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Levels of linkage disequilibrium in a wild bird population
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. (Molecular Evolution)
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. (Zooekologi)ORCID iD: 0000-0002-1178-4053
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. (Zooekologi)
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. (Molecular Evolution)
2006 (English)In: Biology Letters, ISSN 1744-9561, E-ISSN 1744-957X, Vol. 2, no 3, 435-438 p.Article in journal (Refereed) Published
Abstract [en]

Population-based mapping approaches are attractive for tracing the genetic background to phenotypic traits in wild species, given that it is often difficult to gather extensive and well-defined pedigrees needed for quantitative trait locus analysis. However, the feasibility of association or hitch-hiking mapping is dependent on the degree of linkage disequilibrium. (LD) in the population, on which there is yet limited information for wild species. Here we use single nucleotide polymorphism (SNP) markers from 23 genes in a recently established linkage map of the Z chromosome of the collared flycatcher, to study the extent of LD in a natural bird population. In most but not all cases we find SNPs within the same intron (less than 500 bp) to be in perfect LD. However, LD then decays to background level at a distance 1 cM or 400-500 kb. Although LD seems more extensive than in other species, if the observed pattern is representative for other regions of the genome and turns out to be a general feature of natural bird populations, dense marker maps might be needed for genome scans aimed at identifying association between marker and trait loci.

Place, publisher, year, edition, pages
2006. Vol. 2, no 3, 435-438 p.
Keyword [en]
collared flycatcher, recombination, Z chromosome
National Category
Biological Sciences
Identifiers
URN: urn:nbn:se:uu:diva-97943DOI: 10.1098/rsbl.2006.0507ISI: 000241863400032PubMedID: 17148424OAI: oai:DiVA.org:uu-97943DiVA: diva2:173069
Available from: 2008-12-22 Created: 2008-12-22 Last updated: 2016-03-07
In thesis
1. Gene Mapping in Ficedula Flycatchers
Open this publication in new window or tab >>Gene Mapping in Ficedula Flycatchers
2009 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

In order to get full understanding of how evolution proceeds in natural settings it is necessary to reveal the genetic basis of the phenotypic traits that play a role for individual fitness in different environments. There are a few possible approaches, most of which stem from traditional mapping efforts in domestic animals and other model species. Here we set the stage for gene mapping in natural populations of birds by producing a large number of anchor markers of broad utility for avian genetical research and use these markers to generate a genetic map of the collared flycatcher (Ficedula albicollis). The map reveals a very high degree of synteny and gene order conservation between bird species separated by as much as 100 million years. This is encouraging for later stages of mapping procedures in natural populations since this means that there is a possibility to use the information from already characterized avian genomes to track candidate genes for detailed analysis in non-model species. One interesting aspect of the low degree of rearrangements occurring in the avian genomes is that this could play a role in the low rate of hybridization barriers formed in birds compared to for instance mammals. An analysis of Z-linked gene markers reveals relatively long-range linkage disequilibrium (LD) in collared flycatchers compared to other outbred species but still, LD seems to decay within < 50 kb indicating that > 20.000 markers would be needed to cover the genome in an association scan. A detailed scan of 74 Z-linked genes evenly distributed along the chromosome in both the collared flycatcher and the pied flycatcher (Ficedula hypoleuca) indicates that there are regions that evolve under directional selection, regions that might harbor loci of importance for adaptive divergence and/or hybrid inviability.

Place, publisher, year, edition, pages
Uppsala: Universitetsbiblioteket, 2009. 82 p.
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 587Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 587
Keyword
collared flycatcher, SNP, linkage disequilibrium, genetic map, pedigree
Identifiers
urn:nbn:se:uu:diva-9513 (URN)978-91-554-7380-8 (ISBN)
Public defence
2009-01-16, Zootissalen, EBC, Villavägen 9, Uppsala, 09:00
Opponent
Supervisors
Available from: 2008-12-22 Created: 2008-12-22 Last updated: 2011-02-24Bibliographically approved

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Backström, NiclasQvarnström, AnnaGustafsson, LarsEllegren, Hans

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