Molecular Phylogenetic Research Articles

DNA sequencing of topotypes helps delineate species distributions in the Ischnocnema verrucosa complex (Anura, Brachycephalidae)

As many new evolutionary lineages are being discovered and formally named, sequencing topotypes when holotypes are not available becomes essential for taxonomy. This study uses a DNA-taxonomy approach to sequence new populations of the Ischnocnema verrucosa species complex (Brazilian Wart Frogs) from different locations, including, for the first time, individuals from the type localities. Phylogenetic analysis of the mitochondrial 16S gene recovered a monophyletic Ischnocnema verrucosa species series composed of three main clades. The most recent common ancestor was estimated to be 33.76 million years ago, and diversification within the three main clades occurred primarily during the Miocene. We delimited eight species-level lineages with high levels of sequence divergence (7% to 16%). Our study highlights the importance of DNA taxonomy and the necessity of protecting and sequencing topotypes in taxonomic studies. Our study also contributes to the conservation and understanding of the genus Ischnocnema and the biodiversity of the Brazilian Atlantic Forest region.

Feline Hemotropic Mycoplasma Species of Apparently Healthy Domestic Cats in Konya Province of Türkiye

Feline hemotropic mycoplasmosis is an emerging infectious disease in domestic cats caused by a group of hemotropic Mycoplasma species, including three main species: Mycoplasma hemofelis (Mhf), Candidatus Mycoplasma hemominutum (CMhm), and Candidatus Mycoplasma turicensis (CMt). The primary objective of this investigation was to ascertain the molecular prevalence and characterization of hemotropic mycoplasmas in domestic cats from twenty-three districts of Konya province in Türkiye. For this purpose, 384 apparently healthy cats belonging to different breeds were enrolled in this study. The molecular prevalence of Mycoplasma spp. in cats was 9.4%, and the identified species included Mhf, Mycoplasma hemocanis (Mhc), CMt, and CMhm. The molecular prevalence was not significantly associated with district, breed, or gender (p > 0.05) but was significantly associated with age and ownership status (p < 0.05). The study found that all cats with Mycoplasma spp. were older than one year and that the infection had a higher prevalence in stray cats than in owned cats (p < 0.05). Although there are studies conducted in different provinces, data on the molecular and phylogenetic characterization of the species causing feline hemotropic mycoplasmosis are scarce in Türkiye. This study, which provides updated data concerning the molecular characterization and phylogeny of hemotropic Mycoplasma species of cats in Türkiye, revealed the Mycoplasma spp. molecular prevalence in Konya province for the first time and provided remarkable findings that will fill the scientific gap in the country. The molecular characterization of these hemotropic mycoplasmas is crucial for understanding their epidemiology and developing effective diagnostic and treatment strategies for feline hemotropic mycoplasmosis. It is anticipated that the data from the study will raise awareness among pet owners, veterinarians, and healthcare professionals of feline hemotropic Mycoplasma agents with zoonotic potential.

Molecular phylogenetic and biogeographic evidence of Lepidagathis Willd. (Acanthaceae, Barlerieae) focusing on Indian endemics

Lepidagathis Willd., a genus belonging to the Acanthaceae family, is primarily distributed in tropical and subtropical regions worldwide, encompassing approximately 153 species. While considerable morphological research has been conducted on Lepidagathis, it has not completely dispelled taxonomic ambiguities and conflicting interpretations. Molecular analysis emerges as a valuable tool for resolving these taxonomic uncertainties, but the availability of nucleotide sequence data for Lepidagathis has been limited thus far. This study delivers a phylogenetic analysis of Lepidagathis species, utilizing both chloroplast and nuclear regions. The results of Bayesian Inference and Maximum Likelihood phylogenetic analyses consistently segregate the studied Lepidagathis species into two principal clades, denoted as Clade A and Clade B. Notably, this analysis firmly positions the Indian endemic Lepidagathis within Clade A, supported by robust statistical evidence. Furthermore, our biogeographical analysis strongly suggests that the origin of Lepidagathis might be traced back to Eurasia. This research establishes a foundational molecular phylogeny of Lepidagathis, offering valuable insights for future taxonomic investigations. Additionally, it sheds light on the evolutionary history and biogeographical origins of the Lepidagathis genus.

First report of leaf spot disease caused by Fusarium asiaticum on Lonicera caerulea L. in Heilongjiang Province, China.

Heilongjiang is the largest province with the small, cultivated fruit plant, blue honeysuckle (Lonicera caerulea L.), in China (Sun et al. 2024). Between September 2022 and September 2023, a leaf spot disease was observed on about 10 percent of blue honeysuckles of the 'Lanjingling' cultivar grown in a 6.66-ha field in Mudanjiang (129.38°E, 44.59°N), Heilongjiang Province, China. The typical symptoms include a few small brown sunken leaf spots (approximately 2 mm) in the fruiting stage that gradually expand into larger brown sunken lesions (approximately 10 mm) in the senescence stage (Fig. S1). Small 3-4-mm segments of infected tissue from 100 randomly selected leaf samples with typical symptoms were surface sterilized with 75% ethanol and 5% sodium hypochlorite, rinsed in sterile distilled water, and transferred to 9-cm Petri dishes containing potato dextrose agar (PDA) after drying. Finally, 10 isolated fungi were obtained through single-spore culture on PDA, and their conidia displayed a morphology consistent with Fusarium spp. (Zheng et al. 2023), and no other fungi were isolated. The fungal colonies on PDA were pink to dark red with fluffy aerial mycelium and pigmentation (Fig. S2). Microconidia were not observed, and the macroconidia of fungi had 2 to 6 septa, which were slender, sickle-shaped to nearly curved, with an average size of 38.83 (21.30 to 55.20) × 3.87 (2.70 to 6.60) μm (n = 50) on carnation leaf agar (Fig. S3). Genomic DNA was extracted from the representative isolate LD-245 for molecular verification, and PCR amplification was performed with ITS1/ITS4 (White et al. 1990), RPB2-5F2/RPB2-7CR (Liu et al. 1999), and EFl/EF2 (O'Donnell et al. 1998) primers. Sequences of LD-245 ITS (OR565903), RPB2 (OR584061), and TEF (PP965657) revealed 99 to 100% (494/494, 722/726, and 654/654) of identity with Fusarium asiaticum (MT322117, MH582121, and MT330257). Phylogenetic tree was constructed based on the concatenated sequences of ITS, RPB2, and TEF genes, and LD-245 was clustered with F. asiaticum (Fig. S4, Table S1). Therefore, based on the morphological characteristics and molecular phylogeny, LD-245 was identified as F. asiaticum. Six two-year-old healthy plants of the 'Lanjingling' cultivar were selected for a pathogenicity test. Three plants were inoculated with LD-245 conidial suspension (1 × 106 spores/ml) or with sterile water as an experimental control. All plants were cultured in a greenhouse (28℃, 75% relative humidity, 12 h light and dark cycle), and each experiment was replicated three times. Typical leaf spot symptoms were observed on inoculated leaves after 10 days (Fig. S5), whereas no symptoms were detected on water-treated leaves. The pathogens re-isolated from infected leaves displayed the same morphological and molecular traits as the initial isolate, and were again identified as F. asiaticum, confirming Koch's postulate. F. asiaticum was previously reported on giant elephant's ear (Alocasia macrorrhizos) (Zheng et al. 2023), causing leaf spot disease in China. This study is the first report of blue honeysuckle leaf spot disease caused by F. asiaticum in China. China has the largest blue honeysuckle cultivation area globally, and the production of blue honeysuckle with horticultural value is important for growers (Sun et al. 2024). Therefore, we hope researchers can develop efficient measures to manage emerging plant diseases in the future.

Molecular Variation and Phylogeny of Thymidylate Kinase Genes of Candidatus Phytoplasma ziziphi from Different Resistant and Susceptible Jujube Cultivars in China

The thymidylate kinase (tmk) gene is indispensable for the proliferation and survival of phytoplasma. To reveal the molecular variation and phylogeny of the tmk genes of Candidatus phytoplasma ziziphi, in this study, the tmk genes of 50 phytoplasma strains infecting different resistant and susceptible jujube cultivars from different regions in China were amplified and analyzed. Two sequence types, tmk-x and tmk-y, were identified using clone-based sequencing. The JWB phytoplasma strains were classified into three types, type-X, type-Y, and type-XY, based on the sequencing chromatograms of the tmk genes. The type-X and type-Y strains contained only tmk-x and tmk-y genes, respectively. The type-XY strain contained both tmk-x and tmk-y genes. The type-X, type-Y, and type-XY strains comprised 42%, 12%, and 46% of all the strains, respectively. The type-X and type-XY strains were identified in both susceptible and resistant jujube cultivars, while type-Y strain was only identified in susceptible cultivars. Phylogenetic analysis indicated that the tmk genes of the phytoplasmas were divided into two categories: phylo-S and phylo-M. The phylo-S tmk gene was single-copied in the genome, with an evolutionary pattern similar to the 16S rRNA gene; the phylo-M tmk gene was multi-copied, related to PMU-mediated within-genome transposition and between-genome transfer. Furthermore, the phylogenetic tree suggested that the tmk genes shuttled between the genomes of the Paulownia witches’ broom phytoplasma and JWB phytoplasma. These findings provide insights into the evolutionary and adaptive mechanisms of phytoplasmas.

Molecular phylogeny of Boninia (Platyhelminthes: Polycladida), with description of a new species from the Pacific coasts of Panama.

Mesopsammic polyclad members in the family Boniniidae have attracted attention in terms of their evolutionary shifts of microhabitat and their unique morphology such as a pair of pointed tentacles extending from the anterolateral margins and prostatoid organs harbouring stylets. Here, we establish a new species of this family as Boninia panamensis sp. nov. from the Pacific coasts of Panama, based on its morphological characteristics of (i) four cerebral and 61-80 marginal eyespots, (ii) two prostatoid organs located anterior and posterior to the penis papilla, and (iii) two uterine canals departing from the anterior part of the Lang's vesicle. We also report Boninia cf. uru from Hawai'i, USA, based on its morphological identity with B. uru from Okinawa, Japan, along with their genetic distances for the partial cytochrome c oxidase subunit I (COI ) sequences, which were beyond the range of intraspecific differences observed in congeners in this study. Boninia oaxaquensis is also reported from Panama as a new locality for the species. Involving the above-mentioned three species sequenced herein, we reconstructed molecular phylogenetic trees of Boninia based on the four gene markers (18S rDNA, 28S rDNA, 16S rDNA and COI ). Our phylogenetic trees indicated the synapomorphy within the genus Boninia of the small numbers of stylets (2-4) and the connection route of the uterine canals to the Lang's vesicle. The results also showed a characteristic distribution pattern in which pairs of species in distinct lineages occurred sympatrically with different microhabitats, as observed in Boninia uru and Boninia yambarensis in Okinawa and B. panamensis sp. nov. and B. oaxaquensis in Panama. In addition, we discuss possible speciation pathways in this genus based on the tree topology. ZooBank: urn:lsid:zoobank.org:pub:D414BACD-C14A-4B34-8AF9-7ACBA28F46D0.

Transcriptomic analysis identifies enrichment of cAMP/PKA/CREB signaling in invasive lobular breast cancer

ObjectiveInvasive lobular breast cancer (ILC) is the most common special type of breast cancer and has unique clinicopathological and molecular hallmarks that differentiate it from the more common invasive carcinoma—no special type (NST). Despite these differences, ILC and NST are treated as a single entity and there is a lack of ILC-targeted therapies. To fill this gap, we sought to identify novel molecular alterations in ILC that could be exploited for targeted therapies.MethodsDifferential gene expression and Geneset Enrichment and Variation analyses were performed on RNA-seq data from three large public breast cancer databases—the Sweden Cancerome Analysis Network-Breast (SCAN-B; luminal A ILC N = 263, luminal A NST N = 1162), The Cancer Genome Atlas (TCGA; luminal A ILC N = 157, luminal A NST N = 307) and Molecular Taxonomy of Breast Cancer International Consortium (METABRIC; luminal A ILC N = 65, luminal A NST N = 533). Pathways enriched in overlapping differentially expressed genes from these datasets were clustered using Jaccard similarity to identify pathways enriched in ILC. The cAMP/PKA/CREB signaling was studied in ILC, ILC-like and NST cell lines and patient-derived organoids (PDOs) using forskolin, an activator of the pathway.ResultsClinicopathological features of patients with ILC and NST in SCAN-B were similar to prior population-based studies. There was a consistent pattern of up-regulation of cAMP/PKA/CREB related signaling in ILC compared to NST in SCAN-B, TCGA and METABRIC. Treatment with forskolin resulted in a greater increase in phospho-CREB in ILC cell lines and organoids than NST. CRISPR deletion of CDH1 in NST cell lines did not alter response of cells to forskolin as measured by phospho-CREB. Forskolin treatment caused growth inhibition in ILC and NST, with ILC cell lines being more sensitive to forskolin-mediated growth inhibition.ConclusionIn three separate datasets, cAMP/PKA/CREB signaling was identified to be higher in ILC than NST. This in silico finding was validated in cell line and organoid models. Loss of CDH1 was not sufficient to mediate this phenotype. Future studies should investigate the mechanisms for differential cAMP/PKA/CREB signaling and the potential for therapeutic targeting in patients with ILC.Graphical abstract

Integrative Systematics Reveals Cryptic Diversity in Paraphrynus Whip Spiders (Amblypygi: Phrynidae) from Southwestern North America

Due to their continuous growth, reclusive nature, and low vagility, the distributions and species limits of many whip spiders (Amblypygi Thorell, 1883) remain poorly understood, and much cryptic diversity remains unrecognized. Past attempts to separate the historical “forms” of Paraphrynus Moreno, 1940 into morphologically diagnosable species resulted, for example, in the division of Paraphrynus mexicanus (Bilimek, 1867) into three species—the nominotypical form, Paraphrynus cubensis Quintero, 1983, and Paraphrynus carolynae Armas, 2012. Nevertheless, the limitations of conservative morphology continue to hinder progress towards clarifying the diversity of Paraphrynus. One such example concerns P. carolynae, distributed from Arizona to central Mexico as currently defined. Through the acquisition of new, freshly collected material, the discovery of novel morphological characters, and molecular systematics analyses, it became apparent that P. carolynae comprises at least two morphologically diagnosable species. In this present contribution, the northernmost population of P. carolynae occurring in Arizona and California is described as a new species, Paraphrynus tokdod, sp. nov., raising the number of species in the genus to 22. This investigation also revealed more variation than expected in the secondary spine counts of the pedipalps and the trichobothrial counts of leg IV, previously used for species delimitation in Paraphrynus, suggesting that such characters should be used with caution.

Four New Families of Arbuscular Mycorrhizal Fungi Within the Order Glomerales

Based on molecular phylogenetic analyses, and also considering morphological characters, four new families are separated from the family Glomeraceae within the order Glomerales and the class Glomeromycetes. The revised family Glomeraceae comprises only four genera: the type genus Glomus, Complexispora, Sclerocarpum and Simiglomus. Septoglomeraceae fam. nov. comprises, besides Septoglomus, Funneliformis, Funneliglomus, Blaszkowskia and Viscospora. Sclerocystaceae fam. nov. is represented by the type genus Sclerocystis but also by Halonatospora, Oehlia, Parvocarpum, Rhizoglomus and Silvaspora. Kamienskiaceae fam. nov. encompasses Kamienskia, Microkamienskia and Epigeocarpum. Finally, Dominikiaceae fam. nov. includes the genera Dominikia, Macrodominikia gen. nov. Microdominikia, Nanoglomus and Orientoglomus. The genera Oehlia and Halonatospora form two other clades well separated from Silvaspora, Sclerocystis and Rhizoglomus and might represent two further families within Glomerales. This deeper separation is, in our opinion, fully supported by molecular phylogeny, but in view of the low numbers of taxa, the separation is not yet proposed at this stage of research progress.

Discovery of the genus Dishkeya (Lepidoptera: Tischeriidae) in Honduras: unveiling the unique traits of D. gouaniae

This publication records the endemic genus Dishkeya Stonis in Honduras and, for the first time, documents the female genitalia and leaf mines of D. gouaniae (Stonis & Diškus). Additionally, it provides the first barcodes and molecular considerations regarding the genus Dishkeya. The article is illustrated with 34 figures, including photographs of male and female genitalia, leaf mines, exuviae, and a molecular tree based on mtDNA COI sequences.

Multigene phylogenetics of Sargassum (Phaeophyceae) revealed low molecular diversity in contrast to high morphological variability in the NE Atlantic Ocean.

Sargassum species play a key role in habitat formation in tropical and subtropical regions; however, species identification has been hampered by the phenological plasticity exhibited in response to environmental conditions and life history. Molecular phylogenetics has challenged taxa circumscriptions and proven critical in delimiting species in this genus. Yet, the Atlantic species of Sargassum remain poorly understood, and recent studies have shown low molecular diversity between the species in the NW Atlantic. Here, we expand the taxon sampling to the NE Atlantic to assess the diversity of Sargassum in the Atlantic basin, based on a comprehensive morphological and multigene approach. We selected genes commonly used in delineating species in this genus (ITS2, rbcLS, cox3, mtsp) and explored additional markers (cox2, nad6, psbC, clpC, atpB) to infer the phylogenetic relationships between the morphospecies observed in the NE Atlantic. Phylogenetic analyses using single-gene and multigene alignments including 185 new sequences confirmed the low molecular diversity and supported the distinction of a single clade in Sargassum section Sargassum of N Atlantic benthic species. In contrast, morphological analysis resulted in the identification of 10 species and three new morphospecies that we described here but opt not to equate to species until further molecular evidence is available. Our results were congruent with previous findings from the NW Atlantic and highlight the morphological and ecological diversity of Sargassum in the Atlantic. These results suggest a recent colonization and incipient speciation of Sargassum in the Atlantic basin and showcase the need of further high-throughput analyses.

Biofertilizer based on <i>Agrobacterium </i>as a key to food security

Background: The concept of food security is contingent upon the fulfillment of two fundamental requirements: physiological and socioeconomic. The former comprises providing sustenance that is both safeguarded and enhanced in line with people’s nutritional needs and priorities, whereas the latter includes the mechanisms by which these needs are supplied. The objective is to ensure a state of robust and healthy well-being. As a sustainable solution, biofertilizers play a pivotal role in addressing the challenges of food security. Biofertilizers represent a cost-effective and environmentally friendly solution, with the potential to enhance soil productivity through nitrogen fixation. They also enhance crop yield by increasing the concentration of nutrients. Access to functional foods derived from biofertilizer-enhanced yields may contribute to improved dietary diversification and overall well-being. Objective: The objective is to isolate and screen the most active nitrogen-fixing bacterium as a basis to a new biofertilizer. Methods: The isolation of nitrogen-fixing bacteria was conducted using the soil sowing technique. The selection of nitrogen-fixing bacteria was based on their morphophysiological characteristics. Bacterial growth was evaluated by viable cell count. Cultivation of the selected bacterium occurred in both flasks (on a shaker) and a bioreactor to compare growth conditions. The stimulatory effect of the selected bacterium on seed germination was assessed based on the final germination rate. The selected bacterium identified through molecular taxonomy. Results: A total of 100 pure cultures were isolated, from which nitrogen-fixing bacteria were selected. The cultivation conditions for these bacteria were optimized regarding pH, temperature and process duration in a flask on a shaker. Strain NB4 exhibited the most favorable development under optimal settings. Additionally, cultivation parameters for this strain were optimized in a laboratory bioreactor. Notably, a bacterial liquid culture water solution comprising 1.5% strain NB4 facilitated complete germination of wheat (Triticum aestivum L.), seeds and produced high-quality sprouts. The 16S rRNA gene sequence of strain NB4 was submitted to the GenBank database under accession number MT670424.1, identifying it as Agrobacterium Pusense RP 1. Conclusion: This research aimed to develop an effective biofertilizer to tackle the pressing issue of food security. The project’s cornerstone was Agrobacterium pusense RP 1, nitrogen-fixing strain isolated and identified through rigorous research. Keywords: Isolation and identification of nitrogen-fixing bacteria, cultivation in bioreactor, germination of wheat seeds, Agrobacterium pusense.

Biology, morphometric and integrative taxonomy of litchi fruit borer, Conopomorpha sinensis Bradley, 1986: A major pest of litchi (Litchi chinensis Sonn.)

Abstract Conopomorpha sinensis (Lepidoptera: Gracillariidae), commonly known as the litchi fruit borer, is a devastating pest of litchi, leading to substantial economic losses in fruit production. The present study was incepted to supplement updated information on biology, morphometrics, integrative taxonomy, and phylogenetic analysis of C. sinensis. The duration of developmental stages such as egg, larval, pre-pupal, pupal, male and female adult lasts for 3.45 ± 1.13, 11.10 ± 2.52, 2.05 ± 0.51, 5.85 ± 0.88, 5.55 ± 1.00, and 9.00 ± 1.12 days, respectively. The average fecundity was 33.10 ± 6.84 eggs/female. The head capsule width for five larval instars was 0.11 ± 0.01, 0.18 ± 0.02, 0.34 ± 0.01, 0.58 ± 0.04, and 0.64 ± 0.06 mm, respectively. Phylogenetic analysis revealed distinct species-groups formed by C. sinensis with other fruit borer species considered (C. cramerella, C. litchiella Bradley, and Thaumatotibia batrachopa (Meyrick)). Understanding the life cycle of C. sinensis and its correct identification is crucial for targeted pest control strategies. Traditional and molecular taxonomy assist in rapid and accurate species identification and understanding of the evolutionary relationships among Conopomorpha species.

Prognostic nomograms for young breast cancer: A retrospective study based on the SEER and METABRIC databases.

Young breast cancer (YBC) is a subset of breast cancer that is often more aggressive, but less is known about its prognosis. In this study, we aimed to generate nomograms to predict the overall survival (OS) and breast cancer-specific survival (BCSS) of YBC patients. Data of women diagnosed with YBC between 2010 and 2020 were obtained from the Surveillance, Epidemiology, and End Results (SEER) database. The patients were randomly allocated into a training cohort (n = 15,227) and internal validation cohort (n = 6,526) at a 7:3 ratio. With the Cox regression models, significant prognostic factors were identified and used to construct 3-, 5-, and 10-year nomograms of OS and BCSS. Data from the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) database were used as an external validation cohort (n = 90). We constructed nomograms incorporating 10 prognostic factors for OS and BCSS. These nomograms demonstrated strong predictive accuracy for OS and BCSS in the training cohort, with C-indexes of 0.806 and 0.813, respectively. The calibration curves verified that the nomograms have good prediction accuracy. Decision curve analysis demonstrated their practical clinical value for predicting YBC patient survival rates. Additionally, we provided dynamic nomograms to improve the operability of the results. The risk stratification ability assessment also showed that the OS and BCSS rates of the low-risk group were significantly better than those of the high-risk group. Here, we generated and validated more comprehensive and accurate OS and BCSS nomograms than models previously developed for YBC. These nomograms can help clinicians evaluate patient prognosis and make clinical decisions.

Genome sequencing in the management of myelodysplastic syndromes and related disorders.

Myeloid neoplasms originate from the clonal proliferation of hematopoietic stem cells, which is driven by the acquisition of somatic genetic mutations. Within these disorders, myelodysplastic syndromes (MDS) are specifically characterized by morphologic abnormalities (dysplasia) and impaired maturation of myeloid precursors (ineffective hematopoiesis), resulting in peripheral blood cytopenia. Several studies have advanced the field of MDS, with a few landmark papers leading to a paradigm shift, opening new avenues of research and enabling a molecular revolution. These seminal papers include the first description of the 5q- syndrome, the identification of somatic mutations of TET2 in myeloid neoplasms, the detection of common pathway mutations in the splicing machinery, and the discovery of clonal hematopoiesis. The somatic genomic landscape of MDS is now well-defined. Genes that are recurrently mutated include epigenetic regulators, as well as genes of RNA splicing machinery, transcription regulation, DNA repair control, cohesin complex, and signal transduction. Furthermore, several disorders with a germline genetic predisposition to MDS have been identified, collectively accounting for up to 15% of all MDS cases. Genomic profiling can significantly improve the diagnostic approach to MDS, allowing the identification of distinct nosologic entities such as SF3B1-mutant or TP53-mutant MDS. The Molecular International Prognostic Scoring System for MDS (IPSS-M) has already proven to be a valuable tool for individualized risk assessment and treatment decisions. In addition, the recently developed molecular taxonomy of MDS will likely facilitate the implementation of precision medicine approaches for these disorders. This will necessitate the establishment of specialized infrastructures within public health systems, involving close collaboration between healthcare institutions, academia, and the life sciences industry.

Whole-genome-based taxonomy as the most accurate approach to identify Flavobacterium species.

The genus Flavobacterium comprises a diversity of species, including fish pathogens. Multiple techniques have been used to identify isolates of this genus, such as phenotyping, PCR genotyping, and in silico whole-genome taxonomy. In this study, we demonstrate that whole-genome-based taxonomy, using Average Nucleotide Identity (ANI) and molecular phylogeny, is the most accurate approach for Flavobacterium species. We obtained various isolated strains from official collections; these strains had been previously characterized by a third party using various identification methodologies. We analyzed isolates by PCR genotyping using previously published primers targeting gyrB and gyrA genes, which are supposedly specific to the genus Flavobacterium and F. psychrophilum, respectively. After genomic analysis, nearly half of the isolates had their identities re-evaluated: around a quarter of them were re-assigned to other genera and two isolates are new species of flavobacteria. In retrospect, the phenotyping method was the least accurate. While gyrB genotyping was accurate with the isolates included in this study, bioinformatics analysis suggests that only 70% of the Flavobacterium species could be appropriately identified using this approach. We propose that whole-genome taxonomy should be used for accurate Flavobacterium identification, and we encourage bacterial collections to review the identification of isolates identified by phenotyping.

The carrot cyst nematode Heterodera carotae: a major plant-parasitic nematode requiring more investigation

Summary The present study reviews the knowledge to date on the carrot cyst nematode Heterodera carotae, which has become the primary threat to the carrot sector following the withdrawal of the last chemical soil fumigants in Europe. A keyword co-occurrence network was used to structure this review into five research areas: i) biology and epidemiology of H. carotae; ii) molecular identification and phylogeny; iii) population genetics and genomics; iv) control methods and strategies; and v) root exudates and hatching stimulation. Our findings indicate that H. carotae is an under-studied plant-parasitic nematode species, with several identified alternative control methods that require further investigation.

Molecular phylogeny reveals a new genus and species of freshwater mussel (Bivalvia, Unionidae, Gonideinae) from Jiangxi, China

Freshwater mussels of the tribe Gonideini (Bivalvia: Unionidae: Gonideinae) constitute one of the most taxonomically diverse groups and serve as keystone species in riverine and lacustrine ecosystems across East Asia. A new genus and species of Gonideini (Bivalvia: Unionidae) is described from Jiangxi, China, as Pseudopostolata angulagen. et sp. nov. based on an integrative analysis of shell morphology and molecular data. The validity of the new genus and species is supported by distinct conchological features: a short, rounded anterior; a long, wide posterior; a slightly downward-curved dorsal margin; and a distinctly obtuse angle at the center of the posterior margin. The multi-locus (COI + 16S rRNA + 28S rRNA) phylogeny showed that the species formed a monophyletic group in the tribe Gonideini of the subfamily Gonideinae. Pseudopostolata angulagen. et sp. nov. is identified as the sister group to a clade comprising the genera Postolata, Cosmopseudodon, Obovalis, Ptychorhynchus, Parvasolenaia, and Koreosolenaia. We emphasize the significant morphological convergence in freshwater mussels, particularly within Gonideini, highlighting the necessity of an integrated taxonomic approach for accurate generic classification of this group.

Pollen morphology and fruit anatomy of the enigmatic monotypic genus Dicranocarpus (Coreopsideae, Asteraceae)

Dicranocarpus is a monotypic genus endemic to the Chihuahuan Desert with atypical attributes among species of tribe Coreopsideae. Phylogenetic position of Dicranocarpus parviflorus has been controversial. A molecular phylogeny showed that the taxon was closely related to Dahlia; however, further analyses with a wider sampling of Dahlia, also including Hidalgoa, identified the genus in a more distant clade. The objective of this study is to gather anatomical attributes from the cypselae as well as palynological characters along with macromorphology to determine whether Dicranocarpus shares characters with these genera in Coreopsideae. Our results show that although the pollen of D. parviflorus does not possess attributes that distinguish it from the rest of the tribe Coreopsideae, they were useful to confirm its membership in the tribe. The cypselae anatomy identified that D. parviflorus has characters of taxonomic value that differentiate this species from the rest of the Coreopsideae. The three most significant novel characters in Dicranocarpus were in the outer mesocarp, consisting of tracheoidal-like cells forming irregular rows up to 250 μm in length, an aerenchyma in the middle mesocarp, and the lack of phytomelanin and calcium oxalate crystals. Furthermore, the results of the phytomelanin patterns in the studied taxa highlight the need for further anatomical studies of the cypselae to fully understand the evolution of phytomelanin deposition in the tribe Coreopsideae and even in the Heliantheae Alliance. Macromorphological, palynological and anatomical attributes of the cypsela in Dicranocarpus were not shared with Dahlia. Moreover, the sexual condition of the disc and ray florets shared with Hidalgoa has evolved independently in lineages of Asteraceae.

Do morphometric data improve phylogenetic reconstruction? A systematic review and assessment

BackgroundIsolating phylogenetic signal from morphological data is crucial for accurately merging fossils into the tree of life and for calibrating molecular dating. However, subjective character definition is a major limitation which can introduce biases that mislead phylogenetic inferences and divergence time estimation. The use of quantitative data, e.g., geometric morphometric (GMM; shape) data can allow for more objective integration of morphological data into phylogenetic inference. This systematic review describes the current state of the field in using continuous morphometric data (e.g., GMM data) for phylogenetic reconstruction and assesses the efficacy of these data compared to discrete characters using the PRISMA-EcoEvo v1.0. reporting guideline, and offers some pathways for approaching this task with GMM data. A comprehensive search string yielded 11,123 phylogenetic studies published in English up to Oct 2023 in the Web of Science database. Title and abstract screening removed 10,975 articles, and full-text screening was performed for 132 articles. Of these, a total of twelve articles met final inclusion criteria and were used for downstream analyses.ResultsPhylogenetic performance was compared between approaches that employed continuous morphometric and discrete morphological data. Overall, the reconstructed phylogenies did not show increased resolution or accuracy (i.e., benchmarked against molecular phylogenies) as continuous data alone or combined with discrete morphological datasets.ConclusionsAn exhaustive search of the literature for existing empirical continuous data resulted in a total of twelve articles for final inclusion following title/abstract, and full-text screening. Our study was performed under a rigorous framework for systematic reviews, which showed that the lack of available comparisons between discrete and continuous data hinders our understanding of the performance of continuous data. Our study demonstrates the problem surrounding the efficacy of continuous data as remaining relatively intractable despite an exhaustive search, due in part to the difficulty in obtaining relevant comparisons from the literature. Thus, we implore researchers to address this issue with studies that collect discrete and continuous data sets with directly comparable properties (i.e., describing shape, or size).