Transposable elements drive much of naturally occurring genetic lethality in Drosophila melanogaster

Recessive lethal mutations are widespread across studied species, with estimates suggesting that each individual carries at least one. Numerous lethal alleles persist in wild populations at higher frequencies than expected given their extreme deleterious nature. Though these findings spurred historical debate whether classical balancing selection maintains some lethal alleles at elevated frequencies (versus mutation-selection balance acting alone), we propose the question remained unanswered, especially given that the genetic basis of most naturally occurring lethal effects is still unknown. Given current genome-wide point mutation rate estimates, mutation–selection balance alone cannot explain some of this lethal variation in nature. However, evolutionary biologists have historically studied genetic variation through a lens of single nucleotide variants, when in fact the spectrum of mutational changes is far broader than point mutations alone, including indels, structural variants, short tandem repeats, and transposable element insertions. We uncover the genetic basis of lethality in nature and provide insight on the possible evolutionary forces allowing some to persist at higher frequencies. By locating hundreds of recessive lethal mutations in Drosophila melanogaster via complementation testing, fine-mapping, and sequencing a subset, we determine candidate lethal mutations in specific genes. We discover that many lethal disruptions are caused by transposable element insertions, potentially suggesting a higher mutation rate more compatible with mutation-selection balance. The most common transposable element in our data is estimated to have recently invaded D. melanogaster (between 2013-2016). This finding demonstrates that the many lethal alleles studied in D. melanogaster in the last century had a distinct genetic basis. Hence, we propose a model that could explain lethal variation in natural populations of D. melanogaster: lethal mutation frequencies are driven by invasions of new transposable elements and as time passes after each invasion, those frequencies decline as D. melanogaster evolves suppression mechanisms, allowing for natural selection to more efficiently remove lethal insertions. Upon the invasion of a new TE, the cycle repeats. The ubiquity of lethal alleles in natural populations is a classic conundrum for evolutionary geneticists for over a century, and this study utilized modern tools and sequencing technology to provide novel insight into this age-old mystery.