RU T H B . M c C O L E E T A L . endogenous mRNAs of “parent” genes and inserting the cDNA into the genome at a new location (Esnault et al. 2000; Wei et al. 2001). The products of retroposition events often have, in the past, been dismissed as nonfunctional. The term “retrogene” refers to a product of retroposition that generates a functional protein, and so direct evidence of protein function is formally required for a product of a retroposition event to be classified as a retrogene. Retroposition creates an interesting evolutionary scenario for the genes involved. The new gene, in terms of the open reading frame, is often an exact copy of its parent (although retropo- sition can also result in truncation of the open reading frame). Retrogenes may also co-opt existing exons around them to form chimeric genes (Wang et al. 2006; Zhu et al. 2009). What impact has this retroposition process had on the evolution of these genes? Possibilities include neofunctionalization, (Ohno 1970), subfunc- tionalization (Force et al. 1999), and others, reviewed in Conant and Wolfe (2008). Retroposition is akin to gene duplication although the evo- lutionary consequences in terms of rate variation have not been widely studied in the case of retrogenes. There is a conflict in the literature as regards the evolutionary rates of gene duplicates, certain studies conclude that pairs of duplicate genes evolve at different rates, with one gene per pair undergoing changes in function (Zhang et al. 2003; Kellis et al. 2004). Other analyses have concluded that gene duplication has no effect on the rate of evolution of either duplicate (Robinson-Rechavi and Laudet 2001). Additionally, it has been proposed that duplicate genes evolve faster than nonduplicates, but that there is no asymmetry in the rate of evolution between the two duplicates (Kondrashov et al. 2002). In general, gene duplications involving the relocation of a gene duplicate to a new genomic context result in different evolu- tionary rates in those duplicate copies, specifically new duplicates evolve faster than their “parent” genes (Cusack and Wolfe 2007). Retroposition can create this precise scenario as broadly supported Table 1. Information on the retrogenes studied, their “parent” and “host” genes. by analyses of retroposed genes (Gayral et al. 2007). Similarly, genomic context has been found to affect the rate of duplicate gene evolution, both in drosophila (Zhang and Kishino 2004a) and yeast (Zhang and Kishino 2004b). In summary, retrogenes seem to evolve faster than their parent genes, although this reflects broad trends rather than gene-by-gene studies. Here, we present a new case study of the evolution of four retrogenes with similar origins and genomic environments, together with their “parent” genes. We wished to determine if the similar mode of origination of these genes, their shared classification as imprinted, and their similar regulation have all contributed to a similar evolutionary rate variation in these genes. We examine the evolution of the mouse retrogenes Inpp5f_v2, Mcts2, Nap1l5, and U2af1-rs1, or Zrsr1, together with their par- ent genes. All four retrogenes are subject to genomic imprinting (Nabetani et al. 1997; Smith et al. 2003; Choi et al. 2005; Wood et al. 2007). Although direct evidence for functional protein products has yet to be obtained, transcription of these genes occurs in a wide variety of tissues and each contains an intact open reading frame. Imprinted genes are epigenetically marked so that they are exclusively or predominantly expressed from the chromosome of a particular parental origin. The above four genes are exclusively paternally expressed. All four genes possess a CpG island promoter, which is differentially methylated in the gametes (unmethylated in sperm, methylated in oocytes) (Zhang et al. 2006; Wood et al. 2007). Each is located within the intron of a “host” gene (Table 1), and has a parent gene on the X chromosome (reviewed by McCole and Oakey 2008 and Wood and Oakey 2006). Understanding how imprinted genes evolved can inform on their function, which is an important facet of understanding imprinting in general. The parent genes for mouse Inpp5f_v2, Mcts2 and U2af1-rs1 have been identified unambiguously as Tmem114a, Mcts1 (Wood et al. 2007) and U2af1-rs2 or Zrsr2, (Smith et al. 2003) respec- tively. We retain the “U2af1-rs” nomenclature here because of Imprinted retrogene Inpp5f_v2 Mcts2 Nap1l5 U2af1-rs1 (or Zrsr1) Accession number DQ648020 NM_025543 NM_021432 NM_011663 Parent gene Vma21 (or Tmem114a) Mcts1 (or Mct1) Nap1l2 Nap1l3 U2af1-rs2 (or Zrsr2) 1 4 1 4 EVOLUTION MAY 2011 Parent gene accession number BC028317 NM_026902 NM_008671 NM_138742 NM_178754 Position of retrogene in mouse genome build mm9 chr7:135,832,012– 135,832,332 chr2:152,512,884– 152,513,678 chr6:58,855,227– 58,857,120 chr11:22,872,029– 22,874,908 Host gene Inpp5f H13 Herc3 Commd1 (or Murr1) Host intron size (bp) 5,329 2,480 21,751 25,337