Genetic diversity, spatial connectivity, and population structure of Asian silurid catfish Wallago attu (Bloch and Schneider, 1801) in the Ganga River System: insights from mitochondrial DNA analysis

BACKGROUND

The Ganga River System (GRS) is a biodiversity hotspot, its ecological richness is shaped by a complex geological history. In this study, we examined the genetic diversity, spatial connectivity, and population structure of the Asian Silurid catfish, Wallago attu, across seven tributaries of the GRS.

METHODS AND RESULTS

We employed three mitochondrial DNA (mtDNA) regions: cytochrome c oxidase subunit I (COXI), cytochrome b (Cyt b), and control region (CR). Our comprehensive dataset encompassed 2420 bp of mtDNA, derived from 176 W. attu individuals across 19 sampling sites within the seven rivers of GRS. Our findings revealed high gene diversity (Hd:0.99) within W. attu populations. Analysis of Molecular Variance (AMOVA) highlighted that maximum genetic variations were attributed within the populations, and the observed genetic differentiation among the seven populations of W. attu ranged from low to moderate. Network analysis uncovered the presence of three distinct genetic clades, showing no specific association with seven studied rivers. Bayesian skyline plots provided insights into the demographic history of W. attu, suggesting a recent population expansion estimated to have occurred approximately 0.04 million years ago (mya) during the Pleistocene epoch.

CONCLUSIONS

These results significantly enhance our understanding of the genetic diversity and spatial connectivity of W. attu, serving as a vital foundation for developing informed conservation strategies and the sustainable management of this economically valuable resource within the Ganga River System.

In silico prospecting of the mtDNA of Macrobrachium amazonicum from transcriptome data

BACKGROUND

Macrobrachium amazonicum is a freshwater prawn widely distributed in South America that is undergoing speciation, so the denomination "M. amazonicum complex" is used for it. The mitochondrial cytochrome c oxidase subunit I (COI) gene has been used to elucidate this speciation, but heteroplasmies and pseudogenes have been recorded, making separation difficult. Obtaining genes from cDNA (RNA) rather than genomic DNA is an effective tool to mitigate those two types of occurrences. The aim of this study was to assemble in silico the mitochondrial DNA (mtDNA) of the Amazonian coastal population of M. amazonicum inhabiting the state of Pará.

RESULTS

Sequences were obtained from the prawn's transcriptome using the de novo approach. Six libraries of cDNA from the androgen gland, hepatopancreas, and muscle tissue were used. The mtDNA of M. amazonicum was 14,960 bp in length. It contained 13 protein-coding genes, 21 complete transfer RNAs, and the 12S and 16S subunits of ribosomal RNA. All regions were found on the light strand except tRNAGln, which was on the heavy strand. The control region (D-loop) was not recovered, making for a gap of 793 bp. The cladogram showed the formation of the well-defined Macrobrachium clade, with high support value in the established branches (91-100). The three-dimensional spatial conformation of the mtDNA-encoded proteins showed that most of them were mainly composed of major α-helices that typically shows in those proteins inserted in the membrane (mitochondrial).

CONCLUSIONS

It was possible to assemble a large part of the mitochondrial genome of M. amazonicum in silico using data from other genomes deposited in GenBank and to validate it through the similarities between its COI and 16S genes and those from animals of the same region deposited in GenBank. Depositing the M. amazonicum mtDNA sequences in GenBank may help solve the taxonomic problems recorded for the species, in addition to providing complete sequences of candidate coding genes for use as biomarkers in ecological studies.

Pilot study of a comprehensive resource estimation method from environmental DNA using universal D-loop amplification primers

Many studies have investigated the ability of environmental DNA (eDNA) to identify the species. However, when individual species are to be identified, accurate estimation of their abundance using traditional eDNA analyses is still difficult. We previously developed a novel analytical method called HaCeD-Seq (haplotype count from eDNA by sequencing), which focuses on the mitochondrial D-loop sequence for eels and tuna. In this study, universal D-loop primers were designed to enable the comprehensive detection of multiple fish species by a single sequence. To sequence the full-length D-loop with high accuracy, we performed nanopore sequencing with unique molecular identifiers (UMI). In addition, to determine the D-loop reference sequence, whole genome sequencing was performed with thin coverage, and complete mitochondrial genomes were determined. We developed a UMI-based Nanopore D-loop sequencing analysis pipeline and released it as open-source software. We detected 5 out of 15 species (33%) and 10 haplotypes out of 35 individuals (29%) among the detected species. This study demonstrates the possibility of comprehensively obtaining information related to population size from eDNA. In the future, this method can be used to improve the accuracy of fish resource estimation, which is currently highly dependent on fishing catches.

Multiple genetic lineages of anadromous migratory Mekong catfish Pangasius krempfi revealed by mtDNA control region and cytochrome b

Population genetic structure of migratory fishes can reflect ecological and evolutionary processes. Pangasius krempfi is a critically important anadromous catfish in the Mekong River, and its migration pathways and genetic structure have attracted much interest. To investigate, we quantified the genetic diversity of this species using the control region (D-loop) and Cytochrome b (Cytb) of the mitochondrial genome. Fish were sampled (n = 91) along the Mekong tributaries from upstream to estuaries and coastal areas in the Mekong Delta and compared to three samples from Pakse (Laos). The D-loop haplotype (0.941 ± 0.014) and nucleotide diversity (0.0083 ± 0.0005) were high in all populations, but that of Cytb was low (0.331 ± 0.059 and 0.00063 ± 0.00011, respectively). No genetic difference was detected between populations, indicating strong gene flow and confirming a long migration distance for this species. Pangasius krempfi was not genetically structured according to geographical populations but was delineated into three haplogroups, suggesting multiple genetic lineages. The presence of haplogroups in each sampling location implies that migration downstream is random but parallel when the fish enter two river tributaries bifurcating from the main Mekong River. Individuals can also migrate along the coast, far from the estuaries, suggesting a longer migration path than previously reported, which is crucial for maintaining diverse genetic origin and migration pathways for P. krempfi.

Comparative mitogenomics and phylogenetics of the family Carangidae with special emphasis on the mitogenome of the Indian Scad Decapterus russelli

Carangids are abundant and commercially important marine fish that contribute to a significant portion of the fisheries in many parts of the world. In the present study, we characterized the complete mitogenome of the Indian scad, Decapterus russelli and performed a comprehensive comparative mitogenomic analysis of the family Carangidae. The comparative mitogenomics provided valuable insights into the structure, variability, and features of the coding and non-coding regions that evolved across species over millions of years. The structural features of tRNAs revealed changes in the frequency of mismatched and wobble base pairs, which is reflected in the base composition of H and L strands. The highly conserved sequence motif of the mTERF binding site in carangids over the ~ 400 MYA of their divergence demonstrated the functional importance of these sites. The control region of carangids was characterized by the presence of discontinuous repeat units with a high rate of sequence divergence in the form of base substitutions, insertions, and deletions. The maintenance of secondary structures in the control region independent of the rapid evolution of primary structure suggested the effect of selective constraints on their maintenance. Maximum likelihood (ML) and Bayesian inference (BI) phylogeny revealed a similar topology consistent with previous taxonomic studies. The extant carangids diverged through the evolutionary events experienced during the Cretaceous, Paleogene, and Neogene periods.

Reduced genetic diversity and the success of the invasive peacock bass (Cichliformes: Cichlidae)

Several species of Cichla successfully colonized lakes and reservoirs of Brazil, since the 1960's, causing serious damage to local wildlife. In this study, 135 peacock bass were collected in a reservoir complex in order to identify if they represented a single dominant species or multiple ones, as several Cichla species have been reported in the basin. Specimens were identified by color pattern, morphometric and meristic data, and using mitochondrial markers COI, 16S rDNA and Control Region (CR). Overlapping morphological data and similar coloration patterns prevented their identification using the taxonomic keys to species identification available in the literature. However, Bayesian and maximum likelihood from sequencing data demonstrated the occurrence of a single species, Cichla kelberi. A single haplotype was observed for the 16S and CR, while three were detected for COI, with a dominant haplotype present in 98.5% of the samples. The extreme low diversity of the transplanted C. kelberi evidenced a limited number of founding maternal lineages. The success of this colonization seems to rely mainly on abiotic factors, such as increased water transparency of lentic environments that favor visual predators that along with the absence of predators, have made C. kelberi a successful invader of these reservoirs.

Characterization of the complete mitochondrial genome of Chrysochir aureus and phylogenetic studies of Sciaenidae

The complete mitochondrial genome of Chrysochir aureus was sequenced. The full length of the mitochondrial genome was 16,501 bp, including 13 protein-coding genes (PCGs), two ribosomal RNAs, 22 transfer RNA genes, a non-coding control region (CR) and one origin of replication on the light-strand (OL). The total nucleotide composition of mitochondrial DNA was 26.95% A, 29.99% C, 26.29% T, and 16.77% G. Twelve PCGs used the canonical ATG as their initiation codon, whereas COI gene started with an alternative start codon GTG. The mitochondrial genome of C. aureus described in this study could be a useful basis for management of this species and laid a foundation for further research involved with phylogenetic relationship within Sciaenidae.

Characterization of the complete mitochondrial genome of Ostorhinchus novemfasciatus and phylogenetic studies of Apogoninae

The complete mitochondrial genome of Ostorhinchus novemfasciatus was first presented in this study. The full length of the mitochondrial genome was 16,779 bp, including 13 protein-coding genes (PCGs), two ribosomal RNAs, 22 transfer RNA genes, a non-coding control region (CR) and one origin of replication on the light-strand (OL). The total nucleotide composition of mitochondrial DNA was 26.0% A, 30.2% C, 26.2% T and 17.5% G. 12 PCGs used the canonical ATG as their initiation codon, whereas COI gene started with an alternative start codon GTG. The mitochondrial genome of O. novemfasciatus described in this study could be a useful basis for the management of this species and laid a foundation for further research involved with phylogenetic relationship within Apogoninae.

Genetic legacy of tertiary climatic change: a case study of two freshwater loaches, Schistura fasciolata and Pseudogastromyzon myersi, in Hong Kong

The high biodiversity and strong population structure of freshwater fauna has often been attributed to historical geological and climatic alterations. The impact of these historical changes on obligate freshwater species on a small geographical scale has not been well understood due to the lack of fine-scale comparative phylogeographic studies. Strong population structure has been reported in a goby and a caridean shrimp in Hong Kong, a small but highly developed city in South China, but the common drivers of population differentiation in freshwater fauna in this region remain unclear. This study examined the fine-scale phylogeographic patterns of two freshwater loaches, Schistura fasciolata and Pseudogastromyzon myersi in Hong Kong, using sequence data of mitochondrial control region and two nuclear markers (interphotoreceptor retinoid binding protein gene 2 and ribosomal protein S13 gene). Results show that they exhibit pronounced population structure as supported by high and significant Φ_ST. Phylogenetic analyses based on the control region reveal six and three distinct lineages in S. fasciolata and P. myersi, respectively. Phylogeographic structure of both species generally follows the paleodrainage pattern, though P. myersi shows a shallower structure on the Mainland, perhaps due to their higher mobility. Most of these lineages diverged during the Pliocene and Late Pleistocene, a period with marked sea-level fluctuations. In a broader context, this suggests that sea-level fluctuation played an important role in shaping even the fine-scale population structure of freshwater fish in South China, implying that the genetic diversity of this fauna may be higher than expected.

Complete mitochondrial genome of Japanese bigeye (Pristigenys niphonia): genome characterization and phylogenetic analysis

The Japanese bigeye (Pristigenys niphonia) is a species in the genus Pristigenys and in the family Priacanthidae. To understand the phylogenetic relationship of Japanese bigeye in teleost, we firstly determined the complete mitochondrial genome of Japanese bigeye. The entire mitochondrial genome of Japanese bigeye is 16,519bp in length, including 13 protein-coding genes and 2 ribosomal RNA genes (rRNA), 22 transfer RNA genes (tRNAs), and 2 main non-coding regions. The overall base composition is 24.9% of T, 30.6% of C, 27.7% of A, and 16.8% of G. The gene arrangement, base composition, and tRNA structures of the complete mitochondrial genome of Japanese bigeye is consistent with those of other teleost. The complete mitochondrial genome of Japanese bigeye was used to construct phylogenetic tree, which shows that Japanese bigeye is clustered with the fishes of the order Perciformes. We expect that the availability of mitochondrial genome of Japanese bigeye will facilitate the further investigations of the taxonomic resolution, biogeography, and molecular systematic.

Panmixia in a Critically Endangered Fish: The Totoaba (Totoaba macdonaldi) in the Gulf of California

Conservation of the evolutionary legacy of endangered species is a key component for long-term persistence. Totoaba is a long-lived fish endemic to the Gulf of California and is considered critically endangered. There is currently a debate concerning its conservation status and whether it can be used as a fishery resource. Unfortunately, basic information on biological and genetic population structure of the species is lacking. We sampled 313 individuals and employed 16 microsatellite loci and 3 mitochondrial DNA markers (16S, 547 pb; COI, 619 pb; control region, 650 pb) to assess population structure and demography of totoaba in the Gulf of California, with samples from locations that encompass nearly all of its recognized geographic distribution. We could not reject a hypothesis of panmixia for totoaba, using nuclear or mitochondrial markers. Demographic analysis of mtDNA suggests a sudden population expansion model. The results have important implications for totoaba conservation because poaching is a significant conservation challenge and could have additive negative effects over the single population of totoaba in the Gulf of California.

Secondary contact and asymmetrical gene flow in a cosmopolitan marine fish across the Benguela upwelling zone

The combination of oceanographic barriers and habitat heterogeneity are known to reduce connectivity and leave specific genetic signatures in the demographic history of marine species. However, barriers to gene flow in the marine environment are almost never impermeable which inevitably allows secondary contact to occur. In this study, eight sampling sites (five along the South African coastline, one each in Angola, Senegal and Portugal) were chosen to examine the population genetic structure and phylogeographic history of the cosmopolitan bluefish (Pomatomus saltatrix), distributed across a large South-east Atlantic upwelling zone. Molecular analyses were applied to mtDNA cytochrome b, intron AM2B1 and 15 microsatellite loci. We detected uncharacteristically high genetic differentiation (F_ST 0.15-0.20; P<0.001) between the fish sampled from South Africa and the other sites, strongly influenced by five outlier microsatellite loci located in conserved intergenic regions. In addition, differentiation among the remaining East Atlantic sites was detected, although mtDNA indicated past isolation with subsequent secondary contact between these East Atlantic populations. We further identified secondary contact, with unidirectional gene flow from South Africa to Angola. The directional contact is likely explained by a combination of the northward flowing offshore current and endogenous incompatibilities restricting integration of certain regions of the genome and limiting gene flow to the south. The results confirm that the dynamic system associated with the Benguela current upwelling zone influences species distributions and population processes in the South-east Atlantic.

Complete mitochondrial genome of black-banded trevally (Seriolina nigrofasciata): Genome characterization and phylogenetic considerations

The black-banded trevally (Seriolina nigrofasciata) is a species of the family Carangidae and the only known member of genus Seriolina. To understand the phylogenetic relationship of black-banded trevally in teleost, we first determined the complete mitochondrial genome of black-banded trevally. The entire mitochondrial genome of black-banded trevally is 16 531 bp in length, containing 13 protein-coding genes and 2 ribosomal RNA genes (rRNA), 22 transfer RNA genes (tRNAs), and 2 main non-coding regions. The overall base composition is T 25.8%, C 30.0%, A 26.7%, and G 17.5%. The gene arrangement, base composition, and tRNA structures of black-banded trevally are consistent with those of other teleost. Two of the central conserved sequence blocks (CSB-2 and CSB-3) were identified and the core sequence (TACATGTATGTA) of terminal-associated sequences was recognized in the control region. Meanwhile, the conserved motif 5'-GCCGG-3' was identified in the origin of light-strand replication of black-banded trevally. The complete mitochondrial genome of black-banded trevally was used to construct phylogenetic tree, which shows that black-banded trevally is clustered with the fishes of the genus Seriola. We expect that the availability of the mitochondrial genome of black-banded trevally will facilitate the further investigations of molecular systematic and phylogenetic analysis of the Carangidae.

Genetic differentiation in the populations of red piranha, Pygocentrus nattereri Kner (1860) (Characiformes: Serrasalminae), from the river basins of northeastern Brazil

The red piranha, Pygocentrus nattereri, is an important resource for artisanal and commercial fisheries. The present study determines the genetic differentiation among P. nattereri populations from the northeastern Brazilian state of Maranhão. The DNA was isolated using a standard phenol-chloroform protocol and the Control Region was amplified by PCR. The PCR products were sequenced using the didesoxyterminal method. A sequence of 1039 bps was obtained from the Control Region of 60 specimens, which presented 33 polymorphic sites, 41 haplotypes, һ =0.978 and π =0.009. The neutrality tests (D and Fs) were significant (P < 0.05) for most of the populations analyzed. The AMOVA indicated that most of the molecular variation (72%) arises between groups. The fixation index was highly significant (FST = 0.707, P < 0.00001). The phylogenetic analyses indicated that the specimens represented a monophyletic group. Genetic distances between populations varied from 0.8% to 1.9%, and were <0.5% within populations. The degree of genetic differentiation found among the stocks of P. nattereri indicates the need for the development of independent management plans for the different river basins in order to preserve the genetic variability of their populations.

Population genetic structure of Indian oil sardine, Sardinella longiceps along Indian coast

Genetic stock structure and historical demography of Indian oil sardine, a commercially and ecologically important small pelagic fish, was studied using mitochondrial control region and Cytochrome C Oxidase I (COI) sequences. A 758 bp portion of the control region in 287 individuals and a 576 bp portion of the COI gene in 291 individuals from 10 locations along the distribution range were amplified resulting in 236 and 84 haplotypes, respectively. The high haplotype and low nucleotide diversity values (0.99 and 0.19 for control region and 0.85 and 0.004 for COI, respectively) are characteristic of populations having undergone a demographic expansion. Genetic differentiation, ΦST, was low and insignificant between populations using both control region and COI gene markers. Mismatch analysis showed a recent demographic and spatial expansion coinciding with the late Pleistocene epoch. Mantel tests revealed the lack of isolation by distance which is attributable either to high levels of migration overriding the effect of genetic drift or to insufficient time for accomplishing a balance between migration and drift after a recent range expansion.

Complete mitochondrial genome sequence of Tridentiger bifasciatus and Tridentiger barbatus (Perciformes, Gobiidae): a mitogenomic perspective on the phylogenetic relationships of Gobiidae

The fishes of suborder Gobioidei is the largest group of those in present living Perciformes, which contains about 2,200 species belonging to 270 genera of 9 families in the world. The monophyly and phylogenetic relationships of gobies have been controversial and disputable for a long time. In the present study, the complete mitochondrial genome of the shimofuri goby Tridentiger bifasciatus (T. bifasciatus) and shokihaze goby Tridentiger barbatus (T. barbatus) were firstly determined. The two mitochondrial genomes were both consisted of 2 ribosomal RNA (rRNA) genes, 13 protein-coding genes, 22 transfer RNA (tRNA) genes, and one major control region (CR). They shared similar features with those of other gobies in terms of gene arrangement, base composition, and tRNA structures. The CR was absence of typical conserved blocks (CSB-E, and CSB-F) respectively for the T. bifasciatus and T. barbatus. Phylogenomic analyses, which based on 12 concatenated protein-coding genes and complete mitochondrial genome sequences, revealed that there were two groups within the Gobiidae. A large group consisted of the Amblyopinae, Gobionellinae, Oxudercinae and Sicydiinae, and Amblyopinae was nested in Oxudercinae and they were both paraphyletic to Sicydiinae. The other group was the Gobiinae. As a whole, our phylogenetic data was different from the traditionally classification of Gobiidae, but supported the new phylogenetic taxonomy view of Thacker (Copeia 2009:93-104, 2009).