View Program - 2022 Population, Evolutionary, and Quantitative Genetics Conference

While the contribution of retrogenes (new genes originated from the reintegration of reverse-transcribed RNA into the genome) to genome evolution and adaptations has long been recognized, the evolutionary patterns of very recently derived gene retrocopies that are still polymorphic within natural populations have not been much studied so far. To trace the evolutionary dynamics of these new gene retrocopies, we use a unique genomic dataset from nine house mouse populations and show the biological effects of these new gene retrocopies from two distinct aspects. In the first study, we show for natural house mouse populations that the primary rate of gene retroposition is orders of magnitude higher than the long-term rate. Comparisons with single-nucleotide polymorphism distribution patterns in the same populations show that most new gene retrocopies are deleterious. Transcriptomic profiling analysis shows that new gene retrocopies become easily subject to transcription and have an influence on the expression levels of their parental genes, especially when transcribed in the antisense direction. While most gene retrocopies are detrimental and quickly purged, we find a subset of them that appears neutral or even adaptive in the second study. We show that gene retrocopies from X-chromosomal parental genes have a higher likelihood of reaching elevated frequencies in the populations, confirming the notion of adaptive effects for “out-of-X” retrogenes. Also, retrocopies in intergenic regions are more likely to achieve higher population frequencies than introns of genes, implying a more detrimental effect when they land within transcribed regions. For a small subset of retrocopies, we find signatures of positive selection, indicating they were involved in a recent adaptation process of these house mouse natural populations. Taken together, these two lines of work represent a comprehensive coverage of the evolutionary dynamics of gene retrocopies in a range of natural populations.

Tracing the evolutionary dynamics of gene retrocopies in house mouse natural populations