RT Journal
A1 Li, Gang
A1 Davis, Brian
A1 Raudsepp, Terje
A1 Pearks Wilkerson, Alison
A1 Mason, Victor
A1 Ferguson-Smith, Malcolm
A1 O'Brien, Patricia
A1 Waters, Paul
A1 Murphy, William J
T1 Comparative analysis of mammalian Y chromosomes illuminates ancestral structure and lineage-specific evolution
JF Genome Research 
JO Genome Research 
YR 2013 
FD June 20 
DO 10.1101/gr.154286.112 
SP gr.154286.112 
UL http://genome.cshlp.org/content/early/2013/06/19/gr.154286.112.abstract 
AB Although more than thirty mammalian genomes have been sequenced to draft quality, very few of these include the Y chromosome. This has limited our understanding of the evolutionary dynamics of gene persistence and loss, our ability to identify conserved regulatory elements, as well our knowledge of the extent to which different types of selection act to maintain genes within this unique genomic environment. Here we present the first MSY (male-specific region of the Y chromosome) sequences from two carnivores, the domestic dog and cat. By combining these with other available MSY data, our multi-ordinal comparison allows for the first accounting of levels of selection constraining the evolution of eutherian Y chromosomes. Despite gene gain and loss across the phylogeny, we show the eutherian ancestor retained a core set of 15 MSY genes, most being constrained by negative selection for nearly 100 million years (My). The X-degenerate and ampliconic gene classes are partitioned into distinct chromosomal domains in most mammals, but were radically restructured on the human lineage. We identified multiple conserved non-coding elements that potentially regulate eutherian MSY genes. The acquisition of novel ampliconic gene families was accompanied by signatures of positive selection, and has differentially impacted the degeneration and expansion of MSY gene repertoires in different species.