Two DNA barcodes and morphology for multi-method species delimitation in Bonnetina tarantulas (Araneae: Theraphosidae)

Three new species of the spider genus Naphrys Edwards (Araneae, Salticidae) under morphology and molecular data with notes in the distribution of Naphrys acerba (Peckham & Peckham) from Mexico

Herein, we describe three new species of the spider genus Naphrys Edwards, 2003 from Mexico: Naphrys echeri sp. nov., Naphrys tecoxquin sp. nov., and Naphrys tuuca sp. nov. An integrative taxonomic approach was applied, utilizing data from morphology, ultra-morphology, the mitochondrial gene COI, and distribution records. Four molecular methods for species delimitation were implemented under the corrected p-distance Neighbor-Joining (NJ) criteria: (1) Assemble Species by Automatic Partitioning (ASAP); (2) general mixed Yule coalescent (GMYC); (3) Bayesian Poisson tree process (bPTP); and (4) multi-rate Poisson tree process (mPTP). Both morphological and molecular data supported the delimitation and recognition of the three new species. The average interspecific genetic distance (p-distance) within the genus Naphrys is 14%, while the intraspecific genetic distances (p-distance) is <2% for most species. We demonstrate that the natural distribution of Naphrys is not restricted to the Nearctic region. Furthermore, the reported localities herein represent the first with precise locations in the country for Naphrys acerba. In addition, a taxonomic identification key is provided for the species in the genus.

A consequential one-night stand: Episodic historical hybridization leads to mitochondrial takeover in sympatric desert ant-eating spiders

Disentangling the genomic intricacies underlying speciation and the causes of discordance between sources of evidence can offer remarkable insights into evolutionary dynamics. The ant-eating spider Zodarion nitidum, found across the Middle East and Egypt, displays yellowish and blackish morphs that co-occur sympatrically. These morphs additionally differ in behavioral and physiological features and show complete pre-mating reproductive isolation. In contrast, they possess similar sexual features and lack distinct differences in their mitochondrial DNA. We analyzed both Z. nitidum morphs and outgroups using genome-wide and additional mitochondrial DNA data. The genomic evidence indicated that Yellow and Black are reciprocally independent lineages without signs of recent admixture. Interestingly, the sister group of Yellow is not Black but Z. luctuosum, a morphologically distinct species. Genomic gene flow analyses pinpointed an asymmetric nuclear introgression event, with Yellow contributing nearly 5 % of its genome to Black roughly 320,000 years ago, intriguingly aligning with the independently estimated origin of the mitochondrial DNA of Black. We conclude that the blackish and yellowish morphs of Z. nitidum are long-diverged distinct species, and that the ancient and modest genomic introgression event registered resulted in a complete mitochondrial takeover of Black by Yellow. This investigation underscores the profound long-term effects that even modest hybridization events can have on the genome of organisms. It also exemplifies the utility of phylogenetic networks for estimating historical events and how integrating independent lines of evidence can increase the reliability of such estimations.

A new species of the spider genus Mexentypesa Raven (Araneae: Nemesiidae) from Hidalgo, Mexico and taxonomic comments on M. chiapas Raven

A new species of the enigmatic spider genus Mexentypesa (Raven, 1987) from a cloud forest in Hidalgo state, Mexico is described: M. hidalguensis sp. nov. The description of the species is based on both male and female adult specimens. This discovery increases the diversity of the genus to two species: Mexentypesa chiapas (Raven, 1987) and the new species described herein. Additionally, Aptostichus sabinae syn. nov. (=M. chiapas), which was previously described as a different species, is formally synonymized.

Violins we see, species we don't… Species delimitation of the spider genus Loxosceles Heineken & Lowe (Araneae: Sicariidae) from North America using morphological and molecular evidence

In modern systematics, different sources of evidence are commonly used for the discovery, identification, and delimitation of species, especially when morphology fails to delineate between species or in underestimated species complexes or cryptic species. In this study, morphological data and two DNA barcoding markers-cytochrome c oxidase subunit I (COI) and internal transcribed spacer 2 (ITS2)-were used to delimit species in the spider genus Loxosceles from North America. The molecular species delimitation analyses were carried out using three different methods under the corrected p-distance Neighbor-Joining (NJ) criteria: 1) Assemble Species by Automatic Partitioning (ASAP), 2) General Mixed Yule Coalescent model (GMYC), and 3) Bayesian Poisson Tree Processes (bPTP). The analyses incorporated 192 terminals corresponding to 43 putative species of Loxosceles, of which 15 are newly recognized herein, as putative new species, based on morphology and congruence between molecular methods with COI. The average intraspecific genetic distance (p-distance) was <2%, whereas the average interspecific genetic distance was 15.6%. The GMYC and bPTP molecular methods recovered 65-79 and 69 species respectively, overestimating the diversity in comparison with morphology, whereas the ASAP method delimited 60 species. The morphology of primary sexual structures (males palps and female seminal receptacles) was congruent with most of the molecular methods mainly with COI, showing that they are robust characters for identification at the species level. For species delimitation COI was more informative than ITS2. The diversity of Loxosceles species is still underestimated for North America, particularly in Mexico which holds the highest diversity of this genus worldwide.

A new bunting species in South China revealed by an integrative taxonomic investigation of the Emberiza godlewskii complex (Aves, Emberidae)

Species boundaries of birds across the Euro-Asian continent, especially the widely distributed passerines with multiple subspecies, are not completely resolved. The Rock Bunting complex, Emberiza cia and E. godlewskii, is subject to ongoing debate due to geographic variation in its morphology, and deep genetic splits. In this study, the phylogenetic relationships of the E. cia/godlewskii complex were evaluated based on multilocus coalescence methods combined with analyses of plumage color and morphological variation. Although the northern and southern populations of E. godlewski formed reciprocally monophyletic groups, the northern E. godlewskii clade is the sister group to E. cia, rendering E. godlewskii as currently defined paraphyletic. The significant differences in morphometry and plumage color reflectance are complementary and support the phenotypic validity of northern and southern E. godlewskii. Thus, we recommend the following taxonomic revisions: the northern and southern E. godlewskii subspecies should be recognized as different full species, such as E. godlewskii and E. yunnanensis, respectively. This resolves the issue that E. godlewskii, as currently defined, is paraphyletic. Our research provides direct evidence of cryptic species in old world buntings and highlights the underestimation of species diversity in birds in East Asia.

To be or not to be… Integrative taxonomy and species delimitation in the daddy long-legs spiders of the genus Physocyclus (Araneae, Pholcidae) using DNA barcoding and morphology

Integrative taxonomy is crucial for discovery, recognition, and species delimitation, especially in underestimated species complex or cryptic species, by incorporating different sources of evidence to construct rigorous species hypotheses. The spider genus Physocyclus Simon, 1893 (Pholcidae, Arteminae) is composed of 37 species, mainly from North America. In this study, traditional morphology was compared with three DNA barcoding markers regarding their utility in species delimitation within the genus: 1) Cytochrome c Oxidase subunit 1 (CO1), 2) Internal Transcribed Spacer 2 (ITS2), and 3) Ribosomal large subunit (28S). The molecular species delimitation analyses were carried out using four methods under the corrected p-distances Neighbor-Joining (NJ) criteria: 1) Automatic Barcode Gap Discovery (ABGD), 2) Assemble Species by Automatic Partitioning (ASAP), 3) General Mixed Yule Coalescent model (GMYC), and 4) Bayesian Poisson Tree Processes (bPTP). The analyses incorporated 75 terminals from 22 putative species of Physocyclus. The average intraspecific genetic distance (p-distance) was found to be < 2%, whereas the average interspecific genetic distance was 20.6%. The ABGD, ASAP, and GMYC methods were the most congruent, delimiting 26 or 27 species, while the bPTP method delimited 33 species. The use of traditional morphology for species delimitation was congruent with most molecular methods, with the male palp, male chelicerae, and female genitalia shown to be robust characters that support species-level identification. The barcoding with CO1 and 28S had better resolution for species delimitation in comparison with ITS2. The concatenated matrix and traditional morphology were found to be more robust and informative for species delimitation within Physocyclus.

Nor SA, Lavoué S, A. Rahim M, Jamaludin NA, Mohammed Akib NA. DNA-based taxonomy of a mangrove-associated community of fishes in Southeast Asia

The Merbok Estuary comprises one of the largest remaining mangrove forests in Peninsular Malaysia. Its value is significant as it provides important services to local and global communities. It also offers a unique opportunity to study the structure and functioning of mangrove ecosystems. However, its biodiversity is still partially inventoried, limiting its research value. A recent checklist based on morphological examination, reported 138 fish species residing, frequenting or subject to entering the Merbok Estuary. In this work, we reassessed the fish diversity of the Merbok Estuary by DNA barcoding 350 specimens assignable to 134 species initially identified based on morphology. Our results consistently revealed the presence of 139 Molecular Operational Taxonomic Units (MOTUs). 123 of them are congruent with morphology-based species delimitation (one species = one MOTU). In two cases, two morphological species share the same MOTU (two species = one MOTU), while we unveiled cryptic diversity (i.e. COI-based genetic variability > 2%) within seven other species (one species = two MOTUs), calling for further taxonomic investigations. This study provides a comprehensive core-list of fish taxa in Merbok Estuary, demonstrating the advantages of combining morphological and molecular evidence to describe diverse but still poorly studied tropical fish communities. It also delivers a large DNA reference collection for brackish fishes occurring in this region which will facilitate further biodiversity-oriented research studies and management activities.

A review of the taxonomy of spiny-backed orb-weaving spiders of the subfamily Gasteracanthinae (Araneae, Araneidae) in Thailand

Spiny-backed orb-weaving spiders of the subfamily Gasteracanthinae are broadly distributed in the Old World. Despite their use as a model species in biology, evolution, and behavior because of their extraordinary characteristics, the systematics of this group of spiders are still poorly understood. This study elucidates the systematics of Gasteracanthinae in Thailand based on morphological and molecular-based analyses. In total, seven species from three genera, namely Gasteracantha, Macracantha, and Thelacantha, were recorded in Thailand. Shape of abdominal spines, pattern of sigilla, and female genitalia are significant characters for species identification. In contrast, coloration shows highly intraspecific variation in most species within Gasteracanthinae. A phylogenetic tree based on partial sequences of COI, 16S, and H3 genes recovered Gasteracanthinae as a monophyletic group and supports the existence of three clades. Gasteracantha hasselti is placed as a sister taxon to Macracantha arcuata. Hence, we propose to transfer G. hasselti to Macracantha. Moreover, molecular species delimitation analyses (ABGD, bPTP, and GMYC) using 675 bp of COI gene support all nominal species, with evidence of possible additional cryptic species.

Morphological and molecular evidence support the taxonomic separation of the medically important Neotropical spiders Phoneutria depilata (Strand, 1909) and P. boliviensis (F.O. Pickard-Cambridge, 1897) (Araneae, Ctenidae)

The species of the genus Phoneutria (Ctenidae), also called banana spiders, are considered amongst the most venomous spiders in the world. In this study we revalidate P. depilata (Strand, 1909), which had been synonymized with P. boliviensisis (F.O. Pickard-Cambridge, 1897), using morphological and nucleotide sequence data (COI and ITS-2) together with species delimitation methods. We synonymized Ctenus peregrinoides, Strand, 1910 and Phoneutria colombiana Schmidt, 1956 with P. depilata. Furthermore, we designated Ctenus signativenter Strand, 1910 as a nomen dubium because the exact identity of this species cannot be ascertained with immature specimens, but we note that the type locality suggests that the C. signativenter syntypes belong to P. depilata. We also provide species distribution models for both species of Phoneutria and test hypotheses of niche conservatism under an allopatric speciation model. Our phylogenetic analyses support the monophyly of the genus Phoneutria and recover P. boliviensis and P. depilata as sister species, although with low nodal support. In addition, the tree-based species delimitation methods also supported the separate identities of these two species. Phoneutria boliviensis and P. depilata present allopatric distributions separated by the Andean mountain system. Species distribution models indicate lowland tropical rain forest ecosystems as the most suitable habitat for these two Phoneutria species. In addition, we demonstrate the value of citizen science platforms like iNaturalist in improving species distribution knowledge based on occurrence records. Phoneutria depilata and P. boliviensis present niche conservatism following the expected neutral model of allopatric speciation. The compiled occurrence records and distribution maps for these two species, together with the morphological diagnosis of both species, will help to identify risk areas of accidental bites and assist health professionals to determine the identity of the species involved in bites, especially for P. depilata.

ASAP: assemble species by automatic partitioning

Here, we describe Assemble Species by Automatic Partitioning (ASAP), a new method to build species partitions from single locus sequence alignments (i.e., barcode data sets). ASAP is efficient enough to split data sets as large 10⁴ sequences into putative species in several minutes. Although grounded in evolutionary theory, ASAP is the implementation of a hierarchical clustering algorithm that only uses pairwise genetic distances, avoiding the computational burden of phylogenetic reconstruction. Importantly, ASAP proposes species partitions ranked by a new scoring system that uses no biological prior insight of intraspecific diversity. ASAP is a stand-alone program that can be used either through a graphical web-interface or that can be downloaded and compiled for local usage. We have assessed its power along with three others programs (ABGD, PTP and GMYC) on 10 real COI barcode data sets representing various degrees of challenge (from small and easy cases to large and complicated data sets). We also used Monte-Carlo simulations of a multispecies coalescent framework to assess the strengths and weaknesses of ASAP and the other programs. Through these analyses, we demonstrate that ASAP has the potential to become a major tool for taxonomists as it proposes rapidly in a full graphical exploratory interface relevant species hypothesis as a first step of the integrative taxonomy process.

DNA barcoding reveals cryptic diversity in the underestimated genus Triplophysa (Cypriniformes: Cobitidae, Nemacheilinae) from the northeastern Qinghai-Tibet Plateau

Background

The northeastern part of the Qinghai-Tibet Plateau (QTP) presents a high number of plateau loach species. As one of the three major groups of fishes distributed on the QTP, plateau loach has high ecological value. However, the taxonomy and systematics of these fish are still controversial, and a large number of new species have been reported. The reason for this phenomenon is that the degree of morphological variation is low, the phylogenetic information provided by morphological and anatomical features used for species identification is relatively poor, and many cryptic species are observed. Based on the high-density sampling points from the biodiversity hotspots surveyed, this study aims to evaluate the biodiversity of plateau loach in the northeastern part of the QTP and reveal the hidden diversity by comparing morphological species with molecular operational taxonomic units (MOTUs).

Results

After careful identification and comparison of the morphology and DNA barcoding of 1630 specimens, 22 species were identified, with 20 considered valid local species and two identified as new species that had not been previously described. Based on the combination of morphological and molecular methods, a total of 24 native species were found, two of which were cryptic species: Triplophysa robusta sp1 and Triplophysa minxianensis sp1. Fourteen of the 24 species form clusters of barcodes that allow them to be reliably identified. The remaining cases involved 10 closely related species, including rapidly differentiated species and species that seemed to have experienced incomplete lineage sorting or showed introgressions.

Conclusions

The results highlight the need to combine traditional taxonomies with molecular methods to correctly identify species, especially closely related species, such as the plateau loach. This study provides a basis for protecting the biodiversity of plateau loach.

Poor performance of DNA barcoding and the impact of RAD loci filtering on the species delimitation of an Iberian ant-eating spider

Genomic data provide unprecedented power for species delimitation. However, current implementations are still time and resource consuming. In addition, bioinformatic processing is contentious and its impact on downstream analyses is insufficiently understood. Here we employ ddRAD sequencing and a thorough sampling for species delimitation in Zodarion styliferum, a widespread Iberian ant-eating spider. We explore the influence of the loci filtering strategy on the downstream phylogenetic analyses, genomic clustering and coalescent species delimitation. We also assess the accuracy of one mitochondrial (COI) and one nuclear (ITS) barcode for fast and inexpensive species delineation in the group. Our genomic data strongly support two morphologically cryptic but ecologically divergent lineages, mainly restricted to the central-eastern and western parts of the Iberian Peninsula, respectively. Larger matrices with more missing data showed increased genomic diversity, supporting that bioinformatic strategies to maximize matrix completion disproportionately exclude loci with the highest mutation rates. Moderate loci filtering gave the best results across analyses: although larger matrices returned concatenated phylogenies with higher support, middle-sized matrices performed better in genetic structure analyses. COI displayed high diversity and a conspicuous barcode gap, revealing 13 mitochondrial lineages. Mitonuclear discordance is consistent with ancestral isolation in multiple groups, probably in glacial refugia, followed by range expansion and secondary contact that produced genomic homogenization. Several apparently (unidirectionally) introgressed specimens further challenge the accuracy of species identification through mitochondrial barcodes in the group. Conversely, ITS failed to separate both lineages of Z. styliferum. This study shows an extreme case of mitonuclear discordance that highlights the limitations of single molecular barcodes for species delimitation, even in presence of distinct barcode gaps, and brings new light on the effects of parameterization on shallow-divergence studies using RAD data.

Another stripe on the tiger makes no difference? Unexpected diversity in the widespread tiger tarantula Davus pentaloris (Araneae: Theraphosidae: Theraphosinae)

Integrative taxonomy is relevant for the discovery and delimitation of cryptic species by incorporating different sources of evidence to construct rigorous species hypotheses. The genus Davus was recently revised and it was found that Davus pentaloris presents high morphological variation across its widespread distribution. However, tarantulas usually present low dispersal capabilities that occasionally result in local endemism. In order to evaluate species boundaries within this taxon, we examine the morphological variation and, additionally, employ four strategies based on mtDNA data (COI): two distance-based [automatic barcode gap discovery (ABGD) and Neighbor-Joining (NJ)] and two tree-based methods [general mixed Yule coalescent (GMYC) and Bayesian Poisson tree process (bPTP)]. Available morphological evidence recovers 13 putative morphospecies, but the different methods based on molecular data recover a variable number of candidate species (16–18). Based on the congruence across all analyses and the available morphological data, we recognize 13 clearly diagnosable species, 12 of them new to science. We conclude that the underestimation of the diversity in D. pentaloris was mainly caused by deficient practices in taxonomy, rather than by the presence of cryptic diversity. Although COI is a functional barcoding marker and it gives reliable results in our study, we recommend combining multiple sources of evidence and strategies to construct better species delimitation hypotheses.

Under an integrative taxonomic approach: the description of a new species of the genus Loxosceles (Araneae, Sicariidae) from Mexico City

A new species of the spider genus Loxosceles Heineken & Lowe, 1832, Loxosceles tenochtitlan Valdez-Mondragón & Navarro-Rodríguez, sp. nov., is described based on adult male and female specimens from the states of Mexico City, Estado de Mexico and Tlaxcala. Integrative taxonomy including traditional morphology, geometric and lineal morphology, and molecules (DNA barcodes of cytochrome c oxidase subunit 1 (CO1) and internal transcribed spacer 2 (ITS2)), were used as evidence to delimit the new species. Four methods were used for molecular analyses and species delimitation: 1) corrected p-distances under neighbor joining (NJ), 2) automatic barcode gap discovery (ABGD), 3) general mixed yule coalescent model (GMYC), and 4) poisson tree processes (bPTP). All molecular methods, traditional, geometric and lineal morphology were consistent in delimiting and recognizing the new species. Loxosceles tenochtitlan sp. nov. is closely related to L. misteca based on molecular data. Although both species are morphologically similar, the average p-distance from CO1 data was 13.8% and 4.2% for ITS2 data. The molecular species delimitation methods recovered well-supported monophyletic clusters for samples of L. tenochtitlan sp. nov. from Mexico City + Tlaxcala and for samples of L. misteca from Guerrero. Loxosceles tenochtitlan sp. nov. is considered a unique species for three reasons: (1) it can be distinguished by morphological characters (genitalic and somatic); (2) the four different molecular species delimitation methods were congruent to separate both species; and (3) there is variation in leg I length of males between both species, with the males of L. misteca having longer legs than males of L. tenochtitlan sp. nov., also morphometrically, the shape of tibiae of the palp between males of both species is different.

Systematic revision of Mexican threatened tarantulas Brachypelma (Araneae: Theraphosidae: Theraphosinae), with a description of a new genus, and implications on the conservation

The tarantula genus Brachypelma includes colourful species that are highly sought after in the commercial pet trade. They are all included in CITES appendix II. We present phylogenetic analyses using molecular and morphological characters to revise Brachypelma, in which we include all currently known species. Our results agree with a previous study that shows the non-monophyly of Brachypelma. Both phylogenies strongly favour the division of Brachypelma into two smaller genera. The first clade (Brachypelma s.s.) is formed by B.albiceps, B. auratum, B. baumgarteni, B. boehmei, B. emilia, B. hamorii, B. klaasi and B. smithi. The species included in the second clade are transferred to the new genus Tliltocatl and is formed by T. albopilosum comb. nov., T. epicureanum comb. nov., T. kahlenbergi comb. nov., T. sabulosum comb. nov., T. schroederi comb. nov., T. vagans comb. nov. and T. verdezi comb. nov. Both genera can be differentiated by their coloration and the shape of the genitalia. We transfer to Tliltocatl: T. alvarezi, T. andrewi and T. aureoceps, but should be considered as nomina dubia. In addition, we transfer B. fossorium to Stichoplastoris. We discuss the implications of these taxonomical changes for CITES and for the Mexican Laws for wildlife protection.

Tarantula phylogenomics: A robust phylogeny of deep theraphosid clades inferred from transcriptome data sheds light on the prickly issue of urticating setae evolution

Mygalomorph spiders of the family Theraphosidae, known to the broader public as tarantulas, are among the most recognizable arachnids on earth due to their large size and widespread distribution. Their use of urticating setae is a notable adaptation that has evolved exclusively in certain New World theraphosids. Thus far, the evolutionary history of Theraphosidae remains poorly understood; theraphosid systematics still largely relies on morphological datasets, which suffer from high degrees of homoplasy, and traditional Sanger sequencing of preselected genes failed to provide strong support for supra-generic clades. In this study, we provide the first robust phylogenetic hypothesis of theraphosid evolution inferred from transcriptome data. A core ortholog approach was used to generate a phylogeny from 2460 orthologous genes across 25 theraphosid genera, representing all of the major theraphosid subfamilies, except Selenogyrinae. Our phylogeny recovers an unprecedented monophyletic group that comprises the vast majority of New World theraphosid subfamilies including Aviculariinae, Schismatothelinae and Theraphosinae. Concurrently, we provide additional evidence for the integrity of questionable subfamilies, such as Poecilotheriinae and Psalmopoeinae, and support the non-monophyly of Ischnocolinae. The deeper relationships between almost all subfamilies are confidently inferred. We also used our phylogeny in tandem with published morphological data to perform ancestral state analyses on urticating setae, and contextualize our reconstructions with emphasis on the complex evolutionary history of the trait.

Untangling a mess of worms: Species delimitations reveal morphological crypsis and variability in Southeast Asian semi-aquatic earthworms (Almidae, Glyphidrilus)

Semi-aquatic freshwater earthworms in the genus Glyphidrilus from Southeast Asia are characterized by both an extreme morphological crypsis among divergent phylogenetic lineages and a high morphological variability within the same phylogenetic lineages. The present study provides a new taxonomic framework for this problematic genus in SE Asia by integrating DNA sequence and morphological data. When single-locus and multilocus multispecies coalescent-based (MSC) species delimitation methods were applied to DNA sequence data, they usually yielded highly incongruent results compared to morphology-based species identifications. This suggested the presence of several cryptic species and high levels of intraspecific morphological variation. Applying reciprocal monophyly to the cytochrome c oxidase subunit 1 (COI) gene tree allowed us to propose the existence of 33 monophyletic species. Yet, often substantially more molecular operational taxonomic units (MOTUs) were obtained when species delimitation was based on COI and 16S rRNA sequences. In contrast, the ITS1 and ITS2 sequences suggested fewer MOTUs and did not recover most of the monophyletic species from the Mekong basin. However, several of these latter taxa were better supported when MSC species delimitation methods were applied to the combined mtDNA and ITS datasets. The ITS2 secondary structure retrieved one unnamed Mekong basin species that was not uncovered by the other methods when applied to ITS2 sequences. In conclusion, based on an integrative taxonomic workflow, 26 Glyphidrilus candidate species were retained and two remained to be confirmed. As such, this study provides evidence to suggest nine species new to science and to synonymize 12 nominal morphospecies. It also illustrates that the uncritical use of COI as a universal DNA barcode may overestimate species diversity because COI may be unable to distinguish between divergent conspecific lineages and different candidate species.

Invisible apple snail invasions: importance of continued vigilance and rigorous taxonomic assessments

BACKGROUND

Due to the similarities of overall shell morphology among apple snail species and considerable variability within species, substantial taxonomic confusion has plagued the accurate identification of Pomacea species. Many invasive apple snails have been mistakenly identified as P. canaliculata since their introduction to Asia around 1980. In 2008, three other introduced species in addition to P. canaliculata were recognized. In 2013, a fifth, previously unrecognized lineage was reported from China, indicating that despite the taxonomic clarity brought by previous work, continued surveys and taxonomic research are necessary to prevent additional introductions and continued spread, as well as to develop effective management strategies.

RESULTS

Phylogenetic analysis of mitochondrial COI sequences confirmed the presence of a widespread unidentified Pomacea lineage in China. All sequences from samples of this newly documented lineage were recovered in a monophyletic clade delineated from closely related species; however, different DNA barcoding methods yielded inconsistent species boundaries. Additionally, nuclear EF1α sequences indicated incomplete lineage sorting or recent hybridization of the unidentified lineage with the other two established species.

CONCLUSION

Barcoding is a valuable tool for species discovery, and a powerful approach for delineating introduced species. However, determining the identity of the newly discovered invasive lineage in China will require an integrated taxonomic approach incorporating individuals from the native range, and examination of natural history collections at museums around the world. To manage and prevent additional spread of already established species, and to stop the introduction of new taxa, continued monitoring and rigorous taxonomic assessments must be undertaken. © 2018 Society of Chemical Industry.

Singleton molecular species delimitation based on COI-5P barcode sequences revealed high cryptic/undescribed diversity for Chinese katydids (Orthoptera: Tettigoniidae)

Background

DNA barcoding has been developed as a useful tool for species discrimination. Several sequence-based species delimitation methods, such as Barcode Index Number (BIN), REfined Single Linkage (RESL), Automatic Barcode Gap Discovery (ABGD), a Java program uses an explicit, determinate algorithm to define Molecular Operational Taxonomic Unit (jMOTU), Generalized Mixed Yule Coalescent (GMYC), and Bayesian implementation of the Poisson Tree Processes model (bPTP), were used. Our aim was to estimate Chinese katydid biodiversity using standard DNA barcode cytochrome c oxidase subunit I (COI-5P) sequences.

Results

Detection of a barcoding gap by similarity-based analyses and clustering-base analyses indicated that 131 identified morphological species (morphospecies) were assigned to 196 BINs and were divided into four categories: (i) MATCH (83/131 = 64.89%), morphospecies were a perfect match between morphospecies and BINs (including 61 concordant BINs and 22 singleton BINs); (ii) MERGE (14/131 = 10.69%), morphospecies shared its unique BIN with other species; (iii) SPLIT (33/131 = 25.19%, when 22 singleton species were excluded, it rose to 33/109 = 30.28%), morphospecies were placed in more than one BIN; (iv) MIXTURE (4/131 = 5.34%), morphospecies showed a more complex partition involving both a merge and a split. Neighbor-joining (NJ) analyses showed that nearly all BINs and most morphospecies formed monophyletic cluster with little variation. The molecular operational taxonomic units (MOTUs) were defined considering only the more inclusive clades found by at least four of seven species delimitation methods. Our results robustly supported 61 of 109 (55.96%) morphospecies represented by more than one specimen, 159 of 213 (74.65%) concordant BINs, and 3 of 8 (37.5%) discordant BINs.

Conclusions

Molecular species delimitation analyses generated a larger number of MOTUs compared with morphospecies. If these MOTU splits are proven to be true, Chinese katydids probably contain a seemingly large proportion of cryptic/undescribed taxa. Future amplification of additional molecular markers, particularly from the nuclear DNA, may be especially useful for specimens that were identified here as problematic taxa.

Electronic supplementary material

The online version of this article (10.1186/s12862-019-1404-5) contains supplementary material, which is available to authorized users.

Biodiversity, Evolution and Ecological Specialization of Baculoviruses: A Treasure Trove for Future Applied Research

The Baculoviridae, a family of insect-specific large DNA viruses, is widely used in both biotechnology and biological control. Its applied value stems from millions of years of evolution influenced by interactions with their hosts and the environment. To understand how ecological interactions have shaped baculovirus diversification, we reconstructed a robust molecular phylogeny using 217 complete genomes and ~580 isolates for which at least one of four lepidopteran core genes was available. We then used a phylogenetic-concept-based approach (mPTP) to delimit 165 baculovirus species, including 38 species derived from new genetic data. Phylogenetic optimization of ecological characters revealed a general pattern of host conservatism punctuated by occasional shifts between closely related hosts and major shifts between lepidopteran superfamilies. Moreover, we found significant phylogenetic conservatism between baculoviruses and the type of plant growth (woody or herbaceous) associated with their insect hosts. In addition, we found that colonization of new ecological niches sometimes led to viral radiation. These macroevolutionary patterns show that besides selection during the infection process, baculovirus diversification was influenced by tritrophic interactions, explained by their persistence on plants and interactions in the midgut during horizontal transmission. This complete eco-evolutionary framework highlights the potential innovations that could still be harnessed from the diversity of baculoviruses.

A hyper-diverse genus of acanthocephalans revealed by tree-based and non-tree-based species delimitation methods: Ten cryptic species of Neoechinorhynchus in Middle American freshwater fishes

The genus Neoechinorhynchus represents a hyper-diverse group of acanthocephalans, parasites of fresh and brackish water fish and freshwater turtles, with approximately 116 species described worldwide. Forty-nine species have been recorded in the Americas, nine of them in Middle America. Even though species delimitation methods using DNA sequences have been rarely used for parasitic helminths, the genetic library for species of Neoechinorhynchus has grown in the past few years, enhancing the possibility of using these methods for inferring evolutionary relationships and for establishing more robust species boundaries. In this study, we used non-tree-based and tree-based methods through a coalescent approach to explore the species limits of specimens of Neoechinorhynchus collected in 57 localities across Middle America. We sequenced a large number of individuals to build a comprehensive dataset for three genes: the mitochondrial cytochrome c oxidase subunit I (352 individuals), the internal transcribed spacers (330 individuals), and the D2 + D3 domains of the large subunit (278 individuals). Several species delimitation methods were implemented, i.e., Automatic Barcode Gap Discovery (ABGD), General Mixed Yule-Coalescent Model (GMYC), Bayesian species delimitation (BPP) and species tree (∗BEAST). Additionally, we conducted a detailed morphological study of the diagnostic traits associated with the proboscis of 184 males and 169 females. Overall, our analyses allowed us to validate nine nominal species of Neoechinorhynchus and to identify 10 additional genetic lineages herein regarded as candidate species. This unexpected genetic diversity and the lack of reliable morphological traits show that the genus Neoechinorhynchus includes a group of cryptic species, at least in Middle America.

Unexpected species diversity within Japanese Mundochthonius pseudoscorpions (Pseudoscorpiones : Chthoniidae) and the necessity for improved species diagnosis revealed by molecular and morphological examination

Using the complementary approaches of morphological and molecular taxonomy is essential to further our understanding of invertebrate diversity, including the identification of cryptic species. Although the species classification of a widespread group of arachnids, the pseudoscorpions, has been based on traditional diagnostic characters for a long time, recent taxonomic studies have suggested that some of these are unreliable for distinguishing species. Thus, the application of molecular taxonomy may be particularly useful in this group. Here, we performed molecular phylogenetic analyses and species delimitation analyses based on partial sequences of mitochondrial DNA cytochrome c oxidase I and nuclear DNA 18S rRNA genes to assess the taxonomy of species and the reliability of morphological characteristics for distinguishing species in the Japanese soil-dwelling genus Mundochthonius (Chthoniidae). Our results revealed the existence of seven major genetic clades, likely corresponding to three described species and four cryptic species. Although two described species, M. kiyoshii and M. itohi, were represented by single clades in the phylogenetic analysis, a third, M. japonicus, was composed of multiple clades, highlighting inconsistencies between phylogenetic relationships and current species classifications using traditional morphological diagnostics. This study exemplifies the need for further exploration of pseudoscorpion taxonomy and species diversity. In particular, detailed morphological examinations are expected to help determine differences among cryptic species.

Discovering the silk road: Nuclear and mitochondrial sequence data resolve the phylogenetic relationships among theraphosid spider subfamilies

The mygalomorph spiders in the family Theraphosidae, also known as "tarantulas", are one of the most popular and diverse groups of arachnids, but their evolutionary history remains poorly understood because morphological analyses have only provided mostly controversial results, and a broad molecular perspective has been lacking until now. In this study we provide a preliminary molecular phylogenetic hypothesis of relationships among theraphosid subfamilies, based on 3.5 kbp of three nuclear and three mitochondrial markers, for 52 taxa representing 10 of the 11 commonly accepted subfamilies. Our analysis confirms the monophyly of the Theraphosidae and of most recognized theraphosid subfamilies, supports the validity of the Stromatopelminae and Poecilotheriinae, and indicates paraphyly of the Schismatothelinae. The placement of representatives of Schismatothelinae also indicates possible non-monophyly of Aviculariinae and supports the distinction of the previously contentious subfamily Psalmopoeinae. Major clades typically corresponded to taxa occurring in the same biogeographic region, with two of them each occurring in Africa, South America and Asia. Because relationships among these major clades were poorly supported, more extensive molecular data sets are required to test the hypothesis of independent colonization and multiple dispersal events among these continents.

Systematic revision of Brachypelma red-kneed tarantulas (Araneae : Theraphosidae), and the use of DNA barcodes to assist in the identification and conservation of CITES-listed species

Mexican red-kneed tarantulas of the genus Brachypelma are regarded as some of the most desirable invertebrate pets, and although bred in captivity, they continue to be smuggled out of the wild in large numbers. Species are often difficult to identify based solely on morphology, therefore prompt and accurate identification is required for adequate protection. Thus, we explored the applicability of using COI-based DNA barcoding as a complementary identification tool. Brachypelma smithi (F. O. Pickard-Cambridge, 1897) and Brachypelma hamorii Tesmongt, Cleton &amp; Verdez, 1997 are redescribed, and their morphological differences defined. Brachypelma annitha is proposed as a new synonym of B. smithi. The current distribution of red-kneed tarantulas shows that the Balsas River basin may act as a geographical barrier. Morphological and molecular evidence are concordant and together provide robust hypotheses for delimiting Mexican red-kneed tarantula species. DNA barcoding of these tarantulas is further shown to be useful for species-level identification and for potentially preventing black market trade in these spiders. As a Convention on International Trade in Endangered Species (CITES) listing does not protect habitat, or control wildlife management or human interactions with organisms, it is important to support environmental conservation activities to provide an alternative income for local communities and to avoid damage to wildlife populations.

By how much do we underestimate species diversity of liverworts using morphological evidence? An example from Australasian Plagiochila (Plagiochilaceae: Jungermanniopsida)

As a framework for revisionary study of the leafy liverwort Plagiochila in Australia, two methods for species delimitation on molecular sequence data, General Mixed Yule Coalescence model (GMYC) and Automatic Barcode Gap Discovery (ABGD) were applied to a dataset including 265 individuals from Australia, New Zealand, and the Pacific. Groups returned by GMYC and ABGD were incongruent in some lineages, and ABGD tended to lump groups. This may reflect underlying heterogeneity in the history of diversification within different lineages of Plagiochila. GMYC from trees calculated using three different molecular clocks were compared, in some lineages different primary species hypotheses were returned by analyses of trees estimated under different clock models, suggesting clock model selection should be a routine component of phylogeny reconstruction for tree-based species delimitation methods, such as GMYC. Our results suggest that a minimum of 71 Plagiochilaceae species occur in Australasia, 16 more than currently accepted for the region, comprising 8 undetermined species and 8 synonyms requiring reinstatement. Despite modern taxonomic investigation over a four decade period, (1) real diversity is 29% higher than currently recognized; and (2) 12 of 33, or 36%, of currently accepted and previously untested Australasian species have circumscription issues, including polyphyly, paraphyly, internal phylogenetic structure, or combinations of two or more of these issues. These both reflect the many challenges associated with grouping decisions based solely on morphological data in morphologically simple yet polymorphic plant lineages. Our results highlight again the critical need for combined molecular-morphological datasets as a basis for resolving robust species hypotheses in species-rich bryophyte lineages.

On the trapdoor spiders of Mexico: description of the first new species of the spider genus Aptostichus from Mexico and the description of the female of Eucteniza zapatista (Araneae, Mygalomorphae, Euctenizidae)

A new species of the spider genus Aptostichus Simon, 1891 is described from a cave in Huautla de Jiménez, Oaxaca, Mexico: Aptostichus sabinaesp. n. This species represents the first new species described from Mexico and the southernmost record in North America for the genus so far. Aptostichus sabinaesp. n. represents the forty-first species described for the genus, which has the highest species diversity in the family Euctenizidae. Eucteniza zapatista is redescribed based on five new males and the first known female from the Parque Nacional La Malinche (PNLM), Tlaxcala Mexico. Eucteniza zapatista is the fourth species of the genus where a female is known, and one of fourteen species described for the genus to date.