Eco-genomic analysis uncovers precision-conservation targets for the western Pacific’s southernmost salmonid Article Swipe
Yi‐Chien Lee
,
Zong‐Yu Shen
,
Wei-Ren Lin
,
Tzi‐Yuan Wang
,
MingLiang Liu
,
Ying‐Tung Yeh
,
Shih‐Fan Chan
,
Mei‐Yeh Jade Lu
,
Hui‐Yu Wang
,
Lin‐Yan Liao
,
Wen‐Hsiung Li
,
Jen‐Pan Huang
,
Isheng Jason Tsai
,
Sheng‐Feng Shen
·
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.1101/2025.09.09.675276
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.1101/2025.09.09.675276
Understanding how isolated small populations persist and adapt in adverse environments is instrumental to evolutionary and conservation biology. We combine a chromosome-level genome assembly, population resequencing and forward-time simulations to reconstruct the history and viability of the Formosan landlocked salmon ( Oncorhynchus formosanus ), now restricted to a handful of high-mountain headwaters in Taiwan. We estimate that this lineage has diverged from Japanese masu salmon over one million years ago and has no detectable gene flow for ∼50,000 years. It has accumulated extensive chromosome fusions and expansions of cold-adaptation gene families, qualifying it as a new species rather than a subspecies of Japanese masu salmon. Whole-stream sampling reveals an overlooked Hehuan-Creek population that retains high heterozygosity and has gained unique alleles. Life-table simulations show that the Hehuan population has a notably lower extinction risk and can persist or even grow under low-to-moderate typhoon frequency, whereas Qijiawan-Creek population would decline precipitously under the same or higher frequency . These findings contradict the notion that peripheral populations are likely genetically depleted and support stream-specific “precision conservation” in place of broad, untargeted translocations that could erode local adaptation potential. Thus, our genomic-ecological analysis has uncovered hidden strong resilience in a critically endangered, climate-threatened salmonid lineage.
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- preprint
- Language
- en
- Landing Page
- https://doi.org/10.1101/2025.09.09.675276
- https://www.biorxiv.org/content/biorxiv/early/2025/09/15/2025.09.09.675276.full.pdf
- OA Status
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- References
- 105
- OpenAlex ID
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Eco-genomic analysis uncovers precision-conservation targets for the western Pacific’s southernmost salmonidWork title
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preprintOpenAlex work type
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enPrimary language
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2025Year of publication
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2025-09-15Full publication date if available
- Authors
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Yi‐Chien Lee, Zong‐Yu Shen, Wei-Ren Lin, Tzi‐Yuan Wang, MingLiang Liu, Ying‐Tung Yeh, Shih‐Fan Chan, Mei‐Yeh Jade Lu, Hui‐Yu Wang, Lin‐Yan Liao, Wen‐Hsiung Li, Jen‐Pan Huang, Isheng Jason Tsai, Sheng‐Feng ShenList of authors in order
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https://doi.org/10.1101/2025.09.09.675276Publisher landing page
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https://www.biorxiv.org/content/biorxiv/early/2025/09/15/2025.09.09.675276.full.pdfDirect link to full text PDF
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greenOpen access status per OpenAlex
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https://www.biorxiv.org/content/biorxiv/early/2025/09/15/2025.09.09.675276.full.pdfDirect OA link when available
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| abstract_inverted_index.Abstract | 0 |
| abstract_inverted_index.Formosan | 38 |
| abstract_inverted_index.Japanese | 63, 103 |
| abstract_inverted_index.alleles. | 121 |
| abstract_inverted_index.analysis | 190 |
| abstract_inverted_index.biology. | 18 |
| abstract_inverted_index.depleted | 169 |
| abstract_inverted_index.diverged | 61 |
| abstract_inverted_index.estimate | 56 |
| abstract_inverted_index.findings | 159 |
| abstract_inverted_index.isolated | 3 |
| abstract_inverted_index.lineage. | 202 |
| abstract_inverted_index.salmonid | 201 |
| abstract_inverted_index.sampling | 107 |
| abstract_inverted_index.assembly, | 24 |
| abstract_inverted_index.extensive | 83 |
| abstract_inverted_index.families, | 91 |
| abstract_inverted_index.frequency | 156 |
| abstract_inverted_index.uncovered | 192 |
| abstract_inverted_index.viability | 35 |
| abstract_inverted_index.∼50,000 | 78 |
| abstract_inverted_index.Life-table | 122 |
| abstract_inverted_index.adaptation | 185 |
| abstract_inverted_index.chromosome | 84 |
| abstract_inverted_index.contradict | 160 |
| abstract_inverted_index.critically | 198 |
| abstract_inverted_index.detectable | 74 |
| abstract_inverted_index.expansions | 87 |
| abstract_inverted_index.extinction | 133 |
| abstract_inverted_index.formosanus | 43 |
| abstract_inverted_index.frequency, | 144 |
| abstract_inverted_index.headwaters | 52 |
| abstract_inverted_index.landlocked | 39 |
| abstract_inverted_index.overlooked | 110 |
| abstract_inverted_index.peripheral | 164 |
| abstract_inverted_index.population | 25, 112, 128, 147 |
| abstract_inverted_index.potential. | 186 |
| abstract_inverted_index.qualifying | 92 |
| abstract_inverted_index.resilience | 195 |
| abstract_inverted_index.restricted | 46 |
| abstract_inverted_index.subspecies | 101 |
| abstract_inverted_index.untargeted | 179 |
| abstract_inverted_index.accumulated | 82 |
| abstract_inverted_index.endangered, | 199 |
| abstract_inverted_index.genetically | 168 |
| abstract_inverted_index.populations | 5, 165 |
| abstract_inverted_index.reconstruct | 31 |
| abstract_inverted_index.simulations | 29, 123 |
| abstract_inverted_index.Hehuan-Creek | 111 |
| abstract_inverted_index.Oncorhynchus | 42 |
| abstract_inverted_index.Whole-stream | 106 |
| abstract_inverted_index.conservation | 17 |
| abstract_inverted_index.environments | 11 |
| abstract_inverted_index.evolutionary | 15 |
| abstract_inverted_index.forward-time | 28 |
| abstract_inverted_index.instrumental | 13 |
| abstract_inverted_index.resequencing | 26 |
| abstract_inverted_index.“precision | 173 |
| abstract_inverted_index.Understanding | 1 |
| abstract_inverted_index.high-mountain | 51 |
| abstract_inverted_index.precipitously | 150 |
| abstract_inverted_index.Qijiawan-Creek | 146 |
| abstract_inverted_index.heterozygosity | 116 |
| abstract_inverted_index.translocations | 180 |
| abstract_inverted_index.cold-adaptation | 89 |
| abstract_inverted_index.conservation” | 174 |
| abstract_inverted_index.low-to-moderate | 142 |
| abstract_inverted_index.stream-specific | 172 |
| abstract_inverted_index.chromosome-level | 22 |
| abstract_inverted_index.climate-threatened | 200 |
| abstract_inverted_index.genomic-ecological | 189 |
| cited_by_percentile_year | |
| countries_distinct_count | 0 |
| institutions_distinct_count | 14 |
| citation_normalized_percentile.value | 0.42520062 |
| citation_normalized_percentile.is_in_top_1_percent | False |
| citation_normalized_percentile.is_in_top_10_percent | False |