No evidence for Z-chromosome rearrangements between the pied flycatcher and the collared flycatcher as judged by gene-based comparative genetic maps NICLAS BACKSTRO ¨ M,* ELEFTHERIA PALKOPOULOU,* ANNA QVARNSTRO ¨ M† and HANS ELLEGREN* *Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyva ¨gen 18D, SE-752 36 Uppsala, Sweden, †Department of Animal Ecology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala, Sweden Abstract Revealing the genetic basis of reproductive isolation is fundamental for understanding the speciation process. Chromosome speciation models propose a role for chromosomal rearrangements in promoting the build up of reproductive isolation between diverging populations and empirical data from several animal and plant taxa support these models. The pied flycatcher and the collared flycatcher are two closely related species that probably evolved reproductive isolation during geographical separation in Pleistocene glaciation refugia. Despite the short divergence time and current hybridization, these two species demonstrate a high degree of intrinsic post-zygotic isolation and previous studies have shown that traits involved in mate choice and hybrid viability map to the Z-chromosome. Could rearrangements of the Z-chromosome between the species explain their reproductive isolation? We developed high coverage Z-chromosome linkage maps for both species, using gene-based markers and large-scale SNP genotyping. Best order maps contained 57–62 gene markers with an estimated average density of one every 1–1.5 Mb. We estimated the recombination rates in flycatcher Z-chromosomes to 1.1–1.3 cM ⁄ Mb. A comparison of the maps of the two species revealed extensive co-linearity with no strong evidence for chromosomal rearrangements. This study does therefore not provide support the idea that sex chromosome rearrangements have caused the relatively strong post-zygotic reproductive isolation between these two Ficedula species. Keywords: chromosomal speciation, Ficedula, flycatcher, linkage mapping, sex chromosomes Received 11 February 2010; revision received 16 April 2010; accepted 27 April 2010 Introduction The observation that closely related species sometimes show differences in karyotype structure has lead to hypotheses suggesting a role for chromosomal rear- rangements in the speciation process. Two main models have been proposed, the ‘underdominance model’ and the ‘suppression of recombination model’ (Hoffman & Rieseberg 2008). The underdominance model postulates that the chromosome rearrangements themselves induce hybrid inviability or sterility due to the formation of unbalanced gametes during meiosis. The suppression of recombination model instead proposes an indirect role of chromosome rearrangements. The assumption is that gene combinations that promote reproductive isolation positioned within rearranged regions are masked from gene flow by means of reduced crossing over between, for example, inverted and non-inverted segments (But- lin 2005; Hoffman & Rieseberg 2008). Empirical data support the idea that chromosome rearrangements can result in the build-up of reproductive isolation and examples of taxa in which this has been demonstrated include sunflowers, (Helianthus sp.) (Rieseberg 2001; Strasburg et al. 2009), fruitflies (Drosophila sp.) (Noor et al. 2001; Machado et al. 2007), mosquitoes (Anopheles Correspondence: Hans Ellegren, Fax: +46 18 4716310; E-mail: hans.ellegren@ebc.uu.se The authors Niclas Backstro ¨m and Eleftheria Palkopoulou contributed equally to the study. Ó 2010 Blackwell Publishing Ltd Molecular Ecology (2010) 19, 3394–3405 doi: 10.1111/j.1365-294X.2010.04742.x