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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. [ABSTRACT FROM AUTHOR]

Metabarcoding is emerging as an alternative to morphological methods in noninvasive carnivore diet analysis based on scats. A number of metabarcoding markers have been developed but their comparative performance to recover DNA from scats remains mostly untested. We tested three markers covering a wide taxonomic range of prey items and compared them with the results of a morphological analysis. Morphological and genetic methods performed comparably regarding the identity of detected prey species, but the number of identified species varied strongly between markers. Only one, 12S-V5, amplified successfully in all samples and proved to be robust and reliable when working with the highly degraded DNA obtained from scats. [ABSTRACT FROM AUTHOR]

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.

The Large-crested toad is an endemic species of the mountain cloud forests of the Sierra Madre Oriental in Mexico. It is listed as endangered, and the population trend is decreasing. We used mitochondrial fragments 12S (450 bp) and cytochrome b (410 bp) from four toads' populations from remnant fragments of mountain cloud forest in Puebla and Veracruz to estimate the genetic' structure, gene flow, and demographic history. The 12S gene had a single haplotype and null nucleotide diversity. The cytochrome b fragment showed 4 haplotypes, intermediate nucleotide diversity (π = 0.0068), and strong genetic structuring ( F ST = 0.8). Demographic history suggests that there is a low effective population size (Ne = 37.42), possibly due to post-bottleneck expansion and contraction events in some populations. Current difficulty finding individuals at localities where they had been previously documented suggests that the population continues to decline, resulting in low diversity and gene flow. Habitat fragmentation and loss, as well as water pollution at breeding sites, increases the probability of extinction of this species. The importance of establishing conservation strategies for the habitat and genetic diversity of the remaining populations is highlighted. [ABSTRACT FROM AUTHOR]

The coastline of Sub‐Saharan Africa hosts highly diverse fish communities of great conservation value, which are also key resources for local livelihoods. However, many costal ecosystems are threatened by overexploitation and their conservation state is frequently unknown due to their vast spatial extent and limited monitoring budgets. Here, we evaluated the potential of citizen science‐based eDNA surveys to alleviate such chronic data deficiencies and assessed fish communities in Mozambique using two 12S metabarcoding primer sets. Samples were either collected by scientific personnel or trained community members and results from the two metabarcoding primers were combined using a new data merging approach. Irrespective of the background of sampling personnel, a high average fish species richness was recorded (38 ± 20 OTUs per sample). Individual sections of the coastline largely differed in the occurrence of threatened and commercially important species, highlighting the need for regionally differentiated management strategies. A detailed comparison of the two applied primer sets revealed an important trade‐off in primer choice with MiFish primers amplifying a higher number of species but Riaz primers performing better in the detection of threatened fish species. This trade‐off could be partly resolved by applying our new data‐merging approach, which was especially designed to increase the robustness of multiprimer assessments in regions with poor reference libraries. Overall, our study provides encouraging results but also highlights that eDNA‐based monitoring will require further improvements of, for example, reference databases and local analytical infrastructure to facilitate routine applications in Sub‐Saharan Africa. [ABSTRACT FROM AUTHOR]

Abstract Freshwater mussels (family Unionidae) are among the world's most endangered taxa, with almost 75% of North American taxa classified as a species of concern, threatened, or endangered. Despite the critical importance of comprehensive distributional data for the conservation of unionids and fishes, these data are often lacking because of the labor and resources associated with traditional survey methods. During their larval stage, unionid mussels use various fish species as obligate hosts, making native fish species vital to unionid persistence and an understanding of host distribution similarly important. Here, we utilized an eDNA metabarcoding approach to evaluate patterns of co‐distribution of unionid mussels and fishes along ~362 km of the densely sampled Grand River network as well as the outlets of 19 tributaries along the eastern shore of Lake Michigan, USA. We detected a total of 21 mussel and 40 fish taxa, with distinctive composition of both mussel and fish assemblages across tributaries and differences in fish taxa between sampling periods. Notably, we detected more mussel taxa within the Grand River watershed than at the outlets of all 20 rivers combined. Within the Grand River network, two fish taxa (Pylodictus olivaris and Cyprinella) were found more frequently in areas of high mussel diversity, and three fish taxa more frequently in areas of low mussel diversity (Umbra, Leuciscidae, and Etheostoma). There was little difference between eDNA detections of mussels from samples collected in June versus August, but we detected significantly more fish taxa in August compared to June. Taken together, our findings demonstrate the value of eDNA metabarcoding for evaluating co‐distribution of ecologically connected taxa. The use of eDNA as a tool for determining distributions of mussels and their obligate hosts may facilitate conservation efforts for these imperiled taxa.

This study analyzed the molecular and phylogenetic profiles of Theileria annulata , the causative agent of tropical theileriosis in cattle, and its tick vector Hyalomma scupense in Algeria. Forty H. scupense ticks were collected in Medea, with 5 testing positive for Theileria spp. based on partial COXIII gene sequences. Positive ticks were further analyzed using COX1 and 12S rRNA genes. Two novel H. scupense 12S rRNA haplotypes and one novel COX1 haplotype were identified. One T. annulata haplotype previously reported in Algerian cattle was detected. This represents the first molecular characterization of T. annulata from H. scupense ticks in Algeria, providing insights into the genetic diversity of the parasite vector in this region. Overall, the study reveals new haplotypes for both the tick vector and parasite, furthering our understanding of their molecular profiles and phylogenetics in Algeria. [Display omitted] • This study represents the first molecular characterization of T. annulata from its vector H. scupense in Algeria. • COXIII gene reveals five ticks positive for T. annulata with an haplotype previously reported from blood cattle in Algeria. • 2 novel 12S and 1 original COX1 haplotypes specific to H. scupense were identified in Algeria. • Phylogeographic analysis: genetic proximity between H. scupense populations from Algeria and some Asian countries. • H. scupense , vector of T. annulata , represents a major threat to cattle farming and animal health in Algeria. [ABSTRACT FROM AUTHOR]

High-throughput DNA metabarcoding of mitochondrial 12S rRNA and Cyt b gene sequences was coupled with a morphology-based identification tool to assess ichthyoplankton community structure in Oujiang River Estuary, China. The performances of 12S and Cyt b barcoding markers were compared in terms of taxonomic resolution, detection and coverage, and their suitability was established for use as a quick and powerful ichthyoplankton assessment tool. A total of 30,138 ichthyoplankton (2462 eggs and 27,676 larvae) samples were collected from April to August 2015 and identified to 145 taxa belonging to 57 families and 105 genera. June and July were the main spawning months. Ichthyoplankton were more abundant around Lingkun and Qidu Islands and the upper parts of Oujiang River Estuary. The 12S gene marker presented higher species coverage and detection rate than Cyt b. DNA metabarcoding exhibited more representative species identification power than morphology. The findings reported in this study provided a key attempt towards the development of time-efficient and cost-effective ichthyoplankton identification and assessment tool. [ABSTRACT FROM AUTHOR]

Holotype designation is mandatory for animal species descriptions, yet we are lacking studies on its selection. Landmark-based geometric morphometrics (LBGM) can be used to detect subtle phenotypic variations and to calculate mean shapes of groups for certain characters, which should provide reliable tools for selecting holotypes that are most representative even of cryptic species. Western Australian copepods from the genus Halicyclops Norman, 1903 (Halicyclopidae) were studied here in a subterranean archipelago of calcretes by a combination of molecular phylogenetics (using mitochondrial COI and 12S markers) and LBGM, on the same specimens. Bayesian analyses of molecular markers resulted in five deeply divergent and congruent clades, supported with maximum posterior probabilities. ANOVA analysis of LBGM data showed that the effect of these clades was a much larger contributor to shape variation than the effects of locality or individual. Therefore, five new endemic species were described, employing a condensed format appropriate for cryptic species. All of them are destined for extinction due to approved uranium mining in the region. Four morphological structures used for LBGM analyses provided different degrees of phenotypic species separation in both sexes, and representative holotypes and allotypes for one structure were sometimes close to species' extremes of variability for another structure. Résumé: La désignation de l'holotype est indispensable pour la description des espèces animales, cependant nous manquons d'études sur sa sélection. La morphométrie géométrique basée sur des landmarks (points de repère) (LBGM) peut être utilisée pour détecter des variations phénotypiques subtiles et pour calculer des formes moyennes de groupes pour certains caractères, qui pourraient fournir des outils fiables pour sélectionner des holotypes les plus représentatifs même pour les espèces cryptiques. Les copépodes de l'Australie occidentale du genre Halicyclops Norman, 1903 (Halicyclopidae) ont été étudiés ici dans un archipel souterrain de calcrète par une combinaison de phylogénie moléculaire (utilisant les marqueurs mitochondriaux COI et 12S) et la LBGM, sur les mêmes spécimens. Des analyses bayésiennes, ont résulté cinq clades congruents et profondément divergents, soutenus par des probabilités postérieures maximales. L'analyse ANOVA des données de la LBGM a montré que l'effet de ces clades était un contributeur beaucoup plus important pour la variation de forme que les effets de la localité ou de l'individu. Ainsi, cinq espèces nouvelles endémiques ont été décrites, en utilisant un format condensé adapté aux espèces cryptiques. Toutes sont vouées à l'extinction en raison de l'exploitation d'uranium approuvée dans la région. Quatre structures morphologiques utilisées pour les analyses de LBGM ont fourni différents degrés de séparation phénotypique des espèces dans les deux sexes, et des holotypes et allotypes représentatifs pour une structure étaient quelquefois proches des extrêmes de variabilité d'une espèce pour une autre structure. [ABSTRACT FROM AUTHOR]

Abstract Early life stages of aquatic organisms are particularly vulnerable to climatic stressors; however, they are difficult to monitor due to challenges in sampling and morphological identification. Environmental DNA (eDNA) from water samples represents an opportunity for rapid, nondestructive monitoring of aquatic community composition as well as single species monitoring. eDNA can also detect spawning events, although has not been yet tested in offshore spawning grounds. Here, we used metabarcoding of water samples to detect the presence of key fish taxa in spawning areas that are difficult to monitor using traditional means. We analyzed DNA from water samples and fish larvae samples at 14 offshore sites, using 12S mitochondrial metabarcoding and compared taxa detections, diversity, and community structure estimated by both sample types. Species richness and diversity did not differ between water and larvae samples. Both sample types detected a core of 12 taxa across the survey, with an average agreement in detections of 75% at sampling site level. Water samples detected two of the three most abundant taxa, the sandeel, Ammodytes marinus, and clupeids, Clupea harengus/Sprattus sprattus, at 31% and 38% more sites than larvae samples respectively, while Callionymus sp. was more prevalent in larvae samples. Mackerel (Scomber scombrus) and blue whiting (Micromestius poutassou) were only detected in water samples despite sampling taking place at peak spawning times for these species. Our results demonstrate that eDNA metabarcoding provides a rapid and feasible monitoring method for the management of key taxa, such as sandeel, that cannot be easily monitored using traditional capture surveys.

Abstract Metabarcoding studies using environmental DNA (eDNA) and high‐throughput sequencing (HTS) are rapidly becoming an important tool for assessing and monitoring marine biodiversity, detecting invasive species, and supporting basic ecological research. Several barcode loci targeting teleost fish and elasmobranchs have previously been developed, but to date primer sets focusing on other marine megafauna, such as marine mammals, have received less attention. Similarly, there have been few attempts to identify potentially “universal” barcode loci which may be informative across multiple marine vertebrate orders. Here we describe the design and validation of two new sets of primers targeting hypervariable regions of the vertebrate mitochondrial 12S and 16S rRNA genes, which have conserved priming sites across virtually all cetaceans, pinnipeds, elasmobranchs, boney fish, sea turtles, and birds, and amplify fragments with consistently high levels of taxonomically diagnostic sequence variation. “In silico” validation using the OBITOOLS software showed our new barcode loci outperformed most existing vertebrate barcode loci for taxon detection and resolution. We also evaluated sequence diversity and taxonomic resolution of the new barcode loci in 680 complete marine mammal mitochondrial genomes demonstrating that they are effective at resolving amplicons for most taxa to the species level. Finally, we evaluated the performance of the primer sets with eDNA samples from aquarium communities with known species composition. These new primers will potentially allow surveys of complete marine vertebrate communities in single HTS metabarcoding assessments, simplifying workflows, reducing costs, and increasing accessibility to a wider range of investigators.

Two new species of lung-dwelling nematodes are described from North American frogs: Rhabdias aurorae n. sp. from Rana aurora and Rhabdias conni n. sp. from Rana clamitans and Rana catesbeiana from Arkansas; the latter species was also found in Oklahoma and Georgia. Rhabdias aurorae n. sp. differs from other Nearctic congeners in the combination of the following characteristics: buccal capsule 22-25 μm wide, elongated tail covered with inflated cuticle, esophagus with prominent dilatation in anterior part and 6 small circumoral lips. Rhabdias conni n. sp. is morphologically closest to Rhabdias ranae Walton, 1929 and Rhabdias joaquinensisIngles, 1936; it differs from them in the shape of lateral pseudolabia, the dimensions of the body, and the egg size. Both new species were found to be significantly different from the Nearctic congeners in the nucleotide sequences of nuclear ribosomal DNA (18S-ITS-28S region), 12S, and CO1 mitochondrial genes. The 2 new species differ from other currently sequenced Nearctic congeners by 1.1-2.7% of nucleotide positions in the nuclear rDNA region, 1.3-3.4% in the 12S gene, and 3.4-9.4% in CO1 gene. Molecular phylogenetic analysis based on nuclear ribosomal DNA sequences placed both new species into the clade consisting of Nearctic and Neotropical Rhabdias spp. The position of Rh. aurorae n. sp. within the clade is uncertain because of a polytomy, but Rh. conni n. sp. is nested within the "Rh. joaquinensis complex" related to Rh. ranae and Rhabdias tarichaeKuzmin, Tkach, and Snyder, 2003. The phylogenetic analysis based on nuclear ribosomal DNA sequences has revealed 3 evolutionary host-switching events from anuran to caudatan hosts among Rhabdias spp. that occurred in the Nearctic and Palearctic. The molecular phylogeny also suggests that Rhabdias may have originally evolved in what is now Africa., (© American Society of Parasitologists 2024.)

The accuracy and reliability of DNA metabarcoding analyses depend on the breadth and quality of the reference libraries that underpin them. However, there are limited options available to obtain and curate the huge volumes of sequence data that are available on public repositories such as NCBI and BOLD. Here, we provide a pipeline to download, clean and annotate mitochondrial DNA sequence data for a given list of fish species. Features of this pipeline include (a) support for multiple metabarcode markers; (b) searches on species synonyms and taxonomic name validation; (c) phylogeny assisted quality control for identification and removal of misannotated sequences; (d) automatically generated coverage reports for each new GenBank release update; and (e) citable, versioned DOIs. As an example we provide a ready‐to‐use curated reference library for the marine and freshwater fishes of the U.K. To augment this reference library for environmental DNA metabarcoding specifically, we generated 241 new MiFish‐12S sequences for 88 U.K. marine species, and make available new primer sets useful for sequencing these. This brings the coverage of common U.K. species for the MiFish‐12S fragment to 93%, opening new avenues for scaling up fish metabarcoding across wide spatial gradients. The Meta‐Fish‐Lib reference library and pipeline is hosted at https://github.com/genner-lab/meta-fish-lib. [ABSTRACT FROM AUTHOR]

Aim: To evaluate the ability of precipitation‐based environmental DNA (eDNA) sample collection and mitochondrial 12S metabarcoding sequencing to reconstruct well‐studied fish communities in lakes and rivers. Specific objectives were to 1) determine correlations between eDNA species detections and known community composition based on conventional field sampling, 2) compare efficiency of eDNA to detect fish biodiversity among systems with variable morphologies and trophic states, and 3) determine if species habitat preferences predict eDNA detection. Location: Upper Great Lakes Region, North America. Methods: Fish community composition was estimated for seven lakes and two Mississippi River navigation pools using sequence data from the mitochondrial 12S gene amplified from 10 to 50 water samples per waterbody collected in 50‐mL centrifuge tubes at a single time point. Environmental DNA (eDNA) was concentrated without filtration by centrifuging samples to reduce per‐sample handling time. Taxonomic detections from eDNA were compared to established community monitoring databases containing up to 40 years of sampling and a detailed habitat/substrate preference matrix to identify patterns of bias. Results: Mitochondrial 12S gene metabarcoding detected 15%–47% of the known species at each waterbody and 30%–76% of known genera. Non‐metric multidimensional scaling (NMDS) assessment of the community structure indicated that eDNA‐detected communities grouped in a similar pattern as known communities. Discriminant analysis of principal components indicated that there was a high degree of overlap in habitat/substrate preference of eDNA‐detected and eDNA‐undetected species suggesting limited habitat bias for eDNA sampling. Main conclusions: Large numbers of small volume samples sequenced at the mitochondrial 12S gene can describe the coarse community structure of freshwater systems. However, additional conventional sampling and environmental DNA sampling may be necessary for a complete diversity census. [ABSTRACT FROM AUTHOR]

High-throughput DNA metabarcoding of mitochondrial 12S rRNA and Cyt b gene sequences was coupled with a morphology-based identification tool to assess ichthyoplankton community structure in Oujiang River Estuary, China. The performances of 12S and Cyt b barcoding markers were compared in terms of taxonomic resolution, detection and coverage, and their suitability was established for use as a quick and powerful ichthyoplankton assessment tool. A total of 30,138 ichthyoplankton (2462 eggs and 27,676 larvae) samples were collected from April to August 2015 and identified to 145 taxa belonging to 57 families and 105 genera. June and July were the main spawning months. Ichthyoplankton were more abundant around Lingkun and Qidu Islands and the upper parts of Oujiang River Estuary. The 12S gene marker presented higher species coverage and detection rate than Cyt b. DNA metabarcoding exhibited more representative species identification power than morphology. The findings reported in this study provided a key attempt towards the development of time-efficient and cost-effective ichthyoplankton identification and assessment tool.

A new species of Nanorana Günther, 1896 is described from Yunnan Province, China, based on morphological and molecular evidence. Morphologically, Nanorana xuelinensis sp. nov. is distinguished from its congeners by a combination of the following diagnostic characters: body size large; adult males with keratinized spines on chest, belly, lateral body, posterior dorsum, buttocks, outer side of the fore limbs, the inner metacarpal tubercle, fingers I and II, and upper eyelids; no spines on the inner side of the lower and upper arm; forelimbs strongly hypertrophied in adult males; anterior dorsum skin smooth; dorsolateral folds absent; finger I longer than finger II; webbing deeply incurved between tips of toes; present outer metacarpal tubercle and absent outer metatarsal tubercle. The new species is separated from all other congeners by uncorrected genetic distances ranging from 5.2% to 7.3% based on mitochondrial 16S rRNA gene and ranging from 3.9% to 7.6% based on mitochondrial 12S rRNA gene. [ABSTRACT FROM AUTHOR]

[Display omitted] • The tropical brown dog tick (Rhipicephalus linnaei) was studied and resurrected as a dominant species globally. • Global distribution was confirmed using all available cox1 , 12S rDNA and 16S rDNA sequences. • Whole genome sequencing of R. linnaei from Australia, Fiji and Laos was completed to establish mtDNA references. The brown dog tick (Rhipicephalus sanguineus) parasitises dogs. Over the past decade, two distinct lineages have been recognised – R. sanguineus sensu lato "temperate lineage" and R. sanguineus sensu lato "tropical lineage". The nominal taxon R. sanguineus (Latreille, 1806) was recently associated with the "temperate lineage". We here identify the "tropical lineage" as Rhipicephalus linnaei (Audouin, 1826) using material from Australia, where no other Rhipicephalus species parasitises dogs. Whole genome sequencing of R. linnaei from Australia, Fiji and Laos, and assembly of their complete mitochondrial DNA (~15 kb) confirms the genetic identity and distinctness from all other known species within the brown dog tick species complex. Designation of the species R. linnaei is unequivocally supported by material available through the Australian National Insect Collection, Australia. Accordingly, we are formally justified in using R. linnaei for the "tropical lineage". [ABSTRACT FROM AUTHOR]

Animal dietary information provides the foundation for understanding trophic relationships, which is essential for ecosystem management. Yet, in marine systems, high‐resolution diet reconstruction tools are currently under‐developed. This is particularly pertinent for large marine vertebrates, for which direct foraging behaviour is difficult or impossible to observe and, due to their conservation status, the collection of stomach contents at adequate sample sizes is frequently impossible. Consequently, the diets of many groups, such as sharks, have largely remained unresolved. To address this knowledge gap, we applied metabarcoding to prey DNA in faecal residues (fDNA) collected on cotton swabs from the inside of a shark's cloaca. We used a previously published primer set targeting a small section of the 12S rRNA mitochondrial gene to amplify teleost prey species DNA. We tested the utility of this method in a controlled feeding experiment with captive juvenile lemon sharks (Negaprion brevirostris) and on free‐ranging juvenile bull sharks (Carcharhinus leucas). In the captive trial, we successfully isolated and correctly identified teleost prey DNA without incurring environmental DNA contamination from the surrounding seawater. In the field, we were able to reconstruct high‐resolution teleost dietary information from juvenile C. leucas fDNA that was generally consistent with expectations based on published diet studies of this species. While further investigation is needed to validate the method for larger sharks and other species, it is expected to be broadly applicable to aquatic vertebrates and provides an opportunity to advance our understanding of trophic interactions in marine and freshwater systems. [ABSTRACT FROM AUTHOR]

The limpet Lottia cf. borealis, a gastropod species widely distributed in the Far Eastern Seas of Russia, has been subjected to genetic analysis. Three genetic markers (COI, 16S, and 12S) showed no evidence of a distinct genetic structure of this species within the studied part of its range (the southern coast of Primorsky Krai and the coasts of Sakhalin Island and the southern Kuril Islands). A phylogenetic analysis revealed that Lottia cf. borealis is a sister taxon to L. paradigitalis (Fritchman, 1960). [ABSTRACT FROM AUTHOR]

Accurate assessment of larval community composition in spawning areas is essential for fisheries management and conservation but is often hampered by the cryptic nature of many larvae, which renders them difficult to identify morphologically. Metabarcoding is a rapid and cost‐effective method to monitor early life stages for management and environmental impact assessment purposes but its quantitative capability is under discussion. We compared metabarcoding with traditional morphological identification to evaluate taxonomic precision and reliability of abundance estimates, using 332 fish larvae from multinet hauls (0–50 m depth) collected at 14 offshore sampling sites in the Irish and Celtic seas. To improve quantification accuracy (relative abundance estimates), the amount of tissue for each specimen was standardized and mitochondrial primers (12S gene) with conserved binding sites were used. Relative family abundance estimated from metabarcoding reads and morphological assessment were positively correlated, as well as taxon richness (RS = 0.81, P = 0.007) and diversity (RS = 0.90, P = 0.002). Spatial patterns of community composition did not differ significantly between metabarcoding and morphological assessments. Our results show that DNA metabarcoding of bulk tissue samples can be used to monitor changes in fish larvae abundance and community composition. This represents a feasible, efficient, and faster alternative to morphological methods that can be applied to terrestrial and aquatic habitats. [ABSTRACT FROM AUTHOR]

The cannonball jellyfish Stomolophus meleagris display colour variations from blue to purple, and different pigmentation patterns on the umbrella surface. Although these colour phenotypes are common in this organism, surprisingly, little is known about the causes and the adaptive significance of these polymorphisms. In this study, we investigated the population genetic structure of S. meleagris distributed in the Gulf of California based on the partial regions of mitochondrial COI and 12S rRNA genes. Sample collections were carried out, and morphological data from organisms, as well as physicochemical parameters of the seawater at the collection sites, were recorded. White and blue phenotypes were found in April, and blue specimens were the more abundant. No specimens of the white phenotype were found in May, and the purple phenotype was present only in June. A correlation was found between the occurrences of white jellyfish and lower seawater temperatures (23.5 °C). Ten different COI gene haplotypes were detected, and 20 12S rRNA gene haplotypes. The clustering of haplotypes was not correlated with their geographical distributions. Moderate and low values of FST were obtained between samples collected in different locations. These results suggest that S. meleagris in the Gulf of California exist as a single genetic stock, and the different pigmentation patterns observed may result from specific environmental conditions. [ABSTRACT FROM AUTHOR]

The land snail genus Schileykula Gittenberger, 1983 is distributed in arid limestone areas from western Turkey to north‐western Iran. It comprises eight species, which display high variation in shell size and morphology. The cylindrical shells are 5–12 mm in height and the last shell whorls bear several inner lamellae and plicae. Two taxa differ in their chirality having sinistral shells, while all the others are dextrals such as the vast majority of orculids. The aim of this study was to establish a molecular genetic phylogeny of Schileykula and to test whether it conforms to the current morphology‐based classification. Furthermore, we were interested in the phylogenetic position of the two sinistral forms in order to assess whether one or two reversals happened in the evolution of the genus. Nine out of ten species, including all four subspecies of Schileykula trapezensis and three of six subspecies of Schileykula scyphus, were investigated. A section of the mitochondrial cytochrome c oxidase subunit I gene was analyzed in 54 specimens of Schileykula and from a subsample, partial sequences of the mitochondrial genes for the 12S rRNA and the 16S rRNA, and a section of the nuclear H4/H3 histone gene cluster were obtained. The phylogenetic trees based on the mitochondrial sequences feature high support values for most nodes, and the species appear well differentiated from each other. The two chiral forms evolved independently and are not sister lineages. However, some groupings disagree with the present morphology‐based classification and taxonomical conclusions are drawn. Schileykula trapezensis is polyphyletic in the molecular genetic trees; therefore, three of its subspecies are elevated to species level: Schileykula acampsis Hausdorf, 1996 comb. nov., Schileykula neuberti Hausdorf, 1996 comb. nov., and Schileykula contraria Neubert, 1993 comb. nov. Furthermore, Schileykula sigma is grouped within S. scyphus in the mitochondrial and nuclear trees and consequently treated as a subspecies of the latter (Schileykula scyphus sigma Hausdorf, 1996 comb. nov.). Schileykula nordsiecki, whose shell morphology is indistinguishable from that of the neighboring Schileykula scyphus lycaonica, but who differs in its genital anatomy, was confirmed to represent a distinct lineage. The phylogenies produced by the mitochondrial and nuclear data sets are to some extent conflicting. The patterns differ concerning the grouping of some specimens, suggesting at least two independent hybridization events involving S. contraria, S. scyphus and S. trapezensis. The results exemplify the importance of integrating both mitochondrial and nuclear sequence data in order to complement morphology‐based taxonomy, and they provide further evidence for hybridization across distantly related lineages in land snails. [ABSTRACT FROM AUTHOR]

For many years, methods based on the molecular analysis of conservative genome segments have been used to solve controversial issues of phylogeny by calculating the divergence of organisms. In the present study, a marker fragment of the 12S rRNA gene was used to clarify the phylogenetic position of a poorly studied faunistic group, ancient leech-like parasites of the genus Acanthobdella. The mosaic combination of oligochaete (Oligochaeta) and modern leech (Hirudinea) traits points to the intermediate evolutionary position of acanthobdells. Our results suggest that the 12S marker fragment is efficient for phylogenetic analysis at the genus and species levels. The phylogenetic history of acanthobdellids reconstructed in the present study is not consistent with the results of earlier studies. Low statistical support suggests that the 12S marker is not efficient for phylogenetic analysis at the supergenus level. [ABSTRACT FROM AUTHOR]

Metabarcoding extra‐organismal DNA from environmental samples is now a key technique in aquatic biomonitoring and ecosystem health assessment. Of critical consideration when designing experiments, and especially so when developing community standards and legislative frameworks, is the choice of genetic marker and primer set. Mitochondrial cytochrome c oxidase subunit I (COI), the standard DNA barcode marker for animals, with its extensive reference library, taxonomic discriminatory power and predictable sequence variation, is the natural choice for many metabarcoding applications. However, for targeting specific taxonomic groups in environmental samples, the utility of COI has yet to be fully scrutinized.Here, by using a case study of marine and freshwater fishes from the British Isles, we quantify the in silico performance of twelve primer pairs from four mitochondrial loci – COI, cytochrome b, 12S and 16S – in terms of reference library coverage, taxonomic discriminatory power and primer universality. We subsequently test in vitro four primer pairs – three COI and one 12S – for their specificity, reproducibility, and congruence with independent datasets derived from traditional survey methods at five estuarine and coastal sites around the English Channel and North Sea.Our results show that for aqueous extra‐organismal DNA at low template concentrations, both metazoan‐targeted and fish‐targeted COI primers perform poorly in comparison to 12S, exhibiting low levels of reproducibility due to non‐specific amplification of prokaryotic and non‐target eukaryotic DNAs.An ideal metabarcode would have an extensive reference library upon which custom primers could be designed, either for broad assessments of biodiversity, or taxon specific surveys. Such a database is available for COI, but low primer specificity hinders practical application, while conversely, 12S primers offer high specificity, but lack adequate references. The latter, however, can be mitigated by expanding the concept of DNA barcodes to include whole mitochondrial genomes generated by genome‐skimming existing tissue collections. [ABSTRACT FROM AUTHOR]

Viruses alter a multitude of host-cell processes to create a more optimal environment for viral replication. This includes altering metabolism to provide adequate substrates and energy required for replication. Typically, viral infections induce a metabolic phenotype resembling the Warburg effect, with an upregulation of glycolysis and a concurrent decrease in cellular respiration. Human adenovirus (HAdV) has been observed to induce the Warburg effect, which can be partially attributed to the adenovirus protein early region 4, open reading frame 1 (E4orf1). E4orf1 regulates a multitude of host-cell processes to benefit viral replication and can influence cellular metabolism through the transcription factor avian myelocytomatosis viral oncogene homolog (MYC). However, E4orf1 does not explain the full extent of Warburg-like HAdV metabolic reprogramming, especially the accompanying decrease in cellular respiration. The HAdV protein early region 1A (E1A) also modulates the function of the infected cell to promote viral replication. E1A can interact with a wide variety of host-cell proteins, some of which have been shown to interact with metabolic enzymes independently of an interaction with E1A. To determine if the HAdV E1A proteins are responsible for reprogramming cell metabolism, we measured the extracellular acidification rate and oxygen consumption rate of A549 human lung epithelial cells with constitutive endogenous expression of either of the two major E1A isoforms. This was followed by the characterization of transcript levels for genes involved in glycolysis and cellular respiration, and related metabolic pathways. Cells expressing the 13S encoded E1A isoform had drastically increased baseline glycolysis and lower maximal cellular respiration than cells expressing the 12S encoded E1A isoform. Cells expressing the 13S encoded E1A isoform exhibited upregulated expression of glycolysis genes and downregulated expression of cellular respiration genes. However, tricarboxylic acid cycle genes were upregulated, resembling anaplerotic metabolism employed by certain cancers. Upregulation of glycolysis and tricarboxylic acid cycle genes was also apparent in IMR-90 human primary lung fibroblast cells infected with a HAdV-5 mutant virus that expressed the 13S, but not the 12S encoded E1A isoform. In conclusion, it appears that the two major isoforms of E1A differentially influence cellular glycolysis and oxidative phosphorylation and this is at least partially due to the altered regulation of mRNA expression for the genes in these pathways.

Canids are definitive hosts of Taenia and Echinococcus species, which infect a variety of mammals as intermediate or accidental hosts including humans. Parasite transmission is based on domestic, semi-domestic and wildlife cycles; however, little is known of the epidemiological significance of wild large definitive hosts such as the wolf. In this study, 179 scats of wolves (Canis lupus italicus) collected throughout the Italian region of Liguria were analyzed for the detection of taeniid infection. Taeniid egg isolation was performed using a sieving/flotation technique, and the species level was identified by PCR (gene target: 12S rRNA and nad 1) followed by sequence analyses. Based on sequence homologies of ≥99%, Taenia hydatigena was identified in 19.6%, Taenia krabbei in 4.5%, Taenia ovis in 2.2%, Taenia crassiceps in 0.6%, Hydatigera taeniaeformis in 0.6% and Echinococcus granulosus in 5.6% of the samples. According to these results, Canis lupus italicus can be considered as involved in the wild (including cervids and rodents) and semi-domestic cycles (including sheep and goats) of taeniids in this area.

Anthropogenic translocations are the main vectors of intercontinental invasions. Molecular tools have been important in the study of biological invasions, helping to identify the source of non‐native species mainly when these species are rapidly colonizing the new territories. The aims of this study were: (i) to characterize genetic sequences of the Daphnia lumholtzi population in Brazil (Upper Paraná River floodplain) for the first time; (ii) to compare these sequences with available sequences at GenBank; and (iii) to contribute new sequences of gene 12S from D. lumholtzi. Specimens were collected from a lake of the Paraná River for gene comparison (COI and 12S sequences). Genetic sequences from populations outside Brazil were obtained from GenBank. D. lumholtzi specimens sequenced in this study are genetically close to populations from the United States and Mexico and considerably distant from Australian populations. Our data confirm that populations present in the Paraná River floodplain probably came from the United States, where they arrived through introduction of African fish. The genetic similarity between our specimens and populations from Mexico and the morphological discrepancy between them reinforces the importance of molecular analysis for accurate identification of a species and its origin. [ABSTRACT FROM AUTHOR]

The complete larval development of the lobster shrimp Leonardsaxius amurensis (Kobjakova, 1937) (Decapoda: Axiidea: Axiidae) is described and illustrated for the first time. The first zoeae of this species were collected from the plankton samples and reared in the laboratory before moulting to the megalopa. A molecular genetic analysis based on comparison of partial mitochondrial COI, 12S rDNA and 16S rDNA sequence data confirmed the identity of axiid larvae found in the plankton and L. amurensis adults collected in the same area. The larval development of L. amurensis includes five zoeal stages and a single megalopa. Zoeae I of L. amurensis are characterized by the presence of one short posterodorsal spine on the fifth pleonite in contrast to the larvae of related sympatric species Boasaxius princeps having four posterodorsal spines on the pleonites 2–5. Leonardsaxius amurensis occupies an intermediate position between lobster shrimps with abbreviated pelagic development (2–3 zoeal stages) and species with long development (up to eight zoeal stages). Thus, the number of zoeal stages in the family Axiidae varies widely, similarly to that in the families Callianassidae and Upogebiidae. [ABSTRACT FROM AUTHOR]

Insects use sensitive olfactory systems to detect relevant host volatiles and avoid unsuitable hosts in a complex environmental odor landscape. Insects with short lifespans, such as gall midges (Diptera: Cecidomyiidae), are under strong selection pressure to detect and locate suitable hosts for their offspring in a short period of time. Ephemeral gall midges constitute excellent models for investigating the role of olfaction in host choice, host shift, and speciation. Midges mate near their site of emergence and females migrate in order to locate hosts for oviposition, thus females are expected to be more responsive to olfactory cues emitted by the host compared to males. In this study, we explored the correlation between host choice and the function of the peripheral olfactory system in 12 species of gall midges, including species with close phylogenetic relationships that use widely different host plants and more distantly related gall midge species that use similar hosts. We tested the antennal responses of males and females of the 12 species to a blend of 45 known insect attractants using coupled gas chromatographic-electroantennographic detection. When the species-specific response profiles of the gall midges were compared to a newly generated molecular-based phylogeny, we found they responded to the compounds in a sex- and species-specific manner. We found the physiological response profiles of species that use annual host plants, and thus have to locate their host every season, are similar for species with similar hosts despite large phylogenetic distances. In addition, we found closely related species with perennial hosts demonstrated odor response profiles that were consistent with their phylogenetic history. The ecology of the gall midges affects the tuning of the peripheral olfactory system, which in turn demonstrates a correlation between olfaction and speciation in the context of host use. [ABSTRACT FROM AUTHOR]

So far there has been no consensus regarding the definition of the land snail family Orculidae (Gastropoda, Stylommatophora, Orthurethra). Here, we present the outcome of a phylogenetic study on the Orculidae including all genus-level taxa ever mentioned to be members of this family except for Speleodentorcula and Walklea. Analyses were performed based on a data set including three mitochondrial (COI, 12S, 16S) and two nuclear (H4/H3, ITS1/5.8S/ITS2) sequence regions. We found polyphyly in multiple cases, and several genera previously assigned to Orculidae are shown to represent distinct lineages within the clade Orthurethra. Only the following genera are included in Orculidae: Alvariella, Orcula, Orculella, Pilorcula, Schileykula and Sphyradium. The sister group of Orculidae is the family Pyramidulidae. The subfamilies Odontocycladinae and Pagodulininae previously have been considered as members of Orculidae, but they represent distinct orthurethran lineages and are both elevated to family level. Argna and Agardhiella have been so far treated as members of Argnidae, but they are neither closely related to each other nor to Orculidae. The family Agardhiellidae Harl & Páll-Gergely fam. nov. is established for Agardhiella. Fauxulus s.l. is also not closely related to Orculidae; therefore, the family Fauxulidae Harl & Páll-Gergely fam. nov. is established for the genus Fauxulus (with the subgenera Fauxulella, Fauxulus and Anisoloma). [ABSTRACT FROM AUTHOR]

Species of the genus Nipponacmea inhabit only the Pacific coast of Asia, including the Russian Far East. Their external morphological characters are highly variable and often lead to misidentifications of species. So far, little research has been conducted using molecular markers. We used sequences from three mitochondrial genes (fragments of cytochrome c oxidase subunit I gene (COI), 12S and 16S rDNA). For comparison, additional genetic and taxonomic data on other species belonging to this genus were derived from GenBank. The molecular phylogenetic trees suggest that the species N. fuscoviridis and N. nigrans are species complexes. N. fuscoviridis is divided into three subgroups with high support and relatively large distances between them (N. fuscoviridisA, B and C); N. nigrans fall into two subgroups and one of them (N. nigransA) is more closely related to N. moskalevi than to the other subgroup of N. nigrans (B). [ABSTRACT FROM AUTHOR]

Snails of the genus Coralliophila (Muricidae: Coralliophilinae) are common corallivores in the Caribbean, feeding on a wide range of host species. In the present study, the morphological and genetic variation in C. galea and C. caribaea were studied in relation to their association with host coral species at Curaçao. Differences in shell shape among snails living on different hosts were quantified using geometric morphometric and phylogenetic relationships were studied using two mitochondrial markers (12S and COI). Based on these analyses, a new species, C. curacaoensis sp. nov., was found in association with the scleractinian coral Madracis auretenra. Both C. galea and C. caribaea showed host-specific differences in shell shape, size, and shell allometry (i.e. changes in morphological development during growth). Shell spire variability contributed foremost to the overall variation in shell shape. In C. caribaea minor genetic differences existed between snails associated with scleractinian and alcyonacean corals, whereas in C. galea such intraspecific variation was not found. These results shed more light on morphological and genetic differences among coral-associated fauna living on different host species. [ABSTRACT FROM AUTHOR]

This study examined the phylogeography of the barnacle Fistulobalanus albicostatus, which inhabits mangroves and estuarine shores in the West Pacific. Differentiation in the mitochondrial cytochrome c oxidase subunit I ( COI) and 12S ribosomal RNA ( 12S) genes of 401 specimens of F. albicostatus was examined in samples from 16 locations in the West Pacific, ranging from Honshu to Southern China. Our results revealed that F. albicostatus comprises two major clades exhibiting a COI divergence ranging from 1.25% to 2.8%. Clade A demonstrated the widest distribution, ranging from Japan to China, and was divided into three subclades occurring in the South China Sea (A1), Okinawa (A2), and Honshu, Korea and Qingdao (A3). Clade B was determined to be endemic to Okinawa; i.e. two endemic lineages occur in this island. Thus, F. albicostatus resembles several inter-tidal species in having clades that are endemic to Okinawan waters. Nevertheless, in contrast to the rocky inter-tidal barnacles Tetraclita spp. and Chthamalus malayensis, F. albicostatus was not found to be separated into continental and oceanic populations, but instead is divided into northern and southern clades, probably because of the Yangtze River discharge, which limits gene flow between the northern and southern populations. [ABSTRACT FROM AUTHOR]

The molecular characterization of the parasitoid, Blaesoxipha rufipes was studied for the first time using cytochrome oxidase subunit I (COI) and the ribosomal 12S genes to assist with species identification. Parasitoid samples were collected from five localities to examine the molecular variability of B. rufipes in western Saudi Arabia. The partial 12S and COI sequences were investigated using two analytical methods (maximum-parsimony and neighbor-joining). The A, C, G and T base compositions were 37.9%, 10.6%, 14.5% and 37%, respectively, for the 12S genes, and 27.9%, 17.5%, 16.8% and 37.8%, respectively, for the COI genes. The pairwise genetic distances (D) among the studied populations ranged from 0.006 to 0.012 in the 12S gene and from 0.002 to 0.05 in COI gene. The sequence of COI showed 97 base substitutions among and within the populations. Of these substitutions, only one amino acid changed at position 189. The array of amino acid sequences resembles the sequences of previously studied species of Blaesoxipha. Consequently, it could be concluded that the studied populations of B. rufipes showed low genetic variability, indicating that fragmentation and/or other ecological factors have some impact on them. [ABSTRACT FROM AUTHOR]

Cestodes or tapeworms belong to a diverse group of helminths. The adult Taenia saginata and Taenia solium tapeworm can infest the human gut and the larval stage of Echinococcus spp. and T. solium can infect tissues of the human body, causing serious disease. Molecular diagnostics can be performed on proglottids, eggs and on cyst fluids taken by biopsy. Detection of cestodes when a helminthic infection is suspected is of vital importance and species determination is required for appropriate patient care. For routine diagnostics a single test that is able to detect and type a range of cestodes is preferable. We sought to improve our diagnostic procedure that used to rely on PCR and subsequent sequencing of the Cox1 and Nad1 genes. We have compared these PCRs with novel PCRs on the 12S rRNA and Nad5 gene and established the sensitivity and specificity. A single PCR on the 12S gene proved to be very suitable for detection and specification of Taenia sp. and Echinococcus sp. Both targets harbour enough polymorphic sites to determine the various Echinococcus species. The 12S PCR was most sensitive of all tested. [ABSTRACT FROM AUTHOR]

The phylogenetic relationships of the suborder Erpobdelliformes, a group of non-sanguivorous leeches, were investigated with the use of mitochondrial cytochrome c oxidase subunit I, mitochondrial 12S rDNA and nuclear 18S rDNA. The resulting hypothesis indicates that Erpobdellidae and Salifidae are monophyletic and each other closest relatives. We detect, for first time in leeches, intra-specific variation of similar amount than inter-specific variation. We formally resurrect the name Erpobdella mexicana, proposed by Dugès for Mexican specimens, and recommend the use of the name Erpobdella ochoterenai rather than Erpobdella microstoma for Mexican specimens. We record an invasive species of the family Salifidae: Barbronia arcana in Mexico, representing the first record of the species outside Australia, first record of the family in Mexico and third in the New World.Se estudian las relaciones filogenéticas del suborden Erpobdelliformes, un grupo de sanguijuelas no hematófagas de vertebrados, con base en secuencias de la subunidad I del citocromo c oxidasa del ADN mitocondrial, 12S ADNr del ADN mitocondrial y 18S ADNr del ADN nuclear. La hipótesis resultante señala que las familias Salifidae y Erpobdellidae son monofiléticas y hermanas entre sí. Se detecta por primera vez en sanguijuelas variación interespecífica de magnitud similar a la variación interespecífica. Formalmente se reslece el nombre empleado por Dugès: Erpobdella mexicana para las formas mexicanas, así como se argumenta sobre el uso del nombre Erpobdella ochoterenai en lugar de Erpobdella microstoma para las formas mexicanas. Se registra a una especie invasora de la familia Salifidae en México: Barbronia arcana, el cual constituye el primer registro de la especie fuera de Australia, primer registro de la familia en México y tercero en el continente americano.

Canids are definitive hosts of Taenia and Echinococcus species, which infect a variety of mammals as intermediate or accidental hosts including humans. Parasite transmission is based on domestic, semi-domestic and wildlife cycles; however, little is known of the epidemiological significance of wild large definitive hosts such as the wolf. In this study, 179 scats of wolves ( Canis lupus italicus ) collected throughout the Italian region of Liguria were analyzed for the detection of taeniid infection. Taeniid egg isolation was performed using a sieving/flotation technique, and the species level was identified by PCR (gene target: 12S rRNA and nad 1 ) followed by sequence analyses. Based on sequence homologies of ≥99%, Taenia hydatigena was identified in 19.6%, Taenia krabbei in 4.5%, Taenia ovis in 2.2%, Taenia crassiceps in 0.6%, Hydatigera taeniaeformis in 0.6% and Echinococcus granulosus in 5.6% of the samples. According to these results, Canis lupus italicus can be considered as involved in the wild (including cervids and rodents) and semi-domestic cycles (including sheep and goats) of taeniids in this area. [ABSTRACT FROM AUTHOR]

Chemical investigation of the ethanol extract of the roots of Cudrania cochinchinensis led to the isolation of a new flavonoid, (6S,12S,13R)-1-methoxy cyanomaclurin (1), together with seven known compounds, 1,3,5-trihydroxy-4-(3′-hydroxy-3′-methylbutyl)xanthone (2), 1,3,6-trihydroxy-4-prenylxanthone (3), 1,3,6,7-tetrahydroxyxanthone (4), 1,3,5,6-tetrahydroxyxanthone (5), 1,3,6-trihydroxy-5-methoxyxanthone (6), resveratrol (7) and oxyresveratrol (8). The structure of compound 1 was elucidated on the basis of 1D and 2D NMR spectra and the HR-ESI-MS data. The absolute stereochemistry was deduced via Rh2(OCOCF3)4-induced CD and NOESY spectra. [ABSTRACT FROM AUTHOR]