The complete nucleotide sequence of Gymnodiptychus dybowskii mitogenome (16 677 bp) has been determined, containing 13 protein-coding genes, two ribosomal RNA genes, 22 tRNA genes, and one non-coding control region. The base composition is 28.04% A, 26.92% T, 18.94% G, 26.10% C, with an AT bias of 54.97%. The origin of light-strand replication (O_L) is found between tRNA^Asn and tRNA^Cys, which has the potential to fold in a step-loop secondary structure with a stem formed by 11 pairs of nucleotides and a loop of 14 nucleotides. The phylogenetic analysis indicates close relationship between genus Gymnodiptychus and Diptychus.

Schizothoracins are a group of cyprinid fishes distributed throughout the Qinghai–Tibet Plateau, which can be classified in three grades: primitive, specialised and highly specialised according to adaptation ability to plateau environments. As the only specialised schizothoracins in Xinjiang, China, Diptychus maculates and Gymnodiptychus dybowskii are ideal materials for adaptive evolution research. Based on single-nucleotide polymorphism (SNP) loci detected by specific-locus amplified fragment (SLAF) technology, the genome-wide genetic diversities of these two species from nine sites in Xinjiang were evaluated. D.maculates in the Muzat River (BM) and G. dybowskii in the Kaidu River (LKG) presented the lowest genetic diversity levels, whereas D. maculates in the Kumarik River (BK) and G.dybowskii in the Kashi River (LK) were just the opposite. Cluster and principal component analysis demonstrated a distant genetic affinity between D. maculates in the Tashkurgan River (BT) and other populations. Outlier SNP loci were discovered both in D. maculates and G. dybowskii. The coalescent Bayenv and latent factor mixed model (LFMM) methods showed that a total of thirteen and eighteen SNPs in D. maculates were associated with altitude and temperature gradient, respectively. No intersection was revealed in G. dybowskii. The results indicated that D. maculates was subject to much greater divergent selection pressure. A strong signal of isolation-by-distance (IBD) was detected across D. maculates (Mantel test, rs = 0.65; p = 0.05), indicating an evident geographical isolation in the Tarim River. Isolation-by-environment (IBE) analysis implied that temperature and altitude selections were more intensive in D. maculates, with greater environmental variation resulting in weak gene flow.

The Larimichthys crocea represents a critically important economic marine species in China’s East Yellow Sea. However, its populations have experienced significant decline due to overexploitation. Despite implemented conservation measures—including stock enhancement, spawning ground protection, and seasonal fishing moratoria—the recovery of yellow croaker resources remains markedly slow. To address this, our study employed the Maximum Entropy (MaxEnt) model to evaluate and characterize the habitat selection patterns of Larimichthys crocea, thereby providing a theoretical foundation for scientifically informed stock enhancement and resource recovery strategies. Species occurrence data were compiled from field surveys conducted during April and November (2019–2023), supplemented with records from the GBIF database and peer-reviewed literature. Concurrent environmental variables, including primary productivity, current velocity, depth, temperature, salinity, silicate, nitrate, phosphate, and pH, were obtained from the Copernicus and NOAA databases. After rigorous screening, 136 distribution points (April) and 369 points (November) were retained for analysis. The model performance was robust, with an AUC (Area Under the Curve) value of 0.935 for April (2019–2023) and 0.905 for November (2019–2023), indicating excellent predictive accuracy (AUC > 0.9). April (2019–2023): Nitrate, salinity, phosphate, and silicate were identified as the primary environmental factors influencing habitat suitability. November (2019–2023): Silicate, salinity, nitrate, and primary productivity emerged as the dominant drivers. Spatially, Larimichthys crocea exhibited high-density distributions in offshore regions of Zhejiang and Jiangsu, particularly near the Yangtze River estuary. Populations were also associated with island-reef systems, forming continuous distributions along Zhejiang’s offshore waters. In Jiangsu, aggregations were concentrated between Nantong and Yancheng. This study delineates habitat suitability zones for Larimichthys crocea, offering a scientific basis for optimizing stock enhancement programs, designing targeted conservation measures, and establishing marine protected areas. Our findings enable policymakers to develop sustainable fisheries management strategies, ensuring the long-term viability of this ecologically and economically vital species.