Genetic adaptation to polyploidy in animals: a case study in Australian burrowing frogs Neobatrachus

Whole-genome duplication can be adaptive in the long term but in the short term can impair chromosome segregation and fertility, obstacles polyploids must overcome to regain fitness. To investigate how animals adapt to polyploidy, we focused on Australian burrowing frogs (genus Neobatrachus), three species of which are polyploid: N. aquilonius, N. kunapalari and N. sudellae. We assembled a reference genome for diploid N. pictus and sequenced 96 individuals from all nine Neobatrachus species, finding tetraploid-specific selection on genes with meiotic roles in synaptonemal complex and crossover distribution (SYCE2, PRR19), or chromosome and spindle size (Condensin-2, KifC1). These changes may represent a genetic adaptation in vertebrate polyploids with tetrasomic and mixed inheritance that raises crossover interference and scales chromosome and spindle size to ensure successful chromosomal segregation. Finally, we show that adaptive alleles are shared between the tetraploids via interspecific introgression.

全基因组复制（Whole-genome duplication）从长期维度来看具备适应性，但在短期内会损害染色体分离（chromosome segregation）与生育能力，这是多倍体（polyploid）恢复适合度（fitness）必须克服的障碍。为探究动物如何适应多倍化进程，我们将研究对象聚焦于澳大利亚掘蛙属（Neobatrachus），该属下共有3个多倍体物种：北澳掘蛙（N. aquilonius）、库纳帕拉掘蛙（N. kunapalari）以及苏德拉掘蛙（N. sudellae）。我们组装了二倍体斑掘蛙（N. pictus）的参考基因组（reference genome），并对掘蛙属全部9个物种的96个个体开展测序，最终发现针对参与联会复合体（synaptonemal complex）与交叉分布（crossover distribution）的减数分裂（meiotic）基因（SYCE2、PRR19），或调控染色体与纺锤体大小的基因（凝缩蛋白-2 Condensin-2、KifC1）存在四倍体特异性选择。上述改变或代表了具备四体遗传（tetrasomic inheritance）与混合遗传（mixed inheritance）模式的脊椎动物多倍体的一类遗传适应性机制——该机制可增强交叉干涉（crossover interference）效应，并校准染色体与纺锤体大小，以保障染色体分离顺利完成。最后，我们证实适应性等位基因可通过种间渐渗（interspecific introgression）在不同四倍体物种间实现共享。