-09 09:00:00
ISBN
978-91-7895-782-8
978-91-7895-781-1
language
English
LU publication?
yes
id
bd276405-16c9-4e46-9e50-fdd8cfccb0ba
date added to LUP
2021-03-12 09:28:03
date last changed
2021-03-19 11:46:33
@phdthesis{bd276405-16c9-4e46-9e50-fdd8cfccb0ba,
  abstract     = {Sex chromosomes were discovered more than 100 years ago. They have been studied intensely from a theoretical perspective since then, giving rise to a large body of testable predictions about their evolution from autosomes. A common feature of sex chromosomes is recombination suppression between the sex chromosome copies (X and Y in male heterogametic systems, or Z and W in female heterogametic systems). Without recombination, the sex-limited chromosome (Y or W) is expected to degenerate through the accumulation of deleterious mutations and repeat elements. Over long evolutionary time scales, this degeneration may leave the Y/W chromosomes short and almost completely devoid of functional genes.<br/><br/>Using genome sequencing technology, we can now study the full DNA sequence of sex chromosomes. The analysis of sequence data from a wide range of taxonomic groups has revealed that sex chromosomes are more dynamic and variable than previously believed. Several aspects of sex chromosome evolution, however, remain poorly understood, especially relating to the early stages of evolution from autosomes. This is partly because some hypotheses are challenging to test, but also because most well-studied sex chromosome systems are evolutionarily old and biased towards XY systems.<br/><br/>In this thesis, I study the evolution of sex chromosomes across Sylvioidea songbirds using genomic data and bioinformatic methodology. All members of this superfamily have a shared “neo-sex chromosome”: a fusion between an autosome (chromosome 4A) and the existing sex chromosomes. The sex chromosomes of birds (ZW) formed in a common ancestor more than 100 million years ago. Since then, the W chromosome has undergone severe degradation and shortening, obscuring almost all traces of their early evolution. Additions of new genetic material through autosome-sex chromosome fusions, however, allow us to study the early stages of sex chromosome evolution.<br/><br/>I developed a computational pipeline aimed at discovering and visualizing sex chromosomes. I applied this pipeline to genomic data from species belonging to 13 different Sylvioidea families, and found that four additional autosome-sex chromosome fusions have occurred in different lineages within the group (involving chromosomes 3, 4, 5 and 8). These different fused regions have intermediate to extremely low W degeneration levels, with dosage sensitive and evolutionarily constrained genes being retained to a higher degree than other genes. I also studied the structure of these neo-sex chromosomes, how female gene expression changes in response to W degeneration and how recombination suppression extends along newly added sex chromosome regions. The work in this thesis shows that Sylvioidea songbirds are an ideal system for testing theory relating to sex chromosome evolution, and that bird sex chromosomes are more variable than previously believed.},
  author       = {Sigeman, Hanna},
  isbn         = {978-91-7895-782-8},
  language     = {eng},
  month        = {03},
  publisher    = {Lund University (Media-Tryck)},
  school       = {Lund University},
  title        = {Evolution of sex chromosomes in Sylvioidea songbirds},
  url          = {https://lup.lub.lu.se/search/ws/files/95215500/Hanna_Sigeman_avh_E_spik.pdf},
  year         = {2021},
}