Population structure based on whole-genome resequencing and adaptive evolutionary mechanisms of circadian entrainment in the endangered fish Percocypris pingi

📖 Top 20% JournalJan 13, 2026BMC genomics

Genetic differences and adaptation of daily rhythm control in the endangered fish Percocypris pingi

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Abstract

Low genetic diversity was observed in 69 wild and 90 hatchery samples of the endangered fish Percocypris pingi.

Eight wild populations and nine hatchery populations showed relatively low genetic diversity and a simple population structure based on whole-genome resequencing.
The Datuo and Woluo wild populations, along with the Jinping and Yaan hatchery populations, exhibited relatively high genetic diversity compared to 13 other populations.
Enriched gene ontology terms related to circadian entrainment included MAP kinase activity and monoatomic ion channel activity.
Several candidate genes were identified as enriched in the circadian entrainment pathway, including pkc, pkd, and mapk6.
Circadian oscillation was demonstrated in the expression patterns of specific clock genes and melatonin levels in the livers of P. pingi.
The Wuoluo River and Litang River may serve as new refuges for wild P. pingi, while hatchery populations are essential for sustainable conservation efforts.

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BACKGROUND: The endangered fish Percocypris pingi is a national second-class protected animal in China. Comprehensive evaluation of the genetic structure according to more reliable data and exploration of effective conservation measures are urgently needed for P. pingi. In this study, the genetic diversity, population structure, and adaptive evolutionary mechanism of circadian entrainment for P. pingi were performed.

RESULTS: Our results revealed that eight wild populations (69 samples) and nine hatchery populations (90 samples) presented relatively low genetic diversity and simple population structure on the basis of whole-genome resequencing data. Compared to other 13 populations, the Datuo (DT) and Woluo (WL) wild populations and the Jinping (JP) and Yaan (YA) hatchery populations presented relatively high genetic diversity. The Fst‒Pi and XP‒EHH sites from the population group differentiation from DT, WL, JP, and YA were screened. Several GO terms (e.g. MAP kinase activity and monoatomic ion channel activity] and KEGG pathways (e.g. aldosterone synthesis and secretion and MAPK signaling) were enriched in circadian entrainment-related signaling. Then, the multiple candidate genes, such as pkc, pkd, Ac, mapk6, ampar, rorcb, rorab1, rorab2, lamb4, and ck1[Formula: see text]/∂ were shown to be enriched in the circadian entrainment pathway. Furthermore, the expression patterns of cry1a, cry2, per2a, per1b, clock1a, clock1b, baml2a, lamb4, and rorab1 and the melatonin levels in the livers demonstrated circadian oscillation within 24 h.

CONCLUSIONS: Low genetic diversity and a simple population structure of P. pingi were determined. The Wuoluo River and Litang River can be recognized as new refuges for wild P. pingi and that the JP and YA hatchery populations are needed for the sustainable conservation and utilization of resources in the Yalong River and Jinsha River. The circadian entrainment may be an important adaptive evolutionary mechanism of P. pingi. The above results can help formulate science-based breeding protocols and provide necessary genetic data for managing both captive propagation and wild population reinforcement.

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