Comparing the retention mechanisms of tandem duplicates and retrogenes in human and mouse genomes

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.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.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) polyploidization. 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 duplications play significant roles in the evolution of various organisms [5]. Although the molecular basis of gene duplication has been well understood, how the newly created 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 independent dimensions: 1) the extent of functional divergence for the new duplicates, and 2) whether positive (adaptive) selection is involved in the process. The outcomes of functional divergence are usually classified as gene conservation, subfunctionalization and neofunctionalization [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 analy