The quest for Y‐chromosomal markers – methodological strategies for mammalian non‐model organisms

Abstract

Tracing maternal and paternal lineages independently to explore breeding systems and dispersal strategies in natural populations has been high on the wish-list of evolutionary biologists. 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 populations 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 currently 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.

Development of Y-chromosomal Polymorphic Markers in Two Gibbon Species （<i>Hylobates lar and Hylobates pileatus</i>）

“…The application of the Y-chromosomal markers developed in this study will help us to uncover the genetic diversity of these two gibbon species. [6,7]. A distinctive structure and a low genetic variability in the Y-chromosome made it difficult to establish useful markers in many animal species [6].…”

“…Haploidy of Y-chromosomal markers are advantageous in their absence of null alleles and genotyping errors derived from allelic dropouts that are problematic for autosomal markers [5]. Despite these advantages, Y-chromosomal markers have been thus far developed for only a limited number of taxa [6,7]. A distinctive structure and a low genetic variability in the Y-chromosome made it difficult to establish useful markers in many animal species [6].…”

“…Despite these advantages, Y-chromosomal markers have been thus far developed for only a limited number of taxa [6,7]. A distinctive structure and a low genetic variability in the Y-chromosome made it difficult to establish useful markers in many animal species [6]. In the gibbons, a small number of Y-chromosomal single nucleotide polymorphisms/ variants (SNPs/SNVs) were reported in a phylogenetic study [8], but most of them were inter-species variants and its power of detecting intra-species differences was limited (e.g.…”

Discovery of lost diversity of paternal horse lineages using ancient DNA

“…However, very few Y chromosome studies have focused on non-model taxa. This may in part be due to challenges associated with developing Y chromosomal markers which include a proliferation of repeat elements and the low genetic diversity characteristic of the Y chromosome 2 .…”

Sex-linked and autosomal microsatellites provide new insights into island populations of the tammar wallaby

“…Further, sex-linked microsatellites have the potential to illuminate patterns of sex-biased dispersal: previously their application to this field was limited by the poor availability of variable sex chromosome markers for non-model species (Prugnolle and de Meeus, 2002), but the application of sex-linked microsatellites to studies of sex-biased dispersal is becoming more common (Li and Merila, 2010;Yannic et al, 2012). Importantly, large-scale genome sequencing efforts targeting an ever-wider range of species (Genome 10K Community of Scientists, 2009) are likely to enable the development of sex chromosome markers for non-model organisms (Greminger et al, 2010) bringing the analysis of sex chromosomes for many mammals within grasp.…”