Search Results (32)

To date, five species of reddish-brown Neotriplax have been described, but their highly similar body color and other phenotypic traits make accurate taxonomy challenging. To clarify species-level taxonomy and validate potential new species, the cytochrome oxidase subunit I (COI) was used for phylogenetic analysis and the geometric morphometrics of elytron, pronotum, and hind wing were employed to distinguish all reddish-brown Neotriplax species. Phylogenetic results using maximum likelihood and Bayesian analyses of COI sequences aligned well with the current taxonomy of the Neotriplax species group. Significant K₂P divergences, with no overlap between intra- and interspecific genetic distances, were obtained in Neotriplax species. The automatic barcode gap discovery (ABGD), assemble species by automatic partitioning (ASAP), and generalized mixed Yule coalescent (GMYC) approaches concurred, dividing the similar species into eight molecular operational taxonomic units (MOTUs). Geometric morphometric analysis using pronotum, elytron, hind wing shape and wing vein patterns also validated the classification of all eight species. By integrating these analytical approaches with morphological evidence, we successfully delineated the reddish-brown species of Neotriplax into eight species with three new species: N. qinghaiensis sp. nov., N. maoershanensis sp. nov., and N. guangxiensis sp. nov. Furthermore, we documented the first record of N. lewisii in China. This study underscores the utility of an integrative taxonomy approach in species delimitation within Neotriplax and serves as a reference for the taxonomic revision of other morphologically challenging beetles through integrative taxonomy. Full article

(1) Background: Although Physaloptera retusa is one of the most widespread species infecting reptiles in the Americas, numerous taxonomic problems and little genetic data are associated with it. To clarify the taxonomy of this species, we used an integrative approach. (2) Methods: Physaloptera retusa-infecting Erythrolamprus typhlus (snake) from the Pantanal wetlands, Brazil, was morphologically and genetically characterised (18S and 28S rDNA; COI mtDNA) and compared with conspecific sequences available in GenBank, from parasites of Tupinambis teguixin (lizard), using species delimitation methods. Type specimens of P. liophis were re-evaluated given its morphological similarities with P. retusa. (3) Results: The morphology of the present specimens was equal to that of P. retusa, in which the only difference from P. liophis was the relative position of the vulva. Species delimitation methods were more accurate for the COI dataset; all of them (except ABGD) indicated interspecificity among P. retusa sequences. However, a lack of morphological data or voucher material, associated with the deposited sequences, prevented more assertive conclusions. (4) Conclusions: The present results highlight the importance of a clear association between genetic data and morphology of the isolation source, or at least its adequate vouchering. Moreover, P. retusa may represent a species complex in cryptic speciation, since it is widespread and has low hosts specificity. Full article

Fishes of the Mugilidae family are poorly known from a taxonomic perspective, largely because of their conservative morphology. In this paper, we aim to fill the knowledge gap and data deficiency regarding the genetic diversity of mullets occurring in southern peninsular India. A comprehensive mitochondrial phylogeny based on 238 COI sequences (78 newly generated) and three species delimitation methods (ASAP, RESL, and ABGD) confirmed the presence of 21 species of mullets within eight genera in southern peninsular India. These include one species each under the genera Rhinomugil Gill 1863, Minimugil Durand, Chen, Shen, Fu, and Borsa, 2012, Plicomugil Schultz 1953, and Ellochelon Whitley 1930; seven species of Planiliza Whitley 1945; four species of Crenimugil Schultz 1946; four species of Osteomugil Luther 1982; and two species of the “Mugil cephalus Linnaeus 1758” complex—though with uncertainty regarding the exact geographic origin of one of the two species of the “Mugil cephalus” complex and one species phylogenetically close to Planiliza subviridis (Valenciennes 1836). We provide an overview of the specific geographical regions in southern peninsular India, and “species groups”, which require future research using an integrative approach, so as to unravel the true extent of mullet diversity and their distribution in the region. Full article

The genus Lasiodiplodia, a member of the family Botryosphaeriaceae, is an important fungal disease genus in agriculture. However, the Lasiodiplodia species survey and genetic diversity in Taiwan remain unclear. This study aimed to investigate the Lasiodiplodia species associated with various fruit species to explore the cryptic Lasiodiplodia species diversity, validate species delimitation, and unveil cryptic genetic diversity. Overall, six Lasiodiplodia species were identified, with several new records of infection identified. Additionally, phylogenetic analyses indicated that the relations of all isolates of L. theobromae might be paraphyletic. They were grouped with L. brasiliense based on Automatic Barcode Gap Discovery (ABGD), Automatic Partitioning (ASAP) and structure-based clustering analyses. These analyses did not provide conclusive evidence for L. brasiliensis as a stable species. It may be necessary to gather more information to clarify the species delineation. The multiple new records of Lasiodiplodia species with high genetic diversity and differentiation revealed that the diversity of Lasiodiplodia in Taiwan was underestimated in the past. We found that L. theobromae has the highest number of haplotypes but the lowest number of haplotype and nucleotide diversities, indicating a recent population expansion. This was supported by the significant negative Tajima’s D and Fu and Li’s D* tests. The high genetic diversity, low gene flow, and host-associated differentiation of Lasiodiplodia species indicate that they might harbour powerful evolutionary potential in Taiwan. This study provided critical insights into genetic variation, host-associated differentiation, and demography of Lasiodiplodia species, which would be helpful for disease management of related pathogens. Full article

Pangasiids are an economically significant group of catfish, and many pangasiids are threatened in the wild from anthropogenic pressures, including increases in fishing pressure, habitat degradation, and improperly managed aquaculture practices. This study demonstrates the usage of DNA barcoding of the Cytochrome Oxidase subunit I (COI) gene as an identification tool in detecting potentially threatening invasive pangasiid species by establishing the diversity and phylogenetic relationship of Pangasiidae catfishes in Peninsular Malaysia. A neighbour-joining (NJ) dendrogram (Kimura-2-parameter model) generated five clades to represent distinct genera. Pangasius was further subdivided into two clades (Clade A: Pangasius bocourti-P. djambal and Clade B: P. nasutus-P. conchophilus). Given the marginal genetic divergence, indigenous and non-native species should be treated cautiously in allopatrically distributed species. The analysis used Automatic Barcode Gap Discovery (ABGD) and revealed barcode gaps between the intraspecific and interspecific distances. The sequences were partitioned into five groupings, corresponding with the species delineation based on the distribution of pairwise differences, which could not be differentiated using the NJ dendrogram. ABGD allows the recognition of one or two additional species using the recursive approach, but other taxonomic methods should be considered for a solid conclusion. DNA barcoding demonstrates the identification of closely related species, thus justifying its application towards the conservation of these fish. Full article

During scientific expeditions in Indonesia and Vietnam, several sponge specimens belonging to the genus Cladocroce were collected. The integration of morphological and molecular analyses, incorporating species delimitation models (ABGD, ASAP, and bPTP) and phylogenetic approaches using three molecular markers (COI, 28S, and 18S–ITS1–5.8S–ITS2–28S), allowed us to discriminate three congeneric species. Two of these species (C. burapha and C. pansinii sp. nov.) were supported by morphological and molecular data, whereas a third species (C. lamellata sp. nov.) was delimited by morphological data only. We formally describe two new species, C. pansinii sp. nov. and C. lamellata sp. nov. C. aculeata is a newly recorded species for Indonesia and the first documented finding after the original description. The re-examination of the type material of C. burapha, and indirectly the molecular approach, allowed us to confirm that C. burapha lives in sympatry with C. pansinii sp. nov. in Vietnam and with C. lamellata in Indonesia. Thanks to these findings, we relocated the paratype of C. burapha to the new species described here, i.e., C. pansinii sp. nov. Full article

The airbreathing walking catfish (Clariidae: Clarias) comprises 32 species that are endemic to African freshwater systems. The species-level identification of this group is challenging due to their complex taxonomy and polymorphism. Prior to this study, the biological and ecological studies were restricted to a single species, Clarias gariepinus, resulting in a biased view of their genetic diversity in African waters. Here, we generated the 63-mitochondrial Cytochrome c oxidase subunit 1 (COI) gene sequences of Clarias camerunensis and Clarias gariepinus from the Nyong River in Cameroon. Both C. camerunensis and C. gariepinus species maintained adequate intra-species (2.7% and 2.31%) and inter-species (6.9% to 16.8% and 11.4% to 15.1%) genetic distances with other Clarias congeners distributed in African and Asian/Southeast Asian drainages. The mtCOI sequences revealed 13 and 20 unique haplotypes of C. camerunensis and C. gariepinus, respectively. The TCS networks revealed distinct haplotypes of C. camerunensis and shared haplotypes of C. gariepinus in African waters. The multiple species delimitation approaches (ABGD and PTP) revealed a total of 20 and 22 molecular operational taxonomic units (MOTUs), respectively. Among the two Clarias species examined, we found more than one MOTU in C. camerunensis, which is consistent with population structure and tree topology results. The phylogeny generated through Bayesian Inference analysis clearly separated C. camerunensis and C. gariepinus from other Clarias species with high posterior probability supports. The present study elucidates the occurrence of possible cryptic diversity and allopatric speciation of C. camerunensis in African drainages. Further, the present study confirms the reduced genetic diversity of C. gariepinus across its native and introduced range, which might have been induced by unscientific aquaculture practices. The study recommends a similar approach to the same and related species from different river basins to illuminate the true diversity of Clarias species in Africa and other countries. Full article

Spiders of the genus Pholcus were collected for the first time during an expedition to the Lüliang Mountains in Shanxi Province, North China. Phylogenetic analyses of DNA sequence data from COI, H3, wnt, and 28S genes allowed us to group them into nine well-supported clades. We used morphology and four methods of molecular species delimitation, namely Automatic Barcode Gap Discovery (ABGD), the Generalized Mixed Yule Coalescent (GMYC), Bayesian Poisson Tree Processes (bPTP), and Bayesian Phylogenetics and Phylogeography (BPP), to investigate species boundaries. These integrative taxonomic analyses identified the nine clades as nine distinct species, comprising Pholcus luya Peng & Zhang, 2013 and eight other species new to science: Pholcus jiaocheng sp. nov., Pholcus linfen sp. nov., Pholcus lishi sp. nov., Pholcus luliang sp. nov., Pholcus wenshui sp. nov., Pholcus xiangfen sp. nov., Pholcus xuanzhong sp. nov., and Pholcus zhongyang sp. nov. The species occur in geographic proximity and show many morphological similarities. All of them belong to the P. phungiformes species group. The records from the Lüliang Mountains represent the westernmost distribution limit of this species group. Full article

Tai Lake, an important biodiversity hotspot of the lower reaches of the Yangtze River in China, possesses its characteristic fish fauna. Barcoding on native species is important for species identification and biodiversity assessment with molecular-based methods, such as environmental DNA (eDNA) metabarcoding. Here, DNA-barcoding coupled with high-throughput sequencing (HTS) and traditional Sanger sequencing was introduced to barcoding 180 specimens belonging to 33 prior morphological species, including the most majority of fish fauna in Tai Lake. HTS technology, on the one hand, significantly enhances the capture of barcode sequences of fish. The successful rate of fish barcoding was 74% and 91% in Sanger and HTS, respectively. On the other hand, the HTS output has a large number (64%) of insertions and deletions, which require strict bioinformatics processing to ensure that the ‘‘true’’ barcode sequence is captured. Cross-contamination and parasites were the primary error sources that compromised attempts at the DNA barcoding of fish species. The barcode gap analysis was 100% successful at delimiting species in all specimens. The automatic barcode gap discovery (ABGD) method grouped barcode sequences into 34 OTUs, and some deep divergence and closed species failed to obtain corresponding OTUs. Overall, the local species barcode library established by HTS barcoding here is anticipated to shed new light on conserving fish diversity in Tai Lake. Full article

We provide a diversity assessment of the agamid genus Phrynocephalus Kaup, 1825. We analyze COI mtDNA barcodes from 385 individuals sampled all over Phrynocephalus range. We apply the ABGD, ASAP, bGMYC, mlPTP and hsPTP species delimitation algorithms to analyze the COI gene fragment variation and assess the species diversity in Phrynocephalus. Nine species groups are revealed in Phrynocephalus in agreement with earlier studies on the phylogenetic relationships of the genus. We demonstrate that the present taxonomy likely underestimates the actual diversity of the genus. Alternative species delimitation algorithms provide a confusingly wide range of possible number of Phrynocephalus species—from 54 to 103 MOTUs (molecular operational taxonomic units). The ASAP species delimitation scheme recognizing 63 MOTUs likely most closely fits the currently recognized taxonomic framework of Phrynocephalus. We also report on 13 previously unknown Phrynocephalus lineages as unverified candidate species. We demonstrate that the ASAP and the ABGD algorithms likely most closely reflect the actual diversity of Phrynocephalus, while the mlPTP and hsPTP largely overestimate it. We argue that species delimitation in these lizards based exclusively on mtDNA markers is insufficient, and call for further integrative taxonomic studies joining the data from morphology, mtDNA and nuDNA markers to fully stabilize the taxonomy of Phrynocephalus lizards. Full article

This study is devoted to the investigation of Azygia (Digenea: Azygiidae) species diversity using classical morphological, recent molecular tools (28S rRNA and cox1 mtDNA for genetic-based inference) and robust statistical techniques (Principal component analysis, PCA). The analysis revealed that the genus Azygia included four valid species: A. lucii, A. longa, A. hwangtsiyui, and A. sibirica n. sp. The distribution of the type species A. lucii was confirmed in the largest Russian rivers: the Volga and the Ob. The worms isolated from Perccottus glenii were determined as the Chinese species A. hwangtsiyui, according to the genetic data for the cox1 mtDNA gene, at 1.32–1.56%. The new species, Azygia sibirica n. sp, was described from Esox lucius in the Ob River and differentiated from the type species A. lucii by the smaller ovary, testes and prostatic sac, wider body, very narrow pharyngeal lumen and form of anterior margin of ovary. In addition, multivariate analysis and three methods for species delimitation (ABGD, GMYC, bPTP) showed the subdivision of A. lucii and A. sibirica n. sp. into two separate groups, one from the Volga River and another from the Ob River, respectively. To conclude, A. lucii infects Esox lucius in the western (European part of Russia, the Volga River basin), and northern (Western Siberia, the Ob River basin) parts of Russia; A. sibirica n. sp. has also been found to infect Esox lucius in the Ob River, while A. hwangtsiyui infects Perccottus glenii in the South of the Russian Far East (the Artymovka River basin). Full article

Mites of the genus Geckobia (Acariformes: Pterygosomatidae) are permanent and highly specialised ectoparasites of geckos (Gekkota). We conducted a local study on Geckobia mites associated with the geckos of the family Gekkonidae found mainly in the territory of the Indian Institute of Science’s campus (Bangalore, India). In total, we examined 208 lizards belonging to two genera: Hemidactylus and Cnemaspis. We assessed the prevalence of the mites and identified the preferred site for their infestation. We extended the standard morphological identification of the mite species by using DNA barcode markers, partial sequences of the mitochondrial cytochrome c oxidase subunit I (COI) gene and nuclear ribosomal gene sequences: 18S rRNA and hypervariable region D2 of nuclear 28S rRNA. We checked the suitability of COI and nuclear (D2 of 28S rRNA) markers for species delimitations and identification purposes of the genus. The distance- and phylogeny-based approaches were applied: (i) to test the presence of a barcoding gap, we used the automated barcoding gap discovery tool (ABGD) and investigated intra- and interspecific genetic distances, and (ii) to reconstruct evolutionary relationships within the species, we performed maximum likelihood (ML) and Bayesian inference with Markov-Chain Monte Carlo (BI) analyses. As a result, we described five new species—Geckobia gigantea sp. n., G. treutleri sp. n., G. unica sp. n. and G. brevicephala sp. n.—from four Hemidactylus species: H. giganteus, H. treutleri, H. parvimaculatus and H. frenatus, respectively, and G. mysoriensis sp. n. from Cnemaspis mysoriensis. Additionally, we found three already described species: Geckobia indica Hirst, 1917 on H. treutleri (new host), Geckobia bataviensis Vitzhum, 1926 on H. parvimaculatus (new host) and H. frenatus (new locality) and Geckobia phillipinensis Lawrence, 1953 on H. frenatus (new locality). The diagnoses of G. indica and G. phillipinensis were improved and supplemented by descriptions of the males and juveniles. Both topologies of the BI and ML phylogenetic trees, as well as genetic distances, supported the species boundaries in the mite population shown by the morphological data. Hemidactylus frenatus was the most infected gecko species (61% prevalence), with the highest number of mite species (three spp.). The scale-mite richness was higher than expected; therefore, further research is required to evaluate the true diversity of Geckobia mites. Full article

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

Megascolex (Oligochaeta: Megascolecidae) are endemic species to India and Sri Lanka, however, to date their molecular taxonomy and phylogenetic relationships have not been reported. We applied the first integrative approach using morpho-anatomical features and a COI dataset to unveil species delimitation (SD), molecular taxonomy, and phylogenetic relationships in Megascolex species. Our morpho-anatomical results revealed nine Megascolex species, namely, M. auriculata, M. cochinensis cochinensis, M. filiciseta, M. ratus, M. travancorensis travancorensis, M. triangularis, M. konkanensis konkanensis, M. polytheca polytheca, and M. polytheca zonatus. We also reported the occurrence of two new species, namely, M. papparensis sp. nov, and M. vazhichlensis sp. nov. Such findings were also supported by the analysed COI dataset, in which these new species appeared distinct on the phylogenetic trees with strong support. The studied Megascolex species appeared paraphyletic and formed three subclades on Bayesian inference (BI) and Maximum Likelihood (ML) phylogenetic trees. The first clade consisted of six species: M. cochinensis cochinensis, M. polytheca polytheca, M. polytheca zonatus, M. konkanensis konkanensis, M. filiciseta, and M. auriculata with strong posterior probability support. The second clade consisted of M. travancorensis travancorensis, M. papparensis sp. nov, and M. vazhichlensis sp. nov with strong support. The third clade consisted of M. ratus and M. triangularis with good support. In addition, the validation of species was confirmed by SD methods, in which the congruence among OTUs was observed with the clear barcode gap of 12–14% suggested by ABGD analysis. However, the species M. ratus and M. travancorensis travancorensis show deep intraspecific divergence and, therefore, require more sampling data. Such findings are essential to study the phylogenetics and evolution of the genus and, nonetheless, demand larger COI datasets to make concrete conclusions. Full article

Parrotfish are an important group in the coral reef ecosystem that maintain ecological stability and have a close relationship with coral reefs. Around the world, parrotfish and coral reefs are being destroyed due to human activities and global climate change. Here, we investigated the diversity of parrotfish in the South China Sea (SCS) using DNA barcoding, and initially established a DNA barcode database of the SCS parrotfish. A total of 1620 parrotfish specimens, belonging to 23 species of 6 genera in the family Scaridae, were collected in the SCS, accounting for 64% of the parrotfish species in the SCS. Genetic distance analysis at each taxonomic level showed that the average genetic distance was 0.23% within species, 8.52% within genus and 13.89% within family. The average inter-specific distance was 37.04-fold the intra-specific distance. Barcode gap analysis showed that 6 of the 21 parrotfish species with multiple samples had no barcode gap, resulting in an overall identification success rate of 74%. The ABGD analysis revealed that there could be 37 potential operational taxonomic units (OTUs) and the BIN analysis showed 32 identifiable taxonomic units, which by far exceed the number of morphologically previously known species. Overall, this study complements the lack of parrotfish DNA barcode sequences, and our findings provide an important stepping-stone to further study the diversity of parrotfish in South China. Full article