Emergence of young human genes after a burst of retroposition in primates

Abstract

The origin of new genes through gene duplication is fundamental to the evolution of lineage- or species-specific phenotypic traits. In this report, we estimate the number of functional retrogenes on the lineage leading to humans generated by the high rate of retroposition (retroduplication) in primates. Extensive comparative sequencing and expression studies coupled with evolutionary analyses and simulations suggest that a significant proportion of recent retrocopies represent bona fide human genes. We estimate that at least one new retrogene per million years emerged on the human lineage during the past approximately 63 million years of primate evolution. Detailed analysis of a subset of the data shows that the majority of retrogenes are specifically expressed in testis, whereas their parental genes show broad expression patterns. Consistently, most retrogenes evolved functional roles in spermatogenesis. Proteins encoded by X chromosome-derived retrogenes were strongly preserved by purifying selection following the duplication event, supporting the view that they may act as functional autosomal substitutes during X-inactivation of late spermatogenesis genes. Also, some retrogenes acquired a new or more adapted function driven by positive selection. We conclude that retroduplication significantly contributed to the formation of recent human genes and that most new retrogenes were progressively recruited during primate evolution by natural and/or sexual selection to enhance male germline function.

Figure 1. K_S Distribution for 3,951 Retrocopies

The peak at K _S ≍ 0.1 suggests a burst of retroposition on the primate lineage (see also text and Figure S1). Retrocopies with K _S > 1 were pooled in a single bin.

Figure 2. K_A /K _S Distributions for 475 Intact Retrocopies and 1,554 Retropseudogenes with K _S < 0.15

Note that we tested that the differences observed for K _A /K _S < 0.5 are not explained by differences in GC content (see Materials and Methods for details). The bin with K _A /K _S > 1.5 includes estimates where K _S = 0 (K _A /K _S = ∞).

Figure 3. Illustration of the Simulation Results Used to Support Functionality of Retrogenes for One Case (RBMXL1)

(A) Distribution of the number of disablements observed in 10⁵ simulations of the RBMXL1 retrogene evolution under neutrality. The frequency distribution of stop codons is shown in white, and that of deleterious indels in black. All of the simulations showed at least one mutation disrupting the ORF (see text); simulations without stop codons all showed several frame-disrupting indels (the minimum number of such indels in each simulation is four). (B) Nonsynonymous (N _A) and synonymous (N _S) substitutions observed in 10⁵ simulations of neutral RBMXL1 retrogene evolution (diamonds). The black square indicates the observed nonsynonymous and synonymous substitutions in the RBMXL1 primate phylogeny. (C) Ratio of nonsynonymous to synonymous substitutions in 10⁵ simulations of RBMXL1 retrogene evolution in the primate lineages. The arrow indicates the observed ratio of nonsynonymous to synonymous substitutions in the RBMXL1 primate phylogeny.

Figure 4. Expression Pattern of Retrogenes and Parents Determined by RT-PCR

Black boxes indicate retrogenes; hatched boxes indicate parental genes. Note that in all cases testis expression of the retrogene was the strongest, as indicated by the semiquantitative PCR procedure (data not shown).

Figure 5. Evidence for Positive Selection on PABP3 Codons

The rectangles correspond to the different domains of the PABP1 protein: RNA poly(A)-tail-binding domains (vertical lines), RNA-binding domains (hatched), protein–protein interaction domain (white), and PABP homo-oligomerization domain (black). Positions of positively selected codons with high posterior probabilities (>0.95) are indicated by arrows.