Gene family amplification facilitates adaptation in freshwater Unionid bivalve Megalonaias nervosa

As organisms are faced with intense rapidly changing selective pressures, new genetic material is required to facilitate adaptation. Among sources of genetic novelty, gene duplications and transposable elements (TEs) offer new genes or new regulatory patterns that can facilitate evolutionary change. With advances in genome sequencing it is possible to gain a broader view of how gene family proliferation and TE content evolve in non-model species when populations become threatened. Freshwater bivalves (Unionidae) currently face severe anthropogenic challenges. Over 70% of species in the United States are threatened, endangered or extinct due to pollution, damming of waterways, and overfishing. We have created a reference genome for M. nervosa to determine how genome content has evolved in the face of these widespread environmental challenges. We observe a burst of recent transposable element proliferation causing a 382 Mb expansion in genome content. Gene family expansion is common, with a duplication rate of 1.16 x 10^-8 per gene per generation. Cytochrome P450, ABC transporters, Hsp70 genes, von Willebrand proteins, chitin metabolism genes, mitochondria eating proteins, and opsin gene families have experienced significantly greater amplification and show signatures of selection. We use evolutionary theory to assess the relative contribution of SNPs and duplications in evolutionary change. Estimates suggest that gene family evolution may offer an exceptional substrate of genetic variation in M. nervosa, with Psgv=0.185 compared with Psgv=0.067 for single nucleotide changes. Hence, we suggest that gene family evolution is a source of "hopeful monsters" within the genome that facilitate adaptation.