Shen Zong-Yu, Le My-Hanh, Chou Ming-Hsun, Huang Jen-Pan
Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.
Department of Life Science, National Taiwan Normal University, Taipei, Taiwan.
BMC Biol. 2025 Jul 9;23(1):205. doi: 10.1186/s12915-025-02307-7.
Genomic data are vital for conservation biology and recent advances in sequencing technology have facilitated their applicability. However, the role of reference genomes in conservation planning remains largely underexplored. Specifically, while reference genomes can improve the accuracy of estimating genetic indices and help detect genomic regions under selection, they are still limited for non-model species. We explored whether a reference genome can help reveal novel insights not detected by previous genome-wide SNP analyses in a stag beetle system, especially in understanding recent demographic changes and local adaptation, which are critical information for conservation planning.
We used Oxford Nanopore Technology (ONT) to sequence and assemble a draft genome of an endemic stag beetle Lucanus miwai in Taiwan. With this newly generated genome map, we reanalyzed a previously published ddRADseq dataset. Our results revealed that the three geographical lineages of L. miwai exhibit varying levels of runs of homozygosity (ROH), with the lineage experiencing the most severe and recent habitat disturbance showing the longest ROH. Furthermore, the inferred timing and duration of a recent bottleneck coincide with historical records of recent habitat destruction. We also identified putative genomic regions showing signals of divergent selection between the lineages, indicating the importance of maintaining geographical lineages as separate conservation units.
The impact of anthropogenic disturbance among different geographical lineages of L. miwai can be detected using genomic data only when a reference genome is available. Furthermore, a reference genome helps us identify a genomic region that may have experienced a recent selective sweep. Our findings thus provide empirical evidence supporting the crucial roles of reference genomes in conservation planning.
基因组数据对保护生物学至关重要，测序技术的最新进展促进了其应用。然而，参考基因组在保护规划中的作用在很大程度上仍未得到充分探索。具体而言，虽然参考基因组可以提高估计遗传指标的准确性并有助于检测受选择的基因组区域，但对于非模式物种来说，它们仍然存在局限性。我们探讨了参考基因组是否有助于揭示在锹甲系统中先前全基因组SNP分析未检测到的新见解，特别是在理解近期种群动态变化和局部适应性方面，这些是保护规划的关键信息。
我们使用牛津纳米孔技术（ONT）对台湾特有锹甲米氏锹甲的基因组进行测序和组装，得到了一个草图。利用这个新生成的基因组图谱，我们重新分析了之前发表的ddRADseq数据集。我们的结果表明，米氏锹甲的三个地理谱系表现出不同程度的纯合子连续片段（ROH），经历最严重和近期栖息地干扰的谱系显示出最长的ROH。此外，推断的近期瓶颈的时间和持续时间与近期栖息地破坏的历史记录相吻合。我们还确定了在谱系之间显示出趋异选择信号的假定基因组区域，这表明将地理谱系作为单独的保护单元的重要性。
只有当有参考基因组时，才能利用基因组数据检测米氏锹甲不同地理谱系间人为干扰的影响。此外，参考基因组有助于我们识别可能经历了近期选择性清除的基因组区域。因此，我们的研究结果提供了实证证据，支持参考基因组在保护规划中的关键作用。
