The Isthmosacanthidae acanthocephalan species of the genus Serrasentis are parasites of marine teleosts and an elasmobranch. In this study, Serrasentis gibsoni n. sp. is described from the intestines of four flatfish species (Paralichthyidae), namely Ancyclopsetta quadrocellata, Cyclopsetta chittendeni, Syacium gunteri, and S. papillosum from 10 oceanic sites in the Gulf of Mexico (GoM). Twenty sequences of the ‘barcoding’ region of cytochrome C oxidase subunit I gene were obtained from 20 adults of Serrasentis gibsoni n. sp. Additionally, five sequences of the barcoding region were obtained from five adults of rhadinorhynchid Gorgorhynchus lepidus from C. chittendeni, S. papillosum and one species of Haemulidae, Haemulom aurolineatum, from five oceanic sites from the GoM. Two phylogenetic approaches were followed: Bayesian inference and maximum likelihood. In both phylogenetic reconstructions, the sequences of Serrasentis gibsoni n. sp. were recovered as a monophyletic group within the genus Serrasentis and placed as a sister group to G. lepidus. However, due to the lack of molecular data for species of the Isthmosacanthidae and Rhadinorhynchidea, these phylogenetic inferences must be taken with caution. Serrasentis gibsoni n. sp. is the first species of Serrasentis described from Paralichthyidae flatfish species from marine waters of the Americas and from the GoM. Based on the barcoding data set analyzed, Serrasentis gibsoni n. sp. appears to have high intraspecific genetic variation; thus, it is necessary to continue exploring the genetic diversity of this species to infer its intraspecific evolutionary patterns.

Larval trombiculid (chigger) mites are common ectoparasites of terrestrial vertebrates including humans, causing itching and skin inflammation known as trombiculiasis. Investigation of their diversity, distribution and seasonal abundance is therefore important from a veterinary and public health point of view. Although researchers have paid increased attention to these parasites in recent years, there is still little ecological data available on chiggers associated with birds inhabiting different types of habitats such as wetlands, for example. In 2021, we investigated the mite fauna in a specialist reedbed passerine, the bearded tit (Panurus biarmicus), and their effects on this host in the south-west Slovakia, Central Europe. A total of 1134 larvae of 1 mite species Blankaartia acuscutellaris were found in 99 out of 267 examined bearded tits. Juveniles were more infested than adult birds, but no differences were found between sexes. The larvae of mites first appeared on the host during the second half of June and peaked in the second half of July. After that, their numbers decreased gradually until October. Despite the relatively high prevalence and intensity of mite infestation in the bearded tit, no differences in body condition between infested and uninfested birds suggest that infestation by B. acuscutellaris may not have serious negative effects on the host health. Bearded tits can therefore be a reliable indicator of the presence of the chigger mites in wetland habitats.

We conducted a molecular survey on microsporidian diversity in different lineages (operational taxonomic units = OTUs) of Asellus aquaticus from 30 sites throughout Europe. Host body length was determined, and DNA was extracted from host tissue excluding the intestine and amplified by microsporidian-specific primers. In total, 247 A. aquaticus specimens were analysed from which 26.7% were PCR-positive for microsporidians, with significantly more infections in larger individuals. Prevalence ranged between 10 and 90%. At 9 sites, no microsporidians were detected. A significant relationship was found between the frequency of infected individuals and habitat type, as well as host OTU. The lowest proportion of infected individuals was detected in spring-habitats (8.7%, n = 46) and the highest in ponds (37.7%, n = 53). Proportion of infected individuals among host OTUs A, D and J was 31.7, 21.7 and 32.1%, respectively. No infections were detected in OTU F. Our results are, however, accompanied by a partially low sample size, as only a minimum of 5 individuals was available at a few locations. Overall, 17 different microsporidian molecular taxonomic units (MICMOTUs) were distinguished with 5 abundant isolates (found in 4–17 host individuals) while the remaining 12 MICMOTUs were “rare” and found only in 1–3 host individuals. No obvious spatio-genetic pattern could be observed. The MICMOTUs predominantly belonged to Nosematida and Enterocytozoonida. The present study shows that microsporidians in A. aquaticus are abundant and diverse but do not show obvious patterns related to host genetic lineages or geography.

Since 2017, a sea anemone species has been registered in central Portugal with a morphology comparable to Phymactis papillosa, from the Pacific shore of south and central America. In this paper, we have collected two individuals from Cascais, Portugal, extracted their DNA and amplified and sequenced the internal transcribed spacers I and II, markers frequently used in Cnidaria barcoding. The sequences obtained were compared with the ones available on GenBank, using the Basic Local Alignment Search Tool (BLAST) on the NCBI website. This procedure allowed the identification of P. papillosa. This is the first confirmed record of P. papillosa in European coasts. Citizen science data suggest occurrences in the Alentejo coast (south-west Portugal) and Mediterranean coast around Murcia, although no genetic or morphological confirmations of these records have been made. The potential effects of this species introduction are discussed.

Blood parasites comprise some of the most prevalent pathogens in nature, and their detection and identification are major objectives in varied fields such as ecology and biomedicine. Two approaches were compared, one based on Sanger sequencing and the other next-generation sequencing (NGS) based, in terms of their performance in detecting avian blood parasites across tropical Southeast Asian birds. Across a panel of 528 bird individuals, 43 birds were ascertained to be infected with avian haemosporidians using a polymerase chain reaction-based detection method. Among these samples, NGS-based barcoding confirmed co-infections by multiple blood parasites in all eight cases where Sanger sequencing produced double peaks. Importantly however, the NGS-based method produced another five diagnoses of co-infections (62.5%) in which Sanger-based barcoding remained equivocal. In contrast to Sanger sequencing, the NGS-based method was able to identify co-infecting haemosporidian lineages via their barcodes. The accuracy of avian haemosporidian lineage identification was not compromised by the shorter length of NGS sequences, with ~94% of NGS barcodes producing matches identical to those of the Sanger barcodes. The application of NGS-based barcoding methods promises to enhance parasite identification and reduce erroneous inferences based on artefacts.

In this study we report a new record of a cryptogenic polychaete from southern Africa. The species was found inhabiting sand tubes in intertidal sand flats in the Knysna Estuary on the southern coast of South Africa. Morphological comparisons using light and scanning electron microscopy showed extensive taxonomic similarities with Dipolydora socialis described from other localities and from museum vouchers. In addition, 18S rRNA and COI barcodes were generated for the species. Genetic analysis of the assembled polydorid dataset corroborated the morphological data in delineating the species as a taxonomic unit with >99% genetic similarity to available sequences of D. socialis in the GenBank database. Dipolydora socialis has been reported as having a widespread distribution, and since it can reside within tubes associated with fouling communities or as a shell borer, several vectors may have been responsible for its global spread and introduction to southern Africa. Finally, considering the many cryptic complexes that are currently being uncovered within polychaetes, including spionids, future taxonomic studies should incorporate additional genetic data from other regions of the world to determine whether D. socialis may also be part of a larger species complex.

The poorly known sponge species Axinella vellerea (Topsent, 1904), Acarnus levii (Vacelet, 1960) and Haliclona poecillastroides (Vacelet, 1969) are reported from bottom-trawl samples off the Balearic Islands, Western Mediterranean. A re-description is provided for all three species and the Folmer fragment of cytochrome oxidase subunit I (COI) obtained for A. levii and H. poecillastroides. This is the second report of A. vellerea in the Mediterranean, the first time that A. levii is reported outside Corsica and the first time that H. poecillastroides is documented outside the Gulf of Lion, France. The systematic allocation of A. levii and H. poecillastroides is discussed based on a COI phylogenetic analysis and morphology. The poorly understood phylogeny of the Haplosclerida does not permit us to find a proper allocation for H. poecillastroides, although its current position in the genus Haliclona or the family Chalinidae is not defensible. On the other hand, A. levii currently fits best in the family Microcionidae, and seems related to some Clathria species with mixed features between Clathria and Acarnus. Considering that the species of the genus Acarnus shares a strong synapomorphy (the possession of Cladotylotes), it is plausible for all Acarnus species to be Microcionids. We conclude that H. poecillastroides needs to be reallocated to a new genus: Xestospongia poecillastroides comb. nov. (Petrosiidae). However, a reallocation of A. levii is not advisable for the moment, as this would imply major systematic changes such as the reallocation of the whole genus Acarnus to Microcionidae, and the redescription of Microcionidae and Acarnidae.

The Parmelia saxatilis aggregate is comprised of three species in Europe, proposed to differ in morphological, distributional or chemical characters. In this study, we sampled nearly 200 thalli from five sites across a steep ecological gradient in Scotland to investigate the distribution of the species in the aggregate, and we characterized all specimens by morphological, chemical and ITS sequence variation. In our sample, 191 specimens were identified to species using ITS. We confirm that a PCR length assay can be used for separation of P. saxatilis s. str. from P. ernstiae and P. serrana because across our sample, P. saxatilis s. str. consistently includes a group I intron c. 200 bp. Using sequences for specimen identification, we test previously proposed characters to diagnose specimens and use multivariate analysis to identify the most consistent features which may be used for identification among species. First, we test lobe morphology, presence and amount of pruina, distribution of isidia, lobe tip colour, and chemistry. Second, we use classification trees that quantify the contributions of 1) morphological and chemical factors, and 2) morphological and ecological factors, to a priori ITS-barcoded specimens. Parmelia saxatilis s. str., P. ernstiae and P. serrana all occur across the sampled gradient but differ in the frequency of occurrence, with P. saxatilis s. str. more frequent in the relatively drier east, and P. ernstiae more frequent in the wetter west. Parmelia serrana was collected around a third as often as the other two species, but more frequently on tree branches than expected. For all the morphological characters examined, all the species show some overlap and no morphological features are diagnostic, though trends are apparent by species. The classification tree approach holds promise for discovering the most meaningful variation for field workers to approach correct identifications. Chemical variation using TLC is perhaps the best way to distinguish most specimens but, even here, overlap in chemosyndromes exists among the species.

Hybridization events between Schistosoma species (Digenea, Platyhelminthes) are reported with increasing frequency, largely due to improved access to molecular tools. Nevertheless, little is known about the distribution and frequency of hybrid schistosomes in nature. Screening for hybrids on a large scale is complicated by the need for nuclear and mitochondrial sequence information, precluding a ‘simple’ barcoding approach. Here we aimed to determine and understand the spatiotemporal distribution of Schistosoma haematobium × Schistosoma bovis hybrids in the Senegal River Basin. From ten villages, distributed over the four main water basins, we genotyped a total of 1236 schistosome larvae collected from human urine samples using a partial mitochondrial cox1 fragment; a subset of 268 parasites was also genotyped using ITS rDNA. Hybrid schistosomes were unevenly distributed, with substantially higher numbers in villages bordering Lac de Guiers than in villages from the Lampsar River and the Middle Valley of the Senegal River. The frequency of hybrids per village was not linked with the prevalence of urinary schistosomiasis in that village. However, we did find a significant positive association between the frequency of hybrids per village and the prevalence of Schistosoma mansoni. We discuss the potential consequences of adopting a barcoding approach when studying hybrids in nature.

Growing evidence demonstrates that bacterial species diversity is substantial, and many of these species are pathogenic in some contexts or hosts. At the same time, laboratories and museums have collected valuable animal tissue and ectoparasite samples that may contain substantial novel information on bacterial prevalence and diversity. However, the identification of bacterial species is challenging, partly due to the difficulty in culturing many microbes and the reliance on molecular data. Although the genomics revolution will surely add to our knowledge of bacterial systematics, these approaches are not accessible to all researchers and rely predominantly on cultured isolates. Thus, there is a need for comprehensive molecular analyses capable of accurately genotyping bacteria from animal tissues or ectoparasites using common methods that will facilitate large-scale comparisons of species diversity and prevalence. To illustrate the challenges of genotyping bacteria, we focus on the genus Bartonella, vector-borne bacteria common in mammals. We highlight the value and limitations of commonly used techniques for genotyping bartonellae and make recommendations for researchers interested in studying the diversity of these bacteria in various samples. Our recommendations could be applicable to many bacterial taxa (with some modifications) and could lead to a more complete understanding of bacterial species diversity.

Leptospirosis is a zoonotic bacterial disease of global importance. A large spectrum of asymptomatic animal hosts can carry the infection and contribute to the burden of human disease. Environmental sources of human contamination also point to the importance of a hydrotelluric reservoir. Leptospirosis can be caused by as many as 15 different pathogenic or intermediate Leptospira species. However, classification of these bacteria remains complicated through the use of both serological and genetic classification systems that show poor correlation. With the advent of molecular techniques, DNA-based barcoding offers a conceptual framework that can be used for leptospirosis surveillance as well as source tracking. In this review, we summarize some of the current techniques, highlight significant successes and weaknesses and point to the future opportunities and challenges to successfully establish a widely applicable barcoding scheme for Leptospira.

Hybrid parasites may have an increased transmission potential and higher virulence compared to their parental species. Consequently, hybrid detection is critical for disease control. Previous crossing experiments showed that hybrid schistosome eggs have distinct morphotypes. We therefore compared the performance of egg morphology with molecular markers with regard to detecting hybridization in schistosomes. We studied the morphology of 303 terminal-spined eggs, originating from 19 individuals inhabiting a hybrid zone with natural crosses between the human parasite Schistosoma haematobium and the livestock parasite Schistosoma bovis in Senegal. The egg sizes showed a high variability and ranged between 92·4 and 176·4 µm in length and between 35·7 and 93·0 µm in width. No distinct morphotypes were found and all eggs resembled, to varying extent, the typical S. haematobium egg type. However, molecular analyses on the same eggs clearly showed the presence of two distinct partial mitochondrial cox1 profiles, namely S. bovis and S. haematobium, and only a single nuclear ITS rDNA profile (S. haematobium). Therefore, in these particular crosses, egg morphology appears not a good indicator of hybrid ancestry. We conclude by discussing strengths and limitations of molecular methods to detect hybrids in the context of high-throughput screening of field samples.

The results of the first molecular phylogenetic study of Pseudephebe are presented; a three-locus phylogeny. The genus is confirmed as monophyletic within the alectorioid clade of Parmeliaceae. Two major clades were recovered, which can be assigned to the two traditional taxa, P. minuscula and P. pubescens, with modifications of the species delimitation, especially the variable P. minuscula. These species are cryptic and cannot be confidently distinguished morphologically due to phenotypic convergence. Therefore, the use of P. pubescens aggr. is recommended for samples not molecularly analyzed. Contrary to previous studies, specimens of both species might have indistinct pseudocyphellae and also contain lichen substances; norstictic acid was detected in c. 60% of specimens tested. An SSU 1516 Group I intron is usually present in P. minuscula but always absent in P. pubescens. The species-level nomenclature is summarized and sequenced reference specimens (RefSpec) for both Pseudephebe species are selected. Sequences from Bryoria mariensis established that this name was a synonym of P. minuscula.

Mucuna pruriens (L.) DC is a tropical legume cover crop with promising nutritional and agronomic potentials. It is also a key source of 3,4 dihydroxy-L-phenylalanine (L-Dopa) – a precursor of dopamine used in the treatment of Parkinson's disease. However, lack of well-characterized germplasm plus poor accessibility to genomic resources has hindered its breeding programs. Furthermore, the cause and effect of various biotic and abiotic stresses impacting yield is also little studied. Systematic collection and evaluation of Indian germplasm by our group revealed presence of a diverse gene pool in India that can support a variety of breeding needs. The stability of L-Dopa trait across environments examined through Genotype and environment (G × E) interaction studies, as well as feasibility check on barcoding and phylogenetic analyses based on karyotype and conserved nuclear and chloroplast genes showed promising outcome. Germplasm screening for select biotic abiotic stresses identified resilient genotypes. Advances in use of DNA markers for diversity analysis, linkage map development, tagging of genes/quantitative trait loci for qualitative and quantitative traits, and progress in genomics are presented.

Conservation organisations are tasked with protection of biodiversity but are challenged by limited resources; consequently, the highest conservation priority species have designations that should correspond with the level of protection needed. In Britain, the saxicolous Calicium corynellum receives the highest conservation priority as a consequence of its rarity, combined with dramatic population declines over the last several decades, having disappeared from 2 of its 4 British sites and declined in one other. However, there is some uncertainty associated with the taxonomic status of the entity referred to as C. corynellum in Britain, partly because its common congener, C. viride has been recorded on trees overhanging several of the populations of C. corynellum, but also because the morphology of British material is very similar to the common C. viride, but found on rock. Standard fungal barcode nr ITS sequences of C. corynellum from both extant British populations of C. corynellum were successfully amplified, along with C. viride from trees overhanging one of the sites and from other British sites. In addition, morphological features were compared among specimens of both taxa. There is no evidence to support the distinction of British C. corynellum from its more common congener, and its conservation status is Britain should be re-evaluated.

Epitrix species (Coleoptera: Chrysomelidae) feed mostly on plants from the family Solanaceae and some of them are major pests of potato crops. All Epitrix species are morphologically highly similar, which makes them difficult to identify and limits their study and management. Identification of species is mostly based on the observation of the genitalia and requires a high level of expertise. Here, we propose a tool to reliably identify all developmental stages of the most economically important Epitrix species feeding on potato in Europe and North America (Epitrix cucumeris, Epitrix similaris, Epitrix tuberis, Epitrix subcrinita and Epitrix hirtipennis). We first sequenced two DNA markers (mitochondrial cytochrome c oxidase I (COI) and nuclear internal transcribed spacer 2 (ITS2)) to test their effectiveness in differentiating among six Epitrix species (126 specimens). Morphospecies of Epitrix were well-differentiated by both DNA barcodes and no mitochondrial introgression was detected. Then, we developed an RFLP-based diagnostic method and showed that unambiguous species discrimination can be achieved by using the sole restriction enzyme TaqI on COI polymerase chain reaction products. The tool proposed here should improve our knowledge about Epitrix species biology, distribution and host range, three capacities that are particularly important in the detection and management of these pest species. Specifically, this tool should help prevent the introduction of E. tuberis and E. subcrinita in Europe and limit the spread of the recently introduced E. cucumeris and E. similaris, with minimal disruption to Solanaceae trade.

The synergism facilitated by a series of recent developments has conspired to catalyze rapid advancements in the taxonomy and systematics of elasmobranch tapeworms. These developments are: (1) increased interest in global biodiversity; (2) globalization-facilitated communication; (3) enhanced microscopic and digital technologies; (4) availability of web-based taxonomic resources; (5) ease of use and low cost of molecular techniques and (6) the impressive repertoire of available phylogenetic methods. As a consequence, an estimation of global elasmobranch tapeworm diversity is now within our grasp, as is a basic understanding of the effort and resources required to complete the discovery and description of this fauna globally. The generation of robust hypotheses of the phylogenetic relationships for most elasmobranch-parasitizing cestode orders is also well underway. An international community of cestodologists has emerged and through their sharing of knowledge and specimens is making great strides towards expanding knowledge of the cestode fauna of vertebrates worldwide. It is important that these efforts continue to move forward in a collaborative fashion, integrating morphological and molecular data, but also fully engaging elasmobranch taxonomists and systematists. It is equally important that efforts to characterize and describe global biodiversity are not derailed by such seductive, but ultimately unrewarding impracticable initiatives as molecular taxonomy. Integrated taxonomy is certainly not for the feint of heart, but those with the courage to pursue this strategy will be responsible for maintaining and enhancing the biologically relevant context required for effective species recognition well into the future.

Molecular approaches for identifying aquatic macroinvertebrate species are increasingly being used but there is ongoing debate about the number of DNA markers needed to differentiate species accurately. Here, we use two mitochondrial genes (cytochrome oxidase I, cytochrome b) and a nuclear gene (carbamoylphosphate synthetase) to differentiate species variation within the taxonomically challenging chironomid genus Procladius from southern Australia, a genus which is important for pollution monitoring. The mitochondrial genes indicated cryptic species that were subsequently linked to morphological variation at the larval and pupal stage. Two species previously described based on morphological criteria were linked to molecular markers, and there was evidence for additional cryptic species. Each genetic marker provided different information, highlighting the importance of considering multiple genes when dissecting taxonomically difficult groups, particularly those used in pollution monitoring.

Click beetle larvae within the genus Agriotes (Coleoptera: Elateridae), commonly known as wireworms, are abundant ground-dwelling herbivores which can inflict considerable damage to field crops. In Central Europe up to 20 species, which differ in their distribution, ecology and pest status, occur in arable land. However, the identification of these larvae based on morphological characters is difficult or impossible. This hampers progress towards controlling these pests. Here, we present a polymerase chain reaction (PCR)-based approach to identify, for the first time, 17 Agriotes species typically found in Central Europe. Diagnostic sequence information was generated and submitted to GenBank, allowing the identification of these species via DNA barcoding. Moreover, multiplex PCR assays were developed to identify the nine most abundant species rapidly within a single-step reaction: Agriotes brevis, A. litigiosus, A. obscurus, A. rufipalpis, A. sordidus, A. sputator, A. ustulatus, A. lineatus and A. proximus. The latter two species remain molecularly indistinguishable, questioning their species status. The multiplex PCR assays proved to be highly specific against non-agrioted elaterid beetles and other non-target soil invertebrates. By testing the molecular identification system with over 900 field-collected larvae, our protocol proved to be a reliable, cheap and quick method to routinely identify Central European Agriotes species.

Intestinal schistosomiasis continues to be a major public health problem in sub-Saharan Africa, and is endemic in communities around Lake Victoria. Interest is growing in the molecular evolution and population genetic structure of Schistosoma mansoni and we describe a detailed analysis of the molecular epidemiology and phylogeography of S. mansoni from Lake Victoria. In total, 388 cytochrome oxidase 1 (COI) sequences were obtained from 25 sites along the Ugandan, Tanzanian and Kenyan shorelines of Lake Victoria, and 122 unique barcodes were identified; 9 corresponded to previously discovered barcodes from Lakes Victoria and Albert. A subset of the data, composed of COI sequences from miracidia from 10 individual children, was used for population genetics analyses; these results were corroborated by microsatellite analysis of 4 isolates of lab-passaged adult worms. Overall, 12 barcodes were found to be shared across all 3 countries, whereas the majority occurred singly and were locally restricted. The population genetics analyses were in agreement in revealing high diversity at the level of the human host and negligible population structuring by location. The lack of correlation between genetic distance and geographical distance in these data may be attributed to the confounding influence of high intra-individual diversity as well as human migration between communities.