Wang et al. Genetics Selection Evolution 2010, 42:24 http://www.gsejournal.org/content/42/1/24 R E S E A R C H G e n e t i c s Se l e c t i o n Ev o l u t i o n Open Access RCesoeamrchparing the retention mechanisms of tandem duplicates and retrogenes in human and mouse genomes Zhen Wang1,2, Xiao Dong1,2, Guohui Ding*1,3 and Yixue Li*1,3 Abstract Background: Multiple models have been proposed to interpret the retention of duplicated genes. In this study, we attempted to compare whether the duplicates arising from tandem duplications and retropositions are retained by the same mechanisms in human and mouse genomes. Results: Both sequence and expression similarity analyses revealed that tandem duplicates tend to be more conserved, whereas retrogenes tend to be more divergent. The duplicability of tandem duplicates is also higher than that of retrogenes. However, positive selection seems to play significant roles in the retention of both types of duplicates. Conclusions: We propose that dosage effect is more prevalent in the retention of tandem duplicates, while 'escape from adaptive conflict' (EAC) effect is more prevalent in the retention of retrogenes. Background Gene duplication is one of the most important sources of genomic novelty and complexity [1]. There are three main molecular mechanisms leading to new duplicates [2,3]: 1) unequal crossing-over during homologous recombination, 2) duplicative transposition at the DNA level and retroposition mediated by mRNA, and 3) poly- ploidization. While polyploidization is characterized by bursts of large-scale genome duplication, the former two processes are often small-scale and proceed continuously [4]. Recently, the investigations of full genome sequences have revealed that both large- and small-scale duplica- tions play significant roles in the evolution of various organisms [5]. Although the molecular basis of gene duplication has been well understood, how the newly cre- ated duplicates are fixed in the population is still quite controversial [6]. Several evolutionary models for this issue have been proposed, and according to the current perspective [3], they can be distinguished from two inde- * Correspondence: gwding@sibs.ac.cn, yxli@sibs.ac.cn 1 Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, PR China 3 Shanghai Center for Bioinformation Technology, 100 Qinzhou Road, Shanghai, PR China Full list of author information is available at the end of the article pendent dimensions: 1) the extent of functional diver- gence for the new duplicates, and 2) whether positive (adaptive) selection is involved in the process. The out- comes of functional divergence are usually classified as gene conservation, subfunctionalization and neofunc- tionalization [2,3], though the definitions for the latter two are often ambiguous. Theoretically, the duplicates can undergo adaptive evolution or neutral genetic drift to achieve each outcome. Statistical analyses on empirical data have suggested that none of the mechanisms alone can interpret the maintenance of all duplicates [3]. However, we suspect that these retention mechanisms may not contribute equally for duplicates stemming from different molecular bases. In fact, by examining the substitution rate between duplicated pairs, Jun et al. [7] have found that retrotrans- posed and interspersed segmental duplicates diverge more quickly than tandem duplicates. To further com- pare the underlying retention mechanisms, we attempted to investigate the tandem duplicates arising from unequal crossing-over and retrogenes arising from retroposition in human and mouse genomes. We chose both types of duplicates because: 1) tandem duplicates and retrogenes are easier to screen, and 2) after ancient large-scale genome duplications at the origin of vertebrates, most © 2010 Wang et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.