We describe a new species of the genus Alippistrongylus (Nematoda: Trichostrongylina) in the small intestine of Delomys dorsalis (Rodentia: Sigmodontinae) found in Itatiaia National Park (Parque Nacional do Itatiaia, PNI), state of Rio de Janeiro, Brazil. The new species can be distinguished between the other two species previously described by the following morphological characteristics: pattern of the rays from the caudal bursa rays in males and the spherical-shaped appendage in the female. Additionally, we provide molecular genetic data from the new species. The discovery of Alippistrongylus itatiaiaensis sp. n. expands our understanding of nematode diversity and underscores the importance of parasite studies in biodiversity conservation. Its occurrence in a preserved area like the PNI emphasises the role of such habitats in maintaining unique ecological interactions.

Philometroides Yamaguti, 1935 is a genus of dracunculoid nematodes of the family Philometridae Baylis & Daubney, 1926 comprising tissue-infecting species worldwide. In the present study, a new species of Philometroides is described from the Tyrrhenian Sea (central-western Mediterranean Sea) using integrative approaches such as light and scanning microscopy, histopathology and 18S rRNA sequencing. Philometroides giginosantoroi n. sp. found in the skeletal muscles of the Mediterranean moray Muraena helena can be distinguished from its congeners by a combination of morphological traits and in particular by having the oral aperture with 3 large sclerotized triangular oesophageal teeth. The molecular analyses and phylogenetic reconstructions support its status as a new taxon and placed it within a clade of tissue-infecting species, although also confirmed mismatches in the generic assignment of several species. Philometroides giginosantoroi n. sp. is the second species of the genus found in the Mediterranean Sea and in general in the European marine waters and the third species of the family known to infect the family Muraenidae.

Taxonomic intricacies and high interspecific similarity have hampered the identification of scyllarid phyllosoma larvae to the species level. The pygmy locust lobster, Scyllarus pygmaeus, is distributed across the Mediterranean Sea and in the eastern Atlantic; however, its phyllosoma larvae were previously recorded only from the western Mediterranean. We employed DNA barcoding using the mitochondrial COI gene to identify S. pygmaeus phyllosoma collected from the offshore waters of the southeastern Mediterranean Sea and described its morphology. We further discuss the lack of genetic structure in S. pygmaeus with potential implications for species connectivity and conservation.

During the study of ectoparasites (Platyhelminthes) of fish in the floodplain of the Upper Paraná River - Brazil, a new species of Urocleidoides, present in the gill filaments of Hemiodus orthonops (Hemiodontidae), is described using morphological description and molecular data from the mitochondrial region of cytochrome c oxidase, subunit 1 (COI) and the partial region of the 28S rDNA gene. Urocleidoides luquei n. sp. differs from all its congeners by the presence of a filament that joins the accessory piece to the base of the male copulatory organ and resembles U. paradoxus and U. surianoae. Phylogenetic analyses using molecular data revealed that U. luquei n. sp. forms a paraphyletic group concerning the other Urocleidoides species. In this way, as well as contributing to the description of a new species, we seek to encourage and contribute to the increase in research using integrative taxonomy, thus making it possible to elucidate some unresolved questions about the genus Urocleidoides.

Clinostomidae is a diverse family of digenean parasitizing fish-eating birds as adults and fishes as metacercariae. The species composition, within the genus Clinostomum has been steadily increasing in recent years. In Argentina, four named species of Clinostomum have been documented, accompanied by four metacercariae representing distinct genetic lineages whose adults have not been identified. This study focused on examining clinostomids in three fish species – Australoheros scitulus (ASI), Cichlasoma dimerus (CDIM), and Pimelodella laticeps (PLA) – at various localities in Argentina. We conducted both morphological and molecular characterizations of the Clinostomum metacercariae collected from these fish species. Molecular phylogenetic analyses using COI mtDNA were performed to determine the placement of these metacercariae within the clinostomid phylogenetic tree. Clinostomum ASC represents a distinct lineage, morphologically distinguishable from other sequenced metacercariae due to its body shape (widest anteriorly and becoming slender towards the posterior end); this lineage was found to be closely related to C. caffarae. While Clinostomum CDIM and Clinostomum PLA exhibited morphological differences, they clustered together genetically with metacercariae reported in previous studies as Clinostomum L3 and Clinostomum CVI. This outcome, coupled with a low genetic distance (0 to 3%), suggests that they are conspecific with metacercariae found in fish across Mexico, Costa Rica, and Argentina. In light of the extensive diversity of fish species in Argentine freshwater ecosystems (over 500 species), and considering the relatively constrained extent of prior investigations, the anticipation of unearthing additional Clinostomum species or lineages is plausible.

Incomplete original descriptions, the unavailability or poor conditions of specimens and the lack of detailed redescriptions have caused the validity of several species of the genus Encotyllabe Diesing, 1850 to be questioned. To date, seven of the recognized species were described upon one or two specimens, hindering study of intraspecific variations. This was made worse by considering few morphoanatomical differences sufficient to erect new species. Among Encotyllabe spp. occurring in Mediterranean waters, E. vallei was first described from the gilt-head bream Sparus aurata (Sparidae) off Italy. Although beautifully illustrated for a paper from that century, morphometric data for E. vallei from the type-host S. aurata remain unavailable. Previous records of E. vallei provided either morphometrical or molecular data, and its validity was questioned. We provide a redescription of E. vallei based on newly collected specimens from the S. aurata from the southwestern Mediterranean (off Algeria) using integrative taxonomy. Analysis of cox1 sequences of E. vallei from S. aurata, compared to sequences from other sparid hosts, mainly Pagellus bogaraveo, revealed a divergence not exceeding 2%, suggesting a stenoxenic specificity for this monogenean. Given that P. bogaraveo is the type-host for Encotyllabe pagelli, we were tempted to suggest a synonymy between E. vallei and E. pagelli. We refrained from doing so because E. pagelli was first described from the Atlantic coast off Brest, France. Morphological data for Encotyllabe from P. bogaraveo are warranted assessing the host specificity of E. vallei and whether there might be a species complex within individual sparid fish species.

Larval stages of the widely distributed digenean species Proctoeces maculatus (Looss, 1901) were reported 40 years ago from South Africa in the common octopus, Octopus vulgaris Cuvier (Octopodidae). However, the absence of adult specimens and molecular data from this region has hindered a comprehensive understanding of its distribution. In this study, we collected three species of intertidal and near-shore marine fishes [Clinus superciliosus (L.) (Clinidae), Diplodus capensis (Smith) (Sparidae) and Sparodon durbanensis (Castelnau) (Sparidae)] along the South African coast and discovered adult specimens of P. maculatus at five localities. By employing a combination of morphological and molecular techniques, including 28S rDNA, 18S rDNA and COI mtDNA analyses, the first report of adult P. maculatus from South Africa is presented. The findings encompass a comprehensive morphological description and molecular data, illuminating the true distribution of this species in the region.

Species of lichen-forming fungi (LFF) display an array of geographical distribution patterns. Among the broadly distributed lichen-forming fungal species, the degree of reproductive isolation and genetic substructure among populations varies widely, in some cases masking unrecognized diversity or meaningful biogeographical patterns. Lecidea atrobrunnea (Raymond ex Lam. & DC.) Schaer. s. lat. (Lecideaceae) is a widespread species complex that has been studied for over two centuries since its initial description. The diversity of the L. atrobrunnea group is highest in western North America, where a dizzying array of morphologies and chemistry can occur at local scales. Here we investigate whether the assumed cosmopolitan distribution of L. atrobrunnea s. lat. is an artifact of taxonomic limitations and masks biogeographical patterns in this species complex. To address these questions, we compiled sequence data from the standard fungal barcoding marker (ITS) for over 100 specimens within this complex, in addition to genome-scale data from a subset of these representing over 1600 single-copy nuclear genes spanning over 3 Mb of the genome. Our study corroborates the perspective that the morphologically and chemically variable Lecidea atrobrunnea group reflects a complex of distinct species-level lineages, with 42–83 candidate species inferred from the ITS region and high levels of diversity inferred from a subset of specimens using genome-scale data. However, both phenotype- and molecular-based species boundaries remained unsettled, with the most common nominal taxa recovered as highly polyphyletic and with conflict among different molecular species delimitation approaches. Our study also highlights the potential for geographically restricted species, with fascinating biogeographical patterns, challenging, in part, the assumed cosmopolitan distribution of L. atrobrunnea s. lat. This study provides valuable direction for future research that will be crucial in understanding diversification and establishing a robust taxonomy for this well-known species complex.

We present a novel identification tool called PhyloKey, based on the method of morphology-based, phylogenetic binning developed within the software package RAxML. This method takes a reference data set of species for which both molecular and morphological data are available, computes a molecular reference tree, maps the morphological characters on the tree, and computes weights based on their level of consistency versus homoplasy using maximum likelihood (ML) and maximum parsimony (MP). Additional units for which only morphological data are known are then binned onto the reference tree, calculating bootstrap support values for alternative placements. This approach is modified here to work as an identification tool which uses the same character coding approach as interactive keys. However, rather than identifying individual samples through a progressive filtering process when entering or selecting characters, query samples are binned in batch mode to all possible alternative species in the tree, with each placement receiving a bootstrap support adding to 100% for all alternative placements. In addition to the fact that, after scoring a character matrix, a large number of specimens can be identified at once in short time, all possible alternative identifications are immediately apparent and can be evaluated based on their bootstrap support values. We illustrate this approach using the basidiolichen genus Cora, which was recently shown to contain hundreds of species. We also demonstrate how the PhyloKey approach can aid the restudying of herbarium samples, adding further value to these collections and contributing with large quantitative data matrices to ‘non-molecular museomics’. Our analysis showed that PhyloKey identifies species correctly with as low as 50% of the characters sampled, depending on the nature of the reference tree and the character weighting scheme. Overall, a molecular reference tree worked best, but a randomized reference tree gave more consistent results, whereas a morphological reference tree performed less well. Surprisingly, even character weighting gave the best results, followed by parsimony weighting and then maximum likelihood weighting.

The brittle stars of the family Ophiocomidae inhabit shallow waters and coral reefs of tropical regions. The species of Ophiocoma are difficult to identify due to high morphological variation, especially when different stages of development are observed. Here, based on morphological analyses, two Brazilian morphotypes of Ophiocoma were studied and characterized, Ophiocoma sp. NB (Northeastern Brazil) and Ophiocoma sp. TMV (Trindade and Martin Vaz Archipelago), and subsequently thoroughly analysed to confirm whether they were the same species or not. After the morphological studies, including external morphology, morphometry and microstructural characters, and analysis of molecular data, involving the 16S gene, it was concluded that Ophiocoma sp. NB and Ophiocoma sp. TMV do not correspond to the same species, the first being identified as Ophiocoma echinata (Lamarck, 1816) and the latter being a new species. This new species is characterized by two tentacle scales on the first arm segment and then one on all following segments, and the dorsalmost arm spines are robust and rounded, as wide as long or almost as wide as long.

A new species of the genus Stephanostomum is described for the southeastern Gulf of Mexico based on morphological and nucleotide evidence. Stephanostomum minankisi n. sp. infects the intestine of the dusky flounder Syacium papillosum in the Yucatan Continental Shelf, Mexico (Yucatan Peninsula). Sequences of the 28S ribosomal gene were obtained and compared with available sequences of the other species and genera of the families Acanthocolpidae and Brachycladiidae from GenBank. A phylogenetic analysis was conducted, including 39 sequences, 26 of which represented 21 species and six genera of the family Acanthocolpidae. The new species is characterized by the absence of circumoral spines and spines on the tegument. Nonetheless, scanning electron microscopy consistently revealed the pits of 52 circumoral spines distributed in a double row with 26 spines each, and forebody spined. Other distinctive features of this species are testes in contact (sometimes overlapping), the vitellaria running along the body lateral fields to the mid-level of the cirrus-sac, pars prostatica and ejaculatory duct similar in length, and uroproct present. The phylogenetic tree showed that the three species found as parasites of dusky flounder (the new adult species and two in metacercaria stages) were grouped into two different clades. S. minankisi n. sp. was the sister species of Stephanostomum sp. 1 (Bt = 56) and formed a clade with S. tantabiddii, supported by high bootstrap values (100).

In this paper we re-describe Trichuris muris based on morphological data following isolation from two commensal rodent species, Mus musculus from Mexico and Rattus rattus from Argentina. Furthermore, we provide a molecular characterization based on mitochondrial (cytochrome c oxidase subunit 1 mitochondrial gene) and nuclear (internal transcribed spacer 2 region) markers in order to support the taxonomic identification of the studied specimens of T. muris from M. musculus. We distinguished T. muris from 29 species of Trichuris found in American rodents based on morphological and biometrical features, such as the presence of a spicular tube, length of spicule, size of proximal and distal cloacal tube and non-protrusive vulva. We suggest that spicular tube patterns can be used to classify Trichuris species in three groups. Considering that the diagnosis among the species of this genus is mainly based on morphometry, this proposal represents a relevant contribution. We provide molecular studies on two markers, making this the first contribution for T. muris in the Americas. This study makes an important contribution to the integrative taxonomy of cosmopolitan nematode species, and its correct determination from the parasitological study of commensal rodents.

In this study, a new dactylogyrid species is described from the gills of two ariid fish species of the Brazilian coast, Genidens barbus and Genidens genidens, by combining morphological characters with partial 18S rDNA sequences. The new species can be distinguished from its congeners by the following morphological characteristics: a male copulatory organ (MCO), a coiled tubular shaft of around one counterclockwise ring, base with a sclerotized cap; MCO with tapered distal region; a T-shaped accessory piece; a vagina, a cup-shaped vaginal vestibule, slightly sclerotized; and a pharynx comprising a muscular, glandular bulb. Supplementary taxonomic data for Chauhanellus velum from Sciades couma (type-host) are also presented and new 18S rDNA sequences of Chauhanellus spp. from other ariid fish from South America are provided. Phylogenetic analyses based on partial 18S rDNA gene sequences placed Chauhanellus riograndinensis n. sp. and Chauhanellus velum as two early divergent lineages within Chauhanellus from South America. Finally, a way to test the monophyly of Chauhanellus and Hamatopeduncularia is also discussed, which may be useful for future studies.

A new species of Ancyracanthus, parasite of the electric eel Electrophorus varii, in the Brazilian Amazon, is described based on morphological and molecular characterization. Ancyracanthus electrophori n. sp. differs from the two congeners namely, Ancyracanthus pinnatifidus and Ancyracanthus schubarti, based on the structure of cephalic appendages, number and arrangement of caudal papillae in males, vulva very close to anus in females, eggs with smoothly mamillated shell, host taxon and geographical origin. Moreover, the new species is the first in the genus to be described with thorny cuticular rings and to be observed with the use of scanning electron microscopy (SEM). The morphology of A. pinnatifidus and A. schubarti is still poorly-known and should be revised in details; however, the separation between them and the new species was clear. Genetic characterization based on 28S rDNA and cytochrome c oxidase subunit I (cox1) mtDNA partial sequences, performed for the first time in Acyracanthus, along with phylogenetic reconstructions using both genetic markers, placed Ancyracanthus electrophori n. sp. in a suggestive basal position within Gnathostomatidae. Phylogenetic reconstructions using cox1 sequences also suggested lack of monophyly in the genera Gnathostoma and Spiroxys and, consequently, in the subfamilies Gnathostominae and Spiroxyinae. However, such results are preliminary. With the first genetic characterization and observations using SEM in Ancyracanthus, resulting in the discovery of a new species and in the expansion of the geographical occurrence of the genus to Amazonian fish, an important step towards a better understanding of these nematodes has been taken.

Cosmocercoides Wilkie, 1930 are gastrointestinal parasites commonly found in amphibians and reptiles, with 4 species reported from the Neotropical region. In the present study, a new species of Cosmocercoides, namely Cosmocercoides amapari n. sp. is described using integrated approaches such as light and scanning microscopy, and DNA sequencing of the mitochondrial cytochrome c oxidase subunit 1 gene. The specimens were collected from the large intestine of 3 species of hylid frogs in Amapá, Brazil. The new species can be distinguished from its congeners by morphological traits, including the pattern of caudal papillae, absence of the gubernaculum, 2 poorly sclerotized spicules, presence of lateral alae and somatic papillae along the body. In addition, our molecular analyses and phylogenetic reconstructions strongly support the status of the new taxon, which clustered poorly with a large clade of Cosmocerca spp. Cosmocercoides amapari n. sp. is the 29th species of the genus, the 5th from the Neotropical region, the third reported in Brazil, the second described from the Amazon region and the first belonging to the Neotropical region with molecular data.

Echinostoma paraensei, described in Brazil at the end of the 1960s and used as a biological model for a range of studies, belongs to the ‘revolutum’ complex of Echinostoma comprising species with 37 collar spines. However, molecular data are available only for a few isolates maintained under laboratory conditions, with molecular prospecting based on specimens originating from naturally infected hosts virtually lacking. The present study describes Echinostoma maldonadoi Valadão, Alves & Pinto n. sp., a species cryptically related to E. paraensei found in Brazil. Larval stages (cercariae, metacercariae and rediae) of the new species were found in the physid snail Stenophysa marmorata in the State of Minas Gerais, Brazil, the same geographical area where E. paraensei was originally described. Adult parasites obtained experimentally in Meriones unguiculatus were used for morphological (optical microscopy) and molecular [28S, internal transcribed spacer (ITS), nad1 and cox1] characterization. The morphology of larval and adult parasites (most notable the small-sized dorsal spines in the head collar), associated with low (0–0.1%) molecular divergence for 28S gene or ITS region, and only moderate divergence for the mitochondrial cox1 gene (3.83%), might suggest that the newly collected specimens should be assigned to E. paraensei. However, higher genetic divergence (6.16–6.39%) was found in the mitochondrial nad1, revealing that it is a genetically distinct, cryptic lineage. In the most informative phylogenetic reconstruction, based on nad1, E. maldonadoi n. sp. exhibited a strongly supported sister relationship with E. paraensei, which may indicate a very recent speciation event giving rise to these 2 species.

Although Echinostoma robustum (currently a synonym of E. miyagawai) was reported in the Americas based on molecular data, morphological support on adult parasites is still required. Herein, a new species of Echinostoma is described based on worms found in a chicken from Brazil. Molecular phylogenetic analyses based on 28S (1063 bp), ITS (947 bp) and Nad-1 (442 bp) datasets reveal the inclusion of the new species within Echinostoma ‘revolutum’ species complex. Moreover, it was verified the conspecificity between cercariae previously identified as E. robustum in Brazil [identical ITS and only 0.3% of divergence (1 nucleotide) in Nad-1]. Species discovery analyses show that these two isolates form an independent lineage (species) among Echinostoma spp. Compared to E. miyagawai, the new species presents relatively high divergence in Nad-1 (7.88–9.09%). Morphologically, the specimens are distinguished from all nominal species from the ‘revolutum’ species complex by the more posterior position of the testes (length of post-testicular field as a proportion of body length about 20%). They further differ from E. miyagawai and South American Echinostoma spp. by the higher proportion of forebody to the body length. Therefore, combined molecular and morphological evidence supports the proposal of the species named here as Echinostoma pseudorobustum sp. nov.

Six Dipetalonema species have been reported from Neotropical monkeys, Dipetalonema gracile, Dipetalonema graciliformis and Dipetalonema caudispina being the dominant species found in French Guiana primates. Adult filarioids isolated from the abdominal cavity of tamarins (Saguinus midas) in French Guiana were morphologically and molecularly identified as D. graciliformis. Phylogenetic analysis based on DNA and amino acid sequences of the cox1 gene as well as the concatenated sequences of the cox1 and the 18S genes indicated that D. graciliformis belongs to the clade 4 (ONC4) of Onchocercidae. Blast analysis of the 18S rDNA revealed that D. graciliformis in the studied tamarins is conspecific with the filarioid circulating in howler monkeys (Alouatta macconnelli) in French Guiana, previously referred to as unidentified Onchocercidae species.