COI Markers Research Articles

Germplasm evaluation and identification of the population source of hard clam (Mercenaria mercenaria) in China using SSR and COI markers

In aquaculture, good germplasm resources are nearly decisive for its development. The hard clam (Mercenaria mercenaria), a significant marine aquaculture bivalve in China, has flourished quickly since being introduced from North America in 1997. However, for numerous reasons, it has suffered from germplasm deterioration and uncertain origins. To address these issues, seven microsatellite DNA loci (SSRs) and mtCOI were employed to evaluate germplasm and trace the origins of various Chinese populations. The results of these two molecular genetic markers revealed weak genetic differentiation among all Chinese populations, with high genetic diversity observed across most individuals, except for a few outliers. This suggests an alarming situation regarding germplasm resources in China. Based on results of traceability analysis, the most likely areas of origin for the Chinese populations are Chesapeake Bay and the southern region of Cape Hatteras. This study provides a crucial theoretical foundation for the cultivation, conservation, and subsequent introduction of hard clam populations in China, thereby ensuring the sustainable growth of the hard clam breeding sector.

Fifty shades of white: morphological and molecular diversity of the Cadlina laevis species complex (Gastropoda: Nudibranchia) in the North-West Pacific

We provide a morphological examination and a barcoding study to investigate the species identity and variation limits within the Cadlina laevis species complex. Our molecular analysis based on the COI marker revealed seven new clades in the North-West Pacific Cadlina diversity. The distances between these clades are low in some cases (2.08-7.51% overall), and the species delimitation tests gave controversial results (1, 2, 13, 14 groups, depending on the analysis method). This does not allow to conclusively classify this diversity as interspecific or intraspecific. Morphological analysis showed a significant similarity of all examined groups, with minor differences found in the morphology of the central tooth of the radula and the reproductive system. However, these variations fit into the morphological variability of the North Atlantic species Cadlina laevis s.str. and cannot serve as evidence of the isolation of these identified groups. The discovered diversity may represent both a complex of at least 11 very close and cryptic species with not well-established species boundaries, or be a part of a single amphiboreal species Cadlina laevis s.l. This indicates an extremely complex evolutionary history of Cadlina laevis species complex, making this group is an interesting model object for studying speciation in boreal and Arctic communities.

Molecular identification of intertidal rock oyster species in north-eastern Australia reveals new candidates for aquaculture

Oyster aquaculture in Australia is currently centred on two species, Saccostrea glomerata (Gould, 1850) and Magallana gigas (Thunberg, 1793) which are both susceptible to disease. Disease outbreaks have caused significant losses to the industry and there is currently an appetite for diversification to mitigate risk. Development of other, native oyster species for aquaculture is limited by a poor understanding of their biodiversity and distribution, which is primarily due to the difficulty in distinguishing species based on morphology alone. In this study we sampled intertidal rock oysters from 19 localities in north-eastern Australia and performed phylogenetic analyses based on partial COI and 16S mitochondrial markers. A total of 14 distinct oyster lineages (most likely representing distinct species) were identified from the 357 specimens collected and sequenced. In total, we report the presence of 8 Saccostrea lineages, 4 Ostreinae lineages, one Magallana lineage (Magallana bilineata (Röding, 1798), a recent introduction), and one Talonostrea lineage (likely undescribed). A number of these lineages have broad distributions and attain large sizes, and several are currently cultured in other parts of the world. Although morphological identification is challenging we argue that the large size of the tropical black-lip oyster, Saccostrea lineage J, enables it to be definitively identified as Saccostrea spathulata (Lamarck 1819), thus providing taxonomic certainty for this commercially important species. The identification of these oyster lineages and their distributions is a fundamental step towards development of viable alternatives for oyster aquaculture in the region.

DNA Barcoding of Locusta migratoria manilensis (Orthoptera: Acrididae) Reveals Insights into the Species and Subspecies Differentiation

Abstract Accurate identification and classification of insect species, especially those with significant economic and ecological implications, have historically presented challenges. Migratory locusts, Locusta migratoria manilensis (Meyen) (Orthoptera: Acrididae), are notorious for their destructive impact on crops. Traditional morphological methods often face limitations in distinguishing closely related species and require taxonomic expertise. However, the emergence of DNA barcoding as a powerful tool for species identification has revolutionized the field of entomology. DNA barcoding utilizes a standardized DNA sequence, a molecular barcode, which serves as a distinct genetic signature for rapid and accurate species identification. In this study, DNA barcoding techniques were employed to identify and differentiate the migratory locust subspecies manilensis, in both its solitary and gregarious forms, as well as to determine its phylogenetic relationship with other related species within the Acrididae family. GenBank reference sequences were used to identify the locusts at the molecular subspecies level. Although the COI marker did not exhibit significant differences between the solitary and migratory forms, it was valuable in resolving the identification of L. migratoria subspecies. This lack of significant differences may be attributed to limited genetic variation of COI at the subspecies level and substantial genetic similarities between the solitary and migratory forms, likely stemming from a recent common ancestor. Nonetheless, using COI remains beneficial for subspecies identification in migratory locusts.

From caves to seamounts: the hidden diversity of tetractinellid sponges from the Balearic Islands, with the description of eight new species

The sponge fauna of the Western Mediterranean stands as one of the most studied in the world. Yet sampling new habitats and a poorly studied region like the Balearic Islands highlights once again our limited knowledge of this group of animals. This work focused on demosponges of the order Tetractinellida collected in several research surveys (2016–2021) on a variety of ecosystems of the Balearic Islands, including shallow caves, seamounts and trawl fishing grounds, in a broad depth range (0–725 m). Tetractinellid material from the North Atlantic and more than twenty type specimens were also examined and, for some, re-described in this work. All species were barcoded with the traditional molecular markers COI (Folmer fragment) and 28S (C1-C2 or C1-D2 fragment). A total of 36 species were identified, mostly belonging to the family Geodiidae (15 species), thereby bringing the number of tetractinellids recorded in the Balearic Islands from 15 to 39. Eight species from this study are new: Stelletta mortarium sp. nov., Penares cavernensis sp. nov., Penares isabellae sp. nov., Geodia bibilonae sp. nov., Geodia microsphaera sp. nov. and Geodia matrix sp. nov. from the Balearic Islands; Geodia phlegraeioides sp. nov. and Caminus xavierae sp. nov. from the North East Atlantic. Stelletta dichoclada and Erylus corsicus are reported for the first time since their description in Corsica in 1983. Pachastrella ovisternata is documented for the first time in the Mediterranean Sea. Finally, after comparisons of type material, we propose new synonymies: Geodia anceps as a junior synonym of Geodia geodina, Erylus cantabricus as a junior synonym of Erylus discophorus and Spongosorites maximus as a junior synonym of Characella pachastrelloides.

Molecular Characterization Analysis and Adaptive Responses of Spodoptera frugiperda (Lepidoptera: Noctuidae) to Nutritional and Enzymatic Variabilities in Various Maize Cultivars.

The fall armyworm, Spodoptera frugiperda Smith (Lepidoptera: Noctuidae), a common agricultural pest known for its extensive migration and wide host ranges, causes considerable harm to maize (Zea mays L.). In this study, we utilized two molecular marker genes, COI and Tpi, to compare the genetic characteristics of the collected original samples. Additionally, through an interactive study between S. frugiperda larvae and six maize varieties aiming to understand the insect's adaptability and resistance mechanisms, our analysis revealed that both the COI and Tpi genes identified S. frugiperda as the corn strain. Further examination of the larvae showed significant differences in nutritional indices, digestive, and detoxification enzyme activities. Special maize varieties were found to offer higher efficiency in nutrient conversion and assimilation compared with common varieties. This study revealed adaptations in S. frugiperda's digestive and detoxification processes in response to the different maize varieties. For instance, larvae reared on common maize exhibited elevated amylase and lipase activities. Interestingly, detoxification enzyme activities exhibited different patterns of variation in different maize varieties. The Pearson correlation analysis between nutritional indices, enzyme activities, and the nutritional content and secondary metabolites of maize leaves provided deeper insights into the pest's adaptability. The results highlighted significant relationships between specific nutritional components in maize and the physiological responses of S. frugiperda. Overall, our findings contribute substantially to the understanding of S. frugiperda's host plant adaptability, offering critical insights for the development of sustainable pest management strategies.

Kinship relationship of Uroteuthis chinensis in the waters of western Kalimantan and northern Java based on morphometric characters and genetic structure

Uroteuthis chinensis was a squid species with a wide distribution and rapid reproduction. It was commonly found in the waters of western Kalimantan and northern Java, which were the highest squid fishing grounds in Indonesia. Exploitation of U. chinensis in these waters was intensive and increasing, which might have affected the sustainability of U. chinensis squid resources. Therefore, proper and responsible management was needed to maintain the sustainability of this squid resource. For exploitation to be sustainable and optimal, management based on stock units of the managed resources was required. Therefore, information was needed on the stock units of U. chinensis squid in the western waters of Kalimantan and northern Java. Currently, the Indonesian government has separated the management of these two interconnected waters. The method used was to analyze 12 morphometric characters and genetic structures with COI and Rhodopsin markers. Sampling locations included the Sungailiat and Pontianak, for the waters of western Kalimantan, Jakarta, Pekalongan, and Lamongan for the waters of northern Java. Morphometric data were analyzed using Principal Component Analysis (PCA) and Discriminant Analysis (DA) approaches. Genetic analysis (COI and Rhodopsin) included genetic diversity, AMOVA, and haplotype distribution. The results of the morphometric analysis showed that the 12 morphometric size characters in this study showed a close relationship between the five U. chinensis sample populations. Genetic variation between populations and FST values on COI and Rhodopsin showed very low values; P-values also showed results that were not significantly different between populations. The haplotype distribution of both COI and Rhodopsin showed almost the same composition in both observed waters. The results of these analyses suggested that U. chinensis species in both waters showed indications of connectivity and close kinship or could be regarded as a single stock. Therefore, collaborative management across fisheries management areas in both waters (western Kalimantan and northern Java) was required.

Fine-Scale Genetic Structure of Curculio chinensis (Coleoptera: Curculionidae) Based on Mitochondrial COI: The Role of Host Specificity and Spatial Distance.

The Camellia weevil, Curculio chinensis (Chevrolat, 1978), is a dominant oligophagous pest that bores into the fruit of oil-tea Camellia. Genetic differentiation among populations in various hosts can easily occur, which hinders research on pest management. In this study, the genetic structure, genetic diversity, and phylogenetic structure of local C. chinensis populations were examined using 147 individuals (from 6 localities in Jiangxi), based on 2 mitochondrial COI markers. Results indicated that the C. chinensis population in Jiangxi exhibits a high haplotype diversity, especially for the populations from Cam. meiocarpa plantations. Structural differentiation was observed between Haplogroup 1 (73 individuals from Ganzhou, Jian, and Pingxiang) in the monoculture plantations of Cam. meiocarpa and Haplogroup 2 (75 individuals from Pingxiang and Jiujiang) in Cam. oleifera. Two haplogroups have recently undergone a demographic expansion, and Haplogroup 1 has shown a higher number of effective migrants than Haplogroup 2. This suggests that C. chinensis has been spreading from Cam. meiocarpa plantations to other oil-tea Camellia, such as Cam. oleifera. The increased cultivation of oil-tea Camellia in Jiangxi has contributed to a unique genetic structure within the C. chinensis population. This has, in turn, expanded the distribution of C. chinensis and increased migration between populations.

Population structure of commercially important groupers in the coral triangle Gorontalo, Indonesia to support conservation

Abstract. Achmad DS, Nurdin MS, Taslim I, Moore AM. 2023. Population structure of commercially important groupers in the coral triangle Gorontalo, Indonesia to support conservation. Biodiversitas 24: 6592-6601. Appropriate management units are fundamental to the conservation of species and ecosystems. In the case of exploited fishes, sustainable approaches to fisheries management are generally based on population units (stocks). This study aimed to address the lack of data to define the population structure of the stocks of two commercially important grouper species (Variola albimarginata (Baissac, 1953) and Variola louti (Forsskål, 1775)) in the Sulawesi Sea and Tomini Bay waters of Gorontalo Province, Sulawesi, Indonesia, in the Wallacea biodiversity hotspot. We used a combined morphometric and molecular (DNA barcoding, COI marker). We used truss network analysis with 14 characters to evaluate inter and intraspecies morphometric differences. DNA was extracted (Qiagen protocols) from tissue samples from individuals of both species in both sea areas, followed by polymerase chain reaction (PCR) and Sanger sequencing. Sequence processing and phylogenetic analyses conducted in MEGA X. Both approaches show clear separation between V. albimarginata and V. louti but indicate close kinship between the north coast (Sulawesi Sea) and south coast (Tomini Bay) populations of these groupers. Under the authority of the Gorontalo Province Marine and Fisheries Service, these two populations could be managed as one stock without compromising fisheries sustainability or the conservation of these ecologically and economically valuable species.

A transoceanic journey: Melanochlamys diomedea's first report in the North Atlantic

Abstract Egg masses from an unknown mollusc have been found in South-West Iceland since 2020, but it was not until September 2023 that the adult organism was collected. Morphological analysis of both adults and egg masses pointed towards the identification of the species as Melanochlamys diomedea. This was further confirmed through DNA analyses using COI, H3, and 16S rRNA markers, which established the presence of a new non-indigenous species in the North Atlantic. Members of the genus Melanochlamys have predominantly been found in the Indo-Pacific basin and the Pacific Ocean, with only one species known to exist across the Madeira Islands, Canary Islands, and Cape Verde in the Atlantic. The known distribution range of M. diomedea extends from Alaska to California on the Pacific side of North America, where it typically inhabits sandy-muddy areas of the littoral in the tidal zone and below. It is not known how the species arrived in Iceland. However, maritime transport through either ballast water or biofouling is being considered as the most likely mode of dispersal.

Is it worth the extra mile? Comparing environmental DNA and RNA metabarcoding for vertebrate and invertebrate biodiversity surveys in a lowland stream.

Environmental DNA (eDNA) metabarcoding has emerged as a promising approach to assess biodiversity and derive ecological status classes from water samples. However, a limitation of eDNA surveys is that detected DNA molecules may originate from other places or even dead organisms, distorting local biodiversity assessments. Environmental RNA (eRNA) metabarcoding has recently been proposed as a complementary tool for more localized assessments of the biological community. In this study, we evaluated the effectiveness of eDNA and eRNA metabarcoding for inferring the richness and species distribution patterns of vertebrates and invertebrates in a Central European lowland river. We collected water samples and analyzed them using a 12S marker for vertebrates and a COI marker for invertebrates. We detected 31 fish, 16 mammal, 10 bird and one lamprey species in the vertebrate dataset. While results were largely consistent, we detected a higher number of species when analysing eRNA (mean = 30.89) than eDNA (mean = 26.16). Also, eRNA detections had a stronger local signature than eDNA detections when compared against species distribution patterns from traditional fish monitoring data. For invertebrates, we detected 109 arthropod, 22 annelid, 12 rotiferan, eight molluscan and four cnidarian species. In contrast to the pattern of vertebrate richness, we detected a higher richness using eDNA (mean = 41.37) compared to eRNA (mean = 22.42). Our findings primarily show that eDNA and eRNA-based detections are comparable for vertebrate and invertebrate taxa. Biological replication was important for both template molecules studied. Signal detections for vertebrates were more localized for eRNA compared to eDNA. Overall, the advantages of the extra steps needed for eRNA analyses depend on the study question but both methods provide important data for biodiversity monitoring and research.

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

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

MkLTG: a command-line tool for taxonomic assignment of metabarcoding sequences using variable identity thresholds.

Metabarcoding is now a widely used method for biodiversity studies. Taxonomic assignment of environmental sequences is one of the key steps of metabarcoding. Assignments based on lowest common ancestor (LCA) method generally rely on fixed arbitrary thresholds, and this is generally not well adapted for assignment of taxonomically diverse groups with variable coverage in reference databases. The mkLTG is a LCA-based method that uses a series of percentage of identity thresholds starting from stringent parameters and decreasing it if necessary. All parameters can be set separately for each percentage of identity threshold, which makes this tool adaptable for different databases, genetic markers and diverse taxonomic groups. The optimization step was included using the COI marker and a comprehensive, non-redundant database. The mkLTG tool is a command-line application with few dependencies that runs in all operating systems, therefore, it is easy to include into complex pipelines. All scripts are freely available including the benchmarking at https://github.com/meglecz/mkLTG .

Filter no more: A modified plankton sampler for rapid in‐water eDNA capture

Abstract The combination of an efficient sampling method and high‐throughput analysis of environmental DNA (eDNA) can be a powerful approach for characterising biodiversity across aquatic ecosystems. Plankton net tows are one of the oldest, simplest, and least expensive methods for seston and eDNA collection, but require laborious filtration steps which often lead to clogging and/or the introduction of contaminants. In this study, we used a cruising speed net (CSN) device enabling the collection of seston‐derived eDNA at 5 knots speed combined with a novel modified cod‐end with 20 μm nylon mesh inserts enabling eDNA capture while towing. We compared the performance of the CSN sampling protocol with the original conventional filtration of water sample versus the modified cod‐end. Samples were collected in parallel horizontal tows along New Zealand's North‐Eastern coastline. Concentrated water was filtered on conventional 5 μm cellulose acetate membranes, while the 20 μm nylon mesh inserts were immediately isolated post‐towing. Metabarcoding of bacterial 16S rRNA, eukaryotic nuclear 18S rRNA and mitochondrial COI genes, revealed no significant difference in alpha diversity between filtration techniques. In terms of community composition, a clear and significant shift could be observed between sampling sites and environments. Significant differences could be detected between filtration methods for 16S and COI markers, likely driven by fine‐scale differences at more turbid sheltered sites. Nonetheless, each technique could detect shifts in communities between sites and environments with similar sensitivity. Our results demonstrate the promising potential of the modified cod‐end to enable practical and cost‐effective isolation of eDNA‐derived biodiversity data from any vessel types (at ≤5 knots) across a large range of aquatic ecosystems and biogeographic scales.

Insights on Pinna nobilis population genetic structure in the Aegean and Ionian Sea.

The fan mussel Pinna nobilis Linnaeus, 1758 is an endemic species of the Mediterranean Sea, protected by international agreements. It is one of the largest bivalves in the world, playing an important role in the benthic communities; yet it has been recently characterized as Critically Endangered by the IUCN, due to mass mortality events. In this context, the assessment of the genetic variation of the remaining P. nobilis populations and the evaluation of connectivity among them are crucial elements for the conservation of the species. For this purpose, samples were collected from six regions of the Eastern Mediterranean Sea; the Islands of Karpathos, Lesvos and Crete; the Chalkidiki and Attica Peninsulas; and the Amvrakikos Gulf. Sampling was performed either by collecting tissue from the individuals or by using a non-invasive method, i.e., by scraping the inside of their shells aiming to collect their mucus and thus avoid stress induction to them. Conventional molecular techniques with the use of the COI and 16S rRNA mitochondrial markers were selected for the depiction of the intra-population genetic variability. The analyses included 104 samples from the present study and publicly available sequences of individuals across the whole Mediterranean Sea. The results of this work (a) suggest the use of eDNA as an efficient sampling method for protected bivalves and (b) shed light to the genetic structure of P. nobilis population in the Eastern Mediterranean; this latter knowledge might prove to be fundamental for the species conservation and hence the ecosystem resilience. The haplotype analyses reinforced the evidence that there is a certain degree of connectivity among the distinct regions of the Mediterranean; yet there is evidence of population distinction within the basin, namely between the Western and the Eastern basins. The combination of both genetic markers in the same analysis along with the inclusion of a large number of individuals produced more robust results, revealing a group of haplotypes being present only in the Eastern Mediterranean and providing insights for the species' most suitable conservation management.

Using eRNA/eDNA metabarcoding to detect community-level impacts of nanoplastic exposure to benthic estuarine ecosystems

Plastic particles are ubiquitous in marine systems and fragment into smaller pieces, such as nanoplastics (NPs). The effects of NPs on marine organisms are of growing concern but are not well understood. Marine sediments act as a sink for many contaminants, like microplastics, and are rich habitats for benthic micro- and meiofauna which are ecologically-important components of marine food webs; however, little is known about the sensitivities of specific organisms to NPs or the effects on community diversity and composition. Utilizing molecular methods, such as metabarcoding of environmental DNA/RNA, allows for the rapid and comprehensive detection of microscopic organisms via high-throughput sequencing to assess adverse effects at the community level. The objective of this study was to use a metabarcoding approach to investigate the effects of NPs on benthic micro- and meiofaunal community diversity. Mesocosms were created with sediment cores collected from the Narrow River estuary (Rhode Island, USA) and exposed to 900 nm diameter weathered polystyrene beads at concentrations of 0.1, 1, 10, or 100 mg/kg dry weight in sediment for two weeks. Following exposure, RNA and DNA were co-extracted from the sediment, RNA was reverse-transcribed, 18S and COI markers were PCR-amplified, and amplicons were sequenced on an Illumina MiSeq. Using the 18S marker and eRNA template, increases to α-diversity and significant differences to β-diversity were observed in the highest NP exposures relative to the control. Observed differences in community composition were driven by the differential abundance of several types of protists and arthropods. Significant dose-dependent shifts in composition were observed in β-diversity Jaccard and Unweighted-Unifrac metrics with the 18S marker using the RNA template. To our knowledge, this is the first demonstration of a dose-response relationship for NPs at a community level, and it highlights the value of using community-level endpoints to assess environmental impacts of nanoparticles.

Phylogenetic review of the comb-tooth blenny genus Hypleurochilus in the northwest Atlantic and Gulf of Mexico

As some of the smallest vertebrates, yet largest producers of consumed reef biomass, cryptobenthic reef fishes serve a disproportionate role in reef ecosystems and are one of the most poorly understood groups of fish. The blenny genera Hypleurochilus and Parablennius are currently considered paraphyletic and the interrelationships of Parablennius have been the focus of recent phylogenetic studies. However, the interrelationships of Hypleurochilus remain understudied. This genus is transatlantically distributed and comprises 11 species with a convoluted taxonomic history. In this study, relationships for ten Hypleurochilus species are resolved using multi-locus nuclear and mtDNA sequence data, morphological data, and mined COI barcode data. Mitochondrial and nuclear sequence data from 61 individuals collected from the western Atlantic and northern Gulf of Mexico (N. GoM) delimit seven species into a temperate clade, a tropical clade, and a third distinct lineage. This lineage, herein referred to as H. cf. aequipinnis, may represent a species of Hypleurochilus whose range has expanded into the N. GoM. Inclusion of publicly available COI sequence for an additional three species provides further phylogenetic resolution. H. bananensis forms a new eastern Atlantic clade with H. cf. aequipinnis, providing further evidence for a western Atlantic range expansion. Single marker COI delimitation was unable to elucidate the relationships between H. springeri/H. pseudoaequipinnis and between H. multifilis/H. caudovittatus due to incomplete lineage sorting. Mitochondrial data are also unable to accurately resolve the placement of H. bermudensis. However, a comprehensive approach using multi-locus phylogenetic and species delimitation methods was able to resolve these relationships. While mining publicly available sequence data allowed for the inclusion of an increased number of species in the analysis and a more comprehensive phylogeny, it was not without drawbacks, as a handful of sequences are potentially mis-identified. Overall, we find that the recent divergence of some species within this genus and potential introgression events confound the results of single locus delimitation methods, yet a combination of single and multi-locus analyses has allowed for insights into the biogeography of this genus and uncovered a potential transatlantic range expansion.

Exploring Genetic and Morphological Integrity across Ocean Basins: A Case Study of the Mesopelagic Shrimp Systellaspis debilis (Decapoda: Oplophoridae)

Plankton communities often consist of cosmopolitan species with an extensive gene flow between populations. Nevertheless, populations of some plankton species are genetically structured, owing to various barriers such as ocean currents, hydrological fronts, and continents. Drivers that could explain the genetic structures of most mesopelagic species remain unknown on an ocean-basin scale, and our study aims to analyze the genetic and morphological differences between populations of a cosmopolitan mesopelagic shrimp, Systellaspis debilis, from the Southern and Northern Atlantic Ocean, and the Southwest Indian Ocean. We analyzed the ITS-1 and COI markers of 75 specimens and assessed the genetic integrity and within-species variability of these genes. We also coded 32 morphological characteristics in 73 specimens, analyzed their variability, and assessed the correlation between morphological and genetic characteristics using a Redundancy analysis and Mantel test. Systellaspis debilis was genetically cohesive across the whole Atlantic and Southwest Indian Oceans, which is possibly a result of an intensive gene flow through ecological barriers, the resistance of species to hydrological gradients, a purifying selection of mitochondrial genes, etc. In contrast, we found significant morphological differences between populations from different regions, which mirrors morphological diversification and calls for further genomic approaches in order to understand the basis of these variations and uncover potential local adaptations.

Dead‐end hollow fiber ultrafiltration capture of environmental DNA for freshwater mussel (Unionidae) species detection with metabarcoding

AbstractInsufficient water sample volumes can be a limiting factor for detecting species with environmental DNA (eDNA) from aquatic habitats. We compared detections of freshwater mussel (Unionidae) communities using large water sample volumes and dead‐end hollow fiber ultrafiltration (D‐HFUF or DEUF) with traditional eDNA filtration methods that use relatively small water sample volumes. Unionid species were detected in approximately 50‐L D‐HFUF eDNA samples with two mitochondrial DNA metabarcoding markers (COI and ND1) and compared to species detection results from eDNA captured from commonly used 1‐L samples filtered with polyethersulfone (PES) filters at three lotic sites in Georgia and Missouri. Of the 431,560 COI and 1,035,472 ND1 reads from all environmental samples of both filter types that passed quality control, 95% (410,755 reads) of COI reads and 85% (883,472 reads) of ND1 reads were assigned to a unionid species. Nineteen different freshwater mussel species were detected across all D‐HFUF samples, and 11 species were detected across all PES samples. Reads assigned to the genus Elliptio could not be resolved beyond the genus level with either marker. From D‐HFUF samples, 15 and 16 mussel species were detected with the COI and ND1 markers, respectively. From PES samples, nine and seven species were detected with the COI and ND1 markers, respectively. More mussel species were detected at each site in D‐HFUF samples than in PES samples regardless of whether results from both markers were combined or evaluated separately. Our results demonstrate the merit of further exploration and optimization of D‐HFUF for capturing eDNA from high‐volume water samples to facilitate detection of unionids and likely other aquatic organisms.

Integrative Analysis of Retusa pertenuis (Heterobranchia: Cephalaspidea) from Arctic and Russian Far East Seas with Discussion of Its Morphology, Validity and Population Structure

Retusa pertenuis is still formally considered a junior subjective synonym of Retusa obtusa, despite previous data indicating R. pertenuis and R. obtusa differ significantly in copulatory system morphology. In this paper, we study the species identity and population structure of R. pertenuis with an integrative approach combining morphological and molecular data. The external morphology, head copulatory system and gizzard plates were studied using light microscopy and scanning electron microscopy. We also obtained two mitochondrial (COI and 16S) and two nuclear (H3 and 28S) markers to test the monophyly of R. pertenuis and R. obtusa. Populations from the White Sea, Sea of Okhotsk and Sea of Japan were studied using COI and 18S molecular markers. Our results show that Retusa obtusa sensu lato represents a species complex of at least four species: the nominative species occurring in the North Atlantic, the widely distributed R. pertenuis and two additional species whose identities should be clarified in further studies. Retusa pertenuis geographic range encompasses the North Atlantic, Eurasia’s northern seas, the Canadian Arctic, the Bering Sea, the Sea of Okhotsk and the Sea of Japan. Within R. pertenuis’s range, this species demonstrates a wide variability in shell morphology.