Evolutionary ecology of avian neo-sex chromosomes
Jacobsen Ellerstrand, Simon LU
(2026)
- Abstract
- Females and males are alternative reproductive phenotypes that can differ through striking suites of correlated phenotypic traits, such as behaviour, morphology and life-history traits. These sex-specific adaptations are sometimes facilitated through supergenes — sex chromosomes — which link sexually antagonistic alleles and the sex-determining locus into sex-specific haplotypes. However, recombination cessation reduces the ability of selection to maintain sex-limited Y/W haplotypes, often leading to progressive Y/W degeneration and fitness consequences for the heterogametic sex (male XY or female ZW). Despite their acknowledged importance in adaptation, life-history variation and speciation, sex chromosomes remain understudied in many... (More)
- Females and males are alternative reproductive phenotypes that can differ through striking suites of correlated phenotypic traits, such as behaviour, morphology and life-history traits. These sex-specific adaptations are sometimes facilitated through supergenes — sex chromosomes — which link sexually antagonistic alleles and the sex-determining locus into sex-specific haplotypes. However, recombination cessation reduces the ability of selection to maintain sex-limited Y/W haplotypes, often leading to progressive Y/W degeneration and fitness consequences for the heterogametic sex (male XY or female ZW). Despite their acknowledged importance in adaptation, life-history variation and speciation, sex chromosomes remain understudied in many areas of evolutionary ecology. Recent advances in DNA sequencing technology and sequencing initiatives have accumulated evidence that sex chromosome systems across the tree of life vary extensively in age, turnover, evolutionary transitions, autosomal fusions and stratum formation. Thus, now is an ideal time for biologists to investigate the role of sex chromosomes in evolutionary ecology. In this thesis, I studied sex chromosomes in larks (Alaudidae). Several autosomal translocations with subsequent recombination cessation in larks have resulted in greatly expanded neo-sex chromosomes. This system, with multiple evolutionary strata formed at different times, provides a powerful framework for studying different stages of sex chromosome evolution and for performing comparative analyses. I developed a bioinformatic pipeline that extracts Y/W sequences from short-read data, which enabled me to address questions regarding sex chromosome evolution and its role in evolutionary ecology. I studied Z–W gametolog evolution to characterise the longevity and functional role of W chromosomes under extreme demographic scenarios, and dissected the faster-Z effect using a gametolog-level approach. I studied sex chromosomes during speciation, characterising the evolutionary history of a large recombination-cessation polymorphism, and described factors influencing introgression across the Z chromosome. I studied the predictability of sex chromosome evolution and found that several gene properties predict gametolog co-evolution. I characterised remarkable variation in recombination cessation among lark species, with repeated formation of evolutionary strata, linking this variation to sexual dimorphism, pace-of-life strategy, and IUCN Red List status. Taken together, this thesis provides the first chromosome-level genome assembly for larks and lays a foundation for using larks as a model system to study sex chromosomes in evolutionary ecology. (Less)
Please use this url to cite or link to this publication:
https://lup.lub.lu.se/record/429c8c15-a79e-4336-a706-dd9a25d18de5
- author
- Jacobsen Ellerstrand, Simon
LU
- supervisor
- opponent
-
- Docent Martin, Simon, University of Edinburgh, Institute of Ecology and Evolution, Ashworth Laboratories
- organization
- publishing date
- 2026-09-15
- type
- Thesis
- publication status
- published
- subject
- keywords
- sex chromosome evolution, recombination cessation, evolutionary strata, bioinformatic pipeline, Y/W degeneration, faster-X/Z effect, population genomics, mutational load, conservation genomics, speciation, large-X/Z effect, local adaptation, genome evolution, repeated evolution, sexual dimorphism, life-history variation
- pages
- 316 pages
- publisher
- Lund University (Media-Tryck)
- defense location
- Blå Hallen, Ekologihuset
- defense date
- 2026-10-09 09:00:00
- ISBN
- 978-91-90202-94-4
- 978-91-90202-93-7
- project
- The accumulation of genetic load in shared and sex-specific genes in declining species: the largest know avian sex chromosomes and haplodiploid bumblebees
- High-quality reference genomes of the largest known avian sex chromosome, and declining bumblebee species
- Evolutionary and ecological consequences of genetic sex determination
- language
- English
- LU publication?
- yes
- id
- 429c8c15-a79e-4336-a706-dd9a25d18de5
- date added to LUP
- 2026-09-15 11:26:08
- date last changed
- 2026-09-16 11:59:11
@phdthesis{429c8c15-a79e-4336-a706-dd9a25d18de5,
abstract = {{Females and males are alternative reproductive phenotypes that can differ through striking suites of correlated phenotypic traits, such as behaviour, morphology and life-history traits. These sex-specific adaptations are sometimes facilitated through supergenes — sex chromosomes — which link sexually antagonistic alleles and the sex-determining locus into sex-specific haplotypes. However, recombination cessation reduces the ability of selection to maintain sex-limited Y/W haplotypes, often leading to progressive Y/W degeneration and fitness consequences for the heterogametic sex (male XY or female ZW). Despite their acknowledged importance in adaptation, life-history variation and speciation, sex chromosomes remain understudied in many areas of evolutionary ecology. Recent advances in DNA sequencing technology and sequencing initiatives have accumulated evidence that sex chromosome systems across the tree of life vary extensively in age, turnover, evolutionary transitions, autosomal fusions and stratum formation. Thus, now is an ideal time for biologists to investigate the role of sex chromosomes in evolutionary ecology. In this thesis, I studied sex chromosomes in larks (Alaudidae). Several autosomal translocations with subsequent recombination cessation in larks have resulted in greatly expanded neo-sex chromosomes. This system, with multiple evolutionary strata formed at different times, provides a powerful framework for studying different stages of sex chromosome evolution and for performing comparative analyses. I developed a bioinformatic pipeline that extracts Y/W sequences from short-read data, which enabled me to address questions regarding sex chromosome evolution and its role in evolutionary ecology. I studied Z–W gametolog evolution to characterise the longevity and functional role of W chromosomes under extreme demographic scenarios, and dissected the faster-Z effect using a gametolog-level approach. I studied sex chromosomes during speciation, characterising the evolutionary history of a large recombination-cessation polymorphism, and described factors influencing introgression across the Z chromosome. I studied the predictability of sex chromosome evolution and found that several gene properties predict gametolog co-evolution. I characterised remarkable variation in recombination cessation among lark species, with repeated formation of evolutionary strata, linking this variation to sexual dimorphism, pace-of-life strategy, and IUCN Red List status. Taken together, this thesis provides the first chromosome-level genome assembly for larks and lays a foundation for using larks as a model system to study sex chromosomes in evolutionary ecology.}},
author = {{Jacobsen Ellerstrand, Simon}},
isbn = {{978-91-90202-94-4}},
keywords = {{sex chromosome evolution; recombination cessation; evolutionary strata; bioinformatic pipeline; Y/W degeneration; faster-X/Z effect; population genomics; mutational load; conservation genomics; speciation; large-X/Z effect; local adaptation; genome evolution; repeated evolution; sexual dimorphism; life-history variation}},
language = {{eng}},
month = {{09}},
publisher = {{Lund University (Media-Tryck)}},
school = {{Lund University}},
title = {{Evolutionary ecology of avian neo-sex chromosomes}},
url = {{https://lup.lub.lu.se/search/files/260855187/Avhandling_Simon_Jacobsen_Ellerstrand_LUCRIS.pdf}},
year = {{2026}},
}