Characterization of a divergent chromosome region in the willow warbler Phylloscopus trochilus using avian genomic resources.
(2011) In Journal of evolutionary biology 24. p.1241-1253- Abstract
- Genome scans have made it possible to find outlier markers thought to have been influenced by divergent selection in almost any wild population. However, the lack of genomic information in nonmodel species often makes it difficult to associate these markers with certain genes or chromosome regions. Furthermore, the extent of linkage disequilibrium (LD) in the genome will determine the density of markers required to identify the genes under selection. In this study, we investigated a chromosome region in the willow warbler Phylloscopus trochilus surrounding a single marker previously identified in a genome scan. We first located the marker in the assembled genome of another species, the zebra finch Taeniopygia guttata, and amplified... (More)
- Genome scans have made it possible to find outlier markers thought to have been influenced by divergent selection in almost any wild population. However, the lack of genomic information in nonmodel species often makes it difficult to associate these markers with certain genes or chromosome regions. Furthermore, the extent of linkage disequilibrium (LD) in the genome will determine the density of markers required to identify the genes under selection. In this study, we investigated a chromosome region in the willow warbler Phylloscopus trochilus surrounding a single marker previously identified in a genome scan. We first located the marker in the assembled genome of another species, the zebra finch Taeniopygia guttata, and amplified surrounding sequences in Fennoscandian willow warblers. Within an investigated chromosome region of 7.3 Mb as mapped to the zebra finch genome, we observed elevated genetic differentiation between a southern and a northern population across a 2.5-Mb interval comprising numerous coding genes. Within the southern and northern populations, higher values of LD were mostly found between SNPs within the same locus, but extended across distantly situated loci when the analyses were restricted to sampling sites showing intermediate allele frequencies of southern and northern alleles. Our study shows that cross-species genome information is a useful resource to obtain candidate sequences adjacent to outlier markers in nonmodel species. (Less)
Please use this url to cite or link to this publication:
https://lup.lub.lu.se/record/1883766
- author
- Lundberg, Max LU ; Åkesson, Susanne LU and Bensch, Staffan LU
- organization
- publishing date
- 2011
- type
- Contribution to journal
- publication status
- published
- subject
- keywords
- adaptive divergence, barrier to gene flow, hybrid zone, linkage disequilibrium, Phylloscopus, zebra finch genome
- in
- Journal of evolutionary biology
- volume
- 24
- pages
- 1241 - 1253
- publisher
- John Wiley & Sons Inc.
- external identifiers
-
- wos:000290313500009
- scopus:79955659486
- pmid:21418120
- ISSN
- 1420-9101
- DOI
- 10.1111/j.1420-9101.2011.02259.x
- project
- Genetics of migration
- language
- English
- LU publication?
- yes
- id
- bc205c53-5a14-4f83-8ba5-41417d7a8d68 (old id 1883766)
- date added to LUP
- 2016-04-01 09:51:05
- date last changed
- 2022-01-25 17:18:43
@article{bc205c53-5a14-4f83-8ba5-41417d7a8d68,
abstract = {{Genome scans have made it possible to find outlier markers thought to have been influenced by divergent selection in almost any wild population. However, the lack of genomic information in nonmodel species often makes it difficult to associate these markers with certain genes or chromosome regions. Furthermore, the extent of linkage disequilibrium (LD) in the genome will determine the density of markers required to identify the genes under selection. In this study, we investigated a chromosome region in the willow warbler Phylloscopus trochilus surrounding a single marker previously identified in a genome scan. We first located the marker in the assembled genome of another species, the zebra finch Taeniopygia guttata, and amplified surrounding sequences in Fennoscandian willow warblers. Within an investigated chromosome region of 7.3 Mb as mapped to the zebra finch genome, we observed elevated genetic differentiation between a southern and a northern population across a 2.5-Mb interval comprising numerous coding genes. Within the southern and northern populations, higher values of LD were mostly found between SNPs within the same locus, but extended across distantly situated loci when the analyses were restricted to sampling sites showing intermediate allele frequencies of southern and northern alleles. Our study shows that cross-species genome information is a useful resource to obtain candidate sequences adjacent to outlier markers in nonmodel species.}},
author = {{Lundberg, Max and Åkesson, Susanne and Bensch, Staffan}},
issn = {{1420-9101}},
keywords = {{adaptive divergence; barrier to gene flow; hybrid zone; linkage disequilibrium; Phylloscopus; zebra finch genome}},
language = {{eng}},
pages = {{1241--1253}},
publisher = {{John Wiley & Sons Inc.}},
series = {{Journal of evolutionary biology}},
title = {{Characterization of a divergent chromosome region in the willow warbler Phylloscopus trochilus using avian genomic resources.}},
url = {{http://dx.doi.org/10.1111/j.1420-9101.2011.02259.x}},
doi = {{10.1111/j.1420-9101.2011.02259.x}},
volume = {{24}},
year = {{2011}},
}