Phylogenetic relationships of salangid fishes (Osmeridae, Salanginae) with comments on phylogenetic placement of the salangids based on mitochondrial DNA sequences

Correction of GenBank's taxonomic entry error raises a new issue regarding intergeneric relationships among salangid fishes (Osmeriformes: Salangidae)

The GenBank database of publicly available nucleotide sequences is the largest genetic repository providing vitally important resources for downstream applications in biology and medicine. The concern raised about reliability of GenBank data necessitates monitoring of possible taxonomic entry errors. A case of mitochondrial genome (or mitogenome) misidentification for a salangid fish belonging to the genus Neosalanx (Osmeriformes, Salangidae) is considered in this report. The GenBank database contains four complete mitogenome sequences of N. taihuensis with the accession numbers JX524196, KP170510, MH348204, and MW291630. The overall mean p-distance for these sequences is quite high (7.01 ± 0.14 %) but becomes 29-fold lower (0.24 ± 0.05 %) after excluding the MW291630 mitogenome. An analysis of all available nucleotide sequences of salangids has shown that the observed inconsistency in the level of divergence between N. taihuensis mitogenomes is due to species misidentification. It has turned out that the mitogenome MW291630 available in GenBank does not belong to N. taihuensis, but is, in fact, a mitogenome of N. jordani misidentified as N. taihuensis. The resolved taxonomic identity of the MW291630 mitogenome, as well as an extended sample of species with investigated single-marker sequences, has raised some new issues regarding intergeneric relationships in salangid fishes. In particular, the obtained data do not support synonymization of the genus Neosalanx with Protosalanx, as was suggested in the last revision of the salangid classification. As the comparative analysis of interspecific and intergeneric divergences shows, Protosalanx is not an all-inclusive clade that includes all Neosalanx species. Instead, it consists of (at least) two evolutionary distinct lineages with the level of genetic divergence between them matching well the mean value of divergence between the other salangid genera. Further analysis using nuclear genome-wide data is required to have new insights into the evolution of salangid fishes.

Updated species checklist of fishes from Lake Dongting in Hunan Province, South China: Species diversity and conservation

A lack of an updated checklist of freshwater fish species from Lake Dongting is a great hindrance to further biodiversity analysis. A seasonal survey of fishes in the lake was conducted from October 2017 to January 2019. Based on the data obtained during the field survey and coupled with known literature and the latest taxonomic development of relevant taxa, the species checklist of fishes from Lake Dongting was updated. A total of 130 species from 12 orders, 30 families and 76 genera has been documented, containing 126 native species and four alien species. Its fish fauna is dominated by the Xenocyprididae that has the highest number of included species (30), followed by the Gobionidae (25) and Acheilognathidae (11). This checklist comprises 20 species undergoing nomenclatural changes and 11 new records, eight of which are native and three exotic. It excludes 20 species, which have been reported in error in historical works, due to synonyms, erroneous records, taxonomic changes and unconfirmed records. Unsampled in this survey were 34 species that are ecologically specialised: migratory, rheophilic, predatory, shellfish-dependent or pelagic-egg-spawning. While some of these species eluded capture likely due to the paucity of population, others may have been extirpated in Lake Dongting perhaps owing to human perturbations, such as river damming across affluents or the Chang-Jiang mainstem, sand dredging, overfishing or water pollution. The updated checklist lays a sound foundation for biodiversity conservation of fishes in Lake Dongting.

Recombinant Mitochondrial Genomes Reveal Recent Interspecific Hybridization between Invasive Salangid Fishes

The interspecific recombination of the mitochondrial (mt) genome, if not an experimental artifact, may result from interbreeding of species with broken reproductive barriers, which, in turn, is a frequent consequence of human activities including species translocations, habitat modifications, and climate change. This issue, however, has not been addressed for Protosalanx chinensis and other commercially important and, simultaneously, invasive salangid fishes that were the product of successful aquaculture in China. To assess the probability of interspecific hybridization, we analyzed the patterns of diversity and recombination in the complete mitochondrial (mt) genomes of these fishes using the GenBank resources. A sliding window analysis revealed a non-uniform distribution of the intraspecific differences in P. chinensis with four highly pronounced peaks of divergence centered at the COI, ND4L-ND4, and ND5 genes, and also at the control region. The corresponding divergent regions in P. chinensis show a high sequence similarity (99−100%) to the related salangid fishes, Neosalanx tangkahkeii and N. anderssoni. This observation suggests that the divergent regions of P. chinensis may represent a recombinant mitochondrial DNA (mtDNA) containing mt genome fragments belonging to different salangid species. Indeed, four, highly significant (pairwise homoplasy index test, P < 0.00001) signals of recombination have been revealed at coordinates closely corresponding to the divergent regions. The recombinant fragments are, however, not fixed, and different mt genomes of P. chinensis are mosaic, containing different numbers of recombinant events. These facts, along with the high similarity or full identity of the recombinant fragments between the donor and the recipient sequences, indicate a recent interspecific hybridization between P. chinensis and two Neosalanx species. Alternative hypotheses, including taxonomical misidentifications, sequence misalignments, DNA contamination, and/or artificial PCR recombinants, are not supported by the data. The recombinant fragments revealed in our study represent diagnostic genetic markers for the identification and distinguishing of hybrids, which can be used to control the invasive dynamics of hybrid salangid fishes.

A multilocus phylogeny of Asian noodlefishes Salangidae (Teleostei: Osmeriformes) with a revised classification of the family

A group of small and transparent Asian noodlefishes (Osmeriformes: Salangidae) are commercially important fishery species, however, interrelationships among these fishes remain unresolved in previous studies using mitochondrial markers. We re-examine phylogenetic relationships of Salangidae by including complete taxon sampling, based on seven nuclear loci and one mitochondrial gene using a multilocus coalescence-based species-tree method. Our results show a well-resolved phylogeny of Salangidae that does not agree with previous hypotheses. The topology test suggests that our hypothesis represents the most likely phylogeny. Using the inferred species-tree as criterion, we recombine the rank of subfamilies and genera in the Salangidae, and erect a new genus Neosalangichthys. Our revised classification of Salangidae is well supported by reinterpreting previously proposed diagnostic characters. Finally, re-defined synapomorphic characters are used to erect a key to the genera of Salangidae.

Phylogeographical analysis of an estuarine fish, Salanx ariakensis (Osmeridae: Salanginae) in the north-western Pacific

This study extended the geographic coverage of a previous study to explore population genetic structure and demographic history in the Ariake icefish Salanx ariakensis from three populations of continental coastlines and one island population in the north-western Pacific based on a partial sequence of the mitochondrial cytochrome b gene. The S. ariakensis showed high genetic diversity and strong genetic structure. Phylogenetic analysis showed a shallow gene tree with no clear phylogeographical structure. Contiguous range expansion and restricted gene flow were inferred to be main population events by nested-clade analysis. Significant genetic differentiations between populations could be attributable to negligible gene flow by coalescent analysis. High nucleotide diversity of each population was due to geographic mixing of heterogenous haplotypes during lowering sea levels of the Pleistocene. These findings indicate that cycles of geographic isolation and secondary contact happened in the Pleistocene glacial-interglacial cycles shaping genetic structure and population demography of S. ariakensis.

Molecular resolution of the systematics of a problematic group of fishes (Teleostei: Osmeridae) and evidence for morphological homoplasy

Relationships among the species of Northern Hemisphere smelts (family Osmeridae) have long been debated in the fish systematics literature. Eight independent studies based on morphological characters failed to reach any consensus on osmerid interrelationships. We reconstruct the osmerid phylogeny based on DNA sequence data from three mitochondrial (cytb, 16S, 12S) and three nuclear (ITS2, S71, RAG1) gene regions from multiple individuals of the 14 species in 6 genera, using the Japanese ayu (Plecoglossus altivelis) as the outgroup. Analyses with different combinations of nuclear and mitochondrial datasets yielded a generally well-resolved phylogeny of the genera that conflicts with previous hypotheses of osmerid interrelationships, and Shimodaira-Hasegawa tests suggest our topology with the current molecular dataset is significantly better than earlier reconstructions. In addition, mapping 114 morphological characters used in previous studies onto our phylogeny shows widespread homoplasy, which is likely the source of the systematic disagreement produced in earlier works.

Complex population genetic and demographic history of the Salangid, Neosalanx taihuensis, based on cytochrome b sequences

BACKGROUND

The Salangid icefish Neosalanx taihuensis (Salangidae) is an economically important fish, which is endemic to China, restricted to large freshwater systems (e.g. lakes, large rivers and estuaries) and typically exhibit low vagility. The continuous distribution ranges from the temperate region of the Huai and Yellow River basins to the subtropical region of the Pearl River basin. This wide ranging distribution makes the species an ideal model for the study of palaeoclimatic effects on population genetic structure and phylogeography. Here, we aim to analyze population genetic differentiation within and between river basins and demographic history in order to understand how this species responded to severe climatic oscillations, decline of the sea levels during the Pleistocene ice ages and tectonic activity.

RESULTS

We obtained the complete mtDNA cytochrome b sequences (1141 bp) of 354 individuals from 13 populations in the Pearl River, the Yangze River and the Huai River basin. Thirty-six haplotypes were detected. Haplotype frequency distributions were strongly skewed, with most haplotypes (n = 24) represented only in single samples each and thus restricted to a single population. The most common haplotype (H36) was found in 49.15% of all individuals. Analysis of molecular variance (AMOVA) revealed a random pattern in the distribution of genetic diversity, which is inconsistent with contemporary hydrological structure. Significant levels of genetic subdivision were detected among populations within basins rather than between the three basins. Demographic analysis revealed that the population size in the Pearl River basin has remained relatively constant whereas the populations in the Yangze River and the Huai River basins expanded about 221 and 190 kyr ago, respectively, with the majority of mutations occurring after the last glacial maximum (LGM).

CONCLUSION

The observed complex genetic pattern of N. taihuensis is coherent with a scenario of multiple unrelated founding events by long-distance colonization and dispersal combined with contiguous population expansion and locally restricted gene flow. We also found that this species was likely severely impacted by past glaciations. More favourable climate and the formation of large suitable habitations together facilitated population expansion after the late Quaternary (especially the LGM). We proposed that all populations should be managed and conserved separately, especially for habitat protection.