DNA barcode-based delineation of putative species: efficient start for taxonomic workflows

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.

Phylogeography of Microphis retzii (Bleeker, 1856) and Microphis brachyurus (Bleeker, 1854) in the Pacific

Syngnathidae are a charismatic family of teleost fishes, represented by seahorses, seadragons, and pipefishes. Syngnathidae are mainly composed of marine species, but about 30 species of pipefishes inhabit freshwater insular environments of the Indo-Pacific realm. Recent research has shown that some freshwater pipefish species are amphidromous and exhibit high intraspecific divergences across their distribution range, like Microphis brachyurus (Bleeker, 1854) distributed from Sri Lanka to French Polynesia and Microphis retzii (Bleeker, 1856) distributed from Taiwan to Indonesia. In this study, we used the mitochondrial cytochrome oxidase I (COI) partial gene of 91 specimens of M. brachyurus and 30 specimens of M. retzii from localities representative of their respective distribution area to improve knowledge on the population structure of these two widespread species. Genetic species delimitation and phylogeographic analyses were combined to explore spatial patterns of genetic diversity across the distribution ranges of the two species. We have highlighted deep genetic structuring within the two species and relate these results to various biotic and abiotic factors. For M. brachyurus, the population in Polynesia is distinct from those in the West Pacific, suggesting its distinctiveness and recognition as an evolutionary significant unit (ESU). For M. retzii, three lineages are delimited in its range distribution, suggesting the existence of two distinct species in Southeast Asia (Bali/Java/Lombok and China/Taiwan). Pipefish species are particularly vulnerable to anthropogenic pressures (inherent to Syngnathidae and insular environments). The present results, revising species delimitation and geographic distribution, will help implement effective conservation and management measures.

A Novel Polymerase Chain Reaction (PCR)-Based Method for the Rapid Identification of Chrysodeixis includens and Rachiplusia nu

Chrysodeixis includens and Rachiplusia nu are two species belonging to the Plusiinae subfamily within the Noctuidae family. Due to their morphological similarity, the identification of their larvae is difficult and time-consuming. A rapid and accurate identification of these two species is essential for their management as these species exhibit differential susceptibilities to insecticides and crops engineered to express Bacillus thuringiensis (Bt) proteins, and a molecular tool can easily provide this differentiation. Currently, molecular analysis can identify these species through genetic sequencing, an expensive and time-consuming process. In our study, after sequencing part of the mtDNA cytochrome c oxidase I (COI) gene and based on the differences found in the gene of each species, a set of species-specific primers was developed: one reverse primer common to both species and two forward primers, specific to each species, amplifying fragments of 199 base pairs (bp) for C. includens and 299 bp for R. nu. Our results indicate that the primers were specific for these species, enabling the identification of individuals directly through agarose gel. The new methodology proved to be accurate, rapid, and reliable for the correct identification of these two species of loopers.

Hidden diversity revealed by DNA barcoding of paralichthyidae fish along the caribbean and brazilian coast

DNA barcoding based on COI sequences has been highly informative for the taxonomic assessment of many fish species due to its high rate of species identification. Accordingly, numerous studies have employed this method to encompass species checklists of different areas, assessment of cryptic diversity, biodiversity monitoring, and other applications. Furthermore, most of the success of COI DNA barcoding relies on a comprehensive database (BOLD Systems) that holds sequences and detailed records of millions of species and applies a system (BIN) that clusters short DNA barcodes to generate OTUs. Besides COI, the 16S rDNA has proven to be suitable for the molecular identification of several taxa, and the combination of both markers could be advantageous in investigating species composition in the Neotropics. The family Paralichthyidae comprises over 60 flatfish species. Most of them inhabit tropical areas and remain understudied. Here, we evaluated the diversity of Paralichthyidae species along the Brazilian coast through COI and 16S DNA barcodes. Combining our dataset with BOLD (COI) and GenBank (16S) public records, we conducted tree-based and genetic distance analyses along with BIN-based and species delimitation methods. Our results were consistent for both markers, and we identified eight species of paralichthyids among our samples with high confidence. Interestingly, our analyses indicate several cases where public records assigned to the same species might be sequences from multiple species. Therefore, we provide new records and occurrences and explore important issues regarding misidentification and putative cryptic diversity for several species.

Diving deeper into the taxonomy of the Neoscopelus species complex (Myctophiformes: Neoscopelidae) with the description of Neoscopelus serranoi sp. nov

Previous studies have highlighted possible cryptic biodiversity in the genus Neoscopelus. This hypothesis was tested using new morphological, molecular and biogeographical data on species of this genus caught in the north Atlantic between 2010 and 2022. The information obtained has been combined with available data in an integrative approach, including a review of morphological characters reported in the ichthyological literature and DNA-based species delimitation analyses. The main outcome of the present study is the description of Neoscopelus serranoi sp. nov. from the Atlantic and southwestern Indian Oceans. The new species is morphologically very similar to Neoscopelus microchir from which differs in having a shorter anal-fin base, a shorter pelvic fin, more dorsal and pectoral-fin rays, less anal-fin rays, fewer gillrakers and fewer isthmus and lateral photophores. They also differ in geographic distribution, with the new species occurring in the Atlantic Ocean and the near southwestern Indian Ocean, whereas N. microchir was originally described from Japanese waters of the Pacific Ocean. A literature review of available morphological data between geographic areas for Neoscopelus macrolepidotus and Neoscopelus microchir showed a large intraspecific overlap and no boundaries. However, molecular species delimitation based on the mitochondrial COI gene revealed the existence of cryptic diversity in both species, with eight to ten molecular operational taxonomic units (MOTU), compared to three valid species. Neoscopelus serranoi sp. nov. was considered an independent MOTU in all analyses performed, supporting the morphological identification as a new species. These results highlight that the taxonomy of Neoscopelus is far from settled and show that a greater sampling effort is needed to resolve the uncertainties and to describe unknown putative species. This also exemplifies the virtues of integrative taxonomy in delving into the systematics of deep-sea fishes.

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.

Species delimitation, discovery and conservation in a tiger beetle species complex despite discordant genetic data

In an age of species declines, delineating and discovering biodiversity is critical for both taxonomic accuracy and conservation. In recent years, there has been a movement away from using exclusively morphological characters to delineate and describe taxa and an increase in the use of molecular markers to describe diversity or through integrative taxonomy, which employs traditional morphological characters, as well as genetic or other data. Tiger beetles are charismatic, of conservation concern, and much work has been done on the morphological delineation of species and subspecies, but few of these taxa have been tested with genetic analyses. In this study, we tested morphologically based taxonomic hypotheses of polymorphic tiger beetles in the Eunota circumpicta (LaFerté-Sénectère, 1841) species complex using multilocus genomic and mtDNA analyses. We find multiple cryptic species within the previous taxonomic concept of Eunota circumpicta, some of which were historically recognized as subspecies. We found that the mtDNA and genomic datasets did not identify the same taxonomic units and that the mtDNA was most at odds with all other genetic and morphological patterns. Overall, we describe new cryptic diversity, which raises important conservation concerns, and provide a working example for testing species and subspecies validity despite discordant data.

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

BACKGROUND

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

RESULTS

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

CONCLUSION

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

High species diversity of Phintella and Phintella-like spiders (Araneae: Salticidae) in Vietnam revealed by DNA-based species delimitation analyses

Salticidae (jumping spiders) usually exhibit pronounced sexual dimorphism in adult morphology, particularly body coloration and size and shape of the first legs. Consequently, the male and female from the same species might be erroneously assigned to different species or even different genera, which could generate synonymies in classification if only morphological data were used. Phintella is a species-rich genus of Salticidae, which currently exhibits 76 named species. However, the male-female counterpart is unknown for nearly half of the species. In this study, we used a molecular approach to delineate the species boundaries for Phintella and Phintella-like specimens collected in Vietnam, using morphological information as supporting data. We used three gene fragments (mitochondrial COI, 16S-ND1, and nuclear 28S) and biogeographical considerations for species delimitation. A total of 22 putative species were recognized: 18 species of the genus Phintella, one species of the genus Lechia (L. squamata), and three species of the genus Phinteloides. Eleven undescribed species were discovered, of which seven have a male-female combination, two species have only males, and two species have only females. The crown age of Phintella was estimated at the Serravallian stage of the Miocene after the increase of species number around 16 MYA. The crown ages of most putative species recognized in this study were estimated in the Pleistocene, and the divergence among sister species likely occurred from the mid-Miocene to the Pliocene. Our ancestral range reconstruction results showed that the diversification of our ingroup was governed by progressive dispersal events, i.e., Phintella and their related species in Vietnam diversified while expanding their range on the continent. Our results provide fundamental biodiversity data for a high-diversity genus in Vietnamese Phintella spiders.

Delimiting Species with Single-Locus DNA Sequences

DNA sequences are increasingly used for large-scale biodiversity inventories. Because these genetic data avoid the time-consuming initial sorting of specimens based on their phenotypic attributes, they have been recently incorporated into taxonomic workflows for overlooked and diverse taxa. Major statistical developments have accompanied this new practice, and several models have been proposed to delimit species with single-locus DNA sequences. However, proposed approaches to date make different assumptions regarding taxon lineage history, leading to strong discordance whenever comparisons are made among methods. Distance-based methods, such as Automatic Barcode Gap Discovery (ABGD) and Assemble Species by Automatic Partitioning (ASAP), rely on the detection of a barcode gap (i.e., the lack of overlap in the distributions of intraspecific and interspecific genetic distances) and the associated threshold in genetic distances. Network-based methods, as exemplified by the REfined Single Linkage (RESL) algorithm for the generation of Barcode Index Numbers (BINs), use connectivity statistics to hierarchically cluster-related haplotypes into molecular operational taxonomic units (MOTUs) which serve as species proxies. Tree-based methods, including Poisson Tree Processes (PTP) and the General Mixed Yule Coalescent (GMYC), fit statistical models to phylogenetic trees by maximum likelihood or Bayesian frameworks.Multiple webservers and stand-alone versions of these methods are now available, complicating decision-making regarding the most appropriate approach to use for a given taxon of interest. For instance, tree-based methods require an initial phylogenetic reconstruction, and multiple options are now available for this purpose such as RAxML and BEAST. Across all examined species delimitation methods, judicious parameter setting is paramount, as different model parameterizations can lead to differing conclusions. The objective of this chapter is to guide users step-by-step through all the procedures involved for each of these methods, while aggregating all necessary information required to conduct these analyses. The "Materials" section details how to prepare and format input files, including options to align sequences and conduct tree reconstruction with Maximum Likelihood and Bayesian inference. The Methods section presents the procedure and options available to conduct species delimitation analyses, including distance-, network-, and tree-based models. Finally, limits and future developments are discussed in the Notes section. Most importantly, species delimitation methods discussed herein are categorized based on five indicators: reliability, availability, scalability, understandability, and usability, all of which are fundamental properties needed for any approach to gain unanimous adoption within the DNA barcoding community moving forward.

Species delimitation by DNA barcoding reveals undescribed diversity in Stelliferinae (Sciaenidae)

Stelliferinae is the third most speciose subfamily of Sciaenidae, with 51 recognized species arranged in five genera. Phylogenies derived from both morphological and molecular data support the monophyly of this subfamily, although there is no general consensus on the intergeneric relationships or the species diversity of this group. We used the barcoding region of the cytochrome oxidase C subunit I (COI) gene to verify the delimitation of Stelliferinae species based on the Automatic Barcode Gap Discovery (ABGD), Generalized Mixed Yule Coalescence (GMYC), and Bayesian Poisson Tree Process (bPTP) methods. In general, the results of these different approaches were congruent, delimiting 30-32 molecular operational taxonomic units (MOTUs), most of which coincided with valid species. Specimens of Stellifer menezesi and Stellifer gomezi were attributed to a single species, which disagrees with the most recent review of this genus. The evidence also indicated that Odontoscion xanthops and Corvula macrops belong to a single MOTU. In contrast, evidence also indicates presence of distinct lineages in both Odontoscion dentex and Bairdiella chrysoura. Such results are compatible with the existence of cryptic species, which is supported by the genetic divergence and haplotype genealogy. Therefore, the results of the present study indicate the existence of undescribed diversity in the Stelliferinae, which reinforces the need for an ample taxonomic review of the fish in this subfamily.

Species Delimitation in a Polyploid Group of Iberian Jasione (Campanulaceae) Unveils Coherence between Cryptic Speciation and Biogeographical Regionalization

Groups with morphological stasis are an interesting framework to address putative cryptic species that may be hidden behind traditional taxonomic treatments, particularly when distribution ranges suggest disjunct and environmentally heterogeneous biogeographic patterns. New hypotheses of delimitation of evolutionary independent units can lead to the identification of different biogeographic processes, laying the foundation to investigate their historical and ecological significance. Jasione is a plant genus with a distribution centered in the Mediterranean basin, characterized by significant morphological stasis. Within the western Mediterranean J. gr. crispa species complex, J. sessiliflora s.l. and allied taxa form a distinct group, occupying environmentally diverse regions. At least two ploidy levels, diploid and tetraploid, are known to occur in the group. The internal variability is assessed with phylogenetic tools, viz. GMYC and ASAP, for species delimitation. The results are compared with other lines of evidence, including morphology and cytology. The fitting of distribution patterns of the inferred entities to chorological subprovinces is also used as a biogeographical and environmental framework to test the species hypothesis. Despite the scarcity of diagnostic morphological characters in the group, phylogenetic delimitation supports the description of at least one cryptic species, a narrow endemic in the NE Iberian Peninsula. Moreover, the results support the segregation of a thermophilic group of populations in eastern Iberia from J. sessiliflora. Ploidy variation from a wide geographical survey supports the systematic rearrangement suggested by species delimitation. Taxonomic reorganization in J. sessiliflora s.l. would allow ecological interpretations of distribution patterns in great accordance with biogeographical regionalization at the subprovince level, supporting geobotanical boundaries as a framework to interpret species ecological coherence of cryptic lineages. These results suggest that species differentiation, together with geographic isolation and polyploidization, is associated with adaptation to different environments, shifting from more to less thermophilic conditions. Thus, the recognition of concealed evolutionary entities is essential to correctly interpret biogeographical patterns in regions with a complex geologic and evolutionary history, such as the Mediterranean basin, and biogeographical units emerge as biologically sound frameworks to test the species hypothesis.

DNA barcoding the ichthyofauna of the Beibu Gulf: Implications for fisheries management in a seafood market hub

The Beibu Gulf in China is situated in the tropics, in the western Pacific Ocean. It is an emblematic region combining proximity to a marine biodiversity hotspot and a major seafood hub. Intensification of marine fishing and ocean warming led to a drastic decline in fish populations in the Beibu Gulf during the last decades. This situation urges the development of molecular resources of the Beibu Gulf fish fauna in order to enable automated molecular identifications at the species level for next-generation monitoring. With this objective, we present the results of a large-scale campaign to DNA barcode fishes of the Beibu Gulf. We successfully generated 789 new DNA barcodes corresponding to 263 species which, together with 291 sequences mined from Genbank and BOLD, resulted in a reference library of 1080 sequences from 285 species. Based on the use of four DNA-based species delimitation methods (BIN, ASAP, mPTP, mGMYC), a total of 285 Molecular Operational Taxonomical Units (MOTUs). A single case of cryptic diversity was detected in Scomberomorus guttatus and a single species pair was not captured by delimitation methods. Intraspecific K2P genetic distances averaged 0.36% among sequences within species, whereas K2P genetic distances among species within genera averaged 6.96%. The most speciose families in open water trawling differ from those at fish market, and discrepancies with historical data are discussed in the light of recently documented stock collapses.

DNA Barcode library of the endemic-rich avifauna of the oceanic islands of the Gulf of Guinea

Background

The BioSTP: DNA Barcoding of endemic birds from oceanic islands of the Gulf of Guinea dataset contains records of 155 bird specimens belonging to 56 species in 23 families, representing over 80% of the diversity of the breeding landbird community. All specimens were collected on Príncipe, São Tomé and Annobón Islands between 2002 and 2021 and morphologically identified to species or subspecies level by qualified ornithologists. The dataset includes all endemic species and 3/4 of the extant endemic subspecies of the islands. This dataset is the second release by BioSTP and it greatly increases the knowledge on the DNA barcodes of Gulf of Guinea birds. All DNA extractions are deposited at Associação BIOPOLIS - CIBIO, Research Center in Biodiversity and Genetic Resources.

New information

The dataset includes DNA barcodes for all 29 endemic bird species and for 11 of the 15 extant endemic bird subspecies from the oceanic islands of the Gulf of Guinea. This is the first major DNA barcode set of African birds. The three endemic subspecies of Crithagrarufobrunnea, an island endemic with three allopatric populations within the Archipelago, are also represented. Additionally, we obtained DNA barcodes for 16 of the 21 non-endemic landbirds and for one vagrant (Sylviacommunis). In total, forty-one taxa were new additions to the Barcode of Life Data System (BOLD), with another 11 corresponding to under-represented taxa in BOLD. Furthermore, the submitted sequences were found to cluster in 55 Barcode Index Numbers (BINs), 37 of which were new to BOLD. All specimens have their DNA barcodes publicly accessible through BOLD online database and GenBank.

DNA barcodes provide insights into the diversity and biogeography of the non-biting midge Polypedilum (Diptera, Chironomidae) in South America

South America, particularly within its tropical belt, is renowned for its unparalleled high levels of species richness, surpassing other major biomes. Certain neotropical areas harbor fragmented knowledge of insect diversity and face imminent threats from biodiversity loss and climate change. Hence, there is an urgent need for rapid estimation methods to complement slower traditional taxonomic approaches. A variety of algorithms for delimiting species through single-locus DNA barcodes have been developed and applied for rapid species diversity estimates across diverse taxa. However, tree-based and distance-based methods may yield different group assignments, leading to potential overestimation or underestimation of putative species. Here, we investigate the performance of different DNA-based species delimitation approaches to rapidly estimate the diversity of Polypedilum (Chironomidae, Diptera) in South America. Additionally, we test the hypothesis that significant differences exist in the community structure of Polypedilum fauna between South America and its neighboring regions, particularly the Nearctic. Our analysis encompasses a dataset of 1492 specimens from 598 locations worldwide, with a specific focus on South America. Within this region, we analyzed a subset of 247 specimens reported from 37 locations. Using various methods including the Barcode Index Number (BIN), Bayesian Poisson tree processes (bPTP), multi-rate Poisson tree processes (mPTP), single-rate Poisson tree processes (sPTP), and generalized mixed Yule coalescent (sGMYC), we identify molecular operational taxonomic units (MOTUs) ranging from 267 to 520. Our results indicate that the sGMYC method is the most suitable for estimating putative species in our dataset, resulting in the identification of 75 species in the Neotropical region, particularly in South America. Notably, this region exhibited higher species richness in comparison to the Palearctic and Oriental realms. Additionally, our findings suggest potential differences in species composition of Polypedilum fauna between the Neotropical and the adjacent Nearctic realms, highlighting high levels of endemism and species richness in the first. These results support our hypothesis that there are substantial differences exist in species composition between the Polypedilum fauna in South America and the neighboring regions.

Combining morphological and mitochondrial DNA data to describe a new species of Austroniscus Vanhöffen, 1914 (Isopoda, Janiroidea, Nannoniscidae) linking abyssal and hadal depths of the Puerto Rico Trench

Hadal trenches are perceived as a unique deep-sea ecosystem with fundamentally different communities compared to the nearby abyss. So far, however, scarce information exists about how populations are genetically linked within a trench and about mechanisms for species divergence. The present study presents the morphological and molecular-genetic characterization and description of a new nannoniscid species within the genus Austroniscus Vanhöffen, 1914 obtained from abyssal and hadal depths of the Puerto Rico Trench, NW Atlantic. Samples were collected as part of the Vema-TRANSIT expedition onboard RV Sonne in January 2015. Because of the large depth differences between sampling locations (4,552-8,338 m), we expected to find different species within the genus inhabiting abyssal and hadal sites. Initial morphological examination using traditional light microscopy and Confocal Laser Scanning Microscopy was paired with subsequent molecular analysis based on mtDNA (COI and 16S). Contrary to our assumptions, combined morphological and molecular species delimitation analyses (sGMYC, mPTP, ABGD) revealed the presence of only one species spanning the abyssal and hadal seafloor of the Puerto Rico Trench. In addition, comparison with type material could show that this species belongs to a new species, Austroniscus brandtae n. sp., which is described herein. Incongruence between some species delimitation methods suggesting the presence of multiple species is interpreted as strong genetic population structuring within the trench, which is also supported by the analysis of the haplotype networks. The geographic and bathymetric distribution of Austroniscus species is discussed. The species described herein represents the first in the genus Austroniscus from the Atlantic Ocean and the deepest record of the genus to date, and hence significantly expanding previously known limits of its geographic and bathymetric range.

Diversification and evolutionary history of the African laminated-toothed rats (Rodentia, Otomyini)

The African continent was subjected to periodic climatic shifts during the Pliocene and Pleistocene. These habitat changes greatly affected the evolutionary processes and tempo of diversification in numerous, widely distributed mammals. The Otomyini (Family Muridae) comprises three African rodent genera, Parotomys, Otomys and Myotomys, characterized by unique laminated-shaped molars. Species within this tribe generally prefer open-habitat and show low dispersal capabilities, with previous studies suggesting that their diversification was closely associated with climatic oscillations over the last four million years. Our phylogenetic reconstructions, based on three mitochondrial (mtDNA) genes (Cytb, COI and 12S) and four nuclear introns (EF, SPTBN, MGF and THY), identified eight major genetic clades that are distributed across southern, eastern and western Africa. Our data permit the re-examination of the taxonomic status of the three genera as well as the previously proposed mesic-arid dichotomy of the 10 South African species. Moreover, multiple mtDNA species delimitation methods incorporating 168 specimens estimated the number of Otomyini species to be substantially higher than the ∼30 recognized, suggesting that the current taxonomy will necessitate an integrative approach to delimit extant species diversity within the Otomyini. The data suggests that the origin of the tribe can be dated back to ∼5.7 million years ago (Ma) in southern Africa. The distribution and phylogenetic associations among the eight major otomyine evolutionary lineages can best be explained by several waves of northward colonization from southern Africa, complemented by independent reversed dispersals from eastern back to southern Africa at different time periods. There is strong support for the hypothesis that the radiation, dispersion, and diversification of the otomyine rodents is closely linked to recent Plio-Pleistocene climatic oscillations.

DNA barcoding of Chinese snakes reveals hidden diversity and conservation needs

DNA barcoding has greatly facilitated studies of taxonomy, biodiversity, biological conservation, and ecology. Here, we establish a reliable DNA barcoding library for Chinese snakes, unveiling hidden diversity with implications for taxonomy, and provide a standardized tool for conservation management. Our comprehensive study includes 1638 cytochrome c oxidase subunit I (COI) sequences from Chinese snakes that correspond to 17 families, 65 genera, 228 named species (80.6% of named species) and 36 candidate species. A barcode gap analysis reveals gaps, where all nearest neighbour distances exceed maximum intraspecific distances, in 217 named species and all candidate species. Three species-delimitation methods (ABGD, sGMYC, and sPTP) recover 320 operational taxonomic units (OTUs), of which 192 OTUs correspond to named and candidate species. Twenty-eight other named species share OTUs, such as Azemiops feae and A. kharini, Gloydius halys, G. shedaoensis, and G. intermedius, and Bungarus multicinctus and B. candidus, representing inconsistencies most probably caused by imperfect taxonomy, recent and rapid speciation, weak taxonomic signal, introgressive hybridization, and/or inadequate phylogenetic signal. In contrast, 43 species and candidate species assign to two or more OTUs due to having large intraspecific distances. If most OTUs detected in this study reflect valid species, including the 36 candidate species, then 30% more species would exist than are currently recognized. Several OTU divergences associate with known biogeographic barriers, such as the Taiwan Strait. In addition to facilitating future studies, this reliable and relatively comprehensive reference database will play an important role in the future monitoring, conservation, and management of Chinese snakes.

Integrative Taxonomy Approach Reveals Cryptic Diversity within the Phoretic Pseudoscorpion Genus Lamprochernes (Pseudoscorpiones: Chernetidae)

Pseudoscorpions represent an ancient, but homogeneous group of arachnids. The genus Lamprochernes comprises several morphologically similar species with wide and overlapping distributions. We implemented an integrative approach combining molecular barcoding (cox1), with cytogenetic and morphological analyses in order to assess species boundaries in European Lamprochernes populations. The results suggest ancient origins of Lamprochernes species accompanied by morphological stasis within the genus. Our integrative approach delimited three nominal Lamprochernes species and one cryptic lineage Lamprochernes abditus sp. nov. Despite its Oligocene origin, L. abditus sp. nov. can be distinguished from its closest relative only by molecular and cytogenetic differences, or alternatively, by a complex multivariate morphometric analysis involving other Lamprochernes species. The population structure and common haplotype sharing across geographically distant populations in most Lamprochernes species suggest that a phoretic manner of dispersal is efficient in this group.

Molecular analyses of pseudoscorpions in a subterranean biodiversity hotspot reveal cryptic diversity and microendemism

Nested within the Mediterranean biodiversity hotspot, the Dinaric Karst of the western Balkans is one of the world's most heterogeneous subterranean ecosystems and renowned for its highly diverse and mostly endemic fauna. The evolutionary processes leading to both endemism and diversity remain insufficiently understood, and large-scale analyses on taxa that are abundant in both subterranean and surface habitats remain infrequent. Here, we provide the first comprehensive molecular study on Croatian pseudoscorpions, a lineage of arachnids that is common and diverse in both habitats. Phylogenetic reconstructions using 499 COI sequences derived from 128 morphospecies collected across the Dinaric Karst show that: (i) occurrence in karstic microhabitats boosters speciation and endemism in the most diverse genera Chthonius C.L. Koch, 1843 (37 morphospecies) and Neobisium Chamberlin, 1930 (34 morphospecies), (ii) evidence for ongoing diversification is found in many species and species complexes through low optimal thresholds (OTs) and species delineation analyses, and (iii) landscape features, such as mountain ranges, correlate with patterns of genetic diversity in the diverse genus Neobisium. We present two synonymies: Protoneobisium Ćurčić, 1988 = Neobisium, syn. nov., and Archaeoroncus Ćurčić and Rađa, 2012 = Roncus L. Koch, 1873, syn. nov. Overall, our study suggests that karstic microhabitats promote diversification in soil- and cave-dwelling arthropods at all taxonomic levels, but also provide important refugia for invertebrates in past and present periods of environmental change.

Characterization of the Complete Chloroplast Genome of Four Species in Callerya

BACKGROUND

Callerya reticulata (Bentham) Schot, Callerya dielsiana (Harms) P.K. Loc ex Z. Wei & Pedley, Callerya nitida var. hirsutissima (Z. Wei) X.Y. Zhu, and Callerya nitida (Bentham) R. Geesink, which belongs to the Leguminosae family, are important medicinal plants in China. The genus Callerya includes 26 species, 18 species are distributed in China, and the vine stems of some species are used as traditional medicinal herbs because they have important pharmacological activity. Due to the high similarity of appearance, it is difficult to identify them in the market by appearance alone. Therefore, circulating of Callerya-related materia medica on the market is confusing, sometimes even leading to drug safety problems. It is urgent to develop molecular methods for their identification.

OBJECTIVE

To sequence and analyze the complete chloroplast (cp) genomes of C. reticulata, C. dielsiana, C. nitida var. hirsutissima, and C. nitida and to analyze their cp genome differences as a basis for seeking easier DNA barcoding for their identification.

METHOD

After using Illumina high-throughput sequencing and nanopore sequencing to obtain the genome data, some bioinformatics software was used to assembly and analyze the molecular structure of cp genomes.

RESULTS

The complete cp genomes of the four species were circular molecules, which ranged from 130 435 to 132 546 bp, and GC contents ranged from 33.89% to 34.89%. Each of them includes a large single-copy region, a small single-copy region, and without large inverted repeat regions.

CONCLUSIONS

These results suggested that highly variable regions of the four cp genomes would provide useful plastid markers, which could be used as a potential genomic resource to resolve phylogenetic questions and provide a reference for mining specific DNA barcodes of these species.

HIGHLIGHTS

Our study provided highly effective molecular markers for subsequent phylogenetic analysis, species identification, and biogeographic analysis of Callerya.

DNA Barcoding of Lepidoptera Species from the Maltese Islands: New and Additional Records, with an Insight into Endemic Diversity

This work presents the first outcomes resulting from a DNA barcode reference library of lepidopteran species from Malta. The library presented here was constructed from the specimens collected between 2015 and 2019 and covers the genetic barcodes of 146 species (ca. 25% of lepidopterous Maltese fauna), including four newly recorded Lepidoptera species from the Maltese islands: Apatema baixerasi, Bostra dipectinialis, Oiketicoides lutea, and Phereoeca praecox. The DNA reference barcode library constructed during this study was analyzed in conjunction with publicly available DNA barcodes and used to assess the ability of the local DNA barcodes to discriminate species. Results showed that each species occupies a different BOLD BIN; therefore, DNA barcoding was able to discriminate between the studied species. Our data led to the formation of 12 new BOLD BINs—that is, OTUs that were identified during this work—while nearly 46% of the barcodes generated during this study were never recorded on conspecifics, further indicating the uniqueness of genetic diversity on these central Mediterranean islands. The outcomes of this study highlight the integrative taxonomic approach, where molecular taxonomy plays an important role for biodiversity investigation in its entirety.

Super-Mitobarcoding in Plant Species Identification? It Can Work! The Case of Leafy Liverworts Belonging to the Genus Calypogeia

Molecular identification of species is especially important where traditional taxonomic methods fail. The genus Calypogeia belongs to one of the tricky taxons. The simple morphology of these species and a tendency towards environmental plasticity make them complicated in identification. The finding of the universal single-locus DNA barcode in plants seems to be 'the Holy Grail'; therefore, researchers are increasingly looking for multiloci DNA barcodes or super-barcoding. Since the mitochondrial genome has low sequence variation in plants, species delimitation is usually based on the chloroplast genome. Unexpectedly, our research shows that super-mitobarcoding can also work! However, our outcomes showed that a single method of molecular species delimitation should be avoided. Moreover, it is recommended to interpret the results of molecular species delimitation alongside other types of evidence, such as ecology, population genetics or comparative morphology. Here, we also presented genetic data supporting the view that C. suecica is not a homogeneous species.

Comparing the Efficiency of Single-Locus Species Delimitation Methods within Trochoidea (Gastropoda: Vetigastropoda)

In the context of diminishing global biodiversity, the validity and practicality of species delimitation methods for the identification of many neglected and undescribed biodiverse species have been paid increasing attention. DNA sequence-based species delimitation methods are mainly classified into two categories, namely, distance-based and tree-based methods, and have been widely adopted in many studies. In the present study, we performed three distance-based (ad hoc threshold, ABGD, and ASAP) and four tree-based (sGMYC, mGMYC, PTP, and mPTP) analyses based on Trochoidea COI data and analyzed the discordance between them. Moreover, we also observed the performance of these methods at different taxonomic ranks (the genus, subfamily, and family ranks). The results suggested that the distance-based approach is generally superior to the tree-based approach, with the ASAP method being the most efficient. In terms of phylogenetic methods, the single threshold version performed better than the multiple threshold version of GMYC, and PTP showed higher efficiency than mPTP in delimiting species. Additionally, GMYC was found to be significantly influenced by taxonomic rank, showing poorer efficiency in datasets at the genus level than at higher levels. Finally, our results highlighted that cryptic diversity within Trochoidea (Mollusca: Vetigastropoda) might be underestimated, which provides quantitative evidence for excavating the cryptic lineages of these species.

Taxonomy of Aspergillus series Versicolores: species reduction and lessons learned about intraspecific variability

Aspergillus series Versicolores members occur in a wide range of environments and substrates such as indoor environments, food, clinical materials, soil, caves, marine or hypersaline ecosystems. The taxonomy of the series has undergone numerous re-arrangements including a drastic reduction in the number of species and subsequent recovery to 17 species in the last decade. The identification to species level is however problematic or impossible in some isolates even using DNA sequencing or MALDI-TOF mass spectrometry indicating a problem in the definition of species boundaries. To revise the species limits, we assembled a large dataset of 518 strains. From these, a total of 213 strains were selected for the final analysis according to their calmodulin (CaM) genotype, substrate and geography. This set was used for phylogenetic analysis based on five loci (benA, CaM, RPB2, Mcm7, Tsr1). Apart from the classical phylogenetic methods, we used multispecies coalescence (MSC) model-based methods, including one multilocus method (STACEY) and five single-locus methods (GMYC, bGMYC, PTP, bPTP, ABGD). Almost all species delimitation methods suggested a broad species concept with only four species consistently supported. We also demonstrated that the currently applied concept of species is not sustainable as there are incongruences between single-gene phylogenies resulting in different species identifications when using different gene regions. Morphological and physiological data showed overall lack of good, taxonomically informative characters, which could be used for identification of such a large number of existing species. The characters expressed either low variability across species or significant intraspecific variability exceeding interspecific variability. Based on the above-mentioned results, we reduce series Versicolores to four species, namely A. versicolor, A. creber, A. sydowii and A. subversicolor, and the remaining species are synonymized with either A. versicolor or A. creber. The revised descriptions of the four accepted species are provided. They can all be identified by any of the five genes used in this study. Despite the large reduction in species number, identification based on phenotypic characters remains challenging, because the variation in phenotypic characters is high and overlapping among species, especially between A. versicolor and A. creber. Similar to the 17 narrowly defined species, the four broadly defined species do not have a specific ecology and are distributed worldwide. We expect that the application of comparable methodology with extensive sampling could lead to a similar reduction in the number of cryptic species in other extensively studied Aspergillus species complexes and other fungal genera. Citation: Sklenář F, Glässnerová K, Jurjević Ž, Houbraken J, Samson RA, Visagie CM, Yilmaz N, Gené J, Cano J, Chen AJ, Nováková A, Yaguchi T, Kolařík M, Hubka V (2022). Taxonomy of Aspergillus series Versicolores: species reduction and lessons learned about intraspecific variability. Studies in Mycology 102 : 53-93. doi: 10.3114/sim.2022.102.02.

Cryptic diversity impacts model selection and macroevolutionary inferences in diversification analyses

Species persist in landscapes through ecological dynamics but proliferate at wider spatial scales through evolutionary mechanisms. Disentangling the contribution of each dynamic is challenging, but the increasing use of dated molecular phylogenies opened new perspectives. First, the increasing use of DNA sequences in biodiversity inventory shed light on a substantial amount of cryptic diversity in species-rich ecosystems. Second, explicit diversification models accounting for various eco-evolutionary models are now available. Integrating both advances, we explored diversification trajectories among 10 lineages of freshwater fishes in Sundaland, for which time-calibrated and taxonomically rich phylogenies are available. By fitting diversification models to dated phylogenies and incorporating DNA-based species delimitation methods, the impact of cryptic diversity on diversification model selection and related inferences is explored. Eight clades display constant speciation rate model as the most likely if cryptic diversity is accounted, but nine display a signature of diversification slowdowns when cryptic diversity is ignored. Cryptic diversification occurs during the last 5 Myr for most groups, and palaeoecological models received little support. Most cryptic lineages display restricted range distribution, supporting geographical isolation across homogeneous landscapes as the main driver of diversification. These patterns question the persistence of cryptic diversity and its role during species proliferation.

OTU Delimitation with Earthworm DNA Barcodes: A Comparison of Methods

Although DNA barcodes-based operational taxonomic units (OTUs) are increasingly used in earthworm research, the relative efficiency of the different methods available to delimit them has not yet been tested on a comprehensive dataset. For this study, we used three datasets containing 651, 2304 and 4773 COI barcodes of earthworms from French Guiana, respectively, to compare five of these methods: two phylogenetic methods—namely Poisson Tree Processes (PTP) and General Mixed Yule Coalescence (GMYC)—and three distance matrix methods—namely Refined Single Linkage (RESL, used for assigning Barcode Index Numbers in the Barcode of Life Data systems), Automatic Barcode Gap Discovery (ABGD), and Assemble Species by Automatic Partitioning (ASAP). We found that phylogenetic approaches are less suitable for delineating OTUs from DNA barcodes in earthworms, especially for large sets of sequences. The computation times are unreasonable, they often fail to converge, and they also show a strong tendency to oversplit species. Among distance-based methods, RESL also has a clear tendency to oversplitting, while ABGD and ASAP are less prone to mismatches and have short computation times. ASAP requires less a priori knowledge for model parameterisation than AGBD, provides efficient graphical outputs, and has a much lower tendency to generate mismatches.

DNA barcoding echinoderms from the East Coast of South Africa. The challenge to maintain DNA data connected with taxonomy

Echinoderms are marine water invertebrates that are represented by more than 7000 extant species, grouped in five classes and showing diverse morphologies (starfish, sea lilies, feather stars, sea urchins, sea cucumbers, brittle and basket stars). In an effort to further study their diversity, DNA barcodes (DNA fragments of the 5' end of the cytochrome c oxidase subunit I gene, COI) have been used to complement morphological examination in identifying evolutionary lineages. Although divergent clusters of COI sequences were reported to generally match morphological species delineations, they also revealed some discrepancies, suggesting overlooked species, ecophenotypic variation or multiple COI lineages within one species. Here, we sequenced COI fragments of 312 shallow-water echinoderms of the East Coast of South Africa (KwaZulu-Natal Province) and compared morphological identifications with species delimitations obtained with four methods that are exclusively based on COI sequences. We identified a total of 103 morphospecies including 18 that did not exactly match described species. We also report 46 COI sequences that showed large divergences (>5% p-distances) with those available to date and publish the first COI sequences for 30 species. Our analyses also identified discordances between morphological identifications and COI-based species delimitations for a considerable proportion of the morphospecies studied here (49/103). For most of them, further investigation is necessary to keep a sound connection between taxonomy and the growing importance of DNA-based research.

Consolidation of Chloridium: new classification into eight sections with 37 species and reinstatement of the genera Gongromeriza and Psilobotrys

Chloridium is a little-studied group of soil- and wood-inhabiting dematiaceous hyphomycetes that share a rare mode of phialidic conidiogenesis on multiple loci. The genus has historically been divided into three morphological sections, i.e. Chloridium, Gongromeriza, and Psilobotrys. Sexual morphs have been placed in the widely perceived genus Chaetosphaeria, but unlike their asexual counterparts, they show little or no morphological variation. Recent molecular studies have expanded the generic concept to include species defined by a new set of morphological characters, such as the collar-like hyphae, setae, discrete phialides, and penicillately branched conidiophores. The study is based on the consilience of molecular species delimitation methods, phylogenetic analyses, ancestral state reconstruction, morphological hypotheses, and global biogeographic analyses. The multilocus phylogeny demonstrated that the classic concept of Chloridium is polyphyletic, and the original sections are not congeneric. Therefore, we abolish the existing classification and propose to restore the generic status of Gongromeriza and Psilobotrys. We present a new generic concept and define Chloridium as a monophyletic, polythetic genus comprising 37 species distributed in eight sections. In addition, of the taxa earlier referred to Gongromeriza, two have been redisposed to the new genus Gongromerizella. Analysis of published metabarcoding data showed that Chloridium is a common soil fungus representing a significant (0.3 %) proportion of sequence reads in environmental samples deposited in the GlobalFungi database. The analysis also showed that they are typically associated with forest habitats, and their distribution is strongly influenced by climate, which is confirmed by our data on their ability to grow at different temperatures. We demonstrated that Chloridium forms species-specific ranges of distribution, which is rarely documented for microscopic soil fungi. Our study shows the feasibility of using the GlobalFungi database to study the biogeography and ecology of fungi. Taxonomic novelties: New genus: Gongromerizella Réblová; New sections: Chloridium section Cryptogonytrichum Réblová, Hern.-Restr., M. Kolařík & F. Sklenar, Chloridium section Gonytrichopsis Réblová, Hern.-Restr., M. Kolařík & F. Sklenar, Chloridium section Metachloridium Réblová, Hern.-Restr., M. Kolařík & F. Sklenar, Chloridium section Volubilia Réblová, Hern.-Restr., M. Kolařík & F. Sklenar; New species: Chloridium bellum Réblová & Hern.-Restr., Chloridium biforme Réblová & Hern.-Restr., Chloridium detriticola Réblová & Hern.-Restr., Chloridium gamsii Réblová & Hern.-Restr., Chloridium guttiferum Réblová & Hern.-Restr., Chloridium moratum Réblová & Hern.-Restr., Chloridium peruense Réblová & Hern.-Restr., Chloridium novae-zelandiae Réblová & Hern.-Restr., Chloridium elongatum Réblová & Hern.-Restr., Chloridium volubile Réblová & Hern.-Restr.; New varieties: Chloridium bellum var. luteum Réblová & Hern.-Restr., Chloridium detriticola var. effusum Réblová & Hern.-Restr., Chloridium chloridioides var. convolutum Réblová & Hern.-Restr.; New combinations: Chloridium section Gonytrichum (Nees & T. Nees) Réblová, Hern.-Restr., M. Kolařík & F. Sklenar, Chloridium section Mesobotrys (Sacc.) Réblová, Hern.-Restr., M. Kolařík & F. Sklenar, Chloridium section Pseudophialocephala (M.S. Calabon et al.) Réblová, Hern.-Restr., M. Kolařík & F. Sklenar, Chloridium simile (W. Gams & Hol.-Jech.) Réblová & Hern.-Restr., Chloridium chloridioides (W. Gams & Hol.-Jech.) Réblová & Hern.-Restr., Chloridium subglobosum (W. Gams & Hol.-Jech.) Réblová & Hern.-Restr., Chloridium fuscum (Corda) Réblová & Hern.-Restr., Chloridium ypsilosporum (Hol.-Jech.) Réblová & Hern.-Restr., Chloridium costaricense (G. Weber et al.) Réblová & Hern.-Restr., Chloridium cuneatum (N.G. Liu et al.) Réblová & Hern.-Restr., Fusichloridium cylindrosporum (W. Gams & Hol.-Jech.) Réblová, Gongromeriza myriocarpa (Fr.) Réblová, Gongromeriza pygmaea (P. Karst.) Réblová, Gongromerizella lignicola (F. Mangenot) Réblová, Gongromerizella pachytrachela (W. Gams & Hol.-Jech) Réblová, Gongromerizella pini (Crous & Akulov) Réblová; New name: Chloridium pellucidum Réblová & Hern.-Restr.; Epitypifications (basionyms): Chaetopsis fusca Corda, Gonytrichum caesium var. subglobosum W. Gams & Hol.-Jech.; Lectotypification (basionym): Gonytrichum caesium Nees & T. Nees. Citation: Réblová M, Hernández-Restrepo M, Sklenář F, Nekvindová J, Réblová K, Kolařík M (2022). Consolidation of Chloridium: new classification into eight sections with 37 species and reinstatement of the genera Gongromeriza and Psilobotrys. Studies in Mycology 103: 87-212. doi: 10.3114/sim.2022.103.04.

An integrative insight into the diversity, distribution, and biogeography of the freshwater endemic clade of the Ponticola syrman group (Teleostei: Gobiidae) in the Caucasus biodiversity hotspot

Freshwater habitats of the Caucasus biodiversity hotspot represent a center of endemism for the gobiid genus Ponticola Iljin, 1927. Hitherto, large-scale molecular studies, owing to restricted taxon and geographical sampling, have failed to give an elaborate picture of diversity and evolutionary history of these species. Here, to contribute to filling this gap, we assessed taxonomic diversity, phylogeography and evolutionary history for the south Caspian populations of Ponticola presently classified as P. iranicus and P. patimari, using an integrative taxonomic approach comprising an entire geographic range sampling, and analyses of mitochondrial DNA haplotypes, the head lateral line system, otolith shape, and meristic and morphometric variation. All freshwater samples of the P. syrman group belong to a monophyletic clade with two main subclades: a small subclade confined to the upper Sefidroud sub-basin including the type locality of P. iranicus and a large subclade with three geographically constrained haplogroups (Hg1, Hg2, and Hg3), comprising the rest of the distribution. Hg1 showed an eastern distribution including the type locality of P. patimari, while Hg2 and Hg3 are sister groups with central and western-central distributions, respectively. The freshwater clade diverged from P. syrman during the Tyurkyanian low stand (~150 m b.s.l. lasting ~0.1 Myr), while the divergence of P. iranicus and P. patimari and radiations within P. patimari took place during the Bakunian high stand (up to 50 m a.s.l. lasting ~378-480 kya). Species delimitation analyses indicated two distinct species, corresponding to each main subclade. Although the otolith shape and lateral line analyses did not reflect with phylogeographic pattern, PCA and DFA plots of meristic and morphometric data showed a clear separation of the two major subclades corresponding to P. iranicus and P. patimari, suggesting the presence of significant morphological variation meriting formal taxonomic recognition. Overall, our findings (i) reveal the presence of two freshwater endemic species in the P. syrman group, and pending further investigation, hypothesize the presence of a third cryptic species; (ii) revise and document a narrow distributional range and low diversity for P. iranicus, in contrast to a wider distributional range and high diversity for P. patimari; (iii) suggest that the climatic oscillations of the Pleistocene were associated with the cladogenesis within the P. syrman group; and (iv) allowed for the recognition of conservation units and proposition of management measures.

Towards Large-scale Integrative Taxonomy (LIT): resolving the data conundrum for dark taxa

New, rapid, accurate, scalable, and cost-effective species discovery and delimitation methods are needed for tackling “dark taxa,” here defined as groups for which \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$<$\end{document}10\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$\%$\end{document} of all species are described and the estimated diversity exceeds 1,000 species. Species delimitation for these taxa should be based on multiple data sources (“integrative taxonomy”) but collecting multiple types of data risks impeding a discovery process that is already too slow. We here develop large-scale integrative taxonomy (LIT), an explicit method where preliminary species hypotheses are generated based on inexpensive data that can be obtained quickly and cost-effectively. These hypotheses are then evaluated based on a more expensive type of “validation data” that is only obtained for specimens selected based on objective criteria applied to the preliminary species hypotheses. We here use this approach to sort 18,000 scuttle flies (Diptera: Phoridae) into 315 preliminary species hypotheses based on next-generation sequencing barcode (313 bp) clusters (using objective clustering [OC] with a 3\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$\%$\end{document} threshold). These clusters are then evaluated with morphology as the validation data. We develop quantitative indicators for predicting which barcode clusters are likely to be incongruent with morphospecies by randomly selecting 100 clusters for in-depth validation with morphology. A linear model demonstrates that the best predictors for incongruence between barcode clusters and morphology are maximum p-distance within the cluster and a newly proposed index that measures cluster stability across different clustering thresholds. A test of these indicators using the 215 remaining clusters reveals that these predictors correctly identify all clusters that are incongruent with morphology. In our study, all morphospecies are true or disjoint subsets of the initial barcode clusters so that all incongruence can be eliminated by varying clustering thresholds. This leads to a discussion of when a third data source is needed to resolve incongruent grouping statements. The morphological validation step in our study involved 1,039 specimens (5.8\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$\%$\end{document} of the total). The formal LIT protocol we propose would only have required the study of 915 (5.1\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$\%$\end{document}: 2.5 specimens per species), as we show that clusters without signatures of incongruence can be validated by only studying two specimens representing the most divergent haplotypes. To test the generality of our results across different barcode clustering techniques, we establish that the levels of incongruence are similar across OC, Automatic Barcode Gap Discovery (ABGD), Poisson Tree Processes (PTP), and Refined Single Linkage (RESL) (used by Barcode of Life Data System to assign Barcode Index Numbers [BINs]). OC and ABGD achieved a maximum congruence score with the morphology of 89\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$\%$\end{document} while PTP was slightly less effective (84\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$\%$\end{document}). RESL could only be tested for a subset of the specimens because the algorithm is not public. BINs based on 277 of the original 1,714 haplotypes were 86\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$\%$\end{document} congruent with morphology while the values were 89\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$\%$\end{document} for OC, 74\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$\%$\end{document} for PTP, and 72\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$\%$\end{document} for ABGD. [Biodiversity discovery; dark taxa; DNA barcodes; integrative taxonomy.]

Lack of Statistical Rigor in DNA Barcoding Likely Invalidates the Presence of a True Species' Barcode Gap

DNA barcoding has been largely successful in satisfactorily exposing levels of standing genetic diversity for a wide range of taxonomic groups through the employment of only one or a few universal gene markers. However, sufficient coverage of geographically-broad intra-specific haplotype variation within genomic databases like the Barcode of Life Data Systems (BOLD) and GenBank remains relatively sparse. As reference sequence libraries continue to grow exponentially in size, there is now the need to identify novel ways of meaningfully analyzing vast amounts of available DNA barcode data. This is an important issue to address promptly for the routine tasks of specimen identification and species discovery, which have seen broad adoption in areas as diverse as regulatory forensics and resource conservation. Here, it is demonstrated that the interpretation of DNA barcoding data is lacking in statistical rigor. To highlight this, focus is set specifically on one key concept that has become a household name in the field: the DNA barcode gap. Arguments outlined herein specifically center on DNA barcoding in animal taxa and stem from three angles: (1) the improper allocation of specimen sampling effort necessary to capture adequate levels of within-species genetic variation, (2) failing to properly visualize intra-specific and interspecific genetic distances, and (3) the inconsistent, inappropriate use, or absence of statistical inferential procedures in DNA barcoding gap analyses. Furthermore, simple statistical solutions are outlined which can greatly propel the use of DNA barcoding as a tool to irrefutably match unknowns to knowns on the basis of the barcoding gap with a high degree of confidence. Proposed methods examined herein are illustrated through application to DNA barcode sequence data from Canadian Pacific fish species as a case study.

Genome Skimming Contributes to Clarifying Species Limits in Paris Section Axiparis (Melanthiaceae)

Paris L. section Axiparis H. Li (Melanthiaceae) is a taxonomically perplexing taxon with considerable confusion regarding species delimitation. Based on the analyses of morphology and geographic distribution of each species currently recognized in the taxon, we propose a revision scheme that reduces the number of species in P. sect. Axiparis from nine to two. To verify this taxonomic proposal, we employed a genome skimming approach to recover the plastid genomes (plastomes) and nuclear ribosomal DNA (nrDNA) regions of 51 individual plants across the nine described species of P. sect. Axiparis by sampling multiple accessions per species. The species boundaries within P. sect. Axiparis were explored using phylogenetic inference and three different sequence-based species delimitation methods (ABGD, mPTP, and SDP). The mutually reinforcing results indicate that there are two species-level taxonomic units in P. sect. Axiparis (Paris forrestii s.l. and P. vaniotii s.l.) that exhibit morphological uniqueness, non-overlapping distribution, genetic distinctiveness, and potential reproductive isolation, providing strong support to the proposed species delimitation scheme. This study confirms that previous morphology-based taxonomy overemphasized intraspecific and minor morphological differences to delineate species boundaries, therefore resulting in an overestimation of the true species diversity of P. sect. Axiparis. The findings clarify species limits and will facilitate robust taxonomic revision in P. sect. Axiparis.

How to Accurately Delineate Morphologically Conserved Taxa and Diagnose Their Phenotypic Disparities: Species Delimitation in Cryptic Rhinolophidae (Chiroptera)

Systematics and taxonomy are the backbone of all components of biology and ecology, yet cryptic species present a major challenge for accurate species identification. This is especially problematic as they represent a substantial portion of undiscovered biodiversity, and have implications for not only species conservation, but even assaying potential risk of zoonotic spillover. Here, we use integrative approaches to delineate potential cryptic species in horseshoe bats (Rhinolophidae), evaluate the phenotypic disparities between cryptic species, and identify key traits for their identification. We tested the use of multispecies coalescent models (MSC) using Bayesian Phylogenetic and Phylogeography (BPP) and found that BPP was useful in delineating potential cryptic species, and consistent with acoustic traits. Our results show that around 40% of Asian rhinolophid species are potentially cryptic and have not been formally described. In order to avoid potential misidentification and allow species to be accurately identified, we identified quantitative noseleaf sella and acoustic characters as the most informative traits in delineating between potential cryptic species in Rhinolophidae. This highlights the physical differences between cryptic species that are apparent in noseleaf traits which often only qualitatively described but rarely measured. Each part of the noseleaf including the sella, lateral lappets, and lancet furrows, play roles in focusing acoustic beams and thus, provide useful characteristics to identify cryptic Rhinolophus species. Finally, species delimitation for cryptic species cannot rely on genetic data alone, but such data should be complemented by other evidence, including phenotypic, acoustic data, and geographic distributions to ensure accurate species identification and delineation.

Identifying cryptic fern gametophytes using DNA barcoding: A review

Ferns and lycophytes are unique among land plants in having sporophyte (diploid) and gametophyte (haploid) generations that can grow independently of each other. While most studies of fern ecology focus on the more visible sporophytic stage, the gametophyte is critically important, as it is the sexual phase of the life cycle. Yet, fern gametophytes have long been neglected in field studies due to their small size and cryptic morphology. DNA barcoding is a powerful method that can be used to identify field-collected gametophytes to species and allow for detailed study of their ecology. Here, we review the state of DNA barcoding as applied to fern gametophytes. First, we trace the history of DNA barcoding and how it has come to be applied to fern gametophytes. Next, we summarize case studies that show how DNA barcoding has been used to better understand fern species distributions, gametophyte ecology, and community ecology. Finally, we propose avenues for future research using this powerful tool, including next-generation DNA sequencing for in-field identification of cryptic gametophytes.

Re-evaluating the case for poecilogony in the gastropod Planaxis sulcatus (Cerithioidea, Planaxidae)

Background

Planaxis sulcatus has been touted as a textbook example of poecilogony, with members of this wide-ranging Indo-Pacific marine gastropod said to produce free-swimming veligers as well as brooded juveniles. A recent paper by Wiggering et al. (BMC Evol Biol 20:76, 2020) assessed a mitochondrial gene phylogeny based on partial COI and 16S rRNA sequences for 31 individuals supplemented by observations from the brood pouch of 64 mostly unsequenced individuals. ABGD and bGYMC supported three reciprocally monophyletic clades, with two distributed in the Indo-Pacific, and one restricted to the northern Indian Ocean and Red Sea. Given an apparent lack of correlation between clade membership and morphological differentiation or mode of development, the reported 3.08% maximum K2P model-corrected genetic divergence in COI among all specimens was concluded to represent population structuring. Hence, the hypothesis that phylogenetic structure is evidence of cryptic species was rejected and P. sulcatus was concluded to represent a case of geographic poecilogony.

Results

Our goal was to reassess the case for poecilogony in Planaxis sulcatus with a larger molecular dataset and expanded geographic coverage. We sequenced an additional 55 individuals and included published and unpublished sequence data from other sources, including from Wiggering et al. Our dataset comprised 108 individuals (88 COI, 81 16S rRNA) and included nine countries unrepresented in the previous study. The expanded molecular dataset yielded a maximum K2P model-corrected genetic divergence among all sequenced specimens of 12.09%. The value of 3.08% erroneously reported by Wiggering et al. is the prior maximal distance value that yields a single-species partition in ABGD, and not the maximum K2P intraspecific divergence that can be calculated for the dataset. The bGMYC analysis recognized between two and six subdivisions, while the best-scoring ASAP partitions recognized two, four, or five subdivisions, not all of which were robustly supported in Bayesian and maximum likelihood phylogenetic analyses of the concatenated and single gene datasets. These hypotheses yielded maximum intra-clade genetic distances in COI of 2.56–6.19%, which are more consistent with hypothesized species-level thresholds for marine caenogastropods.

Conclusions

Based on our analyses of a more comprehensive dataset, we conclude that the evidence marshalled by Wiggering et al. in support of Planaxis sulcatus comprising a single widespread, highly variable species with geographic poecilogony is unconvincing and requires further investigation in an integrative taxonomic framework.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-022-01961-7.

DNA reconciles morphology and colouration in the drunk blenny genus Scartichthys (Teleostei: Blenniidae) and provides insights into their evolutionary history

The blenniids of the genus Scartichthys are one of the most common fishes of Central and South American Pacific coastal reefs. This being said, Scartichthys spp. remain difficult to identify in the field, and identification is particularly challenging across the c. 6000 km where three of the four currently accepted species are known to occur in sympatry. A reason for this is that the main taxonomic characters from traditional taxonomy are indeed elusive. In addition, at the same time, species can display multiple colour patterns in the field, depending on their ontogenetic stage, habitat association and reproductive behaviour. Overall, molecular characterization is warranted to help address these issues. In this study, the authors have used a novel approach to revise the genus by combining colouration, morphological and molecular data of representative specimens of the four currently valid species and seven described colour patterns. From this, the authors show that only three of the four species should be considered as valid; Scartichthys gigas (Steindachner, 1876), Scartichthys variolatus (Valenciennes, 1836) and Scartichthys viridis (Valenciennes, 1836), whereas Scartichthys crapulatus (Williams, 1990) should be synonymized with S. viridis. In the same way, the analyses in this study show that one of the colour patterns attributed so far only to S. gigas is characteristic of the juvenile stages of S. viridis. The time-calibrated phylogeny of this study shows that this genus is relatively young and that the estimated time of divergence between S. gigas and S. viridis is c. 1.71 Ma. In comparison, the Desventuradas and Juan Fernandez Islands endemic S. variolatus diverged c. 1.95 Ma. The results of this study help to clarify the taxonomy of Scartichthys.

Thainema gen. nov. (Leptolyngbyaceae, Synechococcales): A new genus of simple trichal cyanobacteria isolated from a solar saltern environment in Thailand

Simple trichal types constitute a group of cyanobacteria with an abundance of novel, often cryptic taxa. Here, we investigated material collected from wet surface-soil in a saline environment in Petchaburi Province, central Thailand. A morphological comparison of the isolated strain with similar known species, as well as its phylogenetic and species delimitation analyses based on the combined datasets of other related organisms, especially simple trichal cyanobacteria, revealed that the material of this study represented an independent taxon. Using a multifaceted method, we propose that this material represents a new genus, Thainema gen. nov., belonging to the family Leptolyngbyaceae, with the type species Thainema salinarum sp. nov. This novel taxon shares similar ecological habitats with strains previously placed in the same lineage.

Eight in One: Hidden Diversity of the Bagrid Catfish Tachysurus albomarginatus s.l. (Rendhal, 1928) Widespread in Lowlands of South China

There is increasing evidence that species diversity is underestimated in the current taxonomy of widespread freshwater fishes. The bagrid species T. albomarginatus s.l. is mainly distributed in the lowlands of South China, as currently identified. A total of 40 localities (including the type locality), which covers most of its known range, were sampled. Molecular phylogenetic analyses based on concatenated mtDNA and nuclear genes recover nine highly supported lineages clustering into eight geographic populations. The integration of molecular evidence, morphological data, and geographic distribution demonstrates the delineation of T. albomarginatus s.l. as eight putative species. Four species, namely, T. albomarginatus, T. lani, T. analis, and T. zhangfei sp. nov. and the T. similis complex are taxonomically recognized herein. Moreover, T. zhangfei sp. nov. comprises two genetically distinct lineages with no morphological and geographical difference. This study also reveals aspects of estimation of divergence time, distribution, and ecological adaption within the T. albomarginatus group. The unraveling of the hidden species diversity of this lowland bagrid fish highlights the need for not only the molecular scrutiny of widely distributed species of South China but also the adjustment of current biodiversity conservation strategies to protect the largely overlooked diversity of fishes from low-elevation rapids.

Molecular phylogeny and phylogeography of the freshwater-fish genus Pethia (Teleostei: Cyprinidae) in Sri Lanka

BACKGROUND

Sri Lanka is a continental island separated from India by the Palk Strait, a shallow-shelf sea, which was emergent during periods of lowered sea level. Its biodiversity is concentrated in its perhumid south-western 'wet zone'. The island's freshwater fishes are dominated by the Cyprinidae, characterized by small diversifications of species derived from dispersals from India. These include five diminutive, endemic species of Pethia (P. bandula, P. cumingii, P. melanomaculata, P. nigrofasciata, P. reval), whose evolutionary history remains poorly understood. Here, based on comprehensive geographic sampling, we explore the phylogeny, phylogeography and morphological diversity of the genus in Sri Lanka.

RESULTS

The phylogenetic analyses, based on mitochondrial and nuclear loci, recover Sri Lankan Pethia as polyphyletic. The reciprocal monophyly of P. bandula and P. nigrofasciata, and P. cumingii and P. reval, is not supported. Pethia nigrofasciata, P. cumingii, and P. reval show strong phylogeographic structure in the wet zone, compared with P. melanomaculata, which ranges across the dry and intermediate zones. Translocated populations of P. nigrofasciata and P. reval in the Central Hills likely originate from multiple sources. Morphological analyses reveal populations of P. nigrofasciata proximal to P. bandula, a narrow-range endemic, to have a mix of characters between the two species. Similarly, populations of P. cumingii in the Kalu basin possess orange fins, a state between the red-finned P. reval from Kelani to Deduru and yellow-finned P. cumingii from Bentara to Gin basins.

CONCLUSIONS

Polyphyly in Sri Lankan Pethia suggests two or three colonizations from mainland India. Strong phylogeographic structure in P. nigrofasciata, P. cumingii and P. reval, compared with P. melanomaculata, supports a model wherein the topographically complex wet zone harbors greater genetic diversity than the topographically uniform dry-zone. Mixed morphological characters between P. bandula and P. nigrofasciata, and P. cumingii and P. reval, and their unresolved phylogenies, may suggest recent speciation scenarios with incomplete lineage sorting, or hybridization.

The dark side of pseudoscorpion diversity: The German Barcode of Life campaign reveals high levels of undocumented diversity in European false scorpions

DNA barcoding is particularly useful for identification and species delimitation in taxa with conserved morphology. Pseudoscorpions are arachnids with high prevalence of morphological crypsis. Here, we present the first comprehensive DNA barcode library for Central European Pseudoscorpiones, covering 70% of the German pseudoscorpion fauna (35 out of 50 species). For 21 species, we provide the first publicly available COI barcodes, including the rare Anthrenochernes stellae Lohmander, a species protected by the FFH Habitats Directive. The pattern of intraspecific COI variation and interspecific COI variation (i.e., presence of a barcode gap) generally allows application of the DNA barcoding approach, but revision of current taxonomic designations is indicated in several taxa. Sequences of 36 morphospecies were assigned to 74 BINs (barcode index numbers). This unusually high number of intraspecific BINs can be explained by the presence of overlooked cryptic species and by the accelerated substitution rate in the mitochondrial genome of pseudoscorpions, as known from previous studies. Therefore, BINs may not be an appropriate proxy for species numbers in pseudoscorpions, while partitions built with the ASAP algorithm (Assemble Species by Automatic Partitioning) correspond well with putative species. ASAP delineated 51 taxonomic units from our data, an increase of 42% compared with the present taxonomy. The Neobisium carcionoides complex, currently considered a polymorphic species, represents an outstanding example of cryptic diversity: 154 sequences from our dataset were allocated to 23 BINs and 12 ASAP units.

Diversity and taxonomic revision of tribes Rhipileae and Rhipiliopsideae (Halimedaceae, Chlorophyta) based on molecular and morphological data

Genera and species of the tribes Rhipileae and Rhipiliopsideae are abundant in most coral reef ecosystems worldwide. However, the group has been largely overlooked, and very little genetic data is available to accurately assess its diversity, phylogenetic relationships, and geographic distribution. Our study provided an in-depth reassessment of tribes Rhipileae and Rhipiliopsideae based on a species-rich dataset and the combination of molecular species delimitation, multilocus phylogenetic analyses (tufA, rbcL, and 18S rDNA), and morpho-anatomic observations. Our results revealed an unexpected diversity of 38 morphologically validated species hypotheses, including 20 new species, two of which are described in this paper and one resurrected species (Rhipilia diaphana). Based on our phylogenetic results we proposed to redefine the genera Rhipilia and Rhipiliopsis and described two new genera, Kraftalia gen. nov. (Rhipileae) and Rhipiliospina gen. nov. (Rhipiliopsideae). Finally, we validated Rhipiliella Kraft and included it in the tribe Rhipileae. Although Rhipilia and Rhipiliopsis have a pantropical distribution, none of the species studied here appeared cosmopolitan; instead, they have restricted distributions.

Cryptic Diversity in Cladosporium cladosporioides Resulting from Sequence-Based Species Delimitation Analyses

Cladosporium cladosporioides is an extremely widespread fungus involved in associations ranging from mutualistic to pathogenic and is the most frequently represented Cladosporium species in sequence databases, such as Genbank. The taxonomy of Cladosporium species, currently based on the integration of molecular data with morphological and cultural characters, is in frequent need of revision. Hence, the recently developed species delimitation methods can be helpful to explore cryptic diversity in this genus. Considering a previous study that reported several hypothetical species within C. cladosporioides, we tested four methods of species delimitation using the combined DNA barcodes internal transcribed spacers, translation elongation factor 1-α and actin 1. The analyses involved 105 isolates, revealing that currently available sequences of C. cladosporioides in GenBank actually represent more than one species. Moreover, we found that eight isolates from this set should be ascribed to Cladosporium anthropophilum. Our results revealed a certain degree of discordance among species delimitation methods, which can be efficiently treated using conservative approaches in order to minimize the risk of considering false positives.

A re-analysis of the data in Sharkey et al.'s (2021) minimalist revision reveals that BINs do not deserve names, but BOLD Systems needs a stronger commitment to open science

Halting biodiversity decline is one of the most critical challenges for humanity, but monitoring biodiversity is hampered by taxonomic impediments. One impediment is the large number of undescribed species (here called "dark taxon impediment") whereas another is caused by the large number of superficial species descriptions, that can only be resolved by consulting type specimens ("superficial description impediment"). Recently, Sharkey et al. (2021) proposed to address the dark taxon impediment for Costa Rican braconid wasps by describing 403 species based on COI barcode clusters ("BINs") computed by BOLD Systems. More than 99% of the BINs (387 of 390) were converted into species by assigning binominal names (e.g. BIN "BOLD:ACM9419" becomes Bracon federicomatarritai) and adding a minimal diagnosis (consisting only of a consensus barcode for most species). We here show that many of Sharkey et al.'s species are unstable when the underlying data are analyzed using different species delimitation algorithms. Add the insufficiently informative diagnoses, and many of these species will become the next "superficial description impediment" for braconid taxonomy because they will have to be tested and redescribed after obtaining sufficient evidence for confidently delimiting species. We furthermore show that Sharkey et al.'s approach of using consensus barcodes as diagnoses is not functional because it cannot be applied consistently. Lastly, we reiterate that COI alone is not suitable for delimiting and describing species, and voice concerns over Sharkey et al.'s uncritical use of BINs because they are calculated by a proprietary algorithm (RESL) that uses a mixture of public and private data. We urge authors, reviewers and editors to maintain high standards in taxonomy by only publishing new species that are rigorously delimited with open-access tools and supported by publicly available evidence.

DNA barcoding of Lutzomyia longipalpis species complex (Diptera: Psychodidae), suggests the existence of 8 candidate species

The sand fly Lutzomyia (L.) longipalpis has been implicated as the primary vector of Leishmania infantum, the causative agent of visceral leishmaniasis VL. In addition, it has been associated with atypical cutaneous leishmaniasis transmission in the Neotropic and Central America, respectively. The existence of a L. longipalpis complex species has been suggested with important implications for leishmaniasis epidemiology; however, the delimitation of species conforming it remains a topic of controversy. The DNA Barcoding Initiative based on cox1 sequence variation was used to identify the MOTUs in L. longipalpis including previously described L. pseudolongipalpis. The genetic variation was analyzed based on tree and distance methods. Fifty-five haplotypes were obtained from 103 sequences which were assigned to MOTUs, with a clear separation and a high correspondence of individuals to the groups. Maximum likelihood and Bayesian phylogenetic analysis showed eight MOTUs (100% bootstrap) with high genetic divergence (12.6%). Data obtained in the present study suggest that L. longipalpis complex consists of at least 8 lineages that may represent species. It would be desirable perform additional morphological and molecular analysis of L. longipalpis from Colosó (Caribbean ecoregion) considering that specimens from that area were grouped with L. pseudolongipalpis one of the complex species previously described from Venezuela, which has not been registered in Colombia.

Species diversity of freshwater shrimp in Henan Province, China, based on morphological characters and COI mitochondrial gene

Freshwater shrimp are a rich species group, with a long and problematic taxonomic history attributed to their wide distribution and similar morphological characteristics. Shrimp diversity and species identification are important cornerstones for fisheries management. However, identification based on morphological characteristics is a difficult task for a nonspecialist. Abundant freshwater shrimp species are distributed in the waters of Henan Province, but investigations of freshwater shrimp are limited in this region, especially concerning molecular features. Here, we combined morphology and DNA barcodes to reveal the species diversity of freshwater shrimp in Henan province. A total of 1,200 freshwater shrimp samples were collected from 46 sampling sites, and 222 samples were chosen for further microscopic examination and molecular delimitation. We used tree-based methods (NJ, ML, and bPTP) and distance-based methods (estimation of the paired genetic distances and ABGD) to delimit species. The results showed that there were nine morphospecies based on morphological characteristics; all could effectively be defined by molecular methods, among which bPTP and ABGD defined 13 and 8 MOTUs, respectively. The estimation of the paired genetic distances of K2P and the p-distances had similar results. Mean K2P distances and p-distances within species were both equal to 1.2%. The maximum intraspecific genetic distances of all species were less than 2%, with the exception of Palaemon modestus and M. maculatum. Various analyses have shown that P. modestus and M. maculatum have a large genetic differentiation, which may indicate the existence of cryptic species. By contrast, DNA barcoding could unambiguously discriminate 13 species and detect cryptic diversity. Our results demonstrate the high efficiency of DNA barcoding to delimit freshwater shrimp diversity and detect the presence of cryptic species.

The InBIO Barcoding Initiative Database: DNA barcodes of Portuguese Hemiptera 01

Background

The InBIO Barcoding Initiative (IBI) Hemiptera 01 dataset contains records of 131 specimens of Hemiptera. Most specimens have been morphologically identified to species or subspecies level and represent 88 species in total. The species of this dataset correspond to about 7.3% of continental Portuguese hemipteran species diversity. All specimens were collected in continental Portugal. Sampling took place from 2015 to 2019 and specimens are deposited in the IBI collection at CIBIO, Research Center in Biodiversity and Genetic Resources.

New information

This dataset increases the knowledge on the DNA barcodes and distribution of 88 species of Hemiptera from Portugal. Six species, from five different families, were new additions to the Barcode of Life Data System (BOLD), with another twenty five species barcodes' added from under-represented taxa in BOLD. All specimens have their DNA barcodes publicly accessible through BOLD online database and the distribution data can be accessed through the Global Biodiversity Information Facility (GBIF). Eutettixvariabilis and Fieberiellaflorii are recorded for the first time for Portugal and Siphantaacuta, an invasive species, previously reported from the Portuguese Azores archipelago, is recorded for the first time for continental Portugal.

Aquatic Organisms Research with DNA Barcodes

Since their inception, DNA barcodes have become a powerful tool for understanding the biodiversity and biology of aquatic species, with multiple applications in diverse fields such as food security, fisheries, environmental DNA, conservation, and exotic species detection. Nevertheless, most aquatic ecosystems, from marine to freshwater, are understudied, with many species disappearing due to environmental stress, mostly caused by human activities. Here we highlight the progress that has been made in studying aquatic organisms with DNA barcodes, and encourage its further development in assisting sustainable use of aquatic resources and conservation.