Phylogeny and biogeography of highly diverged freshwater fish species (Leuciscinae, Cyprinidae, Teleostei) inferred from mitochondrial genome analysis

Fifth mass extinction event triggered the diversification of the largest family of freshwater gastropods (Caenogastropoda: Truncatelloidea: Hydrobiidae)

The fifth mass extinction event (MEE) at the Cretaceous-Palaeogene (K-Pg) boundary 66 million years ago (Ma) led to massive species loss but also triggered the diversification of higher taxa. Five models have been proposed depending on whether this diversification occurred before, during or after the K-Pg boundary and the rate of species accumulation. While the effects of the K-Pg MEE on vertebrate evolution are relatively well understood, the impact on invertebrates, particularly in freshwater ecosystems, remains controversial. One example is the hyperdiverse Hydrobiidae-the most species-rich family of freshwater gastropods. Whereas some studies place its origin in the Jurassic or even Carboniferous, most fossil records postdate the K-Pg event. We therefore used robustly time-calibrated multi-locus phylogenies of >400 species representing >100 hydrobiid genera to unravel its evolutionary history and patterns of diversification. We found that the family started diversifying shortly after the K-Pg boundary (∼60 Ma; 95% highest posterior density 52-69 Ma). Lineage richness gradually increased to the present and phylogenetic diversity until ∼25 Ma. These findings suggest that diversification was not initially driven by ecological opportunity. Combining the two criteria of timing and rate of diversification, a soft-explosive diversification model of aquatic vertebrates best fits the patterns observed. We also show that most higher hydrobiid taxa (i.e. subfamilies) diversified from the Middle Oligocene to Middle Miocene (i.e. 12-28 Ma). Two of the 15 major clades delimited are described here as new subfamilies (i.e. Bullaregiinae n. subfam. and Pontobelgrandiellinae n. subfam.), whose members are restricted to subterranean waters. Our results are an important contribution to understanding how the fifth MEE has shaped evolution and patterns of biodiversity in continental aquatic systems. Given the high extinction risks faced by many hydrobiids today, they also emphasise the need to study the biodiversity of vulnerable ecosystems.

Pleistocene Landscape Dynamics Drives Lineage Divergence of a Temperate Freshwater Fish Gobio rivuloides in Coastal Drainages of Northern China

Understanding historical processes underlying lineage distribution patterns is a primary goal of phylogeography. We selected Gobio rivuloides (Cypriniformes: Gobionidae) as a model to improve our knowledge about how intraspecific genetic divergence of freshwater fishes arises in coastal drainages of northern China via statistical analysis using cytochrome b gene. The time-calibrated phylogeny of G. rivuloides showed the divergence of two major lineages (I and II) at ~0.98 Ma (million years ago). Lineage I can be divided into two sub-lineages (I-A and I-B) with a divergence time of ~0.83 Ma. Sub-lineage I-A inhabits the Amur River, and sub-lineage I-B lives in the Luan River and Liao River. Lineage II is distributed in the Yellow River and Hai River, with close genetic relationships between the two drainages, and can be split into two sub-lineages (II-C and II-D) with a divergence time of ~0.60 Ma. Our findings indicate that the splitting of lineages and sub-lineages could be attributed to geographic isolation caused by the formation of the Bohai Sea, river capture, and the episodic hydrologic closing of a paleolake during the late Lower-Middle Pleistocene. It is also the first report we know of displaying a clear phylogeographic break for freshwater fishes across coastal drainages in northern China.

The complete mitochondrial genome and phylogenetic analysis of Anabarilius duoyiheensis Li, Mao & Lu, 2002 (Cypriniformes: Xenocyprididae)

Anabarilius duoyiheensis is a native and rare fish in Yunnan. In this study, the complete mitochondrial genome of A. duoyiheensis was sequenced and published for a total of 16,614 bp, including 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs, and one control region. The phylogenetic analysis based on the complete mitochondrial genome showed that A. duoyiheensis belongs to the clade of the genus Anabarilius and was sister to the clade of Hemiculter. This study also contributes to the genus phylogeny of Anabarilius and other members of the family Xenocyprididae.

Molecular Barcoding: A Tool to Guarantee Correct Seafood Labelling and Quality and Preserve the Conservation of Endangered Species

The recent increase in international fish trade leads to the need for improving the traceability of fishery products. In relation to this, consistent monitoring of the production chain focusing on technological developments, handling, processing and distribution via global networks is necessary. Molecular barcoding has therefore been suggested as the gold standard in seafood species traceability and labelling. This review describes the DNA barcoding methodology for preventing food fraud and adulteration in fish. In particular, attention has been focused on the application of molecular techniques to determine the identity and authenticity of fish products, to discriminate the presence of different species in processed seafood and to characterize raw materials undergoing food industry processes. In this regard, we herein present a large number of studies performed in different countries, showing the most reliable DNA barcodes for species identification based on both mitochondrial (COI, cytb, 16S rDNA and 12S rDNA) and nuclear genes. Results are discussed considering the advantages and disadvantages of the different techniques in relation to different scientific issues. Special regard has been dedicated to a dual approach referring to both the consumer's health and the conservation of threatened species, with a special focus on the feasibility of the different genetic and genomic approaches in relation to both scientific objectives and permissible costs to obtain reliable traceability.

The complete mitochondrial genomes of the Leuciscus baicalensis and Rutilus rutilus: a detailed genomic comparison among closely related species of the Leuciscinae subfamily

Cyprinidae is the largest family in the order of freshwater fish Cypriniformes. Increased subfamily members of Cyprinidae have been suggested to be re-classified for decades. In this study, we sequenced the mitochondrial genomes (mitogenomes) of Leuciscus baicalensis and Rutilus rutilus collected from northwest China and compared with other closely related species to determine their associated family or subfamily. We used Illumina NovaSeq to sequence the entire mitochondrial genomes of Leuciscus baicalensis and Rutilus rutilus and characterized the mitogenomes by the gene structure, gene order, and the secondary structures of the 22 tRNA genes. We compared mitogenome features of Leuciscinae with other subfamilies in Cyprinidae. We used the analytic Bayesian Information and Maximum Likelihood methods to determine phylogenetic trees of 13 PCGs. The mitogenomes of Leuciscus baicalensis and Rutilus rutilus were 16,607 bp and 16,606 bp, respectively. Organization and location of these genes were consistent with already studied Leuciscinae fishes. Synonymous codon usage was conservative in Leuciscinae as compared with other subfamilies in Cyprinidae. Phylogenetic analysis indicated that Leuciscinae was a monophyletic group, and genus Leuciscus was a paraphyletic group. Our approach, for the first time, of studying comparative mitochondrial genomics and phylogenetics together provided a supportive platform to the analysis of population genetics and phylogeny for Leuciscinae. Our results indicated a promising potential of comparative mitochondrial genomics in the manifestation of phylogenetic relationships between fishes, leading us to a suggestion that mitogenomes should be routinely considered in clarifying phylogenetics of family and subfamily members of fish.

Historical dispersal and host-switching formed the evolutionary history of a globally distributed multi-host parasite - The Ligula intestinalis species complex

Studies on parasite biogeography and host spectrum provide insights into the processes driving parasite diversification. Global geographical distribution and a multi-host spectrum make the tapeworm Ligula intestinalis a promising model for studying both the vicariant and ecological modes of speciation in parasites. To understand the relative importance of host association and biogeography in the evolutionary history of this tapeworm, we analysed mtDNA and reduced-represented genomic SNP data for a total of 139 specimens collected from 18 fish-host genera across a distribution range representing 21 countries. Our results strongly supported the existence of at least 10 evolutionary lineages and estimated the deepest divergence at approximately 4.99-5.05 Mya, which is much younger than the diversification of the fish host genera and orders. Historical biogeography analyses revealed that the ancestor of the parasite diversified following multiple vicariance events and was widespread throughout the Palearctic, Afrotropical, and Nearctic between the late Miocene and early Pliocene. Cyprinoids were inferred as the ancestral hosts for the parasite. Later, from the late Pliocene to Pleistocene, new lineages emerged following a series of biogeographic dispersal and host-switching events. Although only a few of the current Ligula lineages show narrow host-specificity (to a single host genus), almost no host genera, even those that live in sympatry, overlapped between different Ligula lineages. Our analyses uncovered the impact of historical distribution shifts on host switching and the evolution of host specificity without parallel host-parasite co-speciation. Historical biogeography reconstructions also found that the parasite colonized several areas (Afrotropical and Australasian) much earlier than was suggested by only recent faunistic data.

The complete mitochondrial genome of Leuciscus merzbacheri (Cypriniformes: Cyprinidae)

Leuciscus merzbacheri (Zugmayer, 1912) is a cyprinid fish endemic to China, with a distribution range limited to Xinjiang Province. As a landmark species in the Junggar Basin, L. merzbacheri is of considerable significance regarding our understanding of the adaptive evolution of salt and alkali tolerance. In this study, the complete mitochondrial sequence of L. merzbacheri was obtained for the first time by high-throughput sequencing. The circular mitogenome is 16,609 bp in length and contains the standard 37 genes, including 13 protein-coding, 22 transfer RNA, and 2 ribosomal RNA genes, which is similar to that of other fish. The mitogenome contents of A, T, C, and G were 27.9, 26.3, 27.1, and 18.7%, respectively. Phylogenetically, L. merzbacheri was located on a new branch near the base of the phylogenetic tree, thereby suggesting an early origin.

The complete mitogenome and phylogeny analysis of Pseudohemiculter hainanensis (Boulenger, 1900) (Cyprinidae: Cultrinae)

The Pseudohemiculter hainanensis (Boulenger, 1900) is a small Cyprinidae fish that has a wide distribution in China. In this study, we characterized the complete mitochondrial genome of P. hainanensis by the Illumina NovaSeq sequencing platform in Guangxi, China. The assembled mitogenome is 16,647 base pairs (bp) and consists of 13 protein-coding genes (PCGs), 22 transfer RNAs, two ribosomal RNAs, and a control region (D-loop). Nucleotide composition of the complete mitogenome is 29.69% (A), 24.82% (T), 27.97% (C), and 17.52% (G), with an A + T bias of 54.51%. The maximum-likelihood tree based on 13 PCGs showed that Pseudohemiculter hainanensis formed an independent lineage and P. hainanensis was closer to T. houdemeri.

Development of loop-mediated isothermal amplification (LAMP) assay for rapid and direct screening of yellowfin tuna (Thunnus albacares) in commercial fish products

Tuna is one of the most widely consumed fish on the European market, being available in various consumable options. Among them, Thunnus albacares, also called yellowfin tuna, is a delicacy and is consumed by millions of people around the world. Due to its comparatively high cost and demand, it is more vulnerable to fraud, where low-cost tuna or other fish varieties might be replaced for economic gain. In this study, a loop-mediated isothermal amplification (LAMP) assay was developed and validated for targeting the mitochondrial cytochrome b gene for fast and direct detection of Thunnus albacares, which is a valuable tuna species. The analytical specificity was confirmed using 18 target samples (Thunnus albacares) and 18 samples of non-target fish species. The analytical sensitivity of the LAMP assay was 540 fg DNA per reaction. In addition, a simple and direct swab method without time-consuming nucleic acid extraction procedures and the necessity for cost-intensive laboratory equipment was performed that allowed LAMP detection of Thunnus albacares samples within 13 minutes. Due to its high specificity and sensitivity, the LAMP assay can be used as a rapid and on-site screening method for identifying Thunnus albacares, potentially providing a valuable monitoring tool for food authenticity control by the authorities.

Phylogenomics and classification of Notropis and related shiners (Cypriniformes: Leuciscidae) and the utility of exon capture on lower taxonomic groups

North American minnows of the Shiner Clade, within the family Leuciscidae, represent one of the most taxonomically complex clades of the order Cypriniformes due to the large number of taxa coupled with conserved morphologies. Species within this clade were moved between genera and subgenera until the community decided to lump many of the unclassified taxa with similar morphologies into one genus, Notropis, which has held up to 325 species. Despite phylogentic studies that began to re-elevate some genera merged into Notropis, such as Cyprinella, Luxilus, Lythrurus, and Pteronotropis, the large genus Notropis remained as a taxonomic repository for many shiners of uncertain placement. Recent molecular advances in sequencing technologies have provided the opportunity to re-examine the Shiner Clade using phylogenomic markers. Using a fish probe kit, we sequenced 90 specimens in 87 species representing 16 genera included in the Shiner Clade, with a resulting dataset of 1,004 loci and 286,455 base pairs. Despite the large dataset, only 32,349 bp (11.29%) were phylogenetically informative. In our maximum likelihood tree, 78% of nodes are 100% bootstrap supported demonstrating the utility of the phylogenomic markers at lower taxonomic levels. Unsurprisingly, species within Notropis as well as Hudsonius, Luxilus, and Alburnops are not resolved as monophyletic groups. Cyprinella is monophyletic if Cyprinella callistia is excluded, and Pteronotropis is monophyletic if it includes Hudsonius cummingsae. Taxonomic changes we propose are: restriction of species included in Alburnops and Notropis, elevation of the subgenus Hydrophlox, expansion of species included in Miniellus, movement of Hudsonius cummingsae to Pteronotropis, and resurrection of the genera Coccotis and Paranotropis. We additionally had two specimens of three species, Notropis atherinoides, Ericymba amplamala, and Pimephales vigilax and found signficant differences between the localities (1,086, 1,424, and 845 nucleotides respectively).

The minnow Phoxinus lumaireul (Leuciscidae) shifts the Adriatic-Black Sea basin divide in the north-western Dinaric Karst region

Karst landscapes are characterized by intermittent and sinking streams. The most common method used to study underground hydrological connections in karst is tracing tests. However, a more biologically oriented approach has been suggested: analysis of the genetic structure of aquatic organisms. Biological tracers can be sought among trogloxenes, that is, surface species that occasionally enter caves and groundwater. One such example is the fish genus Phoxinus, which exhibits high genetic diversity and complex phylogeography in the Balkan Peninsula. In the north-western Dinaric Karst, the complex hydrological network was digitalized in 2020. Contemporaneously, Phoxinus lumaireul populations in the Slovenian Dinaric Karst were intensively sampled and analysed for fragments of two mitochondrial genes and one nuclear gene. The derived phylogeographic structure and data on hydrological connections were compared to evaluate support for three alternative scenarios: The genetic structure (1) is a consequence of the ongoing geneflow through underground connections, (2) reflects a previous hydrological network or (3) is an outcome of anthropogenic translocations. The results suggest that the first two scenarios seem to have played a major role, while the third has not had profound effects on the genetic composition. Comparison between the genetic structure of Slovenian Dinaric Karst sampling sites and that of hydrologically isolated reference sampling sites indicated a greater genetic connectivity in the former. Moreover, the range of Adriatic (1a) and Black Sea (1c) haplotypes does not correspond to the Adriatic-Black Sea basin divide but is shifted northwards.

Integration of Morphometrics and Machine Learning Enables Accurate Distinction between Wild and Farmed Common Carp

Morphology and feature selection are key approaches to address several issues in fisheries science and stock management, such as the hypothesis of admixture of Caspian common carp (Cyprinus carpio) and farmed carp stocks in Iran. The present study was performed to investigate the population classification of common carp in the southern Caspian basin using data mining algorithms to find the most important characteristic(s) differing between Iranian and farmed common carp. A total of 74 individuals were collected from three locations within the southern Caspian basin and from one farm between November 2015 and April 2016. A dataset of 26 traditional morphometric (TMM) attributes and a dataset of 14 geometric landmark points were constructed and then subjected to various machine learning methods. In general, the machine learning methods had a higher prediction rate with TMM datasets. The highest decision tree accuracy of 77% was obtained by rule and decision tree parallel algorithms, and “head height on eye area” was selected as the best marker to distinguish between wild and farmed common carp. Various machine learning algorithms were evaluated, and we found that the linear discriminant was the best method, with 81.1% accuracy. The results obtained from this novel approach indicate that Darwin’s domestication syndrome is observed in common carp. Moreover, they pave the way for automated detection of farmed fish, which will be most beneficial to detect escapees and improve restocking programs.

A comprehensive DNA barcode inventory of Austria’s fish species

Austria is inhabited by more than 80 species of native and non-native freshwater fishes. Despite considerable knowledge about Austrian fish species, the latest Red List of threatened species dates back 15 years and a systematic genetic inventory of Austria’s fish species does not exist. To fulfill this deficit, we employed DNA barcoding to generate an up-to-date and comprehensive genetic reference database for Austrian fish species. In total, 639 newly generated cytochrome c oxidase subunit 1 (COI) sequences were added to the 377 existing records from the BOLD data base, to compile a near complete reference dataset. Standard sequence similarity analyses resulted in 83 distinct clusters almost perfectly reflecting the expected number of species in Austria. Mean intraspecific distances of 0.22% were significantly lower than distances to closest relatives, resulting in a pronounced barcoding gap and unique Barcode Index Numbers (BINs) for most of the species. Four cases of BIN sharing were detected, pointing to hybridization and/or recent divergence, whereas in Phoxinus spp., Gobio spp. and Barbatula barbatula intraspecific splits, multiple BINs and consequently cryptic diversity were observed. The overall high identification success and clear genetic separation of most of the species confirms the applicability and accuracy of genetic methods for bio-surveillance. Furthermore, the new DNA barcoding data pinpoints cases of taxonomic uncertainty, which need to be addressed in further detail, to more precisely assort genetic lineages and their local distribution ranges in a new National Red-List.

The phylogeographical pattern of the Amur minnow Rhynchocypris lagowskii (Cypriniformes: Cyprinidae) in the Qinling Mountains

In this study, the phylogeographical pattern of the Amur minnow (Rhynchocypris lagowskii) widely distributed in the cold freshwaters of the Qinling Mountains was examined. A total of 464 specimens from 48 localities were sequenced at a 540-bp region of the mitochondrial cytochrome b (Cytb) gene, and 69 haplotypes were obtained. The mean ratio of the number of synonymous and nonsynonymous substitutions per site (dN/dS) was 0.028 and indicated purifying selection. Haplotype diversity (h) and nucleotide diversity (π) of natural populations of R. lagowskii varied widely between distinct localities. Phylogenetic trees based on Bayesian inference (BI), maximum likelihood (ML), and maximum parsimony (MP) methods, and network analysis showed five well-differentiated lineages, but these did not completely correspond to localities and geographic distribution. Meanwhile, analysis of molecular variances (AMOVA) indicated the highest proportion of genetic variation was attributed to the differentiation between populations rather than by our defined lineages. In addition, there was no significant correlation between the pairwise Fst values and geographic distance (p > .05). Based on the molecular clock calibration, the time to the most recent common ancestor (TMRCA) was estimated to have emerged from the Late Miocene to the Early Pleistocene. Finally, the results of demographic history based on the neutrality test, mismatch distribution, and Bayesian skyline plot (BSP) analyses showed that collectively, the populations were stable during the Pleistocene while one lineage (lineage E) probably underwent a slight contraction during the Middle Pleistocene and a rapid expansion from the Middle to the Late Pleistocene. Therefore, the study suggests the current phylogeographical pattern of R. lagowskii was likely shaped by geological events that led to vicariance followed by dispersal and secondary contact, river capture, and climatic oscillation during the Late Miocene to the Early Pleistocene in the Qinling Mountains.

Host-Specific Parasites Reveal the History and Biogeographical Contacts of Their Hosts: The Monogenea of Nearctic Cyprinoid Fishes

Simple Summary

Parasites exhibiting close associations with their hosts may represent a useful tool when investigating historical biogeography, especially in the case of hosts associated with a once contiguous landmass. Host-specific gill parasites (Monogenea) were applied as a supplementary tool to reveal the historical biogeographical contacts between freshwater fish from North America and Europe and their contemporary contacts in North America. Cyprinoidei is the most species-rich lineage of cypriniform fish with Leuciscidae exhibiting a Holarctic distribution. Monogenean parasites of the genus Dactylogyrus are mostly restricted to this freshwater fish group, and the high species diversity of Dactylogyrus follows the high diversity of their cyprinoid fish hosts. Using a phylogenetic approach, two Nearctic clades of Dactylogyrus spp. with different origins were revealed indicating two different historical routes of cyprinoid dispersion to the North American continent. Our study showed that the historical contacts between European and North American leuciscids were accompanied by the host switching of gill monogeneans. The phylogenetic relationships among North American Dactylogyrus spp. indicated numerous colonizations of cypriniform fish resulting from ancient paleogeographic events and contemporary drainage reorganization, thereby, facilitating contacts among phylogenetically distant fish species.

Abstract

Host-specific parasites exhibit close co-evolutionary associations with their hosts. In the case of fragmented/disjunct host distribution, host-specific parasites may reflect the biogeographical history of regions and/or the role played by contacts of hosts. The present study was focused on Dactylogyrus (Monogenea) species almost exclusively parasitizing cyprinoid fishes. We investigated the phylogenetic relationships between Dactylogyrus parasites of Nearctic cyprinoids (Leuciscidae) and Dactylogyrus parasites of Palearctic cyprinoids and used Dactylogyrus phylogeny to explore the biogeography of fish hosts in Europe and North America. Phylogenetic analyses revealed that two Nearctic clades of Dactylogyrus spp. have different origins. Historical contacts between European and North American leuciscids were accompanied by the host switching of Dactylogyrus species. In the Nearctic region, Dactylogyrus parasites also colonized non-leuciscid fishes. Dactylogyrus spp. of three Nearctic leuciscid clades were included in the phylogenetic reconstruction; only Dactylogyrus spp. of the Plagopterinae had a common origin. Dactylogyrus species did not reflect the phylogenetic relationships among leuciscid clades, suggesting that past co-diversification was overshadowed by colonization events mediated by paleogeographic and climatological changes and extensive drainage reorganization. Host-specific monogeneans serve as a supplementary tool to reveal the historical biogeographical contacts between freshwater fish from the North America and Europe and also contemporary contacts of leuciscids in North America.

The complete mitochondrial genome of Microphysogobioelongatus (Teleostei, Cyprinidae) and its phylogenetic implications

Mitochondria are important organelles with independent genetic material of eukaryotic organisms. In this study, we sequenced and analyzed the complete mitogenome of a small cyprinid fish, Microphysogobioelongatus (Yao & Yang, 1977). The mitogenome of M.elongatus is a typical circular molecule of 16,612 bp in length containing 13 protein-coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes, and a 930 bp control region. The base composition of the M.elongatus mitogenome is 30.8% A, 26.1% T, 16.7% G, and 26.4% C. All PCGs used the standard ATG start codon with the exception of COI. Six PCGs terminate with complete stop codons, whereas seven PCGs (ND2, COII, ATPase 6, COIII, ND3, ND4, and Cyt b) terminate with incomplete (T or TA) stop codons. All tRNA genes exhibited typical cloverleaf secondary structures with the exception of tRNA^Ser(AGY), for which the dihydrouridine arm forms a simple loop. The phylogenetic analysis divided the subfamily Gobioninae in three clades with relatively robust support, and that Microphysogobio is not a monophyletic group. The complete mitogenome of M.elongatus provides a valuable resource for future studies about molecular phylogeny and/or population genetics of Microphysogobio.

Some Examples of the Use of Molecular Markers for Needs of Basic Biology and Modern Society

Application of molecular genetic markers appeared to be very fruitful in achieving many goals, including (i) proving the theoretic basements of general biology and (ii) assessment of worldwide biodiversity. Both are provided in the present meta-analysis and a review as the main signal. One of the basic current challenges in modern biology in the face of new demands in the 21st century is the validation of its paradigms such as the synthetic theory of evolution (STE) and biological species concept (BSC). Another of most valuable goals is the biodiversity assessment for a variety of social needs including free web-based information resources about any living being, renovation of museum collections, nature conservation that recognized as a global project, iBOL, as well as resolving global trading problems such as false labeling of species specimens used as food, drug components, entertainment, etc. The main issues of the review are focused on animals and combine four items. (1) A combination of nDNA and mtDNA markers best suits the identification of hybrids and estimation of genetic introgression. (2) The available facts on nDNA and mtDNA diversity seemingly make introgression among many taxa obvious, although it is evident, that introgression may be quite restricted or asymmetric, thus, leaving at least the "source" taxon (taxa) intact. (3) If we consider sexually reproducing species in marine and terrestrial realms introgressed, as it is still evident in many cases, then we should recognize that the BSC, in view of the complete lack of gene flow among species, is inadequate because many zoological species are not biological ones yet. However, vast modern molecular data have proven that sooner or later they definitely become biological species. (4) An investigation into the fish taxa divergence using the BOLD database shows that most gene trees are basically monophyletic and interspecies reticulations are quite rare.

Morphological and molecular differentiation of Diplostomum spp. metacercariae from brain of minnows (Phoxinus phoxinus L.) in four populations of northern Europe and East Asia

Metacercariae of trematodes from the genus Diplostomum are major helminth pathogens of freshwater fish, infecting the eye or the brain. The taxonomy of the genus Diplostomum is complicated, and has recently been based mainly on the molecular markers. In this study, we report the results of the morphological and molecular genetic analysis of diplostomid metacercaria from the brain of the minnow Phoxinus phoxinus from three populations in Fennoscandia (Northern Europe) and one population in Mongolia (East Asia). We obtained the data on the polymorphism of the partial mitochondrial cox1 gene and ribosomal ITS1-5.8S-ITS2 region of these parasites. РСА-based morphological analysis revealed that the parasites in the Asian and the European groups of Diplostomum sp. were distinctly different. Metacercariae from the brain of Mongolian minnows were much larger than those from the brain of Fennoscandian minnows but had much fewer excretory granules. Considering that the two study regions were separated by a distance of about 4500 km, we also tested the genetic homogeneity of their host, the minnow, using the mitochondrial cytb gene. It was shown that Diplostomum-infected minnows from Mongolia and Fennoscandia represented two previously unknown separate phylogenetic lineages of the genus Phoxinus. Both molecular and morphological analysis demonstrated that the parasites from Fennoscandia belonged the species Diplostomum phoxini, while the parasites from Mongolia belonged to a separate species, Diplostomum sp. MТ.Each of the two studied Diplostomum spp. was associated with a specific, and previously unknown, genealogical lineage of its second intermediate host, P. phoxinus.

High-Resolution Melting Analysis of COI Sequences Distinguishes Pufferfish Species (Takifugu spp.) in China

Pufferfish is a traditional, delicious dish in Asia. However, eating wild or improperly processed pufferfish causes serious poisoning. This study aimed to exploit the high-resolution melting (HRM) method for authenticating four species of Takifugu pufferfish (Takifugu xanthopterus, T. fasciatus, T. flavidus, and T. rubripes). Candidate DNA barcodes, including the cytochrome c oxidase subunit I (COI), cytochrome oxidase b (Cytb), and the control region (D-loop), were analyzed, with COI selected as the optimal DNA barcode. An HRM method was developed to identify 57 commercial fish samples in China, including 33 commercial pufferfish products and 24 unlabeled fish products. The findings revealed that the pufferfish products were T. rubripes or T. fasciatus, and four T. xanthopterus samples were detected in unlabeled fish products. These results showed that DNA barcode coupled with HRM analysis was a rapid and efficient tool to identify pufferfish, which might aid in the prevention of consumer fraud or mislabeling of fish products.

High diversity of fish ectoparasitic monogeneans (Dactylogyrus) in the Iberian Peninsula: a case of adaptive radiation?

The epicontinental fauna of the Iberian Peninsula is strongly influenced by its geographical history. As the possibilities for dispersion of organisms into and from this region were (and still are) limited, the local fauna consists almost exclusively of endemic species. Almost all Iberian freshwater fishes of the families Leuciscidae and Cyprinidae are endemic and on-going research on these taxa continually uncovers new species. Nevertheless, information on their host-specific parasites remains scarce. In this study, we investigate the diversity and phylogenetic relationships in monogeneans of the genus Dactylogyrus (gill ectoparasites specific to cyprinoid fish) in the Iberian Peninsula. Twenty-two species were collected and identified from 19 host species belonging to Cyprinidae and Leuciscidae. A high degree of endemism was observed, with 21 Dactylogyrus species reported from Iberia only and a single species, D. borealis, also reported from other European regions. Phylogenetic analysis split the endemic Iberian Dactylogyrus into two well-supported clades, the first encompassing Dactylogyrus parasitizing endemic Luciobarbus spp. only, and the second including all Dactylogyrus species of endemic leuciscids and four species of endemic cyprinids. Species delimitation analysis suggests a remarkable diversity and existence of a multitude of cryptic Dactylogyrus species parasitizing endemic leuciscids (Squalius spp. and representatives of Chondrostoma s.l.). These results suggest a rapid adaptive radiation of Dactylogyrus in this geographically isolated region, closely associated with their cyprinoid hosts. Moreover, phylogenetic analysis supports that Dactylogyrus parasites colonized the Iberian Peninsula through multiple dispersion events.

European minnows through time: museum collections aid genetic assessment of species introductions in freshwater fishes (Cyprinidae: Phoxinus species complex)

Massive fish introductions have taken place throughout much of the world, mostly over the last 70 years, and present a major threat to the genetic diversity of native fishes. Introductions have been reported for European Phoxinus, a ubiquitous small cyprinid that populates a wide variety of habitats. Species delineation in European Phoxinus has proven difficult with one reason being ranges of distribution that often traverse drainage boundaries. The present study combines recent samples with museum samples to better understand the current distribution of Phoxinus species and their distributions prior to the massive introductions of fishes in Europe, and to evaluate the use of museum specimens for species distribution studies. For these purposes, genetic lineages from sites collected prior to 1900 (n = 14), and between 1900 and 1950 (n = 8), were analysed using two mitochondrial and nuclear markers. Although possible fish introductions were detected, our results show that the distribution of genetic lineages of museum samples is comparable to that of the extant lineages of European Phoxinus present in those areas. These observations suggest that in the studied ranges the distribution of Phoxinus lineages has been driven by natural processes.

Population genetic structure and phylogenetic analysis of gray's pipefish, Halicampus grayi in the South China Sea

BACKGROUND

The evolution of male pregnancy is the most distinctive characteristic of syngnathids, and they were recognized as flagship species for marine conservation. Genus Halicampus is an important branch of syngnathid fishes that has not received the attention it deserves.

OBJECTIVE

To sequence the mitochondrial genome of Halicampus grayi, and investage the genetic structure of its populations.

METHODS

Degenerate primers were designed to amplify the entire mitochondrial genome of H. grayi. The phylogenetic relationship between H. grayi and other syngnathids were conducted using maximum-likelihood method. Population genetic structure of three geographic population of H. grayi were determined using median-joining haplotype network based on COI and Cytb sequences.

RESULTS

The complete mitochondrial genome of Halicampus grayi was assembled into a 17,059 bp circular sequence, which contains 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and 1 D-loop region. The overall base composition of H. grayi is 29.93% A, 29.31% T, 16.23% G and 24.54% C, with a slight A + T rich feature (59.24%). Phylogenetic analysis indicated that H. grayi has a close relationship with Trachyrhamphus serratus. Population genetic analysis revealed a relatively high genetic diversity across different geographic populations of H. grayi, and the results of median-joining haplotype network indicated a lack of structure in populations of H. grayi.

CONCLUSION

The mitogenome of H. grayi will provided important information about the origin and evolution issues of syngnathid fishes, and the high-level genetic diversity detected in their populations will provide insight into the gene flow pattern of marine fishes.

The complete mitochondrial genome information of Phoxinus phoxinus (Cypriniformes: Cyprinidae) on the Korean Peninsula and the phylogenetic implication

Phoxinus phoxinus is a small Leuciscinae species predominantly found in cool and well-oxygenated streams throughout a wide area encompassing Europe, Siberia and East Asia. It is believed that the populations in Korea hold important clues to how the species has been distributed south along the Eurasian continent to the Korean Peninsula. We characterized the complete mitochondrial genomes of two individual fin-clip samples collected from the two Korean river systems. The whole sequences were 17,665 and 18,220 bp, respectively, and included 13 protein-coding genes, 2 ribosomal RNA genes and 22 transfer RNA genes. The genome size difference was due to the considerably different sizes of the control region. The overall genome structures were identical to those observed in other Leuciscinae species.

Toxicity in aquatic model species exposed to a temporal series of three different flowback and produced water samples collected from a horizontal hydraulically fractured well

In the present study, we compared the toxicity and associated chemical characterizations of flowback and produced water (FPW) collected from a single horizontal hydraulically fractured well at different time points during FPW production. Since few studies on whole mixture toxicity related to FPW exist, our aims were to determine both overall toxicity of the FPW mixture in a suite of organisms (Daphnia magna, Lumbriculus variegatus, Danio rerio, and Oncorhynchus mykiss) and also determine if toxicity changes depending on variation in FPW chemical properties as a function of time sampled (1.33, 72, and 228 h FPW samples collected immediately post-well production onset were analyzed in current study). FPW chemical composition was determined via quadra-pole inductively coupled plasma - mass spectrometry/mass spectrometry (ICP-MS/MS), full-scan high performance liquid chromatography/Orbitrap mass spectrometry (HPLC/Orbitrap-MS), and gas chromatography-mass spectrometry (GC-MS). We observed that FPW sampled later in the production process contained higher ion and total dissolved solids concentrations, whereas the highest concentrations of dissolved organic compounds were observed in the earliest FPW sample analyzed. Toxicity associated with FPW exposure was deemed to be species-specific to a certain extent, but general trends revealed the earliest FPW sampled contained highest toxic potential. Accordingly, we theorize that although the saline conditions of FPW are the foremost toxicological drivers to freshwater organisms, dissolved organics associated with FPW significantly contribute to the overall toxicity of exposed organisms.

The complete mitochondrial genome of Rhynchocypris oxycephalus (Teleostei: Cyprinidae) and its phylogenetic implications

Rhynchocypris oxycephalus (Teleostei: Cyprinidae) is a typical small cold water fish, which is distributed widely and mainly inhabits in East Asia. Here, we sequenced and determined the complete mitochondrial genome of R. oxycephalus and studied its phylogenetic implication. R. oxycephalus mitogenome is 16,609 bp in length (GenBank accession no.: MH885043), and it contains 13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes, and two noncoding regions (the control region and the putative origin of light-strand replication). 12 PCGs started with ATG, while COI used GTG as the start codon. The secondary structure of tRNA-Ser (AGN) lacks the dihydrouracil (DHU) arm. The control region is 943bp in length, with a termination-associated sequence, six conserved sequence blocks (CSB-1, CSB-2, CSB-3, CSB-D, CSB-E, CSB-F), and a repetitive sequence. Phylogenetic analysis was performed with maximum likelihood and Bayesian methods based on the concatenated nucleotide sequence of 13 PCGs and the complete sequence without control region, and the result revealed that the relationship between R. oxycephalus and R. percnurus is closest, while the relationship with R. kumgangensis is farthest. The genus Rhynchocypris is revealed as a polyphyletic group, and R. kumgangensis had distant relationship with other Rhynchocypris species. In addition, COI and ND2 genes are considered as the fittest DNA barcoding gene in genus Rhynchocypris. This work provides additional molecular information for studying R. oxycephalus conservation genetics and evolutionary relationships.

Characterization of the mitochondrial genome of Megalobrama terminalis in the Heilong River and a clearer phylogeny of the genus Megalobrama

Megalobrama terminalis distributed in Sino-Russian Heilong-Amur River basin has decreased dramatically in the last few decades. It has been listed in the Red Book of the Russian Federation as an endangered fish species. Here, the complete mitochondrial (mt) genome sequence of M. terminalis in the Heilong River (MTH) was first determined and characterized. Additionally, we identified a population-specific single nucleotide polymorphism (SNP) locus in MTH which could effectively separate MTH from the six other populations of the genus Megalobrama in the absence of hybridization. Moreover, phylogenetic analyses determined that the Xi River M. hoffmanni is located at the basal branch of the clade, and the rest of the group is divided into two assemblages, namely, one containing M. terminalis from Qiantang River and Jinsha River Reservoir/Longxi River M. Pellegrini/MTH and the other containing M. amblycephala from Liangzi Lake and Yi River. We clarify the intraspecies identity of MTH and construct a clearer phylogeny of the genus Megalobrama, which will contribute to the germplasm identification, protection and development of MTH in the future.

Preserving the tree of life of the fish family Cyprinidae in Africa in the face of the ongoing extinction crisis

Our understanding of how the phylogenetic tree of fishes might be affected by the ongoing extinction risk is poor. This is due to the unavailability of comprehensive DNA data, especially for many African lineages. In addition, the ongoing taxonomic confusion within some lineages, e.g., Cyprinidae, makes it difficult to contribute to the debate on how the fish tree of life might be shaped by extinction. Here, we combine COI sequences and taxonomic information to assemble a fully sampled phylogeny of the African Cyprinidae and investigate whether we might lose more phylogenetic diversity (PD) than expected if currently threatened species go extinct. We found evidence for phylogenetic signal in extinction risk, suggesting that some lineages might be at higher risk than others. Based on simulated extinctions, we found that the loss of all threatened species, which approximates 37% of total PD, would lead to a greater loss of PD than expected, although highly evolutionarily distinct species are not particularly at risk. Pending the reconstruction of an improved multi-gene phylogeny, our results suggest that prioritizing high-EDGE species (evolutionary distinct and globally endangered species) in conservation programmes, particularly in some geographic regions, would contribute significantly to safeguarding the tree of life of the African Cyprinidae.

Phylogenetic relationships and classification of the Holarctic family Leuciscidae (Cypriniformes: Cyprinoidei)

The phylogenetic relationships and classification of the freshwater fish order Cypriniformes, like many other species-rich groups of vertebrates, has evolved over time with some consistency and inconsistencies of relationships across various studies. Within Cypriniformes, the Holarctic family Leuciscidae is one of the most widely distributed and highly diverse monophyletic groups of cyprinoids. Despite several studies conducted on this group, alternative hypotheses exist as to the composition and relationships within Leuciscidae. Here we assess the extent, composition, phylogenetic relationships, and taxonomy of this highly diverse group of fishes, using multiple mitochondrial and nuclear loci and a comprehensive and dense taxonomic sampling. Analyses of 418 specimens (410 species) resolve a well-supported Leuciscidae including 362 specimens (358 taxa) in six well-supported subfamilies/major clades: Pseudaspininae/Far East Asian clade (FEA); Laviniinae/North American Western clade (WC); Plagopterinae/North American Creek Chub-Plagopterin clade (CC-P); Leuciscinae/Eurasian Old World clade (OW) (minus Phoxinus) plus North American Notemigonus; Phoxininae/Eurasian Phoxinus clade (PHX); and Pogonichthyinae/North American clade (NA) including all remaining leuciscids. Within Leuciscidae, neither the traditional phoxinins (Phoxinus, FEA, Nearctic genera) nor all Nearctic genera (minus Notemigonus) are resolved as monophyletic; whereas the WC and CC-P form two independent lineages from remaining North American cyprinoids. A close relationship exists between Eurasian Phoxinus, NA, and OW clades, while FEA is the sister group to all remaining Leuciscidae. Major lineages resolved within these six subfamilies are mostly congruent with some previous studies. Our results suggests a complex evolutionary history of this diverse and widespread group of fishes.

Characterization and phylogenetic analysis of the complete mitogenome of a rare cavefish, Sinocyclocheilus multipunctatus (Cypriniformes: Cyprinidae)

The genus Sinocyclocheilus is a representative group of cave creatures. However, genetic studies on Sinocyclocheilus are rare. The primary objective of this study was to explore the structure and feature of the complete mitochondrial genome of S. multipunctatus, and reconstruct the mitogenomic phylogeny of Sinocyclocheilus. The mitochondrial DNA of S. multipunctatus was amplified by overlapping PCR fragments. The mitogenome was assembled by the SeqMan and annotated using MitoAnnotator. The phylogenetic tree was established using the Bayesian inference and Maximum likelihood methods. The mitogenome of S. multipunctatus is a typical circular molecule of 16,586 bp with base composition A (31.25%), T (25.90%), G (16.35%), and C (26.50%), and consists of 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs) genes, two ribosomal RNAs, and a 931 bp control region. Phylogenetic analysis reveals two clades in the Sinocyclocheilus with robust support. S. multipunctatus is close to a newly discovered cavefish, S. ronganensis. We obtained and described the complete mitogenome of S. multipunctatus, and investigated its phylogenetic status, which may provide a valuable resource for future phylogenetic analyses and population genetic studies in Sinocyclocheilus.

Re-evaluation of the discriminatory power of DNA barcoding on some specimens of African Cyprinidae (subfamilies Cyprininae and Danioninae)

Specimen identification in the absence of diagnostic morphological characters (e.g., larvae) can be problematic even for experts. The goal of the present study was to assess the performance of COI in discriminating specimens of the fish family Cyprinidae in Africa, and to explore whether COI-phylogeny can be reliably used for phylogenetic comparative analysis. The main objective was to analyse a matrix of COI sequences for 315 specimens from 15 genera of African Cyprinidae using various distance-based identification methods alongside multiple tests of DNA barcode efficacy (barcode gap, species monophyly on NJ tree). Some morphological and biological characters were also mapped on a COI-phylogeny reconstructed using Maximum Parsimony. First, the results indicated the existence of barcode gaps, a discriminatory power of COI ranging from 79 % to 92 %, and that most nodes form well-supported monophyletic clades on an NJ tree. Second, it was found that some morphological and biological characters are clustered on the COI-phylogeny, and this indicates the reliability of these characters for taxonomic discrimination within the family. Put together, our results provide not only an additional support for the COI as a good barcode marker for the African Cyprinidae but it also indicate the utility of COI-based phylogenies for a wide spectrum of ecological questions related to African Cyprinidae.

Re-evaluation of the discriminatory power of DNA barcoding on some specimens of African Cyprinidae (subfamilies Cyprininae and Danioninae)

Specimen identification in the absence of diagnostic morphological characters (e.g., larvae) can be problematic even for experts. The goal of the present study was to assess the performance of COI in discriminating specimens of the fish family Cyprinidae in Africa, and to explore whether COI-phylogeny can be reliably used for comparative phylogenetic analysis. The main objective was to analyse a matrix of COI sequences for 315 specimens from 15 genera of African Cyprinidae using various distance-based identification methods alongside multiple tests of DNA barcode efficacy (barcode gap, species monophyly on NJ tree). Some morphological and biological characters were also mapped on a COI-phylogeny reconstructed using Maximum Parsimony. First, the results indicated the existence of barcode gaps, a discriminatory power of COI ranging from 79 % to 92 %, and that most nodes form well-supported monophyletic clades on an NJ tree. Second, it was found that some morphological and biological characters are clustered on the COI-phylogeny, and this indicates the reliability of these characters for taxonomic discrimination within the family. Put together, our results provide not only an additional support for the COI as a good barcode marker for the African Cyprinidae but it also indicate the utility of COI-based phylogenies for a wide spectrum of ecological questions related to African Cyprinidae.

Re-evaluation of the discriminatory power of DNA barcoding on some specimens of African Cyprinidae (subfamilies Cyprininae and Danioninae)

Specimen identification in the absence of diagnostic morphological characters (e.g., larvae) can be problematic even for experts. The goal of the present study was to assess the performance of COI in discriminating specimens of the fish family Cyprinidae in Africa, and to explore whether COI-phylogeny can be reliably used for phylogenetic comparative analysis. The main objective was to analyse a matrix of COI sequences for 315 specimens from 15 genera of African Cyprinidae using various distance-based identification methods alongside multiple tests of DNA barcode efficacy (barcode gap, species monophyly on NJ tree). Some morphological and biological characters were also mapped on a COI-phylogeny reconstructed using Maximum Parsimony. First, the results indicated the existence of barcode gaps, a discriminatory power of COI ranging from 79 % to 92 %, and that most nodes form well-supported monophyletic clades on an NJ tree. Second, it was found that some morphological and biological characters are clustered on the COI-phylogeny, and this indicates the reliability of these characters for taxonomic discrimination within the family. Put together, our results provide not only an additional support for the COI as a good barcode marker for the African Cyprinidae but it also indicate the utility of COI-based phylogenies for a wide spectrum of ecological questions related to African Cyprinidae.

Evolution of the connection patterns of the cephalic lateral line canal system and its use to diagnose opsariichthyin cyprinid fishes (Teleostei, Cyprinidae)

The cephalic lateral line canal systems were compared among 12 species of the cyprinid tribe Opsariichthyini. All species were characterized by the separation of the supraorbital canal from both the infraorbital and the temporal canals, and the left side of the supratemporal canal from the right side of the canal. In species of Candidia, Opsariichthys, Parazacco, and Zacco, and Nipponocyprissieboldii the temporal canal was separated from the preoperculomandibular canal. In Nipponocypristemminckii and N.koreanus, the temporal canal was connected to the preoperculomandibular canal. Separation of the left and right sides of the supratemporal canal is a possible synapomorphy of the opsariichthyin cyprinids. Opsariichthysuncirostris and O.bidens are unique among the opsariichthyins in that the connection between the infraorbital and temporal canals is retarded. The variation in arrangement of the cephalic lateral line canal system can be used as diagnostic characters for the opsariichthyin species.

Analysis of sequence divergence in redfin (Cypriniformes, Cyprinidae, Tribolodon) based on mtDNA and nDNA markers with inferences in systematics and genetics of speciation

To clarify relationship of species of the genus Tribolodon in the Russian part of their distribution ranges, two mitochondrial markers (Co-1 and Cyt-b), a nuclear marker (Rho), and a gene marker of rDNA internal transcribed spacer (ITS-1,2) were used. Depending on the marker, different numbers of species groups were detected by the ABGD method, but in combination with the analysis of phylograms, these data generally support the known species clusters and regional intraspecies groups. A complex analysis of sequences from three redfin species within the area of the study, based on four marker genes and using the methods of molecular phylogenetics, ordination of genetic distances, recombinant analysis, and population genetic approaches, has revealed clusters of three commonly recognized species, regional intraspecific groups or individuals of local populations, and few hybrid individuals. DNA barcoding technique proved to be efficient with the use of two mtDNA markers: Co-1 and Cyt-b. It has been found that analysis of insertions and substitutions within the ITS-1,2 gene marker is also suitable for identification of Tribolodon species. Results of the studies of local groups do not confirm a sufficient level of differences for defining any new taxa of a species rank in the genus Tribolodon.

Barcode index number, taxonomic rank and modes of speciation: examples from fish

Species delimitation by DNA sequence data or DNA barcoding is successful, as confirmed by the vast BOLD data base. However, the theory that would explain this fact has not been developed yet. An approach based on Barcoding Index Number (BIN), suggested in the assignment, allows delimiting of taxa of three ranks (species, genera, and families) and statistical validation with a high precision of delimiting (over 80%), as well as shows for majority of Co-1-based single gene trees good correspondence between their topology and conventional taxa content for analyzed fish species (R² ≈ 0.84-0.98). Knowledge of deviations from these data can help to find out new taxa and improve biodiversity description. It is concluded that delimiting is successful for bulk of cases because the geographic mode of speciation prevails in nature. It takes a long time for new taxa to form in isolation, which allows accumulation of random mutations and many different nucleotide substitutions between them that can be detected by molecular markers and give unique DNA barcodes. The use of BIN approach, described here, can aid greatly in making this important question clearer especially under wider examination of other organisms.

Resolving Cypriniformes relationships using an anchored enrichment approach

BACKGROUND

Cypriniformes (minnows, carps, loaches, and suckers) is the largest group of freshwater fishes in the world (~4300 described species). Despite much attention, previous attempts to elucidate relationships using molecular and morphological characters have been incongruent. In this study we present the first phylogenomic analysis using anchored hybrid enrichment for 172 taxa to represent the order (plus three out-group taxa), which is the largest dataset for the order to date (219 loci, 315,288 bp, average locus length of 1011 bp).

RESULTS

Concatenation analysis establishes a robust tree with 97 % of nodes at 100 % bootstrap support. Species tree analysis was highly congruent with the concatenation analysis with only two major differences: monophyly of Cobitoidei and placement of Danionidae.

CONCLUSIONS

Most major clades obtained in prior molecular studies were validated as monophyletic, and we provide robust resolution for the relationships among these clades for the first time. These relationships can be used as a framework for addressing a variety of evolutionary questions (e.g. phylogeography, polyploidization, diversification, trait evolution, comparative genomics) for which Cypriniformes is ideally suited.