The record of mammal declines and extinctions in Australia raises concerns regarding geographically restricted and poorly known taxa. For many taxa, the existing data are insufficient to assess their conservation status and inform appropriate management. Concerns regarding the persistence of the subspecies of yellow-footed rock-wallaby Petrogale xanthopus celeris, which is endemic to Queensland, have been expressed since the 1970s because of red fox Vulpes vulpes predation, competition with feral goats Capra hircus and land clearing. This rock-wallaby is rarely observed, occupies rugged mountain ranges and, prior to our surveys, had not been surveyed for 25 years. We surveyed 138 sites across the range of this rock-wallaby during 2010–2023, including revisiting sites surveyed in the 1970s–1980s and locations of historical records. We examined occurrence in relation to habitat variables and threats. Occupancy and abundance remained similar over time at most sites. However, by 2023 the subspecies had recolonized areas in the north-east of its range where it had disappeared between surveys in the 1980s and 2010s, and three south-western subpopulations that were considered extinct in the 1980s were rediscovered. Recolonization and increases in abundance at numerous sites between the 2010s and 2020s are associated with declines in feral goat abundance, indicating dietary and habitat competition are major threats. Exclusion fences erected since 2010 could limit genetic exchange between rock-wallaby subpopulations whilst allowing domestic goats to be commercially grazed. Petrogale xanthopus celeris should remain categorized as Vulnerable based on these ongoing threats. Repeated monitoring approximately every decade should underpin management of this endemic taxon.

Sculpins (coastrange and slimy) and sticklebacks (ninespine and threespine) are widely distributed fishes cohabiting 2 south-central Alaskan lakes (Aleknagik and Iliamna), and all these species are parasitized by cryptic diphyllobothriidean cestodes in the genus Schistocephalus. The goal of this investigation was to test for host-specific parasitic relationships between sculpins and sticklebacks based upon morphological traits (segment counts) and sequence variation across the NADH1 gene. A total of 446 plerocercoids was examined. Large, significant differences in mean segment counts were found between cestodes in sculpin (mean = 112; standard deviation [s.d.] = 15) and stickleback (mean = 86; s.d. = 9) hosts within and between lakes. Nucleotide sequence divergence between parasites from sculpin and stickleback hosts was 20.5%, and Bayesian phylogenetic analysis recovered 2 well-supported clades of cestodes reflecting intermediate host family (i.e. sculpin, Cottidae vs stickleback, Gasterosteidae). Our findings point to the presence of a distinct lineage of cryptic Schistocephalus in sculpins from Aleknagik and Iliamna lakes that warrants further investigation to determine appropriate evolutionary and taxonomic recognition.

There is still a high diversity of lichen-forming fungi that remains undescribed, especially cryptic lineages at the species level. Integrating morphological, chemical, and DNA sequence data has proved useful in corroborating species descriptions and delimitations. Here we reviewed morphological features, secondary metabolites and the DNA sequences of ITS, mtSSU and nuLSU markers to study the diversity of Xanthoparmelia in southern Africa. A total of 37 species were recorded. Three of these appear undescribed, and we therefore describe them here as new: Xanthoparmelia nimisii, with a sorediate thallus and broad lobes, is well supported as a clade separate from X. annexa; X. pseudochalybaeizans with a white medulla is phylogenetically distinct from the otherwise similar X. chalybaeizans; and X. sipmaniana, well supported as a separate clade from the similar X. hypoprocetrarica. In addition, the separation of Xanthoparmelia capensis and X. tinctina requires further studies.

Our floristic work in British ancient forests resulted in a description of a frequently reported but misidentified species, Coenogonium nimisii. Its thallus is very similar to Porina rosei, but the apothecia and pycnidia correspond with C. luteum. Sterile collections are not easy to distinguish but the new species differs from P. rosei in several microscopic characters of the isidia. Coenogonium nimisii is so far known from bark and epiphytic bryophytes, rarely mossy rocks, in ancient humid forests of Great Britain and Ireland. The genus Coenogonium is poorly represented by molecular data in the GenBank database. Our preliminary results revealed distinct genetic lineages within two traditionally circumscribed species, C. luteum and C. pineti, which may represent cryptic species.

Cryptic species in coral reefs, such as sea slugs, represent an important portion of their biodiversity, which is usually underestimated. Autonomous Reef Monitoring Structures (ARMS) have been implemented to estimate cryptic diversity in coral reefs. Therefore, this research aimed to contribute to the southern Gulf of Mexico (GM) and the Caribbean Sea (CAR) coral reefs’ sea slugs’ diversity and distribution using ARMS as a collection method. Fifty-eight ARMS were placed at three coral reefs in the GM and CAR, recovered after 1–2 years and then, disassembled at the laboratory. Plates were individually placed in trays with seawater, where we searched for sea slugs. A total of 242 organisms were found belonging to 31 species; 20 of them were identified to the species level, while 11 were determined up to genus or family. More than half of the species (19) were found in Bajo de 10 (GM), while 15 species were found in the CAR localities. Unlike previous studies, we assessed sea slugs’ diversity exclusively by an indirect sampling method. In this work, we found 9.4% of the sea slug diversity recorded in the Caribbean, and we report four determined species for the first time in the country. New records of species, and even one family for the GM stress the gap of information that we still need to fulfil in the area. We recognize ARMS as a useful tool to find juvenile, cryptic and rare species of sea slugs, as well as to standardize their quantification and record their diversity.

Gastrointestinal nematodes threaten the productivity of grazing livestock and anthelmintic resistance has emerged globally. It is broadly understood that wild ruminants living in sympatry with livestock act as a positive source of refugia for anthelmintic-susceptible nematodes. However, they might also act as reservoirs of anthelmintic-resistant nematodes, contributing to the spread of anthelmintic resistance at a regional scale. Here, we sampled managed sheep and cattle together with feral goats within the same property in New South Wales, Australia. Internal transcribed spacer 2 (ITS-2) nemabiome metabarcoding identified 12 gastrointestinal nematodes (Cooperia oncophora, Cooperia punctata, Haemonchus contortus, Haemonchus placei, Nematodirus spathiger, Ostertagia ostertagi, Teladorsagia circumcincta, Oesophagostomum radiatum, Oesophagostomum venulosum, Trichostrongylus axei, Trichostrongylus colubriformis and Trichostrongylus rugatus). Isotype-1 β-tubulin metabarcoding targeting benzimidazole resistance polymorphisms identified 6 of these nematode species (C. oncophora, C. punctata, H. contortus, H. placei, O. ostertagi and T. circumcincta), with the remaining 3 genera unable to be identified to the species level (Nematodirus, Oesophagostomum, Trichostrongylus). Both ITS-2 and β-tubulin metabarcoding showed the presence of a cryptic species of T. circumcincta, known from domestic goats in France. Of the gastrointestinal nematodes detected via β-tubulin metabarcoding, H. contortus, T. circumcincta, Nematodirus and Trichostrongylus exhibited the presence of at least one resistance genotype. We found that generalist gastrointestinal nematodes in untreated feral goats had a similarly high frequency of the benzimidazole-resistant F200Y polymorphism as those nematodes in sheep and cattle. This suggests cross-transmission and maintenance of the resistant genotype within the wild ruminant population, affirming that wild ruminants should be considered potential reservoirs of anthelmintic resistance.

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.

Recent studies have demonstrated that species boundaries among the lichen-forming fungi are in need of revision with the discovery of cryptic species in numerous clades, especially in parmelioid lichens. Here we focus on addressing the species boundaries in Canoparmelia texana, a sorediate species with a pantropical distribution that extends into temperate regions. We extracted DNA sequences of the nuclear ribosomal internal transcribed spacer region (ITS), large subunit (nuLSU) and mitochondrial small subunit (mtSSU) from samples mostly collected in Kenya, and analyzed them in a phylogenetic framework. We illustrate that our samples of the species as currently circumscribed do not form a monophyletic group but fall into two distinct clades, with the apotheciate C. nairobiensis nested within. Both of the discovered lineages have a wide distributional range and are common in Kenya, and Parmelia albaniensis C. W. Dodge is resurrected to accommodate one of the clades; consequently a new combination, Canoparmelia albaniensis (C. W. Dodge) Divakar & Kirika comb. nov., is proposed.

Ascaridia galli (Nematoda: Ascaridiidae) is the most common intestinal roundworm of chickens and other birds with a worldwide distribution. Although A. galli has been extensively studied, knowledge of the genetic variation of this parasite in detail is still insufficient. The present study examined genetic variation in the mitochondrial cytochrome c oxidase subunit 1 (cox1) gene among A. galli isolates (n = 26) from domestic chickens in Hunan Province, China. A portion of the cox1 (pcox1) gene was amplified by polymerase chain reaction separately from adult A. galli individuals and the amplicons were subjected to sequencing from both directions. The length of the sequences of pcox1 is 441 bp. Although the intra-specific sequence variation within A. galli is 0–7.7%, the inter-specific sequence differences among other members of the infraorder Ascaridomorpha were 11.4–18.9%. Phylogenetic analyses based on the maximum likelihood method using the sequences of pcox1 confirmed that all of the Ascaridia isolates were A. galli, and also resolved three distinct clades. Taken together, the findings suggest that A. galli may represent a complex of cryptic species. Our results provide an additional genetic marker for the management of A. galli in chickens and other birds.

Pomatomus saltatrix is a high-value marine pelagic coastal fish, that is fished throughout subtropical and temperate coastal waters around the world. Despite its large economic potential, there are no global data on its genetic diversity, which could compromise the conservation of the species. The aim of this study was to analyse the genetic-evolutionary structuring of the species, with the intention of evaluating different genetic P. saltatrix stocks that may indicate potential species. Based on 157 Cytochrome C Oxidase Subunit 1 sequences, the molecular delimitation analyses of species (distance and coalescence methods), as well as the haplotype network, found profound geographic structuring related to five distinct units with high and significant FST pairwise values. The divergence of these molecular units is mostly related to the Pleistocene glacial and interglacial cycles of climatic oscillations. It is hypothesized that one ancestral lineage, adapted to cold water environments, diversified into two lineages, with one more adapted to warmer environments. The high values of global genetic diversity (π = 0.016; h = 0.96) may be related to the existing profound genetic differentiation. Due to the presence of five Molecular Operational Taxonomic Units (MOTUs) within the species it is necessary to employ different regional management strategies. Traits of low haplotype richness and shallow population contraction were identified in the MOTUs V (Venezuela and Brazil) and III (Turkey and Australia), respectively, representing conservation priorities. Other molecular markers, as well as morphological data, should be explored with the aim of defining the taxonomic status of P. saltatrix stocks.

The taxonomy of species of Bivesicula Yamaguti, 1934 is analysed for samples from holocentrid, muraenid and serranid fishes from Japan, Ningaloo Reef (Western Australia), the Great Barrier Reef (Queensland), New Caledonia and French Polynesia. Analysis of three genetic markers (cox1 mtDNA, ITS2 and 28S rDNA) identifies three strongly supported clades of species and suggests that Bivesicula as presently recognized is not monophyletic. On the basis of combined morphological, molecular and biological data, 10 species are distinguished of which five are proposed as new. Bivesicula Clade 1 comprises seven species of which three are effectively morphologically cryptic relative to each other; all seven infect serranids and four also infect holocentrids. Bivesicula Clade 2 comprises three species of which two are effectively morphologically cryptic relative to each other; all three infect serranids and one also infects a muraenid. Bivesicula Clade 3 comprises two known species from apogonids and a pomacentrid, and forms a clade with species of Paucivitellosus Coil, Reid & Kuntz, 1965 to the exclusion of other Bivesicula species. Taxonomy in this genus is made challenging by the combination of low resolving power of ribosomal markers, the existence of regional cox1 mtDNA populations, exceptional and unpredictable host-specificity and geographical distribution, and significant host-induced morphological variation.

We report specimens of monorchiids infecting Haemulidae from the waters off Japan and Australia; these specimens represent five species of Helicometroides Yamaguti, 1934, three of which are unambiguously new. Helicometroides murakamii n. sp. infects Diagramma pictum pictum from off Minabe, Japan; Helicometroides gabrieli n. sp. infects Plectorhinchus chrysotaenia from off Lizard Island, Australia; and Helicometroides wardae n. sp. infects Plectorhinchus flavomaculatus and Plectorhinchus multivittatus from off Heron Island, Australia. Helicometroides murakamii n. sp. and H. gabrieli n. sp. conform to the most recent diagnosis of Helicometroides in lacking a terminal organ, but H. wardae n. sp. possesses a terminal organ with distinct, robust spines; despite this morphological distinction, the three form a strongly-supported clade in phylogenetic analyses. We also report specimens morphologically consistent with Helicometroides longicollis Yamaguti, 1934, from D. pictum pictum from off Minabe, Japan, and Diagramma pictum labiosum on the Great Barrier Reef, Australia. Genetic analyses of ITS2 rDNA, 28S rDNA and cox1 mtDNA sequence data for the Japanese specimens reveal the presence of two distinct genotypes. Specimens of the two genotypes were discovered in mixed infections and are morphologically indistinguishable; neither genotype can be associated definitively with H. longicollis as originally described. We thus identify them as H. longicollis lineage 1 and 2, pending study of further fresh material. Genetic analyses of specimens from the Great Barrier Reef are consistent with the presence of only H. longicollis lineage 1. This species thus has a range that incorporates at least Australia and Japan, localities separated by over 7000 km.

Delimiting and describing Plasmodium species in reptiles remains a pressing problem in Haemosporida taxonomy. The few morphological characters used can overlap, and the significance of some life-history traits is not fully understood. Morphologically identical lizard Plasmodium forms have been reported infecting different cell types (red and white blood cells) in the same host and have been considered the same species. An example is Plasmodium tropiduri tropiduri, a species known to infect erythrocytes, thrombocytes and lymphocyte-like cells. Here, both forms of P. t. tropiduri were analysed using light microscope-based morphological characteristics and phylogenetic inferences based on almost complete mitochondrial genomes of parasites naturally infecting lizards in southeastern Brazil. Although morphologically similar, two distinct phylogenetic lineages infecting erythrocytes and non-erythrocytic cells were found. The lineage found in the erythrocytes forms a monophyletic group with species from Colombia. However, the non-erythrocytic lineage shares a recent common ancestor with Plasmodium leucocytica, which infects leucocytes in lizards from the Caribbean islands. Here, Plasmodium ouropretensis n. sp. is described as a species that infects thrombocytes and lymphocyte-like cells.

Estimates of trematode diversity are inaccurate due to unrecognized cryptic species and phenotypic plasticity within species. Integrative taxonomy (genetics, morphology and host use) increases the clarity of species delineation and improves knowledge of parasite biology. In this study, we used this approach to resolve taxonomic issues and test hypotheses of cryptic species in a genus of trematode, Quinqueserialis. Specimens from throughout North America were field collected from hosts and obtained from museums. We found three morphologically distinct groups and successfully sequenced specimens from two of these groups. DNA sequencing at the 28S and CO1 gene regions revealed that two of the three groups were genetically distinct. One genetic group included two morphological clusters demonstrating host-induced phenotypic plasticity within Quinqueserialis quinqueserialis. The other unique genetic group is a novel species, Quinqueserialis kinsellai n. sp., which is described herein. Our study illustrates the importance of integrating multiple sources of evidence when investigating trematode diversity to account for the influence of cryptic species or phenotypic plasticity. However, further sampling is needed to understand Quinqueserialis spp. diversity as some species have no genetic information associated with them.

The morphology of sexual adults is the cornerstone of digenean systematics. In addition, life cycle data have always been significant. The integration of these approaches, supplemented with molecular data, has allowed us to detect a new species that many researchers may have previously seen, but not recognized. Sexual adults from common eiders that we found in northern European seas were extremely similar to other notocotylids, but the discovery of their intermediate host, a marine snail, revealed the true nature of this material. Here we describe sexual adults, rediae and cercariae of Catatropis onobae sp. nov. We discuss how ‘Catatropis verrucosa’ should be regarded, justify designation of the new species C. onobae for our material and explain why it can be considered a cryptic species. The phylogenetic position of C. onobae within Notocotylidae, along with other evidence, highlights the challenges for the taxonomy of the family, for which two major genera appear to be polyphyletic and life cycle data likely undervalued.

Acanthocephalans are obligate parasites of vertebrates, mostly of fish. There is limited knowledge about the diversity of fish-parasitizing Acanthocephala in Austria. Seven determined species and an undetermined species are recorded for Austrian waters. Morphological identification of acanthocephalans remains challenging due to their sparse morphological characters and their high intraspecific variations. DNA barcoding is an effective tool for taxonomic assignment at the species level. In this study, we provide new DNA barcoding data for three genera of Acanthocephala (Pomphorhynchus Monticelli, 1905, Echinorhynchus Zoega in Müller, 1776 and Acanthocephalus Koelreuter, 1771) obtained from different fish species in Austria and provide an important contribution to acanthocephalan taxonomy and distribution in Austrian fish. Nevertheless, the taxonomic assignment of one species must remain open. We found indications for cryptic species within Echinorhynchus cinctulus Porta, 1905. Our study underlines the difficulties in processing reliable DNA barcodes and highlights the importance of the establishment of such DNA barcodes to overcome these. To achieve this goal, it is necessary to collect and compare material across Europe allowing a comprehensive revision of the phylum in Europe.

The principal goal of our study was to test whether ecologically and chemically different populations of lichens in the Physconia muscigena group belong to a single, or multiple, species. We used sequence data from three markers (ITS rDNA, mtSSU rDNA and TEF1-α) for the reconstruction of phylogenetic trees based on a sampling of mostly European and Canadian populations of P. muscigena (Ach.) Poelt, P. muscigena var. bayeri (Nádv.) Poelt and P. isidiomuscigena Essl. In addition, we sought any possible geographical or ecological trends among chemotypes and haplotypes. Results show that: 1) sequence data of ITS rDNA and TEF1-α show large genetic variation in the Physconia muscigena group, which does not correlate with geographical distribution or thallus chemistry; 2) Physconia muscigena var. bayeri and P. isidiomuscigena appear undifferentiated with P. muscigena in our phylogenetic trees, and the three species cannot be distinguished on the basis of ITS rDNA, mtSSU rDNA and TEF1-α sequences. We therefore synonymized Physconia muscigena var. bayeri with P. muscigena and we recombine P. isidiomuscigena as a variety of P. muscigena.