ABGD, Automatic Barcode Gap Discovery for primary species delimitation

Genomic divergence across the tree of life

Nucleotide sequence data are being harnessed to identify species, even in cases in which organisms themselves are neither in hand nor witnessed. But how genome-wide sequence divergence maps to species status is far from clear. While gene sequence divergence is commonly used to delineate bacterial species, its correspondence to established species boundaries has yet to be explored across eukaryotic taxa. Because the processes underlying gene flow differ fundamentally between prokaryotes and eukaryotes, these domains are likely to differ in the relationship between reproductive isolation and genome-wide sequence divergence. In prokaryotes, homologous recombination, the basis of gene flow, depends directly on the degree of genomic sequence divergence, whereas in sexually reproducing eukaryotes, reproductive incompatibility can stem from changes in very few genes. Guided by measures of genome-wide sequence divergence in bacteria, we gauge how genomic criteria correspond to species boundaries in eukaryotes. In recognized species of eukaryotes, levels of gene sequence divergence within species are typically very small, averaging <1% across protein-coding regions in most animals, plants, and fungi. There are even instances in which divergence between sister species is the same or less than that among conspecifics. In contrast, bacterial species, defined as populations exchanging homologous genes, show levels of divergence both within and between species that are considerably higher. Although no single threshold delineates species, eukaryotic populations with >1% genome-wide sequence divergence are likely separate species, whereas prokaryotic populations with 1% divergence are still able to recombine and thus can be considered the same species.

Expanding the known haemosporidian parasite diversity in Eurasian bluethroat (Luscinia svecica) subspecies through amplicon sequencing

Monitoring haemosporidian parasites in birds is essential to comprehend the dynamics of avian malaria, a disease that significantly affects bird populations worldwide. This study concentrated on the prevalence and diversity of haemosporidian parasites in 198 specimens from two subspecies of the Eurasian bluethroat (Luscinia svecica), aiming to explore the genetic diversity and species richness of haemosporidian fauna across the host populations. By utilizing next-generation amplicon high-throughput sequencing (NGS), we observed a marked increase in the detection of haemosporidian diversity, revealing cryptic variants and species previously unidentified by Sanger sequencing. A high prevalence of Plasmodium was seen in all studied sites, accompanied by a less frequent Leucocytozoon infection in the red-spotted subspecies and minimal occurrence of Haemoproteus. Both previously known and new, low prevalence cryptic variants were detected, underscoring the complexity of haemosporidian infections in avian hosts. The use of species delimitation tools provided a detailed understanding of haemosporidian species diversity, their coexistence within hosts, and their phylogenetic relationships. Despite the varying ecological characteristics of the study sites, no significant difference in haemosporidian alpha diversity among populations was found. However, significant differences in beta diversity were identified, suggesting that habitat characteristics and geographic distance influence parasite distribution. These findings highlight the importance of advanced molecular techniques in revealing the hidden diversity of parasites, offering valuable insights into the ecology and evolution of haemosporidian infections. Given the threatened status of one of the host's populations, knowledge on local diversity of haemosporidian parasites also has implications for possible conservation strategies.

Diversity, Phylogeny, and historical biogeography of the genus Coccocarpia (lichenized Ascomycota: Peltigerales) in the tropics

Coccocarpia Pers. currently comprises 28 mostly broadly distributed tropical species of fungi associated with cyanobacteria. Three of these taxa, C. erythroxyli, C. palmicola, and C. pellita, are presumably pantropical to subcosmopolitan, with broad morphological variation across their range. This study provides the first global phylogeny of the genus, to test current species concepts and infer distribution patterns, based on samples from Colombia, Puerto Rico, Gabon, Kenya, Thailand, Fiji, and Hawaii. We also estimate divergence times within the clade and provide a first reconstruction of its biogeographic history. Based on phylogenetic reconstructions inferred from maximum likelihood and Bayesian approaches of four molecular markers (mtSSU, nuLSU, ITS, RPB2), Coccocarpia was recovered as monophyletic. However, the currently accepted taxa are largely polyphyletic entities and the underlying diversity in this genus is much higher than currently understood. Different methods for species delimitation boundaries came to agree on a scenario involving more than 150 species in the available, albeit still small, dataset. This suggests that with broader sampling, Coccocarpia may indeed represent a hyper-diverse genus, potentially containing over 200 species. The phylogeny is geographically structured: one clade is exclusive to the Paleotropics, one to the Neotropics, and one is pantropical. Coccocarpia likely emerged during the Late Cretaceous (90 ± 10 Mya) in the tropical regions of Australasia-Oceania, initially colonizing Oceania, and Asia and subsequently the Neotropics. The three main clades diverged between the Late Cretaceous and the Paleocene, with significant diversification in the Oligocene, during which the neotropical clade gave rise to morphological novelties, including the epiphylla and stellata clades.

Study of epiphytic non-geniculate coralline algae Reveals an Evolutionarily significant Genus, Pseudoderma gen. nov. (Lithophylloideae, Corallinophycidae)

Epiphytic non-geniculate coralline algae (ENCA) are distributed broadly, while limited research on their diversity has constrained our understanding of their ecological roles in marine environments, and impeded a comprehensive understanding of coralline algae. In this study, the diversity and ecological characteristics of ENCA epiphytic on 113 red macroalgal specimens collected from coastal China were examined. Three species delimitation algorithms revealed 24 primary species hypotheses (PSH), of which 22 were corroborated through phylogenetic analysis based on the psbA gene. Further multi-gene concatenated phylogenetic analyses and morpho-anatomical assessments revealed a new genus within Lithophylloideae, Pseudoderma gen. nov., which is closely related to the genus Titanoderma and exhibits morphological similarities. A hypothesis concerning the growth patterns was proposed to elucidate the morphological differences among Titanoderma, Lithophyllum, and Pseudoderma: the presence or absence of hypothallial palisade cells indicated distinct thallus thickening patterns, either dominated by elongation of the hypothallial cells or by division of the perithallial cells. These processes resulted in fast-growing thin-crust thalli or longer-lasting thick-crust thalli, adapted to epiphytic or epilithic lifestyles, respectively. Pseudoderma included at least six new taxa, and Pseudoderma sinicarum sp. nov., was designated as the holotype species of this genus. In conclusion, this study has underscored the unexpected biodiversity of ENCA, and the identification of the novel genus Pseudoderma from ENCA groups carried significant evolutionary implications for enhancing our understanding of coralline algae systematics.

"Dark taxonomy": A new protocol for overcoming the taxonomic impediments for dark taxa and broadening the taxon base for biodiversity assessment

We are entering the sixth mass extinction with little data for "dark taxa", although they comprise most species. Much of the neglect is due to the fact that conventional taxonomic methods struggle with handling thousands of specimens belonging to hundreds of species. We thus here propose a new strategy that we call "dark taxonomy". It addresses (i) taxonomic impediments, (ii) the lack of biodiversity baselines and (iii) the low impact of revisionary research. Taxonomic impediments are reduced by carrying out revisions at small geographic scales to keep the number of specimens low. The risk of taxonomic error is reduced by delimiting species based on two types of data. We furthermore show that dark taxonomy can yield important biodiversity baseline data by using samples obtained with biomonitoring traps. Lastly, we argue that the impact of revisionary research can be improved by publishing two papers addressing different readerships. The principles of dark taxonomy are illustrated by our taxonomic treatment of Singapore's fungus gnats (Mycetophilidae) based only on Malaise trap samples. We show that a first batch of specimens (N = 1454) contains 120 species, of which 115 are new to science, thus reducing taxonomic impediments by increasing the number of described Oriental species by 25%. Species delimitation started with using DNA barcodes to estimate the number of Molecular Operational Taxonomic Units (MOTUs) before "LIT" (Large-scale Integrative Taxonomy) was used to obtain the species boundaries for the 120 species by integrating morphological and molecular data. To test the taxonomic completeness of the revision, we next analysed a second batch of 1493 specimens and found that >97% belonged to the 120 species delimited based on the first batch. Indeed, the second batch only contained 18 new and rare MOTUs, i.e. our study suggests that a single revision can simultaneously yield the names for all important species and relevant biodiversity baseline data. Overall, we believe that "dark taxonomy" can quickly ready a large unknown taxon for biomonitoring.

An Integrative Phylogenetic Analysis of the Genus Rhynchium Spinola (Hymenoptera: Vespidae: Eumeninae) from China Based on Morphology, Genomic Data and Geographical Distribution

The species of the genus Rhynchium Spinola are important natural insect control resources and widespread in the Old World. Due to the various color patterns of several species in China, it is difficulty to accurately classify and identify the genus. We combined their morphology with population genetic differentiation, phylogenetic relationship and geographical distribution to delimitate the species of Rhynchium from China. Within the genus, more than 600 pinned specimens were examined and a total of 37 whole genomes were analyzed, of which 35 were newly sequenced. Firstly, COI sequences, 13 PCGs and 2 rRNAs sequences of the mitochondrial genomes, USCO nucleotide matrix of 90% completeness (USCO90_fna), and USCO amino acid matrix of 90% completeness (USCO90_faa) were extracted from the whole-genome data. Then, genetic distances were calculated using the COI sequences, and ABGD species delimitation analysis identified three valid species. By integrating the four phylogenetic trees inferred from the four datasets and morphological analysis, the specimens of Rhynchium from China were recognized as R. carnaticum (newly recorded), R. quinquecinctum, and R. brunneum; the last is the most widely distributed in China, while the remaining two only occur in Hainan and Yunnan, respectively, markedly different from previous records. Finally, it is interesting that color patterns of the species R. brunneum seem to closely relate to the geographical distribution, embodying two different modes in the South and the North of China, as well as a transitional state in the middle. The roles of the color patterns are still not resolved and their underlying evolutionary mechanisms need further exploration.

COI Insights into Diversity and Species Delimitation of Immature Stages of Non-Biting Midges (Diptera: Chironomidae)

The diversity of non-biting midges (Chironomidae, Diptera) remains an unresolved topic, with estimates of species numbers ranging from 6000 to 15,000 according to various authors. To assess Chironomidae diversity in Lithuania, we evaluate the effectiveness of COI gene-based species delimitation methods for providing rapid diversity estimates. Nevertheless, differences between tree-based and distance-based approaches can result in varying group classifications, which may cause species numbers to be overestimated or underestimated. For our study, we analyzed a dataset of 109 specimens sampled from six Lithuanian streams. By applying multiple methods, such as Assemble Species by Automatic Partitioning (ASAP), Automatic Barcode Gap Discovery (ABGD), the generalized mixed Yule-coalescent (GMYC) model, and the Bayesian implementation of the Poisson Tree Processes (bPTP) model, we found that species estimates ranged from 28 to 58. Among these methods, ASAP proved to be the most effective for our dataset, identifying 58 putative species. These results reinforce our assumption that the current understanding of Chironomidae species diversity is incomplete.

Species delimitation and historical biogeography of Sturisoma Swainson, 1838 (Loricariidae: Loricariinae): Hidden diversity along the Amazon River

In the present study, we used DNA sequences from three mitochondrial (COI, Cytb, and nd2) and one nuclear (RAG2) marker, to perform species delimitation analyses (ABGD, GMYC, BPP, and bPTP) within Sturisoma to test the validity of currently recognized and potential new species for the genus. Additionally, a historical biogeographic analysis was carried out to test the age and centers of origin for species of the genus. Results found here indicate a high degree of genetic divergence with overlapping morphological characteristics suggesting a greater diversity than previously proposed for the genus. All valid species currently included in Sturisoma were confirmed here, and one potentially undescribed species was recovered. Based on genetic distances, geographical patterns and historical biogeography, the diversification of the group could be related to dispersal events from Western to Eastern Amazonia resulting in sympatric species that are highly divergent genetically but conservative morphologically. The lower (eastern) Amazonas and the Orinoco River basins were identified as the main centers of origin for the genus, with an approximate age of origin of 13 Mya, during the Miocene. The diversity of the genus is likely to be even higher because the Amazon River is a hotspot of hidden biodiversity.

Integrative taxonomy of the cycad-associated weevils of the Tranes group, with a revision of Tranes Schoenherr, a key to all taxa and an assessment of host specificity in the group (Coleoptera: Curculionidae: Molytinae)

Australia is a main centre of diversity for extant cycads (Cycadophyta), harbouring 4 genera and 85 named species and subspecies. Three cycad genera, Bowenia , Lepidozamia and Macrozamia , serve as hosts for four weevil genera of the Tranes group, Tranes Schoenherr, Miltotranes Zimmerman, Demyrsus Pascoe and Siraton Hustache. Several morphologically based taxonomic studies have been undertaken on some of these genera recently, but their classification, diversity and species delineations have not been evaluated using an integrative taxonomic approach. In the present study, we combine morphological characters and mitochondrial DNA data to assess the taxonomic status of taxa in this group. Different methods of molecular species delimitation, especially distance-based ones, generally provide strong support for taxon concepts derived from morphological characteristics, demonstrating that these are well able to delineate natural species and assess taxonomic diversity in this group of weevils. Exceptions are that molecular analyses indicate Siraton internatus (Pascoe) to be more closely related to Demyrsus than to S. roei (Boheman), rendering Siraton a paraphyletic taxon, and a genetically distinct but morphologically cryptic species of Miltotranes to occur south of Cairns. A key to all genera and species of the Tranes group is presented. The genus Tranes and its four previously named species are redescribed and six species are newly described, T. chadwicki sp. nov., T. forsteri sp. nov., T. kgariensis sp. nov., T. occidentalis sp. nov., T. terryae sp. nov. and T. tinctipennis sp. nov., and a lectotype is designated for the name Tranes insignipes Lea, 1929. The salient characters and distribution ranges of all Tranes species are illustrated, and their host specificities are assessed. ZooBank: urn:lsid:zoobank.org:pub:45DE986E-A8B3-4247-B056-DF3126D4B31D.

Intraspecific genetic variation in the lymphatic filariasis vector Mansonia dives (Diptera: Culicidae) in Thailand: Hidden species or genetically divergent populations?

Mansonia dives is recognized as a vector for brugian filariasis in Thailand. A recent study analyzing the cytochrome c oxidase subunit I (COI) gene revealed two distinct clades within the Ma. dives population in Thailand. This study aimed to examine the genetic diversity and structure of Ma. dives using the COI gene and the internal transcribed spacer 2 (ITS2) region to determine the presence of distinct species or genetically divergent populations. We analyzed 60 COI and 60 ITS2 sequences from Ma. dives populations in Narathiwat, Ranong, Tak, and Trat. The results showed a nucleotide diversity of 0.019 and a haplotype diversity of 0.979 for the COI gene, while the ITS2 region displayed a nucleotide diversity of 0.005 and a haplotype diversity of 0.545. Phylogenetic and haplotype network analyses of the COI gene identified two genetic lineages: one confined to Trat and another encompassing the other sites. However, species delimitation methods suggested that these genetic differences were insufficient to classify the lineages as distinct species. In contrast, the ITS2 analysis indicated a uniform genetic pattern across all populations. We conducted neutrality tests and mismatch distribution to examine the demographic history. For the COI gene, Tajima's D was slightly positive and non-significant (0.014), while Fu's Fs was negative (-9.750), indicating a potential expansion phase. Conversely, for the ITS2 region, Tajima's D and Fu's Fs were positive and non-significant, suggesting that the population might be in equilibrium or undergoing contraction. Moreover, the mismatch distribution analysis for the ITS2 region was inconclusive. The apparent discrepancies between these markers indicate the presence of genetically divergent populations, rather than distinct species.

Identifications of Common Species and Descriptions of Two New Species of Siphonaria (Mollusca: Gastropoda) in China

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Deep cryptic diversity in the Craugastor podiciferus Species Group (Anura: Craugastoridae) of Isthmian Central America revealed by mitochondrial and nuclear data

The Craugastor podiciferus Species Group contains eleven species of terraranan frogs distributed from eastern Honduras to eastern Panama. All species have remarkable color pattern polymorphisms, which may contribute to potential taxonomic problems. We performed exhaustive sampling throughout the geographic distribution of the group to evaluate the phylogenetic relationships and biogeographic history of all named species based on two mitochondrial markers and nuclear ddRAD loci. We also implemented various species delimitation methods to test for the presence of unconfirmed candidate species within the group. Molecular phylogenetic analyses showed that the group contains four major clades. All currently named species are supported by molecular data, yet species richness within the group is clearly underestimated. Species delimitation was discordant between the mitochondrial and nuclear datasets and among analytical methods. Adopting a conservative approach, we propose that the C. podiciferus species group contains at least 12 unconfirmed candidate species. Ancestral area reconstruction showed that the group originated and diversified in the highlands of the Talamancan montane forest ecoregion of Costa Rica and western Panama.

Integrative phylogenetic analysis of the genus Episoriculus (Mammalia: Eulipotyphla: Soricidae)

Shrews in the genus Episoriculus are among the least-known mammals in China, where representatives occur mainly in the Himalayan and Hengduan mountains. We sequence one mitochondrial and three nuclear genes from 77 individuals referable to this genus, collect morphometric data for five shape and 11 skull measurements from 56 specimens, and use museum collections and GenBank sequences to analyze phylogenetic relationships between this and related genera in an integrated molecular and morphometric approach. Whereas historically anywhere from two to eight species have been recognized in this genus, we conclude that six (Episoriculus baileyi, E. caudatus, E. leucops, E. macrurus, E. sacratus, E. soluensis) are valid. We dissent from recent systematic reviews of this genus and regard E. sacratus to be a valid taxon, E. umbrinus to be a subspecies of E. caudatus, and transfer E. fumidus to Pseudosoriculus. Our record of E. soluensis is the first for China, and expands the previously recognized distribution of this taxon from Nepal and NE India into the adjacent Yadong and Nyalam counties. One further undescribed Episoriculus taxon may exist in Xizang.

Taxonomic study of the genus Campylomyza Meigen (Diptera, Cecidomyiidae) in Korea with descriptions of seven new species

The genus Campylomyza Meigen, 1818, belongs to the subfamily Micromyinae (Diptera, Cecidomyiidae). The genus, comprising 40 species, is best known in the Palearctic Region. To date, four species are recorded in Korea: Campylomyzaappendiculata, C.flavipes, C.furva, and C.spinata. Based on our field investigations from 2017 to 2020, five species are newly recorded from Korea (C.abjecta, C.aborigena, C.cornuta, C.cavitata, and C.cingulata) and seven new species are described (C.ambulata sp. nov., C.angusta sp. nov., C.convexa sp. nov., C.cornigera sp. nov., C.hori sp. nov., C.odae sp. nov., and C.salicia sp. nov.), based on morphological identification and molecular analyses. Detailed morphological and molecular data, including mitochondrial COI sequences are provided, with species diagnosis, descriptions, and keys for identification of those species.

An integrative taxonomic approach reveals two putatively novel species of phlebotomine sand fly (Diptera: Psychodidae) in Thailand

BACKGROUND

The subfamily Phlebotominae comprises 1028 species of sand fly, of which only 90 are recognized as vectors of pathogenic agents such as Trypanosoma, Leishmania, and Bartonella. In Thailand, leishmaniasis-a sand fly-borne disease-is currently endemic, with 36 documented sand fly species. However, many cryptic species likely remain unidentified. To improve our understanding of the distribution, habitat preferences, and role in disease transmission of these sand flies, further research is necessary.

METHODS

Sand flies were collected using CDC light traps from 13 locations across four provinces in Thailand between October 2022 and October 2023. Initially, species identification was based on morphological characteristics, employing identification keys, and subsequently confirmed through mitochondrial cytochrome oxidase c subunit I (COI) and cytochrome b (Cytb) sequencing. Species identities were verified using BLASTN and BOLD searches. Species delimitation was conducted using Automatic Barcode Gap Discovery (ABGD) and Assemble Species by Automatic Partitioning (ASAP) with three substitution models. Additionally, intraspecific and interspecific genetic variation, neutrality tests (including Tajima's and Fu and Li's D* tests), phylogenetic analyses, and TCS haplotype network analysis were performed using the obtained sequences.

RESULTS

A total of 3693 phlebotomine sand flies were collected, with 2261 (61.22%) identified as female. Integrative analyses combining morphological data, BLASTN searches, phylogenetic assessments, and species delimitation confirmed the identification of four genera: Sergentomyia, Grassomyia, Phlebotomus, and Idiophlebotomus, encompassing 12 species: Sergentomyia anodontis, Se. sylvatica, Se. perturbans, Se. barraudi, Se. hivernus, Se. khawi, Se. siamensis, Grassomyia indica, Phlebotomus barguesae, Ph. stantoni, Idiophlebotomus asperulus, and Id. longiforceps. Furthermore, molecular analysis revealed cryptic and complex species, including two putatively novel species, Se. sp. 1 and Se. sp. 2, as well as a unique haplotype.

CONCLUSIONS

This study, which integrated genetic and morphological identification techniques, identified 12 sand fly species and unveiled cryptic and complex species, including two putatively novel species (Se. sp. 1 and Se. sp. 2) and a unique haplotype. The findings underscore the utility of mitochondrial genes, combined with species delimitation methodologies, as reliable approaches for identifying diverse sand fly species.

Phylogenomic analyses of hamsters (Cricetinae) inferred from GBS data and mitochondrial genomes

Accurate species delimitation and identification is crucial for species conservation, providing a foundation for studies on evolutionary biology, ecology, and essentially all biological disciplines. The subfamily Cricetinae (Cricetidae, Rodentia), known as hamsters, is widely distributed in the Palearctic region. At present, there are nine genera and 18 species of hamsters are recognized worldwide, although the taxonomic status of certain taxa remains unclear. In this study, we collected 146 hamster specimens representing 14 species and generated new mitochondrial genomes and nuclear genome-wide single nucleotide polymorphisms (SNPs) to explore their relationships among these hamsters using multiple species delimitation approaches. Results showed: (1) strong phylogenetic support for the classification of Urocricetus, Nothocricetulus, and Cansumys as separate genera; (2) Urocricetus contained two separate species, U. kamensis and U. lama, with U. alticola and U. tibetanus considered synonyms of U. lama; (3) U. kamensis and U. lama are separated by the Nujiang River, with the matching divergence time suggesting that the formation of the river was the primary evolutionary factor driving the species differentiation, and (4) genetic differentiation occurred within the Tscherskia genus, which included two cryptic species.

Insights from DNA Barcodes-Based Phylogenetic Analysis of Medicinal Plants and Estimation of Their Conservation Status: A Case Study in the Tianshan Wild Forest, China

The Tianshan wild fruit forest region is a vital repository of plant biodiversity, particularly rich in the unique genetic resources of endemic medicinal plants in this ecological niche. However, human activities such as unregulated mining and excessive grazing have led to a significant reduction in the diversity of these medicinal plants. This study represents the first application of DNA barcoding to 101 medicinal plants found in the Tianshan wild fruit forests, using three genetic loci along with morphological identification methods. A phylogenetic analysis was performed to delineate species relationships. The results indicate that the internal transcribed spacer (ITS) region has been identified as the most reliable barcode for species identification across different families, while combining data from multiple gene segments can improve species detection. Moreover, the Analytical Hierarchy Process (AHP) was employed to assess and prioritize the 101 medicinal plants, highlighting 23 species as candidates for urgent conservation efforts in the region. The approaches and insights from this study provide a significant benchmark for DNA barcoding studies on medicinal plants with local significance and establish an evaluative framework for the conservation of biodiversity and the surveillance of genetic resources among medicinal plants in the Tianshan wild fruit forest area.

The syntopic occurrence of velvet mites Trombidium spp. (Acariformes: Trombidiidae) with the first characteristics of the larva of Trombidium heterotrichum

Observations of representatives of Trombidium at one locality over two subsequent years revealed the syntopic occurrence of three species: T. holosericeum, T. brevimanum, and T. heterotrichum. The separate identities of the species, which were initially supported by morphological evidence, were confirmed with a molecular approach (COI sequence data) complemented by molecular species delimitation tools (ABGD, ASAP) and phylogenetic inference. Laboratory rearing of ovigerous females of T. heterotrichum resulted in obtaining hitherto unknown larvae of the species. The first characteristic of the larvae is supplemented with extended biometrical data and data on the biology and ecology of the species. We hypothesize that at syntopic and synchronous occurrence of Trombidium spp., the host spectrum contributes to the niche segregation.

Integrated taxonomy to advance species delimitation of the Anopheles maculipennis complex

The Anopheles maculipennis complex consists of several mosquito species, including some primary malaria vectors. Therefore, the presence of a species in a particular area significantly affects public health. In this study, 1252 mosquitoes were collected in northern Italy, representing four identified species of the Anopheles maculipennis complex (Anopheles daciae sp. inq., Anopheles maculipennis s. s., Anopheles atroparvus and Anopheles melanoon). The sequences of two DNA markers, mitochondrial cytochrome c oxidase I (COI) and nuclear internal transcribed spacer 2 (ITS2), were generated. DNA-based species delimitation analyses were performed, incorporating public sequences, with distance-based and coalescent tree-based methods to confirm the actual species boundaries within the complex. While some morphospecies were unequivocally delimited by all methods and markers, COI analysis splitted An. maculipennis s. s. into two well-supported groups. However, molecular delimitation failed in recognizing An. daciae sp. inq. and An. messeae as two separate evolutionary entities. Species delimitation was further tested with a morphometric approach, which clearly differentiated species collected in the survey area. These findings underscore how challenging the characterization of the taxonomy of the complex is, providing evidence of potential introgression events in An. maculipennis s. s. and suggesting the need for robust evidence to support An. daciae sp. inq. and An. messeae as distinct species.

Species diversity in the new lamprey genus Occidentis, formerly classified as western North American 'Lampetra'

Accurate taxonomy is fundamental to the study and conservation of biodiversity. Because of their morphological similarities, most brook and river lampreys in western North America have been placed in the genus Lampetra along with lampreys from Eurasia and eastern North America. However, molecular-based phylogenetic studies dating back several decades indicate that lampreys from Pacific drainages are genetically distinct from Atlantic Lampetra. Reviewing previous phylogenetic analysis of two mitochondrial and two nuclear genes for Northern Hemisphere lampreys, we assign these western North American brook and river lampreys to a new genus, Occidentis. To assess species diversity within Occidentis, we performed a species delimitation analysis using all publicly available cytochrome b sequences of the genus. Similar to previous studies, O. ayresii and O. richardsoni were not reciprocally monophyletic and are best categorized as life history variants of a single species. In addition to O. pacifica, O. hubbsi, and the diverse O. ayresii species complex, as many as seven undescribed candidate species from Oregon and California were identified, supporting results from previous studies with more geographically limited datasets. One specimen from Paynes Creek, California, was identified as a candidate species, although this single individual showed minimal interspecific divergence (1.34%) with O. hubbsi. Further genetic assessment along with information on morphology and phylogeography is needed to determine whether the variation observed between groups of candidate species represents distinct species or divergent lineages within a species complex. Additional sampling will inform whether there are additional species not currently represented in this dataset. Thus, the number of species formally recognized under Occidentis is subject to change with new information. Systematic assessment of the distribution and phylogenetic complexity within Occidentis will enhance our understanding of its evolutionary history and taxonomic diversity, which will guide efforts to conserve the biodiversity of lampreys.

Molecular identification, genetic diversity, and secondary structure predictions of Physalis species using ITS2 DNA barcoding

BACKGROUND

The genus Physalis belongs to the Solanaceae family and has different species with important nutritional and medicinal values. Species within this genus have limited morphological differences, a characteristic that hinders accurate identification, safe utilization and genetic conservation of promising genotypes. In addition, to prevent the perceived loss of Physalis diversity due to habitat destruction, species delimitation needs attention. In this study, we used the sequence and structural information of the internal transcribed spacer 2 (ITS2) barcode to efficiently identify and discriminate Physalis species from a collection of 34 Physalis accessions.

METHODOLOGY

Physalis plant samples were collected from eight Counties in Kenya based on the availability of the germplasm. The voucher specimens were identified using the botanical taxonomy method and were deposited in the University of Nairobi herbarium. A total of 34 Physalis accessions were identified and accessed for diversity based on the ITS2 barcode region. The sequence similarity of the ITS2 genes was analyzed through the Basic Local Alignment Search Tool (BLAST), the nearest Kimura-2-parameter (K2P) genetic distances were calculated and a phylogenetic tree was constructed using the Bayesian inference (BI) method in MrBayes 3.2.7a software. The differences in the ITS2 secondary structure between the species were analyzed.

RESULTS

The success rate of PCR amplification and sequencing was 75% and 67%, respectively. The analyzed ITS2 sequences displayed significant inter-specific divergences, clear DNA barcoding gaps and high species identification efficiency. Based on the constructed phylogenetic tree, three Physalis species (Physalis peruviana, Physalis purpurea and Physalis cordata) were identified and were clustered in a homogenized distribution. High genetic diversity (0.36923) and genetic distance (0.703) were observed between Physalis peruviana and Physalis cordata. The highest genetic nucleotide diversity (0.26324) and distance (0.46) within species was obtained for Physalis peruviana. The differences in the secondary structures generated from this study discriminated between the Physalis species.

CONCLUSIONS

Our study demonstrated that ITS2 is a potential DNA barcode for effective identification and discrimination of Physalis species. The results of this study provide insights into the scientific basis of species identification, safe utilization, genetic conservation and future breeding strategies for this important nutritional and medicinal plant species.

Reversing a reported case of transoceanic dispersal: Nudibranch identifications among tsunami debris

In the aftermath of the 2011 east Japanese earthquake and tsunami, anthropogenic debris from the east coast of Japan floated across the Pacific Ocean to the west coast of North America. One such vessel from Iwate Prefecture arrived on the coast of Oregon, and the fouling community included specimens identified as the nudibranch Hermissenda crassicornis, which was previously thought to range from Japan to Baja California but has since been split into three species: H. crassicornis (northeastern Pacific), H. opalescens (southeastern Pacific), and H. emurai (western Pacific). Also aboard were nudibranchs of the genera Dendronotus and Eubranchus. Previous work suggested that all of the motile invertebrates found in the tsunami debris fouling community were either pelagic or Japanese in origin. Our study sought to determine whether the Hermissenda nudibranch specimens collected from the Iwate vessel were, according to the most updated classification system, only H. emurai as would be the case if the nudibranchs were Japanese in origin. In addition, we also sought to identify the Dendronotus and Eubranchus aboard. Results from DNA sequencing and limited morphological analysis indicate that specimens of H. crassicornis, as it is currently recognized, and H. opalescens were found on the vessel. Morphological or genetic data resolved the other nudibranchs as the Eastern Pacific Dendronotus venustus and Eubranchus rustyus. These findings indicate that these species settled after arrival to the west coast of North America. Data shared on GBIF and the iNaturalist platform were also used to map where eastern Pacific Hermissenda are currently understood to occur.

DNA Barcodes and Morphology Reveal Two New Species of the Genus Prochas Walkley, 1959 (Ichneumonidae, Campopleginae), from China

DNA barcoding is an effective modern tool in taxonomy, evolutionary biology, and biodiversity research. Many new species have been discovered and described with DNA barcodes as part of their diagnostic features. We combined morphological examination and molecular species delimitation of the mitochondrial cytochrome c oxidase 1 (COI) gene using the automatic barcode gap discovery (ABGD) to investigate species boundaries. The genus Prochas Walkley (Hymenoptera, Ichneumonidae, Campopleginae) was first reported from China and is new for the Oriental and Eastern Palearctic regions. Using an integrative taxonomy method, two new species P. rugipunctata sp. nov. and P. striata sp. nov. are hereby described and illustrated. A key to the world species and a distribution map are provided.

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.

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.

Eco-phylogenetic study of Trebouxia in southern Africa reveals interbiome connectivity and potential endemism in a green algal lichen photobiont

PREMISE

Southern Africa is a biodiversity hotspot rich in endemic plants and lichen-forming fungi. However, species-level data about lichen photobionts in this region are minimal. We focused on Trebouxia (Chlorophyta), the most common lichen photobiont, to understand how southern African species fit into the global biodiversity of this genus and are distributed across biomes and mycobiont partners.

METHODS

We sequenced Trebouxia nuclear ribosomal ITS and rbcL of 139 lichen thalli from diverse biomes in South Africa and Namibia. Global Trebouxia phylogenies incorporating these new data were inferred with a maximum likelihood approach. Trebouxia biodiversity, biogeography, and mycobiont-photobiont associations were assessed in phylogenetic and ecological network frameworks.

RESULTS

An estimated 43 putative Trebouxia species were found across the region, including seven potentially endemic species. Only five clades represent formally described species: T. arboricola s.l. (A13), T. cf. cretacea (A01), T. incrustata (A06), T. lynniae (A39), and T. maresiae (A46). Potential endemic species were not significantly associated with the Greater Cape Floristic Region or desert. Trebouxia species occurred frequently across multiple biomes. Annual precipitation, but not precipitation seasonality, was significant in explaining variation in Trebouxia communities. Consistent with other studies of lichen photobionts, the Trebouxia-mycobiont network had an anti-nested structure.

CONCLUSIONS

Depending on the metric used, ca. 20-30% of global Trebouxia biodiversity occurs in southern Africa, including many species yet to be described. With a classification scheme for Trebouxia now well established, tree-based approaches are preferable over "barcode gap" methods for delimiting new species.

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.

Morphology and molecular evidence of a new species of Characidium (Characiformes: Crenuchidae) from the edges of a protected area at Rio Itararé, upper Rio Paraná, southern Brazil

A new species of Characidium is described from the headwaters of the Rio Itararé, upper Rio Paraná basin, at the boundaries of the Ponta Grossa Arch and the Devonian Escarpment Environmental Protection Area. The new species is supported by both morphological and molecular data, including species delimitation methods (Assemble Species by Automatic Partitioning, Barcode Index Number, Poisson Tree Process and its Bayesian implementation, and Generalized Mixed Yule Coalescent). The species is genetically close to other species that also exhibit the presence of scales on the isthmus, including Characidium litorale, Characidium satoi, Characidium xanthopterum, and Characidium aff. zebra. The high genetic diversity among Characidium species underscores the necessity of employing a complementary perspective in studies of this group. The discovery of a new species in the headwaters of the Rio Itararé further reinforces the importance of this biogeographic region for the conservation of ichthyofauna.

Diaporthe species on palms - integrative taxonomic approach for species boundaries delimitation in the genus Diaporthe, with the description of D. pygmaeae sp. nov

The application of traditional morphological and ecological species concepts to closely related, asexual fungal taxa is challenging due to the lack of distinctive morphological characters and frequent cosmopolitan and plurivorous behaviour. As a result, multilocus sequence analysis (MLSA) has become a powerful and widely used tool to recognise and delimit independent evolutionary lineages (IEL) in fungi. However, MLSA can mask discordances in individual gene trees and lead to misinterpretation of speciation events. This phenomenon has been extensively documented in Diaporthe, and species identifications in this genus remains an ongoing challenge. However, the accurate delimitation of Diaporthe species is critical as the genus encompasses several cosmopolitan pathogens that cause serious diseases on many economically important plant hosts. In this regard, following a survey of palm leaf spotting fungi in Lisbon, Portugal, Diaporthe species occurring on Arecaceae hosts were used as a case study to implement an integrative taxonomic approach for a reliable species identification in the genus. Molecular analyses based on the genealogical concordance phylogenetic species recognition (GCPSR) and DNA-based species delimitation methods revealed that speciation events in the genus have been highly overestimated. Most IEL identified by the GCPSR were also recognised by Poisson tree processes (PTP) coalescent-based methods, which indicated that phylogenetic lineages in Diaporthe are likely influenced by incomplete lineage sorting (ILS) and reticulation events. Furthermore, the recognition of genetic recombination signals and the evaluation of genetic variability based on sequence polymorphisms reinforced these hypotheses. New clues towards the intraspecific variation in the common loci used for phylogenetic inference of Diaporthe species are discussed. These results demonstrate that intraspecific variability has often been used as an indicator to introduce new species in Diaporthe, which has led to a proliferation of species names in the genus. Based on these data, 53 species are reduced to synonymy with 18 existing Diaporthe species, and a new species, D. pygmaeae, is introduced. Thirteen new plant host-fungus associations are reported, all of which represent new host family records for Arecaceae. This study has recognised and resolved a total of 14 valid Diaporthe species associated with Arecaceae hosts worldwide, some of which are associated with disease symptoms. This illustrates the need for more systematic research to examine the complex of Diaporthe taxa associated with palms and determine their potential pathogenicity. By implementing a more rational framework for future studies on species delimitation in Diaporthe, this study provides a solid foundation to stabilise the taxonomy of species in the genus. Guidelines for species recognition, definition and identification in Diaporthe are included. Taxonomic novelties: New species: Diaporthe pygmaeae D.S. Pereira & A.J.L. Phillips. New synonyms: Diaporthe afzeliae Monkai & Lumyong, Diaporthe alangii C.M. Tian & Q. Yang, Diaporthe araliae-chinensis S.Y. Wang et al., Diaporthe australiana R.G. Shivas et al., Diaporthe australpacifica Y.P. Tan & R.G. Shivas, Diaporthe bombacis Monkai & Lumyong, Diaporthe caryae C.M. Tian & Q. Yang, Diaporthe chimonanthi (C.Q. Chang et al.) Y.H. Gao & L. Cai, Diaporthe conferta H. Dong et al., Diaporthe diospyrina Y.K. Bai & X.L. Fan, Diaporthe durionigena L.D. Thao et al., Diaporthe etinsideae Y.P. Tan & R.G. Shivas, Diaporthe eucalyptorum Crous & R.G. Shivas, Diaporthe fujianensis Jayaward. et al., Diaporthe fusiformis Jayaward. et al., Diaporthe globoostiolata Monkai & Lumyong, Diaporthe hainanensis Qin Yang, Diaporthe hongkongensis R.R. Gomes et al., Diaporthe hubeiensis Dissan. et al., Diaporthe infecunda R.R. Gomes et al., Diaporthe italiana Chethana et al., Diaporthe juglandigena S.Y. Wang et al., Diaporthe lagerstroemiae (C.Q. Chang et al.) Y.H. Gao & L. Cai, Diaporthe lithocarpi (Y.H. Gao et al.) Y.H. Gao & L. Cai, Diaporthe lutescens S.T. Huang et al., Diaporthe machili S.T. Huang et al., Diaporthe megabiguttulata M. Luo et al., Diaporthe middletonii R.G. Shivas et al., Diaporthe morindae M. Luo et al., Diaporthe nannuoshanensis S.T. Huang et al., Diaporthe nigra Brahman. & K.D. Hyde, Diaporthe orixae Q.T. Lu & Zhen Zhang, Diaporthe passifloricola Crous & M.J. Wingf., Diaporthe pimpinellae Abeywickrama et al., Diaporthe pseudoinconspicua T.G.L Oliveira et al., Diaporthe pungensis S.T. Huang et al., Diaporthe rhodomyrti C.M. Tian & Qin Yang, Diaporthe rosae M.C. Samar. & K.D. Hyde, Diaporthe rumicicola Manawas et al., Diaporthe salicicola R.G. Shivas et al., Diaporthe samaneae Monkai & Lumyong, Diaporthe subcylindrospora S.K. Huang et al., Diaporthe tectonae Doilom et al., Diaporthe tectonigena Doilom et al., Diaporthe theobromatis H. Dong et al., Diaporthe thunbergiicola Udayanga & K.D. Hyde, Diaporthe tuyouyouiae Y.P. Tan et al., Diaporthe unshiuensis F. Huang et al., Diaporthe vochysiae S.A. Noriler et al., Diaporthe xishuangbannaensis Hongsanan & K.D. Hyde, Diaporthe xylocarpi M.S. Calabon & E.B.G. Jones, Diaporthe zaobaisu Y.S. Guo & G.P. Wang, Diaporthe zhaoqingensis M. Luo et al. Citation: Pereira DS, Phillips AJL (2024). Diaporthe species on palms - integrative taxonomic approach for species boundaries delimitation in the genus Diaporthe, with the description of D. pygmaeae sp. nov. Studies in Mycology 109: 487-594. doi: 10.3114/sim.2024.109.08.

A new species of giant gecko of the genus Rhacodactylus from New Caledonia (Squamata, Gekkota, Diplodactylidae)

We describe a new species of giant gecko, Rhacodactylus willihenkeli sp. nov. from New Caledonia. The new species is most similar in external appearance and molecular data (16S and ND2 sequences) with R. leachianus from which it differs in coloration as well as having a genetic distance of 5.0% in the 16S gene fragment and 8.5% in the ND2 fragment, respectively.

Identification of two new species of Mecistocephalus (Chilopoda, Geophilomorpha, Mecistocephalidae) from southern China and the re-description of Mecistocephalussmithii Pocock, 1895

Mecistocephalus Newport, 1843 is the most diverse genus in the family Mecistocephalidae; however, only two species have been recorded in mainland China to date. Therefore, taxonomic research on Chinese Mecistocephalus needs further research. In this study, the species diversity of Mecistocephalus in southern China was investigated using the mitochondrial marker COI integrated with morphological evidence. Species delimitation using Automatic Barcode Gap Discovery, Poisson Tree Processes, and phylogenetic and morphological analyses revealed ten species, including two newly described species, M.chuensis Jiang & You, sp. nov. and M.huangi Jiang & You, sp. nov. Furthermore, based on newly collected specimens, the presence of the little-known species M.smithii Pocock, 1895 was confirmed in China and thoroughly re-described.

Revalidation of Enteromius crocodilensis (Fowler, 1934) from synonymy with the disjunctly distributed Enteromius argenteus (Günther, 1868) based on molecular and morphological evidence

The rosefin barb, Enteromius argenteus, as currently described, is a freshwater fish with a distribution that is geographically separated and divided into the northern population in the Kwanza River system in Angola, and the southern population in the Inkomati River system in South Africa and Eswatini. Due to this disjunct distribution pattern, it is likely that the two populations represent distinct species. mtDNA sequence data and detailed examination of morphometric characters revealed considerable genetic (2.8%-3.5%) and morphological differentiation of the two populations, suggesting their recognition as two distinct species. Enteromius crocodilensis is revalidated and redescribed for the southern population that is readily distinguished from E. argenteus by nonoverlapping circumpeduncular scale counts (12-13 vs. 14) and color pattern (presence of a conspicuous dark band along the midline vs. absence of characteristic melanin patterns). Phylogenetic analysis based on mtDNA cytochrome oxidase subunit I (COI) data places both E. argenteus and E. crocodilensis in a well-supported clade that includes a number of morphologically similar sawfin barb species from southern and central Africa.

Hidden diversity in anthropophilic sand flies of the Monticola Series (Diptera, Psychodidae)

The Monticola series comprises two anthropophilic and widely distributed species in Brazil: Pintomyia (Pifanomyia) monticola (Costa Lima, 1932) and Pintomyia (Pifanomyia) misionensis (Castro, 1959). They mainly occur in the Atlantic Rainforest, and it is known that Pi. monticola comprises at least two well-structured genetic lineages regarding a fragment of the cytochrome c oxidase subunit I (COI) gene. Here, we aim to elucidate the taxonomic status of this group using integrative taxonomy tools. Collections were performed in nine localities of four Brazilian states, and COI fragments were sequenced and merged with publicly available data. Several single-locus species delimitation algorithms, genetic distance metrics, phylogenetic trees, and haplotype networks were used to uncover cryptic diversity and population structure within Pi. monticola and Pi. misionensis. The resulting genetic clusters were then tested for morphological differences through linear and geometric morphometry of several characters. We analyzed 152 COI sequences, comprising 48 haplotypes. The maximum intraspecific p distances were 8.21% (mean 4.17%) and 9.12% (mean 4.4%) for Pi. monticola and Pi. misionensis, respectively, while interspecific ones ranged from 10.94 to 14.09% (mean 12.33%). Phylogenetic gene trees showed well-supported clades for both species, with clear structuring patterns within them. Species-delimitation algorithms split our dataset into at least three putative species for each taxon. Moreover, population structure analysis showed a strong correlation between Atlantic Forest areas of endemism as sources of molecular variation in Pi. monticola. Morphometric analyses were significant for wing shape variation and some linear measurements (mainly of the head) when comparing specimens of different genetic clusters for both taxa. These results indicate strong genetic structuring of Monticola series species, confirmed by morphometry, indicating two possible cryptic species complexes.

A DNA-based approach to infer species diversity of larvae and adults from the white grub genus Phyllophaga (Coleoptera: Scarabeidae)

Scarabaeoidea is a diverse and widely distributed insect group; many are agricultural pests including species within the genus Phyllophaga. Species diversity studies in this taxonomic group are done mainly using morphological identification. However, despite existing taxonomic keys for adults and larvae, identification may be difficult due to their complex morphology. Molecular taxonomy can increase the value and accuracy of morphological species identification of larvae and adults. To test this, larvae collected from soil close to maize plants were identified using molecular taxonomy, and compared with adults captured using light traps. The larvae (2021) and adults (2022) were sampled on maize at the same locations in central Mexico. Molecular identification was achieved using three regions within the Cytochrome oxidase gene (cox), two in the Cytochrome c oxidase subunit 1 (cox1), Cytochrome b (CytB) and 28S rDNA. Cox gene information was more useful than nuclear information (28S). Combined morphological and molecular taxonomy of adults distinguished between seven Phyllophaga species. Although two closely related species, P. polyphyla and P. ravida, were distinguished using cox gene information, greater resolution was obtained using CytB. All analyses identified cryptic species within P. vetula. Species found amongst sampled adults were similar to those found amongst larvae. However, the number of species was greater in adults than in larvae at the same locations. Larval information showed Phyllophaga community structure changed over time. Our findings will contribute to a better understanding of Phyllophaga's ecology in maize.

Two new species of Diamesinae (Diptera: Chironomidae) from the Central Iranian Range and Elburz Mountains (Iran), with new faunistic records for the subfamily

As part of our continuous investigation into the biodiversity of Chironomidae of Iran, we expanded our collection area to the Elburz Mountains and the Central Iranian Range in East Azerbaijan and Kurdistan Provinces. As a result of this, we discovered and described Diamesa sahandensis sp. nov. and Sympotthastia golalae sp. nov., two new Diamesinae, adding to the diversity of these genera in Iran and the Palaearctic region. We also provide new Iranian faunistic records, Diamesa kasymovi Kownacka et Kownacki, 1973, describe its female for the first time, and provide an updated key to the adult males of Sympotthastia Pagast, 1947. Based on the molecular analysis of cytochrome oxidase (COI) genes and methods for delimiting species, the average interspecific distance between S. golalae sp. nov. and other species of Sympotthastia was high enough (13.9%) to maintain a species level.

Phlebotomine sand fly survey, blood meal source identification, and description of Sergentomyia imihra n. sp. in the central Sahara of Algeria

BACKGROUND

Phlebotomine sand flies (Diptera: Psychodidae) are important vectors of various pathogens, mainly Leishmania parasites. In the Old World, the most important genus in term of pathogens transmission is the genus Phlebotomus, which includes many proven or suspected vectors of several Leishmania species, while the genus Sergentomyia remains so far unproven as a vector of human pathogens. Algeria is one of the most affected countries by human leishmaniasis.

METHODS

In the present study, an entomological survey was carried out in two provinces, Ghardaïa and Illizi, located in the north and central Sahara, respectively, where cases of human leishmaniasis are recorded. Our goal was to understand the role of the local sand fly species in the transmission of Leishmania parasites and to analyze their blood meal preferences. Collected sand flies were identified by a combination of morphological and molecular approaches that included DNA-barcoding and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) protein profiling. In addition, female blood meals were analyzed by peptide mass mapping using MALDI-TOF MS.

RESULTS

In total, 640 sand fly specimens belonging to Phlebotomus and Sergentomyia genera were collected in the two provinces. Sergentomyia antennata and Se. fallax were most abundant species in Ghardaïa, and Ph. papatasi and Ph. alexandri in Illizi. In addition, a new sand fly species was described in Illizi named Sergentomyia (Sergentomyia) imihra n. sp. Blood meal analysis of the engorged females revealed various mammalian hosts, especially goats, but also humans for Phlebotomus papatasi and Ph. alexandri, suggesting that these vector species are opportunistic feeders.

CONCLUSIONS

Integrative approach that combined morphological analysis, sequencing of DNA markers, and protein profiling enabled the recognition and description of a new Sergentomyia species, raising the number of the Algerian sand fly fauna to 27 species. Further sand fly surveillance in the central Sahara is recommended to identify the thus-far unknown males of Se. imihra n. sp.

Cryptic diversity patterns of subterranean estuaries

Subterranean estuaries are coastal ecosystems characterized by vertically stratified groundwater. The biota within these ecosystems is relatively understudied due to the inherent difficulty of accessing such extreme environments. The fauna inhabiting these ecosystems is considered vulnerable to extinction, and the presence of cryptic species has major implications for research and conservation efforts. Most species lack molecular data; however, the evaluation of genetic data for some taxa has revealed that undocumented species are common. This study employs molecular species delimitation methods and DNA barcoding through the analysis of publicly and newly generated sequences, including individuals from type localities and non-crustacean phyla; the latter are typically overlooked in biodiversity assessments of subterranean estuaries. We analysed 376 cytochrome c oxidase subunit I (COI) gene sequences and 154 16S rRNA gene sequences. The COI sequences represented 32% of previously described species and 50% of stygobiont species from the Yucatan Peninsula and Cozumel Island, while sequences of the 16S rRNA represented 14% of described species and 22% of stygobionts. Our results revealed cryptic genetic lineages and taxonomic misidentification of species. As several species from these ecosystems are recognized as endangered, the use of molecular approaches will improve biodiversity estimates and highlight overlooked cryptic lineages in need of evaluation of conservation status.

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.

New Records and New Species of Dacnusini (Hymenoptera: Braconidae, Alysiinae) Based on Morphological and Molecular Evidence

Dacnusini is a species-rich tribe in the subfamily Alysiinae, with most species exclusively serving as parasitoids of leaf-mining Diptera (Agromyzidae). The number of genera discovered in China remains limited, which is apparently insufficient considering the global diversity of species and genera within this tribe, particularly given the vast and ecologically diverse landscapes of China. In the present study, three new record genera, Victorovita Tobias, Coloneura Foerster, and Laotris Nixon, were documented for the first time in China. In addition, the species delimitation approach and haplotype network analyses based on the COI sequences, combined with morphological evidence, were employed to delimit species. The findings indicated three new species: Laotris glabella sp. nov., Laotris aethidentata sp. nov., and Victorovita aequalis sp. nov. Additionally, K2P divergences showed no overlap between intra- and interspecific genetic distances in the Laotris and Victorovita species. Detailed descriptions for new species and keys to the species of Laotris and Victorovita are provided in this paper, along with the documentation of two new species records for China: Victorovita caudata (Szépligeti, 1901) and Coloneura stylata Foerster, 1863.

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.

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.

A new species of Dainty Frog (Anura: Pyxicephalidae: Cacosternum) and the first endemic anuran to the Cederberg region of South Africa

Within the genus Cacosternum, the species C. capense and C. namaquense form a clade defined by their robust morphology, large size, and distinct dorsolateral glands. In this study, we describe a third member of the group endemic to the Cederberg region of South Africa. Specimens from this area have historically been assigned to C. karooicum, but here we show that this population is genetically unrelated. Using a combination of molecular, morphological, and acoustic data, we provide evidence to show that the Cederberg population of C. karooicum represents an undescribed species within the C. capense group. The new species can be diagnosed from its closest phylogenetic relatives, C. capense and C. namaquense, by the absence of a dark streak running downwards from the pupil into the iris, the presence of large rictal glands that form an uninterrupted arc with the angle of the jaw, heart-shaped palmar tubercles, and an advertisement call with a dominant frequency below 2 kHz. We further discuss their natural history, distribution, and conservation.

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.

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.