Exploring the genomic landscape of gene flow between willow warblers (Phylloscopus trochilus) and chiffchaffs (P. collybita)
(2019) BINP50 20191Degree Projects in Bioinformatics
- Abstract
- Hybridisation and subsequent backcrossing allows alleles to migrate between populations in a process known as ‘gene flow’. This provides an alternative source of new alleles for a population, meaning that gene flow can give rise to new adaptive phenotypes. Consequently, to understand the evolution of a given phenotype, the possibility that the underlying alleles have been introgressed from another population must be considered. Here I show that the willow warbler (P. trochilus), which is a model system for investigating the genetic basis of migratory phenotypes, has undergone a period of ancient gene flow with the common chiffchaff (P. collybita). At regions of the genome containing polymorphic chromosomal rearrangements associated with... (More)
- Hybridisation and subsequent backcrossing allows alleles to migrate between populations in a process known as ‘gene flow’. This provides an alternative source of new alleles for a population, meaning that gene flow can give rise to new adaptive phenotypes. Consequently, to understand the evolution of a given phenotype, the possibility that the underlying alleles have been introgressed from another population must be considered. Here I show that the willow warbler (P. trochilus), which is a model system for investigating the genetic basis of migratory phenotypes, has undergone a period of ancient gene flow with the common chiffchaff (P. collybita). At regions of the genome containing polymorphic chromosomal rearrangements associated with migratory phenotypes, I found that the rate of gene flow between P. trochilus and P. collybita varied depending on the P. trochilus subspecies analysed, demonstrating that recombination suppression has resulted in differential gene flow at these regions. Additionally, one of these chromosomal rearrangements, which is currently polymorphic within P. trochilus, shows high genetic divergence between P. trochilus and P. collybita, thus suggesting that this region may have acted as a barrier to gene flow during the early stages of speciation. My results add to a growing body of work showing that both chromosomal rearrangements and gene flow are important processes in evolution that often interact. While the exact genetic mechanisms underlying migration remain elusive, this work provides valuable context to their evolution in a model system. (Less)
- Popular Abstract
- Ancient hybridisation between willow warblers and chiffchaffs
The species on earth today have each been shaped by their own unique evolutionary history. This means that the characteristics of a species often have their roots in events that happened thousands or millions of years ago. In my thesis, I investigated whether the evolution of willow warblers (Phylloscopus trochilus) has been shaped an ancient period hybridisation with another species.
Willow warblers and common chiffchaffs (P. collybita) are species of migratory songbirds that diverged from one another approximately 5 million years ago (Mya). Willow warbler individuals vary in their appearance (plumage and wing length) and migratory behavior, and have consequently been... (More) - Ancient hybridisation between willow warblers and chiffchaffs
The species on earth today have each been shaped by their own unique evolutionary history. This means that the characteristics of a species often have their roots in events that happened thousands or millions of years ago. In my thesis, I investigated whether the evolution of willow warblers (Phylloscopus trochilus) has been shaped an ancient period hybridisation with another species.
Willow warblers and common chiffchaffs (P. collybita) are species of migratory songbirds that diverged from one another approximately 5 million years ago (Mya). Willow warbler individuals vary in their appearance (plumage and wing length) and migratory behavior, and have consequently been delimited into subspecies. While these differences may have evolved within the species, it is also possible that gene copies (alleles) from the common chiffchaff may have moved into the willow warbler population through hybridisation, causing this variation. Although the two species do not hybridise today, signals of ancient hybridisation would persist in the DNA of either species.
I used whole genome DNA sequences from multiple individuals to look for evidence of hybridisation between the species. This involved modelling when the two species separated and whether there was hybridised after this time. I also tested whether regions in the willow warbler genome associated with subspecies shared more/less genetic variants with the common chiffchaff depending on the subspecies analysed. This was done to test whether the willow warbler subspecies had been affected differently by hybridisation with the common chiffchaff.
A history of ancient hybridisation and uneven gene sharing
I found that the two species separated approximately 3 Mya (more recently than previously thought) and that alleles moved between them for another 2 million years, suggesting that hybridisation was frequent. At the genomic regions associated with willow warbler subspecies, the common chiffchaff often shares more genetic variants with one subspecies than the other. This result is consistent with chromosomal rearrangements stopping alleles from moving from the common chiffchaff to just one of the willow warbler subspecies. While my results do not conclusively show that the regions separating willow warbler subspecies came from hybridisation with the common chiffchaff, they do demonstrate that gene sharing with the subspecies has been uneven. Given that the willow warbler subspecies are a model system for understanding the evolution of divergent migratory behaviour, I am hopeful that my results will provide valuable information that can be used in future studies.
Master’s Degree Project in Bioinformatics 30 credits 2019
Department of Biology, Lund University
Advisors: Staffan Bensch and Max Lundberg
Molecular Ecology (Less)
Please use this url to cite or link to this publication:
http://lup.lub.lu.se/student-papers/record/8995376
- author
- Mackintosh, Alexander
- supervisor
-
- Staffan Bensch LU
- Max Lundberg LU
- organization
- course
- BINP50 20191
- year
- 2019
- type
- H2 - Master's Degree (Two Years)
- subject
- language
- English
- id
- 8995376
- date added to LUP
- 2019-09-19 08:44:52
- date last changed
- 2019-09-19 08:44:52
@misc{8995376,
abstract = {{Hybridisation and subsequent backcrossing allows alleles to migrate between populations in a process known as ‘gene flow’. This provides an alternative source of new alleles for a population, meaning that gene flow can give rise to new adaptive phenotypes. Consequently, to understand the evolution of a given phenotype, the possibility that the underlying alleles have been introgressed from another population must be considered. Here I show that the willow warbler (P. trochilus), which is a model system for investigating the genetic basis of migratory phenotypes, has undergone a period of ancient gene flow with the common chiffchaff (P. collybita). At regions of the genome containing polymorphic chromosomal rearrangements associated with migratory phenotypes, I found that the rate of gene flow between P. trochilus and P. collybita varied depending on the P. trochilus subspecies analysed, demonstrating that recombination suppression has resulted in differential gene flow at these regions. Additionally, one of these chromosomal rearrangements, which is currently polymorphic within P. trochilus, shows high genetic divergence between P. trochilus and P. collybita, thus suggesting that this region may have acted as a barrier to gene flow during the early stages of speciation. My results add to a growing body of work showing that both chromosomal rearrangements and gene flow are important processes in evolution that often interact. While the exact genetic mechanisms underlying migration remain elusive, this work provides valuable context to their evolution in a model system.}},
author = {{Mackintosh, Alexander}},
language = {{eng}},
note = {{Student Paper}},
title = {{Exploring the genomic landscape of gene flow between willow warblers (Phylloscopus trochilus) and chiffchaffs (P. collybita)}},
year = {{2019}},
}