Freshwater unionid bivalves 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. These species are notable for their unusual life history strategy, parasite–host co‐evolution and biparental mitochondrial inheritance. Among this clade, the washboard mussel Megalonaias nervosa is one species that remains prevalent across the Southeastern United States, with robust population sizes. 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 dynamic changes in genome content, with a burst of recent transposable element proliferation causing a 382 Mb expansion in genome content. Birth–death models suggest rapid expansions among gene families, with a mutation rate of 1.16 × 10⁻⁸ duplications per gene per generation. Cytochrome P450 gene families have experienced exceptional recent amplification beyond expectations based on genome‐wide birth–death processes. These genes are associated with increased rates of amino acid changes, a signature of selection driving evolution of detox genes. Fitting evolutionary models of adaptation from standing genetic variation, we can compare adaptive potential across species and mutation types. The large population size in M. nervosa suggests a 4.7‐fold advantage in the ability to adapt from standing genetic variation compared with a low diversity endemic E. hopetonensis. Estimates suggest that gene family evolution may offer an exceptional substrate of genetic variation in M. nervosa, with P_sgv = 0.185 compared with P_sgv = 0.067 for single nucleotide changes. Hence, we suggest that gene family evolution is a source of 'hopeful monsters’ within the genome that may facilitate adaptation when selective pressures shift. These results suggest that gene family expansion is a key driver of adaptive evolution in this key species of freshwater Unionidae that is currently facing widespread environmental challenges. This work has clear implications for conservation genomics on freshwater bivalves as well as evolutionary theory. This genome represents a first step to facilitate reverse ecological genomics in Unionidae and identify the genetic underpinnings of phenotypic diversity.

中文翻译：

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基因家族扩增促进淡水联合双壳类Megalonaias nervosa的适应

淡水联合双壳贝类目前面临严重的人为挑战。由于污染、水道筑坝和过度捕捞，美国超过 70% 的物种受到威胁、濒临灭绝或灭绝。这些物种以其不同寻常的生活史策略、寄生虫-宿主共同进化和双亲线粒体遗传而著称。在这个进化枝中，搓板贻贝Megalonaias nervosa是一种在美国东南部仍然普遍存在的物种，具有强大的种群规模。我们为M. nervosa创建了参考基因组以确定基因组内容在面对这些广泛的环境挑战时是如何进化的。我们观察到基因组内容的动态变化，近期转座因子的激增导致基因组内容扩大了 382 Mb。生死模型表明基因家族之间的快速扩张，每代每个基因的突变率为 1.16 × 10 ^{-8个重复。}细胞色素 P450基因家族最近经历了超出基于全基因组出生-死亡过程的预期的异常扩增。这些基因与氨基酸变化率增加有关，这是选择驱动排毒基因进化的标志。根据常设遗传变异拟合适应进化模型，我们可以比较跨物种和突变类型的适应潜力。M. nervosa的大种群规模表明，与低多样性的地方性E. Hopetonensis相比，在适应遗传变异的能力方面具有 4.7 倍的优势。估计表明，基因家族进化可能为M. nervosa的遗传变异提供了一个特殊的底物，其中P _sgv = 0.185 与 单核苷酸变化的P _{sgv = 0.067 相比。}Hence, we suggest that gene family evolution is a source of 'hopeful monsters' within the genome that may facilitate adaptation when selective pressures shift. 这些结果表明，基因家族的扩展是目前面临广泛环境挑战的淡水联合科这一关键物种适应性进化的关键驱动力。这项工作对淡水双壳类动物的保护基因组学以及进化理论具有明显的意义。该基因组代表了促进联合科逆向生态基因组学和确定表型多样性的遗传基础的第一步。