  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.
