A reference genome enhances the power to detect signatures of recent anthropogenic impact in genomic data: a lesson learned from a stag beetle system
Abstract Background 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...
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2025-07-01
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| Online Access: | https://doi.org/10.1186/s12915-025-02307-7 |
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| author | Zong-Yu Shen My-Hanh Le Ming-Hsun Chou Jen-Pan Huang |
| author_facet | Zong-Yu Shen My-Hanh Le Ming-Hsun Chou Jen-Pan Huang |
| author_sort | Zong-Yu Shen |
| collection | DOAJ |
| description | Abstract Background 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. Results 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. Conclusions 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. |
| format | Article |
| id | doaj-art-cd0fc5aab1ea4400be7d1d5185ad9a35 |
| institution | DOAJ |
| issn | 1741-7007 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Biology |
| spelling | doaj-art-cd0fc5aab1ea4400be7d1d5185ad9a352025-08-20T03:06:05ZengBMCBMC Biology1741-70072025-07-0123111410.1186/s12915-025-02307-7A reference genome enhances the power to detect signatures of recent anthropogenic impact in genomic data: a lesson learned from a stag beetle systemZong-Yu Shen0My-Hanh Le1Ming-Hsun Chou2Jen-Pan Huang3Biodiversity Research Center, Academia SinicaBiodiversity Research Center, Academia SinicaBiodiversity Research Center, Academia SinicaBiodiversity Research Center, Academia SinicaAbstract Background 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. Results 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. Conclusions 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.https://doi.org/10.1186/s12915-025-02307-7Demographic historyHabitat lossLocal adaptationLucanusNanoporeROH |
| spellingShingle | Zong-Yu Shen My-Hanh Le Ming-Hsun Chou Jen-Pan Huang A reference genome enhances the power to detect signatures of recent anthropogenic impact in genomic data: a lesson learned from a stag beetle system BMC Biology Demographic history Habitat loss Local adaptation Lucanus Nanopore ROH |
| title | A reference genome enhances the power to detect signatures of recent anthropogenic impact in genomic data: a lesson learned from a stag beetle system |
| title_full | A reference genome enhances the power to detect signatures of recent anthropogenic impact in genomic data: a lesson learned from a stag beetle system |
| title_fullStr | A reference genome enhances the power to detect signatures of recent anthropogenic impact in genomic data: a lesson learned from a stag beetle system |
| title_full_unstemmed | A reference genome enhances the power to detect signatures of recent anthropogenic impact in genomic data: a lesson learned from a stag beetle system |
| title_short | A reference genome enhances the power to detect signatures of recent anthropogenic impact in genomic data: a lesson learned from a stag beetle system |
| title_sort | reference genome enhances the power to detect signatures of recent anthropogenic impact in genomic data a lesson learned from a stag beetle system |
| topic | Demographic history Habitat loss Local adaptation Lucanus Nanopore ROH |
| url | https://doi.org/10.1186/s12915-025-02307-7 |
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