Genome evolution in an endangered freshwater mussel

Nearly neutral theory predicts that evolutionary processes will differ in small populations compared to large populations, a key point of concern for endangered species. The nearly-neutral threshold, the span of neutral variation, and the adaptive potential from new mutations all differ depending on N_e. To determine how genomes respond in small populations, we have created a reference genome for a US federally endangered IUCN Red List freshwater mussel, Elliptio spinosa, and compare it to genetic variation for a common and successful relative, Elliptio crassidens. We find higher rates of background duplication rates in E. spinosa consistent with proposed theories of duplicate gene accumulation according to nearly-neutral processes. Along with these changes we observe fewer cases of adaptive gene family amplification in this endangered species. However, TE content is not consistent with nearly-neutral theory. We observe substantially less recent TE proliferation in the endangered species with over 500 Mb of newly copied TEs in Elliptio crassidens. These results suggest a more complex interplay between TEs and duplicate genes than previously proposed for small populations. They further suggest that TEs and duplications require greater attention in surveys of genomic health for endangered species.