ASAP: assemble species by automatic partitioning

Molecular characterisation of Amblyomma integrum circulating in southern India

Amblyomma integrum is a large gooseberry sized longirostrate tick (when fully repleted) found in India and Sri Lanka. In Kerala (India), this tick is commonly found in the forest and its fringe areas frequently infesting deer and hence it is locally known as "maan chellu / maanunny" (deer tick). In the present study, molecular characterisation and phylogenetic analysis of A. integrum collected from the area grazed by the sambar deer (Rusa unicolor) of Kerala, south India was performed using three molecular markers viz., the mitochondrial cytochrome c oxidase subunit 1 (COI), mitochondrial 16S ribosomal RNA, and nuclear 18S ribosomal RNA genes. Cytochrome c oxidase subunit 1 (COI) gene showed better resolving ability for elucidating the evolutionary relationship of A. integrum and identified two distinct clades, viz., A and B. The Tamil Nadu isolates of south India and Marayoor isolate 1 (from Idukki district of Kerala bordering with Tamil Nadu) belonged to clade A. Majority of Wayanad isolates from Kerala, occupied clade B. The intraspecific genetic distance among the A. integrum species ranged from 0.00 to 13.34%. Between clades A and B, the genetic distance observed was 11.49%. The clade B isolates were genetically close to A. geoemydae (GD: 1.22%). Morphological variations between the clades included darker exoskeletal coloration in clade A and distinct differences in the shape of basis capitulum. Further analysis using Assemble Species by Automatic Partitioning (ASAP) and Generalized Mixed Yule Coalescent (GMYC) provided additional insights. Assemble Species by Automatic Partitioning (ASAP) identified 26 Molecular Operational Taxonomic Units (MOTUs) at a threshold distance of 5.38%, supporting the species partition of A. integrum clade B. Generalized Mixed Yule Coalescent (GMYC) analysis retained the same species complex (A. integrum-geoemydae Complex) inferred from the ASAP analyses. It could be inferred from the present study that the A. integrum clades A and B could be two different putative pseudocryptic species.

Of sea, rivers and symbiosis: Diversity, systematics, biogeography and evolution of the deeply diverging florideophycean order Hildenbrandiales (Rhodophyta)

The Hildenbrandiales, a typically saxicolous red algal order, is an early diverging florideophycean group with global significance in marine and freshwater ecosystems across diverse temperature zones. To comprehensively elucidate the diversity, phylogeny, biogeography, and evolution of this order, we conducted a thorough re-examination employing molecular data derived from nearly 700 specimens. Employing a species delimitation method, we identified Evolutionary Species Units (ESUs) within the Hildenbrandiales aiming to enhance our understanding of species diversity and generate the first time-calibrated tree and ancestral area reconstruction for this order. Mitochondrial cox1 and chloroplast rbcL markers were used to infer species boundaries, and subsequent phylogenetic reconstructions involved concatenated sequences of cox1, rbcL, and 18S rDNA. Time calibration of the resulting phylogenetic tree used a fossil record from a Triassic purportedly freshwater Hildenbrandia species and three secondary time points from the literature. Our species delimitation analysis revealed an astounding 97 distinct ESUs, quintupling the known diversity within this order. Our time-calibration analysis placed the origin of Hildenbrandiales (crown age) in the Ediacaran period, with freshwater species emerging as a monophyletic group during the later Permian to early Triassic. Phylogenetic reconstructions identified seven major clades, experiencing early diversification during the Silurian to Carboniferous period. Two major evolutionary events-colonization of freshwater habitats and obligate systemic symbiosis with a marine fungus-marked this order, leading to significant morphological alterations without a commensurate increase in species diversification. Despite the remarkable newly discovered diversity, the extant taxon diversity appears relatively constrained when viewed against an evolutionary timeline spanning over 800 million years. This limitation may stem from restricted geographic sampling or the prevalence of asexual reproduction. However, species richness estimation and rarefaction analyses suggest a substantially larger diversity yet to be uncovered-potentially four times greater. These findings drastically reshape our understanding of the deeply diverging florideophycean order Hildenbrandiales species diversity, and contribute valuable insights into this order's evolutionary history and ecological adaptations. Supported by phylogenetic, ecological and morphological evidence, we established the genus Riverina gen. nov. to accommodate freshwater species of Hildenbrandiales, which form a monophyletic clade in our analyses. This marks the first step toward refining the taxonomy of the Hildenbrandiales, an order demanding thorough revisions, notably with the creation of several genera to address the polyphyletic status of Hildenbrandia. However, the limited diagnostic features pose a challenge, necessitating a fresh approach to defining genera. A potential solution lies in embracing a molecular systematic perspective, which can offer precise delineations of taxonomic boundaries.

Exploring the biological diversity and source species of medicinal horseflies through metabarcoding

Horseflies from the Tabanidae family play a significant role in traditional Chinese medicine to treat various health conditions, including coronary heart disease, stroke, headaches, liver cirrhosis, psoriasis, and hepatic carcinoma. There are 27 species of Tabaninae (Tabanidae) used as medicine, and they showed high morphological similarities with those for which medicinal properties have not been reported. Nonetheless, there have been reports suggesting that medicinal crude drugs sometimes contain irrelevant or false species, impacting the drug's efficacy. In this current study, we collected 14 batches, totaling 13,528 individuals, from various provinces in China. Instead of "classic" DNA barcoding strategy, we employed a high-throughput metabarcoding approach to assess the biological composition of crude drug mixtures derived from horseflies. Our analysis identified 40 Amplicon Sequence Variants (ASVs) with similarity percentages ranging from 92% to 100% with 12 previously reported species. Species delimitation methods revealed the presence of 11 Molecular Operational Taxonomic Units (MOTUs), with ten belonging to the Tabanus genus and one to Hybomitra. Tabanus sp6 displayed the highest relative abundance, and its ASVs showed close resemblance to Tabanus pleski. Our investigations revealed that the medicinal batches were biologically composed of 6 to 12 species. Some batches contained ASVs that closely resembled species previously associated with false Tabanus species. In conclusion, our findings offer valuable insights into the biological composition of crude drugs derived from horseflies and have the potential to enhance the quality of these traditional medicines.

DNA barcoding reveals cryptic species in the sea slater Ligia italica (Crustacea, Isopoda) from Tunisia

Barcoding studies have provided significant insights into phylogenetic relationships among species belonging to the genus Ligia (Crustacea, Isopoda). Herein the diversity of the Italian sea slater Ligia italica from Tunisia is studied for the first time. Samples were collected from 18 localities in Tunisia, and the analysis included previously published sequences from Italy and Greece available in GenBank. Bayesian and Maximum Likelihood phylogenetic analyses were carried out using a fragment of the mitochondrial COI gene. Putative cryptic species were explored using the 'barcode gap' approach in the software ASAP. A genetic landscape shape analysis was carried out using the program Alleles in Space. The analyses revealed highly divergent and well-supported clades of L. italica dispersed across Tunisia (Clades A1 and A2), Greece (Clade B) and Italy (Clades C1 and C2). High genetic dissimilarity among clades suggested that L. italica constitute a cryptic species complex. Divergence among different L. italica lineages (Clades A, B and C) occurred around 7-4.5 Ma. The detected high genetic distances among clades did not result from atypical mitochondrial DNAs or intracellular infection by Wolbachia bacteria. The complex history of the Mediterranean Sea appears to have played a significant role in shaping the phylogeographic pattern of Ligia italica. Additional morphological and molecular studies are needed to confirm the existence of cryptic species in Ligia italica in Mediterranean.

Integrative taxonomy reveals a new species of the glass knifefish genus Eigenmannia Jordan & Evermann, 1896 (Teleostei: Gymnotiformes: Sternopygidae) from the Rio Branco basin, Brazil

A new species of Eigenmannia is described from the Rio Branco basin, Roraima, Brazil, based on morphological and molecular datasets. It is distinguished from all congeners by the following combination of characters: lateral line stripe extending from first perforated lateral line scale to distal portion of caudal filament, presence of superior midlateral stripe with origin posterior to end of body cavity anal-fin hyaline, caudal filament corresponding to 15.2%-43.1% LEA, subterminal mouth, ii,14-16 pectoral-fin rays, 166-219 anal-fin rays, 10-13 scale rows above lateral line at vertical through posterior tip of pectoral fin, 100-128 scales on lateral line, 22-28 premaxillary teeth, 19-23 dentary teeth, 7-10 endopterygoid teeth, depth of posterodorsal expansion on infraorbitals 1 + 2 half as long as infraorbitals 1 + 2 length, basibranchial 1 unossified, 13 precaudal vertebrae, and length of coronomeckelian bone corresponding to 20% of Meckel's cartilage length. The new species has significant genetic divergence from species with accessible DNA sequences in public repositories, ranging from 10.8% to 17.7%. An osteological description of the new species, a review of Eigenmannia cytochrome c oxidase subunit I (COI) sequences available in public repositories based on voucher examination, and a hypothesis of phylogenetic relationships for the new species based on COI are provided. The critical importance of including voucher examination as one of the steps in the pipeline for using DNA sequences present in public repositories in taxonomic and phylogenetic studies is discussed.

A new species of the genus Yoldiella (Bivalvia, Protobranchia, Yoldiidae) from Haima Cold Seep, South China Sea, China

In present study, a previously unidentified but frequently encountered species of deep-sea protobranch, Yoldiellahaimaensis sp. nov., is described new to science from the Haima Cold Seep on the northwestern slope of the South China Sea. A morphological analysis confirmed that this species belongs to a previously undescribed species of the genus Yoldiella A.E. Verrill & K.J. Bush, 1897. It differs morphologically from other known species within the genus in its shell shape, degree of inflation, beaks, and number of hinge teeth. Furthermore, we sequenced three gene segments of Y.haimaensis sp. nov., comprising a nuclear ribosomal gene (18S rRNA), a nuclear protein-coding gene (histone H3), and a mitochondrial gene (cytochrome c oxidase subunit I, COI). Our phylogenetic analysis performed on the superfamily Nuculanoidea and family Yoldiidae indicates that the genus Yoldiella is non-monophyletic, and the widely recognized families within the superfamily Nuculanoidea are also not monophyletic. Our results provide molecular insights into the Protobranchia and highlight the necessity for further samples and data to revise the classification of families and genera within the superfamily using an integrative approach that combines morphological analysis and molecular data.

Integrative taxonomy, phylogenetics and historical biogeography of subgenus Aeschyntelus Stål, 1872 (Hemiptera: Heteroptera: Rhopalidae)

The subgenus Aeschyntelus includes six species that show variations in body color and shape, thus making it difficult to identify them based on morphological identification alone. To date, no genetic study has evaluated species within this genus. Herein, we collected 171 individuals from 90 localities of Rhopalus and employed an integrative taxonomic approach that incorporated morphological data, mitochondrial genomic data (COI, whole mitochondrial data) and nuclear genomic data (18S + 28S rRNAs, nuclear genome-wide SNPs) to delineate species boundaries. Our analyses confirmed the status of nine described species of Rhopalus and proposed the recognition of one new species known as Rhopalus qinlinganus sp. nov., which is classified within the subgenus Aeschyntelus. Discrepancies arising from nuclear and mitochondrial data suggest the presence of mito-nuclear discordance. Specifically, mitochondrial data indicated admixture within Clade A, comprising R. kerzhneri and R. latus, whereas genome-wide SNPs unambiguously identified two separate species, aligning with morphological classification. Conversely, mitochondrial data clearly distinguished Clade B- consisting of R. sapporensis into two lineages, whereas genome-wide SNPs unequivocally identified a single species. Our study also provides insights into the evolutionary history of Aeschyntelus, thus indicating that it likely originated in East Asia during the middle Miocene. The development of Aeschyntelus biodiversity in the southwestern mountains of China occurred via an uplift-driven diversification process. Our findings highlight the necessity of integrating both morphological and multiple molecular datasets for precise species identification, particularly when delineating closely related species. Additionally, it reveals the important role of mountain orogenesis on speciation within the southwestern mountains of China.

The expansion of invasive species to the East: new sites of the bullheads (genus Ameiurus Rafinesque 1820) in Ukraine with morphological and genetic identification

This study confirms the extended distribution of two invasive species of the genus Ameiurus in Ukraine. Specifically, A. melas is recorded for the first time in the Southern Buh basin and A. nebulosus has expanded further eastward within the Dnipro basin. Material collected in 2019 and 2022 was identified by morphological features and confirmed by molecular genetic analysis. The most reliable morphological characters for distinguishing these two species include anal-fin membrane pigmentation (light or black), gill raker count (fewer or more than 16), and serrations on the pectoral-fin spine (well-developed along the full length or small, absent near the tip). The analysis of the cytochrome oxidase subunit I barcoding marker identified all samples from the Dnipro Basin (Tnia and Velykyi Luh localities) as A. nebulosus, while all specimens from the Vinnytsia region within the Southern Buh basin (Sotskoho and Vyshenske lakes) were attributed to A. melas. The maximum-likelihood analysis revealed clearly separated clades with high bootstrap support (>75%), strongly supporting the presence of the two separate species. This study suggests the potential for further eastward expansion of both species within Ukraine: A. nebulosus in the northern direction and A. melas in the southern direction.

Ribbon worms (phylum Nemertea) from Bodega Bay, California: A largely undescribed diversity

The diversity of nemerteans along the Pacific coast of the United States is regarded as well characterized, but there remain many cryptic, undescribed, and "orphan" species (those known only in their larval form). Recent sampling of nemerteans in Oregon and Washington has begun to fill in these taxonomic gaps, but nemertean diversity in California has received relatively little attention over the past 60 years. During the summers of 2019 and 2020, nemertean specimens were collected from 20 locations in the Bodega Bay region of northern California, USA, including rocky intertidal shores, sandy beaches, mudflats, and other habitats. Based on morphological assessment and DNA sequence analysis (partial Cytochrome Oxidase I and 16S rRNA genes), our surveys identified 34 nemertean species. Only 13 of these (38%) can be confidently assigned to described species. Another 11 represent species that are new to science, including members of the genera Riserius, Nipponnemertes, Poseidonemertes, Zygonemertes, Nemertellina, Oerstedia, and three species of uncertain affiliation. The remaining ten species include undescribed or cryptic species of uncertain status that have been found previously along the Pacific Coast of North America. Our surveys also document extensions of known geographic ranges for multiple species, including the first records in California of Antarctonemertesphyllospadicola, Cephalothrixhermaphroditica, and Maculauraoregonensis. This is the first report of the genus Nemertellina in the northeast Pacific and Riserius in California. Overall, our findings highlight how much remains to be learned about the diversity and distribution of nemerteans in the northeast Pacific.

Deep divergences among inconspicuously colored clades of Epipedobates poison frogs

Poison frogs (Dendrobatidae) are famous for their aposematic species, having a combination of diverse color patterns and defensive skin toxins, yet most species in this family are inconspicuously colored and considered non-aposematic. Epipedobates is among the youngest genus-level clades of Dendrobatidae that includes both aposematic and inconspicuous species. Using Sanger-sequenced mitochondrial and nuclear markers, we demonstrate deep genetic divergences among inconspicuous species of Epipedobates but relatively shallow genetic divergences among conspicuous species. Our phylogenetic analysis includes broad geographic sampling of the inconspicuous lineages typically identified as E. boulengeri and E. espinosai, which reveals two putative new species, one in west-central Colombia (E. sp. 1) and the other in north-central Ecuador (E. aff. espinosai). We conclude that E. darwinwallacei is a junior subjective synonym of E. espinosai. We also clarify the geographic distributions of inconspicuous Epipedobates species including the widespread E. boulengeri. We provide a qualitative assessment of the phenotypic diversity in each nominal species, with a focus on the color and pattern of inconspicuous species. We conclude that Epipedobates contains eight known valid species, six of which are inconspicuous. A relaxed molecular clock analysis suggests that the most recent common ancestor of Epipedobates is ∼11.1 million years old, which nearly doubles previous estimates. Last, genetic information points to a center of species diversity in the Chocó at the southwestern border of Colombia with Ecuador. A Spanish translation of this text is available in the supplementary materials.

Integrative phylogenetic, phylogeographic and morphological characterisation of the Unio crassus species complex reveals cryptic diversity with important conservation implications

The global decline of freshwater mussels and their crucial ecological services highlight the need to understand their phylogeny, phylogeography and patterns of genetic diversity to guide conservation efforts. Such knowledge is urgently needed for Unio crassus, a highly imperilled species originally widespread throughout Europe and southwest Asia. Recent studies have resurrected several species from synonymy based on mitochondrial data, revealing U. crassus to be a complex of cryptic species. To address long-standing taxonomic uncertainties hindering effective conservation, we integrate morphometric, phylogenetic, and phylogeographic analyses to examine species diversity within the U. crassus complex across its entire range. Phylogenetic analyses were performed using cytochrome c oxidase subunit I (815 specimens from 182 populations) and, for selected specimens, whole mitogenome sequences and Anchored Hybrid Enrichment (AHE) data on ∼ 600 nuclear loci. Mito-nuclear discordance was detected, consistent with mitochondrial DNA gene flow between some species during the Pliocene and Pleistocene. Fossil-calibrated phylogenies based on AHE data support a Mediterranean origin for the U. crassus complex in the Early Miocene. The results of our integrative approach support 12 species in the group: the previously recognised Unio bruguierianus, Unio carneus, Unio crassus, Unio damascensis, Unio ionicus, Unio sesirmensis, and Unio tumidiformis, and the reinstatement of five nominal taxa: Unio desectusstat. rev., Unio gontieriistat. rev., Unio mardinensisstat. rev., Unio nanusstat. rev., and Unio vicariusstat. rev. Morphometric analyses of shell contours reveal important morphospace overlaps among these species, highlighting cryptic, but geographically structured, diversity. The distribution, taxonomy, phylogeography, and conservation of each species are succinctly described.

Morphological and molecular characterization of brown-banded broodsacs and metacercariae of Leucochloridium (Trematoda: Leucochloridiidae) parasitizing the semi-slug Omalonyx unguis (Succineidae) in Argentina

Trematodes of the genus Leucochloridium exhibit an unusual transmission strategy among mollusks (intermediate host). The fully developed sporocyst, housing encysted metacercariae, displays vivid coloration and rhythmic activity in the snail's tentacle, mimicking insect larvae. These strategies attract insectivorous birds, their final hosts, thereby increasing the chances of completing their life cycle. In South America, the reports of adults and larval stages of Leucochloridium are scarce. Brown-banded broodsac of Leucochloridium sp. were obtained from Omalonyx unguis collected in a shallow lake from Corrientes Province, Argentina. Here, we morphologically characterized the larval stages (broodsac and metacercaria), identified the parasite through DNA sequences from nuclear 28S-rRNA (28S) and the mitochondrial cytochrome c oxidase I (COI) genes, and explored its evolutionary affinities with the Leucochloridium species available in GenBank. The present broodsac displays brown bands, with a yellowish background in the first two-thirds and yellowish-white in the last third. Based on morphological comparisons, the broodsac and metacercaria described in this study could not be conclusively categorized under any known South American species of Leucochloridium. In relation to the phylogenetic reconstructions, Leucochloridium sp. consistently clustered with L. perturbatum, and species delimitation analyses resulted in recognized Leucochloridium sp. from Argentina as a distinct species. The DNA sequences obtained in this study constitute the first genetic data generated for sporocyst broodsacs in South America. Future studies, incorporating morphology, genetic, and biological data, will be essential for both species identification and the elucidation of leucochloridiid diversity in the region.

Parvatrema spp. (Digenea, Gymnophallidae) with parthenogenetic metacercariae: diversity, distribution and host specificity in the palaearctic

There are several species of gymnophallid digeneans in the genus Parvatrema that are unique in developing metacercariae that reproduce by parthenogenesis in the second intermediate host. Transmission of these digeneans takes place in coastal ecosystems of the North Pacific and North Atlantic seas. The first intermediate hosts are bivalves, the second ones are gastropods, and the definitive hosts are migratory birds. We integrated data accumulated over 25 years of research and differentiated a complex of five closely related species. They differ in the molluscan second intermediate hosts, distribution ranges, and life cycles patterns. The type I life cycle includes two generations of parthenogenetic metacercariae, followed by development of metacercariae which are invasive for the definitive host. In the type II life cycle, the number of generations of parthenogenetic metacercariae is unlimited, and they can also produce cercariae. These cercariae emerge into the environment and can infect new individuals of the second intermediate host. We conclude that the type I life cycle is a derived option that has evolved as a better fit to transmission in the unstable conditions in the intertidal zone. Another evolutionary trend in Parvatrema is transition from inhabiting the extrapallial space of the gastropod second intermediate host to endoparasitism in its mantle and internal organs. rDNA sequence analysis highlighted that Parvatrema spp. with parthenogenetic metacercariae form a monophyletic clade and suggested the Pacific origin of the group, with two transfers to the North Atlantic and colonisation of new second intermediate host species. Apparently the group formed in the late Pliocene-Pleistocene and diversified as a result of recurrent isolation in inshore refugia during glacial periods. We argue that parthenogenetic metacercariae in Parvatrema may serve as a model for early digenean evolution, demonstrating the first steps of adopting the molluscan first intermediate host and becoming tissue parasites.

Machine learning approaches delimit cryptic taxa in a previously intractable species complex

Cryptic species are not diagnosable via morphological criteria, but can be detected through analysis of DNA sequences. A number of methods have been developed for identifying species based on genetic data; however, these methods are prone to over-splitting taxa with extreme population structure, such as dispersal-limited organisms. Machine learning methodologies have the potential to overcome this challenge. Here, we apply such approaches, using a large dataset generated through hybrid target enrichment of ultraconserved elements (UCEs). Our study taxon is the Aoraki denticulata species complex, a lineage of extremely low-dispersal arachnids endemic to the South Island of Aotearoa New Zealand. This group of mite harvesters has been the subject of previous species delimitation studies using smaller datasets generated through Sanger sequencing and analytical approaches that rely on multispecies coalescent models and barcoding gap discovery. Those analyses yielded a number of putative cryptic species that seems unrealistic and extreme, based on what we know about species' geographic ranges and genetic diversity in non-cryptic mite harvesters. We find that machine learning approaches, on the other hand, identify cryptic species with geographic ranges that are similar to those seen in other morphologically diagnosable mite harvesters in Aotearoa New Zealand's South Island. We performed both unsupervised and supervised machine learning analyses, the latter with training data drawn either from animals broadly (vagile and non-vagile) or from a custom training dataset from dispersal-limited harvesters. We conclude that applying machine learning approaches to the analysis of UCE-derived genetic data is an effective method for delimiting species in complexes of low-vagility cryptic species, and that the incorporation of training data from biologically relevant analogues can be critically informative.

Revision of the 'Acanthephyra purpurea' species complex (Crustacea: Decapoda), with an emphasis on species diversification in the Atlantic

We inventoried all nine species of the 'Acanthephyra purpurea' complex, one of the most abundant and cosmopolitan group of mesopelagic shrimps. We used 119 specimens at hand and genetic data for 124 specimens from GenBank and BOLD. Phylogenetic analysis of four genes (COI, 16S, NaK, and enolase) showed that the 'Acanthephyra purpurea' complex is polyphyletic and encompasses two species groups, 'A. purpurea' (mostly Atlantic) and 'A. smithi' (Indo-West Pacific). The 'A. purpurea' species group consists of two major molecular clades A. pelagica and A. kingsleyi - A. purpurea - A. quadrispinosa. Molecular data suggest that hitherto accepted species A. acanthitelsonis, A. pelagica, and A. sica should be considered as synonyms. The Atlantic is inhabited by at least two cryptic genetic lineages of A. pelagica and A. quadrispinosa. Morphological analyses of qualitative and quantitative (900 measurements) characters resulted in a tabular key to species and in a finding of four evolutionary traits. Atlantic species showed various scenarios of diversification visible on mitochondrial gene level, nuclear gene level, and morphological level. We recorded and discussed similar phylogeographic trends in diversification and in distribution of genetic lineages within two different clades: A. pelagica and A. kingsleyi - A. purpurea - A. quadrispinosa.

Molecular detection of blood protozoa and identification of black flies of the Simulium varicorne species group (Diptera: Simuliidae) in Thailand

Species of the Simulium varicorne group in Thailand have veterinary significance as vectors of haemosporidian parasites. Accurate identification is, therefore, critical to the study of vectors and parasites. We used morphology and molecular markers to investigate cryptic genetic lineages in samples identified as Simulium chumpornense Takaoka & Kuvangkadilok, 2000. We also tested the efficiency of the nuclear internal transcribed spacer 2 (ITS2) marker for the identification of species in this group. Morphological examinations revealed that S. chumpornense lineage A is most similar to S. khelangense Takaoka, Srisuka & Saeung, 2022, with minor morphological differences. They are also genetically similar based on mitochondrial cytochrome c oxidase I (COI) sequences. Geographically, the sampling site where paratypes of S. khelangense were originally collected is <50 km from where S. chumpornense lineage A was collected. We concluded that cryptic lineage A of S. chumpornense is actually S. khelangense. COI sequences could not differentiate S. kuvangkadilokae Pramual and Tangkawanit, 2008 from S. chumpornense and S. khelangense. In contrast, ITS2 sequences provided perfect accuracy in the identification of these species. Molecular analyses of the blood protozoa Leucocytozoon and Trypanosoma demonstrated that S. khelangense carries L. shoutedeni, Leucocytozoon sp., and Trypanosoma avium. The Leucocytozoon sp. in S. khelangense differs genetically from that in S. asakoae Takaoka & Davies, 1995, signaling the possibility of vector-parasite specificity.

Ice-inhabiting species of Bdelloidea Rotifera reveal a pre-Quaternary ancestry in the Arctic cryosphere

Historical climate data indicate that the Earth has passed through multiple geological periods with much warmer-than-present climates, including epochs of the Miocene (23-5.3 mya BP) with temperatures 3-4°C above present, and more recent interglacial stages of the Quaternary, for example, Marine Isotope Stage 11c (approx. 425-395 ka BP) and Middle Holocene thermal maximum (7.5-4.2 ka BP), during which continental glaciers may have melted entirely. Such warm periods would have severe consequences for ice-obligate fauna in terms of their distribution, biodiversity and population structure. To determine the impacts of these climatic events in the Nordic cryosphere, we surveyed ice habitats throughout mainland Norway and Svalbard ranging from maritime glaciers to continental ice patches (i.e. non-flowing, inland ice subjected to deep freezing overwinter), finding particularly widespread populations of ice-inhabiting bdelloid rotifers. Combined mitochondrial and nuclear DNA sequencing identified approx. 16 undescribed, species-level rotifer lineages that revealed an ancestry predating the Quaternary (> 2.58 mya). These rotifers also displayed robust freeze/thaw tolerance in laboratory experiments. Collectively, these data suggest that extensive ice refugia, comparable with stable ice patches across the contemporary Norwegian landscape, persisted in the cryosphere over geological time, and may have facilitated the long-term survival of ice-obligate Metazoa before and throughout the Quaternary.

Improving DNA barcoding library of armored scale insects (Hemiptera: Diaspididae) in China

DNA barcoding is used to identify cryptic species, survey environmental samples, and estimate phyletic and genetic diversity. Armored scale insects are phytophagous insects and are the most species-rich taxa in the Coccoidea superfamily. This study developed a DNA barcode library for armored scale insect species collected from southern China during 2021-2022. We sequenced a total of 239 specimens, recognized as 50 morphological species, representing two subfamilies and 21 genera. Sequencing analysis revealed that the average G + C content of the cytochrome oxidase subunit I (COI) gene sequence was very low (~18.06%) and that the average interspecific divergence was 10.07% while intraspecific divergence was 3.20%. The intraspecific divergence value was inflated by the high intraspecific divergence in ten taxa, which may indicate novel species overlooked by current taxonomic treatments. All the Automated Barcode Gap Discovery, Assemble Species by Automatic Partitioning, Taxon DNA analysis and Bayesian Poisson Tree Process methods yielded largely consistent results, indicating a robust and credible species delimitation. Based on these results, an intergeneric distance threshold of ≤ 5% was deemed appropriate for the differentiation of armored scale insect species in China. This study establishes a comprehensive barcode library for the identification of armored scale insects, future research, and application.

Island mosquitoes of Thailand: an update on species diversity and DNA barcoding

Mosquitoes (Diptera: Culicidae) are among the most medically significant insects, with several species acting as vectors for human pathogens. Although there are frequent reports of mosquito-borne diseases in the border island areas of Thailand, comprehensive data on the diversity and DNA barcoding of these mosquito species remain limited. This study investigated mosquito diversity in two main archipelagos in Thailand-the Trat archipelago (comprising Chang Island and Kood Island) and the Ranong archipelago (comprising Chang Island and Phayam Island)-and generated DNA barcode data from the mosquitoes found there. The survey across these islands discovered a total of 41 species, highlighting the presence of several species known to be vectors for human diseases. Thirty-seven mosquito species from the island areas were documented to provide reference DNA barcode sequences for mosquitoes in Thailand's island regions. Two species, Aedes fumidus and Finlaya flavipennis, have been added as new COI sequence records in the database. DNA barcoding was highly effective in classifying almost all species by identifying barcoding gaps, except for Anopheles baimaii and Anopheles dirus, which could not be distinguished. Additionally, the study noted that geographical variations might influence certain mosquito species, such as Anopheles barbirostris A3 and Mansonia dives, causing them to be split into two distinct subgroups. The findings of this study are crucial, as they aid in classifying mosquito species using molecular techniques and expand our knowledge of disease vectors in these biodiverse regions.

Oxynoemacheilus fatmae, a new species from the Güzelhisar Stream in the Aegean Sea basin, Türkiye (Teleostei: Nemacheilidae)

Oxynoemacheilus fatmae, a new species, is found in the Güzelhisar Stream in the northern Aegean Sea basin. It is differentiated from all other species of Oxynoemacheilus in the northern Aegean Sea and adjacent basins by having four to eight irregularly shaped narrow black bars on the posterior part of flank, and anterior parts of the flank with a marbled pattern. O. fatmae is differentiated from the closest species Oxynoemacheilus theophilii by having 14 fixed diagnostic nucleotide substitution sites, and the pair-wise genetic distance is 2.22%. It further differs from O. theophilii by having a slenderer body (body at dorsal-fin origin: 15%-17% standard length [SL] vs. 17%-18%), a slenderer caudal peduncle (10%-12% SL vs. 12%-13%), a more forked caudal fin (length of middle caudal-fin lope: 16%-19% SL vs. 19%-23%), and the absence the dorsal and ventral adipose crests on the caudal peduncle behind the vertical of the posterior anal-fin base (vs. present). Three species delimitation tests (assemble species by automatic partitioning (ASAP), automatic barcode gap discovery (ABGD) and generalized mixed yule-coalescent (GMYC)) and phylogenetic analyses reinforce the validity of O. fatmae as a distinct species.

Molecular diversity of Diplura in southern High Appalachian leaf litter

The fauna of Diplura, the two-pronged bristletails (Hexapoda), of the southern Appalachians has received little focused systematic attention. Existing literature suggests the fauna to comprise around a dozen species. Based on a broader DNA barcode-based survey of high elevation litter arthropods in the region, we suggest the fauna to be much richer, with automated species delimitation methods hypothesising as many as 35 species, most highly restricted to single or closely proximate localities. Such a result should not be very surprising for such small, flightless arthropods, although it remains to be seen if other markers or morphology support such high diversity. The region still remains sparsely sampled for these more cryptic elements of the arthropod fauna and much larger numbers of species undoubtedly remain to be discovered.

Molecular differentiation analysis of ten putative species of Fannia (Diptera: Fanniidae) collected in carrion-baited traps from Colombia

The genus Fannia is the most representative of the Fannidae family of true flies with worldwide distribution. Some species are attracted to decomposing materials and live vertebrate animals, which makes them important in forensics, medical and veterinary fields. However, identifying Fannia species can be difficult due to the high similarity in the external morphology of females and limited descriptions and morphological keys. Herein, molecular markers could provide a complementary tool for species identification. However, molecular identification has still limited application since databases contain few data for neotropical species of Fannia. This study assessed the potential of two molecular markers, the COI-3' region and internal transcribed spacer 2 (ITS2), to differentiate 10 putative species of the genus Fannia from Colombia using distance-based and tree-based approaches. The partial ITS2 and/or COI-3' regions allowed molecular diagnosis of six species, while pairs of species Fannia colazorrensis + F. dodgei and F. laclara + F. aburrae are conflicting. Although these results might suggest that conflicting pair species are conspecific, consistent morphological differences between males do not support this hypothesis. The lack of differentiation at the nuclear and mitochondrial molecular markers for the conflicting species may be due to incomplete evolutionary lineage separation, hybridization, or introgression events. In addition, sexual selection on male morphological traits before species-specific differences in molecular markers emerge may partially explain the results. Our study provides a valuable dataset to identify and confirm some Fannia species molecularly. Further, they could be used to associate females and immature stages with their conspecifics as a baseline to deep into their biology, ecology, distribution and potential applications in forensic and medico-veterinary entomology.

Characterising the north-western European species of Phaenoglyphis Förster, 1869 (Hymenoptera: Figitidae: Charipinae) with novel insights from DNA barcode data

Background

The taxonomy of the hymenopteran parasitoid subfamily Charipinae (Hymenoptera: Cynipoidea: Figitidae) has, until recently, been in a state of chaos. While this situation has improved significantly in recent years, most of the efforts were focused on morphological data of typically old specimens. Here, we present the first integrative approach to describe the diversity of the genus Phaenoglyphis Förster, 1869 from north-western Europe.

New information

For seven (of a total of 17) species, we provide DNA barcode data. Phaenoglyphisbelizini Pujade-Villar, 2018 and Phaenoglyphisevenhuisi Pujade-Villar & Paretas-Martínez, 2006 are recorded for the first time from Germany. All DNA barcodes and specimen data were added to the publicly available GBOL and BOLD reference database. The presence of a 6 bp long deletion in the CO1 barcode region that is characteristic to the genus and unique amongst Figitidae supports the monophyly of Phaenoglyphis.

Morphological and Molecular Analysis Identified a Subspecies of Crassostrea ariakensis (Fujita, 1913) along the Coast of Asia

Crassostrea ariakensis (Fujita, 1913) is one of the most important economic and ecological oysters that is naturally distributed along the coast of Asia, separated by the Yangtze River estuary. They are usually compared as different populations, while there is no consensus on whether C. ariakensis in northern and southern areas should be considered as two species or subspecies. Here, we analyzed morphological characteristics, COI, 16s rRNA, mitogenome sequences, and species delimitation analysis (ASAP and PTP) to resolve the intraspecific taxonomic status of the C. ariakensis. Phylogenetic and ASAP analysis highlight that C. ariakensis was divided into N-type and S-type. PTP was unable to differentiate between the two types of C. ariakensis. The divergence time of N-type and S-type C. ariakinsis is estimated to be 1.6 Mya, using the relaxed uncorrelated lognormal clock method. Additionally, significant morphological differences exist between the two groups in terms of the adductor muscle scar color. Despite these differences, the COI (0.6%) and 16S rRNA (0.6%) genetic distance differences between N-type and S-type C. ariakensis has not yet reached the interspecific level. These results suggest that N-type and S-type C. ariakensis should be treated as different subspecies and renamed as C. ariakensis ariakensis subsp. nov and C. ariakensis meridioyangtzensis subsp. nov.

A DNA barcode reference library of Croatian mosquitoes (Diptera: Culicidae): implications for identification and delimitation of species, with notes on the distribution of potential vector species

BACKGROUND

Mosquitoes pose a risk to human health worldwide, and correct species identification and detection of cryptic species are the most important keys for surveillance and control of mosquito vectors. In addition to traditional identification based on morphology, DNA barcoding has recently been widely used as a complementary tool for reliable identification of mosquito species. The main objective of this study was to create a reference DNA barcode library for the Croatian mosquito fauna, which should contribute to more accurate and faster identification of species, including cryptic species, and recognition of relevant vector species.

METHODS

Sampling was carried out in three biogeographical regions of Croatia over six years (2017-2022). The mosquitoes were morphologically identified; molecular identification was based on the standard barcoding region of the mitochondrial COI gene and the nuclear ITS2 region, the latter to identify species within the Anopheles maculipennis complex. The BIN-RESL algorithm assigned the COI sequences to the corresponding BINs (Barcode Index Number clusters) in BOLD, i.e. to putative MOTUs (Molecular Operational Taxonomic Units). The bPTP and ASAP species delimitation methods were applied to the genus datasets in order to verify/confirm the assignment of specimens to specific MOTUs.

RESULTS

A total of 405 mosquito specimens belonging to six genera and 30 morphospecies were collected and processed. Species delimitation methods assigned the samples to 31 (BIN-RESL), 30 (bPTP) and 28 (ASAP) MOTUs, with most delimited MOTUs matching the morphological identification. Some species of the genera Culex, Aedes and Anopheles were assigned to the same MOTUs, especially species that are difficult to distinguish morphologically and/or represent species complexes. In total, COI barcode sequences for 34 mosquito species and ITS2 sequences for three species of the genus Anopheles were added to the mosquito sequence database for Croatia, including one individual from the Intrudens Group, which represents a new record for the Croatian mosquito fauna.

CONCLUSION

We present the results of the first comprehensive study combining morphological and molecular identification of most mosquito species present in Croatia, including several invasive and vector species. With the exception of some closely related species, this study confirmed that DNA barcoding based on COI provides a reliable basis for the identification of mosquito species in Croatia.

Integrative species delimitation and five new species of lynx spiders (Araneae, Oxyopidae) in Taiwan

An accurate assessment of species diversity is a cornerstone of biology and conservation. The lynx spiders (Araneae: Oxyopidae) represent one of the most diverse and widespread cursorial spider groups, however their species richness in Asia is highly underestimated. In this study, we revised species diversity with extensive taxon sampling in Taiwan and explored species boundaries based on morphological traits and genetic data using a two-step approach of molecular species delimitation. Firstly, we employed a single COI dataset and applied two genetic distance-based methods: ABGD and ASAP, and two topology-based methods: GMYC and bPTP. Secondly, we further analyzed the lineages that were not consistently delimited, and incorporated H3 to the dataset for a coalescent-based analysis using BPP. A total of eight morphological species were recognized, including five new species, Hamataliwa cordivulva sp. nov., Hamat. leporauris sp. nov., Tapponia auriola sp. nov., T. parva sp. nov. and T. rarobulbus sp. nov., and three newly recorded species, Hamadruas hieroglyphica (Thorell, 1887), Hamat. foveata Tang & Li, 2012 and Peucetia latikae Tikader, 1970. All eight morphological species exhibited reciprocally monophyletic lineages. The results of molecular-based delimitation analyses suggested a variety of species hypotheses that did not fully correspond to the eight morphological species. We found that Hamat. cordivulva sp. nov. and Hamat. foveata showed shallow genetic differentiation in the COI, but they were unequivocally distinguishable according to their genitalia. In contrast, T. parva sp. nov. represented a deep divergent lineage, while differences of genitalia were not detected. This study highlights the need to comprehensively employ multiple evidence and methods to delineate species boundaries and the values of diagnostic morphological characters for taxonomic studies in lynx spiders.

Taxonomic notes on the genus Baetiella Uéno, 1931 (Ephemeroptera, Baetidae), with description of three new species from Thailand

Based on material recently collected in northern Thailand, the present study provides an updated of the genus Baetiella, including Gratia. It comprises six species in Thailand, three of them being new species: Baetiella (Gratia) narumonae, Baetiella (Gratia) sororculaenadinae, Baetiella (Baetiella) bispinosa, Baetiella (Baetiella) baeisp. nov., Baetiella (Baetiella) lannaensissp. nov. and Baetiella (Baetiella) bibranchiasp. nov.Baetiella (Baetiella) baeisp. nov. can be distinguished from other species by the reduction of the posteromedian protuberances on abdominal tergites I-III, the asymmetrical coniform terminal segment of labial palp, the distal margin of abdominal sternites VII-X each with a row of long, spatulate setae, the dorsal margin of femur with two long, robust setae distally. Baetiella (Baetiella) lannaensissp. nov. is diagnosed by the posteromedian protuberances present on tergites I-VIII, dorsal margin of femur with a regular row of long, rounded, ciliated setae and body surface covered with numerous, dense, rounded scale-like setae. Baetiella (Baetiella) bibranchiasp. nov. can be separated from other species by coxal gills present at the base of forelegs and midlegs. The molecular study based on the mitochondrial gene COI and a larval key to species of Thai Baetiella are also provided.

Integrating mitochondrial and nuclear genomic data to decipher the evolutionary history of Eubranchipus species in Japan

Understanding the genetic diversity and evolutionary history of species is crucial for their conservation and management. In this study, we investigated the genetic diversity and phylogenetic relationships among Eubranchipus species occurring in Japan. Phylogenetic analyses revealed that nuclear and mitochondrial data yield incompatible results. In E. uchidai, nuclear data support the monophyly of the Shimokita area, while mitochondrial data indicate a clustering of Higashidori2 individuals with Hokkaido (Ishikari and Wakkanai) E. uchidai. Similar incongruences were observed in E. hatanakai, where nuclear data favor the monophyly of the Chokai area, while mitochondrial data cluster some Chokai pool 3 individuals with Aizu individuals. These incompatibilities might be caused by mitochondrial gene flow. The findings emphasize the importance of considering both nuclear and mitochondrial data during phylogenetic studies and provide valuable insights into the complex dynamics of migration and genetic exchange in Eubranchipus species.

A review of Nearctic Lathrobium (Coleoptera, Staphylinidae), with revision and descriptions of new flightless species from the mountains of the southeastern U.S

Species of the genus Lathrobium Gravenhorst (Coleoptera: Staphylinidae: Paederinae) from North America north of Mexico are reviewed and 41 species are recognized. Morphology and mitochondrial COI sequence data were used to guide species designations in three flightless lineages endemic to the southern Appalachian Mountains, a biologically diverse region known for cryptic diversity. Using a combination of phylogeny, algorithm-based species delimitation analyses, and genitalic morphology, five new cryptic species are described and possible biogeographic scenarios for their speciation hypothesized: L.balsamense Haberski & Caterino, sp. nov., L.camplyacra Haberski & Caterino, sp. nov., L.islae Haberski & Caterino, sp. nov., L.lividum Haberski & Caterino, sp. nov., L.smokiense Haberski & Caterino, sp. nov. Five additional species are described: L.absconditum Haberski & Caterino, sp. nov., L.hardeni Haberski & Caterino, sp. nov., L.lapidum Haberski & Caterino, sp. nov., L.solum Haberski & Caterino, sp. nov., and L.thompsonorum Haberski & Caterino, sp. nov. Two species are transferred from Lathrobium to Pseudolathra Casey: Pseudolathraparcum (LeConte, 1880), comb. nov. and Pseudolathratexana (Casey, 1905), comb. nov. Twenty-six names are reduced to synonymy. Lectotypes are designated for 47 species. Larvae are described where known, and characters of possible diagnostic value are summarized. Species diagnoses, distributions, illustrations of male and female genitalia, and a key to Lathrobium species known from the Nearctic region (including several introduced species) are provided.

Circumtropical distribution and cryptic species of the meiofaunal enteropneust Meioglossus (Harrimaniidae, Hemichordata)

Hemichordata has always played a central role in evolutionary studies of Chordata due to their close phylogenetic affinity and shared morphological characteristics. Hemichordates had no meiofaunal representatives until the surprising discovery of a microscopic, paedomorphic enteropneust Meioglossus psammophilus (Harrimaniidae, Hemichordata) from the Caribbean in 2012. No additional species have been described since, questioning the broader distribution and significance of this genus. However, being less than a millimeter long and superficially resembling an early juvenile acorn worm, Meioglossus may easily be overlooked in both macrofauna and meiofauna surveys. We here present the discovery of 11 additional populations of Meioglossus from shallow subtropical and tropical coralline sands of the Caribbean Sea, Red Sea, Indian Ocean, and East China Sea. These geographically separated populations show identical morphology but differ genetically. Our phylogenetic reconstructions include four gene markers and support the monophyly of Meioglossus. Species delineation analyses revealed eight new cryptic species, which we herein describe using DNA taxonomy. This study reveals a broad circumtropical distribution, supporting the validity and ecological importance of this enigmatic meiobenthic genus. The high cryptic diversity and apparent morphological stasis of Meioglossus may exemplify a potentially common evolutionary 'dead-end' scenario, where groups with highly miniaturized and simplified body plan lose their ability to diversify morphologically.

Distribution and diversification of Adelphobates, emblematic poison frogs from Brazilian Amazonia

Adelphobates contains three species, and the inaccurate identification of A. quinquevittatus and the scarcity of records of A. castaneoticus complicate inference of their distributions; the latter species occurs in sympatry with A. galactonotus. Our objective was to revise the distributions of Adelphobates by compiling data and modeling habitat suitability, as range limits may be shaped by landscape features and biotic interactions. We initially analyzed the existence of operational taxonomic units within the nominal species and subsequently inferred the observed and potential distributions, taking into account the possible independent lineages for the three species, and we also generated a molecular timetree to understand the chronology of interspecific diversification events. Adelphobates quinquevittatus was found to have a more easterly distribution than previously described, and specimens with phenotypic variation were found to occur in areas inconsistent with the modeling, and A. castaneoticus was concentrated in the Tapajós-Xingu interfluve, surrounded by A. galactonotus. Models indicated that the right bank of the Xingu River is suitable for both species, indeed, both were found there. Despite Adelphobates species having their distributions delimited by major Amazonian rivers, estimated divergence times predate the formation of the modern river network, suggesting that other mechanisms were involved in their diversification.

Utilising public sequence databases to investigate genetic diversity of stoneflies in Medvednica Nature Park

In Medvednica Nature Park, near Croatia's capital Zagreb, urbanisation significantly impacts the fauna. Comprehensive field research has never been conducted in this area, despite the presence of diverse microhabitats and the discovery of several rare species previously unknown in the Croatian fauna. This study provides the Park with first insight into the genetic and morphological diversity of stoneflies, one of the most endangered groups of organisms. Phylogenetic reconstructions and species delineation methods revealed intraspecific haplotype variation in most species (e.g. Brachypteraseticornis, Isoperlagrammatica and Leuctrabraueri), except for Leuctraprima. Additionally, our study has identified isolated populations that merit further in-depth investigation concerning morphology, genetics and ecology.

Hidden in the riffles: A new suckermouth catfish (Mochokidae, Chiloglanis) from the middle Zambezi River system, Zimbabwe

The recent surge in the discovery of hidden diversity within rheophilic taxa, particularly in West and East Africa, prompted a closer examination of the extent to which the current taxonomy may obscure the diversity of riffle-dwelling suckermouth catfishes in the genus Chiloglanis in southern Africa. Currently, the region comprises eight valid species within this genus. Seven of them have relatively narrow geographic distribution ranges except for C.neumanni, which is considered to be widely distributed, occurring from the Buzi River system in the south, and its northern limit being the eastward draining river systems in Tanzania. Recent surveys of the middle Zambezi River system revealed Chiloglanis specimens that were distinguishable from the known species of the genus from southern Africa. Integration of molecular and morphological data indicated that these specimens from the Mukwadzi River represent a new species to science, herein described as Chiloglaniscarnatus Mutizwa, Bragança & Chakona, sp. nov. This species is readily distinguished from its southern African congeners by the possession of a distinctive extended dermal tissue covering the base of the dorsal fin and the possession of ten mandibular teeth (vs 8, 12, or 14 in the other taxa). Results from this study add to the growing evidence of a high level of undocumented diversity within riffle-dwelling taxa in southern Africa.

Molecular and morphometric data provide evidence of intraspecific variation in shape and pigmentation pattern in Otocinclus cocama (Siluriformes: Loricariidae) across major river drainages

Otocinclus cocama, a uniquely colored species of the loricariid catfish genus Otocinclus described solely from the type locality in the lower Ucayali River in northern Peru, is reported occurring in the Tigre River, a tributary to the Marañón River that drains a different section of the Andean Mountain range in the western Amazon. Both populations differ in the number of dark bars spanning the flanks of the body, and we investigated whether these morphotypes constitute distinct species. The body shapes of populations from the Tigre and Ucayali rivers were compared using geometric morphometrics. Although principal component analysis detected a broad overlap between populations, multivariate analysis of variance and linear driscriminat analysis revealed a subtle differentiation between the populations of the two hydrographic basins. Average body shape of the Ucayali River population tend to be slightly higher than that of the Tigre River, with the caudal peduncle stretched vertically in the Ucayali population. Multivariate regression of shape and centroid size revealed an allometric effect of 10.7% (p < 0.001), suggesting that the variation between Tigre and Ucayali populations was purely shape variation. Molecular data of coI, cytb, nd2, and 16S mitochondrial genes indicated a nucleotide diversity range from 0.001 to 0.003, and haplotypic diversity range from 0.600 ± 0.11 to 0.79 ± 0.07. The median-joining haplotype network for the concatenated matrix exhibited two divergent haplogroups related to the geographic area and separated by <10 mutational steps. The molecular species delimitation methods based on distance (automatic barcode gap discovery and assemble species by automatic partitioning) recovered two molecular lineages evolving independently, being one of the lineages formed by individuals from both populations. Tree-based methods (generalized mixed Yule coalescent and Bayesian implementation of the Poisson tree process) recovered similar topologies and supported single lineage recognition. Methods of molecular delimitation of species disclosed the high similarity between the two populations of Otocinclus cocama, further supported by the presence of old haplotypes common to both groups which could indicate that the populations still maintain gene flow. Although the morphological data reveal a subtle variation between both river basins, the molecular data suggest a weak population structuration based on hydrographic areas, but not different species lineages, therefore Otocinclus cocama is composed of a single lineage with two distinct morphotypes.

A cryptic radiation of Caribbean sea slugs revealed by integrative analysis: Cyerce 'antillensis' (Sacoglossa: Caliphyllidae) is six distinct species

Integrative studies have revealed cryptic radiations in several Caribbean lineages of heterobranch sea slugs, raising questions about the evolutionary mechanisms that promote speciation within the tropical Western Atlantic. Cyerce Bergh, 1871 is a genus comprising 12 named species in the family Caliphyllidae that lack the photosynthetic ability of other sacoglossans but are noted for vibrant colours on the large cerata (dorsal leaf-like appendages) that characterize many species. Two species are widely reported from the Caribbean: Cyerce cristallina (Trinchese, 1881) and Cyerce antillensis Engel, 1927. Here, we present an integrative assessment of diversity in Caribbean Cyerce. Four methods of molecular species delimitation supported seven species in samples from the Caribbean and adjacent subtropical Western Atlantic. Six delimited species formed a monophyletic lineage in phylogenetic analyses but were > 9% divergent at the barcoding COI locus and could be differentiated using ecological, reproductive and/or morphological traits. We redescribe C. antillensis, a senior synonym for the poorly known Cyerce habanensis Ortea & Templado, 1988, and describe five new species. Evolutionary shifts in algal host use, penial armature and larval life history might have acted synergistically to promote the rapid divergence of endemic species with restricted distributions in this radiation, substantially increasing global diversity of the genus.

Two new records and description of a new Perinereis (Annelida, Nereididae) species for the Saudi Arabian Red Sea region

Annelid biodiversity studies in the Red Sea are limited and integrative taxonomy is needed to accurately improve reference libraries in the region. As part of the bioblitz effort in Saudi Arabia to assess the invertebrate biodiversity in the northern Red Sea and Gulf of Aqaba, Perinereis specimens from intertidal marine and lagoon-like rocky environments were selected for an independent assessment, given the known taxonomic ambiguities in this genus. This study used an integrative approach, combining molecular with morphological and geographic data. Our results demonstrate that specimens found mainly in the Gulf of Aqaba are not only morphologically different from other five similar Perinereis Group I species reported in the region, but phylogenetic analysis using available COI sequences from GenBank revealed different molecular operational taxonomic units, suggesting an undescribed species, P.kaustianasp. nov. The new species is genetically close and shares a similar paragnath pattern to the Indo-Pacific distributed P.helleri, in particular in Area III and Areas VII-VIII. Therefore, we suggest it may belong to the same species complex. However, P.kaustianasp. nov. differs from the latter mainly in the shorter length of the postero-dorsal tentacular cirri, median parapodia with much longer dorsal Tentacular cirri, posteriormost parapodia with much wider and greatly expanded dorsal ligules. Additionally, two new records are reported for the Saudi Neom area belonging to P.damietta and P.suezensis, previously described only for the Egyptian coast (Suez Canal) and are distributed sympatrically with the new species, but apparently not sympatric with each other.

Species divergence in valleys: the phylogeny of Phrynocephalus forsythii complex and description of a new species

Background

Geographic isolation caused by high-altitude valleys promotes the formation of geographic segregation of species, leading to species differentiation. The subgenus Oreosaura contains viviparous species from the Tibetan Plateau and the vicinity of the Tarim Basin, which can be divided into three species complexes according to their geographical distribution: Phrynocephalus vlangalii, Phrynocephalus theobaldi, and Phrynocephalus forsythii. However, molecular data for the P. forsythii complex are limited and the diversity of this species complex has been greatly underestimated. Therefore, this study aimed to explore the species diversity of Oreosaura and species differentiation within the P. forsythii complex.

Methods

We analysed the species diversity of Oreosaura by combining previous data, constructed a phylogenetic tree of the subgenus based on cytochrome c oxidase subunit I and 16S sequences, and estimated the divergence time.

Results

The results suggest significant genetic differences between the Tarim Basin populations and adjacent mountain valley populations of the P. forsythii complex and that the combination of deep valley landscapes in the high mountains and ice-age events have contributed to the differentiation of the viviparous toad-headed agama lizard, which is a key factor in the phylogenetics of the P. forsythii complex. Furthermore, we identified a population collected from Wuqia County, Xinjiang, as a new species, Phrynocephalus kangsuensis sp. nov. The results will provide data for phylogenetic studies following the P. forsythii complex and help demonstrate that valleys promote the formation of Phrynocephalus species.

Unveiling taxonomic diversity in the deep-sea fish genus Notacanthus (Notacanthiformes: Notacanthidae) with description of Notacanthus arrontei n. sp

Notacanthid fishes constitute a common part of benthopelagic deep-sea fish communities on seamounts and continental slopes around the world. However, their highly conserved morphology and the usual lack of information on deep-water organisms make it difficult to appropriately address their biodiversity. A multidisciplinary approach combining morphological data with a DNA-based species delimitation analyses was used to explore the taxonomy of Notacanthus species. For this purpose, morphological and molecular data were obtained from 43 individuals, and the resulting information was combined with the available data. The results showed the occurrence of Notacanthus arrontei n. sp. from the Iberian Peninsula and highlighted several taxonomic conundrums regarding the Notacanthus genus. For instance, no significant differences were found between Notacanthus indicus and the recently described Notacanthus laccadiviensis, questioning its taxonomic status. Similarly, the result of the species delimitation molecular analysis coincided with previous DNA barcoding studies supporting the snubnosed spiny eel Notacanthus chemnitzii as a species complex that requires further research. Moreover, two unidentified records from the Indian Ocean were confirmed to belong to an unknown species pending formal description, and barcoding data show for the first time the occurrence of the shortfin spiny eel Notacanthus bonaparte in the Australia-New Zealand area. This research confirms the existence of important gaps in the knowledge of notacanthid fishes and represents a step forward toward a better understanding of their biological diversity.

A comprehensive DNA barcoding reference database for Plecoptera of Switzerland

DNA barcoding is an essential tool in modern biodiversity sciences. Despite considerable work to barcode the tree of life, many groups, including insects, remain partially or totally unreferenced, preventing barcoding from reaching its full potential. Aquatic insects, especially the three orders Ephemeroptera, Plecoptera, and Trichoptera (EPT), are key freshwater quality indicators worldwide. Among them, Plecoptera (stoneflies), which are among the most sensitive aquatic insects to habitat modification, play a central role in river monitoring surveys. Here, we present an update of the Plecoptera reference database for (meta)barcoding in Switzerland, now covering all 118 species known from this country. Fresh specimens, mostly from rare or localized species, were collected, and 151 new CO1 barcodes were generated. These were merged with the 422 previously published sequences, resulting in a dataset of 573 barcoded specimens. Our CO1 dataset was delimited in 115 CO1 clusters based on a priori morphological identifications, of which 17% are newly reported for Switzerland, and 4% are newly reported globally. Among the 115 CO1 clusters, 85% showed complete congruence with morphology. Distance-based analysis indicated local barcoding gaps in 97% of the CO1 clusters. This study significantly improves the Swiss reference database for stoneflies, enhancing future species identification accuracy and biodiversity monitoring. Additionally, this work reveals cryptic diversity and incongruence between morphology and barcodes, both presenting valuable opportunities for future integrative taxonomic studies. Voucher specimens, DNA extractions and reference barcodes are available for future developments, including metabarcoding and environmental DNA surveys.

Ice cage: new records and cryptic, isolated lineages in wingless snow flies (Diptera, Limoniidae: Chionea spp.) in German lower mountain ranges

In Earth's history warm and cold periods have alternated. Especially, during the Pleistocene, the alternation between these different climatic conditions has led to frequent range expansions and retractions of many species: while thermophilic species dispersed during warm periods, cold adapted species retracted to cold refugia and vice versa. After the last Pleistocene cycle many cold adapted taxa found refuges in relict habitats in mountain ranges. One example for such a cold adapted relict is the flightless snow fly Chionea araneoides (Dalman, 1816). It can be found in lower mountain ranges of Central Europe exclusively in stone runs and stony accumulations which provide cold microclimates. Imagines develop only in winter. They have strongly restricted ranges and hence experienced strong isolation predicting that local populations may show local adaptation and hence also genetic differentiation. We investigated this for several middle mountain ranges of Germany using the COI barcoding gene. Our analyses revealed two distinct lineages, one in the Bavarian Forest and a second one in all other more northern locations up to Scandinavia. These lineages likely go back to post-Pleistocene isolation and should be studied in more detail in the future, also to confirm the taxonomic status of both lineages. Further, we confirmed former records of the species for Germany and report new records for the federal states of Saxony, Lower Saxony, Saxony-Anhalt and Thuringia. Finally, we provide the first evidence of two types of males for the species, a small and a larger male type.

Species delimitation of tea plants (Camellia sect. Thea) based on super-barcodes

BACKGROUND

The era of high throughput sequencing offers new paths to identifying species boundaries that are complementary to traditional morphology-based delimitations. De novo species delimitation using traditional or DNA super-barcodes serve as efficient approaches to recognizing putative species (molecular operational taxonomic units, MOTUs). Tea plants (Camellia sect. Thea) form a group of morphologically similar species with significant economic value, providing the raw material for tea, which is the most popular nonalcoholic caffeine-containing beverage in the world. Taxonomic challenges have arisen from vague species boundaries in this group.

RESULTS

Based on the most comprehensive sampling of C. sect. Thea by far (165 individuals of 39 morphospecies), we applied three de novo species delimitation methods (ASAP, PTP, and mPTP) using plastome data to provide an independent evaluation of morphology-based species boundaries in tea plants. Comparing MOTU partitions with morphospecies, we particularly tested the congruence of MOTUs resulting from different methods. We recognized 28 consensus MOTUs within C. sect. Thea, while tentatively suggesting that 11 morphospecies be discarded. Ten of the 28 consensus MOTUs were uncovered as morphospecies complexes in need of further study integrating other evidence. Our results also showed a strong imbalance among the analyzed MOTUs in terms of the number of molecular diagnostic characters.

CONCLUSION

This study serves as a solid step forward for recognizing the underlying species boundaries of tea plants, providing a needed evidence-based framework for the utilization and conservation of this economically important plant group.

A DNA barcode library of Austrian geometridae (Lepidoptera) reveals high potential for DNA-based species identification

Situated in the Eastern section of the European Alps, Austria encompasses a great diversity of different habitat types, ranging from alpine to lowland Pannonian ecosystems, and a correspondingly high level of species diversity, some of which has been addressed in various DNA barcoding projects. Here, we report a DNA barcode library of all the 476 species of Geometridae (Lepidoptera) that have been recorded in Austria. As far as possible, species were sampled from different Austrian regions in order to capture intraspecific genetic variation. In total, 2500 DNA barcode sequences, representing 438 species, were generated in this study. For complete coverage of Austrian geometrid species in the subsequent analyses, the dataset was supplemented with DNA barcodes from specimens of non-Austrian origin. Species delimitations by ASAP, BIN and bPTP methods yielded 465, 510 and 948 molecular operational taxonomic units, respectively. Congruency of BIN and ASAP partitions with morphospecies assignments was reasonably high (85% of morphospecies in unique partitions), whereas bPTP appeared to overestimate the number of taxonomic units. The study furthermore identified taxonomically relevant cases of morphospecies splitting and sharing in the molecular partitions. We conclude that DNA barcoding and sequence analysis revealed a high potential for accurate DNA-based identification of the Austrian Geometridae species. Additionally, the study provides an updated checklist of the geometrid moths of Austria.

A new species of Svistella Gorochov, 1987 from Xizang, China (Orthoptera, Trigonidiidae, Trigonidiinae)

The genus Svistella Gorochov, 1987 includes 10 species from Asia, with nine documented in China. In this study, a new species, Svistellayayun He, sp. nov., is described from Xizang, China. Morphologically, it resembles S.rufonotata (Chopard, 1932) but can be distinguished by a smaller inner tympanum, dark-brown setae on the 5th segment of the maxillary palp, and a rounded apex on the ectoparamere. To validate our morphological inferences and support the description of S.yayunsp. nov. as a new species, we performed a PCA based on bioacoustics parameters and molecular analysis. All Svistella species documented in China are distinguished by integrating their songs and DNA barcoding.

Comparative Analysis of the Systematics and Evolution of the Pampus Genus of Fish (Perciformes: Stromateidae) Based on Osteology, Population Genetics and Complete Mitogenomes

Pampus is a widespread species of fish in the western Pacific and Indian Oceans that has significant commercial worth. Its evolutionary history and phylogenetics are still poorly understood, and details on its intraspecific taxonomy are debatable, despite some morphological and molecular research. Here, we analyzed this species using skeletal structure data as well as nuclear (S7 gene) and mitochondrial genetic information (COI, D-loop and mitogenomes). We found that the genetic distance between P. argenteus and P. echinogaster was much smaller than that between other Pampus species, and both maximum likelihood and Bayesian phylogenetic trees yielded almost identical tree topologies. An additional and adjacent M repeat was found in the downstream region of the IQM gene cluster of P. argenteus and P. echinogaster, and the trnL2 gene of P. minor was translocated. The genus Pampus experienced early rapid radiation during the Palaeocene with major lineages diversifying within a relatively narrow timescale. Additionally, three different methods were conducted to distinguish the genus Pampus species, proving that P. argenteus and P. echinogaster are the same species, and P. liuorum is speculated to be a valid species. Overall, our study provides new insights not only into the evolutionary history of Pampus but its intraspecific taxonomy as well.

Molecular Evidence Reveals Taxonomic Uncertainties and Cryptic Diversity in the Neotropical Catfish of the Genus Pimelodus (Siluriformes: Pimelodidae)

Pimelodus is the most speciose genus of the family Pimelodidae, and is amply distributed in the Neotropical region. The species-level taxonomy and phylogenetic relationships within this genus are still poorly resolved, however. These taxonomic problems and the general lack of data have generated major uncertainties with regard to the identification of specimens from different localities. In the present study, we applied a single-locus species delimitation approach to identify the MOTUs found within the genus Pimelodus and provide sound evidence for the evaluation of the species richness of this genus in the different river basins of the Neotropical region. The study was based on the analysis of sequences of the mitochondrial COI gene of 13 nominal species, which resulted in the identification of 24 consensus MOTUs. Only six nominal species were recovered as well-defined molecular entities by both the traditional barcoding analysis and the molecular delimitation methods, while the other seven presented cryptic diversity or persistent taxonomic uncertainties. The lineages identified from the Parnaíba ecoregions, Amazonas Estuary and Coastal Drainages may represent a much greater diversity of Pimelodus species than that recognized currently, although a more detailed study of this diversity will be necessary to provide a more definitive classification of the genus.

Description of a new species of the genus Awaous Valenciennes, 1837 (Gobiiformes: Oxudercidae) from the middle stretch of the Mahanadi River, Odisha, India, with comments on the Awaous species from India

A new species of the genus Awaous (Oxudercidae), Awaous motla sp. nov., is described based on 18 specimens collected from the Mahanadi River near Sonepur, Subarnapur District, and 3 specimens from the same river near Boudh bridge, Boudh District of Odisha, India. This species is distinct from its congeners by having a combination of characteristics: relatively small eyes, diameter of 6.6-8.4 in head length (LH); robust and long snout, 2.0-2.6 in LH; eye diameter 2.7-4.1 in snout length; cephalic sensory pore system interrupted with eight pores; predorsal scales 13-15; longitudinal scale series 55-58; gill rakers 2 + 1 + (6-7) on the first gill arch; teeth small, conical, and in a single row on the upper jaw and multiserial (2-3) on the lower jaw. This species is also differentiated from some of its congeners in the nucleotide composition of the cytochrome c oxidase I gene by 8.3%-13.8% Kimura two-parameter (K2P) distance and belongs to a separate cluster in the maximum likelihood tree analysis. This finding is also supported by the species delimitation analysis based on Assemble Species by Automatic Partitioning. The new species holds high commercial value in its locality and needs special conservation attention for sustainable utilization.

A combined phylogenetic strategy illuminates the evolution of Goniodorididae nudibranchs (Mollusca, Gastropoda, Heterobranchia)

Goniodorididae is a family of small dorid nudibranchs distributed worldwide that feed on entoprocts, ascidians, and bryozoans. The evolutionary relationships between its taxa have been uncertain due to the limited taxa available for phylogenetic analyses; some genera being paraphyletic. The family includes a remarkable number of synonymized genera in which the species richness is unequally distributed, while some genera have dozens of species others are monospecific. Some clades are very uniform morphologically while others are considered highly variable. To increase backbone phylogenetic resolution a target enrichment approach of ultra-conserved elements was aimed at representative Goniodorididae species for the first time. Additionally, we increase species representation by including mitochondrial markers cytochrome c oxidase subunit I and ribosomal RNA 16S as well as nuclear Histone 3 and ribosomal RNA 18S from 109 Goniodorididae species, out of approximately 160 currently valid species. Maximum likelihood and Bayesian inference analyses were performed to infer the phylogeny of the family. As a result, two subfamilies and eleven genera were elucidated. The synonymized genera Bermudella, Cargoa, and Ceratodoris are here resurrected and a new genus, Naisdoris gen. nov., is described. The clades included taxa with shared prey preference, showing that trophic behavior could have driven species evolution and morphological uniqueness within the family Goniodorididae.

A Molecular Phylogenetic Study of the Eye Fluke Philophthalmus lacrymosus (Trematoda: Philophthalmidae) Found in Larus dominicanus (Aves: Laridae) from Brazil

PURPOSE

Species of the genus Philophthalmus are eye flukes with a complex taxonomy, which began to be improved with the help of molecular data only recently. However, most described species have never been placed into a phylogenetic context. In this study, eye flukes previously found on kelp gulls, Larus dominicanus, from Brazil and identified as Philophthalmus lacrymosus were subjected to molecular analysis.

METHODS

For the molecular analyses, we analyzed parasites found in six infected gulls (one worm per bird) collected from different municipalities of the state of Santa Catarina, Brazil. We carried out the amplification and sequencing of the partial region of the 28S and cox1 genes and the data obtained were compared with sequences available to philophthalmid species and subjected to phylogenetic analysis.

RESULTS

The isolates of P. lacrymosus from Brazil grouped in well-supported clades with five other species of Philophthalmus with sequences available for comparison. Interspecific divergences of 0.1-1.6% in 28S and 8.2-14.9% in cox1 were found in relation to other isolates of Philophthalmus spp. Two cox1 haplotypes differing in one nucleotide (0.1%) were found between the six eye flukes isolates in gulls from different localities. The Brazilian isolates grouped in a subclade with parasites identified as P. lacrymosus in Portugal; however, the molecular divergences found in cox1 (8.2-8.5%) strongly suggest that these isolates belong to different species. The phylogenetic trees obtained and the intergeneric divergences to species of the genera Cloacitrema and Parorchis did not support the validity of the genus Natterophthalmus, for which P. lacrymosus was proposed as the type species in the past.

CONCLUSION

As P. lacrymosus was described from Brazil, we recommend that this name be applied to the South American isolates and that the Portuguese isolates be provisionally considered as Philophthalmus sp., a probable cryptic species. Moreover, data obtained supports the previous morphology-based synonymizing between Natterophthalmus and Philophthalmus. Considering our results and most of previous reports of P. lacrymosus in South America, we suggest this species presents a marine life cycle.

Enigmatic and extravagant genitalia in the spider genus Mastigusa (Araneae, Cybaeidae) - a taxonomic revision

Mastigusa is a genus of small palearctic spiders that has recently been moved to the family Cybaeidae after the first inclusion of the genus in a phylogenetic matrix. Three species are currently recognised: M. arietina , M. lucifuga and M. macrophthalma . The status and delimitation, though, has always been problematic due to inconsistency in the characters used to discriminate between these, leading to great confusion in identity and distribution. We present a detailed morphological redescription of the genus and a taxonomic revision of the included species by the combined use of morphological data and molecular species-delimitation techniques based on the mitochondrial COI gene. The status of the three currently described species has been reevaluated and Mastigusa diversa was revalidated based on material from the Iberian Peninsula, North Africa and the United Kingdom. The distribution of Mastigusa species is updated based on novel taxonomic considerations, and comments on the natural history and ecological differences observed in the species are provided. ZooBank: urn:lsid:zoobank.org:pub:AAD3FAED-440F-4295-B458-455B1D913F81.

Discovery of a new species of Synergus (Hymenoptera, Cynipidae, Synergini) based on morphology and molecular data

A new species of gall inquiline, Synergusdilatatussp. nov., is described from Hubei Province, China. Morphological descriptions, photographs and biological information are provided. Mitochondrial cytochrome oxidase (COI) sequences of the new species were newly obtained and a molecular species delimitation analysis of 12 species of Synergus performed using the ASAP method recovered 16 molecular operational taxonomic units, providing support for recognition of the new species. The results also highlight a few conflicts between morphological and molecular species delimitations in Synergus.