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Originally published as Genetics Published Articles Ahead of Print on June 18, 2006.
Genetics, Vol. 174, 377-386, September 2006, Copyright © 2006
doi:10.1534/genetics.106.058917
Genetic Mapping in a Natural Population of Collared Flycatchers (Ficedula albicollis): Conserved Synteny but Gene Order Rearrangements on the Avian Z Chromosome
Niclas Backström*,
Mikael Brandström*,
Lars Gustafsson
,
Anna Qvarnström,
Hans Cheng
and
Hans Ellegren*,1
* Department of Evolutionary Biology and Department of Animal Ecology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala, Sweden and United States Department of Agriculture, Agricultural Research Service, Avian Disease and Oncology Laboratory, East Lansing, Michigan 48823
1 Corresponding author: Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D SE-752 36 Uppsala, Sweden.
E-mail: hans.ellegren{at}ebc.uu.se
Data from completely sequenced genomes are likely to open the way for novel studies of the genetics of nonmodel organisms, in particular when it comes to the identification and analysis of genes responsible for traits that are under selection in natural populations. Here we use the draft sequence of the chicken genome as a starting point for linkage mapping in a wild bird species, the collared flycatcher—one of the most well-studied avian species in ecological and evolutionary research. A pedigree of 365 flycatchers was established and genotyped for single nucleotide polymorphisms in 23 genes selected from (and spread over most of) the chicken Z chromosome. All genes were also found to be located on the Z chromosome in the collared flycatcher, confirming conserved synteny at the level of gene content across distantly related avian lineages. This high degree of conservation mimics the situation seen for the mammalian X chromosome and may thus be a general feature in sex chromosome evolution, irrespective of whether there is male or female heterogamety. Alternatively, such unprecedented chromosomal conservation may be characteristic of most chromosomes in avian genome evolution. However, several internal rearrangements were observed, meaning that the transfer of map information from chicken to nonmodel bird species cannot always assume conserved gene orders. Interestingly, the rate of recombination on the Z chromosome of collared flycatchers was only 
50% that of chicken, challenging the widely held view that birds generally have high recombination rates.
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