Taxonomic Research Research Articles

New morphological data for two rare species of sand-dwelling marine dinoflagellates, Amphidiniella sedentaria and Pachena cf. leibnizii

Abstract Benthic dinoflagellates have been the subject of extensive taxonomic research in recent decades. Studies of morphologies of already known species of benthic dinoflagellates from various geographical populations remain relevant, as these allow elucidation of some details that were overlooked in the original species descriptions or assessment of their morphological variability. In the present study, two rare species of dinoflagellates, Amphidiniella sedentaria and Pachena cf. leibnizii, have been studied, for the first time, from coastal sands of the northwestern Sea of Japan. In the cells of A. sedentaria from the Sea of Japan, we have found two anterior intercalar plates instead of one. Therefore, the original formula has been changed to APC 4′ 2a 7″ 5c 4s 6‴ 2⁗. As a result of the examination of P. cf. leibnizii from the Sea of Japan, we have counted seven precingular plates and six cingular plates, instead of six and five, respectively, indicated in the original description. The plate formula of the cells of P. cf. leibnizii from the Sea of Japan is APC 4′ 3a 7″ 6c 5s 5‴ 2⁗. It is currently difficult to judge whether these differences are morphological variations. Therefore, we have identified these cells as P. cf. leibnizii.

Reducing the number of Data Deficient plant species

Although most plant species have yet to have their extinction risk evaluated for the IUCN Red List, current knowledge of plant diversity suggests that tens of thousands (8%–38% of species) are likely to remain assessed as Data Deficient (DD). This impacts evaluations of the overall proportion of threatened species, as well as on setting appropriate priorities for biodiversity conservation. One of the principle causes of Data Deficiency is taxonomic uncertainty: data permitting an IUCN Red List assessment is often lacking, because species that are poorly known are also taxonomically uncertain. Establishing the taxonomic status of DD species thus assists in determining whether confusion over this is causing their evaluation as DD. In this paper, three separate numerical methods – hierarchical clustering, ordination and phylogenetic ordination – were applied to three independent datasets of standardized traits for plant species from China in order to identify, for each DD species, morphologically similar Non-DD species. Semi-automated analysis of morphological disparity quickly identifies which species are in need of further taxonomic research, as shared traits can indicate either potential synonymy or, otherwise, successful adaptations of distinct species to similar ecological conditions. Extinction risk assessments of morphologically and phylogenetically distinct DD species could then be informed by data on habitat preferences, geographic range or population size from Non-DD species with the most similar traits. Ultimately, determination of the morphological distance between DD species and their most similar Non-DD species, and therefore of differences in the trait space occupied by DD and Non-DD species, could be the basis of future research for improved inference of conservation priorities, and help distinct DD species with similar ecological traits as other taxonomically accepted, threatened species to be identified as being threatened themselves.

A botanical oasis rather than a biological desert: Rediscoveries, new species and new records in a tropical city

Societal Impact StatementCities present a unique challenge for conservation. While overall native biodiversity is reduced, remnant habitats in the urban matrix can be important refugia for native and endemic species. This study reviews the rediscovery of 173 presumed nationally extinct plant taxa and discovery of 155 new native plant records, including 22 new to science and five endemics, in the botanically densely‐collected tropical city‐state of Singapore. The findings of this study indicate that plant rediscoveries and new discoveries are still possible in cities and urban areas with remaining fragments of original forest reserved for species protection, and investment in comprehensive botanical surveys and taxonomic research.Summary The conservation of native species‐dominated forest fragments and investment into botanical surveys and taxonomic research have enabled the rediscovery of presumed nationally extinct plant taxa and discovery of new native plant records in the tropical city‐state of Singapore. We compared national plant checklists of 2009, 2022, and the national Red Data Book (third edition in press) to enumerate rediscovered and newly discovered native vascular plant taxa in the last 14 years. We examined if these were from taxonomic specialist redetermination of only pre‐existing specimens or newly collected from field surveys, and if they were from particular sites and vegetation types, disproportionately represented by certain life forms and families, and predominantly threatened. We documented 173 rediscoveries and 155 new records after 2009, including 22 new to science and five endemics. Most rediscoveries were newly collected from field surveys, but most new records resulted from redetermination of pre‐existing specimens. Native species‐dominated forest fragments were the most important sites for the first collection of new records or first re‐collection of rediscoveries. Trees and climbers were well‐represented among the rediscoveries and new records. Epiphytes were significantly under‐represented compared to their proportion in the presumed nationally extinct flora. Most rediscoveries and new records are nationally Critically Endangered but regionally and globally not assessed. Our findings indicate hope for the persistence of rare native plant species and opportunities for conservation in cities.

Trials and tribulations of Neotropical plant taxonomy: Pace of tree species description

Societal Impact StatementGiven the current unprecedented concerns for global biodiversity loss, it is critical to identify best practices for describing new species more efficiently so we can complete the inventory of the Neotropical flora and implement appropriate conservation strategies in a timely manner. This study aims to answer the question of how long it takes to describe a new species of tree in the Neotropics by calculating the time elapsed from collection of the first specimen to the publication of a new species. It demonstrates that enhancing international collaboration and promoting taxonomy training may be the most efficient ways to accelerate species descriptions.Summary One of the main aspects of taxonomic research is the description of new species. Identifying how to describe new species more efficiently is key to completing the inventory of the Neotropical flora in an era of massive biodiversity loss. Here, we calculate the interval between first specimen collection and publication of new species for a group of 2123 Neotropical trees, and discuss the historical context surrounding specimen collection and new species publication events. Our results reveal that on average, it takes almost 16 years from specimen collection to publication of a new Neotropical tree species, which is considerably shorter than previous estimates for other tropical groups. Peru had the longest average time lags by country, while Haiti had the shortest. The average time lags increased until the early 1900s, when a decrease was observed, with the shortest lags between 1941 and 1960. We found that the majority of the species described more rapidly are from plants collected by a field botanist and described by a herbarium‐based researcher as part of ad hoc collaboration, and the ones collected and described by the same researcher. We demonstrate how political instability and conflict can delay or impede the completion of taxonomic research initiatives in the region. We argue that enhancing international collaboration and training opportunities in Latin American countries, as well as ensuring safe plant collection campaigns, are critical to complete the inventory of the Neotropical flora.

New records and range extension of two deep-sea skate genera,AmblyrajaandNotoraja(Elasmobranchii: Rajiformes), in the southeastern Pacific Ocean

AbstractTwo species of deep-sea skates,Amblyraja frerichsiandNotoraja martinezi, are reported for the first time in Peruvian waters, representing the first record of their respective genera from the country. Earlier,A.frerichsiwas known from both the southwestern Atlantic (off Brazil, Uruguay, and Argentina) and southeastern Pacific (off Chile), whileN.martineziwas known from Costa Rica to Ecuador in the eastern-central and southeastern Pacific. This study contributes to the limited knowledge of deep-sea fish diversity along the South American west coast, and stresses the need of further taxonomic research in the region, particularly in light of the ecological importance of this group of fishes in marine ecosystems and its conservation state worldwide.

DNA Barcoding in Species Delimitation: From Genetic Distances to Integrative Taxonomy.

Over the past two decades, DNA barcoding has become the most popular exploration approach in molecular taxonomy, whether for identification, discovery, delimitation, or description of species. The present contribution focuses on the utility of DNA barcoding for taxonomic research activities related to species delimitation, emphasizing the following aspects:(1) To what extent DNA barcoding can be a valuable ally for fundamental taxonomic research, (2) its methodological and theoretical limitations, (3) the conceptual background and practical use of pairwise distances between DNA barcode sequences in taxonomy, and (4) the different ways in which DNA barcoding can be combined with complementary means of investigation within a broader integrative framework. In this chapter, we recall and discuss the key conceptual advances that have led to the so-called renaissance of taxonomy, elaboratea detailed glossary for the terms specific to this discipline (see Glossary in Chap. 35 ), and propose a newly designed step-by-step species delimitation protocol starting from DNA barcode data that includes stepsfrom the preliminary elaboration of an optimal sampling strategy to the final decision-making process which potentially leads to nomenclatural changes.

DNA Barcode-Based Species Diagnosis with MolD.

Rapid biodiversity loss sets new requirements for taxonomic research, prompting updating some long-established practices to maximize timely documentation of species before they have gone extinct. One of the crucial procedures associated with the description of new taxa in Linnean taxonomy is assigning them a diagnosis, which is an account of the specific features of the taxon, differentiating it from already described species. Traditionally, diagnostic characters have been morphological, but especially in the case of morphologically cryptic species, molecular diagnoses become increasingly important. In this chapter, we provide detailed protocols for molecular taxon diagnosis with the bioinformatic tool MolD which is available as open-source Python code, command-line driven binary, GUI-driven executable for Windows and Mac, and Galaxy implementation. MolD identifies diagnostic combinations of nucleotides (DNCs) in addition to single (pure) diagnostic sites, enabling users to base DNA diagnoses on a minimal number of diagnostic sites necessary for reliable differentiation of taxa.

Plant taxonomy: Cooperation, innovation, productivity

Floristic taxonomic research, looking for constant differences between species, is a very time-consuming and slow process. The flora of the Malay Archipelago is estimated to have 45,000 vascular plant species and the Flora Malesiana project that describes them has completed c. 1/3rd in 75 years. Presently, the flora is heavily threatened because of land use and climate change. We have to speed up the flora writing to understand what will be threatened and how to counter the threats. Innovation using Next Generation Sequencing of DNA to find the species in combination with Image Recognition might help to increase speed. Another aspect is cooperation, more international scientists should be involved, also students and citizens via citizen science projects. Citizens can help to gather information (observations and collecting). Once the flora is better known, monitoring of the flora by regular inventories (done by non-scientists in the Netherlands) helps to see which plants are threatened or become plagues and causes can then be investigated. Monitoring will help to change energy consumption (no more fossil energy), agriculture, industry, and living: improve our climate, and save the planet.

An integrated approach to studying tropical plant diversity – Taxonomic monographs, herbarium specimens and the sweet potato

Recent decades have witnessed a massive increase in data accumulation, but our knowledge of the world’s biodiversity is still fragmentary: data accumulation has not been matched by a parallel taxonomic effort, and many groups of organisms have never been comprehensively studied. In the current context of climate change and biodiversity loss, we need to accelerate taxonomy and species discovery. This, however, requires a good taxonomic and phylogenetic framework, which is lacking for most groups of tropical plants. This contribution discusses the role of botanical monographs in accelerating taxonomy. We argue that the increasingly easier access to data in the world’s herbaria and the availability of DNA sequence data place botanists in an unparalleled position to produce taxonomic monographs, the forefront of taxonomic research. We illustrate the discussion with the results of a monographic study of the genus Ipomoea (Convolvulaceae). We integrated herbarium-based morphological studies with techniques of phylogenetic and genomic analysis of thousands of specimens to develop more robust species delimitation hypotheses and a comprehensive phylogenetic framework. Monographs such as ours have implications for other disciplines beyond taxonomy. We specifically show how it enabled important discoveries related to the origin of sweet potato, a worldwide staple crop.

A New Endemic Smilax (Smilacaceae) from Tafelberg, Suriname, Supported by Morphometric and Phylogenetic Evidence

Abstract— Taxonomy of Smilax in the Neotropics is poorly known with many undescribed species, unresolved synonymy, and regional treatments with conflicting taxon concepts. This issue is amplified in the Guiana Shield, which has arguably received the least amount of taxonomic research in Smilax. Here, we investigate multiple specimens from Tafelberg, Suriname that we hypothesized to represent an undescribed species. We used univariate and multivariate morphometrics to analyze linear measurements and leaf outlines to test if and how Tafelberg specimens differ from those of morphologically similar species in the Guiana Shield, Smilax lasseriana and S. maypurensis. We used a genome skimming approach to sequence and assemble plastomes, which also allowed us to extract plastid loci previously employed in Sanger-based studies and place the putative new species in a phylogeny with expanded taxon sampling. We recovered the Smilax from Tafelberg as more closely related to species with ranges centered in eastern Brazil than to its morphologically hypothesized congeners, S. lasseriana and S. maypurensis. We describe this new species as Smilax tafelbergensis with detailed morphological comparisons to similar taxa, a distribution map, and illustration.

Genomic exploration of Sesuvium sesuvioides: comparative study and phylogenetic analysis within the order Caryophyllales from Cholistan desert, Pakistan

BackgroundThe Aizoaceae family’s Sesuvium sesuvioides (Fenzl) Verdc is a medicinal species of the Cholistan desert, Pakistan. The purpose of this study was to determine the genomic features and phylogenetic position of the Sesuvium genus in the Aizoaceae family. We used the Illumina HiSeq2500 and paired-end sequencing to publish the complete chloroplast sequence of S. sesuvioides.ResultsThe 155,849 bp length cp genome sequence of S. sesuvioides has a 36.8% GC content. The Leucine codon has the greatest codon use (10.6%), 81 simple sequence repetitions of 19 kinds, and 79 oligonucleotide repeats. We investigated the phylogeny of the order Caryophyllales’ 27 species from 23 families and 25 distinct genera. The maximum likelihood tree indicated Sesuvium as a monophyletic genus, and sister to Tetragonia. A comparison of S. sesuvioides, with Sesuvium portulacastrum, Mesembryanthemum crystallinum, Mesembryanthemum cordifolium, and Tetragonia tetragonoides was performed using the NCBI platform. In the comparative investigation of genomes, all five genera revealed comparable cp genome structure, gene number and composition. All five species lacked the rps15 gene and the rpl2 intron. In most comparisons with S. sesuvioides, transition substitutions (Ts) were more frequent than transversion substitutions (Tv), producing Ts/Tv ratios larger than one, and the Ka/Ks ratio was lower than one. We determined ten highly polymorphic regions, comprising rpl22, rpl32-trnL-UAG, trnD-GUC-trnY-GUA, trnE-UUC-trnT-GGU, trnK-UUU-rps16, trnM-CAU-atpE, trnH-GUG-psbA, psaJ-rpl33, rps4-trnT-UGU, and trnF-GAA-ndhJ.ConclusionThe whole S. sesuvioides chloroplast will be examined as a resource for in-depth taxonomic research of the genus when more Sesuvium and Aizoaceae species are sequenced in the future. The chloroplast genomes of the Aizoaceae family are well preserved, with little alterations, indicating the family’s monophyletic origin. This study’s highly polymorphic regions could be utilized to build realistic and low-cost molecular markers for resolving taxonomic discrepancies, new species identification, and finding evolutionary links among Aizoaceae species. To properly comprehend the evolution of the Aizoaceae family, further species need to be sequenced.

Redescription and molecular characterization of Panagrellus ceylonensis (Nematoda, Rhabditida, Panagrolaimidae) from India.

A species of genus Panagrellus was discovered from a wet season form of an oriental common evening brown butterfly Melanitis leda. In this study, a detailed description of Panagrellus ceylonensis is provided including the morphometry, light microscopy and molecular (18S and 28S rDNA genes) studies. Morphological studies on the species agree with original description and characterized by having 12501481m long body in females and 9491305m in males, lateral fields with four longitudinal incisures, lip region continuous and 811 m wide, six offset lips with protruding labial sensilla, neck 124173 m long, excretory pore at the level of basal bulb, vulva post-equatorial (V = 6871), vagina anteriorly orientated with heavily muscled vaginal walls, post-vulval uterine sac 111135 m long or 1.72.6 times as long as the corresponding body diameter, tail conical elongate with an acute terminus in both sexes, spicule 7191 m long, ventrally curved having hooked manubrium and bifurcated lamina tip, lamina ventrally curved with dorsal deflexion at about 60% of spicule length, gubernaculum 2631 m long and well developed. Morphologically, the Indian population of P. ceylonensis does not show a significant difference from the type material of P. ceylonensis in the original description. For molecular studies of this species, the sequence of 18S rDNA is obtained for the first time. Phylogenetic trees based on 18S and 28S rDNA sequences are provided in this study. Additionally, bionomics and global distribution of the species of Panagrellus genus are also discussed. In conclusion, our study provides a comprehensive morphological characterisation and molecular marker sequences of 18S, and 28S genes that can be used to support future taxonomical research on this species and emphasizes the importance of combining molecular data with morphological data to describe the species accurately.

A detailed anatomical approach to taxonomically problematic endemic Seseli L. (Apiaceae) taxa in Türkiye.

In this study, the vegetative anatomical features of the taxa, which were previously named as Seseli gummiferum subsp. ilgazense A.Duran, Ö.Çetin & M.Öztürk and S. paphlagonicum Pimenov & Kljuykov, were compared with a closely related species, S. resinosum Freyn & Sint., which is also endemic in Türkiye. The root, the stem, the leaf segment, the petiole, and the rachis parts were examined anatomically and explained in detail for the first time to discuss the results of recent morphological and molecular studies with the anatomy of the taxa. The results show that S. gummiferum subsp. ilgazense and S. paphlagonicum have anatomically similar characters. However, in terms of the same characters, these taxa quite differ from a closely related species, S. resinosum. The most prominent different characters can be listed as the shape of stems, petioles and rachis, the presence of sclereids in the roots, the collenchyma arrangement of stems and petioles, the surface view of rachis and the sclerenchyma above floem in the stems and rachis. This revisional and detailed descriptive study highlights the importance of anatomy in the taxonomy of Apiaceae, and it is obvious that it will assist future taxonomic research in the genus. RESEARCH HIGHLIGHTS: Vegetative anatomical characters are also taxonomically important as well as the fruit anatomy in the family Apiaceae. The vegetative anatomy supports the molecular data that, the taxa named as S. gummiferum in Türkiye seem to be S. paphlagonicum.

Lactifluus subg. Lactariopsis (Russulales/Basidiomycota) from Brazilian tropical forests

Lactifluus subg. Lactariopsis is a well-supported group of milkcaps occurring predominantly in tropical and subtropical ecosystems. This subgenus contains agaricoid and pleurotoid representatives and is the only group with members containing a secondary velum. The results of taxonomic and phylogenetic research into Lactifluus subg. Lactariopsis collected in Brazilian tropical forests (Amazon, Atlantic Rainforests, and Caatinga biomes) of the North and Northeast is presented here. Two new species are described: Lf. aurantioceraceus in sect. Neotropici, and Lf. reniformis in sect. Multicipites, newly delimited here . In addition, Lf. neotropicus has had its distribution expanded to the Caatinga biome, Lf. dunensis was confirmed in Lf. sect. Neotropici with new records from French Guiana, and Lf. annulifer was re-collected from the type locality. A combined dataset of nuclear rDNA internal transcribed spacer region and nuclear large subunit amplified sequences was analyzed and, based on its phylogenetic hypothesis, the two novel taxa and the new section were confirmed .

Agromyces chromiiresistens sp. nov., Novosphingobium album sp. nov., Sphingobium arseniciresistens sp. nov., Sphingomonas pollutisoli sp. nov., and Salinibacterium metalliresistens sp. nov.: five new members of Microbacteriaceae and Sphingomonadaceae from polluted soil

There are many unidentified microbes in polluted soil needing to be explored and nominated to benefit the study of microbial ecology. In this study, a taxonomic research was carried out on five bacterial strains which were isolated and cultivated from polycyclic aromatic hydrocarbons, and heavy metals polluted soil of an abandoned coking plant. Phylogenetical analysis showed that they belonged to the phyla Proteobacteria and Actinobacteria, and their 16S rRNA gene sequence identities were lower than 98.5% to any known and validly nominated bacterial species, suggesting that they were potentially representing new species. Using polyphasic taxonomic approaches, the five strains were classified as new species of the families Microbacteriaceae and Sphingomonadaceae. Genome sizes of the five strains ranged from 3.07 to 6.60 Mb, with overall DNA G+C contents of 63.57–71.22 mol%. The five strains had average nucleotide identity of 72.38–87.38% and digital DNA-DNA hybridization of 14.0–34.2% comparing with their closely related type strains, which were all below the thresholds for species delineation, supporting these five strains as novel species. Based on the phylogenetic, phylogenomic, and phenotypic characterizations, the five novel species are proposed as Agromyces chromiiresistens (type strain H3Y2-19aT = CGMCC 1.61332T), Salinibacterium metalliresistens (type strain H3M29-4T = CGMCC 1.61335T), Novosphingobium album (type strain H3SJ31-1T = CGMCC 1.61329T), Sphingomonas pollutisoli (type strain H39-1-10T = CGMCC 1.61325T), and Sphingobium arseniciresistens (type strain H39-3-25T = CGMCC 1.61326T). Comparative genome analysis revealed that the species of the family Sphingomonadaceae represented by H39-1-10T, H39-3-25T, and H3SJ31-1T possessed more functional protein-coding genes for the degradation of aromatic pollutants than the species of the family Microbacteriaceae represented by H3Y2-19aT and H3M29-4T. Furthermore, their capacities of resisting heavy metals and metabolizing aromatic compounds were investigated. The results indicated that strains H3Y2-19aT and H39-3-25T were robustly resistant to chromate (VI) and/or arsenite (III). Strains H39-1-10T and H39-3-25T grew on aromatic compounds, including naphthalene, as carbon sources even in the presence of chromate (VI) and arsenite (III). These features reflected their adaptation to the polluted soil environment.

Redescription of both Goniogryllus bistriatus Wu & Wang, 1992 and Callogryllus yunnanus Wu & Zheng, 1992 (Orthoptera: Gryllidae, Gryllinae).

Goniogryllus bistriatus Wu & Wang, 1992 was described at the end of the last century, based on the female holotype, and there have been no further studies or reports related to this species since then. Callogryllus yunnanus Wu & Zheng, 1992 also has a similar situation. Although the holotype is a male, its external genitalia have been lost. These issues pose obstacles to subsequent taxonomic research. Recently, we have successively discovered these two species in Huize County, Yunnan Province, China. To address the aforementioned taxonomic problems, this article describes the male specimens of the G. bistriatus and redescribes the female; meanwhile, since the original description of C. yunnanus lacked male genital characteristics, and we have also conducted a complete redescription of this species based on the new specimen.

Taxonomic research, collections and associated databases – and the changing science scene in New Zealand

​

Putting the F into FBD analysis: tree constraints or morphological data?

AbstractThe fossilized birth–death (FBD) process provides an ideal model for inferring phylogenies from both extant and fossil taxa. Using this approach, fossils are directly integrated into the tree, leading to a statistically coherent prior on divergence times. Since fossils are typically not associated with molecular sequences, additional information is required to place fossils in the tree. We use simulations to evaluate two different approaches to handling fossil placement in FBD analyses: using topological constraints, where the user specifies monophyletic clades based on established taxonomy, or using total‐evidence analyses, which use a morphological data matrix in addition to the molecular alignment. We also explore how rate variation in fossil recovery or diversification rates impacts these approaches. We find that the extant topology is well recovered under all methods of fossil placement. Divergence times are similarly well recovered across all methods, with the exception of constraints which contain errors. We see similar patterns in datasets which include rate variation, however, relative errors in extant divergence times increase when more variation is included in the dataset, for all approaches using topological constraints, and particularly for constraints with errors. Finally, we show that trees recovered under the FBD model are more accurate than those estimated using non‐time calibrated inference. Overall, we show that both fossil placement approaches are reliable even when including uncertainty. Our results underscore the importance of core taxonomic research, including morphological data collection and species descriptions, irrespective of the approach to handling phylogenetic uncertainty using the FBD process.

Relevance of molecular systematics in insect pest management

Relevance of molecular systematics in insect pest management

Lepidoptera research in Puerto Rico: Reconnecting with historical legacies to guide future priorities

AbstractThe Caribbean archipelago of Puerto Rico supports a diverse flora and fauna and is located in a region characterized by complex socio‐economic and environmental change. The diversity of entomofauna across Puerto Rico has received considerable attention in wide‐scale research over the last century, with particular emphasis on the order Lepidoptera as the subject of substantial taxonomic and ecological surveys. However, much of this work is incomplete, outdated, or has been obscured in gray literature. Thus, our primary objectives were to contextualize the role of past research in the current understanding of Puerto Rican Lepidoptera and to outline an agenda for future research. Specifically, we provide an overview of taxonomic, ecological, agricultural, and conservation Lepidoptera research in Puerto Rico and highlight key studies and historical datasets. We found that, despite a strong taxonomic legacy, native moth taxonomy remains poorly understood, except for a few major pests. Further, much of the recent Lepidoptera research has focused on short‐term evaluations of agricultural pests, necessitated by immediate economic needs. The current ecological status of Lepidoptera on the islands is unknown. Therefore, prioritizing ecological research could provide timely insight for understanding changing Lepidoptera diversity and distribution and for conserving this biologically and economically significant group. Greater emphasis on long‐term monitoring and digitization of museum collections would be particularly useful for quantifying past and forecasting future impacts of global change.Abstract in Spanish is available with online material.