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A Gene-Based Genetic Linkage Map of the Collared Flycatcher (Ficedula albicollis) Reveals Extensive Synteny and Gene-Order Conservation During 100 Million Years of Avian Evolution
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
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2008 (English)In: Genetics, ISSN 0016-6731, E-ISSN 1943-2631, Vol. 179, 1479-1495 p.Article in journal (Refereed) Published
Abstract [en]

By taking advantage of a recently developed reference markerset for avian genome analysis we have constructed a gene-basedgenetic map of the collared flycatcher, an important "ecologicalmodel" for studies of life-history evolution, sexual selection,speciation, and quantitative genetics. A pedigree of 322 birdsfrom a natural population was genotyped for 384 single nucleotidepolymorphisms (SNPs) from 170 protein-coding genes and 71 microsatellites.Altogether, 147 gene markers and 64 microsatellites form 33linkage groups with a total genetic distance of 1787 cM. Malerecombination rates are, on average, 22% higher than femalerates (total distance 1982 vs. 1627 cM). The ability to anchorthe collared flycatcher map with the chicken genome via thegene-based SNPs revealed an extraordinary degree of both syntenyand gene-order conservation during avian evolution. The greatmajority of chicken chromosomes correspond to a single linkagegroup in collared flycatchers, with only a few cases of inter-and intrachromosomal rearrangements. The rate of chromosomaldiversification, fissions/fusions, and inversions combined isthus considerably lower in birds (0.05/MY) than in mammals (0.6–2.0/MY).A dearth of repeat elements, known to promote chromosomal breakage,in avian genomes may contribute to their stability. The degreeof genome stability is likely to have important consequencesfor general evolutionary patterns and may explain, for example,the comparatively slow rate by which genetic incompatibilityamong lineages of birds evolves.

Place, publisher, year, edition, pages
2008. Vol. 179, 1479-1495 p.
National Category
Biological Sciences
URN: urn:nbn:se:uu:diva-97942DOI: 10.1534/genetics.108.088195ISI: 000258313400028OAI: oai:DiVA.org:uu-97942DiVA: diva2:173068
Available from: 2008-12-22 Created: 2008-12-22 Last updated: 2016-04-15
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.
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
collared flycatcher, SNP, linkage disequilibrium, genetic map, pedigree
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
Available from: 2008-12-22 Created: 2008-12-22 Last updated: 2011-02-24Bibliographically approved

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Backström, NiclasGustafsson, LarsQvarnström, AnnaEllegren, Hans
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Evolutionary BiologyAnimal ecologyDepartment of Evolution, Genomics and Systematics
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