ABGD, Automatic Barcode Gap Discovery for primary species delimitation

Topology Testing and Demographic Modeling Illuminate a Novel Speciation Pathway in the Greater Caribbean Sea Following the Formation of the Isthmus of Panama

Recent genomic analyses have highlighted the prevalence of speciation with gene flow in many taxa and have underscored the importance of accounting for these reticulate evolutionary processes when constructing species trees and generating parameter estimates. This is especially important for deepening our understanding of speciation in the sea where fast-moving ocean currents, expanses of deep water, and periodic episodes of sea level rise and fall act as soft and temporary allopatric barriers that facilitate both divergence and secondary contact. Under these conditions, gene flow is not expected to cease completely while contemporary distributions are expected to differ from historical ones. Here, we conduct range-wide sampling for Pederson's cleaner shrimp (Ancylomenes pedersoni), a species complex from the Greater Caribbean that contains three clearly delimited mitochondrial lineages with both allopatric and sympatric distributions. Using mtDNA barcodes and a genomic ddRADseq approach, we combine classic phylogenetic analyses with extensive topology testing and demographic modeling (10 site frequency replicates × 45 evolutionary models × 50 model simulations/replicate = 22,500 simulations) to test species boundaries and reconstruct the evolutionary history of what was expected to be a simple case study. Instead, our results indicate a history of allopatric divergence, secondary contact, introgression, and endemic hybrid speciation that we hypothesize was driven by the final closure of the Isthmus of Panama and the strengthening of the Gulf Stream Current ~3.5 Ma. The history of this species complex recovered by model-based methods that allow reticulation differs from that recovered by standard phylogenetic analyses and is unexpected given contemporary distributions. The geologically and biologically meaningful insights gained by our model selection analyses illuminate what is likely a novel pathway of species formation not previously documented that resulted from one of the most biogeographically significant events in Earth's history.

Predicting genetic biodiversity in salamanders using geographic, climatic, and life history traits

The geographic distribution of genetic variation within a species reveals information about its evolutionary history, including responses to historical climate change and dispersal ability across various habitat types. We combine genetic data from salamander species with geographic, climatic, and life history data collected from open-source online repositories to develop a machine learning model designed to identify the traits that are most predictive of unrecognized genetic lineages. We find evidence of hidden diversity distributed throughout the clade Caudata that is largely the result of variation in climatic variables. We highlight some of the difficulties in using machine-learning models on open-source data that are often messy and potentially taxonomically and geographically biased.

Intraspecific diversity of Myrmecophilus acervorum (Orthoptera: Myrmecophilidae) indicating an ongoing cryptic speciation

Myrmecophilus acervorum, previously considered a parthenogenetic species widely-distributed in Europe, has been observed to have both sexes in populations inhabiting the central part of the distribution range. Specimens from those heterosexual populations have been found being infected with Wolbachia. New mitochondrial data (COI and 16S markers) revealed the well-supported differentiation of M. acervorum populations inhabiting western Polesie (Poland) and southern Europe. In turn, analyses of EF1α marker support the hypothesis on the unfinished lineage sorting at the nuclear DNA level. Interestingly, we found that parthenogenetic populations inhabiting western Polesie are infected with Wolbachia belonging to supergroup A, while endosymbionts occurring in sexual populations of M. acervorum observed in Romania belong to supergroup B. Furthermore, new and potentially diagnostic characteristics in the external structures of the eyes of M. acervorum were identified. The surface of ommatidia in specimens occurring in southern Europe was smooth. In contrast, the ommatidia surface of individuals collected in Poland was visibly sculptured. To sum up, the significant genetic variability found in the present case, and the differentiating morphological character, are almost certainly effects of cryptic species being present within M. acervorum. This is indicative of ongoing speciation within the populations of this insect, and of simultaneous unfinished lineage sorting at the nuclear DNA level.

Phylogenetics and species delimitation of the recluse spider, Loxosceles rufescens (Araneae: Sicariidae) populations invading Bangkok, Thailand

The Mediterranean recluse spider, Loxosceles rufescens, has been discovered for the first time inhabiting human dwellings in Bangkok, Thailand. Expeditions across 39 localities revealed five establishments with L. rufescens populations. The highest density was recorded in a storage house on Yaowarat Road, located in the heart of Bangkok's Chinatown, where 315 individuals were found, including adults, juveniles, and spiderlings. This medically significant spider's presence in such a densely populated urban area raises concerns about potential envenomation risks. Thirteen specimens of L. rufescens were extracted for DNA and sequenced for molecular phylogenetic analyses. COI and ITS2 markers were used to investigate relationships within L. rufescens and across available Loxosceles species sequences. Results indicate COI is superior for resolving species-level genetic clusters compared to ITS2. Surprisingly, L. rufescens individuals from the same house were found in significantly distant COI lineages, suggesting mtDNA may not be suitable for studying intra-specific phylogeography in this case. Species delimitation methods ABGD and ASAP demonstrated promising results for both COI and ITS2, while bPTP and GMYC tended to overestimate species numbers. ITS2 exhibited high sequence similarity in L. rufescens, suggesting potential utility as a barcoding marker for identification of this globally distributed species. Genetic distance analyses revealed a potential barcoding gap (K2P) of 8-9 % for COI and <2 % for ITS2 in Loxosceles. This study contributes valuable sequence data for the medically important genus Loxosceles and highlights the need for integrative approaches in understanding its evolution and spread. The findings have important implications for pest management strategies and public health in urban environments.

Phylogeography of the Sinica Group of Macaques in the Himalayas: Taxonomic and Evolutionary Implications

Owing to the taxonomic incongruence between the morphological features and genetic relationships of the sinica group of macaques (genus Macaca), the taxonomy of this macaque group has remained inconclusive. We aimed to resolve the taxonomic quandary and improve our understanding of the historical biogeography of the group by including macaque DNA samples from previously unsampled areas in the Himalayas. We sequenced and analyzed three mitochondrial DNA loci [cytochrome b (CYTB), cytochrome oxidase subunit 1 (COI) and D-loop; 2898 bp] for sequence polymorphism, phylogenetics, species delimitation, and ancestral area reconstruction. We confirmed the occurrence of Arunachal macaque (Macaca munzala) on the southern slopes of the Eastern Himalayas in the Xizang Zizhiqu (Tibet Autonomous Region) of China. The results revealed that the sinica group of macaques is a parapatric species group composed of seven distinct species. Phylogenetic and species delimitation analyses revealed that the two previously considered subspecies of Assamese macaques (the eastern subspecies M. assamensis assamensis and the western subspecies M. a. pelops) are two distinct species. The eastern Assamese macaque is a sister species to the Tibetan macaque, whereas the western Assamese macaque and Arunachal macaque are the closest genetic sister species. The sinica group of macaques underwent five vicariance and seven dispersal radiations in the past, which mainly coincided with the Quaternary climatic oscillations between the late Pliocene and the late Pleistocene. By integrating our phylogenetic and ancestral area reconstruction results with findings from previous paleontological and molecular studies, we propose a robust hypothesis about the phylogeography of the sinica group of macaques.

Naming the other cousin: A new goldie barb (Cyprinidae: Smiliogastrininae) from the northeast escarpment in South Africa, with proposed taxonomic rearrangement of the goldie barb group in southern Africa

A growing body of evidence indicates that the global diversity of freshwater fishes has not been fully documented. Studies of freshwater fishes that were previously thought to be morphologically variable have revealed the existence of deeply divergent lineages, with many distinct species. In southern Africa a number of Enteromius species exhibit either exceedingly wide or divided distribution patterns that should be rare for freshwater fishes with limited dispersal opportunities between river systems. One such species is the sidespot barb, Enteromius neefi. As currently defined, E. neefi has a disjunct distribution that is divided between rivers in the northeast escarpment in South Africa and Eswatini, and tributaries of the Upper Zambezi in Zambia and southern Congo in the Democratic Republic of Congo, with a large geographic gap between these two populations. With the use of molecular and morphological methods, the level of divergence between the two populations was examined, and a new species was described from the Steelpoort River in the Limpopo River system of South Africa. Findings from this study provide further evidence for a number of taxonomic problems within the goldie barbs of southern Africa, and some taxonomic rearrangements are proposed for this group.

Biogeography of larval trematodes in the freshwater snail, Semisulcospira libertina: a comparison of the morphological and molecular approaches

While biogeographic patterns of free-living organisms are well documented, the biogeography of parasitic fauna remains largely unclear. Due to morphological similarities, parasites are often difficult to identify without the aid of molecular genetics, further complicating the interpretation of their biogeographic patterns. We investigated trematode parasites infecting the East Asian freshwater snail Semisulcospira libertina to understand their biogeography and to evaluate how molecular approaches influence the interpretation of biogeographic patterns of the trematode fauna. We identified 46 genetically delimited species from 19 morphologically distinguishable trematodes infecting S. libertina and found that their species richness was negatively correlated to latitude. We also found that potential definitive host (fishes) richness and host body size were positively correlated with trematode species richness, suggesting that host attributes are essential factors shaping the biogeographic pattern in trematodes. These trends were observed irrespective of species identification methods, demonstrating that classical morphological identification can also effectively identify the latitudinal gradient pattern in trematodes. We further detected the distance decay of similarity in trematode communities, although this trend was only detectable in the biogeographic dataset based on molecular identification. Our study showed that morphological identification sufficiently reflects the latitudinal richness gradient while molecular identification is essential to estimate accurate local species richness and increase the resolution of the large-scale pattern of population similarities in the trematode communities.

New insights into the phylogeny of Carasobarbus Karaman, 1971 (Actinopterygii, Cyprinidae) with the description of three new species

Fishes from the genus Carasobarbus, widely distributed throughout the river systems of North Africa and West Asia, are commonly referred to as Himris. In the Persian Gulf basin, they are widespread and are also found in fast-flowing rivers or the deeper regions of lakes. In this region, representation of these fishes in scientific collections is scarce, and except for C. luteus, the other species are very poorly documented and frequently misidentified due to their similarities. In this study we analysed the relationships among Carasobarbus species using mitochondrial genes (Cyt b, COI) and present morphological characters based on examinations. Our results revealed three new species which we describe here. Carasobarbus doadrioi, new species, is distinguished by 40-44 scales on the lateral line and a prominent black blotch on end of caudal peduncle in specimens < 85 mm SL. Carasobarbus hajhosseini, new species is distinguished by 32-34 scales on the lateral line and long head length (20-24% SL). Carasobarbus saadatii, new species, is distinguished by 38-40 scales on the lateral line and short head length (19-20% HL). In the Persian Gulf basin, Carasobarbus species exhibit uncorrected genetic distances of 1.6 to 5.5% in the COI barcode region and 2.6% to 9.9% in the Cyt b gene. This study highlights the importance of investigating the unexplored diversity that exists within poorly sampled and understudied freshwater fish group. Such investigations are essential for developing a comprehensive understanding of the true extent of biodiversity, which is critical for informing effective conservation and protection strategies.

Molecular phylogeny and species diversity of the genus Dichaetophora Duda and related taxa (Diptera: Drosophilidae)

Our intensive surveys of wild drosophilids in East and Southeast Asia discovered a great species diversity (more than 100 putatively new species) of the genus Dichaetophora, which is currently comprised of 67 formally described species assigned into five species groups, i.e., agbo, tenuicauda, acutissima, sinensis and trilobita. In the present study, we delimited species from a huge amount of samples of Dichaetophora and allied taxa (the genus Mulgravea and the subgenus Dudaica of Drosophila) collected from a wide range of the Oriental and east Palearctic regions. We first sorted all specimens into morpho-species, and representative specimen(s) selected from each morpho-species were subjected to barcoding of COI (the cytochrome c oxidase subunit I gene) sequences. The applied ASAP (Assemble Species by Automatic Partitioning) analysis estimated a total of 166 to 168 MOTUs (molecular operational taxonomic units). Integrating this result with morphological evidence from re-examined, detailed structures of male terminalia, we recognized a total of 144 (109 new and 35 known) species in our sample. Out of them, 83 species representing the supraspecific taxa of Dichaetophora, Mulgravea and Dudaica were selected, along with 33 species from major genera and subgenera of Drosophila in the tribe Drosophilini, as in-group and four species from the tribe Colocasiomyini as out-group for phylogenetic reconstruction based on 12 nuclear gene markers. In the trees constructed by the maximum likelihood and Bayesian inference methods, the three focal taxa (i.e., Dichaetophora, Mulgravea and Dudaica) formed a clade provisionally called the "pan-Dichaetophora". Within this large clade, the agbo, tenuicauda, sinensis and trilobita groups of Dichaetophora, Mulgravea and Dudaica were recovered as monophyletic groups, but Dichaetophora and its acutissima group were regarded as paraphyletic. In addition, two clusters were recognized among ungrouped species of Dichaetophora. Thus, the present study has uncovered some issues concerning the taxonomy of the pan-Dichaetophora. Such issues will be addressed elsewhere in the phylogenetic reclassification of the pan-Dichaetophora, along with descriptions/redescriptions of a large number of new/known species delimited in the present study.

Unravelling the Molecular Identity of Bulgarian Jumping Plant Lice of the Family Aphalaridae (Hemiptera: Psylloidea)

Psyllids (Hemiptera: Psylloidea) are plant sap-sucking insects whose identification is often difficult for non-experts. Despite the rapid development of DNA barcoding techniques and their widespread use, only a limited number of sequences of psyllids are available in the public databases, and those that are available are often misidentified. Here, we provide 80 sequences of two mitochondrial genes, cytochrome c oxidase I (COI) and cytochrome b (Cytb), for 25 species of Aphalaridae, mainly from Bulgaria. The DNA barcodes for 15 of these species are published for the first time. In cases where standard primers failed to amplify the target gene fragment, we designed new primers that can be used in future studies. The distance-based thresholds for the analysed species were between 0.0015 and 0.3415 for COI and 0.0771 and 0.4721 for Cytb, indicating that the Cytb gene has a higher interspecific divergence, compared to COI, and therefore allows for more accurate species identification. The species delimitation based on DNA barcodes is largely consistent with the differences resulting from morphological and host plant data, demonstrating that the use of DNA barcodes is suitable for successful identification of most aphalarid species studied. The phylogenetic reconstruction based on maximum likelihood and Bayesian inference analyses, while showing similar results at high taxonomic levels to previously published phylogenies, provides additional information on the placement of aphalarids at the species level. The following five species represent new records for Bulgaria: Agonoscena targionii, Aphalara affinis, Colposcenia aliena, Co. bidentata, and Craspedolepta malachitica. Craspedolepta conspersa is reported for the first time from the Czech Republic, while Agonoscena cisti is reported for the first time from Albania.

Unveiling ophiuroid biodiversity across North Atlantic habitats via an integrative perspective

The depths of the North Atlantic Ocean host a species-rich fauna providing heterogeneous habitats from thermal vent fields to cold-water coral reefs. With the increasing threat of destruction of deep-sea habitats due to human impacts, such as demersal fishing and the beginning of deep-sea mining, an analysis of the diversity and distribution of species is crucial for conservation efforts. Brittle stars occur in high biomasses, contributing to the biodiversity of the seafloor. Specimens were collected during several scientific expeditions to gain a more detailed insight into the brittle star diversity in the North Atlantic Ocean. An integrative approach to identify the species with DNA barcoding (mtCOI) in combination with morphological studies revealed 24 species. Most species have been previously identified in the North Atlantic, but sequences for 13 species are newly added to public repositories. Additionally, the MALDI-TOF-MS proteomic analysis was successfully applied for 197 specimens with known COI barcodes. Results are congruent with other molecular species delimitations demonstrating the functionality of proteomics for the identification of brittle stars. This dataset significantly expands our understanding of the taxonomic and genetic diversity of brittle stars and contributes to publicly available data. It emphasizes the importance of considering habitat heterogeneity for large scale patterns of biodiversity.

Congruent patterns of cryptic cladogenesis revealed using RADseq and Sanger sequencing in a velvet worm species complex (Onychophora: Peripatopsidae: Peripatopsis sedgwicki)

In the present study, first generation DNA sequencing (mitochondrial cytochrome c oxidase subunit one, COI) and reduced-representative genomic RADseq data were used to understand the patterns and processes of diversification of the velvet worm, Peripatopsis sedgwicki species complex across its distribution range in South Africa. For the RADseq data, three datasets (two primary and one supplementary) were generated corresponding to 1,259-11,468 SNPs, in order to assess the diversity and phylogeography of the species complex. Tree topologies for the two primary datasets were inferred using maximum likelihood and Bayesian inferences methods. Phylogenetic analyses using the COI datasets retrieved four distinct, well-supported clades within the species complex. Five species delimitation methods applied to the COI data (ASAP, bPTP, bGMYC, STACEY and iBPP) all showed support for the distinction of the Fort Fordyce Nature Reserve specimens. In the main P. sedgwicki species complex, the species delimitation methods revealed a variable number of operational taxonomic units and overestimated the number of putative taxa. Divergence time estimates coupled with the geographic exclusivity of species and phylogeographic results suggest recent cladogenesis during the Plio/Pleistocene. The RADseq data were subjected to a principal components analysis and a discriminant analysis of principal components, under a maximum-likelihood framework. The latter results corroborate the four main clades observed using the COI data, however, applying additional filtering revealed additional diversity. The high overall congruence observed between the RADseq data and COI data suggest that first generation sequence data remain a cheap and effective method for evolutionary studies, although RADseq does provide a far greater resolution of contemporary temporo-spatial patterns.

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.

A window on remarkable cryptic diversity of the Merodon planifacies subgroup (Diptera: Syrphidae) in the Afrotropical Region

The genus Merodon Meigen (Diptera: Syrphidae) is one of the most species-rich hoverfly genera distributed across the Palaearctic and Afrotropical regions. In the Palaearctic, the genus Merodon boasts 195 described species, while its Afrotropical region pales in comparison, with a mere 17 species documented thus far. As a result of 8 years of fieldwork conducted in the Republic of South Africa, in this paper, we present the description of 11 new species for science with a description of immature stages for 2 species, which increases the diversity of this genus in the Afrotropical region by remarkable 39%. These revelations are based on integrating morphology, molecular analysis (COI gene and 28S rRNA) and geometric morphometry. All described species belong to the Merodon planifacies subgroup, the Merodon desuturinus lineage and, within that, to the Afrotropical Merodon melanocerus group. Additionally, we provide an illustrated key to 15 species belonging to the subgroup, a detailed discussion on relevant taxonomic characters, a morphological diagnosis, a distribution map and clarification of the association between M. capi complex and host plants from the genus Merwilla.

An expanded phylogeny of the genus Pseudamnicola (Gastropoda; Truncatelloidea; Hydrobiidae) across the Mediterranean Basin

The genus Pseudamnicola Paulucci, 1878, is commonly found throughout the Mediterranean region. The genus displays considerable levels of endemism, accompanied by notable systematic and taxonomic ambiguity. However, the application of molecular data has proven highly effective in clarifying taxonomy and unveiling the diversity of cryptic species within the genus. Therefore, we employed all cytochrome c oxidase subunit I sequence data available and generated new ones from Greece to infer the phylogeny of the genus throughout its Mediterranean range and estimate the divergence times as well as the ancestral area of diversification. Our phylogenetic and time-estimate analyses demonstrate that with 36 to 38 extant Pseudamnicola species and genetic divergences across species ranging from 0.5% to 11.9% on average, the genus underwent relatively recent diversification during late Miocene (6.53 Ma), and the primary speciation events occurred during Plio-Pleistocene. The Italian Peninsula and Islands and the Ionian Drainages as defined by the Freshwater Ecoregions of the World are the ancestral regions of the genus following two different dispersal routes. Our study contributes to deepening our understanding of Pseudamnicola phylogeny by using data from throughout its range for the first time. This phylogeny provides evidence and confirms previous studies that relatively recent habitat isolation, followed by founder and dispersal events, has been one of the primary reasons for the evolution of the genus Pseudamnicola in the Mediterranean basin.

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.

Intra- and interspecific variation of Amblyomma ticks from southern Africa

BACKGROUND

Amblyomma spp. ticks, known for their long mouthparts, bright ornate appearance and aggressive hunting behaviour, are vectors of a number of important pathogens. In southern Africa, 17 Amblyomma spp. are currently documented. Of these species, Amblyomma hebraeum and Amblyomma variegatum have been well studied due to their wide geographical range and their status as competent vectors of pathogens that are of veterinary and medical importance. Studies on other Amblyomma spp. in southern Africa have been neglected, fostering ongoing debates on the validity of certain species such as Amblyomma pomposum. This study investigated the inter- and intra-species variation of Amblyomma ticks collected in southern Africa, focusing on resolving the dispute about A. pomposum and A. variegatum being distinct species.

METHODS

Four Amblyomma tick species were collected from Angola, Mozambique, South Africa, Zambia and Zimbabwe, and were identified morphologically as Amblyomma eburneum (208), A. hebraeum (4758), A. pomposum (191) and A. variegatum (2577) using identification keys. Gene amplification targeting the 12S and 16S rRNA, cytochrome oxidase I, cytochrome B and internal transcribed spacer-2 genes was conducted for 204 ticks, for which varying success was achieved during amplification for each of the markers. Maximum likelihood analyses were performed in IQ-TREE.

RESULTS

The phylogenetic topologies and ABGD analyses of each individual gene clustered A. pomposum within the A. variegatum clade, while clearly separating A. eburneum and A. hebraeum from all other species. None of the genetic markers indicated intraspecific structuring on the basis of geographical origin, despite great distances between sampling sites.

CONCLUSION

Our study concludes that there is insufficient molecular evidence to differentiate A. pomposum and A. variegatum from each other. We highlight the need for whole mitochondrial genome sequencing of these two species to resolve the ongoing controversies. Furthermore, we propose mating and hybrid viability studies between the two species to confirm their reproductive isolation.

Diversity of lichen mycobionts and photobionts and their relationships in the Ny-Ålesund region (Svalbard, High Arctic)

Lichens are dual organisms, with one major mycobiont and one major photobiont in each lichen symbiosis, which can survive extreme environmental conditions in the Arctic. However, the diversity and distribution of lichen photobionts in the Arctic remain poorly understood compared to their mycobiont partners. This study explored the diversity of lichen mycobionts and photobionts in 197 lichen samples collected from the Ny-Ålesund region (Svalbard, High Arctic). The nuclear ribosomal internal transcribed spacer (ITS) regions were sequenced and phylogenetic analyses were performed. The relationships between mycobionts and photobionts, as well as the association patterns, were also investigated. A total of 48 species of lichen mycobionts (16 families, nine orders) and 31 species/lineages of photobionts were identified. These 31 photobiont species belonged to one class (Trebouxiophyceae) and five genera, including 22 species of Trebouxia, five species of Asterochloris, two species of Chloroidium, one species of Symbiochloris, and one species of Coccomyxa. The results indicated that most analyzed lichen mycobionts could associate with multiple photobiont species, and the photobionts also exhibited a similar pattern. The results provided an important reference dataset for characterizing the diversity of lichen mycobionts and photobionts in the High Arctic region.

Unveiled species diversity of moss-feeding mites (Stigmaeidae: Eustigmaeus): a research on their distribution, habitat, and host plant use in Japan

The genus Eustigmaeus Berlese, 1910 represents the unique phytophagous group within the superfamily Raphignathoidea. Four species within this genus have been known to inhabit mosses and feed on them as larvae, nymphs, and adults. However, the interactions with mosses have remained poorly understood. In order to reveal the diversity and host-plant use of the moss-feeding species, we conducted an extensive field study in Japan. This study revealed an array of moss-feeding species inhabiting various moss species, with 10 morphologically distinctive species newly documented in Japan. Through DNA barcoding based on cytochrome c oxidase subunit I (COI) sequences, these morphospecies were recovered as distinct entities. Notably, the host-plant use of four species was elucidated. Among these, Eustigmaeus sp. 9 exhibited polyphagy, while three species (Eustigmaeus spp. 1-3) demonstrated varying degrees of host specificity, each using moss species from the Hypnales, Philonotis, and Dicranidae, respectively. While a few moss-feeding species were frequently found in the same geographic area, more than one species rarely co-occurred within the same moss colonies. Eustigmaeus offers a unique study system, with its diverse moss-feeding species and indications of specific host plant use. Consequently, the moss-feeding Eustigmaeus serves as a valuable model for exploring the macroevolutionary patterns underlying diversification in moss-feeding arthropods.

Deciphering the Plastome and Molecular Identities of Six Medicinal "Doukou" Species

The genus Amomum includes over 111 species, 6 of which are widely utilized as medicinal plants and have already undergone taxonomic revision. Due to their morphological similarities, the presence of counterfeit and substandard products remains a challenge. Accurate plant identification is, therefore, essential to address these issues. This study utilized 11 newly sequenced samples and extensive NCBI data to perform molecular identification of the six medicinal "Doukou" species. The plastomes of these species exhibited a typical quadripartite structure with a conserved gene content. However, independent variation shifts of the SC/IR boundaries existed between and within species. The comprehensive set of genetic sequences, including ITS, ITS1, ITS2, complete plastomes, matK, rbcL, psbA-trnH, and ycf1, showed varying discrimination of the six "Doukou" species based on both distance and phylogenetic tree methods. Among these, the ITS, ITS1, and complete plastome sequences demonstrated the highest identification success rate (3/6), followed by ycf1 (2/6), and then ITS2, matK, and psbA-trnH (1/6). In contrast, rbcL failed to identify any species. This research established a basis for a reliable molecular identification method for medicinal "Doukou" plants to protect wild plant resources, promote the sustainable use of medicinal plants, and restrict the exploitation of these resources.

Delimitation of the widely distributed Palearctic Stenodema species (Hemiptera, Heteroptera, Miridae): insights from molecular and morphological data

Species delimitation presents a significant challenge in biology, particularly in systematics. Here, an integrative approach is employed to assess the species boundaries of widely distributed Palearctic Stenodema species. Due to their diversity, wide distribution, and the absence of comprehensive morphological and molecular data for most species, revising Stenodema is both daunting and time-consuming. Our study focuses on detailed examinations of male and female genitalia, coupled with phylogenetic analyses based on two mitochondrial markers (cytochrome c oxidase subunit I and 16S rRNA) and species delimitation analyses. Eight species with wide distributions are reviewed, Stenodematrispinosa Reuter, 1904 is synonymized with S.pilosa (Jakovlev, 1889), and a lectotype for Stenodematuranica Reuter, 1904 is designated. Morphological and molecular data effectively distinguish all species, revealing distinct clades and relationships. Notably, S.calcarata and S.pilosa form a well-supported clade, while S.virens and S.turanica share a lineage with Nearctic species. Stenodemarubrinervis and S.sibirica are morphologically similar and form a distinct clade in all phylogenies. Species delimitation analyses confirm the separation of all studied species, and genetic distances suggest the potential existence of cryptic species within S.calcarata and S.pilosa. This study highlights the advantages of integrative taxonomy in delimiting species with intricate and relatively recent phylogeographic histories.

COI Barcodes combined with multilocus data for representative Aporia taxa shed light on speciation in the high altitude Irano-Turanian mountain plateaus (Lepidoptera: Pieridae)

Even though the high plateaus of Qinghai-Tibet and Iran share many faunal elements, the historical biogeography of the species present in this area are not very well understood. We present a complete COI barcode library for Aporia Hübner and a first comprehensive phylogeny for the genus including all known species and majority of subspecies using ten available genes (COI-COII, ND1, ND5, Cytb, EF-1a, Wg, 16S, 28S-D2/D3 and 28S-D8). We then focus on A. leucodice (Eversmann, 1843) and related taxa in order to resolve some long-standing taxonomic issues in this species-group. Based on DNA sequence data as well as morphology, we raise Aporia illumina (Grum-Grshimailo 1890) stat. nov. (= pseudoillumina Tshikolovets 2021 syn. nov.) as a distinct species and designate a lectotype; synonymize Aporia leucodice leucodice Eversmann, 1843 (= A. l. morosevitshae Sheljuzhko, 1908 syn. nov.); and describe a new species, Aporia ahura sp. nov., from the Central Alborz Mountains in northern Iran.

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.

Endless forms most frustrating: disentangling species boundaries in the Ramalina decipiens group (Lecanoromycetes, Ascomycota), with the description of six new species and a key to the group

Oceanic islands have been recognized as natural laboratories in which to study a great variety of evolutionary processes. One such process is evolutionary radiations, the diversification of a single ancestor into a number of species that inhabit different environments and differ in the traits that allow them to exploit those environments. The factors that drive evolutionary radiations have been studied for decades in charismatic organisms such as birds or lizards, but are lacking in lichen-forming fungi, despite recent reports of some lineages showing diversification patterns congruent with radiation. Here we propose the Ramalina decipiens group as a model system in which to carry out such studies. This group is currently thought to be comprised of five saxicolous species, all of them endemic to the Macaronesian region (the Azores, Madeira, Selvagens, Canary and Cape Verde islands). Three species are single-island endemics (a rare geographic distribution pattern in lichens), whereas two are widespread and show extreme morphological variation. The latter are suspected to harbor unrecognized species-level lineages. In order to use the Ramalina decipiens group as a model system it is necessary to resolve the group's phylogeny and to clarify its species boundaries. In this study we attempt to do so following an integrative taxonomy approach. We constructed a phylogenetic tree based on six molecular markers, four of which are newly developed and generated competing species hypotheses based on molecular (species discovery strategies based on both single locus and multilocus datasets) and phenotypic data (unsupervised clustering algorithms based on morphology, secondary chemistry and geographic origin). We found that taxonomic diversity in the Ramalina decipiens group has been highly underestimated in previous studies. In consequence, we describe six new species, most of them single-island endemics and provide a key to the group. Phylogenetic relationships among species have been reconstructed with almost full support which, coupled with the endemic character of the group, makes it an excellent system for the study of island radiations in lichen-forming fungi. Citation: Blázquez M, Pérez-Vargas I, Garrido-Benavent I, et al. 2024. Endless forms most frustrating: disentangling species boundaries in the Ramalina decipiens group (Lecanoromycetes, Ascomycota), with the description of six new species and a key to the group. Persoonia 52: 44-93. https://doi.org/10.3767/persoonia.2024.52.03 .

Substrate specialisation drives an unexpectedly diverse radiation in barking geckos (Ptenopus: Gekkonidae)

Barking geckos (genus Ptenopus) are terrestrial, burrowing lizards endemic to southern Africa, currently with three recognised species. Two species are range-restricted (P. kochi and P. carpi) and display clear differences in substrate preference (soft sand vs. hard gravel). The third and most widespread species, P. garrulus, occurs on a variety of substrates of differing hardness, across potential geographic barriers, and over a steep climatic gradient. Variations in morphology and advertisement calls indicates that P. garrulus may be a species complex. Two subspecies of P. garrulus are currently recognised: P. g. maculatus and P. g. garrulus. To investigate species boundaries, we produced the first comprehensive phylogeny for the genus. We used a novel application of multiple regression on matrices models to assess multiple environmental drivers of diversification, as contrasted to isolation by distance. We show that P. kochi, P. carpi, and P. g. garrulus are valid species, but that P. g. maculatus is a paraphyletic complex of five previously unrecognised taxa. Specialisation onto different substrates was likely the main driver of divergence, with parapatric occurrence of two to four clades occurring at each of the three substrate transition zones identified a priori. The region encompasses diverse bioclimatic regions and potential geographic barriers, and these likely played a role in some divergence events.

An integrative approach to the study of Kempnyia Klapálek, 1914 (Plecoptera: Perlidae) from Brazil: Support for the description of four new species and a basis for future studies

Kempnyia (Plecoptera: Perlidae) is an endemic genus of Brazilian stoneflies that has 36 valid species and is distributed primarily in the Atlantic Forest and the mountainous areas of Central Brazil, particularly in Goiás and Tocantins states. Despite being the Brazilian genus with the most DNA sequences available on GenBank, integrative studies on the genus began only recently, in 2014. In this context, herein we studied the morphology and molecular data of Kempnyia specimens deposited in the Aquatic Biology Laboratory (UNESP, Assis) and the Entomology Museum of the Federal University of Viçosa (UFVB, Viçosa) collections. For the integrative approach adopted, in addition to studying the specimens morphologically, we used sequences of the COI mitochondrial gene combined with the following species delimitation methods: Automatic Barcode Gap Discovery (ABGD), both primary (ABGDp) and recursive (ABGDr) partitions; Assemble Species by Automatic Partitioning (ASAP); Poisson Tree Processes (PTP) and the Bayesian implementation of the Poisson Tree Processes (bPTP). As a result, we provided 28 new COI sequences of 21 species and support the description of four new species, namely, K. guarani sp. nov., K. tupiniquim sp. nov., K. una sp. nov., and K. zwickii sp. nov., consequently increasing the known diversity of the genus to 40 species. We also discuss the morphological variations observed in other species of the genus and provide several new geographic records. Therefore, our study brings new insights into the values of intra- and interspecific molecular divergence within Kempnyia, serving as a basis for new studies.

Phylogenetics, Molecular Species Delimitation and Geometric Morphometrics of All Reddish-Brown Species in the Genus Neotriplax Lewis, 1887 (Coleoptera: Erotylidae: Tritomini)

To date, five species of reddish-brown Neotriplax have been described, but their highly similar body color and other phenotypic traits make accurate taxonomy challenging. To clarify species-level taxonomy and validate potential new species, the cytochrome oxidase subunit I (COI) was used for phylogenetic analysis and the geometric morphometrics of elytron, pronotum, and hind wing were employed to distinguish all reddish-brown Neotriplax species. Phylogenetic results using maximum likelihood and Bayesian analyses of COI sequences aligned well with the current taxonomy of the Neotriplax species group. Significant K2P divergences, with no overlap between intra- and interspecific genetic distances, were obtained in Neotriplax species. The automatic barcode gap discovery (ABGD), assemble species by automatic partitioning (ASAP), and generalized mixed Yule coalescent (GMYC) approaches concurred, dividing the similar species into eight molecular operational taxonomic units (MOTUs). Geometric morphometric analysis using pronotum, elytron, hind wing shape and wing vein patterns also validated the classification of all eight species. By integrating these analytical approaches with morphological evidence, we successfully delineated the reddish-brown species of Neotriplax into eight species with three new species: N. qinghaiensis sp. nov., N. maoershanensis sp. nov., and N. guangxiensis sp. nov. Furthermore, we documented the first record of N. lewisii in China. This study underscores the utility of an integrative taxonomy approach in species delimitation within Neotriplax and serves as a reference for the taxonomic revision of other morphologically challenging beetles through integrative taxonomy.

Geometric Morphometrics and Genetic Diversity Analysis of Chalcidoidea (Diglyphus and Pachyneuron) at Various Elevations

Eulophidae and Pteromalidae are parasitic wasps with a global distribution and import for the biological control of pests. They can be distributed in different altitude regions, but their morphological and genetic adaptations to different altitudes are unclear. Here, we collected specimens that belong to Eulophidae and Pteromalidae from various altitudinal gradients, based on integrated taxonomic approaches to determine the species composition, and we analyzed their body shape and size from different altitudes using geometric morphometrics. Then, we performed an analysis of the D. isaea population's haplotype genes to illustrate their genetic diversity. As a result, eight species that belong to two genera, Diglyphus Walker (Eulophidae) and Pachyneuron Walker (Pteromalidae), were identified, including two newly recorded species from China (D. chabrias and D. sabulosus). Through a geometric morphometrics analysis of body shape, we found that a narrow forewing shape and a widened thorax are the significant characteristics of adaptation to high-altitude environments in D. isaea and P. aphidis. Additionally, the body size studies showed a principal relationship between centroid size and altitude; the size of the forewings and thorax increases at higher altitudes. Next, using haplotype analysis, 32 haplotypes were found in seven geographic populations with high genetic diversity of this species. Our research provides preliminary evidence for the morphological and genetic diversity adaptation of parasitic wasps to extreme environments, and these data can provide important references for investigations on the ecological adaptability of parasitic wasps.

Montane diversification as a mechanism of speciation in neotropical butterflies

The mountains in the Atlantic Forest domain are environments that harbor a high biodiversity, including species adapted to colder climates that were probably influenced by the climatic variations of the Pleistocene. To understand the phylogeographic pattern and assess the taxonomic boundaries between two sister montane species, a genomic study of the butterflies Actinote mantiqueira and A. alalia (Nymphalidae: Acraeini) was conducted. Analyses based on partial sequences of the mitochondrial gene COI (barcode region) failed to recover any phylogenetic or genetic structure discriminating the two species or sampling localities. However, single nucleotide polymorphisms gathered using Genotyping-by-Sequencing provided a strong isolation pattern in all analyses (genetic distance, phylogenetic hypothesis, clustering analyses, and F ST statistics) which is consistent with morphology, separating all individuals of A. alalia from all populations of A. mantiqueira. The three sampled mountain ranges where A. mantiqueira populations occur-Serra do Mar, Serra da Mantiqueira, and Poços de Caldas Plateau-were identified as three isolated clusters. Paleoclimate simulations indicate that both species' distributions changed according to climatic oscillations in the Pleistocene period, with the two species potentially occurring in areas of lower altitude during glacial periods when compared to the interglacial periods (as the present). Besides, a potential path between their distribution through the Serra do Mar Mountain range was inferred. Therefore, the Pleistocene climatic fluctuation had a significant impact on the speciation process between A. alalia and A. mantiqueira, which was brought on by isolation at different mountain summits during interglacial periods, as shown by the modeled historical distribution and the observed genetic structure.

Phylogeographic patterns of Cyphocharax from trans-Andean rivers and northward expansion to lower Central America (Teleostei, Curimatidae)

Phylogenetic analyses of mitochondrial and nuclear data of 31 specimens of Cyphocharax from trans-Andean rivers support the presence of one lineage of Cyphocharax aspilos in Lago Maracaibo and three cryptic lineages of Cyphocharax magdalenae: (1) Cauca-Magdalena and Ranchería, (2) León and Atrato, and (3) Chucunaque-Tuira, Santa María, and Chiriquí basins of Central America. Results suggest that the Serranía del Perijá facilitated Late Miocene cladogenetic events, whereas post-Isthmian C. magdalenae expansion was enabled by gene flow across the lower Magdalena valley and Central American lowlands. Time-calibrated phylogenetics indicate that the C. magdalenae colonized lower Central America in the Pliocene (3.7 MYA; Ma), the divergence Atrato-Magdalena occurred in Late Pliocene (3.0 Ma) and the split Ranchería-Magdalena during the Middle Pleistocene (1.3 Ma). Updated geographic distribution data support the hypothesis that the Cordillera de Talamanca functions as a barrier to northward expansion of C. magdalenae in Central America.

Species boundaries of the whiptail catfish Rineloricaria (Siluriformes: Loricariidae) from the Paraíba do Sul River drainage, southeastern Brazil, with species redescriptions and description of a new species

Species of the catfish genus Rineloricaria are common in the Paraíba do Sul River basin, in southeastern Brazil; here we present a revision of the taxonomic diversity and geographic distribution of the species of the genus inhabiting the basin, based on novel morphologic and molecular data. Five species delimitation methods based on cytochrome C oxidase subunit 1 nucleotide sequences yielded comparable molecular operational taxonomic units. The automatic barcode gap discovery, assemble species by automatic partitioning, barcode index number, and Bayesian implementation of the Poisson tree process methods supported the recognition of five evolutionary lineages. These taxonomic units were assigned to the previously described Rineloricaria nigricauda, Rineloricaria steindachneri, Rineloricaria zawadzkii, and Rineloricaria nudipectoris, and an additional undescribed species. R. zawadzkii was further divided into two intraspecific geographically structured lineages using the generalized mixed Yule coalescent delimitation method. A maximum likelihood phylogenetic analysis revealed that the five lineages from the Paraíba do Sul have closer relationships to different species from southern and southeastern Brazil (Ribeira de Iguape, Lagoa dos Patos, Uruguay, Paraguay, and Parana river basins) than to each other. Based on the analysis of lectotypes, recently collected material, and specimens from ichthyological collections, the poorly described R. nigricauda and R. steindachneri are redescribed following current descriptive standards. The undescribed species from the middle and upper Paraíba do Sul River basin is formally described. The description of a new species, along with the description of species boundaries in R. nigricauda and R. steindachneri, contributes to the knowledge of the ichthyofauna of the Paraíba do Sul River basin and adjacent coastal drainages of southeastern Brazil. An identification key for the species of Rineloricaria occurring in the Paraíba do Sul River basin is provided.

Delimiting species, revealing cryptic diversity in Molytinae (Coleoptera: Curculionidae) weevil through DNA barcoding

The subfamily Molytinae (Coleoptera: Curculionidae), being the second largest group within the family Curculionidae, exhibits a diverse range of hosts and poses a serious threat to agricultural and forestry industries. We used 1,290 cytochrome c oxidase subunit I (COI) barcodes to assess the efficiency of COI barcodes in species differentiation and uncover cryptic species diversity within weevils of Molytinae. The average Kimura 2-parameter distances within species, genus, and subfamily were 2.90%, 11.0%, and 22.26%, respectively, indicating significant genetic differentiation at both levels. Moreover, there exists a considerable degree of overlap between intraspecific (0%-27.50%) and interspecific genetic distances (GDs; 0%-39.30%). The application of Automatic barcode gap discovery, Assemble Species by Automatic Partitioning, Barcode Index Number, Poisson Tree Processes (PTP), Bayesian Poisson Tree Processes (bPTP), and jMOTU resulted in the identification of 279, 275, 494, 322, 320, and 279 molecular operational taxonomic units, respectively. The integration of 6 methods successfully delimited species of Molytinae in 86.6% of all examined morphospecies, surpassing a threshold value of 3% GD (73.0%). A total of 28 morphospecies exhibiting significant intraspecific divergences were assigned to multiple MOTUs, respectively, suggesting the presence of cryptic diversity or population divergence. The identification of cryptic species within certain morphological species in this study necessitates further investigation through comprehensive taxonomic practices in the future.

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.

Integrating phylogenetic, phylogeographic, and morphometric analyses to reveal cryptic lineages within the genus Asaccus (Reptilia: Squamata: Phyllodactylidae) in Iran

The Middle Eastern endemic genus Asaccus comprises Southwest Asian leaf-toed geckos. To date, this genus includes 19 species of leaf-toed geckos (seven in Arabia and 12 in the Zagros Mountains). Despite a recent study on the taxonomy and phylogeny of Asaccus species in Iran, controversies still remain surrounding the phylogeny and phylogeography of the genus. Here, we used an integrative approach to determine the phylogeny and phylogeography of Asaccus species using two mitochondrial genes (12 S and Cyt b), and one nuclear gene (c-mos). Our results uncovered 22 distinct lineages, demonstrating a significant cryptic diversity that challenges the current morphological classifications of these species. Phylogenetic analyses reinforce the monophyly of the Asaccus group, positioning A. montanus as a basal lineage, which supports a deep evolutionary divergence dating back to the Late Oligocene, approximately 27.94 million years ago. This genetic diversity also highlights the impact of historical climatic and geographical changes on species diversification. The findings advocate for an integrative approach combining both molecular and morphological data to resolve species identities accurately, thereby enhancing conservation strategies to protect these genetically distinct lineages.

Towards holistic insect monitoring: species discovery, description, identification and traits for all insects

Holistic insect monitoring needs scalable techniques to overcome taxon biases, determine species abundances, and gather functional traits for all species. This requires that we address taxonomic impediments and the paucity of data on abundance, biomass and functional traits. We here outline how these data deficiencies could be addressed at scale. The workflow starts with large-scale barcoding (megabarcoding) of all specimens from mass samples obtained at biomonitoring sites. The barcodes are then used to group the specimens into molecular operational taxonomic units that are subsequently tested/validated as species with a second data source (e.g. morphology). New species are described using barcodes, images and short diagnoses, and abundance data are collected for both new and described species. The specimen images used for species discovery then become the raw material for training artificial intelligence identification algorithms and collecting trait data such as body size, biomass and feeding modes. Additional trait data can be obtained from vouchers by using genomic tools developed by molecular ecologists. Applying this pipeline to a few samples per site will lead to greatly improved insect monitoring regardless of whether the species composition of a sample is determined with images, metabarcoding or megabarcoding. This article is part of the theme issue 'Towards a toolkit for global insect biodiversity monitoring'.

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.

Comparative Study of Two Himalayan Snow Trouts, Schizothorax esocinus and Schizothorax curvifrons Within the Schizothoracinae and Other Nearest Relatives of Cyprinidae, Inferred from Mitochondrial Sequences of Cytochrome b (Cyt-b) and Cytochrome Oxidase I (Co-I) Gene

The Himalayan region encompasses varied aquatic ecosystems, characterized by the presence of diverse ichthyofauna, particularly represented by members of the Schizothorax genus, commonly referred to as snow trout. The primary objective of this work was to examine the molecular phylogeny of Schizothoracinae, specifically focusing on the two species, Schizothorax esocinus and Schizothorax curvifrons, which are known to inhabit the northern and north-eastern regions of the Himalayas. This investigation was conducted by analyzing the entire mitochondrial Cyt-b and Co-I gene sequences. The aligned Cyt-b and Co-I sequences for S. esocinus, S. curvifrons, and related members within the subfamily Schizothoracinae, spanned 1130 to 1141 and 1536 to 1551 base pairs, respectively. Using these gene, phylogenetic trees were created to compare Schizothoracinae species to other subfamilies of the family Cyprinidae (Barbinae, Alburninae, Leuciscinae, Xenocyprinae, Cyprininae, and Cultrinae). Genetic distances for Cyt-b and Co-I sequence at three hierarchical levels shows significant disparities in their average score. For Cyt-b, average p-distances for intraspecies, intragenus, and intrafamily were 2.13%, 4.1%, and 15.23%, respectively. Similarly, for Co-I, average p-distances were 1.19%, 3.6%, and 13.8% for intraspecies, intragenus, and intrafamily, respectively. Total number of haplotypes (h) based on Cyt-b and Co-I gene were 6 and 12 within the target Schizothorax spp. In the present study, the observed range of haplotype diversity (hd) for the Cyt-b gene varied from 0.00 to 0.847, with an average haplotype diversity of 0.847 ± 0.034. Similarly, for the Co-I gene, the observed haplotype diversity ranged from 0.00 to 0.931, with an average value of haplotype diversity estimated to be 0.931 ± 0.024. The results of the present study clearly shows that the representative species exhibited close affinities with members of Barbinae and Cyprininae, while other subfamilies formed distinct groups. The findings of the study also indicated that the Cyt-b and Co-I gene exhibits polymorphism and has the potential to serve as a marker for identifying genetic differentiation among populations based on ecological habitats. Mitochondrial Cyt-b and Co-I have been established as a universally accepted and validated genetic marker within a comprehensive bio-identification system at the species level.

Genetic diversity and population structure of Physella acuta (Gastropoda: Physidae) in Thailand using mitochondrial gene markers: COI and 16S rDNA

Physella acuta is a freshwater snail native to North America. Understanding the phylogeography and genetic structure of P. acuta will help elucidate its evolution. In this study, we used mitochondrial (COI and 16S rDNA) and nuclear (ITS1) markers to identify the species and examine its genetic diversity, population structure, and demographic history of P. acuta in Thailand. Phylogenetic and network analyses of P. acuta in Thailand pertained to clade A, which exhibits a global distribution. Analysis of the genetic structure of the population revealed that the majority of pairwise comparisons showed no genetic dissimilarity. An isolation-by-distance test indicates no significant correlation between genetic and geographical distances among P. acuta populations, suggesting that gene flow is not restricted by distance. Demographic history and haplotype network analyses suggest a population expansion of P. acuta, as evidenced by the star-like structure detected in the median-joining network. Based on these results, we concluded that P. acuta in Thailand showed gene flow and recent population expansion. Our findings provide fundamental insights into the genetic variation of P. acuta in Thailand.

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.

Genetic and morphometric differentiation between two morphs of Haematobosca sanguinolenta (Diptera: Muscidae) from Thailand

Haematobosca is a genus of biting fly within the subfamily Stomoxyinae of the family Muscidae. It is currently recognized to include 16 species worldwide. These species, acting as ectoparasites, are considered to have significant importance in the veterinary and medical fields. To address the color polymorphism related to the genus Haematobosca in Thailand, herein, we focused on the normal (legs mainly black) and yellow (legs mainly yellow) morphs of Haematobosca sanguinolenta and examined them for genetic differences using three molecular markers: the cytochrome c oxidase subunit 1 (cox1) and cytochrome b (cytb) genes from the mitochondrial genome as well as the internal transcribed spacer 2 (ITS2) region from the nuclear ribosomal DNA. In addition, we analyzed wing differences between the two morphs using geometric morphometrics (GM). The genetic divergences between the two morphs showed that cytb gene showed the greatest divergence, for which the average distance was 5.6%. This was followed by the combination of cox1-cytb-ITS2, exhibiting an average divergence of 4.5%, ITS2 with a divergence of 4.1%, and finally cox1, showing the lowest divergence of 3.5%. Phylogenetic analyses distinctly separated the two morphs of H. sanguinolenta; this separation was supported by high bootstrap values (97-100%). These results were further corroborated by three species delimitation methods, i.e. assemble species by automatic partitioning (ASAP), automated barcode gap discovery (ABGD), and Poisson tree processes (PTP), all of which suggested that the two morphs likely represent separate species. In addition, a GM study identified a statistically significant difference in wing shape between the two morphs of H. sanguinolenta (P < 0.05). This combination of genetic and morphometric results strongly supports the existence of two distinct species within H. sanguinolenta in Thailand.

One Step beyond Species Description: Unveiling a Fine-Scale Diversity within the Genus Dzhanokmenia Kostjukov (Hymenoptera: Eulophidae)

Although Chalcidoidea is one of the megadiverse superfamilies in Hymenoptera, numerous species are still being discovered and described. However, the difficulties in delimiting intra- and interspecific variation hinder this process. In this study, DNA barcoding methods using the COI gene were employed to investigate the morphological variation within Dzhanokmenia Kostjukov, 1977. The nuclear locus, 28S D2, was used to infer a phylogeny to gain an understanding of the relationship of Dzhanokmenia with other potentially close genera. Through a preliminary DNA barcode library established here, including eight species, we calibrated the intraspecific variation in certain diagnostic characters for the new species described here, D. brevifunis Ganbaatar & Cao sp. nov. Maximum likelihood results show that Dzhanokmenia is clustered with the genera associated with Tetrastichus, such as Chaenotetrastichus Graham, 1987, Baryscapus Förster, 1856, Tetrastichus Haliday, 1844, and Oomyzus Rondani, 1870 involved in this study. Our results indicate that the species diversity of Dzhanokmenia is understudied and tentatively confirm that Dzhanokmenia has a potential close relationship with Baryscapus. Along with the DNA barcode library, the referenced phylogeny datasets improve the understanding of the systematic position of Dzhanokmenia within the subfamily Tetrastichinae and the definition of this genus in terms of morphology, thereby facilitating species delimitation, discovery, and description within Dzhanokmenia.

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.

Exploring hidden diversity: Molecular insights into the Leporinus species of the rivers of the Brazilian states of Maranhão and Piauí

The present study delved into the world of hidden diversity by examining specimens identified as Leporinus piau from the river basins of the northern Brazilian states of Maranhão and Piauí. Using genetic analyses that combined data from three mitochondrial markers and one nuclear marker, the study identified two well-supported groups, reinforcing the findings of previous publications. The first group, found in samples from the Itapecuru, Mearim, Turiaçu, and Pericumã basins, in Maranhão, appears to represent a relatively ancient diversification and the possibility of concealed cryptic diversity. The second group, comprising specimens from the Parnaíba (Piauí) and Mearim (Maranhão) basins, appears to have resulted from a more recent process of diversification and has a close relationship with Leporinus friderici from the type locality. Our findings not only confirm the existence of a complex scenario of cryptic diversity in the genus Leporinus from the study basins but also underscore the taxonomic inconsistencies within this group of fish. This study offers a comprehensive analysis of the species diversity of the Maranhão and Piauí basins, which are critical regions for the conservation of Amazonian fish, providing valuable insights for the sustainable management and conservation of these fish.

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.

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.

Complete mitochondrial genome of critically endangered catfish Hemibagrus punctatus (Jerdon, 1849) and comparative analysis for insights into the phylogeny of hemibagrids through mitogenomic approach

BACKGROUND

Hemibagrus punctatus (Jerdon, 1849) is a critically endangered bagrid catfish endemic to the Western Ghats of India, whose population is declining due to anthropogenic activities. The current study aims to compare the mitogenome of H. punctatus with that of other Bagrid catfishes and provide insights into their evolutionary relationships.

METHODS AND RESULTS

Samples were collected from Hemmige Karnataka, India. In the present study, the mitogenome of H. punctatus was successfully assembled, and its phylogenetic relationships with other Bagridae species were studied. The total genomic DNA of samples was extracted following the phenol-chloroform isoamyl alcohol method. Samples were sequenced, and the Illumina paired-end reads were assembled to a contig length of 16,517 bp. The mitochondrial genome was annotated using MitoFish and MitoAnnotator (Iwasaki et al., 2013). A robust phylogenetic analysis employing NJ (Maximum composite likelihood) and ASAP methods supports the classification of H. punctatus within the Bagridae family, which validates the taxonomic status of this species. In conclusion, this research enriches our understanding of H. punctatus mitogenome, shedding light on its evolutionary dynamics within the Bagridae family and contributing to the broader knowledge of mitochondrial genes in the context of evolutionary biology.

CONCLUSIONS

The study's findings contribute to a better understanding of the mitogenome of H. punctatus and provide insights into the evolutionary relationships within other Hemibagrids.

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.

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.