Convergent evolution, the repeated evolution of the same phenotype in independent lineages, is often caused by the same types of mutations at the same genes. Why are there such “hotspot mutations”? One possible cause is that a specific genomic site is highly mutagenic and therefore has a high chance to be captured by natural selection. This hypothesis is rarely tested in convergent evolution of natural systems except in a few cases.
Three-spined stickleback (Gasterosteus aculeatus) fish is widely distributed in the temperate zone of the Northern Hemisphere. Marine ancestors have colonized and rapidly adapted to freshwater habitats recurrently and independently in different continents. This system serves as a good model for studying convergent adaptive evolution. A previous study showed that multiple freshwater populations increased the copy number of the Fatty acid desaturase 2 (Fads2) gene, which encodes an enzyme involved in the synthesis of a polyunsaturated fatty acid, docosahexaenoic acid (DHA). A higher copy number of this gene is adaptive in freshwater fish to cope with low DHA food sources in freshwater habitats.
To elucidate how such copy number variations arise, we analyzed de novo genome assembly of multiple stickleback populations that are recently constructed in our lab. A dot plot analysis of the genomic regions around the Fads2 copy revealed repetitive sequences and palindrome-like structures between Fads2 copies on Chromosome 19 of all the populations that have at least two Fads2 copies on Chromosome 19. These repetitive sequences are similar between populations, suggesting that the Fads2 CNV may be caused by a similar mechanism. These repetitive sequences are composites of several fragmented transposons, including the DNA transposons Helitron-1 and EnSpm1. These sequences are inferred to make non-B DNA structures., such as G-quadruplex motifs, short tandem repeats, and slipped motifs. Because non-B DNA structures can cause stalling of DNA replication and induce replication errors, we hypothesized that these may make this region highly mutagenic and make it easy to increase or decrease the copy number rapidly. Further investigation of these repetitive sequences will give insights into the mechanisms causing recurrent copy number changes.