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

Gap-free genome assembly of Salangid icefish Neosalanx taihuensis

Neosalanx taihuensis is widely distributed in freshwater and brackish water areas in China. Due to its high commercial value, it has been artificially introduced into many lakes and reservoirs, showing strong ecological adaptability. Here, a gap-free chromosome-level reference genome was constructed by combining short reads, PacBio HiFi long reads, Nanopore ultralong reads and Hi-C data. The reference genome of N. taihuensis was 397.29 Mb with a contig N50 of 15.61 Mb. The assembled sequences were anchored to 28 chromosomes. Furthermore, 20,024 protein-coding genes and 98.16% of the predicted genes were annotated in publicly available biological databases. This high-quality gap-free assembled genome will provide an essential reference for studying the evolution and ecological adaptability of N. taihuensis.

mtDNA CR Evidence Indicates High Genetic Diversity of Captive Forest Musk Deer in Shaanxi Province, China

Forest musk deer (Moschus berezovskii) are endangered ruminants whose adult males secrete musk. China has been breeding forest musk deer artificially since the 1950s in an effort to restore wild populations, with Shaanxi and Sichuan provinces as the two main sites for captive breeding. Genetic diversity is a significant indicator that determines the long-term viability and status of a population, particularly for species at risk of extinction. In this study, we analyzed the current genetic makeup of seven captive forest musk deer populations in the Shaanxi province, using the mitochondrial DNA (mtDNA) control region (CR) as the molecular marker. We sequenced 604 bp of mtDNA CR, with an average content of A+T higher than G+C. We observed 111 variable sites and 39 different haplotypes from 338 sequences. The nucleotide diversity (Pi) and haplotype diversity (Hd) were 0.02887 and 0.908, respectively. Genetic differentiation between these populations was not significant, and the populations might not have experienced rapid growth. By combining our sequences with previous ones, we identified 65 unique haplotypes with 26 rare haplotypes and estimated a total of 90 haplotypes in Shaanxi province captive populations. The Shaanxi province and Sichuan province obtained 88 haplotypes, the haplotypes from the two populations were mixed together, and the two populations showed moderate genetic differentiation. Our findings suggested that captive forest musk deer populations in the Shaanxi province had high genetic diversity, with a rich founder population of about 90 maternal lines. Additionally, managers could develop genetic management plans for forest musk deer based on the haplotype database. Overall, our study will provide insights and guidelines for the conservation of genetic diversity in captive forest musk deer populations in the Shaanxi province.

Assessment of Genetic Diversity of the Salangid, Neosalanx taihuensis, Based on the Mitochondrial COI Gene in Different Chinese River Basins

Simple Summary

In the current study, we estimate the genetic diversity of the salangid Neosalanxtaihuensis sampled from 11 populations in the six typical river basins of China. Using the COI gene sequencing technology, the N. taihuensis population’s genetic difference within and between river basins was investigated. Significant levels of genetic subdivision were detected among populations within basins rather than between basins. Population history dynamics showed that N. taihuensis populations experienced a population expansion during the glacial period in the late Pleistocene. These results suggest that different populations should be considered as different management units to achieve effective conservation and management purposes.

Abstract

The salangid Neosalanx taihuensis (Salangidae) is a commercially important economical fish endemic to China and restricted to large freshwater systems with a wide-ranging distribution. This fish species has continuous distribution ranges and a long-introduced aquaculture history in Chinese basins. However, the research on its population genetic differentiation within and between basins is very limited. In this regard, 197 individuals were sampled from 11 populations in the Nenjiang River Basin (A1–A4), Songhua River Basin (B1), Yellow River Basin (C1–C2), Yangtze River Basin (D1), Lanchang River Basin (E1–E2) and Huaihe River Basin (F1). Based on the COI sequence, the N.taihuensis population’s genetic difference within and between river basins was investigated. The haplotypes and their frequency distributions were strongly skewed, with most haplotypes (n = 13) represented only in single samples each and thus restricted to a single population. The most common haplotype (H4, 67/197) was found in all individuals. The analysis of molecular variance (AMOVA) revealed a random pattern in the distribution of genetic diversity, which is inconsistent with contemporary hydrological structure. The mismatch between the distribution and neutrality tests supported the evidence of a population expansion, which occurred during the late Pleistocene (0.041–0.051 million years ago). Significant levels of genetic subdivision were detected among populations within basins rather than between the six basins. Population history dynamics showed that N. taihuensis experienced an expansion during the glacial period in the late Pleistocene. Therefore, different populations should be considered as different management units to achieve effective conservation and management purposes. These results have great significance for the evaluation and exploitation of the germplasm resources of N. taihuensis.

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.

Morphological characterization and phylogenetic relationships of Indochinese box turtles-The Cuora galbinifrons complex

The members of the Indochinese box turtle complex, namely Cuora galbinifrons, Cuora bourreti, and Cuora picturata, rank the most critically endangered turtle species on earth after more than three decades of over-harvesting for food, traditional Chinese medicine, and pet markets. Despite advances in molecular biology, species boundaries and phylogenetic relationships, the status of the C. galbinifrons complex remains unresolved due to the small number of specimens observed and collected in the field. In this study, we present analyses of morphologic characters as well as mitochondrial and nuclear DNA data to reconstruct the species boundaries and systematic relationships within the C. galbinifrons complex. Based on principal component analysis (PCA) and statistical analysis, we found that phenotypic traits partially overlapped among galbinifrons, bourreti, and picturata, and that galbinifrons and bourreti might be only subspecifically distinct. Moreover, we used the mitochondrial genome, COI, and nuclear gene Rag1 under the maximum likelihood criteria and Bayesian inference criteria to elucidate whether C. galbinifrons could be divided into three separate species or subspecies. We found strong support for a sister relationship between picturata and the other two species, and consequently, we recommend maintaining picturata as a full species, and classifying bourreti and galbinifrons as subspecies of C. galbinifrons. These findings provide evidence for a better understanding of the evolutionary histories of these critically endangered turtles.

The impact of one-decade ecological disturbance on genetic changes: a study on the brine shrimp Artemia urmiana from Urmia Lake, Iran

Urmia Lake, the largest natural habitat of the brine shrimp Artemia urmiana, has progressively desiccated over the last two decades, resulting in a loss of 80% of its surface area and producing thousands of hectares of arid salty land. This ecological crisis has seriously affected the lake’s native biodiversity. Artemia urmiana has lost more than 90% of its population during the decade from 1994 (rainy period) to 2004 (drought period) due to salinity increasing to saturation levels (∼300 g/l). We studied the influence of this ecological crisis on the genetic diversity of A. urmiana in Urmia Lake, based on one cyst collections in 1994 and 2004. AMOVA analysis on ISSR data demonstrated a 21% genetic variation and there was a 5.5% reduction of polymorphic loci between samples. PCoA showed that 77.42% and 68.75% of specimens clustered separately in 1994 and 2004, respectively. Our analyses of four marker genes revealed different genetic diversity patterns with a decrease of diversity at ITS1 and an increase for Na⁺/K⁺ ATPase. There was no notable difference in genetic variation detected for COI and 16S genes between the two periods. However, they represented distinctly different haplotypes. ITS1 and COI followed a population expansion model, whereas Na⁺/K⁺ ATPase and 16S were under demographic equilibrium without selective pressure in the 1994 samples. Neutrality tests confirmed the excess of rare historical and recent mutations present in COI and ITS1 in both samples. It is evident that a short-term ecological disturbance has impacted the genetic diversity and structure of A. urmiana.

Phylogeography and genetic population structure of the spadenose shark (Scoliodon macrorhynchos) from the Chinese coast

The population structure of Scoliodon macrorhynchos from the Chinese coast was investigated using the mitochondrial control region. All 19 mtDNA haplotypes from 219 sequences were identified. Relatively high average haplotype diversity (0.797) and relatively low average nucleotide diversity (0.0013) were found together with a recent and sudden population expansion. Analysis of the mismatch distributions, neutrality tests and Bayesian skyline plot showed a pattern consistent with a recent population expansion event that may have taken place during the last glacial maximum (LGM). The analysis of molecular variance (AMOVA) showed the low genetic differentiation between the populations, which may be a general feature of sharks living in coastal areas. The phylogenetic and cluster analysis of the mtDNA indicates that two putative groups (K = 2) existed in S. macrorhynchos, showing that the Taiwan Strait acted as a biogeographic barrier during major drops in the sea level in the late Pliocene epoch.

Genetic diversity and demographic history of the giant river catfish Sperata seenghala inferred from mitochondrial DNA markers

The giant river catfish Sperata seenghala has huge demand in South Asian countries due to its low number of intramuscular bones and nutritive value. However, the culture practises for this fish have not been standardized and the current demand for this fish is being met by capture fisheries only. Unregulated and indiscriminate fishing would lead overexploitation of fish stocks subsequently stock depletion. Genetic diversity between populations would give insight about population structure and demography. In the present study, S. seenghala stocks from three rivers, namely Ganga, Brahmaputra and Mahanadi were characterized using cytochrome b gene and D-loop region. Moderate to high haplotype diversity and low nucleotide diversity values were observed in all populations. Analysis of molecular variance and pairwise F_ST values showed significant genetic differentiation among populations. Patterns of diversity, haplotype networks and mismatch distribution strongly suggest a historical influence on the genetic structure of S. seenghala populations. S. seenghala stocks from these three rivers are genetically distinct units and management measures should be formulated separately for each population.

Complete mitochondrial genome of Hemisalanx brachyrostralis (Osteichthyes: Salangidae)

Hemisalanx brachyrostralis belonging to the family Salangidae is endemic to the Yangtze River. This species has been listed on the Chinese Red List because of the serious decrease in its resources. In this study, we analyzed the complete mtDNA (16588 bp long) of H. brachyrostralis. Overall base composition of the genome is 25.1% A, 25.4% T, 18.7% G, and 30.8% C. The complete mtDNA contains 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes (12S rRNA and 16S rRNA), and 1 control region. Apart from the ND6 gene and nine tRNA genes encoded on the L-strand, most of the genes are on the H-strand. H. brachyrostralis has the lowest genetic diversity among the Salangid species, so further studies on conservation genetics must be conducted.

Population divergence and structure of Cirrhinus mrigala from peninsular rivers of India, revealed by mitochondrial cytochrome b gene and truss morphometric analysis

Genetic diversity and population structure of Cirrhinus mrigala from peninsular riverine systems of India was studied using mitochondrial DNA gene, cytochrome b and truss morphometric analysis. Analysis of 982 bp of the cytochrome b gene from 182 samples collected from six rivers revealed the presence of 28 haplotypes with overall high haplotype diversity value of 0.78981 and nucleotide diversity value of 0.00215. Analysis of molecular variance (AMOVA) showed that genetic variation is mainly harbored within populations rather than among populations. The pairwise Fst values (-0.009 to 0.084) was indicative of a low genetic structure among mrigal populations. Morphometric examination of 243 samples using 10 truss landmarks and principal component analysis showed a similar trend when compared with genetic data. Overall, low genetic and morphometric differences were observed despite those populations from different geographic locations. The results of this study would provide essential information to resource recovery and help in delineating populations for fishery management. Besides, the data will provide a valuable baseline for further investigations on the geographic distribution of this commercially important fish species.

Phylogeographical pattern of Mazocraeoides gonialosae (Monogenea, Mazocraeidae) on the dotted gizzard shad, Konosirus punctatus, along the coast of China

In the present study, we examined the phylogeographical pattern of the monogenean, Mazocraeoides gonialosae, which parasitises the dotted gizzard shad (Konosirus punctatus) along the coast of China. Fragments of 756 bp of the mitochondrial cytochrome c oxidase subunit I gene were sequenced for 147 individuals from seven localities along the coast of China. Phylogenetic analysis revealed no significant genealogical clades of samples corresponding to sampling localities. Analyses of molecular variance and pairwise F(ST) suggested a high rate of gene flow and the lack of a predictable genetic structure between different populations of this parasite. Both neutrality tests and mismatch distribution analyses indicated a recent population expansion in M. gonialosae after the last glacial maximum. Gradually decreasing genetic diversity in more northerly populations implied a historical south-to-north expansion of this parasite. Dispersal of eggs and larvae with ocean currents was considered to be associated with the genetic homogeneity of this species. The limited time to accumulate genetic variation after the last glacial maximum may also account in part for the lack of phylogeographical structure in the studied region.

Genetic evidence of recent population contraction in the southernmost population of giant pandas

Anthropogenic habitat loss and fragmentation have been implicated in the endangerment and extinction of many species. Here we assess genetic variation and demographic history in the southernmost population of giant pandas (Ailuropoda melanoleuca) that continues to be threatened by habitat degradation and fragmentation, using noninvasive genetic sampling, mitochondrial control region sequence and 12 microsatellite loci. Compared to other giant panda populations, this population has medium-level genetic diversity based on the measure of both mitochondrial and nuclear markers. Mitochondrial DNA-based demographic analyses revealed that no historical population expansion or contraction has occurred, indicating a relatively stable population size. However, a Bayesian-coalescent method based on the observed allele distribution and allele frequencies of microsatellite clearly did detect, quantify and date a recent decrease in population size. Overall, the results indicate that a population contraction in the order of 95-96% has taken place over the last 910-999 years and is most likely due to anthropogenic habitat loss. These findings highlight the need for a greater focus on habitat protection and restoration for the long-term survival of this giant panda population.

Multiple unrelated founding events for the long-distance Pleistocene dispersal of the Salangid, Neosalanx taihuensis: a general demographic model for inshore-orientated freshwater fish

The Salangid icefish Neosalanx taihuensis (Salangidae) originated from inshore of the East China seas and underwent adaptive freshwater radiation from the mid-Miocene to the early Pleistocene. The distribution of its genetic diversity presents a random pattern inconsistent with contemporary hydrological structure. In the present study, coalescent simulations were used to analyze its Pleistocene dispersal history. Population history simulation supported the hypothesis of long-distance dispersal during the Pleistocene based on multiple unrelated founding events. This analogous genetic pattern has been described for other inshore-orientated freshwater fish, and may represent a general history dispersal model for the phylogeography of these species. From network analysis, three subclades (Clades 1-3) grouped consistently with three probable ancestral haplotypes (H36, H27, and H33). Demographic analysis also revealed that the ancestral haplotype group (Clade 1) dispersed into freshwater during an interglacial age about 0.35Ma, while Clades 2 and 3 dispersed about 0.12 and 0.145Ma, respectively. The N. taihuensis population remained relatively small for a considerable amount of time during the Pleistocene ages, with population expansion events mainly occurring after the last glacial maximum (LGM).