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Genetics of migration: detection and qPCR- based quantification of transposable elements linked to migratory phenotypes in the willow warbler (Phylloscopus trochilus)

Caballero-López, Violeta (2019) BION02 20182
Degree Projects in Biology
Abstract
The genetics underlying bird migration have been the subject of several studies. Two willow warbler subspecies (Phylloscopus trochilus trochilus and Phylloscopus trochilus acredula) follow different routes during their winter migration to Africa. Their breeding territories overlap in a contact area or “migratory divide” across central Scandinavia and to the east of the Baltic sea. Previous genome-wide analyses have found that the genetic differences between the two subspecies are few and cluster in chromosomes 1 and 5. However, the location of an AFLP-derived biallelic marker (known as WW2) which presents a steep cline along the hybrid zone between these two subspecies failed to be identified in the genome. Here, I investigated the origins... (More)
The genetics underlying bird migration have been the subject of several studies. Two willow warbler subspecies (Phylloscopus trochilus trochilus and Phylloscopus trochilus acredula) follow different routes during their winter migration to Africa. Their breeding territories overlap in a contact area or “migratory divide” across central Scandinavia and to the east of the Baltic sea. Previous genome-wide analyses have found that the genetic differences between the two subspecies are few and cluster in chromosomes 1 and 5. However, the location of an AFLP-derived biallelic marker (known as WW2) which presents a steep cline along the hybrid zone between these two subspecies failed to be identified in the genome. Here, I investigated the origins of WW2 and I characterised its two variants as portions of LTR (long terminal repeat) retrotransposons which result from an ancient infection by an endogenous retrovirus (ERV). I used qPCR techniques to quantify the copy number variation (CNV) of the WW2 northern variant across the two subspecies and F2 hybrids. The resulting pattern suggests that WW2 northern variants occur in higher copy numbers in P. t. acredula and seem to be linked to a third divergent chromosome region which remained unnoticed until now. The divergence analysis of both WW2 variants shows that despite their common origins, WW2 northern variants experienced a recent expansion. In contrast, WW2 southern variants display larger diversity and seem to share more similarities with the LTRs found in the zebra finch (Taeniopygia guttata), indicating earlier formation. Although no candidate genes were found in the proximities of the WW2 northern LTRs, their strong linkage to the migratory phenotype and the low diversity of WW2 northern variants, suggests important structural variations that could link these elements with regions involved in the determination of migratory routes. (Less)
Popular Abstract
CAN A VIRUS INFLUENCE MIGRATION?

The willow warbler (Phylloscopus trochilus) is the most common songbird in Sweden and it is widely distributed across Central and Northern Europe to East Siberia. Two of its subspecies differ in their migratory routes to their wintering grounds. P. t. trochilus (south Sweden and central Europe), the ancestral subspecies, migrates to W Africa whereas P. t. acredula (north Scandinavia), the derived subspecies, migrates towards SE Africa in a longer route. There is a region in Central Sweden where both subspecies hybridize. However, the genomes of these two subspecies are very similar. Except for a few regions.

One of these regions was classified as an AFLP-marker (short DNA sequence that helps in... (More)
CAN A VIRUS INFLUENCE MIGRATION?

The willow warbler (Phylloscopus trochilus) is the most common songbird in Sweden and it is widely distributed across Central and Northern Europe to East Siberia. Two of its subspecies differ in their migratory routes to their wintering grounds. P. t. trochilus (south Sweden and central Europe), the ancestral subspecies, migrates to W Africa whereas P. t. acredula (north Scandinavia), the derived subspecies, migrates towards SE Africa in a longer route. There is a region in Central Sweden where both subspecies hybridize. However, the genomes of these two subspecies are very similar. Except for a few regions.

One of these regions was classified as an AFLP-marker (short DNA sequence that helps in discriminating between the two subspecies). P. t. acredula and P. t. trochilus (Figure 1) differ in the length of this marker. Its many copies were widely distributed across the genome of both subspecies, suggesting the role of transposable elements (TEs). Transposable elements are sequences that can replicate themselves and change position within the genome. They usually behave as genomic parasites disrupting host cell’s functioning, but they also play an important role in genome function and evolution. For my project I identified these markers as Class I TEs which derive from a virus that infected the willow warbler genome around 5 million years ago. I also quantified how many of these TEs were present in the genome of both subspecies and tried to locate their exact place in the genome and find any possible link to the determination of migratory routes.

Overall, whereas the ancestral sequence is present in both subspecies, the derived sequence (northern TE) was mainly detected in P. t. acredula (Fig. 2). P. t. acredula presents more copies of the northern TE variant than P. t. trochilus, and hybrid birds present a much more variable copy number than the parental species. Furthermore, some of the pure individuals captured within the hybrid zone present TE copy numbers very similar to hybrids, suggesting that they are not as “pure” as previously thought. However, it is not yet possible to know the exact location of these TEs in the genome of the willow warbler. They could influence the migratory routes of both subspecies in different ways: by direct regulation of nearby genes, chromosomal rearrangements or epistatic interactions (affecting genes that are elsewhere in the genome). This study highlights the important influence of TEs in genome evolution and speciation. For the future it would be very interesting to be able to locate these TEs in the genome and observe direct correlations between TE copy number and migratory routes of hybrid birds and pure subspecies.

Master’s Degree project in Biology, Animal Ecology. 45 credits. 2019
Department of Biology, Lund University

Supervisor: Staffan Bensch
Department of Biology (Less)
Please use this url to cite or link to this publication:
author
Caballero-López, Violeta
supervisor
organization
course
BION02 20182
year
type
H2 - Master's Degree (Two Years)
subject
language
English
id
8994929
date added to LUP
2019-09-13 15:50:15
date last changed
2019-09-13 15:50:15
@misc{8994929,
  abstract     = {The genetics underlying bird migration have been the subject of several studies. Two willow warbler subspecies (Phylloscopus trochilus trochilus and Phylloscopus trochilus acredula) follow different routes during their winter migration to Africa. Their breeding territories overlap in a contact area or “migratory divide” across central Scandinavia and to the east of the Baltic sea. Previous genome-wide analyses have found that the genetic differences between the two subspecies are few and cluster in chromosomes 1 and 5. However, the location of an AFLP-derived biallelic marker (known as WW2) which presents a steep cline along the hybrid zone between these two subspecies failed to be identified in the genome. Here, I investigated the origins of WW2 and I characterised its two variants as portions of LTR (long terminal repeat) retrotransposons which result from an ancient infection by an endogenous retrovirus (ERV). I used qPCR techniques to quantify the copy number variation (CNV) of the WW2 northern variant across the two subspecies and F2 hybrids. The resulting pattern suggests that WW2 northern variants occur in higher copy numbers in P. t. acredula and seem to be linked to a third divergent chromosome region which remained unnoticed until now. The divergence analysis of both WW2 variants shows that despite their common origins, WW2 northern variants experienced a recent expansion. In contrast, WW2 southern variants display larger diversity and seem to share more similarities with the LTRs found in the zebra finch (Taeniopygia guttata), indicating earlier formation. Although no candidate genes were found in the proximities of the WW2 northern LTRs, their strong linkage to the migratory phenotype and the low diversity of WW2 northern variants, suggests important structural variations that could link these elements with regions involved in the determination of migratory routes.},
  author       = {Caballero-López, Violeta},
  language     = {eng},
  note         = {Student Paper},
  title        = {Genetics of migration: detection and qPCR- based quantification of transposable elements linked to migratory phenotypes in the willow warbler (Phylloscopus trochilus)},
  year         = {2019},
}