Structural variation (SV) constitutes an important type of genetic mutations providing the raw material for evolution. Here, we uncover the genome-wide spectrum of intra- and interspecific SV segregating in natural populations of seven songbird species in the genus Corvus. Combining short-read (N = 127) and long-read re-sequencing (N = 31), as well as optical mapping (N = 16), we apply both assembly- and read mapping approaches to detect SV and characterize a total of 220,452 insertions, deletions and inversions. We exploit sampling across wide phylogenetic timescales to validate SV genotypes and assess the contribution of SV to evolutionary processes in an avian model of incipient speciation. We reveal an evolutionary young (~530,000 years) cis-acting 2.25-kb LTR retrotransposon insertion reducing expression of the NDP gene with consequences for premating isolation. Our results attest to the wealth and evolutionary significance of SV segregating in natural populations and highlight the need for reliable SV genotyping.

结构变异（SV）是一种重要的基因突变类型，为进化提供了原材料。在这里，我们揭示了乌鸦属七种鸣禽自然种群中种内和种间 SV 分离的全基因组谱。结合短读长（N  = 127）和长读重测序（N  = 31）以及光学映射（N  = 16），我们应用组装和读长映射方法来检测 SV 并表征总共220,452 个插入、删除和倒位。我们利用跨广泛系统发育时间尺度的采样来验证 SV 基因型，并评估 SV 对早期物种形成鸟类模型中进化过程的贡献。我们揭示了一个进化年轻（约 530,000 年）顺式作用 2.25-kb LTR 逆转录转座子插入降低了NDP基因的表达，从而导致交配前分离。我们的结果证明了 SV 在自然群体中分离的财富和进化意义，并强调了可靠的 SV 基因分型的必要性。