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The Ficus erecta complex, characterized by its morphological diversity and frequent interspecific overlap, shares pollinating fig wasps among several species. This attribute, coupled with its intricate phylogenetic relationships, establishes it as an exemplary model for studying speciation and evolutionary patterns. Extensive researches involving RADseq (Restriction-site associated DNA sequencing), complete chloroplast genome data, and flow cytometry methods were conducted, focusing on phylogenomic analysis, genetic structure, and ploidy detection within the complex. Significantly, the findings exposed a pronounced nuclear-cytoplasmic conflict. This evidence, together with genetic structure analysis, confirmed that hybridization within the complex is a frequent occurrence. The ploidy detection revealed widespread polyploidy, with certain species exhibiting multiple ploidy levels, including 2×, 3×, and 4×. Of particular note, only five species (F. abelii, F. erecta, F. formosana, F. tannoensis and F. vaccinioides) in the complex were proved to be monophyletic. Species such as F. gasparriniana, F. pandurata, and F. stenophylla were found to encompass multiple phylogenetically distinct lineages. This discovery, along with morphological comparisons, suggests a significant underestimation of species diversity within the complex. This study also identified F. tannoensis as an allopolyploid species originating from F. vaccinioide and F. erecta. Considering the integration of morphological, molecular systematics, and cytological evidences, it is proposed that the scope of the F. erecta complex should be expanded to the entire subsect. Frutescentiae. This would redefine the complex as a continuously evolving group comprising at least 33 taxa, characterized by blurred species boundaries, frequent hybridization and polyploidization, and ambiguous genetic differentiation. [ABSTRACT FROM AUTHOR]

In this work, the diversity of the genus Orbiniella in the Nordic Seas and the North Atlantic waters south of Iceland is studied based on the analyses of molecular markers (mitochondrial COI, 16S rDNA and nuclear ITS2) and morphological characters. Our results showed the presence of at least five genetic lineages in the studied material which could also be morphologically identified by their segmental annulation patterns, the number and the shape of acicular spines, and the length and the shape of pygidial lobes. The species name Orbiniella petersenae is assigned to one of the lineages restricting its geographical and vertical distribution to the deep-sea areas north of Iceland and Jan Mayen, and three lineages are described as new species (i.e., Orbiniella griegi Meca & Budaeva, sp. nov., Orbiniella mayhemi Meca & Budaeva, sp. nov., and Orbiniella parapari Meca & Budaeva, sp. nov.) elevating the number of known species in the genus to 25. Three deep-sea species of Orbiniella in our study are reported only north of the Greenland-Iceland-Scotland Ridge, one deep-sea species found south of the ridge. A single shallow-water species is distributed along the ridge and on the Norwegian shelf. [ABSTRACT FROM AUTHOR]

With up to 137 species worldwide, Myotis ,— a genus of small, insectivorous bats are an example for understanding biogeographic and evolutionary processes such as intercontinental colonization, diversification, speciation, and convergent adaptive evolution. Species limits and associated distributions, however, remain poorly delineated across significant portions of this diverse group and encompassing a vast geographic range. Here, we explore how diversity is partitioned across this radiation with a focus on Neotropical species of Myotis , using a barcoding approach (706 bp of the mitochondrial DNA gene cytochrome-b) that includes 544 individual sequences (116 newly generated sequences and 428 sequences from GenBank, including outgroups). Single-locus molecular barcoding is useful for identifying cryptic diversity and establishing hypotheses that can guide investigations of species boundaries and phylogenetic relationships, an especially important initial step in assessing poorly characterized, diverse clades. The global phylogeny produced from these data is consistent with the hypothesized monophyly of the New World clade and places the evolutionary relationships of Neotropical species of Myotis within the context of the Palearctic and Nearctic clades. We then explore species boundaries for 25 of the 36 nominal species of Neotropical Myotis , using 3 alternative species delimitation approaches (1 distance-based ABGD [Automatic Barcode Gap Discovery]; and 2 coalescent-based mPTP [multi-rate Poisson Tree Processes], GMYC [Generalized Mixed Yule Coalescent] model). The mPTP (n = 29 species) and ABGD (n = 26) approaches inferred different numbers of species than that recognized by current Neotropical Myotis taxonomy, whereas GMYC (n = 25) inferred the same number of species. In addition to the original 36 Neotropical nominal species currently recognized, we suggest that taxonomic revisions are needed to assess whether M. oxyotus gardneri and M. nigricans osculatii should be elevated to the species level and whether M. dinellii is distinct from M. levis. With the 7 potentially cryptic species identified herein that require further study, the number of Neotropical Myotis may approach 45 species. Taken together, our results suggest that rather than a classic example of a temperate radiation, there may be more species of Myotis in the Neotropics than Nearctic, Afrotropic, Indomalayan, and Oceanian Realms, with only the Palearctic region showing higher species richness. [ABSTRACT FROM AUTHOR]

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

The lacertid wall lizards of the genus Podarcis (Wagler, 1830) originate from Western Europe and are divided into 24-25 species (Speybroeck et al., 2020). Despite the abundance of phylogenetic studies referring to the genus, the relationships among certain species, as well as the taxonomic status of some genealogical lineages, remain unclear due to great genetic diversity. The common wall lizard Podarcis muralis has a relatively wide distribution and despite the existence of various molecular studies focused on this species, its Greek populations had never been thoroughly sampled until now. To fill in this geographical gap, we sampled the species' Greek distribution and constructed phylogenies that uncovered the presence of at least five monophyletic lineages that correspond to different geographic regions. Furthermore, species delimitation analyses assigned all lineages to a single species diversifying during the early Pleistocene (c. 1.93 mya). The strong association of the genetic lineages with specific geographical regions coupled with the Pleistocene diversification of the group imply the presence of multiple refugia within Greece and, by extension, the Balkan peninsula, supporting a refugia-within-refugia scenario. Finally, in an effort to clarify the position of these new samples within the larger phylogeny of P. muralis , a larger phylogeny was constructed which indicated that the Greek populations cluster with the central European, Italian and Turkish populations of the species. [ABSTRACT FROM AUTHOR]

The South American central Andes have a great richness of Asteraceae, where the genus Stevia (Eupatorieae, Piqueriinae) is also especially diverse. The taxonomy of Stevia species in the southern part of the central Andes pose a challenge because of the unclear delimitation among the species and overlap of morphological characters. Two species complexes were identified for the region comprising north Argentina and southern Bolivia. In this study, our objectives were to employ morphometric analyses to assess the delimitation of taxa within the Stevia alpina Griseb. and Stevia chamaedrys Griseb. complexes. We aimed to identify informative morphological characters and gain insight into the identity of species in each group. To accomplish this, we utilised cluster analysis, principal-component analysis, non-metric multidimensional scaling and univariate analyses to evaluate 37 morphological traits. In total, 200 specimens were examined, covering the entire geographic distribution of each species complex. We found support for the recognition of nine species: Stevia alpina, S. breviaristata Hook. & Arn., S. chamaedrys, S. mandonii Sch. Bip., S. mercedensis Hieron., S. minor Griseb., S. potrerensis Hieron., S. procumbens Hieron. and S. vaga Griseb. A new combination and status is proposed for S. tarijensis Hieron., incorporating it as a variety of S. mandonii, and S. centinelae Cabrera and S. crassicephala Cabrera are merged as synonyms under the name S. alpina. Two neotypes are designated for the names S. mercedensis and S. potrerensis. [ABSTRACT FROM AUTHOR]

Chrysopidae are a family of Neuroptera of significant importance in biocontrol against agricultural pests because of their predatory larvae. Currently, the taxonomy of Chrysopidae lacks a comprehensive revision, which impedes the exploration of species diversity as well as the selection and the conservation of green lacewings as biocontrol agents. We have established a DNA barcode reference library of the Chinese green lacewings based on an approximately complete sampling (95.63%) in 25 of the 34 provincial regions in China, comprising 1 119 barcodes of 25 genera and 197 species (representing 85% genera and 43.62% species from China). Combining other 1 049 high quality green lacewing DNA barcodes, we first inferred the optimal threshold of interspecific genetic divergence (1.87%) for successful species identification in multiple simulated scenarios based on present data. We further inferred the threshold of genetic divergence (7.77%) among genera with biocontrol significance. The inference and performance of the threshold appears to be mainly associated with the completeness of sampling, the proportion of closely related species, and the analytical approaches. Six new combinations, Apertochrysa platypa (Yang & Yang, 1991) comb. nov., Apertochrysa shennongana (Yang & Wang, 1990) comb. nov., Apertochrysa pictifacialis (Yang, 1988) comb. nov., Apertochrysa helana (Yang, 1993) comb. nov., Plesiochrysa rosulata (Yang & Yang, 2002) comb. nov., and Signochrysa hainana (Yang & Yang, 1991), are proposed according to integrative species delimitation. Our library and optimal threshold will effectively facilitate the exploration of species diversity of green lacewings. Our study also provides a methodological reference in molecular delimitation of other insects. [ABSTRACT FROM AUTHOR]

The use of species as a concept is an important metric for assessing biological diversity and ecosystem function. However, delimiting species based on morphological characters can be difficult, especially in aquatic plants that exhibit high levels of variation and overlap. The Sphagnum cuspidatum complex, which includes plants that dominate peatland hollows, provides an example of challenges in species delimitation. Microscopic characters that have been used to define taxa and the possibility that these characters may simply be phenoplastic responses to variation in water availability make species delimitation in this group especially difficult. In particular, the use of leaf shape and serration, which have been used to separate species in the complex, have resulted in divergent taxonomic treatments. Using a combination of high-resolution population genomic data (RADseq) and a robust morphological assessment of plants representing the focal species, we provide evidence to evaluate putative species in this complex. Our data support the recognition of S. cuspidatum , S. fitzgeraldii , S. mississippiense , and S. trinitense as genetically distinct species that can be separated morphologically. These results indicate that S. viride does not differ genetically from S. cuspidatum. Our results are broadly relevant to other aquatic groups where leaf shape and marginal teeth are used to distinguish species. [ABSTRACT FROM AUTHOR]

Understanding how historical geological processes drive diversification and shape the contemporary distribution of species is fundamental to phylogeography. We take a genomic approach in order to elucidate the deep phylogeographical history and species limits of chuckwallas (Sauromalus), a conspicuous group of lizards of the arid lands of south-western North America. Phylogenetic and population genomic analyses of double digest restriction site-associated DNA sequencing data confirm the presence of at least two major lineages, peninsular and continental groups, within the widespread and morphologically variable common chuckwalla (Sauromalus ater). These lineages diversified in the vicinity of the head of the Gulf of California in north-eastern Baja California in the early Pliocene to late Miocene, during the formation of the northern gulf. The peninsular lineage of S. ater subsequently gave rise to the four insular endemic species of Sauromalus associated with the Baja California peninsula. Genomic analyses strongly support the continued recognition of the insular gigantics Sauromalus varius and Sauromalus hispidus as distinct species, although their relationship as sister species remains unresolved. Weaker phylogenetic signal for the insular species Sauromalus slevini and Sauromalus klauberi is provided by the genomic data; thus, it is advocated to continue recognizing these species until additional data can be analysed to evaluate their distinctiveness. [ABSTRACT FROM AUTHOR]

Morphological and molecular data support the description of a new Aequidens species from the upper rio Correntes, considered herein as endemic to the upper rio Paraguai basin in the Cerrado biome in Brazil. The new species is distinguished from all congeners, except from A. plagiozonatus by having anteriorly oblique dark brown flank bars vs. vertical flank bars, and is additionally distinguished from some congeners by showing a discontinuous lateral band and presence of a dark cheek spot. The new species differs from Aequidens plagiozonatus by having the profile of the dorsal part of head almost straight (in lateral view), with a conspicuous concavity at the interorbital, and by the longer length of upper and lower jaws. Furthermore, delimitation analyses based on mitochondrial data provide additional support for the validity of the species. Our study data also revealed the occurrence, and consequently the first record, of A. plagiozonatus in the upper rio Araguaia basin, which was most likely driven by headwater capture events. [ABSTRACT FROM AUTHOR]

The twisted‐winged parasite genus Stylops has a history of different species concepts with varying host specificity resulting in diverse species diversity estimates in different regions of the Holarctic. The adoption of a supergeneralist species concept in Europe, proposing synonymization of all Western Palaearctic Stylops species, did not facilitate taxonomic clarity and obscured the available life‐history data in the region for decades. Lack of molecular data has allowed divergent opinions on species hypotheses and little opportunity for evaluating them in this morphologically challenging genus. To solve these discrepancies and gain novel information about host associations, we applied whole‐genome sequencing to 163 specimens, representing a significant portion of putative European species. We evaluate the existing and conflicting species hypotheses with molecular species delimitation using Species bOundry Delimitation using Astral (SODA) and use a maximum likelihood phylogeny to investigate host associations of the species. Furthermore, we evaluate the effect of a number of loci used in SODA for the number of inferred species. We find justification for synonymization of multiple species and indications of undescribed species, as well as new host–parasite relationships. We show that the number of inferred species in SODA is exceedingly and positively correlated with the number of loci used, urging for cautious application. The results of our study bring clarity to the Western Palaearctic species diversity of Stylops. Furthermore, the comprehensive molecular dataset generated in this study will be a valuable resource for future studies on Stylops and the evolution of parasites in general. [ABSTRACT FROM AUTHOR]

The complex and dynamic history of the Anatolian Peninsula during the Pleistocene set the stage for species diversification. However, the evolutionary history of biodiversity in the region is shrouded by the challenges of studying species divergence in the recent, dynamic past. Here, we study the Poecilimon bosphoricus (PB) species group to understand how the bush crickets' diversification and the regions' complex history are coupled. Specifically, using sequences of two mitochondrial and two nuclear gene segments from over 500 individuals for a comprehensive set of taxa with extensive geographic sampling, we infer the phylogenetic and geographic setting of species divergence. In addition, we use the molecular data to examine hypothesized species boundaries that were defined morphologically. Our analyses of the timing of divergence confirm the recent origin of the PB complex, indicating its diversification coincided with the dynamic geology and climate of the Pleistocene. Moreover, the geography of divergence suggests a history of fragmentation followed by admixture of populations, suggestive of a ring species. However, the evolutionary history based on genetic divergence conflicts with morphologically defined species boundaries raising the prospects that incipient species divergences may be relatively ephemeral. As such, the morphological differences observed in the PB complex may not to be sufficient to have prevented homogenizing gene flow in the past. Alternatively, with the recent origin of the complex, the lack of time for lineage sorting may underlie the discord between morphological species boundaries and genetic differentiation. Under either hypothesis, geography—not taxonomy—is the best predictor of genetic divergence. [ABSTRACT FROM AUTHOR]

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

Here we present a taxonomic treatment for the Brazilian species of Syrbatus (Reitter, 1882), including the description of three new species (Syrbatus moustache Asenjo & Valois sp. nov., Syrbatus obsidian Asenjo & Valois sp. nov. and Syrbatus superciliata Asenjo & Valois sp. nov.) from the Quadrilátero Ferrífero (Minas Gerais, Brazil). In addition, we designated lectotypes for the Brazilian species of species-group 2, Syrbatus centralis (Raffray, 1898), Syrbatus hetschkoi (Reitter, 1888), Syrbatus hiatusus (Reitter, 1888), Syrbatus transversalis (Raffray, 1898), and Syrbatus trinodulus (Schaufuss, 1887), besides recognizing the holotype for Syrbatus brevispinus (Reitter, 1882), Syrbatus bubalus (Raffray, 1898), and Syrbatus grouvellei (Raffray, 1898). The mitochondrial genomes (mitogenomes) of the three new species are presented, for which we present the phylogenetic placement among Staphylinidae with previously published data.

Abstract The Leptomias group represents one of the most diverse taxonomic group of weevils in the Qinghai‐Tibet Plateau and its adjacent areas. Despite the potential of hidden diversity, relatively few comprehensive studies have been conducted on species diversity in this taxonomic group. In this study, we performed DNA barcoding analysis for species of the Leptomias group using a comprehensive DNA barcode dataset that included 476 sequences representing 54 morphospecies. Within the dataset, our laboratory contributed 474 sequences, and 390 sequences were newly generated for this study. The average Kimura 2‐parameter distances among morphospecies and genera were 0.76% and 19.15%, respectively. In 94.4% of the species, the minimum interspecific distances exceeded the maximum intraspecific distances, indicating the presence of barcode gaps in most species of Leptomias group. The application of Automatic Barcode Gap Discovery, Assemble Species by Automatic Partitioning, Barcode Index Number, Bayesian Poisson tree processes, jMOTU, and Neighbor‐joining tree methods revealed 45, 45, 63, 54, and 55 distinct clusters representing single species, respectively. Additionally, a total of four morphospecies, Leptomias kangmarensis, L. midlineatus, L. siahus, and L. sp.9RL, were found to be assigned to multiple subclade each, indicating the geographical divergences and the presence of cryptic diversity. Our findings of this study demonstrate that Qinghai‐Tibet Plateau exhibits a higher species diversity of the Leptomias group, and it is imperative to investigate cryptic species within certain morphospecies using integrative taxonomic approaches in future studies. Moreover, the construction of a DNA barcode reference library presented herein establishes a robust foundational dataset to support forthcoming research on weevil taxonomy, phylogenetics, ecology, and evolution.

Abstract DNA barcoding is commonly used for species identification. Despite this, there has not been a comprehensive assessment of the utility of DNA barcoding in crayfishes (Decapoda: Astacidea). Here we examined the extent to which local barcoding gaps (used for species identification) and global barcoding gaps (used for species discovery) exist among crayfishes, and whether global gaps met a previously suggested 10× threshold (mean interspecific difference being 10× larger than mean intra specific difference). We examined barcoding gaps using publicly available mitochondrial COI sequence data from the National Center for Biotechnology Information's nucleotide database. We created two versions of the COI datasets used for downstream analyses: one focused on the number of unique haplotypes (NH) per species, and another that focused on total number of sequences (NS; i.e., including redundant haplotypes) per species. A total of 81 species were included, with 58 species and five genera from the family Cambaridae and 23 species from three genera from the family Parastacidae. Local barcoding gaps were present in only 30 species (20 Cambaridae and 10 Parastacidae species). We detected global barcoding gaps in only four genera (Cambarus, Cherax, Euastacus, and Tenuibranchiurus), which were all below (4.2× to 5.2×) the previously suggested 10× threshold. We propose that a ~5× threshold would be a more appropriate working hypothesis for species discovery. While the NH and NS datasets yielded largely similar results, there were some discrepant inferences. To understand why some species lacked a local barcoding gap, we performed species delimitation analyses for each genus using the NH dataset. These results suggest that current taxonomy in crayfishes may be inadequate for the majority of examined species, and that even species with local barcoding gaps present may be in need of taxonomic revisions. Currently, the utility of DNA barcoding for species identification and discovery in crayfish is quite limited, and caution should be exercised when mitochondrial‐based approaches are used in place of taxonomic expertise. Assessment of the evidence for local and global barcoding gaps is important for understanding the reliability of molecular species identification and discovery, but outcomes are dependent on the current state of taxonomy. As this improves (e.g., via resolving species complexes, possibly elevating some subspecies to the species‐level status, and redressing specimen misidentifications in natural history and other collections), so too will the utility of DNA barcoding.

The family Dendrodorididae has a global distribution, with prevalence in tropical and subtropical intertidal zones. Three species of Dendrodorididae were collected from the intertidal zone of the northern coast of the Persian Gulf in Iran. Based on anatomical, histological, and molecular investigations they can be assigned to Dendrodoris fumata, Dendrodoris nigra, and a new species of Doriopsilla, D. aroni sp. nov. Molecular analyses of CO1 and 16S, including all genera of Dendrodorididae, members of the sister taxon Phyllidiidae, and other dorid outgroups resulted in a polyphyletic genus Dendrodoris, which is in contrast to the nuclear gene studies. Our molecular results confirm the differentiation between Dendrodoris rubra and D. fumata. Dendrodoris nigra, D. fumata, and D. krusensternii each consist of several clades, indicating cryptic species complexes requiring further investigation. We describe the presence of bacteria for the first time in the vestibular gland of D. fumata. Validation of the specimens of Doriopsilla from the Persian Gulf as a new species is supported by haplotype networking, genetic distance, and ABGD analyses of mitochondrial genes. Our CO1 analysis confirms a previous hypothesis that Cariopsilla is a junior synonym of Doriopsilla.

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

Species of Baylisascaris (Nematoda: Ascarididae) are of great veterinary and zoonotic significance, owing to cause Baylisascariosis or Baylisascariasis in wildlife, captive animals and humans. However, the phylogenetic relationships of the current 10 Baylisascaris species remain unclear. Moreover, our current knowledge of the detailed morphology and morphometrics of the important zoonotic species B. procyonis is still insufficient. The taxonomical status of B. procyonis and B. columnaris remains under debate. In the present study, the detailed morphology of B. procyonis was studied using light and scanning electron microscopy based on newly collected specimens from the raccoon Procyon lotor (Linnaeus) in China. The results of the ASAP analysis and Bayesian inference (BI) using the 28S, ITS, cox1 and cox2 genetic markers did not support that B. procyonis and B. columnaris represent two distinct species. Integrative morphological and molecular assessment challenged the validity of B. procyonis, and suggested that B. procyonis seems to represent a synonym of B. columnaris. Molecular phylogenetic results indicated that the species of Baylisascaris were grouped into 4 clades according to their host specificity. The present study provided new insights into the taxonomic status of B. procyonis and preliminarily clarified the phylogenetic relationships of Baylisascaris species.

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.

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

Mastigusa is a genus of small palearctic spiders that has recently been moved to the family Cybaeidae after the first inclusion of the genus in a phylogenetic matrix. Three species are currently recognised: M. arietina , M. lucifuga and M. macrophthalma. The status and delimitation, though, has always been problematic due to inconsistency in the characters used to discriminate between these, leading to great confusion in identity and distribution. We present a detailed morphological redescription of the genus and a taxonomic revision of the included species by the combined use of morphological data and molecular species-delimitation techniques based on the mitochondrial COI gene. The status of the three currently described species has been reevaluated and Mastigusa diversa was revalidated based on material from the Iberian Peninsula, North Africa and the United Kingdom. The distribution of Mastigusa species is updated based on novel taxonomic considerations, and comments on the natural history and ecological differences observed in the species are provided. ZooBank: urn:lsid:zoobank.org:pub:AAD3FAED-440F-4295-B458-455B1D913F81 The debatable identity and delimitation of spider species of Mastigusa have confused the taxonomic status and distribution. Broad sampling, and morphological and molecular techniques were used to revise the species' statuses. Three Mastigusa species were recircumscribed and redescribed, and the distributions updated. Based on a reexamination of type material, Mastigusa diversa O. Pichard-Cambridge, 1893 is revalidated. Mastigusa shows strong ecological plasticity, and understanding the species delimitations and distributions will unravel drivers of extreme lifestyles such as myrmecophily and cave-dwelling. (Image credit: F. Castellucci.) [ABSTRACT FROM AUTHOR]

Cephalopod fisheries are increasing, but little is known about the cryptic diversity of some key commercial species. Recent studies have shown that cryptic speciation is common in cephalopods, including several oceanic squids formerly considered 'cosmopolitan species.' Further efforts are needed to investigate the cryptic diversity of commercial species, to inform management and support sustainable fisheries practices. Thysanoteuthis rhombus is an oceanic squid, currently recognized as the single species of the family Thysanoteuthidae. Thysanoteuthis. rhombus has a global distribution in tropical and subtropical waters and is an economically important species, with the highest catches occurring off Okinawa in Japan and of potential fishery resource for other countries due to its high abundance and large size. Here, we used sequences from 12S rRNA, 16S rRNA, and cytochrome c oxidase I to characterize its cryptic diversity using samples collected throughout most of its known geographic range. We identified three different putative species whose distributions are concordant with main ocean basins: Thysanoteuthis major, the most abundant species, is widely distributed in the North Pacific Ocean, North Indian Ocean, and limits of the South Atlantic Ocean; Thysanoteuthis rhombus is distributed in the North and South Atlantic Ocean and Mediterranean Sea; and Thysanoteuthis cf. filiferum, likely the least sampled to date, is found in the southwestern Pacific Ocean. A sister relationship was observed between T. rhombus and T. major, and T. cf. filiferum was found to be the most divergent species. Based on our divergence estimation, we hypothesize that the closure of the Isthmus of Panama during the early Pliocene played a significant role in the split of T. rhombus and T. major, while the split of their ancestor from T. cf. filiferum coincided with an increase in the Pacific Walker Circulation and the longitudinal gradient of surface temperatures in the Pacific Ocean during the Late Oligocene and Early Miocene. Our work identifies three different putative species within Thysanoteuthis and has potential use for improving fishery management and conserving the diversity in these species. [ABSTRACT FROM AUTHOR]

In the present study, we tested the variability of spore morphology in freshly collected plants of Riccia bifurca Hoffm., R. glauca L., R. sorocarpa Bisch. and R. warnstorfii Limpr. ex Warnst. at the individual and population scale, and examined the taxonomical power of distinct characters that are used in the literature for species delimitation in the genus Riccia. Spore size, number of areolae across the distal spore side, and wing width were determined from permanent preparations of spores, using three individuals of each of the four tested species. Statistical analyses, including power analyses, were carried out, in addition to evaluation using light microscopy images. Our results suggest that individual spore characteristics are subject to high variability at the individual and population level. Owing to the high dispersion of the collected data, the boundaries for these characteristics are obscured across different species. Generally, although the specific morphology of the spores does differ across Riccia species, several characters are too strongly specified in the literature and should be used only in a statistical context and in combination with additional, often qualitative, characters. [ABSTRACT FROM AUTHOR]

The deep‐sea corals Dendrophyllia ramea and Dendrophyllia cornigera occur in Mediterranean and Atlantic waters. Both species are found in different environmental conditions, and they can colonize hard and soft substrates. These species then display an important ecological plasticity along with morphological plasticity. Nevertheless, there is a large knowledge gap on the genetic characteristics of the two species, including on the relationships between them and the possibility of cryptic species along their range. The recent discovery of Dendrophyllia populations off Cyprus in the eastern Mediterranean Sea raised new questions in this context. These corals were related to D. ramea but had some morphological differences with other known populations of this species. Here, we study the specific status of Dendrophyllia corals from Cyprus on the basis of morphology and genetics. The genetic data are interpreted by comparison with the same analysis performed on two Caryophyllia species. Both morphological and genetic data confirm that corals found off Cyprus belong to the D. ramea species. We further tested the speciation scenario using transcriptome data: the results indicate an absence of current gene flow between D. ramea and D. cornigera and that the divergence occurred more than 3 million years ago. We discuss the possible historical and ecological factors which may have shaped speciation in these species. [ABSTRACT FROM AUTHOR]

Glass‐perchlets of the genus Ambassis (Teleostei; Ambassidae) form an important component of the brackish and marine coastal fish communities of tropical Asia. However, their species‐level diversity is still poorly documented because of the absence of recent taxonomic revisions in this region and the limited availability of specimens for research. In addition, long‐standing taxonomic and nomenclatural issues complicate the studies of this genus. Herein, we examine the diversity of Ambassis in Peninsular Malaysia using an integrative taxonomic approach and a large set of recently collected specimens from this region. Our initial morphological observations of 260 specimens revealed the presence of eight species, identified as Ambassis dussumieri, Ambassis interrupta, Ambassis kopsii, Ambassis macracanthus, Ambassis nalua, Ambassis octava, Ambassis urotaenia and Ambassis vachellii. We then sequenced the barcode fragment of the mitochondrial cytochrome c oxidase subunit I (COI) gene for 122 of our specimens, representing all eight morpho‐species. Automatic species delimitation methods recovered nine Molecular Operational Taxonomic Units (MOTUs) because A. interrupta is made of two MOTUs. Morphological re‐examination within A. interrupta detected variation at one character, congruent with molecular delimitation. Overall, our integrative approach unveiled rich species‐level diversity within the genus Ambassis in Peninsular Malaysia, with the presence of nine species. Further comparisons between our COI dataset and the COI sequences archived in the Barcode of Life Data System (BOLD) from specimens of Ambassis broadly collected in tropical Asian regions, indicated regional‐scale hidden diversity and identification conflicts, triggering the need for a complete taxonomic revision of this genus. [ABSTRACT FROM AUTHOR]

Simple Summary: The reduviid genus Sycanus Amyot & Serville, 1843, possesses higher aesthetic value and plays a crucial role as a natural enemy in the control of agricultural and forestry pests. However, Sycanus from China has not undergone a comprehensive review for over four decades. Based on both molecular data and morphological evidence, we conducted a systematic review of the 14 Chinese Sycanus species, including a description of three new species. Due to the variability of body coloration and morphological similarity among closely related species, unresolved issues and debates still persist in the taxonomic study of the genus Sycanus from China. In this study, we conducted phylogenetic analyses and species delimitation for Sycanus in China based on a COI DNA barcoding dataset comprising 81 samples. The results revealed that all the samples could be classified into 12 species by integrating molecular analyses with morphological comparison. This paper provides a comprehensive systematic review of the Sycanus species found in China, including descriptions of three new species: S. taiwanensis Zhao & Cai sp. nov., S. flavicorius Li & Cai sp. nov., and S. hainanensis Wang & Cai sp. nov. Furthermore, it is proposed that S. croceovittatus Dohrn, 1859, S. leucomesus Walker, 1873, and S. villicus Stål, 1863, are three synonyms of S. bifidus (Fabricius, 1787); S. bicolor Hsiao, 1979, is a synonym of S. versicolor Dohrn, 1859; and S. hsiaoi Maldonado-Capriles, 1990, is a synonym of S. marginellus Putshkov, 1987. Additionally, brief biological information is provided for two species, S. falleni Stål, 1863, and S. croceus Hsiao, 1979. [ABSTRACT FROM AUTHOR]

Simple Summary: Pampus is a genus of fish of commercial importance in Asia. This is a comprehensive study on the species delimitation and evolution history of Pampus species. This study integrated information on the skeletal structure and mitochondrial and nuclear molecular data of the genus Pampus to define their species delimitation. Based on these findings, we suggest that P. argenteus and P. echinogaster should be classified as the same species and P. liuorum is speculated to be a valid species. P. cinereus is closely related to P. minor, P. chinensis and P. punctatissimus, but these are different species. Pampus can be divided into six species: P. argenteus, P. punctatissimus, P. cinereus, P. chinensis, P. minor, and P. liuorum. The aim of this study was to resolve the controversies about the phylogeny and taxonomy of Pampus and provide a robust delimitation of Pampus for fisheries management. Pampus is a widespread species of fish in the western Pacific and Indian Oceans that has significant commercial worth. Its evolutionary history and phylogenetics are still poorly understood, and details on its intraspecific taxonomy are debatable, despite some morphological and molecular research. Here, we analyzed this species using skeletal structure data as well as nuclear (S7 gene) and mitochondrial genetic information (COI, D-loop and mitogenomes). We found that the genetic distance between P. argenteus and P. echinogaster was much smaller than that between other Pampus species, and both maximum likelihood and Bayesian phylogenetic trees yielded almost identical tree topologies. An additional and adjacent M repeat was found in the downstream region of the IQM gene cluster of P. argenteus and P. echinogaster, and the trnL2 gene of P. minor was translocated. The genus Pampus experienced early rapid radiation during the Palaeocene with major lineages diversifying within a relatively narrow timescale. Additionally, three different methods were conducted to distinguish the genus Pampus species, proving that P. argenteus and P. echinogaster are the same species, and P. liuorum is speculated to be a valid species. Overall, our study provides new insights not only into the evolutionary history of Pampus but its intraspecific taxonomy as well. [ABSTRACT FROM AUTHOR]

The widespread Tantilla melanocephala is a South American snake, which has a convoluted taxonomic history and a poorly addressed systematics. The taxonomic identity and the phylogenetic affinities of their populations are unclear, suggesting the existence of a complex of undescribed species. Here, we preliminarily address the morphological diversity and genetic structure of the T. melanocephala complex through comparative morphological approaches and phylogenetic analyses using maximum likelihood. Our results confirm the presence of hidden diversity within the T. melanocephala complex and strongly indicate that the populations of T. melanocephala from southern South America represent a distinct lineage, which is morphologically diagnosable under a unique combination of character states. Therefore, we formally describe these populations as a new species and present a comparison among all other South American species of Tantilla. We also estimate the divergence times of the main clades within the complex through Bayesian analysis, suggesting a biogeographical scenario of lineage diversification. Finally, our study clarifies aspects of the intricate taxonomy of the T. melanocephala complex, providing a framework for future studies to avoid the description of synonyms. [ABSTRACT FROM AUTHOR]

The genus Elysia comprises about one-third of the species richness in Sacoglossa. However, the species diversity in the genus remains poorly characterized in some areas like the north-eastern Atlantic and Mediterranean waters. To clarify the systematics of this genus and to characterize the species diversity in undersampled regions, we performed an integrative study based on a thorough literature review, molecular and morphological analyses, and species delimitation approaches. We conducted phylogenetic analyses of partial sequences of two mitochondrial genes (COI and 16S) and two nuclear genes (H3 , 28S) using Bayesian inference and maximum likelihood methods, which confirmed the presence of five of the recognized European Elysia species: Elysia viridis , E. timida , E. flava , E. margaritae , and E. rubeni. Moreover, a new species (Elysia azorica sp. nov.) was identified in the Azores, and E. gordanae , currently considered a junior synonym of E. margaritae , was recovered as a distinct species. In addition, we consider E. hetta as a junior synonym of E. gordanae , and E. translucens as a taxon inquirendum. Finally, the tropical E. evelinae is recorded along European coasts for the first time. Our results demonstrate the value of integrative approaches in resolving taxonomic uncertainty surrounding polymorphism and unravelling potential cases of cryptic or pseudocryptic species complexes. [ABSTRACT FROM AUTHOR]

Dendropsophus molitor is a hylid frog endemic to the Eastern Cordillera of the Colombian Andes, where it exhibits extensive geographic variation in size and colour pattern. Previous multivariate analyses of acoustic and genetic data suggested that northern and southern populations of D. molitor were distinct lineages, and consequently, the northern populations were described as Dendropsophus luddeckei. In this study, we conducted morphometric and genetic analyses of populations of D. molitor and D. luddeckei to test the validity of this recent taxonomic split. We sequenced the mitochondrial genes 12S, 16S, and COI , and the nuclear marker POMC , and also tested whether variation in the MC1R gene was associated with colour polymorphism in these frogs. Phylogenetic analyses recovered D. molitor and D. luddeckei as polyphyletic and species delimitation tests failed to recover them as separate lineages. Genetic differentiation between populations was mostly explained by high intra- and interpopulation variation in the absence of a north-south split, and we found no differences in morphometry between northern and southern populations. In addition, the coding region of MC1R is not associated with colour polymorphism. Thus, multiple lines of evidence suggest that D. luddeckei is not a valid species and D. molitor should be considered a single species. Our study highlights the danger of taxonomic inflation in the face of limited geographic sampling and a lack of clear diagnostic characters. [ABSTRACT FROM AUTHOR]

This study was designed to assess whether or not existed interspecific hybrids between the two lesser known African taxa in Solanum Merolloids section Solanum; S. tardremotum and S. florulentum that confused their taxonomy. Hybridization is one of the factors that blur boundary between closely related species. It is an indication that there is semi-permeable boundary through which genes are flowing across. In the African species of section Solanum it has been hypothesized that interspecific hybridization is one of the factors complicating the delimitation of species though this claim has never been examined systematically. Solanum tarderemotum and S. florulentum were all described by Bitter from Tanzania. Through history the two taxa have been considered separate species, different species mixed with hybrids and recently the boundary of S. tarderemotum has been expanded to include S. florulentum s. str. and materials thought to be hybrids. DNA was isolated from 63 individuals belonging to 22 accessions and two amplified fragment length polymorphism (AFLP) primer combinations; EcoRI + AAC/MseI + CAC and EcoRI + ACC/MseI + CAT used. Clustering used PAST software. Five clusters were generated, S. tarderemotum s. str. and S. florulentum s. str., fell in different clusters. The two taxa shared only 41% of their bands which was less that what was shared between them and their supposed hybrids in two of the three remaining clusters. Some individuals from certain accessions segregated in different clusters. Intermediary and segregation indicates exists hybrids in midst of good species S. tarderemotum and S. florulentum and this could be the reason of the confused species delimitation. [ABSTRACT FROM AUTHOR]

Crescent butterflies of the Phyciodes tharos group have a long-standing reputation for taxonomic difficulty. We assessed species boundaries in the P. tharos group using genome-wide single-nucleotide polymorphism (SNP) data, focusing on sampling in western Canada, where 4 species (P. tharos , P. cocyta , P. batesii , and P. pulchella) have classically been recognized. Phylogenetic and cluster-based analyses confirm that there are indeed 4 species based on the maintenance of genomic integrity in the presence of occasional hybridization and low levels of gene flow. Mitochondrial cytochrome c oxidase I (COI) does not consistently distinguish species, with haplotypes extensively shared between species. Limited sampling of P. batesii indicates complex boundaries and interactions with other Phyciodes , especially with P. pulchella and P. cocyta. This study demonstrates the power of a genome-wide perspective to elucidate the integrity of boundaries between recently diverged species that remain capable of occasional hybridization. [ABSTRACT FROM AUTHOR]

Schizosaccharomyces japonicus Yukawa et Maki (1931) and Schizosaccharomyces versatilis Wickerham et Duprat (1945) have been treated as varieties of S. japonicus or as conspecific, based on various approaches including mating trials and nDNA/nDNA optical reassociation studies. However, the type strains of S. japonicus and S. versatilis differ by five substitutions (99.15% identity) and one 1‐bp indel in the sequences of the D1/D2 domain of the 26S rRNA gene, and 23 substitutions (96.3% identity) and 31‐bp indels in the sequences of internal transcribed spacer (ITS) of rRNA, suggesting that they may not be conspecific. To reassess their taxonomic status, we conducted mating trials and whole‐genome analyses. Mating trials using the type strains showed a strong but incomplete prezygotic sterility barrier, yielding interspecies mating products at two orders of magnitude lower efficiency than intraspecies matings. These mating products, which were exclusively allodiploid hybrids, were unable to undergo the haplontic life cycle of the parents. We generated chromosome‐level gap‐less genome assemblies for both type strains. Whole genome sequences yielded an average nucleotide identity (ANI) of 86.4%, indicating clear separation of S. japonicus and S. versatilis. Based on these findings, we propose the reinstatement of S. versatilis as a distinct species (holotype strain: CBS 103T and ex‐types: NRRL Y‐1026, NBRC 1607, ATCC 9987, PYCC 7100; Mycobank no.: 847838). Take‐away: It is shown that an almost complete reproductive barrier exists between S. japonicus and S. versatilis.Gapless genomes of the type strains of S. japonicus and S. versatilis are reported here.Genome‐based analysis estimates that S. japonicus and S. versatilis diverged more than 10 million years ago.S. versatilis is reinstated and a valid species description is provided. [ABSTRACT FROM AUTHOR]

Mushrooms are important organisms because of their human nutritional and medicinal value. With the expansion of the cultivation of edible mushrooms, fungal diseases have become a major problem in limiting their production. Numerous fungi can cause mushroom deformation or rots. In this publication we report on fungal diseases found during Morchella cultivation in China, with emphasis on morphology and phylogeny to characterise species. The key findings include 1) establishment of a new family Albomorchellophilaceae in Hypocreales, and a novel monotypic genus Albomorchellophila with the type species A. morchellae. Divergence time estimates indicate that Albomorchellophilaceae diverged from its sister family Calcarisporiaceae at ca. 105 (92–120) MYA; 2) the phylogeny and morphology of the family Pseudodiploosporeaceae (Hypocreales) is revised. The family contains a single genus Pseudodiploospora. Intraspecific genetic analyses of Pseudodiploospora longispora reveals significant base differences within strains, especially in the regions of protein-coding genes RPB 2 and TEF; 3) four fungicolous taxa, i.e., Cylindrodendrum alicantinum, Hypomyces aurantius, Hypomyces rosellus, and Trichothecium roseum, are reported as putative pathogens on cultivated morels for the first time. In addition, the previously reported pathogens of morels, Clonostachys rosea, Clonostachys solani, Hypomyces odoratus, and Pseudodiploospora longispora are also detailed in their symptoms and morphology; 4) the phylogeny and morphology of "Zelopaecilomyces" previously placed within Pseudodiploosporeaceae are re-assessed. "Zelopaecilomyces" is proved to be introduced through a chimerism of gene fragments sourced from two distinct organisms. Consequently, it is recommended that "Zelopaecilomyces" should not be recognised due to the mixed up molecular data in phylogeny and a lack of support from morphological evidence. Furthermore, this study discusses the voucher specimen Paecilomyces penicillatus (CBS 448.69), which may contain two mixed taxa, i.e., Pseudodiploospora longispora and a member of Penicillium. Publications on pathogenic fungi of cultivated mushrooms is sporadically, which leads to a lack of understanding of causal agents. As a follow up to the diseases of morel cultivation, we also review the fungal diseases of cultivated mushrooms reported over the last four decades. More than 130 pathogens affect the growth and development of the main cultivated mushrooms. The taxonomic diversity of these pathogens is high, distributed in 58 genera, 40 families, 20 orders, 12 classes and six phyla. The host infected are from Ascomycota to Basidiomycota, mainly being reported from Agaricus bisporus, Cordyceps militaris, Morchella spp., and Pleurotus spp. This study not only enriches our current knowledge on the diversity of pathogens of cultivated mushrooms, especially morels, but also recognizes the importance of some taxa as potential pathogens. Taxonomic investigation and accurate identification are initial and key steps to understanding pathogen-mushroom interactions, and will result in better disease management strategies in the mushroom industry. [ABSTRACT FROM AUTHOR]

Among direct-developing rain frogs of the genus Craugastor is a clade of 19 described species (bocourti series) that occur in Mexico and northern Central America. Many of these 19 species have been described based on subtle morphological differences and have never been examined using molecular data. Here, we used a multilocus dataset (one mitochondrial (mtDNA) and four nuclear (nDNA) gene fragments, totalling 3,048 concatenated base pairs) to investigate species limits and phylogenetic relationships among 60 northern rain frogs referable to 12 species, with a focus on species from Guatemala. We inferred phylogenies using maximum likelihood and Bayesian analyses on separate mtDNA and nDNA datasets. Concatenated and coalescent species-tree analyses support the monophyly of multiple species, with interspecific relationships mostly unresolved. These mtDNA and nDNA trees were often incongruent with morphology-based taxonomy. For example, two genetically shallow clades contained individuals referable to at least five described species, whereas a single described species contained deep divergences indicative of multiple cryptic species. These findings indicate that morphology-based taxonomy has both overestimated and underestimated actual species diversity (depending on the species), an interpretation supported by two molecular species-delimitation procedures. Based on these findings, we synonymise C. glaucus (Lynch, 1967) and C. stuarti (Lynch, 1967) with C. xucanebi (Stuart, 1941). We also synonymise C. nefrens (Smith, 2005) and C. cyanochthebius McCranie & Smith, 2006 with C. campbelli (Smith, 2005). The molecular data also support multiple undescribed species, notably within C. decoratus (Taylor, 1942). Overall, we show how morphology-based species delimitation can both underestimate and overestimate species richness in morphologically conservative groups. [ABSTRACT FROM AUTHOR]

Simple Summary: The three sloe bugs, Dolycoris baccarum, D. indicus and D. penicillatus, are distributed across the Chinese mainland and have similar morphology. In this study, the mitochondrial genomes of these three species were generated and compared. Species boundaries and interspecific relationships among the three species were explored for the first time. The mitochondrial genomes of the three Dolycoris species were conservative in terms of nucleotide composition, gene order, and codon usage. The species boundaries of the three species were clarified based on the mitochondrial data, and a clear barcode gap was found between the interspecific and intraspecific genetic distances. The interspecific relationships of the three species were inferred as (D. indicus + (D. baccarum + D. penicillatus)). Our study has enriched the mitogenomic library of Dolycoris, providing insights into the evolution of Dolycoris species. (1) Background: The three sloe bugs, Dolycoris baccarum, Dolycoris indicus, and Dolycoris penicillatus, are found in the Chinese mainland and are morphologically similar. The species boundaries and phylogenetic relationships of the three species remain uncertain; (2) Methods: In this study, we generated multiple mitochondrial genomes (mitogenomes) for each of the three species and conducted comparative mitogenomic analysis, species delimitation, and phylogenetic analysis based on these data; (3) Results: Mitogenomes of the three Dolycoris species are conserved in nucleotide composition, gene arrangement, and codon usage. All protein-coding genes (PCGs) were found to be under purifying selection, and the ND4 evolved at the fastest rate. Most species delimitation analyses based on the COI gene and the concatenated 13 PCGs retrieved three operational taxonomic units (OTUs), which corresponded well with the three Dolycoris species identified based on morphological characters. A clear-cut barcode gap was discovered between the interspecific and intraspecific genetic distances of the three Dolycoris species. Phylogenetic analyses strongly supported the monophyly of Dolycoris, with interspecific relationship inferred as (D. indicus + (D. baccarum + D. penicillatus)); (4) Conclusions: Our study provides the first insight into the species boundaries and phylogenetic relationships of the three Dolycoris species distributed across the Chinese mainland. [ABSTRACT FROM AUTHOR]

Simple Summary: The application of molecular methods in the studies of biological diversity revealed that there are many more species than we can recognise by their appearance. Species pairs or groups, which are difficult to recognise and are known as cryptic species, may differ in their ecological traits, place in trophic networks, and their functional role in ecosystems. It is important to separate cryptic species, particularly if we apply species composition or other diversity metrics for an assessment or monitoring of the ecosystem state or human pressures and impacts. In our study, we revealed a new cryptic species of aphid-hunting wasp that is virtually indistinguishable from a well-known one by morphology. These two species can be easily segregated using molecular characters, and presumably they differ also by nesting habitat. Upon exploring the mitotype diversity of the aphid-hunting wasp, Diodontus tristis, we revealed specimens with highly divergent mitotypes from two localities in Lithuania and nesting in clayey substrate, while the specimens with typical mitotypes were found nesting in sandy sites. The comparison of inter- and intra-specific distances and application of delimitation algorithms supported the species status of the clay-nesting populations. Using a set of DNA markers that included complete or partial sequences of six mitochondrial genes, three markers of ribosomal operon, two homeobox genes, and four other nuclear genes, we clarified the phylogenetic relationships of the new cryptic species. The endosymbiotic bacteria infestation was checked, considering the option that the divergent populations may represent clades isolated by Wolbachia infection; however, it did not demonstrate any specificity. We found only subtle morphological differences in the new clay-nesting species, D. argillicola sp. nov.; the discriminant analysis of morphometric measurements did not reliably segregate it as well. Thus, we provide the molecular characters of the cryptic species, which allow confident identification, its phylogenetic position within the genus, and an updated identification key for the D. tristis species group. [ABSTRACT FROM AUTHOR]

Recent work has suggested exceptional species-level diversity in the lichen-forming Lecanora polytropa complex (Lecanoraceae, Ascomycota). However, biogeographic patterns and the spatial structuring of this diversity remains poorly known. To investigate diversity across multiple spatial scales, we sampled members of this species complex from two distinct regions—the Pacific Coast Ranges in southern Alaska, USA, and montane habitats in Spain. We also included sequence data from several species within this complex that were recently described from populations in France. Using the standard DNA barcoding marker and a sequence-based species delimitation approach (ASAP), we inferred a total of 123 candidate species (SHs) within the Lecanora polytropa complex, 32 of which were sampled for the first time here. Of 123 SHs, 21 had documented intercontinental distributions, while the vast majority were found at much smaller spatial scales. From our samples collected from Alaska, USA, and Spain, representing 36 SHs, we found high genetic diversity occurring within each sampled site, but limited overlap among all sites. Mountain ranges in both regions had high proportions of endemic lineages, with the highest diversity and endemism occurring in mountain ranges in Spain. Our sequence data generally support the recent taxonomic proposals, and an integrative taxonomy may help partly resolve the taxonomic conundrums within this hyper-diverse lineage. [ABSTRACT FROM AUTHOR]

The bushbuck (Tragelaphus scriptus) is an antelope widely distributed throughout sub-Saharan Africa that varies greatly in body size, horn length and coat patterning. Recent taxonomic work has suggested reclassification as two or more species. Molecular studies have shown a deep mitochondrial divergence between north-western (scriptus) and south-eastern (sylvaticus) bushbuck populations, and morphological assessments, based largely on coat patterning, have divided the bushbuck into as many as eight species and 32 subspecies. Molecular and morphological approaches have, to date, not been brought together in a single integrative study. Using 43 museum cranial specimens, we sequenced complete mitochondrial genomes and used three-dimensional geometric morphometrics to compare genetic and phenotypic divergence between the two main subclades of the T. scriptus species complex. We found a significant but weak relationship between phenotypic and genetic distances. Mean body size differed between males of each subclade, but morphological differences attributable to sexual dimorphism within subclades were greater than differences between subclades. Despite a mitochondrial divergence of nearly 3 Myr, cranial morphological differences between subclades were minor and could be accounted for largely by minor size differences between males (size–shape allometry). These results support the recognition of a single bushbuck species, as indicated by nuclear genetic data. [ABSTRACT FROM AUTHOR]

Since first human settlement c. 400 years ago, the Mascarene islands have undergone some of the highest rates of ecosystem transformation and species extinction recorded worldwide. One surviving species, the Mascarene Swiftlet Aerodramus francicus native to the islands of Mauritius and Réunion, is typical among Aerodramus swiftlets in presenting a paucity of distinguishable morphological characters, as well as being particularly vulnerable to anthropogenic activities. In this study, a primary objective was generating genetic data for each island population, allowing genetic divergence between them to be assessed for the first time, employing informative methods regarding the taxonomic status. We find that the two island populations are 0.8% divergent and reciprocally monophyletic in the mitochondrial ND2 gene, with nuclear data (β-fibrinogen intron 7) being largely congruent but showing incomplete lineage sorting and low resolution. Results of barcode gap and coalescent species delimitation analyses are consistent with a comparison of the genetic divergence uncovered within Mascarene Aerodramus with that among other long-established Aerodramus species. The findings of all three approaches are consistent with the two island populations representing two separate species. However, because of lack of resolution in the nuclear locus, we conservatively retain a single species pending future data. To assess the conservation status, we conducted the first quantitative assessment of population size and distribution through extensive nest counts on the islands of Mauritius and Réunion, and by considering the threats to swiftlets on each island. The survey produced estimates of 10,100–10,700 individuals for Mauritius, and 39,600–53,500 individuals for Réunion. Considering the population size data, inferred distributions, and numerous conservation concerns, an updated conservation status to Threatened (Endangered): B2 b(i,ii,iii,iv,v) c(i,ii,iii,iv) is warranted according to IUCN guidelines. Improving protection of the breeding habitat of the Mascarene Swiftlet is crucial to prevent this endemic species from being added to the Mascarene's staggering extinction toll. [ABSTRACT FROM AUTHOR]

The Australian genus Isopogon (Proteaceae) consists of approximately 39 species, most of which occur in southwestern Australia, a region of considerable endemism and biodiversity. Unresolved taxonomic issues exist for two species complexes (nine suspected taxa) allied to I. spathulatus and I. polycephalus. There is uncertainty in how to delimit species in these two complexes due to unclear or overlapping morphological characters, although recognition of four phrase‐named taxa provide starting hypotheses for potential new taxa. We used a genomic approach (ddRAD) to generate SNPs for 146 samples from 32 populations across the two complexes to evaluate the genomic distinction of taxa and delimit species. We used an optimised ipyrad assembly of the sequenced libraries, followed by custom filtering of samples and SNPs for ordination, genetic structure, distance and concatenation and coalescent phylogenetic analyses. Population genetic and phylogenetic analyses consistently supported three geographically overlapping yet genomically distinct groups, two of which showed additional genomic divergence consistent with multiple distinct species. Existing morphological hypotheses were congruent with genomic groupings in some cases but discordant in others, where genomic admixture suggested existing taxa were conspecific. Evaluating morphological characters, geographic distribution and genomic distinction, we recognise five species and three subspecies from nine original taxa. We provide a key to species in the complexes and related taxa, updated descriptions for existing taxa, and describe two new species, I. elatus sp. nov. and I. pallidus sp. nov., and two new subspecies, I. spathulatus subsp. obovatus stat. nov. and I. spathulatus subsp. elongatus subsp. nov. [ABSTRACT FROM AUTHOR]

Polychaetes are annelids predominantly marine and constitute an important part of marine communities. The genus Alitta, of the family Nereididae, comprises nine recognized species, including Alitta succinea, considered cosmopolitan. The species was first described from the Helgoland (Germany) and has been recorded on the Brazilian coast. However, evidence suggests that A. succinea might be a complex of cryptic species. The aim of this short communication is molecularly analyzing specimens of Alitta succinea to ascertain the status of the species in Brazil. The study encompassed molecular analyses of COI and 16S sequences using data obtained from eight specimens collected from three localities at Rio de Janeiro and seven specimens collected from Santa Catarina, in addition to available data from GenBank and BOLD Systems. Molecular analyses clustered specimens from Brazil, the type locality and other localities in the same clade, reinforcing the status of A. succinea as an invasive species. However, additional studies, including more extensive molecular and morphological analyses, are necessary to clarify the distribution of the Alitta succinea along the Brazilian coast. [ABSTRACT FROM AUTHOR]

Traditionally, the apparent paucity of biogeographic barriers in marine environments when compared to terrestrial and freshwater habitats has been associated with high gene flow rates among geographically distant populations. However, physical traits such as tide currents, temperature, and salinity levels may serve as ecological boundaries thus leading to restricted-range phylogeographic patterns (e.g., the outflow plume from the Amazonas-Orinoco rivers between the Caribbean and the Brazilian Province) according to adaptive features of coastal organisms. To assess the degree of cohesiveness among populations and species of marine and estuarine fishes along a latitudinal gradient from Western South Atlantic, we carried out comparative phylogenetic and species delimitation analyses based on Cytochrome C Oxidase I (COI) sequences of 34 fish taxa from the Caribbean and Brazilian coasts. Distinct values of genetic diversity were revealed for both Provinces, ranging from moderate (1 to 2%) to high (≥ 2%) in 11.76% and 20.59% of the analyzed taxa, respectively. Furthermore, a significant genetic differentiation was observed within the nominal taxa Diapterus auratus, Citharichthys spilopterus, and Scorpaena plumieri from the Caribbean, as well as for Haemulon plumierii between the Caribbean and Brazilian Provinces. Such divergence is likely to result from temporal isolation among local populations during sea-level fluctuations during the Pliocene-Pleistocene period. The present findings demonstrate that similar biogeographic boundaries may result in species-specific patterns of genetic connectivity, possibly associated with ecological constraints. Since molecular operational taxonomic units (MOTUs) were identified in certain formal taxa from both Provinces, a systematic revision of these groups is highly recommended. At last, multispecies COI data proved to be helpful to phylogeographic inferences and to support appropriate policies for the conservation of natural resources. [ABSTRACT FROM AUTHOR]

Consistent species identification is foundational to biological research and requires coordination among a diversity of researchers and institutions. However, such consistency may be hindered for rare organisms where specimens, identification resources, and taxonomic experts are few. This is often the case for deep-sea taxonomic groups. For example, the deep-sea gastropod genus Provanna Dall, 1918 is common at chemosynthetic sites throughout the world's oceans, yet no formal guide to these species has yet been produced. Recent exploration has recovered new specimens of Provanna from hydrocarbon seeps off the Pacific Costa Rica Margin. The current work assesses the species identity of these specimens using shell morphology, radular morphology, and genetic barcoding (mitochondrial CO1 and nuclear H3). Records of occurrence for P. laevis Warén & Ponder, 1991, P. ios Warén & Bouchet, 1986, and P. pacifica Warén & Bouchet, 1986 are herein presented from the Costa Rica Margin. A critical taxonomic review of the 29 extant species within this genus was conducted and their genetic, morphological, and biogeographical distinction assessed. In this review, genetic and morphological support was found for nearly all current species delineations except for P. glabra Okutani et al., 1992, syn. nov. and P. laevis, syn. nov., which are herein synonymized to P. laevis, and for P. ios, syn. nov. and P. goniata Warén & Bouchet, 1986, syn. nov., which are synonymized to P. ios. Finally, the first species identification key for the extant species in this genus is presented. This work clarifies the taxonomy and systematics of this deep-sea gastropod genus and contributes a novel polytomous key for use in future research. [ABSTRACT FROM AUTHOR]

Namalycastis abiuma has been recorded as a worldwide distributed species, found in most tropical and subtropical mangroves and estuarine environments. However, this status has been questioned in several publications, which indicate that several distinct species are being identified under the name N. abiuma. In this study, we perform a morphological analysis, along with a series of species delimitation tests and a phylogenetic analysis--using the molecular marker 16S--to evaluate whether analyzed populations previously identified as Namalycastis abiuma belong to the same species. We used sequences from the GenBank database in the analysis, as well as six newly sequenced specimens collected from the coast of Brazil, two of them from the N. abiuma type-locality. For species delimitation, we applied the Generalized Mixed Yule Coalescent (GMYC), the Assemble Species by Automatic Partitioning (ASAP), and the Multi-rate Poisson Tree Processes (mPTP) tests. Results from GMYC and ASAP suggest that Namalycastis abiuma may be endemic to the type-locality and that all other populations studied represent a second distinct species. However, mPTP indicates that all Namalycastis species included should be grouped into one single species. The mPTP results seem to be biased due to data limitation as it showed poor statistical support. Our morphological data, especially on the shape and dentition of the sub-neuroacicular falciger blades, support the GMYC and ASAP results, suggesting restricted endemism for Namalycastis abiuma. Based on these results, we conclude that N. abiuma is restricted to its type-locality and we provide a description of a new species, Namalycastis lanai sp. nov. occurring in Brazilian waters from 22°S to 27°S, including, at its southern range, an overlap with N. abiuma at Florianópolis. Finally, we provide a key to all Namalycastis species found in Brazil. [ABSTRACT FROM AUTHOR]

DNA barcoding often fails to identify species despite its undisputed advantages. Hybridization, sample contamination, incomplete lineage sorting and nuclear copies of mitochondrial genes (NUMTs) are often put forward as explanations but have seldomly been tested. Here I used available RNA-sequencing data to explore this issue in four Chorthippus grasshopper species. I was able to exclude NUMTs, contamination and recent hybridization as probable causes of the low barcoding performance. Using a phylogenetic method, I estimated the nuclear and mitochondrial mutation rates as 1.31 × 10−9–2.27 × 10−9 and 8.1 × 10−9–1.4 × 10−8 mutations/site/year, respectively. These grasshoppers therefore did not exhibit a particularly low mitochondrial mutation rate compared to other insect species. Using coalescence simulation, I was able to show that two simple demographic scenarios, with a divergence period of 1–3 Myr, provided a good fit to the mitochondrial genealogies in three of the four target species. Interestingly, the mitochondrial genealogy of Chorthippus mollis was inconsistent with a neutral evolution pattern, suggesting that it had undergone adaptive selection. [ABSTRACT FROM AUTHOR]