DNA barcode divergence among species and genera of birds and fishes

Integrative morphological, cytogenetic and molecular characterization of the Andean climbing catfish Astroblepus mindoensis (Regan, 1916) (Siluriformes:Astroblepidae)

Astroblepus species, commonly known as Andean climbing catfish, exhibit a unique challenge in species delimitation, leading to ongoing taxonomic debates. Here we report data on Astroblepus mindoensis, a vulnerable species endemic to Ecuador, obtained by an integrative approach that includes cytogenetic analysis, molecular identification of the specimens, and recording of morphological and morphometric characters useful for species diagnosis. Thus, this study aimed to associate the karyotype data of the specimens analyzed with morphological and molecular characters, improving and expanding the existing taxonomic information, thus contributing to the systematics of the species. Our morphology results, unlike Regan's original description, which is brief and ambiguous, provide a more detailed morphometric and meristic description. Molecular phylogenetic reconstruction and genetic distance based on a fragment of the cytochrome c oxidase subunit I (COI) showed that our samples constitute a well-supported and monophyletic clade within the A. grixalvii species complex. The cytogenetic analysis identified distinct chromosomal markers, including a single cluster of major ribosomal genes (on chromosome pair 3) and of minor ribosomal genes (on chromosome pair 12) with their localization differing from those reported in other Astroblepus species analyzed. Additionally, the presence of a heteromorphic chromosome pair in males suggests the presence of an XX/XY sex-determination system that has not been identified in other congeneric species. Further investigation is necessary to determine if these chromosomes are associated with the accumulation of repeated sequences, as typically occurs with sex chromosomes, and to assess their presence in other species of the genus.

Multi-marker DNA metabarcoding for precise species identification in ichthyoplankton samples

Ichthyoplankton monitoring is crucial for stock assessments, offering insights into spawning grounds, stock size, seasons, recruitment, and changes in regional ichthyofauna. This study evaluates the efficiency of multi-marker DNA metabarcoding using mitochondrial cytochrome c oxidase subunit I (COI), 12S rRNA and 16S rRNA gene markers, in comparison to morphology-based methods for fish species identification in ichthyoplankton samples. Two transects with four coastal distance categories were sampled along the southern coast of Portugal, being each sample divided for molecular and morphological analyses. A total of 76 fish species were identified by both approaches, with DNA metabarcoding overperforming morphology-75 versus 11 species-level identifications. Linking species-level DNA identifications with higher taxonomic morphological identifications resolved several uncertainties associated with traditional methods. Multi-marker DNA metabarcoding improved fish species detection by 20-36% compared to using a single marker/amplicon, and identified 38 species in common, reinforcing the validity of our results. PERMANOVA analysis revealed significant differences in species communities based on the primer set employed, transect location, and distance from the coast. Our findings underscore the potential of DNA metabarcoding to assess ichthyoplankton diversity and suggest that its integration into routine surveys could enhance the accuracy and comprehensiveness of fish stock assessments.

Examination of sequence variations in partial mitochondrial 12S gene amongst damselfish species as references for DNA barcoding

Accurate species identification, based on DNA barcoding, can be achieved when sufficient sequence variations are present amongst species in the sampled marker. In general, the ability to discriminate species decreases with shorter sequences; however, shorter regions have a merit in amplification success by the polymerase chain reaction. In either case, it is important to investigate sequence variations amongst species before barcoding to understand its reliability and limitations. In this study, we investigate how accurately short, but hypervariable portion of the mitochondrial 12S ribosomal RNA (12S) gene (MiFish region with approximately 180 bp) is used to identify each species in diversified pomacentrid fishes compared with the longer region of the same gene (approximately 750 bp). We prepared three datasets with 301 sequences of the MiFish region for 150 species, the same 301 of sequences of the longer 12S region and 476 sequences of the MiFish region for 183 species. Neighbour-joining (NJ) analyses and genetic distance analyses revealed several indistinguishable pairs of species in these DNA regions. Although the number of such pairs was larger in the MiFish region, 83.6% (153 of 183) of species possessed respective unique sequences even in the MiFish region (versus 96.0% [144 of 150 species] in the longer 12S region). A part of indistinguishable pairs of species might have caused by mitochondrial DNA introgressions and taxonomically unresolved problems. Our analysis clarified the effectiveness and limitations of species identification using DNA barcoding for Pomacentridae and the sequences we provided here contribute to the expansion of references for pomacentrid mitochondrial 12S sequences.

Unveiling taxonomic diversity in the deep-sea fish genus Notacanthus (Notacanthiformes: Notacanthidae) with description of Notacanthus arrontei n. sp

Notacanthid fishes constitute a common part of benthopelagic deep-sea fish communities on seamounts and continental slopes around the world. However, their highly conserved morphology and the usual lack of information on deep-water organisms make it difficult to appropriately address their biodiversity. A multidisciplinary approach combining morphological data with a DNA-based species delimitation analyses was used to explore the taxonomy of Notacanthus species. For this purpose, morphological and molecular data were obtained from 43 individuals, and the resulting information was combined with the available data. The results showed the occurrence of Notacanthus arrontei n. sp. from the Iberian Peninsula and highlighted several taxonomic conundrums regarding the Notacanthus genus. For instance, no significant differences were found between Notacanthus indicus and the recently described Notacanthus laccadiviensis, questioning its taxonomic status. Similarly, the result of the species delimitation molecular analysis coincided with previous DNA barcoding studies supporting the snubnosed spiny eel Notacanthus chemnitzii as a species complex that requires further research. Moreover, two unidentified records from the Indian Ocean were confirmed to belong to an unknown species pending formal description, and barcoding data show for the first time the occurrence of the shortfin spiny eel Notacanthus bonaparte in the Australia-New Zealand area. This research confirms the existence of important gaps in the knowledge of notacanthid fishes and represents a step forward toward a better understanding of their biological diversity.

Redescription of Cyprinion muscatense (Teleostei: Cyprinidae) with the first phylogenetic analysis of the genus

Members of the genus Cyprinion (Cypriniformes: Cyprinidae) are found in the Indus River basin west to the Arabian Peninsula and the Tigris-Euphrates River drainages (Persian Gulf basin). The taxonomic status of Cyprinion including Cyprinion muscatense is poorly understood when compared to other cyprinid genera. C. muscatense has been considered as a member of the Cyprinion watsoni-microphthalmum group and a valid species endemic to the Arabian Peninsula. Here, we redescribe C. muscatense based on an integrative morphological and molecular approach and freshly sampled material from several localities in the Oman Mountains ecoregion. The results showed that C. muscatense is distinguished from the other Cyprinion species in the Arabian Peninsula by having a short, thin, and slightly serrated last unbranched dorsal fin ray; the lower number of circumpeduncular scales; lateral line scales; and also scales between the lateral line and the dorsal-fin origin. Subterminal mouth, presence of one pair of small barbels at the mouth corner, 3-4 unbranched and 9½-10½ dorsal-fin branched rays, 12-14 pectoral-fin rays, 7-8 pelvic-fin rays, 2-3 unbranched and 6½-7½ branched anal-fin rays, and 37-40 lateral line scales are other morphological characteristics of C. muscatense. C. muscatense is also well distinguished by molecular characters among its congeners. The first molecular phylogenetic analysis of the genus, covering all currently recognized Cyprinion species except for C. watsoni, is also presented. C. muscatense is resolved as the sister species to another endemic fish of the Arabian Peninsula Cyprinion mhalense, with a Kimura-2-Parameter model distance of 5.3%.

Taxonomic position of holothurian Eupentactafraudatrix (Echinodermata, Holothuroidea)

Samples of the holothurian Eupentactafraudatrix (Djakonov & Baranova in Djakonov, Baranova & Saveljeva, 1958) from the Sea of Japan were studied and the relationships of the genera Eupentacta and Sclerodactyla, as well as related taxa, were evaluated on the basis of phylogenetic analysis of the mitochondrial DNA COI and 16S rRNA genes. Using three methods, phylogenetic trees were constructed, and the degree of reliability of topological reconstructions was estimated by means of a nonparametric bootstrap test for the neighbor joining (NJ) and maximum likelihood (ML) techniques, as well as by a posteriori probability for Bayesian inference (BI) analysis. Genetic data confirm the validity of the assignment of Cucumariafraudatrix to the genus Eupentacta Deichmann, 1938. The study of sequences obtained from the holothurian specimens collected in Russian waters, near the city of Vladivostok, and determined by morphological characters clearly indicate that these specimens belong to the genus Eupentacta and are assigned as E.fraudatrix . The specimens from China in GenBank named as Sclerodactylamultipes and used in the present study, were likely misidentified, and after re-examination they may be assigned to the genus Eupentacta, either as E.fraudatrix or another taxon. Analyses of morphological characters of S.multipes unequivocally affirm that this species must be excluded from Sclerodactyla Ayres, 1851 and is provisionally assigned to the genus Sclerothyone Thandar, 1989 based on the external morphological characters and the body wall ossicles.

Comparative ontogeny and phylogenetic relationships of eight lizardfish species (Synodontidae) from the Northwest Pacific, with a focus on Trachinocephalus monophyly

Lizardfish (Aulopiforms: Synodontidae), distributed broadly in temperate to tropical waters, are represented globally by 83 species across four genera, with 10 species in Korea. Despite these numbers, few studies have been conducted on the early life history of lizardfishes compared to their adult counterparts. Thus, we conducted molecular identification of 123 Synodontidae larvae collected from the Northwest Pacific (Korea Strait, Yellow Sea, East China Sea, and East Sea) between June 2017 and July 2021, using mitochondrial DNA COI and 16S rRNA sequences. Significant morphological differences were observed in the larvae and juvenile, including variation in melanophore, count, morphometric characteristics, and body shape. The morphological traits of eight species (Harpadon nehereus, Saurida macrolepis, Saurida wanieso, Saurida sp., Synodus hoshinonis, Synodus kaianus, Synodus macrops, and Trachinocephalus trachinus) served as vital data for interpreting the phylogenetic relationships within the Northwest Pacific Synodontidae. Ultimately, the identification key revealed by this study will enable accurate identification of Synodontid larvae and juveniles, and further facilitate our understanding of the phylogenetic relationships within this family.

Comparative Mitogenomics Reveals Cryptic Species in Sillago ingenuua McKay, 1985 (Perciformes: Sillaginidae)

It is unreliable to identify marine fishes only by external morphological features. Species misidentification brings great challenges to fishery research, resource monitoring and ecomanagement. Sillago ingenuua is an important part of commercial marine fishes, and in which, the morphological differences between different groups are not obvious. Here, we compared different geographical groups of S. ingenuua which were collected from Xiamen, Dongshan, Keelung, Songkhla and Java. The results showed that all samples of S. ingenuua were similar in external morphological characteristics and the shape of the swim bladder, but there were two distinctive lineages which were flagged as cryptic species based on DNA barcoding. The comparative mitogenomic results showed that S. ingenuua A and S. ingenuua B were identical in structural organization and gene arrangement. Their nucleotide composition and codon usage were also similar. A phylogenetic analysis was performed based on 13 concatenated PCGs from eight Sillago species. The results showed that the genetic distance between S. ingenuua A and S. ingenuua B was large (D = 0.069), and this genetic distance was large enough to reveal that S. ingenuua A and S. ingenuua B might be different species.

DNA metabarcoding assessment of Neotropical ichthyoplankton communities is marker-dependent

The study of ichthyoplankton is paramount to understanding fish assemblages' reproductive dynamics. DNA metabarcoding has been applied as a rapid, cost-effective, and accurate taxonomy tool, allowing the identification of multiple individuals simultaneously. However, there remain significant challenges when using DNA metabarcoding, such as molecular marker choice according to the taxonomic resolution and length of the fragment to be sequenced, primer bias, incomplete reference databases, and qualitative inference incongruences. Here, 30 ichthyoplankton pools collected from a Neotropical river were identified at a molecular level using DNA metabarcoding to compare the resolution, sensibility, specificity, and relative read abundance (RRA) recovery of three molecular markers: the standard COI fragment (650 pb, with each end analyzed individually) and two short 12S rRNA genes markers (≅200 bp - NeoFish and MiFish markers). The combined use of the three markers increased the genera detection rates by 25%-87.5%, allowing an increased taxonomic coverage and robust taxonomic identification of complex Neotropical ichthyoplankton communities. RRA is marker-dependent, indicating caution is still needed while inferring species abundance based on DNA metabarcoding data when using PCR-dependent protocols.

DNA barcoding of marine teleost fishes (Teleostei) in Cebu, the Philippines, a biodiversity hotspot of the coral triangle

A morphology-based barcoding library of market teleost fishes (Teleostei) in Cebu is built based on cytochrome c oxidase subunit I (COI) sequences and voucher specimens which aimed to establish a reliable reference of frequently traded fishes in the province, a biodiversity hotspot at the center of the Philippine archipelago. A total of 1721 specimens were collected from 18 fish markets and landing sites around the province, in which 538 specimens were sequenced belonging to 393 species from 229 genera, 86 families, and 37 orders. Most speciose families are coral reef or reef-related shallow-water species. Twelve species from 11 families are newly recorded in the Philippine waters, among which 7 species are deep-sea inhabitants, while 3 species have expanded their distribution range. Only 20 taxa could not be identified to the species level due to the difficulty in morphological examinations, absence of matched reference sequences in online databases, and/or problematic species awaiting further studies. This first comprehensive DNA barcoding survey of Cebu fishes can facilitate further taxonomic research as well as the conservation and management of fisheries in the Philippines.

Taxonomic revision of the Ophidion holbrookii Putnam, 1874 (Ophidiiformes: Ophidiidae) species complex, with description of a new species from Brazil

This study integrates morphological and molecular data to redefine the taxonomic limits of Ophidion holbrookii, as well as its geographic ranges, with the description of a new species from the eastern and southeastern coast of Brazil, South America. Ophidion zavalai n. sp. is described based on variations related to ontogeny and sexual development of swim bladder and sonic apparatus, which are likely important traits for species recognition. The description of O. zavalai n. sp. and the redefinition of distribution limits of O. holbrookii corroborate the existence of different complex species in the western Atlantic, revealing important gaps of knowledge regarding morphological variation and species habits. Ophidion zavalai n. sp. is the first species of Ophidion described from the southwestern Atlantic Ocean and contributes to evidence of a distinct coastal fauna in Brazil and surrounding areas of Argentina province.

A revision of the gudgeon genus Hypseleotris (Gobiiformes: Gobioidei: Eleotridae) of northwest Australia, describing three new species and synonymizing the genus Kimberleyeleotris

Species within the northwest Australian clade of Hypseleotris (six species) and the genus Kimberleyeleotris (two species) are reviewed following the recording of new populations in the region and a molecular study of the group that identified three undescribed candidate species. Based on the analysis of extensive morphological and nuclear and mitochondrial molecular datasets, Kimberleyeleotris is here formally synonymised with Hypseleotris. Furthermore, three species from the Kimberley region, Western Australia, are described to science: Hypseleotris maranda sp. nov., Hypseleotris wunduwala sp. nov., and Hypseleotris garawudjirri sp. nov. The presence of, or number of scales across the head and body, the pattern of sensory papillae on the head, fin ray counts, dorsal and anal fin colouration (particularly in breeding males), and body depth, can be used to distinguish the members of the northwest Australia lineage. Furthermore, the newly described species were genetically separated from all northwest Australian congeners by K2P distances ranging from 7.8-11.3% based on the CO1 gene, and 7.7-16.3 % based on the entire mitochondrial genome. Two of the new species, H. maranda sp. nov. and H. wunduwala sp. nov., have extremely narrow ranges being found in single sub-catchments of the Roe and King Edward Rivers respectively. On the other hand, H. garawudjirri sp. nov. is moderately widespread, being found across the Charnley, Calder, and Sale rivers. While the conservation risk to H. maranda sp. nov. and H. wunduwala sp. nov. is inherently high due to their small range, there are currently no obvious local threatening processes to either of these species given their remote locations that are little impacted by human activities.

Genetic variation and cryptic lineage among the sergestid shrimp Acetes americanus (Decapoda)

The taxonomic status of the sergestid shrimp, Acetes americanus, has been questioned for several decades. No specific study has been performed thus far to resolve the incongruences. This species has a wide geographical range in the western Atlantic and is represented by two formally accepted subspecies: Acetes americanus carolinae, distributed in North America, and Acetes americanus americanus, present in South America. However, there are regions where the coexistence of both subspecies has been reported, such as Central America. This study aimed to genetically compare specimens of A. a. americanus collected in South America with A. a. carolinae sampled in North America to check for possible differences and the existence of more than one subspecies of A. americanus on the Brazilian coast. Based on the sequences of two informative markers, the cytochrome oxidase I region (COI) and 16S rRNA, phylogenetic reconstruction demonstrated well-defined clades with high support values, reinforcing the idea that A. a. americanus is genetically different from A. a. carolinae. Our hypothesis was corroborated as the specimens collected in Brazil were divided into two distinct lineages: the first composed of A. a. americanus sensu stricto (Brazil 1) and the second by Acetes americanus (Brazil 2). The three groups evidenced in the haplotype network were the same as those observed in the phylogenetic tree. The morphometric character (height/length of the thelycum) was effective in distinguishing A. a. Brazil 1 from A. a. carolinae. However, more detailed and conclusive studies comprising other characteristics to propose and describe a possible new entity are necessary. To the best of our knowledge, for the first time, the results of this study provide some insights into the taxonomic status of the sergestid shrimp A. americanus in the western Atlantic.

First record of mudskipper Boleophthalmus dussumieri (Gobiidae: Oxudercinae) on the coast of Mozambique and evidence of two putative lineages along its known distribution range

Boleophthalmus dussumieri is one of the most widely distributed mudskippers and is native to the Persian Gulf in Iran down to the northeast of the Arabian Sea and the coast of India. Nonetheless, the present study is the first to confirm the presence of B. dussumieri in the marine areas of the Mozambique coast. In addition, molecular analysis revealed strong evidence for the existence of two lineages with a high level of nucleotide divergence along the sampled area, revealing a still-neglected taxonomic condition for this lineage/species.

Conjectures and refutations: Species diversity and phylogeny of Australoheros from coastal rivers of southern South America (Teleostei: Cichlidae)

Morphological and genetic analyses of species of Australoheros focusing on those distributed in coastal rivers from the Rio de La Plata north to the Rio Buranhém, support recognition of 17 valid species in the genus. Eight species are represented in coastal rivers: A acaroides, A. facetus, A. ipatinguensis, A. oblongus, A. ribeirae, and A. sanguineus are validated from earlier descriptions. Australoheros mboapari is a new species from the Rio Taquari in the Rio Jacuí drainage. Australoheros ricani is a new species from the upper Rio Jacuí. Specimens from the Rio Yaguarón and Rio Tacuary, affluents of Laguna Merín, and tributaries of the Rio Negro, tributary of the Rio Uruguay are assigned to A. minuano pending critical data on specimens from the type locality of A. minuano. Australoheros taura is a junior synonym of A. acaroides. Australoheros autrani, A. saquarema, A. capixaba, A. macaensis, A. perdi, and A. muriae are junior synonyms of A. ipatinguensis. Heros autochthon, A. mattosi, A. macacuensis, A. montanus, A. tavaresi, A. paraibae, and A. barbosae, are junior synonyms of A. oblongus. Heros jenynsii is a junior synonym of A. facetus.

Hyporthodus griseofasciatus (Perciformes: Epinephelidae), a new species of deep-water grouper from the west coast of Australia

A new species of deep-water epinephelid fish is described from the west coast of Australia based on 14 specimens, 99-595 mm standard length. Hyporthodus griseofasciatus sp. nov. is endemic to Western Australia from Barrow Island to Two Peoples Bay in depths of 76-470 m. It has a series of eight grey bands alternating with eight brown bands along the body and the soft dorsal, soft anal and caudal fin margins are pale cream to white. It is distinguished from its nearest congener, H. ergastularius, by the presence of a star-like pattern of radiating lines on the head versus an overall brownish colour in the latter as well as significant differences in the quantitative analyses of 25 morphological characters. The two species have allopatric distributions on either side of the Australian continent. H. griseofasciatus is distinguished from H. octofasciatus by several grey bands being distinctly narrower than other grey bands (vs. all grey bands subequal in the latter) and the presence of broad white margins on the dorsal, caudal and anal fins (vs. narrow or absent in the latter). Some scale counts appear to also differ. Analyses of mitochondrial cytochrome oxidase subunit 1 sequences revealed reciprocally monophyletic clades with fixed differences and genetic distances typical of recently diverged species of fishes.

Unraveling the Drifting Larval Fish Community in a Large Spawning Ground in the Middle Pearl River Using DNA Barcoding

Simple Summary

DNA barcoding identified 28 species from larvae collected from the Dongta spawning ground. Six invasive species were identified in the larval pool, implying that these species had successfully colonized the middle Pearl River. Several migratory species common in the lower Pearl River were rare or absent in the Dongta spawning ground, suggesting that adverse effects of dam construction posed on these migratory species. Our study provided important reference data for fishery management and conservation in the Pearl River.

Abstract

Resolving the species composition of a larval pool in a spawning ground can provide novel insights into regional fish stocks and can support the development of effective monitoring and conservation policies. However, it is challenging to identify fish larvae to species due to their high diversity and dramatic phenotypic changes over development. In this study, we collected fish larvae in the Dongta spawning ground (Guiping City, Guangxi Province, China) in the middle reaches of the Pearl River between May and August 2018. We used a DNA barcoding approach to determine the species composition of the larval pool. A total of 905 larvae were chosen for molecular identification, of which 750 yielded high-quality barcoding sequences. Of these, 597 (≈79.6%), 151 (≈20.1%)/and 2 (≈0.3%) were assigned to 28 species, 8 genera, and 1 subfamily using the Barcode of Life Data System and GenBank nucleotide databases, respectively. Among the 28 identified species, 21 were cyprinids. Two species (Mugilogobius myxodermus and Pseudolaubuca engraulis) that were present only infrequently in previous adult surveys were abundant in the larval pool. Six invasive species were identified in the larval pool, implying that these species had successfully colonized the studied river section. Several migratory species common in the lower Pearl River were rare or absent in the investigated region, suggesting that dam construction in the Pearl River has had adverse effects on these migratory species. In summary, our study confirmed the applicability of DNA barcoding to studies of fish larval ecology and provided important reference data for fishery management and conservation in the Pearl River.

An integrative insight into the diversity, distribution, and biogeography of the freshwater endemic clade of the Ponticola syrman group (Teleostei: Gobiidae) in the Caucasus biodiversity hotspot

Freshwater habitats of the Caucasus biodiversity hotspot represent a center of endemism for the gobiid genus Ponticola Iljin, 1927. Hitherto, large-scale molecular studies, owing to restricted taxon and geographical sampling, have failed to give an elaborate picture of diversity and evolutionary history of these species. Here, to contribute to filling this gap, we assessed taxonomic diversity, phylogeography and evolutionary history for the south Caspian populations of Ponticola presently classified as P. iranicus and P. patimari, using an integrative taxonomic approach comprising an entire geographic range sampling, and analyses of mitochondrial DNA haplotypes, the head lateral line system, otolith shape, and meristic and morphometric variation. All freshwater samples of the P. syrman group belong to a monophyletic clade with two main subclades: a small subclade confined to the upper Sefidroud sub-basin including the type locality of P. iranicus and a large subclade with three geographically constrained haplogroups (Hg1, Hg2, and Hg3), comprising the rest of the distribution. Hg1 showed an eastern distribution including the type locality of P. patimari, while Hg2 and Hg3 are sister groups with central and western-central distributions, respectively. The freshwater clade diverged from P. syrman during the Tyurkyanian low stand (~150 m b.s.l. lasting ~0.1 Myr), while the divergence of P. iranicus and P. patimari and radiations within P. patimari took place during the Bakunian high stand (up to 50 m a.s.l. lasting ~378-480 kya). Species delimitation analyses indicated two distinct species, corresponding to each main subclade. Although the otolith shape and lateral line analyses did not reflect with phylogeographic pattern, PCA and DFA plots of meristic and morphometric data showed a clear separation of the two major subclades corresponding to P. iranicus and P. patimari, suggesting the presence of significant morphological variation meriting formal taxonomic recognition. Overall, our findings (i) reveal the presence of two freshwater endemic species in the P. syrman group, and pending further investigation, hypothesize the presence of a third cryptic species; (ii) revise and document a narrow distributional range and low diversity for P. iranicus, in contrast to a wider distributional range and high diversity for P. patimari; (iii) suggest that the climatic oscillations of the Pleistocene were associated with the cladogenesis within the P. syrman group; and (iv) allowed for the recognition of conservation units and proposition of management measures.

Mitochondrial marker implies fishery separate management units for spotted sardinella, Amblygaster sirm (Walbaum, 1792) populations in the South China Sea and the Andaman Sea

The spotted sardinella, Amblygaster sirm (Walbaum, 1792), is a commercial sardine commonly caught in Malaysia. Lack of management of these marine species in Malaysian waters could lead to overfishing and potentially declining fish stock populations. Therefore, sustainable management of this species is of paramount importance to ensure its longevity. As such, molecular information is vital in determining the A. sirm population structure and management strategy. In the present study, mitochondrial DNA Cytochrome b was sequenced from 10 A. sirm populations: the Andaman Sea (AS) (two), South China Sea (SCS) (six), Sulu Sea (SS) (one), and Celebes Sea (CS) (one). Accordingly, the intra-population haplotype diversity (Hd) was high (0.91-1.00), and nucleotide diversity (π) was low (0.002-0.009), which suggests a population bottleneck followed by rapid population growth. Based on the phylogenetic trees, minimum spanning network (MSN), population pairwise comparison, and F _ST,and supported by analysis of molecular variance (AMOVA) and spatial analysis of molecular variance (SAMOVA) tests, distinct genetic structures were observed (7.2% to 7.6% genetic divergence) between populations in the SCS and its neighboring waters, versus those in the AS. Furthermore, the results defined A. sirm stock boundaries and evolutionary between the west and east coast (which shares the same waters as western Borneo) of Peninsular Malaysia. In addition, genetic homogeneity was revealed throughout the SCS, SS, and CS based on the non-significant F _STpairwise comparisons. Based on the molecular evidence, separate management strategies may be required for A. sirm of the AS and the SCS, including its neighboring waters.

Phylogeography of Sarmarutilus rubilio (Cypriniformes: Leuciscidae): Complex Genetic Structure, Clues to a New Cryptic Species and Further Insights into Roaches Phylogeny

Italy hosts a large number of endemic freshwater fish species due to complex geological events which promoted genetic differentiation and allopatric speciation. Among them, the South European roach Sarmarutilus rubilio inhabits various freshwater environments in three different ichthyogeographic districts. We investigated the genetic diversity of S. rubilio using two different mitochondrial markers (COI and CR), aiming to define its relationship with other similar taxa from the Balkan area and, from a phylogeographic perspective, test the effects of past hydrogeological dynamics of Italian river basins on its genetic structure and demographic history. Our analysis highlighted a marked genetic divergence between S. rubilio and all other roach species and, among Italian samples, revealed the existence of three deeply divergent geographic haplogroups, named A, B and C. Haplogroup C likely corresponds to a new putative cryptic species and is located at the northern border of the South European roach range; haplogroup B is restricted to Southern Italy; and haplogroup A is widespread across the entire range and in some sites it is in co-occurrence with C or B. Their origin is probably related to the tectonic uplifting of the Apuan Alps in the north and of the Colli Albani Volcano in the south during the Pleistocene, which promoted isolation and vicariance followed by secondary contacts.

Clarifying the taxonomy of some cryptic blennies (Blenniidae) in their native and introduced range

Omobranchus punctatus is native to the Indo-Pacific region and invasive in the Atlantic region, currently being considered one of the most widely distributed blenny species. However, recent molecular studies indicated that O. punctatus is a complex of species, with three divergent mtDNA lineages identified to date, stressing the need for a taxonomic revision. In this study, we used an integrative approach, combining morphological and genetic data, to shed light on the taxonomy and distribution of O. punctatus. Moreover, we provide the first genetic records of introduced populations in Brazil and discuss the introduction pattern of this species in this region. Morphological data shows that O. punctatus consists of at least five distinct and geographically restricted species: O. punctatus sensu stricto, O. dispar, O. sewalli, O. cf. kochi, and O. cf. japonicus. Species delimitation analyses performed using the mtDNA data available confirmed that O. punctatus sensu stricto, O. dispar and O. sewalli correspond to different species that started to diverge about 2.6 Mya. Furthermore, O. sewalli was identified as the invasive species colonizing Atlantic shores. The existence of historical oceanographic barriers, such as the emergence of the Sunda Shelf in the Eastern Indian Ocean during the Pleistocene, and the biological traits of these blennies are the most likely factors responsible for their genetic differentiation and subsequent speciation.

DNA metabarcoding quantifies the relative biomass of arthropod taxa in songbird diets: Validation with camera‐recorded diets

Ecological research is often hampered by the inability to quantify animal diets. Diet composition can be tracked through DNA metabarcoding of fecal samples, but whether (complex) diets can be quantitatively determined with metabarcoding is still debated and needs validation using free‐living animals. This study validates that DNA metabarcoding of feces can retrieve actual ingested taxa, and most importantly, that read numbers retrieved from sequencing can also be used to quantify the relative biomass of dietary taxa. Validation was done with the hole‐nesting insectivorous Pied Flycatcher whose diet was quantified using camera footage. Size‐adjusted counts of food items delivered to nestlings were used as a proxy for provided biomass of prey orders and families, and subsequently, nestling feces were assessed through DNA metabarcoding. To explore potential effects of digestion, gizzard and lower intestine samples of freshly collected birds were subjected to DNA metabarcoding. For metabarcoding with Cytochrome Oxidase subunit I (COI), we modified published invertebrate COI primers LCO1490 and HCO1777, which reduced host reads to 0.03%, and amplified Arachnida DNA without significant changing the recovery of other arthropod taxa. DNA metabarcoding retrieved all commonly camera‐recorded taxa. Overall, and in each replicate year (N = 3), the relative scaled biomass of prey taxa and COI read numbers correlated at R = .85 (95CI:0.68–0.94) at order level and at R = .75 (CI:0.67–0.82) at family level. Similarity in arthropod community composition between gizzard and intestines suggested limited digestive bias. This DNA metabarcoding validation demonstrates that quantitative analyses of arthropod diet is possible. We discuss the ecological applications for insectivorous birds.

The first description of larvae and comments on the taxonomy of Stichaeus ochriamkini Taranetz, 1935 (Perciformes: Stichaeidae)

Stichaeus ochriamkini (Stichaeidae) is common in the northern Japan Sea and the southern Okhotsk Sea. Among the five known representatives of the genus Stichaeus, early ontogenesis is the least studied in S. ochriamkini. In this study, the authors provide the first description of all larval stages of this species. In the north-western Japan Sea, larvae are found in plankton from early April to early June. S. ochriamkini larvae can be identified using the following characters: postanal-lateral pigment (PLP) lines present on the sides of the caudal part of the body and run along the anterior edge of hypaxial myomeres; 14-15 abdominal vertebrae; 32-34 rays in the anal fin; larvae disappear from plankton at a body length of L_T > 25.0 mm (L_S > 20 mm). Larvae of S. ochriamkini are very similar to larvae of Stichaeus punctatus. The melanin pigmentation in larvae of both species shows similar patterns of development. In the genus Stichaeus Reinhardt, 1836, two groups of species are distinguished by the presence/absence of PLP lines in larvae, and by significant divergence (clearly exceeding the species level) in the COI mtDNA gene. It is suggested the differences between these species groups is recognized at the generic level. Thus, the genus Stichaeus Reinhardt, 1836 should include S. punctatus and S. ochriamkini, whereas the other three species should be placed in the genus Dinogunellus Herzenstein, 1890: Dinogunellus fuscus, Dinogunellus nozawae and Dinogunellus grigorjewi.

DNA barcoding identification of Greek freshwater fishes

Biodiversity is a key factor for the functioning and efficiency of an ecosystem. Greece, though covering a relatively small surface area, hosts a great deal of species diversity. This is especially true for freshwater fishes. In recent years, the traditional methods of species identification have been supplemented by the use of molecular markers. The present study therefore aims to extensively produce DNA barcodes for Greek freshwater fish species and investigate thoroughly if the presently accepted species classification is in agreement with molecular data. A 624-bases long fragment of the COI gene was sequenced, from 406 freshwater fish specimens belonging to 24 genera and originating from 18 lake and river sites. These sequences were used along with 596 sequences from the same genera, recovered from BOLD, for the construction of phylogenetic trees and the estimation of genetic distances between individuals. In total, 1002 sequences belonging to 72 species were analyzed. The method was found to be effective for 55 of 72 studied species. 17 closely related species with low interspecific genetic distances were observed, for which further study is proposed. It should also be noted that, in four cases, cryptic diversity was observed, where groups originally identified as one species exhibited genetic distance great enough to be separated into discrete species. Region specific haplotypes were also detected within populations of 14 species, giving the possibility to identify even the geographic origin of a species. Our findings are discussed in the light of the rich history of the Balkan peninsula and provide a significant steppingstone for the further study of Greek and European freshwater fish biodiversity.

High rDNA polymorphisms in Astyanax lacustris (Characiformes: Characidae): new insights about the cryptic diversity in A. bimaculatus species complex with emphasis on the Paraná River basin

Abstract This study aimed to identify species of Astyanax bimaculatus group from four Itaipu Reservoir tributaries (Paraná River Basin) by cytogenetics and molecular markers (COI) to investigate the possible occurrence of cryptic diversity in part of this basin. The four populations showed only one karyotype formula and simple AgNORs. FISH with 18S rDNA probe showed a high variation, and 5S rDNA probes evidenced simple sites in most of the specimens, although multiple sites are present in two specimens. The variations of 5S and 18S cistrons generated 13 cytotypes. The molecular data did not reveal cryptic diversity in the populations; however, its grouping with 82 sequences from other stretches of the Paraná River Basin originated three haplogroups (distances of 3.12% and 8.82%) and 33 haplotypes were identified. DNA Barcode suggests that cytogenetic variations represent a high polymorphism degree, and it identified the analyzed specimens as Astyanax lacustris, which confirms the morphological identification. Our data suggest that the cryptic diversity of this group in the tributaries of the Paraná River Basin is different than the proposed by the synonymizations of A. altiparanae and A. asuncionensis to A. lacustris. This study reinforces the importance of integrative cytogenetics and molecular methods for taxonomy.

Population structuration and chromosomal features homogeneity in Parodon nasus (Characiformes: Parodontidae): A comparison between Lower and Upper Paraná River representatives

ABSTRACT The ichthyofauna of the La Plata hydrographic basin is divided into Upper and Lower Paraná River systems due to the geographic isolation of the Sete Quedas waterfalls, currently flooded by the lake of the Itaipu dam. In Parodontidae, pairs of species, or groups of cryptic species were described between these systems. Although genetic isolation and speciation have already been proposed in other species in the group, Parodon nasus has been maintained as a valid species and distributed throughout the La Plata river basin. In this perspective, specimens of P. nasus from four different sampling sites in the Upper and Lower Paraná River systems were compared regarding the karyotypes, molecular analyzes of population biology and species delimitation to investigate their genetic and population isolation in the La Plata river basin. Despite a geographic barrier and the immense geographic distance separating the specimens sampled from the Lower Paraná River system compared to those from the Upper Paraná River, the data obtained showed P. nasus as a unique taxon. Thus, unlike other species of Parodontidae that showed diversification when comparing the groups residing in the Lower versus Upper Paraná River, P. nasus showed a population structure and a karyotypic homogeneity.

Eight in One: Hidden Diversity of the Bagrid Catfish Tachysurus albomarginatus s.l. (Rendhal, 1928) Widespread in Lowlands of South China

There is increasing evidence that species diversity is underestimated in the current taxonomy of widespread freshwater fishes. The bagrid species T. albomarginatus s.l. is mainly distributed in the lowlands of South China, as currently identified. A total of 40 localities (including the type locality), which covers most of its known range, were sampled. Molecular phylogenetic analyses based on concatenated mtDNA and nuclear genes recover nine highly supported lineages clustering into eight geographic populations. The integration of molecular evidence, morphological data, and geographic distribution demonstrates the delineation of T. albomarginatus s.l. as eight putative species. Four species, namely, T. albomarginatus, T. lani, T. analis, and T. zhangfei sp. nov. and the T. similis complex are taxonomically recognized herein. Moreover, T. zhangfei sp. nov. comprises two genetically distinct lineages with no morphological and geographical difference. This study also reveals aspects of estimation of divergence time, distribution, and ecological adaption within the T. albomarginatus group. The unraveling of the hidden species diversity of this lowland bagrid fish highlights the need for not only the molecular scrutiny of widely distributed species of South China but also the adjustment of current biodiversity conservation strategies to protect the largely overlooked diversity of fishes from low-elevation rapids.

Molecular species delimitation refines the taxonomy of native and nonnative physinine snails in North America

Being able to associate an organism with a scientific name is fundamental to our understanding of its conservation status, ecology, and evolutionary history. Gastropods in the subfamily Physinae have been especially troublesome to identify because morphological variation can be unrelated to interspecific differences and there have been widespread introductions of an unknown number of species, which has led to a speculative taxonomy. To resolve uncertainty about species diversity in North America, we targeted an array of single-locus species delimitation methods at publically available specimens and new specimens collected from the Snake River basin, USA to generate species hypotheses, corroborated using nuclear analyses of the newly collected specimens. A total-evidence approach delineated 18 candidate species, revealing cryptic diversity within recognized taxa and a lack of support for other named taxa. Hypotheses regarding certain local endemics were confirmed, as were widespread introductions, including of an undescribed taxon likely belonging to a separate genus in southeastern Idaho for which the closest relatives are in southeast Asia. Overall, single-locus species delimitation was an effective first step toward understanding the diversity and distribution of species in Physinae and to guiding future investigation sampling and analyses of species hypotheses.

Phylogenomics and loci dropout patterns of deeply diverged Zodarion ant-eating spiders suggest a high potential of RAD-seq for genus-level spider phylogenetics

RAD sequencing yields large amounts of genome-wide data at a relatively low cost and without requiring previous taxon-specific information, making it ideal for evolutionary studies of highly diversified and neglected organisms. However, concerns about information decay with phylogenetic distance have discouraged its use for assessing supraspecific relationships. Here, using Double Digest Restriction Associated DNA (ddRAD) data, we perform the first deep-level approach to the phylogeny of Zodarion, a highly diversified spider genus. We explore the impact of loci and taxon filtering across concatenated and multispecies coalescent reconstruction methods and investigate the patterns of information dropout in reference to both the time of divergence and the mitochondrial divergence between taxa. We found that relaxed loci-filtering and nested taxon-filtering strategies maximized the amount of molecular information and improved phylogenetic inference. As expected, there was a clear pattern of allele dropout towards deeper time and mitochondrial divergences, but the phylogenetic signal remained strong throughout the phylogeny. Therefore, we inferred topologies that were almost fully resolved, highly supported, and noticeably congruent between setups and inference methods, which highlights overall inconsistency in the taxonomy of Zodarion. Because Zodarion appears to be among the oldest and most mitochondrially diversified spider genera, our results suggest that ddRAD data show high potential for inferring intra-generic relationships across spiders and probably also in other taxonomic groups.

Genetic diversity across the mitochondrial genome of eastern oysters (Crassostrea virginica) in the northern Gulf of Mexico

The eastern oyster, Crassostrea virginica, is divided into four populations along the western North Atlantic, however, the only published mitochondrial genome sequence was assembled using one individual in Delaware. This study aimed to (1) assemble C. virginica mitochondrial genomes from Texas with pooled restriction-site-associated DNA sequencing (ezRAD), (2) evaluate the validity of the mitochondrial genome assemblies including comparison with Sanger sequencing data, and (3) evaluate genetic differentiation both between the Delaware and Texas genomes, as well as among three bays in Texas. The pooled-genome-assembled-genomes (PAGs) from Texas exhibited several characteristics indicating that they were valid, including elevated nucleotide diversity in non-coding and the third position of codons, placement as the sister haplotype of the genome from Delaware in a phylogenetic reconstruction of Crassostrea mitochondrial genomes, and a lack of genetic structure in the ND4 gene among the three Texas bays as was found with Sanger amplicons in samples from the same bays several years prior. In the comparison between the Delaware and Texas genome, 27 of 38 coding regions exhibited variability between the two populations, which were differentiated by 273 mutations, versus 1-13 mutations among the Texas samples. Using the full PAGs, there was no additional evidence for population structure among the three Texas bays. While population genetics is rapidly moving towards larger high-density datasets, studies of mitochondrial DNA (and genomes) can be particularly useful for comparing historic data prior to the modern era of genomics. As such, being able to reliably compile mitochondrial genomes from genomic data can improve the ability to compare results across studies.

Comparative Fatty Acid Profiling of Edible Fishes in Kuala Terengganu, Malaysia

The aim of this study was to compare the relative nutritional benefit of edible Malaysian fishes from the coast of Terengganu in Malaysia, as well as to perform a taxonomical characterization and metal assessment. Discrimination between species was carried out by a morphological and molecular approach by evaluating the total concentrations of metals by ICP-MS analyses and the fatty acids (FA) composition using the GC–MS approach on the fish fillet tissues. The taxonomical studies detected fishes of 11 families and 13 species. The heavy metal assessment showed that all detected elements did not exceed the regulatory limit stated by Malaysian Food Regulations. The proportion of saturated fatty acids (SFA) ranged from 33 to 58.34%, followed by the polyunsaturated fatty acids (PUFA) values from 24 to 51.8%, and the lowest proportion was of monounsaturated fatty acids (MUFA), ranging from 12.7 to 35.9%. The ω-3/ω-6 PUFA and PUFA/SFA ratios were determined in the range 1.1 to 7.4 and 0.35 to 1.6, respectively. The C20:5 ω-3 and C22:6 ω-3 acids were detected at levels comparable to those found in the corresponding species from similar tropical marine ecosystems. The high FA values can be useful biochemical tools for comparing the relative nutritional benefits of these biodiverse and non-toxic edible Malaysian fishes.

Cryptic species and grey zone speciation of the Barbodes binotatus complex (Teleostei, Cyprinidae) in Sundaland

Morphology-based taxonomy of freshwater fish is effective when there are representative specimens covering large regions. However, in Sundaland, where the presence of cryptic species is high, the technique has its limitations. This is compounded by uncritical descriptions of holotypes in old literature. We demonstrate the problem using Barbodes binotatus first described from an ink drawing. Several species in the Barbodes genus of Sundaland exhibit morphological similarity to B. binotatus. We applied new DNA sequences of 16S, cytochrome c oxidase subunit I (COI), cytochrome b (Cytb) and recombination-activating gene 1 (RAG1), and pigmentation markers to clarify species complex boundaries in the Malay Peninsula, namely B. aff. binotatus "Malay Peninsula", Barbodes cf. banksi and Barbodes rhombeus. Results suggest B. binotatus-like specimens in the Malay Peninsula are B. rhombeus based on a threshold of 3% COI genetic divergence. B. aff. binotatus recorded in Sumatra, Borneo and the Philippines are likely valid but undescribed species. However, if the 2% COI threshold is applied, some populations in the northern Malay Peninsula would qualify as new and undescribed species. The implications of the 2% threshold and the likelihood of "grey zone" incipient populations are discussed. We further found a rapid visual method, not reported previously, to delineate B. aff. binotatus and B. cf. banksi, but it requires further validation. Additionally, we offer fresh perspectives by discussing the roles of biological species concept, morphological species concept, genetic species concept and mate recognition concept in the B. binotatus complex. Our findings reinforce the standpoint that species delineation is not entirely a binary process, but there is a spectrum to consider, especially in biogeography intersection regions.

A multi-locus approach to elucidating the evolutionary history of the clingfish Tomicodon petersii (Gobiesocidae) in the Tropical Eastern Pacific

Marine species that are widely distributed in the Tropical Eastern Pacific (TEP) has served as a model for studying biogeographic patterns resulting from the effects of intraregional habitat discontinuities and oceanographic processes on the diversification and evolution of cryptobenthic reef fishes. Tomicodon petersii, a clingfish (Gobiesocidae) endemic to the TEP, is found on very shallow rocky reefs from central Mexico to northern Peru, and in the Cocos and Galapagos islands. We evaluated the effect of likely biogeographic barriers in different parts of the TEP on the diversification process of this species. We used one mitochondrial and three nuclear DNA markers from 112 individuals collected across the distribution range of T. petersii. Our phylogenetic results showed the samples constituted a monophyletic group, with three well-supported, allopatric subgroups: in the Mexican province, the Panamic province (from El Salvador to Ecuador), and the Galapagos Islands. The split between the Mexican and more southerly clades was estimated to occur at the end of the Miocene ca. 5.74 Mya, and the subsequent cladogenetic event separating the Galapagos population from the Panamic population at the junction of the Pliocene and Pleistocene, ca. 2.85 Mya. The species tree, Bayesian species delimitation tests (BPP), STACEY, and substantial genetic distances separating these three populations indicate that these three independent evolutionary units likely include two unnamed species. The cladogenetic events that promoted the formation of those genetically differentiated groups are consistent with disruptive effects on gene flow of habitat discontinuities and oceanographic processes along the mainland shoreline in the TEP and of ocean-island isolation, in conjunction with the species intrinsic life-history characteristics.

Diversification of Dawkinsia filamentosa (Valenciennes, 1844) and their growth conditions by the impact of toxic metals in the river Tamiraparani

The concentration of toxic metals in water, sediment, and organs of species Dawkinsia filamentosa and its growth conditions were analyzed from the Tamiraparani river of Tamilnadu, India. The water quality preferred to examine the existence of metals, and the concentration of Pb, Cr and Cd expand the first time were found to be high in sediment, which was followed by water and the organs of the fish gill and liver. Even though, intakes of the toxic metals were highly accumulated in the gill instead of the liver. From that, the histological assessments of organ damages were observed significant variations in the study sites. Within the linear regression parameters for length-weight relationships of coefficient value r², 'a' value and 'b' value were showed the allometric growth rate and condition factor of 'K' was fittest. The phylogenetic tree analyses were showing analogy between the opposite groups of Clade III and Clade II showed that the species were closely correlated with the Puntius sp. of other species. And in Clade I was intimately related within the identical population of D. filamentosa as respectively. However, the comparison of metal concentrations of other Indian rivers and of other parts of the world specified that these metals are getting closer to the standard permissible limits. Altogether, the potential ecological risk factor was slightly increased at the sampling sites; therefore, we conclude that the metal contents might pollute the river. Throughout this research, the observed findings emphasize that fish species from the riverine ecosystem may useful for environmental management and genetic diversity.

Integrative taxonomy reveals the historically poorly defined armoured catfish Hypostomus variipictus (Ihering 1911), from the upper rio Paraná basin, Brazil (Siluriformes, Loricariidae)

In a recent expedition to the rio Grande basin, a tributary of the rio Paraná in southern Brazil, individuals of the armoured catfish genus Hypostomus with a peculiar and beautiful colour pattern composed of pale vermiculations on the head and four to five horizontal stripes on the flanks were collected. Initially, the specimens were identified as a colour morph of the pale-spotted H. margaritifer. However, when we compared their partial cytochrome C oxidase subunit I (COI) mitochondrial gene to sequences of some typically pale-spotted H. margaritifer, the striped specimens were genetically distinct. Further analysis of the striped individuals revealed that they are the poorly known but valid species Hypostomus variipictus, which was described by Ihering in 1911 from the rio Pardo, a tributary of the rio Grande, upper rio Paraná basin, in São Paulo State, Brazil. Since its descriptions, no robust taxonomic work has been published concerning this species. In this study, the newly sampled population was compared to the original description and to the holotype of H. variipictus, providing the foundation for a complete redescription, proper diagnosis, and first live colour illustration and description of the previously hidden H. variipictus.

First record of the pencil cardinal Epigonus denticulatus (Perciformes: Epigonidae) in the Azores archipelago

The pencil cardinal Epigonus denticulatus is a small deep-water fish inhabiting continental slopes usually between 300 and 600 m depth. We report the first record of E. denticulatus in the Azores archipelago, where one specimen was found floating by fisherman off Faial island. Meristic and morphometric characters are in accordance with those reported for the species and molecular analyses further supported species identity. The record of E. denticulatus as a native species in the Azores increases the number of Epigonus species in the region to a total of three.

Molecular classification and comparative phylogeographic study of insectivorous bat species (Pipisitrellus coromandra) from Punjab, Pakistan

Molecular based identification of bat fauna in Pakistan has been relatively less explored. The current study was therefore planned to report for the first time the molecular classification of insectivorous bats (Pipistrellus coromandra) based on mitochondrion gene (COI) from Punjab, Pakistan. Specimens were collected from five different locations followed by DNA extraction with subsequent gene amplification and sequencing. All samples in the study had shown close identity matches with species (Pipistrellus coromandra) from India and (Pipistrellus tenuis) from Vietnam with percentage identity score of 96.11 and 95.58 respectively except one sequence which only revealed 86.78% identity match on Basic Local Alignment Search Tool (BLAST) and could only be assigned to genus level Pipistrellus sp. The results indicated negligible intra-population genetic distance among collected samples whereas the comparison with species from other countries had shown high intraspecific (P. coromandra) and interspecific (P. tenuis) mean genetic distances. The current study hence successfully proved the efficiency of COI gene as a molecular marker for species identification and in analyzing the patterns of genetic variation with species from other countries.

Genetic landscape clustering of a large DNA barcoding data set reveals shared patterns of genetic divergence among freshwater fishes of the Maroni Basin

The Maroni is one of the most speciose basins of the Guianas and hosts a megadiverse freshwater fish community. Although taxonomic references based on morphological identification exist for both the Surinamese and Guianese parts of the basin, there are still taxonomic uncertainties concerning the status of several species. We used COI sequences of 1284 fish in conjunction with morphological and biogeographical evidence to assist with species delineation and discovery in order to validate and standardize the current taxonomy. This resulted in a final DNA barcode data set of 199 fish species (125 genera, 36 families and eight orders; 68.86% of strictly freshwater fishes from the basin), among which 25 are new putative candidate species flagged as requiring taxonomic update. DNA barcoding delineation through Barcode Index Numbers (BINs) revealed further cryptic diversity (230 BINs in total). To explore global genetic patterns across the basin, genetic divergence landscapes were computed for 128 species, showing a global trend of high genetic divergence between the Surinamese southwest (Tapanahony and Paloemeu), the Guianese southeast (Marouini, Litany, Tampok, etc.), and the river outlet in the north. This could be explained by lower levels of connectivity between these three main areas and/or the exchange of individuals between these areas and the neighbouring basins. A new method of ordination of genetic landscapes successfully assigned species into cluster groups based on their respective pattern of genetic divergence across the Maroni Basin: genetically homogeneous species were effectively discriminated from species showing high spatial genetic fragmentation and possible lower capacity for dispersal.