INVITED TECHNICAL REVIEW The quest for Y-chromosomal markers – methodological strategies for mammalian non-model organisms MAJA P. GREMINGER,* MICHAEL KRU ¨ TZEN,* CLAUDE SCHELLING,† ALDONA PIENKOWSKA-SCHELLING‡ and PETER WANDELER§ *Anthropological Institute and Museum, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland, †Animal Genetics Group, Vetsuisse-Faculty Zurich, University of Zurich, Tannenstrasse 1, 8092 Zurich, Switzerland, ‡Department of Animal Sciences, Federal Institute of Technology Zurich, Tannenstrasse 1, CH-8092 Zurich, Switzerland, §Zoological Museum, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland Abstract Tracing maternal and paternal lineages independently to explore breeding systems and dis- persal strategies in natural populations has been high on the wish-list of evolutionary biolo- gists. As males are the heterogametic sex in mammals, such sex-specific patterns can be indirectly observed when Y chromosome polymorphism is combined with mitochondrial sequence information. Over the past decade, Y-chromosomal markers applied to human pop- ulations have revealed remarkable differences in the demographic history and behaviour between the sexes. However, with a few exceptions, genetic data tracing the paternal line are lacking in most other mammalian species. This deficit can be attributed to the difficulty of developing Y-specific genetic markers in non-model organisms and the general low levels of polymorphisms observed on the Y chromosome. Here, we present an overview of the cur- rently employed strategies for developing paternal markers in mammals. Moreover, we review the practical feasibility and requirements of various methodological strategies and highlight their future prospects when combined with new molecular techniques such as next generation sequencing. Keywords: cytogenetics , microsatellite, SNPs, sex-biased dispersal, YCATS, Y chromosome Received 5 August 2009; revision received 24 September 2009; accepted 4 October 2009 Introduction Why Y? Females and males do not pass on their genes equally to the next generation in space and time. In birds, for exam- ple, dispersal is mainly female-biased and males are philopatric, resulting in a higher number of female genes being exchanged between populations. Such sex-biased dispersal has profound consequences for the genetic diversity and genetic makeup of natural populations (Handley & Perrin 2007). Information on sex specific dif- ferences in dispersal patterns gathered using autosomal genetic markers is limited to one generation, given that recombination will obscure independent maternal and paternal lineages in the next generation (reviewed in Goudet et al. 2002; Prugnolle & de Meeus 2002). More- over, sex-biased dispersal is currently still assessed quali- tatively rather than quantitatively (Petit et al. 2002). As a consequence, there remains a considerable gap between empirical data and our theoretical understanding of dis- persal strategies in relation to different mating systems and ecological constraints (Handley & Perrin 2007). The independent demographic population history of either sex can be investigated by contrasting chromosome polymorphisms of the heterogametic sex with mitochon- drial DNA (mtDNA) sequence variation, provided that maternally inherited mtDNA is passed on in the homo- gametic sex. In mammals, for instance, males are the Correspondence: Peter Wandeler, Fax: +41 44 635 6818; E-mail: peter.wandeler@access.uzh.ch Ó 2009 Blackwell Publishing Ltd Molecular Ecology Resources (2010) 10, 409–420 doi: 10.1111/j.1755-0998.2009.02798.x