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The recognition and delineation of cryptic species remains a perplexing problem in systematics, evolution, and species delimitation. Once recognized as such, cryptic species complexes provide fertile ground for studying genetic divergence within the context of phenotypic and ecological divergence (or lack thereof). Herein we document the discovery of a new cryptic species of trapdoor spider, Promyrmekiaphila korematsui sp. nov. Using subgenomic data obtained via target enrichment, we document the phylogeography of the California endemic genus Promyrmekiaphila and its constituent species, which also includes P. clathrata and P. winnemem. Based on these data we show a pattern of strong geographic structuring among populations but cannot entirely discount recent gene flow among populations that are parapatric, particularly for deeply diverged lineages within P. clathrata. The genetic data, in addition to revealing a new undescribed species, also allude to a pattern of potential phenotypic differentiation where species likely come into close contact. Alternatively, phenotypic cohesion among genetically divergent P. clathrata lineages suggests that some level of gene flow is ongoing or occurred in the recent past. Despite considerable field collection efforts over many years, additional sampling in potential zones of contact for both species and lineages is needed to completely resolve the dynamics of divergence in Promyrmekiaphila at the population-species interface.

Orthops is a widely distributed plant bug genus comprising 35 species. Its nominotypical subgenus includes seven species mostly known from the Palearctic, and four of them are widely distributed. Most of them live in sympatry having only little morphological differences. The species limits have never been tested using the molecular data. The aim of this work is to test whether currently defined species represent monophyletic lineages and to find their interrelationships using an integrative approach. Morphological studies on external characters and male and female genitalia were performed. The molecular studies were based on the mitochondrial (cytochrome c oxidase subunit I [COI] and 12S ribosomal RNA [rRNA]) and nuclear (internal transcribed spacer I [ITS1] and calcium ATPase [Ca‐ATPase]) markers and included comparison of the intra‐ and interspecific distances, species delimitation (ABGD, BPP, bGMYC, PTP, and bPTP), and phylogenetic analyses. All markers showed interspecific differences, and COI was the most variable. It was found that all species differed from each other morphologically, and the most reliable character complexes were parameres and female genitalia. In most analyses, Orthops kalmii and O. campestris were monophyletic. Orthops basalis formed a clade in most phylogenetic trees. Most of the species delimitation analyses confirmed the status of those three species. Orthops scutellatus was split into two clades, Palearctic and North American, which was also confirmed by the species delimitation analyses. Those two groups differed in parameres. Orthops campestris and O. scutellatus form a clade in all analyses, and O. basalis forms a clade with O. kalmii in most analyses. [ABSTRACT FROM AUTHOR]

Holoplanktonic organisms are thought to have enormous populations sizes, expansive geographic ranges, and low species diversity. Previous work suggests that pelagic gastropods are no exception to this generalization. However, most of these data are derived from temperate species, whereas the bulk of pteropod diversity occurs in the tropics. Here, we present DNA barcode data for COI focused on the under‐studied limacinoid, gymnosome, and pseudothecosome pteropods collected from the coastal waters of Panama. We applied four molecular species delimitation approaches to determine the number of operational taxonomic units (OTUs) identifiable from our sequences and all data available from Barcode of Life Database (BOLD) and GenBank and compared these to the Barcode Index Number generated by the BOLD. Assemble Species by Automatic Partitioning (ASAP), Poisson Tree Processes (PTP), Bayesian Poisson Tree Processes (bPTP), and Generalized Mixed Yule Coalescent (GMYC) methods generally gave congruent results and suggest that pteropod diversity in the tropics is significantly underrepresented both in DNA sequence databases and in the number of named OTUs. Of 42 specimens collected and sequenced, we recovered 16 OTUs, only one of which belonged to an OTU already represented in sequence databases. Neighbor‐joining trees including the previously published sequences show that in all three groups morphospecies can include genetically divergent lineages. Many very divergent (>15% from nearest neighbor) taxa are also still represented by only a single sequence, suggesting that there is a large amount of cryptic or pseudo‐cryptic diversity still to be described. To aid this future endeavor, we include some preliminary 16S data derived from new pteropod‐specific primers. [ABSTRACT FROM AUTHOR]

Aim: There is an urgent need to explore, characterize, describe and preserve as many species as possible to prevent their decline. Tropical biodiversity hotspots harbour most of the known land diversity and vast amounts of undiscovered and undescribed species. Here, we quantify the taxonomically unassessed amphibian species richness in Madagascar, one of the best‐studied and explored tropical hotspots worldwide, to identify knowledge gaps and conservation implications. Location: Madagascar. Time Period: Present. Major Taxa Studied: Amphibians. Methods: We used the Madagascar amphibian fauna as a model to unveil neglected diversity by analysing 10,873 mitochondrial sequences using species delimitation algorithms and incorporating all previously published bioacoustics, distributional, morphological and nuclear data with an integrative approach. Results: Besides the currently described 413 species, we identified 408 divergent lineages. Among this, 310 fit the category of candidate species pending a taxonomic assessment, while 98 are considered deep conspecific lineages. These figures suggest that species richness could be twice as high as represented in the current taxonomy. Geographically, most of these candidate species occur in well‐studied areas within the island. Main Conclusions: Despite being one of the best‐studied and explored tropical countries worldwide for amphibians, we found that many species are awaiting a taxonomic assessment in Madagascar. Paradoxically, this unassessed diversity concentrates on highly explored regions, emphasizing the importance of exploring and inventorying new areas. Our results highlight the magnitude of the Linnean and Wallacean shortfalls, affecting both species richness estimates and the distribution ranges and biogeographic setting known for this fauna. Current conservation efforts should consider this novel diversity and unexplored areas as they will likely harbour yet many new species to be discovered. We expect similar patterns across less studied tropical realms and encourage researchers to perform such studies in different clades before this neglected biodiversity becomes irremediably lost. [ABSTRACT FROM AUTHOR]

Oceanic islands are hotspots of marine biodiversity, and biogeographic and evolutionary studies can provide important knowledge about the origin and diversification of the species that inhabit them. In the South Pacific, the Juan Fernández Archipelago (JFA) stands out for its high endemic biota, most of them endangered by human activities. Currently, two octopus species are recognized in JFA, but their taxonomic identity is not conclusive. In the present study, we performed morphometric and molecular analyses of both species inhabiting the JFA and contrast them with other species worldwide. Morphological, phylogenetic analysis, genetic diversity, and divergence times between species were estimated. Morphometric analysis did not show significant differences in body shape of males between/within Octopus species from JFA, only between females from different localities. However, phylogenetic and species delimitation analyses support the presence of two species in the JFA, namely Octopus mimus and Octopus vulgaris. In addition, both species show evidence of different divergence and colonization histories into the JFA during the Pleistocene. These findings do not only shed light on the identity, origin, and colonization time of the species, but also provide the basis to generate informed decisions on management and conservation. The recent colonization time and low genetic diversity observed in both species suggest that these populations are vulnerable to drastic changes, such as those caused by anthropic effects. [ABSTRACT FROM AUTHOR]

The structural and environmental heterogeneity within southern Africa has given rise to many morphological forms of Psammophylax rhombeatus distributed throughout the country, with previous studies neglecting the associated molecular significance of these forms. The species' widespread, generalist ecology coupled with the substantial phylogenetic structuring previously acknowledged within the species, makes P. rhombeatus the ideal candidate for phylogeographic analyses. Using 103 samples, representing the full distribution of the species, phylogenetic analyses retrieved four well-supported clades: south-eastern South Africa, south-western South Africa, north-eastern South Africa and western South Africa. Although not variable enough to warrant taxonomic re-evaluation, the clades are phylogenetically distinguishable, with relatively high intraspecific genetic divergence values separating them, irrespective of the small geographic distances separating populations. This is likely a product of the taxon's habitat-generalist lifestyle, enabling them to bypass vicariant barriers that might otherwise cause speciation in less versatile species. The clades are also geographically distinct, with little overlap, indicating previous vicariance, a finding that is supported by the split of P. rhombeatus from P. ocellatus in the mid-Pliocene, followed by the diversification of P. rhombeatus into four clades throughout the Pleistocene. The genetic structuring observed in P. rhombeatus may be a product of population expansion following ancient refugial isolation (potentially Last Glacial Maximum). The morphological groupings highlighted in previous studies are loosely attributable to the molecular clades identified in the phylogenetic reconstruction, highlighting the complex interplay of genetic and morphological characteristics in the process of speciation, and their representation in systematic accounts. [ABSTRACT FROM AUTHOR]

Phylogeographic studies on widespread rainforest species from West and Central Africa often reveal genetic discontinuities. These discontinuities can originate from past barriers to gene flow resulting from long-lasting population fragmentation during glacial periods, according to the forest refuge hypothesis. This study 69 nuclear SNPs, 13 plastid SNPs, and 24 mitochondrial SNPs to characterized the distribution of genetic diversity in 377 individuals of the widespread tropical tree Khaya ivorensis, in western and central African evergreen forests. Two very well-differentiated nuclear genetic clusters (FST = 0.28) are located respectively in West and Central Africa. The gradual transition of allele frequencies between the clusters across a broad geographic area going from Cameroon to Nigeria accords with the recognition of a single species, although we show an incipient divergence that could eventually lead to the separation of two taxa. The two clusters have similar genetic diversity at nuclear SNPs. However, the cytoplasmic data revealed high haplotypic diversity and numerous endemic haplotypes in Central Africa, and only one widespread haplotype in West Africa, suggesting an ancient colonization of West Africa from Central Africa. The genetic diversity inside and outside putative forest refugia (Anhuf et al., Palaeogeogr Palaeoclimatol Palaeoecol 239:510–527, 2006) does not differ significantly in either genetic cluster. Hence, we cannot confirm that forest refugia played a particular role in the pattern of distribution of genetic diversity in K. ivorensis. Owing to the high haplotypic diversity of their populations, Central Africa, especially Gabon, constitutes a priority area for the conservation of the genetic diversity of K. ivorensis. [ABSTRACT FROM AUTHOR]

Eriophyoid mites (Acari: Eriophyoidea) are among the smallest terrestrial arthropods possessing simplified morphological characters, which challenges the traditional morphology‐based species delimitation. The Diptilomiopus spp. exhibit further morphological degeneration (e.g., lack of genus on both legs and some opisthosoma setae). Especially, they possess high similarity in the reticulate prodorsal shield patterns, leading to cryptic species complex and hampering our understanding of species diversity. In this study, we implemented an integrated approach, including genetic distance analysis, phylogenetic analysis, population genetic structure construction, introgression test, and morphometric analysis, to delimitate the Diptilomiopus ligustri complex. We obtained 52 mitochondrial COI gene sequences and 19 whole‐genome sequences across 18 sample sites of this complex. All samples were collected from Ligustrum plants in China, which may cover their main distribution ranges. Our results demonstrate that the D. ligustri complex consists of at least four distinct species (i.e., D. ligustri, D. cf. ligustri sp1., D. cf. ligustri sp2., and D. cf. ligustri sp3.), which are genetically divergent but do not differ morphologically, assessed by principal component analysis of 27 morphological characteristics. No significant gene flow was observed among this complex. Divergence time estimates further showed that most Diptilomiopus species diverged in a short time interval at the Paleogene–Neogene boundary, indicating a rapid radiation. Our results highlight the integrated approaches in eriophyoid mite species complex delimitation. [ABSTRACT FROM AUTHOR]

Five stink bugs, Aelia acuminata, A. fieberi, A. furcula, A. klugii and A. sibirica, are found in China and have similar morphologies. Due to the lack of molecular data, the species boundaries and phylogenetic relationships among these five species remain uncertain. In this study, we integrated mitochondrial DNA and nuclear single nucleotide polymorphisms (SNPs) generated by double‐digest restriction site‐associated DNA sequencing (ddRAD‐seq) to perform species delimitation and phylogenetic analyses of the five Aelia species. Most species delimitation analyses based on the cytochrome c oxidase subunit I (COI) gene, mitochondrial genomes and nuclear SNPs yielded five molecular operational taxonomic units (MOTUs), which correspond well to the five Aelia species identified based on morphological characters. We obtained a clear mito‐nuclear discordance between the tree topologies based on mitochondrial genome and genome‐wide SNP data. The D‐statistic and TreeMix analysis suggested that introgression is the most likely cause of mito‐nuclear discordance in Aelia species, which requires confirmation through more extensive sampling and comprehensive data. This study provides the first molecular evidence of the species boundaries and phylogenetic relationships of these five Aelia stink bugs, which is crucial to our understanding of the biodiversity and evolution of Aelia species. [ABSTRACT FROM AUTHOR]

ABSTRACT The isolated river drainages of eastern North America serve as a natural laboratory to investigate the roles of allopatry and secondary contact in the evolutionary trajectories of recently diverged lineages. Drainage divides facilitate allopatric speciation, but due to their sensitivity to climatic and geomorphological changes, neighboring rivers frequently coalesce, creating recurrent opportunities of isolation and contact throughout the history of aquatic lineages. The freshwater mussel Quadrula quadrula is widely distributed across isolated rivers of eastern North America and possesses high phenotypic and molecular variation across its range. We integrate sequence data from three genomes, including female‐ and male‐inherited mitochondrial markers and thousands of nuclear encoded SNPs with morphology and geography to illuminate the group's divergence history. Across contemporary isolated rivers, we found continuums of molecular and morphological variation, following a pattern of isolation by distance. In contact zones, hybridization was frequent with no apparent fitness consequences, as advanced hybrids were common. Accordingly, we recognize Q. quadrula as a single cohesive species with subspecific variation (Q. quadrula rumphiana). Demographic modeling and divergence dating supported a divergence history characterized by allopatric vicariance followed by secondary contact, likely driven by river rearrangements and Pleistocene glacial cycles. Despite clinal range‐wide variation and hybridization in contact zones, the process‐based species delimitation tool delimitR, which considers demographic scenarios like secondary contact, supported the delimitation of the maximum number of species tested. As such, when interpreting species delimitation results, we suggest careful consideration of spatial sampling and subsequent geographic patterns of biological variation, particularly for wide‐ranging taxa. [ABSTRACT FROM AUTHOR]

The identification of spider species presents many challenges, since in most cases the characters used are from genital structures that are only fully developed in the adult stage, hence the identification of immatures is most often not possible. Additionally, these structures usually also present some intra-specific variability, which in some cases makes the identification of closely related species difficult. The genetic barcode technique (DNA barcodes), based on sequencing of the mitochondrial marker cytochrome c oxidase subunit I (COI), has proven a useful, complementary tool to overcome these limitations. In this work, the contribution of DNA barcoding to the taxonomy of the subfamily Amaurobioidinae is explored using the refined single linkage analysis (RESL) algorithm for the delimitation of operational taxonomic units (OTUs), in comparison with the assemble species by automatic partitioning (ASAP) algorithm, and presented in conjunction with an updated molecular phylogenetic analysis of three other markers (28S rRNA, 16S rRNA, Histone H3), in addition to COI. Of a total of 97 included species identified by morphology, 82 species were concordant with the operational taxonomic units obtained from RESL, representing an 85% correspondence between the two methods. Similar results were obtained using the ASAP algorithm. Previous observations of morphological variation within the same species are supported, and this technique provides new information on genetic structure and potentially cryptic species. Most of the discrepancies between DNA barcoding and morphological identification are explained by low geographic sampling or by divergent or geographically structured lineages. After the addition of many specimens with only COI data, the multi-marker phylogenetic analysis is consistent with previous results and the support is improved. The markers COI , closely followed by 28S , are the most phylogenetically informative. We conclude that the barcode DNA technique is a valuable source of data for the delimitation of species of Amaurobioidinae, in conjunction with morphological and geographic data, and it is also useful for the detection of cases that require a more detailed and meticulous study. Taxonomic identification of spider species from morphological structures has limitations in cases of closely related species or intraspecific variability. We investigate the utility of genetic barcoding with the mitochondrial marker cytochrome c oxidase I (COI) in ghost spiders of the subfamily Amaurobioidinae. Most discrepancies between DNA barcoding and morphological identification are explained by low geographic sampling or by geographically structured lineages. In addition, we show that the marker COI is phylogenetically informative for deeper nodes in the tree. (Image credit: Martín Ramírez.) [ABSTRACT FROM AUTHOR]

Australian salt lakes contain a diverse range of endemic invertebrates. The brine shrimp Parartemia is among the most speciose and salt-tolerant of these invertebrates. The morphotaxonomy of Parartemia is well established but there has only been limited molecular assessment of the phylogenetic relationships and boundaries of the morphospecies. We used multiple genetic markers (nuclear 28S and mitochondrial 16S and COI) and tree-building methods (Bayesian inference and maximum likelihood) to investigate the phylogeny of Parartemia. We also used species delimitation methods to test the validity of morphological species designations. The data set included all but 2 of the 18 described Parartemia morphospecies, collected from a total of 93 sites from across southern Australia plus some sequences from GenBank. The results identified large amounts of molecular divergence (e.g. COI P- values of up to 25.23%), some groups of closely related species (which also usually shared some morphological similarities) and some distinctive species, although the relationships among divergent lineages were generally not well resolved. The most conservative set of results from the species delimitation analyses suggests that the morphotaxonomy is largely accurate, although many morphospecies comprised divergent genetic lineages separated by COI P- values of up to 17.02%. Two putative new morphospecies, three cryptic species and one synonymy were identified. Our findings improve the knowledge of Parartemia taxonomy and will facilitate the development of future studies and conservation of this taxon. The brine shrimp Parartemia is a diverse, salt-tolerant genus found in Australian salt lakes. Its current taxonomy is mainly based on morphological data. We used molecular data to investigate the number and relationships of Parartemia species and found two new morphospecies and three cryptic species. Although most species were valid, molecular divergence among and within some species was substantial. Our results confirm the species richness of the genus and our updated species list will aid in targeted conservation efforts. (Image credit: Md Aminul Islam.) [ABSTRACT FROM AUTHOR]

The stubby-root nematode genus Paratrichodorus comprises species of plant polyphagous ectoparasitic nematodes distributed worldwide and a few of them are plant virus-vectors (tobravirus). This is one of the most difficult nematode genera in terms of species identification, since it is phenotypically conserved with closely related species and is highly sensitive to the specimen fixation and preservation processes. Using an integrative and multidisciplinary taxonomy framework, we determined species boundaries among the Paratrichodorus populations from a P. allius species-complex sampled in cultivated and natural ecosystems across Spain. We support the hypothesis that nematode diversity of the P. allius species-complex remains underestimated and describe here a total of eight new species on the basis of detailed morphological and molecular characterization of 16 Paratrichodorus populations: Paratrichodorus asidonaensis sp. nov. Paratrichodorus benalupensis sp. nov. Paratrichodorus hinogerus sp. nov. Paratrichodorus litoralis sp. nov. Paratrichodorus paraallius sp. nov. Paratrichodorus rocianerus sp. nov. Paratrichodorus tarifaensis sp. nov. and Paratrichodorus uliaensis sp. nov. This study emphasizes the importance of properly applying a broad taxonomic framework in plant-parasitic nematodes. It is also relevant for plant health, since it correctly delimits species morphologically closed to the virus vector nematode, P. allius , and gives proper molecular markers for its unequivocal identification. [ABSTRACT FROM AUTHOR]

The multispecies coalescent (MSC) model accommodates genealogical fluctuations across the genome and provides a natural framework for comparative analysis of genomic sequence data from closely related species to infer the history of species divergence and gene flow. Given a set of populations, hypotheses of species delimitation (and species phylogeny) may be formulated as instances of MSC models (e.g. MSC for 1 species versus MSC for 2 species) and compared using Bayesian model selection. This approach, implemented in the program bpp , has been found to be prone to over-splitting. Alternatively, heuristic criteria based on population parameters (such as population split times, population sizes, and migration rates) estimated from genomic data may be used to delimit species. Here, we develop hierarchical merge and split algorithms for heuristic species delimitation based on the genealogical divergence index (⁠ g d i ⁠) and implement them in a Python pipeline called hhsd. We characterize the behavior of the g d i under a few simple scenarios of gene flow. We apply the new approaches to a dataset simulated under a model of isolation by distance as well as 3 empirical datasets. Our tests suggest that the new approaches produced sensible results and were less prone to oversplitting. We discuss possible strategies for accommodating paraphyletic species in the hierarchical algorithm, as well as the challenges of species delimitation based on heuristic criteria. [ABSTRACT FROM AUTHOR]

Worldwide, humans have strongly altered river networks. Key changes resulted in modified hydromorphology, poor habitat quality and availability, migration barriers, and pollution. Restoration measures aim at mitigating anthropogenic stressors and at restoring connectivity, but the biological success of these measures is not guaranteed. Analyzing genetic diversity and metapopulation structure of target species in the river network with genetic markers can help to understand recolonization processes and to identify persisting gene flow barriers. Here, we studied the population genetic structure of the two pollution‐tolerant detritivorous isopod species, Asellus aquaticus and Proasellus coxalis, in the former heavily degraded and polluted, but now mostly restored Emscher catchment in Germany. For both species, we analyzed mitochondrial cytochrome c oxidase I (COI) gene sequences and nuclear genome‐wide single nucleotide polymorphism (SNP) data. Surprisingly, we found a strong metapopulation structure for both species with several isolated populations on a small‐scale of few kilometers, but a still high genetic diversity, especially in the COI gene. For both taxa, potentially cryptic species are known, but our SNP data showed that the mitochondrial lineages represent only one species, each, in the study area. This highlights the importance of integrating high‐resolution nuclear markers into species identification because species diversity may otherwise be overestimated. While we could identify some migration barriers and find indications for passive dispersal by birds or humans, these factors could not fully explain the local metapopulation structure, suggesting that also other drivers, such as isolation by adaptation, priority effects, or biotic interactions, play a role in shaping the population genetic structure. [ABSTRACT FROM AUTHOR]

Garra, a kind of small‐ to medium‐sized fish, is widely distributed from southern Eurasia to central Africa. As one of the most diverse genera of Cyprinidae, investigating the phylogeny and biogeography of Garra remains challenging. In this study, we combined sequences of Garra samples collected from Myanmar with sequences downloaded from GenBank to investigate the phylogeny, diversification, and biogeography of Garra on a global scale, with an emphasis on Southeast Asia. Species delimitation results indicated that there are at least 22 potential species, including eight undescribed species in Myanmar, suggesting that the diversity of Garra in this region have been largely underestimated. Diversification analysis suggested a relatively high diversification rate in the early branches of Garra. Ancestral distribution reconstruction results revealed that Garra originated from the Irrawaddy River basin in the late Eocene, approximately 34 million years ago, with subsequent dispersals across different drainages influenced by the uplift of the Qinghai‐Tibet Plateau. Our study provided a new insight into the evolutionary history of Garra and the basis for further research on this genus. [ABSTRACT FROM AUTHOR]

A good knowledge of the evolutionary history of organisms and an accurate taxonomic framework are keys for efficient biodiversity conservation measures. This is particularly relevant for European butterflies, which are often used as bioindicator organisms and umbrella species for conservation.The Holarctic butterfly genus Agriades includes seven European arctic‐alpine species of which several have a debated taxonomic status. They are localized and allopatric, and at least two of them are of high conservation concern, namely A. aquilo (in Europe, restricted to northern Scandinavia) and A. zullichi (endemic to southern Spain). Despite high conservation value and taxonomic uncertainty, molecular studies on these taxa are limited to DNA barcodes.We investigated the evolutionary history and species delimitation of West Palearctic Agriades using double‐digest RAD sequencing (ddRADseq).Various analyses using genomic data suggested the presence of one species in the glandon species group and one or two in the pyrenaicus species group. The differentiation within the former group (i.e., glandon, aquilo, zullichi) appears to be relatively recent, although the main allopatric populations represent evolutionary significant units (ESUs). Notable geographic structure was found within the pyrenaicus species group, with four allopatric ESUs detected.Wolbachia screening highlighted the presence of several allele combinations, some associated with particular Agriades populations.Genomic data revealed the evolutionary trajectory of European Agriades and a tendency for taxonomic oversplitting within this genus. These findings aid conservation by providing genetic background for region or population prioritization (including ESUs), and for the management of potential population reinforcement or reintroductions. [ABSTRACT FROM AUTHOR]

Species extinctions increase at a global scale; therefore, rapid inventorying of our planet's biodiversity is becoming more and more important. As insects represent the highest portion of the fauna and play key ecological roles, it is a pressing need to investigate their biodiversity and accelerate species discovery, especially for understudied insect groups, also known as "dark taxa." Phoridae (Diptera) are a great example of a "dark taxon," in particular the genus Megaselia Rondani.The use of integrative methodologies is the best approach to face up to the task of describing hyperdiverse and dark taxa, as morphology alone can be imprecise and slow, and molecular methods alone are often insufficient and lead to errors.Here, we used the Large‐Scale Integrative Taxonomy (LIT) approach to sort 9000 Megaselia into 277 putative species based on DNA barcodes. Each cluster passed through an evaluation of the predictors for incongruence indices between clusters and morphology (maximum p‐distance, stability index), and a subset of specimens were morphologically examined.We provided species estimates with Chao1, and our results suggest a 15% increase in species richness on our dataset. As this estimate was mostly based on samples from southern Germany, the species count will likely increase with expanded geographic sampling. This is a step forward in the study of this taxon, despite the fact that the German insect fauna is one of the best known in Europe and boasts more than one hundred years of study on phorids. [ABSTRACT FROM AUTHOR]

Species delimitation remains a challenge worldwide, especially in highly diverse tropical and subtropical regions. Here, we use an integrative approach that combines morphology, phylogenomics, and species distribution modeling (SDM) to clarify the cryptic differentiation within the enigmatic hemiparasitic love vine Cassytha filiformis (Lauraceae) in China and adjacent regions. We generated complete plastid genomes and nuclear ribosomal sequences for diverse samples from across the species range and compared results with previously published plastid data, recovering two well‐supported monophyletic clades. Further, the analysis revealed significant differences in two morphological characters and SDM, indicating distinct environmental factors influencing their distributions. Fossil‐calibrated analyses to estimate the origins and diversification patterns for the cryptic species gave divergence age estimates corresponding to the Oligo‐Miocene; a period of new ecological opportunities associated with the prevailing East Asian monsoon. Multivariate analyses support the conclusion that southern China and adjacent regions have a different, previously unknown, cryptic lineage of C. filiformis. Our study highlights the importance of using multivariate approach to characterize plant species, as well as the significant role that past climatic changes have played in driving speciation in parasitic plants in tropical and subtropical zones. [ABSTRACT FROM AUTHOR]

The jumping spider Marpissa marina (Goyen, 1892) is endemic to Aotearoa New Zealand. In this paper, we redescribe the species. Marpissa marina was placed in the Northern Hemisphere genus Marpissa due to its subjective similarity to spiders in that genus. The original description lacked modern morphological diagnoses and useful illustrations. The description was based largely on the female, and therefore lacked the taxonomically important characters seen in the male pedipalp. Previous literature has suggested M. marina may be related to the Australian genus, Maratus Karsch, 1878. We applied an integrative taxonomic approach based on diagnostic morphological characters and molecular analysis for a more detailed species description and assignment into an appropriate genus. Morphological features indicate that M. marina belongs to Maratus. This is supported by phylogenetic analyses using DNA sequences from the nuclear gene Actin 5C and the mitochondrial gene 16S ribosomal RNA. We transfer Marpissa marina into the genus Maratus, as Maratus marinus (Goyen, 1892), new combination. [ABSTRACT FROM AUTHOR]

As defining various taxonomic ranks, especially at and within a specific level, can often be difficult, we used an evolutionarily young group of Central Asian beetles, the genus Anoplistes, to examine the limits between species, subspecies and ecotype. The molecular data (COI genetic distance, haplotype network and species delimitation) and detailed morphology (using SEM) of taxa assigned to the rank of species, subspecies and ecotype were used to verify their taxonomic status and attempt to more precisely establish the boundaries between these concepts. The minimum threshold for the COI genetic distance between species was found to be approximately 3%, while at the threshold of 4%–5% the morphology left no doubt as to the species distinctiveness. The threshold of approximately 2% was accepted as adequate for a subspecies rank, whereas intraspecific variability among individuals of the same subspecies (including its ecotypes) ranged from 0% to 2%. A newly presented colour/elytral pattern form, possibly another ecotype of A. halodendri distributed in western Mongolia, exemplifies adaptation to different environmental conditions via ecological speciation. Our results provide support that ecotypes can form phylogenetically distinct clades. Based on the results of the haplotype network, it can be tentatively concluded that the sand ecotype was the incipient form from which further ecotypes and subspecies developed. [ABSTRACT FROM AUTHOR]

The definition of species boundaries in mygalomorph spiders is historically based on morphological characters, which can be problematic due to the homogeneous morphology and continuous variation across species. The male copulatory bulb of Neodiplothele, as of many mygalomorphs, is phenotypically diverse and the differences are displayed mostly by subtle shape variations. The purpose of this research was to evaluate the traditional morphology-based delimitation of species informal groups and assess the significance of morphological characters in the systematics of the highly variable and widespread mygalomorph spiders of the barychelid genus Neodiplothele. We conducted a geometric morphometric analysis on the bulb of specimens of Neodiplothele using Fourier descriptors. The results show that the bulb is rather difficult to apply as a discrete character in a taxonomic context and show the proximity of a group of undescribed species of Neodiplothele to both groups proposed in a previous revision, indicating a continuous variation. As a taxonomic character, the use of the copulatory bulb shape as a discrete character may be uninformative in the case of species that present one or more intermediate states, when the incorrect treatment of the character can result in a misrepresentation of shape diversity and equivocate inference of evolutionary relationships.https://zoobank.org/urn:lsid:zoobank.org:author:471C6BE5-D24C-4805-B2DE-EB89B6D1D8FAhttps://zoobank.org/urn:lsid:zoobank.org:author:D4955FF5-FE7F-4E68-AB2F-4A89593F9850 [ABSTRACT FROM AUTHOR]

Astroblepus species, commonly known as Andean climbing catfish, exhibit a unique challenge in species delimitation, leading to ongoing taxonomic debates. Here we report data on Astroblepus mindoensis, a vulnerable species endemic to Ecuador, obtained by an integrative approach that includes cytogenetic analysis, molecular identification of the specimens, and recording of morphological and morphometric characters useful for species diagnosis. Thus, this study aimed to associate the karyotype data of the specimens analyzed with morphological and molecular characters, improving and expanding the existing taxonomic information, thus contributing to the systematics of the species. Our morphology results, unlike Regan's original description, which is brief and ambiguous, provide a more detailed morphometric and meristic description. Molecular phylogenetic reconstruction and genetic distance based on a fragment of the cytochrome c oxidase subunit I (COI) showed that our samples constitute a well‐supported and monophyletic clade within the A. grixalvii species complex. The cytogenetic analysis identified distinct chromosomal markers, including a single cluster of major ribosomal genes (on chromosome pair 3) and of minor ribosomal genes (on chromosome pair 12) with their localization differing from those reported in other Astroblepus species analyzed. Additionally, the presence of a heteromorphic chromosome pair in males suggests the presence of an XX/XY sex‐determination system that has not been identified in other congeneric species. Further investigation is necessary to determine if these chromosomes are associated with the accumulation of repeated sequences, as typically occurs with sex chromosomes, and to assess their presence in other species of the genus. [ABSTRACT FROM AUTHOR]

Cycas is the second-largest genus of cycads in Australia and the sole cycad genus in Papua New Guinea. In contrast to the other Australian cycads, which are mainly pollinated by weevils of the Tranes group of Molytinae, the Australian Cycas species are pollinated by tiny weevils belonging to the subfamily Cossoninae but representing an unnamed genus. This study evaluates the taxonomic status of these weevils by combining morphological examination with molecular phylogenetic analyses and species delineation based on mitochondrial DNA. The results reveal that the Cycas -pollinating weevils in Australia comprise only one species, here described as Zimmiodes australis gen. et sp. nov. with another species in Papua New Guinea, described as Zimmiodes papuanus sp. nov. The phylogenetic analyses and morphological comparison reveal that Zimmiodes belongs in the tribe Pentarthrini of Cossoninae and that the related Tychiodes group includes not only Tychiodes Wollaston, Tychiosoma Wollaston and Nanoplaxes Heller but also Tyrpetes Heller and is also assignable to Pentarthrini. The conspecificity of Zimmiodes weevils from all Australian Cycas species sampled suggests the likely taxonomic oversplitting of the Australian Cycas species and thus provides new insights into the taxonomy of the Australian cycads. [ABSTRACT FROM AUTHOR]

Simple Summary: The taxonomy of the sinica group of macaques has been unresolved due to inconsistencies between their physical traits and genetic relationships. To clarify this taxonomic issue, we analyzed DNA from previously unsampled populations of the macaques in the Himalayas. Our results revealed that the sinica group consists of seven distinct species, rather than the previously considered six species as the two subspecies of Assamese macaques (Macaca assamensis assamensis and M. a. pelops) are separate candidate species with strong genetic variations. The study also identified Arunachal macaques (M. munzala) in the Shannan area of Xizang Zizhiqu in China. Multiple analyses revealed complex historical patterns of species dispersal and separation, mostly linked to climatic changes during the Quaternary period. We propose a new hypothesis about the sinica group's evolutionary history. Owing to the taxonomic incongruence between the morphological features and genetic relationships of the sinica group of macaques (genus Macaca), the taxonomy of this macaque group has remained inconclusive. We aimed to resolve the taxonomic quandary and improve our understanding of the historical biogeography of the group by including macaque DNA samples from previously unsampled areas in the Himalayas. We sequenced and analyzed three mitochondrial DNA loci [cytochrome b (CYTB), cytochrome oxidase subunit 1 (COI) and D-loop; 2898 bp] for sequence polymorphism, phylogenetics, species delimitation, and ancestral area reconstruction. We confirmed the occurrence of Arunachal macaque (Macaca munzala) on the southern slopes of the Eastern Himalayas in the Xizang Zizhiqu (Tibet Autonomous Region) of China. The results revealed that the sinica group of macaques is a parapatric species group composed of seven distinct species. Phylogenetic and species delimitation analyses revealed that the two previously considered subspecies of Assamese macaques (the eastern subspecies M. assamensis assamensis and the western subspecies M. a. pelops) are two distinct species. The eastern Assamese macaque is a sister species to the Tibetan macaque, whereas the western Assamese macaque and Arunachal macaque are the closest genetic sister species. The sinica group of macaques underwent five vicariance and seven dispersal radiations in the past, which mainly coincided with the Quaternary climatic oscillations between the late Pliocene and the late Pleistocene. By integrating our phylogenetic and ancestral area reconstruction results with findings from previous paleontological and molecular studies, we propose a robust hypothesis about the phylogeography of the sinica group of macaques. [ABSTRACT FROM AUTHOR]

Combating wildlife crimes in South Africa requires accurate identification of traded species and their products. Diagnostic morphological characteristics needed to identify species are often lost when specimens are processed and customs officials lack the expertise to identify species. As a potential solution, DNA barcoding can be used to identify morphologically indistinguishable specimens in forensic cases. However, barcoding is hindered by the reliance on comprehensive, validated DNA barcode reference databases, which are currently limited. To overcome this limitation, we constructed a barcode library of cytochrome c oxidase subunit 1 and cytochrome b sequences for threatened and protected mammals exploited in southern Africa. Additionally, we included closely related or morphologically similar species and assessed the database's ability to identify species accurately. Published southern African sequences were incorporated to estimate intraspecific and interspecific variation. Neighbor-joining trees successfully discriminated 94%–95% of the taxa. However, some widespread species exhibited high intraspecific distances (>2%), suggesting geographic sub-structuring or cryptic speciation. Lack of reliable published data prevented the unambiguous discrimination of certain species. This study highlights the efficacy of DNA barcoding in species identification, particularly for forensic applications. It also highlights the need for a taxonomic re-evaluation of certain widespread species and challenging genera. [ABSTRACT FROM AUTHOR]

Genomic‐scale datasets, sophisticated analytical techniques, and conceptual advances have disproportionately failed to resolve species boundaries in some groups relative to others. To understand the processes that underlie taxonomic intractability, we dissect the speciation history of an Australian lizard clade that arguably represents a "worst‐case" scenario for species delimitation within vertebrates: the Ctenotus inornatus species group, a clade beset with decoupled genetic and phenotypic breaks, uncertain geographic ranges, and parallelism in purportedly diagnostic morphological characters. We sampled hundreds of localities to generate a genomic perspective on population divergence, structure, and admixture. Our results revealed rampant paraphyly of nominate taxa in the group, with lineages that are either morphologically cryptic or polytypic. Isolation‐by‐distance patterns reflect spatially continuous differentiation among certain pairs of putative species, yet genetic and geographic distances are decoupled in other pairs. Comparisons of mitochondrial and nuclear gene trees, tests of nuclear introgression, and historical demographic modelling identified gene flow between divergent candidate species. Levels of admixture are decoupled from phylogenetic relatedness; gene flow is often higher between sympatric species than between parapatric populations of the same species. Such idiosyncratic patterns of introgression contribute to species boundaries that are fuzzy while also varying in fuzziness. Our results suggest that "taxonomic disaster zones" like the C. inornatus species group result from spatial variation in the porosity of species boundaries and the resulting patterns of genetic and phenotypic variation. This study raises questions about the origin and persistence of hybridizing species and highlights the unique insights provided by taxa that have long eluded straightforward taxonomic categorization. [ABSTRACT FROM AUTHOR]

The deep-sea raphitomid genus Gymnobela Verrill, 1884 (Neogastropoda: Conoidea) has historically been a container for a multitude of raphitomid species, assigned to this genus almost exclusively based on shell characters. Consequently, the genus has become taxonomically inflated. However, a 2021 molecular study redefined Gymnobela and taxonomically revised the genus. Herein, we present an integrative taxonomic study that, mainly based on samples from Australian waters, further defines this problematic genus, as well as the closely related genus Pontiothauma E.A. Smith, 1895. An automatic barcode gap discovery (ABGD) analysis of three mitochondrial genes resulted in six primary species hypotheses (four in Gymnobela and two in Pontiothauma). We recognised morpho-anatomical and bathymetric/geographical characters distinct to all six and found available names for four; we name one new species, Pontiothauma transregnasp. n., but abstain from naming one presumably unnamed Pontiothauma due to a lack of well-preserved adult specimen material. We provide clear synapomorphic characters unique to both Gymnobela and Pontiothauma, notably those of the radula. Furthermore, we present the first evidence supported by molecular data of a transoceanic distribution among the raphitomids, namely in Gymnobela angulosa Sysoev, 1988. Additionally, we recognise non-molecular evidence that might indicate similarly wide distributions in Gymnobela agasizzi (Verrill and Smith, 1880), Gymnobela engonia Verrill, 1884 and Gymnobela frielei Verrill, 1885. Consequently, and to avoid taxonomic splitting, we herein advocate for wide-ranging investigation of worldwide material when conducting taxonomic studies on deep-sea conoideans, due to growing evidence of transoceanic distributions in the group. Finally, through an exhaustive search of worldwide repositories and the literature, and in conjunction with our molecular, morpho-anatomical and bathymetric/geographical data, we have reassigned 16 species from Gymnobela to other genera within the family Raphitomidae. [ABSTRACT FROM AUTHOR]

Neogoniolithon is a widespread genus of non‐geniculate coralline algae in the Mediterranean Sea. Three vaguely differentiated species have been reported in the region. This study examined the diversity of Neogoniolithon in the Mediterranean by inferring phylogenies using psbA and COI‐5P markers, applying delimitation algorithms and comparing morpho‐anatomies of putative species. In contrast to previous reports, 13 species were delimited from the Mediterranean in two distant clades. Initial observations suggested that tetrasporangial conceptacle size might be used to separate the two clades. Only three species showed fruticose morphologies. Further morpho‐anatomical differentiation was difficult. One species included Mediterranean, Pacific and Atlantic samples, while three other species occurred in the Mediterranean and the Canary Islands. The global tree revealed that most species were geographically restricted. Crypticity in multiple lineages implied a much higher diversity than currently reported, even lacking samples from the eastern Mediterranean. Only sequence data can be used to identify these cryptic lineages. High endemism emphasizes the importance of conservation of coralline algal bioconstructions to prevent extinctions. The presence of cryptic diversity also invites a reassessment of the knowledge on species distributions that are important in conservation planning and management. [ABSTRACT FROM AUTHOR]

Abstract Fish early-stages constitute useful indicators of the states of marine ecosystems, as well as important fishery resources. Given the spectacular phenotypic changes during ontogeny, and the paucity of diagnostic morphological characters at the species level, the identification of fish early-stages is a challenging task. DNA barcoding, the use of the mitochondrial gene of the cytochrome c oxidase subunit I (COI) as an internal species tag, opened new perspectives for the identifications of both larval fish and fish eggs. However, the accuracy of the identifications assisted by DNA barcoding are dependent of the completeness of the DNA barcode reference libraries used to assigned unknown sequences to known species. Here, we built a DNA barcode reference library for 113 species of larval fish and 85 species of fish eggs involving the production of 741 newly generated DNA barcodes from South China Sea (63 localities). Together with 514 DNA barcodes mined from Genbank for 116 species from the South China Sea regions, a reference library including 1255 DNA barcodes for 308 species (248 locations) was assembled. The present study emphasizes the importance of integrating DNA barcoding to large scale inventories of early stages, as DNA-based species delimitation analyses delimited 305 molecular operational taxonomic units (MOTUs) and multiple cases of discordance with morphological identifications were detected. Cryptic diversity is detected with 14 species displaying two MOTUs and a total of 23 species were lumped into 11 MOTUs due to low interspecific divergence and/or mixed lineages.

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

AbstractThe populations of the loggerhead turtles, Caretta caretta, present four main D-loop mitochondrial haplogroups that are distributed across the Indo-Pacific, Mediterranean, and Atlantic oceans. The Southwestern Atlantic (SWA) is one of the Regional Management Units (RMUs) of loggerheads, characterized by unique haplotypes, high nest density, and distinct life history traits. Detecting new D-loop haplogroups is important, particularly endemic ones, as they can enhance our understanding of their life history within the RMUs and contribute to the resolution of mixed stock analysis. In this study, we conducted a series of phylogenetic delimitation and network analyses to identify, validate, and infer the origin of four new D-loop haplotypes detected in the loggerhead populations from the SWA. Our findings demonstrate that these new D-loop haplotypes are valid and unique to the SWA lineage, potentially aiding in the delimitation of individuals’ origins and the inference of their lineage. [ABSTRACT FROM AUTHOR]

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

Anacolia menziesii sensu lato (Bartramiaceae) is a common and widespread moss in western North America that has been treated as either a single variable species or two distinct taxa, A. menziesii s.s. and A. baueri, with the two variously interpreted as species or subspecies. Interpretation has been hampered historically because the primary character used to separate the two entities, capsule shape, is absent on most specimens of this dioicous moss, and gametophytes have not yielded characters that can be used to separate the two putative entities with confidence. Here, we quantified previously categorical traits to test whether morphological characters are continuous across the geographic range or whether discrete morphological groups exist within A. menziesii s.l. We found that quantitative sporophyte characters replacing analogous categorical characters support the recognition of two entities, and that quantitative gametophyte characters also support the recognition of two entities. Furthermore, the two morphologically defined entities are overlapping geographically but have distinctive ecological niches. This provides strong evidence supporting the recognition of two species and provides new tools for separating sterile material. [ABSTRACT FROM AUTHOR]

The rich genetic and phenotypic diversity of species complexes is best recognized through formal taxonomic naming, but one must first assess the evolutionary history of phylogeographic lineages to identify and delimit candidate taxa. Using genomic markers, mitochondrial DNA barcoding, and morphometric analyses, we examined lineage diversity and distribution in the Iberian endemic frog Rana parvipalmata. We confirmed two deep phylogeographic lineages, one relatively homogenous genetically, found in Asturias and adjacent areas (T2), and one more fragmented and locally genetically impoverished, restricted to Galicia (T1). Analyses of their hybrid zone suggested a shallow transition characterized by far-ranging admixture, which was modelled by a wide geographic cline (~60 km for the genome average) and no obvious barrier loci (i.e. loci showing disproportionally restricted introgression). The relatively young T1 and T2 have thus remained reproductively compatible, which argues against their distinction as biological species, and we accordingly describe T2 as a new subspecies, Rana parvipalmata asturiensis ssp. nov. Remarkably, we highlight striking discordances between mitochondrial and nuclear distributions across their hybrid zones, as well as between their genetic and morphological differentiation. Our study illustrates how genomic-based phylogeographic frameworks can help decipher the high genetic and phenotypic variation of species complexes and substantiate the taxonomic assessment of candidate lineages. [ABSTRACT FROM AUTHOR]

Simple Summary: Chaetogaster is a genus of the subfamily Naidinae (Naididae). It includes a large number of species and is frequent in surface coarse sediments in streams. The aim of the present study is to establish a first inventory of lineages of Chaetogaster (=species) in Switzerland. We analyzed genetically 135 specimens collected at 6 sites in 4 streams of 4 cantons and preserved the anterior part of almost all specimens. We were able to delimit six lineages belonging to the nominal species Chaetogaster diaphanus (one lineage), Chaetogaster diastrophus (three lineages), Chaetogaster langi (one lineage), and Chaetogaster setosus (one lineage), as well as three lineages of unidentified Chaetogaster spp. We described the three cryptic lineages of C. diastrophus and two Chaetogaster spp. lineages as new species. The prospects of the present work are to acquire more data on the molecular diversity of this genus in Switzerland and to describe the newly found Chaetogaster species on a molecular/morphological basis. The genus Chaetogaster belongs to the subfamily Naidinae (Naididae); it includes mostly species of small size and is diverse and abundant in surface coarse sediments in streams. The aim of the present study is to initiate an inventory of lineages (=species) of Chaetogaster in Switzerland. We used 135 specimens collected at 6 sites in 4 streams of 4 cantons. We sequenced the cytochrome c oxidase (COI) gene from all specimens and ITS2 and rDNA 28S from all or several specimens of each lineage that was delimited using COI data, and preserved, for morphological identifications, the anterior part of almost all sequenced specimens. We were able to delimit, based on the calculation of genetic distances and analyses of single-locus data, one lineage for Chaetogaster diaphanus (Gruithuisen, 1828), three within Chaetogaster diastrophus (Gruithuisen, 1828), one for Chaetogaster langi Brestcher, 1896, one for Chaetogaster setosus Svetlov, 1925, and three unidentified Chaetogaster spp. Two lineages of Chaetogaster spp. could correspond to a new morphological group, but this should be confirmed in more specimens. We proposed a new identification key of the nominal species and described the three C. diastrophus lineages and two Chaetogaster spp. as new species. The prospects of the present work are to complete the data of the molecular diversity of this genus in Switzerland and to describe the newly found Chaetogaster species on a molecular/morphological basis. [ABSTRACT FROM AUTHOR]

During the present study, DNA sequence and morphological data were used to delineate species boundaries in the velvet worm, Peripatopsis sedgwicki species complex. The combined mitochondrial cytochrome c oxidase subunit one (COI) and the nuclear 18S rRNA loci were phylogenetically analyzed using Bayesian inference and maximum likelihood platforms that both demonstrated the presence of four, statistically well-supported clades (A–D). In addition, five species delimitation methods (ASAP, bPTP, bGMYC, STACEY and iBPP) were used on the combined DNA sequence data to identify possible novel lineages. All five species delimitation methods supported the distinction of the Fort Fordyce Nature Reserve specimens in the Eastern Cape province, however, in the main P. sedgwicki s.l. species complex, the species delimitation methods revealed a variable number of novel operational taxonomic units. Gross morphological characters were of limited utility, with only the leg pair number in the Fort Fordyce Nature Reserve specimens and the white head-collar of the Van Stadens Wildflower Nature Reserve specimens being diagnostic. The RADseq results from the earlier study of P. sedgwicki s.l. provided highly congruent results with the four clades observed in the present study. The distribution of P. sedgwicki s.s. (clade B) is restricted to the western portions of its distribution in the Afrotemperate forested regions of the Western Cape Province, South Africa. Three novel species, P. collarium sp. nov., (clade C) P. margaritarius sp. nov., (clade A) and P. orientalis sp. nov., (clade D) are described, of which the first two species are narrow range endemics. The present study, along with several recent systematic studies of velvet worms affirms the importance of fine-scale sampling to detect and document the alpha taxonomic diversity of Onychophora. [ABSTRACT FROM AUTHOR]

Species delimitation can be based on the consideration of several different criteria, including the differentiation of ecological or functional traits. Two species of Pacific rockfish, the dark rockfish (Sebastes ciliatus) and the dusky rockfish (Sebastes variabilis), appear to represent recently divergent evolutionary lineages. We evaluate evidence for the differentiation of these two species in somatic shape using geometric morphometrics at two locations in the northeast Pacific where they occur in sympatry. The somatic shape was significantly different between species, but the species' shape did not vary between the two locations. Sebastes ciliatus had an upturned and relatively smaller head, eye, and jaw, and an elongated midbody, whereas S. variabilis had a downturned and larger head, eye, and jaw, and a shorter midbody. These results suggest that S. ciliatus and S. variabilis are morphometrically differentiated in a similar way in both locations. The somatic shape differentiation between these two sympatric species is similar to genus-wide patterns of somatic shape differentiation. [ABSTRACT FROM AUTHOR]

Alternaria is a large genus within Pleosporaceae and consists of fungi that have up to recently been considered to be 15 separate genera, including Ulocladium. The majority of Ulocladium species after incorporation into Alternaria were placed in three sections: Ulocladioides, Pseudoulocladium, and Ulocladium. In this study, phylogeny of 26 reference strains of 22 species and 20 Russian Ulocladium-like isolates was recovered. The partial actin gene (act), Alternaria major allergen (alta1), calmodulin (cal), glyceraldehyde-3-phosphate dehydrogenase (gapdh), RNA polymerase II second largest subunit (rpb2), and translation elongation factor 1-α (tef1) were sequenced for Russian isolates. All these fungi were examined using multilocus phylogenetic analysis according to the genealogical concordance phylogenetic species recognition (GCPSR) principle and the coalescent-based model Poisson tree processes (PTP, mPTP) and evaluated for the presence of recombination. All strains were combined into two clades that corresponded to the Pseudoulocladium and Ulocladioides sections. The Pseudoulocladium clade included four reference strains and nine local isolates and considered to be a single species, whereas the Ulocladioides section comprises 11 species, instead of 17 names previously adopted. Nine species were abolished by joining four other species. Species A. atra and A. multiformis were combined into the single species A. atra. Five species, A. brassicae-pekinensis, A. consortialis, A. cucurbitae, A. obovoidea, and A. terricola, were united in the species A. consortialis. Alternaria heterospora and A. subcucurbitae were combined into one species, A. subcucurbitae. Alternaria aspera, A. chartarum, A. concatenata, and A. septospora were combined into a single species, A. chartarum. Also, amplification with two different primer sets was performed to define mating-type locus 1 (MAT1) idiomorph. All studied isolates were heterothallic, contradicting some prior studies. Twenty Russian Ulocladium-like isolates were assigned to five species of two sections, A. atra, A. cantlous, A. chartarum, A. consortialis, and A. subcucurbitae. Species A. cantlous and A. subcucurbitae were found in Russia for the first time. [ABSTRACT FROM AUTHOR]

An accurate species‐level taxonomy is paramount for biogeographical research, and conversely, biogeographical data are of importance for species delimitation. We here review recent developments and future perspectives of taxonomy of direct relevance for biogeographers. The understanding that species are independently evolving segments of population‐level lineages, the rise of integrative approaches to delimit such lineages, and the advent of high‐throughput sequencing have considerably renewed the discipline of taxonomy. Using genome‐scale molecular datasets, the extent of admixture across hybrid zones can now be effectively assessed and the evolutionary independence of lineages inferred, leading to more reliable and comparable species delimitation criteria. Substantially divergent but admixing phylogeographical lineages can conveniently be named as subspecies, thus avoiding taxonomic oversplitting and taxonomic inflation. At the same time, comprehensive DNA barcoding and DNA metabarcoding efforts are uncovering an enormous proportion of undiscovered biotic diversity, and we encourage the development of bioinformatic pipelines that combine high‐throughput species discovery and delimitation with diagnosis and scientific naming, to approach a biotic inventory of the globe without abandoning the established Linnaean system. [ABSTRACT FROM AUTHOR]

The Atlantic Forest is recognized as a biodiversity hotspot because of the high species richness and the remaining natural areas comprising less than 30% relative to its primary vegetation. Even though many anuran species from this biome are ecologically restricted to pristine ecosystems, there are some examples of new species discovered from anthropized areas. Adenomera represents a widespread and abundant frog genus in Atlantic Forest ecosystems, with species occurring in areas with varying degrees of human disturbance. In this paper, we name and describe a new species of Adenomera endemic to the Atlantic Forest typically found in human-altered ecosystems, such as urban and rural sites. The new species was recovered as belonging to the Adenomera marmorata clade, and sister to A. ajurauna. These two species have allopatric distributions in southeastern and southern Brazil, with a single known sympatric occurrence. They display different calls and occupy distinct habitats. The newly described species of Adenomera is an additional case of new species discovered from urban sites in the Atlantic Forest hotspot. [ABSTRACT FROM AUTHOR]

The taxonomy of the freshwater featherback fish genus Chitala (Osteoglossomorpha: Notopteridae) remains unsettled because delimiting and naming Chitala species based solely on morphology led to different hypotheses. In this study, we aim to determine the number and identity of Chitala species present in Peninsular Malaysia by employing an integrative taxonomic approach that combines morphology and two mitochondrial markers: the cytochrome c oxidase subunit I (COI) and cytochrome b genes. A total of 60 specimens of Chitala were collected throughout Peninsular Malaysia. Initially, all specimens were sorted into three distinct categories based on their body marking patterns. A molecular phylogenetic analysis revealed that each of these groups was monophyletic, and an automated species partition method further recognized them as distinct species. These results support the presence of three Chitala species in Peninsular Malaysia, even though a multivariate morphometric analysis failed to fully differentiate each of these three species. Comparison with original species descriptions and genetic data from an additional 70 Chitala specimens from neighbouring regions allowed us to name these species as Chitala lopis, Chitala borneensis, and Chitala ornata. We also showed the presence of two undescribed species in Indonesia. [ABSTRACT FROM AUTHOR]

The terrestrial isopod genus Ligidium includes 58 species from Europe, Asia, and North America. In Eastern North America four species are recognized: L. floridanum and L. mucronatum, known just from their type localities in Florida and Louisiana respectively, L. blueridgensis, endemic to the southern Appalachians, and L. elrodii, widespread from Georgia to Ontario. The genus shows a marked morphological conservatism, and species are differentiated mostly by small morphological differences; it is not always easy to determine if such variability represents inter‐ or intraspecific variation. Here, we explore the diversity of Ligidium from the southern Appalachian Mountains, exploring the congruence of morphologically defined groups with multilocus phylogenetic reconstructions and molecular species delimitation methods. We have studied a total of 130 specimens from 37 localities, mostly from the southern Appalachians, and analysed mtDNA (Cox1) and nuclear (28S, NaK) sequences. Morphologically, we recognized eight morphotypes, most of them assignable to current concepts of L. elrodii and L. blueridgensis. Phylogenetic analyses supported the evolutionary independence of all morphotypes, and suggest the existence of 8–9 species, including limited cryptic diversity. Single‐locus delimitation analyses based on mtDNA data suggest the existence of a much higher number of species than the multilocus analyses. The estimated age of the ancestors of sampled lineages indicates a long presence of the genus in eastern North America and old speciation events through the Miocene. Our results indicate a higher diversity than previously thought among the Ligidium populations present in the southern Appalachian Mountains, with several species to be described. [ABSTRACT FROM AUTHOR]

Delimitation of allopatric populations into species remains subjective and largely arbitrary. Many cold-adapted species from the sub-Arctic and Central and Southern European Mountain systems provide excellent models to study allopatry problem due to their patchy distributions. The same concerns many Holarctic species, which frequently show varying degrees of differentiation between continents. In this study, we analyze high-throughput target enrichment data for 10 groups of Arctic-alpine and Holarctic lepidopteran species sampled from different regions across the Holarctic realm, i.e. Fennoscandia, European Alps, Altai Mountains, and North America. We first aimed to assess whether the genetic differences in the nuclear genome reflected observed DNA barcode divergences and, secondly, whether the gap between population and species-level differences can be reliably dissected using genomic data. We compared the phylogenetic trees and uncorrected pairwise genetic distances obtained from target enrichment and mitochondrial COI barcodes and performed a suite of population genetic and species delimitation analyses to further explore patterns of intraspecific variation in our study species. We observed that in about one-half of the cases, DNA barcodes showed phylogenetic relationships similar to the target enrichment markers. Nuclear genetic differentiation varied among the populations analyzed, from low differentiation of geographically separated populations to the deeper separation of some Nearctic populations and Arctic-alpine disjunction in the populations from Fennoscandia and Southern European mountains. Our results highlight the need for consistent delimitation of allopatric populations, especially given the prevalence of distributional discontinuities across species. Large sets of standard genetic markers provide a very promising avenue towards this goal. [ABSTRACT FROM AUTHOR]

Jezero Blaca is a unique spring lake situated at the northern coast of the Pelješac Peninsula near the village Duba Pelješka in South Dalmatia, Croatia. The lake supported by a karstic spring located near the Adriatic seashore is inhabited by unusually rich brackish water truncatelloid assemblage. The position of the lake near seashore evokes a model of sea invertebrate gradual adaptation to freshwater spring head allowing them to further invade the stygobiont karst conduits. Similar lakes could be the marine gateways of the extraordinarily rich Dinaric stygobiont fauna. The main aim of this study was to sample and barcode the aquatic snails found in this locality to check their species affiliation and describe conservation needs. The results confirmed that the locality hosts four interesting representatives of the gastropod superfamily Truncatelloidea, which has never been found syntopically so far. One of the species characterized by unique COI sequences and was described herein as Truncatella dalmatica new sp. The conservation need of this unique and understudied habitat type is discussed. [ABSTRACT FROM AUTHOR]

New-generation molecular approaches and methods are currently being developed to accurately identify species and establish species boundaries. Various approaches to species delimitation are utilized to evaluate the species richness of poorly studied and highly diverse taxa. DNA barcoding has proven to be a powerful tool for species identification and delimitation. While DNA barcoding studies have been conducted in the family Heteroderidae, there has been a lack of research on species delimitation. Therefore, in 2024, a study was undertaken at the University of Limpopo to compare species delimitation analyses within the Meloidogyne genus based on the cytochrome c oxidase I (COI) region. In this study, ASAP species delimitation approaches were employed. A total of 73 sequences from South Africa were utilised (GenBank), representing four species (Meloidogyne sp, M. incognita, M. javanica, and M. enterolobii). The phylogenetic analyses grouped all the species into two major clades, with M. enterolobii being distinctly separate. In conclusion, the ASAP results showed no significant differences among the species. Therefore, the COI marker is not a suitable marker for Meloidogyne species. [ABSTRACT FROM AUTHOR]

Modern species delimitation is challenged by past morphological descriptions, a mix of applied species concepts, missing tools for complex evolutionary processes and large multi-approach datasets, and nonstandardized data integration. The vision is to have less subjective and standardized species delimitation approaches based on modern integrative taxon-omics under a unified species concept, integrating the discovery of genetic entities with the fusion of automatically extracted information from multi-approach data to find natural taxonomic units. Artificial Intelligence (AI) approaches have been launched to tackle delimitation issues using classification/clustering methods based on supervised/unsupervised learning, although data fusion and problematic and unknown species represent active fields of research. AI can help accelerate the revision and unraveling of eukaryotic biodiversity on a scale not seen before. Although species are central units for biological research, recent findings in genomics are raising awareness that what we call species can be ill-founded entities due to solely morphology-based, regional species descriptions. This particularly applies to groups characterized by intricate evolutionary processes such as hybridization, polyploidy, or asexuality. Here, challenges of current integrative taxonomy (genetics/genomics + morphology + ecology, etc.) become apparent: different favored species concepts, lack of universal characters/markers, missing appropriate analytical tools for intricate evolutionary processes, and highly subjective ranking and fusion of datasets. Now, integrative taxonomy combined with artificial intelligence under a unified species concept can enable automated feature learning and data integration, and thus reduce subjectivity in species delimitation. This approach will likely accelerate revising and unraveling eukaryotic biodiversity. Although species are central units for biological research, recent findings in genomics are raising awareness that what we call species can be ill-founded entities due to solely morphology-based, regional species descriptions. This particularly applies to groups characterized by intricate evolutionary processes such as hybridization, polyploidy, or asexuality. Here, challenges of current integrative taxonomy (genetics/genomics +morphology +ecology, etc.) become apparent: different favored species concepts, lack of universal characters/markers, missing appropriate analytical tools for intricate evolutionary processes, and highly subjective ranking and fusion of datasets. Now, integrative taxon-omics combined with artificial intelligence under a unified species concept can enable automated feature learning and data integration, and thus reduce subjectivity in species delimitation. This approach will likely accelerate revising and unraveling eukaryotic biodiversity. [ABSTRACT FROM AUTHOR]

Simple Summary: We evaluated linear morphometry of male genitalia as a diagnostic method to distinguish the genera and species of Monomorium and Syllophopsis (Hymenoptera: Formicidae). We measured 10 morphometric characters on the male genitalia from 10 species of Monomorium and 5 species of Syllophopsis. We used three datasets, raw data, ratio data, and RAV data, and analyzed them using multivariate methods: hierarchical clustering (Ward's method), Principal Component Analysis (PCA), Non-Metric Multidimensional Scaling analyses (NMDS), Linear Discriminant Analysis (LDA), and Conditional Inference Trees (CITs). The ratio data were most effective in separating the two genera, while the raw data were more effective at species-level delimitation. The findings highlighted the potential for a broader application of genitalia-based morphometric analyses in ant systematics. Morphometric analyses of male genitalia are routinely used to distinguish genera and species in beetles, butterflies, and flies, but are rarely used in ants, where most morphometric analyses focus on the external morphology of the worker caste. In this work, we performed linear morphometric analysis of the male genitalia to distinguish Monomorium and Syllophopsis in Madagascar. For 80 specimens, we measured 10 morphometric characters, especially on the paramere, volsella, and penisvalvae. Three datasets were made from linear measurements: mean (raw data), the ratios of characters (ratio data), and the Removal of Allometric Variance (RAV data). The following quantitative methods were applied to these datasets: hierarchical clustering (Ward's method), unconstrained ordination methods including Principal Component Analysis (PCA), Non-Metric Multidimensional Scaling analyses (NMDS), Linear Discriminant Analysis (LDA), and Conditional Inference Trees (CITs). The results from statistical analysis show that the ratios proved to be the most effective approach for genus-level differentiation. However, the RAV method exhibited overlap between the genera. Meanwhile, the raw data facilitated more nuanced distinctions at the species level compared with the ratios and RAV approaches. The CITs revealed that the ratios of denticle length of the valviceps (SeL) to the paramere height (PaH) effectively distinguished between genera and identified key variables for species-level differentiation. Overall, this study shows that linear morphometric analysis of male genitalia is a useful data source for taxonomic delimitation. [ABSTRACT FROM AUTHOR]