Taxonomic Problems Research Articles

Natural Hybrid Origin of the Controversial "Species" Clematis × pinnata (Ranunculaceae) Based on Multidisciplinary Evidence.

Interspecific hybridization is common and has often been viewed as a driving force of plant diversity. However, it raises taxonomic problems and thus impacts biodiversity estimation and biological conservation. Although previous molecular phylogenetic studies suggested that interspecific hybridization may be rather common in Clematis, and artificial hybridization has been widely applied to produce new Clematis cultivars for nearly two centuries, the issue of natural hybridization of Clematis has never been addressed in detail. In this study, we tested the hybrid origin of a mesophytic and cold-adapted vine species, Clematis pinnata, which is a rare and taxonomically controversial taxon endemic to northern China. Using field investigations, flow cytometry (FCM), phylogenomic analysis, morphological statistics, and niche modeling, we tested hybrid origin and species status of C. pinnata. The FCM results showed that all the tested species were homoploid (2n = 16). Phylonet and HyDe analyses based on transcriptome data showed the hybrid origins of C. × pinnata from either C. brevicaudata × C. heracleifolia or C. brevicaudata × C. tubulosa. The plastome phylogeny depicted that C. × pinnata in different sampling sites originated by different hybridization events. Morphological analysis showed intermediacy of C. × pinnata between its putative parental species in many qualitative and quantitative characters. Niche modeling results suggested that C. × pinnata had not been adapted to a novel ecological niche independent of its putative parents. These findings demonstrated that plants of C. × pinnata did not formed a self-evolved clade and should not be treated as a species. The present study also suggests that interspecific hybridization is a common mechanism in Clematis to generate diversity and variation, and it may play an important role in the evolution and diversification of this genus. Our study implies that morphological diversity caused by natural hybridization may overstate the real species diversity in Clematis.

Taxonomic notes on the genus Dumasia (Fabaceae)

The phylogenetic relationships between species of the genus Dumasia have been revealed by previous studies. However, some taxonomic problems still remain to be resolved. In this article, we recognize 10 species of Dumasia. We re-circumscribe D. yunnanensis Y. T. Wei & S. K. Lee, promote D. nitida var. kurziana Predeep & M. P. Nayar as a distinct species, and synonymize D. hunanica Y. K. Yang, L. H. Liu & J. K. Wu with D. hirsuta Craib. D. prazeri Predeep & M. P. Nayar is here confirmed as a newly recorded species for China, and D. zhangjiajieensis Y. K. Yang, L. H. Liu & J. K. Wu, a distinct species with winged peduncles which was overlooked in previous studies, is also reported here. We provided detailed descriptions, expanded distributions, habitat and phenological information, conservation status, and taxonomic notes for these five species. An updated key to the genus is also provided.

Classification of weed seeds based on visual images and deep learning

Weeds are mainly spread by weed seeds being mixed with agricultural and forestry crop seeds, grain, animal hair, and other plant products, and disturb the growing environment of target plants such as crops and wild native plants. The accurate and efficient classification of weed seeds is important for the effective management and control of weeds. However, classification remains mainly dependent on destructive sampling-based manual inspection, which has a high cost and rather low flux. We considered that this problem could be solved using a nondestructive intelligent image recognition method. First, on the basis of the establishment of the image acquisition system for weed seeds, images of single weed seeds were rapidly and completely segmented, and a total of 47 696 samples of 140 species of weed seeds and foreign materials remained. Then, six popular and novel deep Convolutional Neural Network (CNN) models are compared to identify the best method for intelligently identifying 140 species of weed seeds. Of these samples, 33 600 samples are randomly selected as the training dataset for model training, and the remaining 14 096 samples are used as the testing dataset for model testing. AlexNet and GoogLeNet emerged from the quantitative evaluation as the best methods. AlexNet has strong classification accuracy and efficiency (low time consumption), and GoogLeNet has the best classification accuracy. A suitable CNN model for weed seed classification could be selected according to specific identification accuracy requirements and time costs of applications. This research is beneficial for developing a detection system for weed seeds in various applications. The resolution of taxonomic issues and problems associated with the identification of these weed seeds may allow for more effective management and control.

Review of Trachysphaera Heller, 1858 (Diplopoda: Glomerida: Glomeridae) in Serbia, with taxonomic notes on the genus.

The glomerid genus Trachysphaera Heller, 1858 in Serbia is revised, based on recently collected specimens and historical material. Six species are presently recorded from Serbia, viz., Trachysphaera corcyraea (Verhoeff, 1900), T. cristangula (Attems, 1943), T. schmidtii Heller, 1858, and T. similicostata (Radu Ceuca, 1951), all new to the fauna of the country, as well as T. costata (Waga, 1857a) and T. lobotarsus (Attems, 1943). All of these species are richly illustrated and mapped. To verify the identity of some species, historical material from the Natural History Museum in Vienna, including syntypes, is also studied, and two lectotypes have been designated. Some misidentifications from the literature have been corrected. Trachysphaera acutula (Latzel, 1884) syn. n., T. cultrifera (Verhoeff, 1906) syn. n. and T. multiclavigera (Verhoeff, 1898) syn. n. are all considered as junior subjective synonyms of T. schmidtii. Trachysphaera attemsi Golovatch, 1976 syn. n. is transferred from the list of synonyms of T. costata to the list of synonyms of T. corcyraea. One species, T. similicostata, is resurrected from synonymy. Relationships between some congeners and the taxonomic problems within the genus are briefly discussed.

Why morphology matters: the negative consequences of hasty descriptions of putative novelties in asexual ascomycetes

ABSTRACTRecent progress in the discovery of fungal diversity has been enabled by intensive mycological surveys in centres of global biodiversity. Descriptions of new fungal species have been almost routinely based on phenotypic studies coupled with single or multigene phylogenetic analyses of DNA sequence data. However, high accessibility of sequencing services together with an increasing amount of available molecular data are providing easier and less critical support for taxonomic novelties without carefully studying the phenotype, particularly morphology. As a result, the accelerated rate of species descriptions has been unfortunately accompanied by numerous cases of overlooking previously described and well documented species, some of them that have been known for more than a century. Here, we critically examined recent literature, phenotypic and molecular data, and detected multiple issues with putative novelties of asexual Ascomycota traditionally known as hyphomycetes. In order to fix these taxonomic problems, three new combinations within the genera Pleopunctum, Camposporium and Sporidesmium, and two new names in Camposporium are proposed. Moreover, three genera, Aquidictyomyces, Fusiconidium and Pseudohelminthosporium, together with nine species are reduced to synonymy. The examples outlined here clearly show the relevance of morphology in modern phylogenetic studies and the importance of more stringent ‘quality controls’ during biodiversity studies documenting the extensive fungal diversity in a speedy manner.

Should we abandon the name Titanosauridae? some comments on the taxonomy of titanosaurian sauropods (Dinosauria)

Titanosaurs were the most abundant and widespread of Cretaceous sauropod dinosaurs. A derived subset of titanosaurian genera, historically termed the Titanosauridae, is beset with multiple taxonomic problems. Because the genus Titanosaurus is founded upon nondiagnostic material, the International Code of Zoological Nomenclature opposes the continued use of the term Titanosauridae. Nevertheless, the newly proposed Phylogenetic Code of Biological Nomenclature advocates the retention of Titanosauridae. To stabilize the taxonomy of derived titanosaurs, I consider Titanosauridae as a node-based taxon and Epachthosaurinae and Eutitanosauria as stern-based taxa, and thereby establish a node-stem triplet at Titanosauridae. I phylogenetically define additional titanosaurian clades including Titanosauroidea, Andesauroidea, Eutitanosauria, Saltasaurinae and Opisthocoelicaudinae. Finally, I return “Titanosaurus” araukanicus to the genus Laplatasaurus.

On the scientific names of mastodont taxa: nomenclature, Chinese translation, and taxonomic problems

On the scientific names of mastodont taxa: nomenclature, Chinese translation, and taxonomic problems

On the classification of simple and complex biological images using Krawtchouk moments and Generalized pseudo-Zernike moments: a case study with fly wing images and breast cancer mammograms.

In image analysis, orthogonal moments are useful mathematical transformations for creating new features from digital images. Moreover, orthogonal moment invariants produce image features that are resistant to translation, rotation, and scaling operations. Here, we show the result of a case study in biological image analysis to help researchers judge the potential efficacy of image features derived from orthogonal moments in a machine learning context. In taxonomic classification of forensically important flies from the Sarcophagidae and the Calliphoridae family (n = 74), we found the GUIDE random forests model was able to completely classify samples from 15 different species correctly based on Krawtchouk moment invariant features generated from fly wing images, with zero out-of-bag error probability. For the more challenging problem of classifying breast masses based solely on digital mammograms from the CBIS-DDSM database (n = 1,151), we found that image features generated from the Generalized pseudo-Zernike moments and the Krawtchouk moments only enabled the GUIDE kernel model to achieve modest classification performance. However, using the predicted probability of malignancy from GUIDE as a feature together with five expert features resulted in a reasonably good model that has mean sensitivity of 85%, mean specificity of 61%, and mean accuracy of 70%. We conclude that orthogonal moments have high potential as informative image features in taxonomic classification problems where the patterns of biological variations are not overly complex. For more complicated and heterogeneous patterns of biological variations such as those present in medical images, relying on orthogonal moments alone to reach strong classification performance is unrealistic, but integrating prediction result using them with carefully selected expert features may still produce reasonably good prediction models.

The complete mitochondrial genome of a parthenogenetic ant Monomorium triviale (Hymenoptera: Formicidae)

Monomorium is one of the most species-rich yet taxonomically problematic ant genus. An East Asian species, M. triviale Wheeler, W.M., 1906, is reproduced by obligate thelytokous parthenogenesis and performs strict reproductive division of labor. We sequenced the M. triviale mitogenome using next-generation sequencing methods. The circular mitogenome of M. triviale was 16,290 bp in length, consisting of 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNAs, and a single non-coding region of 568 bp. The base composition was AT-biased (82%). Gene order rearrangements were detected and likely to be unique to the genus Monomorium. We announce the M. triviale mitogenome as additional genomic resources for elucidating phylogenetic and taxonomic problems of Monomorium and comparative genomics of parthenogenetic ant species.

Species delimitation of the northeastern Anatolian Symphytum (Boraginaceae) taxa

Symphytum is regarded one of the most complicated genera in terms of the classification of its members among the Boraginaceae. In addition to different infrageneric classification methods, several species complex or aggregates have been proposed to deal with the taxonomical problem of genus members. Symphytum asperum aggregate was first introduced by Kurtto, who proposed six taxa within this aggregate. However, according to further studies by different researchers based on morphological data, total number of species of the complex was variable. The number of species was reduced to three, comprising S. asperum, S. savvalense, and S. sylvaticum, after the phylogenetic and morphological studies of Tarıkahya-Hacıoğlu and Erik. However, the taxonomical status of some of these species (i.e., S. savvalense and S. sylvaticum, and S. sepulcrale), which was assigned as a member of this complex by Kurtto, has been regarded as unresolved. To solve this uncertainty, different species delimitation methods were used, including statistical parsimony network analysis (TCS), generalized mixed Yule coalescent (GMYC), and Bayesian Phylogenetics and Phylogeography (BPP) of the ITS, trnL-F and trnS-G sequence data. In addition to members of this complex, S. ibericum, which is phylogenetically nested within the S. asperum aggregate, was also used. The TCS and GMYC analyses demonstrated more complicated clusters, whereas high posterior probabilities of BPP clusters were more compatible with the morphological data. In accordance with the morphological approach of Tarıkahya-Hacıoğlu and Erik, the species delimitation analyses based on molecular data support the recognition of S. asperum, S. ibericum, S. savvalense, and S. sylvaticum as different species.

Taxonomic notes on some species in the genus Clausena (Rutaceae) in China based on molecular and morphological data

Abstract Clausena (Rutaceae) is only one genus native both to the Monsoon region and to tropical and subtropical Africa in the subfamily Aurantioideae. The most distinctive morphological character in this genus is the gynophore supporting the ovary and the morphology of pistil can help to define the natural groups of species. Based on the morphological data of flowers and molecular phylogeny of ITS, trnL-F and atpB-rbcL, the taxonomic problems of some species in China are resolved here. The species C. lenis has a separate status in the genus Clausena, then C. lansium stands apart from other species except C. lenis; the species status of five species, C. odorata, C. vestita, C. dunniana, C. emarginata, and C. anisum-olens are restated.

Taxonomic problems with Gynaikothrips and related genera (Thysanoptera, Phlaeothripinae): the ficorum/uzeli complex and taxa endemic to Australia.

Ten species from Australia in or related to the genus Gynaikothrips are discussed. Variation among specimens of the pest species on Ficus trees, the ficorum/uzeli complex, is examined with the conclusion that recognition of these two species remains questionable. Two species related to this complex are newly recorded from Australia, insulsus Priesner and luzonensis Priesner, and edentatus Priesner is placed as a syn.n. of ficorum. Two new Gynaikothrips are described, jasmini sp.n. and platypodae sp.n., and additamentus Karny is transferred from Gynaikothrips to Eilapinothrips gen.n. A new species of Agynaikothrips is described as the third known member of this genus, lorieni sp.n., and Liothrips umbratus Hood comb.rev. is returned to this original genus from Gynaikothrips. Two species described in Gynaikothrips from the Philippines, capitulatus Reyes and pedanus Reyes, are transferred to the genus Teuchothrips. The monobasic genus, Aiganothrips Bhatti, is considered a syn.n. of Gynaikothrips, and the monobasic genus, Jennythrips Bhatti, is considered a syn.n. of Liothrips.

The Towakkalak System, A Hotspot of Subterranean Biodiversity in Sulawesi, Indonesia

The Towakkalak System located in the Maros karst of South Sulawesi is currently the richest of Southeast Asia in obligate subterranean species. It comprises several caves and shafts that give access to the subterranean Towakkalak river as well as many unconnected fossil caves, stream sinks, and springs located within its footprint. The total length of the caves linked to the active system is 24,319 m and comprises two of the longest caves of Indonesia, Gua Salukkan Kallang and Gua Tanette. Studies of its fauna began in 1985. There are 10 stygobionts and 26 troglobionts that are known from the system. The smaller adjacent system of Saripa has 6 stygobionts and 18 troglobionts, of which 1 and 3, respectively, are absent from Towakkalak. Like all tropical cave inventories, our dataset has limits due to identification uncertainties, gaps in habitat (waters, guano) and taxonomic coverage (micro-crustaceans, mites), sampling methods (pitfall trapping, Karaman–Chappuis), and problems of ecological assignment. A number of additional species are therefore expected to be found in the future. The Towakkalak and Saripa cave systems are included in the Bantimurung-Bulusaraung National Park and are under efficient protection, but parts of the Maros karst outside the park are under serious threat, mainly from quarrying.

A Reassessment of the Little-Known Amazonian Fern Diplazium praestans Based on Molecular and Morphological Evidence

Abstract— Family- and genus-level circumscription of ferns in the suborder Aspleniineae (eupolypods II) has long been controversial, due in part to confusion about the relationship among the families Aspleniaceae and Athyriaceae. Recent studies have demonstrated that character states traditionally used to infer a close relationship between these two families are either symplesiomorphic or homoplastic, and re-examination of numerous taxa has led to the recircumscription of several clades, and the description of several new families and genera. In light of these findings, we re-evaluated the taxonomic affinities of Diplazium praestans, a little-known fern from western Amazonia that is morphologically disparate to the remainder of Neotropical Diplazium. Using sequence data from three chloroplast markers and analysis of eight morphological characters, we demonstrate that Diplazium praestans was erroneously placed in that genus and instead is a Hymenasplenium. We place it in a phylogenetic context, reassess its morphology in light of our findings, evaluate its conservation status under IUCN criteria, and provide a new combination: Hymenasplenium praestans. We also provide an updated key to the Neotropical species of Hymenasplenium and discuss unresolved taxonomic problems in the genus.

Venation pattern and micromorphology of schizocarps of Gaya and related genera within Malveae (Malvaceae)

Few studies have reported the venation pattern and micromorphology of Malveae schizocarpic fruits. These reproductive structures are present in Gaya and other genera of the tribe and may prove useful for solving taxonomic problems and understanding phylogenetic relationships within. We analyzed the mericarp and the seeds of 13 Brazilian species of Gaya and 11 species of related genera to provide useful comparative features for their taxonomy and phylogeny. The samples were subjected to the herborization reversal procedure and followed methods of scanning electron microscopy, light microscopy and diaphanization. The studied species of Gaya were compared on a binary matrix of characters analyzed through UPGMA. Within Gaya, the mericarp constriction corresponds to the dehiscence lines, which may occur at the basal portion or ventrally. Two to three veins in contact with the columella (central structure to which the mericarps are attached) were observed in this region. At the upper ventral margin, we observed only one vein connecting with the columella. The exocarp exhibited simple, biradiate, stellate and multiradiated trichomes. Capitate glandular trichomes were also observed. Species from related genera (Briquetia, Callianthe, Herissantia and Hochreutinera) showed stellate trichomes. Glandular and tector trichomes were observed in Gaya seeds, while other genera exhibited only simple trichomes. Venation pattern and micromorphological characters of mericarps, as well as novel seed trichome types here reported support of Gaya support the delimitation of genera studied and highlight the isolated position of Gaya within Malvaeae.

The anatomical, palynological and micromorphological aspects of three endemic Bellevalia species (Asparagaceae) in Turkey and their taxonomic importance

In the present research, anatomical, palynological and micromorphological characteristics of three endemic Bellevalia species (B. gracilis, B. malatyaensis and B. vuralii) for Turkey are carried out. This work reveals the descriptive characteristics of the examined species, and contribute to solving taxonomic problems. Anatomical studies were carried out on cross sections of root, scape and leaf. The metaxylem, the number of root cortex cells, and the number of cortex and sclerenchyma cells in the scape were found to be significant in terms of taxonomy. Pollen grains of all the examined species were monosulcate and heteropolar. In addition, seed and pollen surface ornamentation were photographed under SEM microscopy, which SEM micrographs showed that the exine sculpturing pattern is reticulate-perforate, and pollen muri walls of were different among the examined species. Conversely, seeds showed a general similarity of the surface among the studied species, all showing a reticulate faveolate ornamentation.

Genome-Wide SNPs Clarify a Complex Radiation and Support Recognition of an Additional Cat Species.

Phylogenetic reconstruction and species delimitation are often challenging in the case of recent evolutionary radiations, especially when postspeciation gene flow is present. Leopardus is a Neotropical cat genus that has a long history of recalcitrant taxonomic problems, along with both ancient and current episodes of interspecies admixture. Here, we employ genome-wide SNP data from all presently recognized Leopardus species, including several individuals from the tigrina complex (representing Leopardus guttulus and two distinct populations of Leopardus tigrinus), to investigate the evolutionary history of this genus. Our results reveal that the tigrina complex is paraphyletic, containing at least three distinct species. While one can be assigned to L. guttulus, the other two remain uncertain regarding their taxonomic assignment. Our findings indicate that the “tigrina” morphology may be plesiomorphic within this group, which has led to a longstanding taxonomic trend of lumping these poorly known felids into a single species.

Tragoportax and Miotragocerus from Nagri Formation type locality, Siwalik Group, Pakistan (early Late Miocene): Taxonomic problems and hypotheses regarding their resolution

This article focuses on some new material of currently called Miotragocerus/Tragoportax complex of species, collected from Nagri type locality, early Late Miocene (10.039 to 9.969Ma) of the Siwalik Group of Pakistan. Along with the material description, the issues regarding the taxonomic status of Tragoportax, Miotragocerus, Sivaceros and Helicoportax are briefly discussed on the basis of preliminary results of ongoing thorough research on the Siwalik bovids. Furthermore, the priority of Graecoryx over Miotragocerus, the synonymy of Sivaceros with Graecoryx, the distinction between Tragoportax and Graecoryx, and some hypotheses have been laid down for future work, based on the morphological study.

Cryptic diversity and significant cophylogenetic signal detected by DNA barcoding the rust fungi (Pucciniaceae) of Cyperaceae–Juncaceae

AbstractPlants play important roles as habitat and food for a tremendous diversity of specialist animals and fungi. The disappearance of any plant species can lead to extinction cascades of its associated biota. In consequence, documenting the diversity and specificity of plant‐associated organisms is of high practical relevance in biodiversity conservation. Here, we present the first large‐scale molecular investigation into the diversity, host specificity, and cophylogenetic congruence of an especially rich plant–fungal association, the rust fungi (Pucciniaceae) of Cyperaceae and Juncaceae. Using the largest rust fungi DNA barcoding dataset published to date (252 sequences, 82 taxa), we reject the presence of a global ITS2‐28S barcode gap, but find a local gap in Cyperaceae–Juncaceae rusts, and suggest the existence of many cryptic species in North America, with some broadly circumscribed species possibly corresponding to >10 cryptic species. We test previous hypotheses of correlations between the phylogenies of rust fungi and their Cyperaceae–Juncaceae hosts using a combination of global‐fit and event‐based cophylogenetic methods. A significant cophylogenetic signal is detected between rusts and their hosts, but the small number of cospeciations argues for preferential host jumps as the driving process behind these correlations. In addition, temporal congruence between the origin of major Carex clades and their rusts suggests that host diversification may have promoted parasite diversification. Finally, we discuss the relevance of rust infection patterns to the systematics of Cyperaceae, highlight some taxonomic problems uncovered by the analyses, and call attention to the promise of DNA barcoding for bridging knowledge gaps in poorly studied plant‐associated microorganisms.

Reassessment of suitable markers for taxonomy of Chaetophorales (Chlorophyceae, Chlorophyta) based on chloroplast genomes.

Filamentous green algae Chaetophorales present numerous taxonomic problems as many other green algae. Phylogenetic analyses based on nuclear genes have limited solutions. Studies with appropriate chloroplast molecular markers may solve this problems; however, suitable molecular markers for the order Chaetophorales are still unknown. In this study, 50 chloroplast genomes of Chlorophyceae, including 15 of Chaetophorales, were subjected to single protein-coding gene phylogenetic analyses, and substitution rate and evolutionary rate assays, and PCR amplification verification was conducted to screen the suitable molecular markers. Phylogenetic analyses of three chloroplast representative genes (psaB, tufA, and rbcL) amplified from 124strains of Chaetophorales showed that phylogenetic relationships were not improved by increasing the number of samples, implying that the genes themselves, rather than limited samples, were the reason for the unsupported Topology I. Seven genes (atpF, atpI, ccsA, cemA, chlB, psbB, and rpl2) with robust support were selected to be the most suitable molecular markers for phylogenetic analyses of Chaetophorales, and the concatenated seven genes could replace the time-consuming and labor-intensive phylogenetic analyses based on chloroplast genome to some extent. To further solve the taxonomic problems of Chaetophorales, suitable chloroplast markers combined with more taxon-rich approach could be helpful and efficient.