The mitochondrial genome of Schizothorax argentatus from Northern Xinjiang and its phylogenetic analysis

In this study, we first sequenced the mitochondrial genome (mitogenome) of Schizothorax argentatus. The circular mitogenome of S. argentatus is 16,587 bp long, containing 13 protein-coding genes, 22 tRNA genes, two ribosomal RNA genes, and a control region (D-loop region). The base composition is AT biased (63.11%). A phylogenetic tree confirms monophyly at the genus level within Cyprinidae and supports S. argentatus as sister to Schizothorax pseudoaksaiensis

Complete Mitogenome of the <i>Triplophysa bombifrons</i>: Comparative Analysis and Phylogenetic Relationships among the Members of <i>Triplophysa</i>

In the last decade, the phylogenetic relationships within the genus Triplophysa have become controversial, due to a lack of molecular data. The mitochondrial genome plays a vital role in the reconstruction of phylogenetic relationships and in revealing the molecular evolution of bony fishes. Herein, we obtained the complete mitogenome of Triplophysa bombifrons via HiFi reads of the Pacbio Sequel II system and DNBSEQ short-reads. We compared all available mitogenomes of the Triplophysa genus and reconstructed the phylogeny of Nemacheilidae, based on the mitogenomes, using maximum likelihood (ML) methods. The results show that the complete mitogenome sequence of T. bombifrons was circular and 16,568 bp in length, including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA), 2 ribosomal RNA (rRNA), and a typical control region (D-loop). The most common start codons were ATG, except for cox1, and TAA/TAG were the stop codons for all PCGs. In total, 677 SNPs and 9 INDELs have been found by comparing the sequence divergence between this study and previous reports. Purity selection was found in all PCGs. Phylogeny was inferred by analyzing the 13 PCGs and the concatenated nucleotide sequences of 30 mitogenomes. The phylogenetic analyses based on the nucleotides of the 13 PCGs supported the assumption that the Triplophysa genus can be divided into 4 main clades and demonstrated that T. bombifrons and T. tenuis are closely related species for the first time. This study laid the foundation for further study on the mitogenome and phylogeny of Nemacheilidae fishes

Otolith Morphology and Population Discrimination of Triplophysa yarkandensis

To study the classification, identification, and discrimination between different geographical populations of Triplophysa yarkandensis and explore the related otolith morphology and fish life history, this study statistically analyzed the morphological otolith indices and fish bodies of 734 T. yarkandensis from the Yarkand River, Hotan River, and Tarim River using otolith morphology and fish ecology methods. The results showed that otoliths were small in T. yarkandensis, approximately elliptic, thicker in the middle, gradually thinning to the outer edge, and with a prominent protrusion in the center of the external surface. Otolith length was obviously larger than otolith width while the excisural notch was not obvious, wherein the rostrum was developed, the ventral otolith edge was smooth with a shallow arc, and the otolith dorsal had a crest-like ridge. No significant difference between left and right lapillus morphology was observed (P > 0.05). The otolith morphological indices followed a logarithmic function with the body length and weight (R2=0.48~0.62). It reflects the ontogenetic adaptation to the environment, and migration behavior mainly affects the relationship between otolith morphology and fish body morphology. The SHAPE software was used to extract the outer otolith contour of T. yarkandensis, revealing morphological differences between T. yarkandensis populations. The parameter with the largest discriminant coefficient, i.e., the one in which the morphological difference has the greatest significant effect, was screened. Therewith, the discriminant formula was set up to calculate the discriminant accuracy. Discriminant analysis between groups using fish morphology, otolith morphometry and elliptical Fourier analysis, respectively. The discriminant accuracy of the Hotan River and Tarim River populations was 96.0%, 61.4%, and 82.2%; the Yarkand River and Hotan River was 93.0%, 79.5%, and 87.9%; the Yarkand River and Tarim River populations was 96.5%, 77.5%, and 86.8%. Environmental factors such as water temperature, spatial niche adaptation, and habitat depth were the main causes of the otolith morphological changes, also affecting the behavior characteristics of typical T. yarkandensis life history, especially fish migration. In this study, the T. yarkandensis was found to live in high altitude, low habitat temperature, and high salinity and alkaline waters, so the fish body growth and the elements deposition rate onto otoliths were low. T. yarkandensis belongs to the sub-cold water and benthic fish group, which only enters deep water during overwintering in winter. In other seasons, it swims along the edge and rests in shallow depth waters, so the otolith grows slowly and has a small size. The relationship between otolith and body growth reflected the T. yarkandensis ontogenetic adaptability to its habitat. As the T. yarkandensis residence time is short in the migration area, mineral elements in the water body cannot be rapidly deposited in a short period of time, and the accelerated body growth is not completely reflected in the otolith growth. Therefore, the short-distance migration behavior under habitat fragmentation mainly affects the correlation between otolith and fish growth in T. yarkandensis. The fish otolith morphology is highly species-specific and population-specific. T. yarkandensis otolith morphology was significantly different among the geographically different populations (P 90.0%) was slightly higher than that of elliptic Fourier analysis (> 80.0%), both of which could be used as the discrimination basis parameter. However, the traditional fish otolith morphology is easy to record, as repetitive operations are robust and less affected by the environment, especially in the contents of a carnivorous fish feeding analysis; therefore, vertebrate paleontology explore has a useful application prospect in these aspects. Moreover, it could serve as an effective tool to identify fish intraspecific differences in the case of growth restriction or bodily injury. Therefore, it is of great research value to introduce the otolith morphology into the population identification of T. yarkandensis. This study explored the T. yarkandensis morphological characteristics and compared otolith morphologies to effectively identify the geographically different population, co-relating otolith shape with T. yarkandensis growth (i.e., body length and quality) and resource management, providing theoretical support to further researches about the composition and migratory population growth. The T. yarkandensis intraspecies differences in different rivers were also compared concerning fish body morphology, otolith measurements, and elliptic Fourier analysis, providing strong evidence for traditional morphological classification. The effective utilization and cost control of incomplete fish samples was greatly favored by this study. Otolith morphology was applied for the first time in the classification and population identification of T. yarkandensis, which laid a foundation for the development and research of its microchemical features and life history strategy, presenting a reference for further identification and evolutionary classification of Triplophysa, strengthening the taxonomic foundation of aquatilia, and providing scientific basis for protecting the plateau fishery germplasm resources

Analyses of Morphological Differences between Geographically Distinct Populations of <i>Gymnodiptychus dybowskii</i>

To study the morphological differences between and the evolutionary mechanisms driving the differentiation of geographically distinct populations of Gymnodiptychus dybowskii, 158 fish were collected from the Turks River and the Manas River in Xinjiang from 2020 to 2021 with the approval of the Academic Ethics Committee. The morphological characteristics of the fish were assessed using classical fish ecology methods such as traditional morphometric measurements and the framework approach. The results showed that the morphological characteristics of the populations in the Turks River and Manas River were significantly different; a one-way ANOVA revealed 22 highly significant differences (p p G. dybowskii. The main characteristics associated with principle component 1 were the terminus of the dorsal fin to the ventral origin of the caudal fin (D—F), the dorsal origin of the caudal fin to the origin of the anal fin (E—H), and the insertion of the pectoral fin to the terminus of the pectoral fin (J—K); the main factors associated with principal component 2 were the body height (BD), the terminus of the dorsal fin to the insertion of the pelvic fin (D—I), the caudal peduncle height (CPH), and the tip of the snout to the last end of the frontal maxilla (A—B); and the main traits associated with principle component 3 were the terminus of the anal fin to the origin of the anal fin (G—H), the body width (BW), the insertion of the pelvic fin to the terminus of the pelvic (I—L), the insertion of the pectoral fin to the terminus of the pectoral fin (J—K), and the insertion of the pelvic fin to the insertion of the pectoral fin (I—J). An OPLS-DA revealed that the two populations could be wholly separated and that the intergroup growth traits of the Manas River population were different and significantly greater than those of the Turks River population. The discriminant functions of the Turks River and Manas River populations of G. dybowskii were as follows: YT = −432.033 + 1787.748X1 + 826.517X2 + 249.002X3 + 1183.050X4 + 554.934X5 + 999.296X6 + 627.428X7; YM = −569.819 + 2041.044X1 + 344.942X2 + 333.737X3 + 940.512X4 + 348.222X5 + 1167.770X6 + 1015.904X7. According to a coefficient of variation analysis, a total of nine traits, namely, EI/BL, C-D/BL, E-F/BL, F-H/BL, H-I/BL, C-J/BL, D-I/BL, D-H/BL, and D-F/BL, had a CD > 1.28, indicating that the differences in these nine traits had reached the subspecies level. The results showed that G. dybowskii significantly differed between the two geographically distinct populations in the Turks River and the Manas River and have differentiated to the subspecies level. This study provides a basis for a better investigation of the population structure of highland endemic fishes and the mechanisms by which they diverged and lays a foundation for developing and utilizing germplasm resources from endemic fishes in Xinjiang