The complete mitochondrial genome of Triplophysa grahami Regan 1906 (Cypriniformes: Nemacheilidae) and phylogenetic analysis

Triplophysa grahami Regan 1906 is a member of the family Nemacheilidae, Cypriniformes, and native loach in Yunnan. In this study, the complete mitochondrial genome (mitogenome) of T. grahami Regan 1906 was firstly reported and analyzed. The mitogenome of T. grahami Regan 1906 is 16,566 bp in length, including 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and one control region (D-loop). The arrangement and orientation of protein coding genes and RNAs in T. grahami Regan 1906 are identical to other species of Nemacheilidae. The base composition of T. grahami Regan 1906 mitogenome was 29.25% A, 28.55% T, 25.03% C, and 17.17% G. The phylogenetic analysis based on the mitogenome showed that T. grahami Regan 1906 belongs to the clade of genus Triplophysa and the monophyly of Triplophysa is identified. This study contributed valuable genetic data for T. grahami Regan 1906 and explored the phylogenetic relationships in Nemacheilidae.

Mitochondrial genome data provide insights into the phylogenetic relationships within Triplophysadalaica (Kessler, 1876) (Cypriniformes, Nemacheilidae)

Due to the detrimental effect of formaldehyde on DNA, ethanol has replaced formalin as the primary preservative for animal specimens. However, short-term formalin fixation of specimens might be applied during field collection. In an increasing number of studies, DNA extraction and sequencing have been successfully conducted from formalin-fixed specimens. Here the DNA from five specimens of Triplophysadalaica (Kessler, 1876) were extracted and performed high-throughput sequencing. Four of the specimens underwent short-term fixation with formalin and were subsequently transferred to ethanol. One was continuously stored in ethanol. No significant difference of DNA quality and amount were observed among these samples. Followed by assembly and annotation, five mitochondrial genomes ranging in length from 16,569 to 16,572 bp were obtained. Additionally, previously published data of other individuals or species were included to perform phylogenetic analyses. In the reconstructed trees, all eight individuals of T.dalaica form a monophyletic group within the Triplophysa branch. The group is divided into three clades: (1) samples from the Yellow River, (2) those from the Yangtze River, and (3) those from the Haihe River, and the Lake Dali Nur. This study sheds initial light on the phylogeographic relationships among different populations of T.dalaica, and will support the research about its evolutionary history in the future.

Adaptive evolution of mitochondrial genomes in Triplophysa cavefishes

Extreme conditions in caves pose survival challenges for cave dwellers, who gradually develop adaptive survival features. Cavefishes are one of the most successful animals among cave dwellers. Triplophysa cavefishes are an important group of cavefishes, and they show remarkable adaptability to the extreme environments of caves. However, there is a limited understanding of their adaptation mechanisms. In this study, eight complete mitochondrial genomes of Triplophysa cavefishes were newly obtained, and their genomic characteristics, including the base composition, base bias, and codon usage, were analyzed. Phylogenetic analysis was carried out based on 13 mitochondrial protein-coding genes from 44 Nemacheilidae species. This showed that Triplophysa cavefishes and non-cavefishes separate into two reciprocally monophyletic clades, suggesting a single origin of the cave phenotype. Positive selection analysis strongly suggested that the selection pressure in cavefishes is higher than that in non-cavefishes. Furthermore, the ND5 gene in cavefishes showed evidence of positive selection, which suggests that the gene may play an important role in the adaptation of cavefishes to the cave environment. Protein structure analysis of the ND5 subunit implied that the sites of positive selection in cavefishes might allow them to acquire lower ND5 protein stability, compared to that in non-cavefishes, which might help the accumulation of nonsynonymous (mildly deleterious) mutations. Together, our study revealed the genetic signatures of cave adaptation in Triplophysa cavefishes from the perspective of energy metabolism.

Triplophysadaryoae, a new nemacheilid loach species (Teleostei, Nemacheilidae) from the Syr Darya River basin, Central Asia

Triplophysadaryoae, new species, is described from the Sokh River, a former tributary of Syr Darya that today fails to reach the river, in the Sokh District, an exclave of Uzbekistan, surrounded by Kyrgyzstan. Triplophysadaryoae is distinguished from other species of Triplophysa in Central Asia by a truncate caudal fin with 13 or 14 branched rays, body without obvious mottling, dorsal-fin origin opposite to pelvic-fin insertion, and absence of the posterior chamber of the air bladder. Molecular data suggest that Triplophysadaryoae is closely related to T.ferganaensis from the Shakhimardan stream, a small tributary of Syr Darya in the Yordon village, another exclave of Uzbekistan in Kyrgyzstan. The two species were separated by a Kimura 2-parameter genetic distance of 2.8% in the mitochondrial DNA cytochrome c oxidase subunit I barcode region; they are also distinguished morphologically. A key to the species of Triplophysa in the Syr Darya basin and adjacent regions is provided.

Pleistocene climate and geomorphology drive the evolution and phylogeographic pattern of Triplophysa robusta (Kessler, 1876)

Montane systems provide excellent opportunities to study the rapid radiation influenced by geological and climatic processes. We assessed the role of Pleistocene climatic oscillations and mountain building on the evolution history of Triplophysa robusta, a cold-adapted species restricted to high elevations in China. We found seven differentiated sublineages of T. robusta, which were established during the Mid Pleistocene 0.87–0.61 Mya. The species distribution modeling (SDM) showed an expansion of T. robusta during the Last Glacial Maximum (LGM) and a considerable retraction during the Last Interglacial (LIG). The deep divergence between Clade I distributed in Qinling Mountains and Clade II in Northeastern Qinghai-Tibet Plateau (QTP) was mainly the result of a vicariance event caused by the rapid uplifting of Qinling Mountains during the Early Pleistocene. While the middling to high level of historical gene flow among different sublineages could be attributed to the dispersal events connected to the repetition of the glacial period during the Pleistocene. Our findings suggested that frequent range expansions and regressions due to Pleistocene glaciers likely have been crucial for driving the phylogeographic pattern of T. robusta. Finally, we urge a burning question in future conservation projection on the vulnerable cold-adapted species endemic to high elevations, as they would be negatively impacted by the recent rapid climate warming.

Population Structure, Genetic Diversity and Differentiation of Triplophysa tenuis in Xinjiang Tarim River

Triplophysa tenuis is an important indigenous fish in the Xinjiang Tarim River. In this study, we collected 120 T. tenuis individuals from 8 T. tenuis populations in the Tarim River. Through genotyping-by-sequencing (GBS), a total of 582,678,756 clean reads were generated for all the genotypes, and after quality filtering, 595,379 SNPs were obtained for the population genetic analyses. Multiple genetic parameters showed that the 8 T. tenuis populations had high genetic diversity. Phylogenetic tree analysis indicated that all T. tenuis individuals were divided into five branches, the individuals from the north of Tarim River were grouped into cluster 1 (SF and WS) and cluster 3 (DWQ, TKX, and KZE), while the AETS, WLWT and LF individuals from the south of Tarim River were clustered into cluster 2. The result was consistent with the admixture analysis, which supported that the 8 T. tenuis populations were clustered into three subgroups. Furthermore, the pairwise F_ST values and genetic distance indicated that there was a large genetic differentiation between WS and other T. tenuis populations. Collectively, this study provides valuable genome-wide data for the conservation of natural T. tenuis populations in the Tarim River.

Triplophysa ferganaensis, a new loach species from Fergana Valley in Central Asia (Teleostei: Nemacheilidae)

Triplophysa ferganaensis sp. nov. is described from the Shakhimardan stream, a small tributary of the Syr Darya, which does not reach the river in Fergana Valley. It can be distinguished from other valid Triplophysa loaches based on the following combination of characters: body smooth and scaleless, lateral line complete, posterior chamber of air bladder degenerated, inner gill rakers 10-11 on the first-gill arch, outer gill rakers absent, vertebrae 4 + 35-36, 8 + 8 branched caudal-fin rays, caudal peduncle depth 2.1-2.7 times its length, two supratemporal pores, dorsal-fin origin closer to the caudal-fin base than to the snout tip, caudal fin emarginated and pelvic-fin tip reaching the anus. The new species can also be distinguished from its congeners based on the molecular analyses of mitochondrial cytochrome oxidase subunit I (coI) gene sequences. The phylogenetic position of this new species indicates that it is a sister taxon of Triplophysa tenuis.

Fine-scale genetic structure of suckermouth Hypostomus ancistroides populations: the importance of Neotropical streams for fish conservation

In the Neotropics, freshwater streams harbour high fish diversity and are constantly threatened by anthropogenic disturbance. However, there are few studies on the genetic diversity of fish populations inhabiting these streams. We aimed to assess, based on microsatellite and mitochondrial DNA markers, the population structure and genetic diversity of the suckermouth catfish, Hypostomus ancistroides, a Neotropical species widely distributed across the Upper Paraná River Basin in South America. Twenty-five locations were sampled, distributed across 18 sites in six tributary streams and another seven sites in the main river channel. Our analyses revealed a spatial heterogeneity in genetic diversity within the basin, indicating fine-scale genetic structuring. Samples from all streams showed exclusive haplotypes and private alleles, reinforcing the importance of preserving the tributaries for the conservation of the genetic diversity of the studied populations. The fine-scale genetic structuring of H. ancistroides is probably related to the limited displacement capacity of this species.

Triplophysa wulongensis, a new species of cave-dwelling loach (Teleostei, Nemacheilidae) from Chongqing, Southwest China

We describe a new species of cave-dwelling loach, Triplophysawulongensissp. nov., based on specimens collected in a subterranean pool in a cave in Wulong County, Chongqing, Southwest China. The pool is connected to the Wujiang River drainage. Triplophysawulongensis differs from its congeners by the following combination of characters: eyes present, caudal fin with 18 branched rays; posterior chamber of the air bladder degenerate; stomach U-shaped; intestine without bends or loops immediately posterior to stomach; body smooth and scaleless, and lateral line complete. The mitochondrial cytochrome b sequence differs from those of other published sequences of species of Triplophysa by 14.9–24.9% in K2P distance. Phylogenetic analysis based on cytochrome b gene sequences recovered T.wulongensis as sister taxon to all other cave-dwelling species of Triplophysa.

Island colonization by a ‘rheophilic’ fish: the phylogeography of Garra ceylonensis (Teleostei: Cyprinidae) in Sri Lanka

Despite exhibiting multiple morphological adaptations to living in swiftly flowing water (rheophily), Garra ceylonensis is one of the most widely distributed freshwater fish in Sri Lanka. It is thus an ideal organism to reconstruct the evolutionary history of a widespread, yet morphologically specialized, freshwater fish in a tropical-island setting. We analysed the phylogenetic and phylogeographic relationships of G. ceylonensis based on two mitochondrial and one nuclear genes. G. ceylonensis is shown to be monophyletic, with a sister-group relationship to the Indian species Garra mullya. Our results suggest a single colonization of Sri Lanka by ancestral Garra, in the late Pliocene. This suggests that the Palk Isthmus, which was exposed for most of the Pleistocene, had a hydroclimate unsuited to the dispersal of fishes such as Garra. G. ceylonensis exhibits strong phylogeographic structure: six subclades are distributed as genetically distinct populations in clusters of contiguous river basins, albeit with two exceptions. Our data reveal one or more Pleistocene extirpation events, evidently driven by aridification, with relict populations subsequently re-colonizing the island. The phylogeographic structure of G. ceylonensis suggests inter-basin dispersal largely through headwater capture, likely facilitated by free-swimming post-larvae. The Peninsular-Indian species G. mullya comprises two genetically distinct parapatric clades, which may represent distinct species.

Variations in the Mitochondrial Genome of a Goldfish-Like Hybrid [Koi Carp (♀) × Blunt Snout Bream (♂)] Indicate Paternal Leakage

Previously, a homodiploid goldfish-like fish (2n = 100; GF-L) was spontaneously generated by self-crossing a homodiploid red crucian carp-like fish (2n = 100; RCC-L), which was in turn produced via the distant hybridization of female koi carp (Cyprinus carpio haematopterus, KOC, 2n = 100) and male blunt snout bream (Megalobrama amblycephala, BSB, 2n = 48). The phenotypes and genotypes of RCC-L and GF-L differed from those of the parental species but were similar to diploid red crucian carp (2n = 100; RCC) and goldfish (2n = 100; GF), respectively. We sequenced the complete mitochondrial DNAs (mtDNAs) of the KOC, BSB, RCC-L, GF-L, and subsequent generations produced by self-crossing [the self-mating offspring of RCC-L (RCC-L-F₂) to the self-mating offspring of RCC-L-F₂ (RCC-L-F₃) and the self-mating offspring of GF-L (GF-L-F₂)]. Paternal mtDNA fragments were stably embedded in the mtDNAs of both lineages, forming chimeric DNA fragments. In addition to these chimeras, several nucleotide positions in the RCC-L and GF-L lineages differed from the parental bases, and were instead identical with RCC and GF, respectively. Moreover, RCC-L and GF-L mtDNA organization and nucleotide composition were more similar to those of RCC and GF, respectively, compared to parental mtDNA. Finally, phylogenetic analyses indicated that RCC-L and GF-L clustered with RCC and GF, not with the parental species. The molecular dating time shows that the divergence time of KOC and GF was about 21.26 Mya [95% highest posterior density (HPD): 24.41-16.67 Mya], which fell within the period of recent. The heritable chimeric DNA fragments and mutant loci identified in the mtDNA of the RCC-L and GF-L lineages provided important evidence that hybridizations might lead to changes in the mtDNA and the subsequent generation of new lineages. Our findings also demonstrated for the first time that the paternal mtDNA was transmitted into the mtDNA of homodiploid lineages (RCC-L and GF-L), which provided evidence that paternal DNA plays a role in inherited mtDNA. These evolutionary analyses in mtDNA suggest that GF might have diverged from RCC after RCC diverged from koi carp.