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Characterization of a divergent chromosome region in the willow warbler Phylloscopus trochilus using avian genomic resources.

Lundberg, Max LU ; Åkesson, Susanne LU and Bensch, Staffan LU (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)
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author
organization
publishing date
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
external identifiers
  • wos:000290313500009
  • scopus:79955659486
ISSN
1420-9101
DOI
10.1111/j.1420-9101.2011.02259.x
project
CAnMove
language
English
LU publication?
yes
id
bc205c53-5a14-4f83-8ba5-41417d7a8d68 (old id 1883766)
date added to LUP
2011-04-11 13:20:31
date last changed
2017-04-23 03:01:05
@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},
  keyword      = {adaptive divergence,barrier to gene flow,hybrid zone,linkage disequilibrium,Phylloscopus,zebra finch genome},
  language     = {eng},
  pages        = {1241--1253},
  publisher    = {John Wiley & Sons},
  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},
  volume       = {24},
  year         = {2011},
}