Search Results (31)

Chionea is classified within the Tipuloidea superfamily and predominantly inhabits cold regions. However, its phylogenetic relationships remain contentious. In this study, the first three mitogenomes of Chionea (Diptera: Limoniidae) sampled in northeastern China (Jilin region) were sequenced, and their phylogenetic relationships were reconstructed by integrating these sequences with 30 additional Tipuloidea mitogenomes retrieved from NCBI. Unlike other Tipuloidea species, which are predominantly distributed in relatively warmer regions, this research investigates whether positive selection has acted on the mitogenomes of these three Chionea species due to environmental pressures, thereby elucidating key evolutionary drivers for Chionea. The three mitogenomes of Chionea exhibit characteristic features typical of insect mitogenomes, comprising 13 protein-coding genes (PCGs), 2 ribosomal RNA genes (16S rRNA and 12S rRNA), 22 transfer RNA genes (tRNA), and a single non-coding control region (D-loop). Notably, the secondary structure of trnS1 lacks the DHU arm in all three samples, and UUA (Leu) emerges as the most frequently utilized codon. Furthermore, the COX2 and ND5 genes utilize incomplete stop codons “T”. Utilizing these 13 PCGs, we reconstructed the internal phylogenetic relationships within Tipuloidea, revealing that Chionea tianhuashana and C. sphaerae form sister branches, while (C. tianhuashana + C. sphaerae) constitutes a sister branch to C. crassipes. Moreover, our analysis confirms the monophyly of Tipulidae, Tipula, and Nephrotoma as well as the polyphyly of Tipulinae, Chioneinae, and Limoniidae. In the branch site model analysis, three positively selected sites were detected when Chionea was designated as the foreground branches: COX3 (at position 242), ND5 (at position 535), and ND6 (at position 138). Full article

Membrane transporters are vital for solute movement and localisation across cellular compartments, particularly in extremophilic organisms such as Galdieriales. These red algae thrive in geothermal and metal-rich environments, where adaptive transporter systems contribute to their metabolic flexibility. While inventories of transporter genes in the species Galdieria sulphuraria have previously been compiled, their phylogenetic origins remain incompletely resolved. Here, we conduct a comparative phylogenetic analysis of three transporter families—Major Facilitator Superfamily (MFS). Amino acid–Polyamine–Organocation (APC) and the natural resistance–associated macrophage protein (Nramp)—selected from overexpressed transcripts in G. sulphuraria strain SAG 107.79. Using sequences from six Galdieriales species and orthologs from diverse taxa, we reconstructed maximum likelihood trees to assess conservation and potential horizontal gene transfer (HGT). The MFS subfamilies revealed contrasting patterns: sugar porters (SPs) exhibited polyphyly and fungal affinity, suggesting multiple HGT events, while phosphate:H⁺ symporters (PHSs) formed a coherent monophyletic group. APC sequences were exclusive in G. sulphuraria and extremophilic prokaryotes, indicating a likely prokaryotic origin. In contrast, Nramp transporters were broadly conserved across eukaryotes and prokaryotes, showing no signs of recent HGT. Together, these findings highlight the mosaic evolutionary history of membrane transporters in Galdieriales, shaped by a combination of vertical inheritance and taxon-specific gene acquisition events, and provide new insight into the genomic strategies underpinning environmental resilience in red algae. Full article

Background: Sedum, with the largest number of species in the family Crassulaceae, is a taxonomically complex genus and an important group of horticultural plants within this family. Despite extensive historical research using diverse datasets, the branching patterns within this genus and the family remain debatable. Methods: In this study, we conducted sequencing and comparative analyses of plastomes from eight Sedum species, focusing on the diversities in nucleotide, microsatellite repeats, putative RNA editing, and gene content at IR junctions. The phylogenetic inferences were further conducted at the order level—Saxifragales. Results: Our IR junction analyses of the eight investigated Sedum species detected a unique 110 bp IR extension into rps19, a feature highly conserved across Crassulaceae species, indicating a remarkably family-specific pattern. Additionally, we obtained 79 PCGs from 148 Saxifragales species and constructed a phylogenetic tree using a larger set of plastomes than in previous studies. Our results confirm the polyphyly of Sedum and reveal that S. emarginatum is more closely related to S. makinoi than to S. alfredii, which is sister to S. plumbizincicola. Furthermore, we also performed analyses of codon usage, putative RNA editing sites, and microsatellite repeats. Conclusions: These findings and the generated sequence data will enrich plastid resources and improve understanding of the evolution of Sedum, Crassulaceae, and Saxifragales. Full article

Anemone altaica Fisch. ex C. A. Mey., a component of the tertiary boreo-nemoral vegetation complex, exhibits a disjunct distribution from European Russia to Central China. The Khamar-Daban Ridge, extending along Lake Baikal’s southern coast, has served as a refugium preserving mesophilic forest remnants in South Siberia since the Pleistocene. This study aimed to elucidate the phylogenetic relationships and historical biogeography of A. altaica within the Khamar-Daban refugium using plastid DNA markers (trnL + trnL-trnF). Phylogenetic and mismatch distribution analysis revealed polyphyly (more specifically diphyly) among A. altaica lineages, suggesting past hybridization events with related species followed by backcrossing. Estimation of isolation by distance effect, spatial autocorrelation analysis, PCoA, and AMOVA indicated a clear spatial genetic structure for A. altaica on the Khamar-Daban Ridge. The most reliable geographical model suggests that during periods of Pleistocene cooling, A. altaica persisted in at least six microrefugia within the ridge. Populations associated with these microrefugia formed western, central, and eastern genetic supergroups with limited gene flow among them. Gene flow likely occurred more easily during glaciations or early interglacials when the subalpine zone shifted closer to Lake Baikal due to the depression of the snow boundary, allowing adjacent populations to intermingle along the glacial edges and terminal moraines in mountain forest belt. Full article

Background: The Satyrinae subfamily represents a taxonomically critical group within Nymphalidae, characterized by its remarkable species diversity. Despite its evolutionary significance, the phylogenetic relationships among tribal and subtribal lineages remain poorly resolved. Although mitochondrial genomes have become crucial molecular markers in Lepidoptera phylogenetics, their potential remains underutilized in the systematics of Satyrinae. Notably, Amathusiini exhibits a particular paucity, with only two congeneric representatives having been comprehensively sequenced to date. Methods: We employed high-throughput sequencing to assemble the complete mitochondrial genomes of two Amathusiini species, Discophora sondaica and Aemona amathusia. Our study revealed novel evolutionary insights through comparative genomics, which encompassed all available Satyrinae mitochondrial genomes. Additionally, we conducted phylogenetic reconstruction using maximum likelihood and Bayesian inference approaches, utilizing the most extensive dataset to date. Results: The closed, circular mitochondrial genomes measure 15,333 bp for D. sondaica and 15,423 bp for A. amathusia, maintaining the ancestral lepidopteran architecture: 13 protein-coding genes (PCGs), 22 tRNAs, 2 rRNAs, and an AT-rich control region. Comparative analyses of 71 mitochondrial genomes revealed strong evolutionary conservation across multiple parameters: nucleotide composition (AT content range: 77.9–81.8%), codon usage bias (ENC = 30.83–37.55), tRNA secondary structures, and control region organization. All PCGs showed purifying selection signals (Ka/Ks < 1.0), with atp8 exhibiting the highest evolutionary rate (Ka/Ks = 0.277). Phylogenetic reconstructions yielded congruent tribal-level topologies with strong nodal support: ((Satyrini + Melanitini) + (Amathusiini + Elymniini) + Zetherini), confirming a sister relationship between Amathusiini and Elymniini. Within Satyrini, five subtribes formed monophyletic groups: Ypthimina, Erebiina, Maniolina, Satyrina, and Melanargiina, arranged as ((Ypthimina + (Erebiina + Maniolina)) + (Satyrina + Melanargiina)). Mycalesina, Lethina, and Parargina comprised a well-supported clade (BS = 100%; PP = 1.0), though internal relationships required further resolution due to Lethina’s polyphyly. Conclusions: This study provides novel insights into mitochondrial genomic evolution within the Satyrinae subfamily while elucidating the efficacy of mitogenomic data for resolving deep phylogenetic relationships within this ecologically significant subfamily. Our findings establish critical genome baselines for further systematic research and underscore essential pathways for refining subtribal-level taxonomy through integrative molecular approaches. Full article

Bassia scoparia is a widespread weedy species in the temperate regions of the world and is valued as a medicinal and ornamental plant. To date, the taxonomic concept of B. scoparia remains insufficiently studied due to a limited number of samples used in the previous phylogenetic analyses. To solve the taxonomy of the B. scoparia complex, we constructed a new phylogeny based on the nuclear ribosomal internal transcribed spacer (ITS), plastid intergenic spacer atpB-rbcL, and plastid region rpL16 intron sequences for numerous samples with diverse morphology. Our analysis revealed a close proximity and intermixed positions of the samples of the B. scoparia group with various morphology. Because of this polyphyly, we prefer to broadly delimit the species. An updated nomenclature of B. scoparia is provided including four new synonyms: Bassia angustifolia, B. littorea, Kochia albovillosa, and K. scoparia subsp. hirsutissima. In its new circumscription, B. scoparia encompasses populations with glabrous or variously hairy leaves and perianths. The original material of Kochia sieversiana, previously considered a species with hairy leaves and inflorescences, has the same diagnostic characters as in B. scoparia s.str. The correct name for more hairy-leaved plants is B. scoparia var. subvillosa. Plants with hairy perianths known as Kochia albovillosa and K. scoparia subsp. hirsutissima have a restricted distribution in Central Asia and South Siberia and have never been recorded as alien in other regions; they can be classified as a separate variety, B. scoparia var. hirsutissima. The ornamental variant of oblong or pyramidal shape may be called B. scoparia var. trichophila. Bassia scoparia is often confused with a similarly looking relative, B. indica, especially in North Africa, a region where secondary ranges of both species overlap. Phylogenetically, these species are sister groups; they share some morphological characters but have different primary distribution ranges. We traced a recent expansion of B. indica in the Mediterranean with the first record reported from the European continent (Spain) and uncovered various introduction pathways of the species in this region. Full article

Southern Brazil is home to a large biodiversity of elasmobranchs from the Brazilian coast. Several genera and species of small sharks of the Triakidae family live in this marine environment. Studies on these shark species are scarce, with few genetic data and little information on animal population structures. The present study aimed to sequence the complete mitochondrial genome (mtDNA) of the endangered species Mustelus schmitti (narrownose smooth-hound shark) and to perform a phylogenetic analysis of the Triakidae family. The mtDNA sequenced here was 16,764 bp long and possessed the usual 13 mitochondrial protein coding genes (PCGs), 22 tRNAs, two rRNAs (12S and 16S) and a large D-loop DNA sequence, presenting an overall organization similar to other species from the genus Mustelus. Phylogenetic analyses were performed using a dataset containing this new mtDNA and 59 other mitochondrial genomes of the Carcharhiniformes species (including 14 from the Triakidae family), using the Maximum Likelihood (ML) method. All the species of the Triakidae family were clustered into a monophyletic topology group. In addition, polyphyly was observed in Galeorhinus galeus, Hemiatrakis japanica, Triakis megalopterus and Triakis semifasciata. In conclusion, this study contributes to a deeper understanding of the genetic diversity of sharks and represents an important step towards the conservation of these endangered animals. Full article

Coxal combs, found only in members of the ‘cydnoid’ complex (comprising four families: Cydnidae, Parastrachiidae, Thaumastellidae, and Thyreocoridae) within the superfamily Pentatomoidea, have long been regarded as a character confirming their close evolutionary relationship. However, many studies have demonstrated that these four families are phylogenetically distant. Others have been treated as subfamilies of the broadly defined Cydnidae, with the coxal combs as the only character linking them. This is the first study on the origin of coxal combs in species of all families and subfamilies that represent the broadly conceived Cydnidae (69 species in 39 genera). Moreover, this study presents the first 16S rDNA gene sequences providing a basis for such analyses. The analyses included DNA sequences of 62 species in 34 genera of Cydnidae sensu stricto, three species in two genera of Thyreocoridae, two species in two genera of Parastrachiidae, and two species in one genus of Thaumastellidae. The sequence analysis in the family Cydnidae covered 35 species representing 19 genera of the subfamily Cydninae, 16 species in eight genera of the subfamily Sehirinae, five species in two genera of Amnestinae, three species in three genera of Garsauriinae, two species in one genus of Cephalocteinae, and one species of Amaurocorinae. The results of our study demonstrate the independent origin of coxal combs in taxa of the ‘cydnoid’ complex within the superfamily Pentatomoidea. They confirm the polyphyly not only of the entire ‘cydnoid’ complex but also of the family Cydnidae itself. Full article

The Anostostomatidae of Aotearoa New Zealand are well-characterized at the genus and species level, but the higher-level systematics of the family as a whole remain poorly resolved. We tested the hypothesis that the New Zealand anaostostomatid fauna consists of a single monophyletic group consistent with a single common ancestor. For phylogenetic analysis, we sampled the genera in Aotearoa New Zealand as well as representatives of the family from Australia and New Caledonia. Maximum likelihood analyses including topological comparison statistics with a DNA alignment of thirteen mitochondrial and four nuclear protein coding genes rejected the monophyly of lineages in New Zealand. We found phylogenetic support for four separate New Zealand lineages; three with their closest relatives in Australia and one in New Caledonia. The New Zealand genus Hemiandrus is paraphyletic and the establishment of a morphologically distinct genus is justified. We determined that six of the valid species previously placed in Hemiandrus form a distinct clade that we designated here as Anderus gen. nov. The putative Hemiandrus that we sampled from Australia was sister to neither of the New Zealand lineages. Full article

A reliable character system is crucial to taxonomy and systematics, and it promises valid downstream inferences, e.g., estimates of diversity and disparity, reconstruction of evolutionary history, and even stratigraphic correlations. Modern taxonomy and systematics of extant cockroaches requires an integrative study involving multiple lines of evidence with emphasis on genital and reproductive characteristics and molecular data. In contrast, many fossil cockroach taxa published recently are based solely on forewings. Many studies have shown that forewing-based taxa are questionable. In order to find out how much of the phylogenetic signal we could ascertain from venational similarity, and how confident we could be, this study used forewing characters to reconstruct phylogenies of the genera of well-recognized family-group taxa. The intuitively reconstructed phylogeny of 75 extant genera failed to recover those taxa or their relationships. Parsimony analyses of various datasets all yielded strong polyphyly and chaotic relationships. In conclusion, the forewing of cockroaches is not a universally competent character system. The underlying causes are the complicated nature of veins and the limitations of current analytical techniques. The uncertainty in forewing-based taxonomy and systematics has been underestimated in the literature. Forewing-based fossil taxa warrant re-evaluation; some of them are herein deemed nomina dubia in their current state. Full article

Tamarisk is an invasive evergreen shrub native to arid regions of Africa and Eurasia and is considered a weed in some countries with dry climates. The complex of gall mites from tamarisks includes fourteen species from four genera of the family Eriophyidae. We reinvestigated the type species of the genus Dicruvasates, D. tamaricis from Egypt, described D. ngubani n. sp. from Tamarix usneoides from South Africa, and revised the generic concept of Dicruvasates. This genus possesses cuticular plates marking longitudinal opisthosomal ridges typical of various phyllocoptine genera, e.g., Echinacrus. We sequenced three genes of Dicruvasates and Phyllocoptes mites from Tamarix and Echinacrus from Frangula, combined our sequences with the data from GenBank, and performed single-gene phylogenetic analyses. All analyses inferred the following: (1) a transcontinental clade Tam comprising Dicruvasates + Aceria + Phyllocoptes from Tamarix; (2) Echinacrus distantly related to Dicruvasates, suggesting the homoplastic nature of the cuticular plates on the opisthosomal ridges, and (3) polyphyly of the genera Aceria and Phyllocoptes. We also investigated partially cleared specimens of Dicruvasates under CLSM and, for the first time, visualized a well-developed anal secretory apparatus (ASA) in the immatures of gall mites, which was previously shown to be a specialized system evolved in Eriophyoidea for silk production. We hypothesize that the ASA contributes to finding nymphs by conspecific males and advocate for the importance of the future molecular biology studies of gall mite silk for developing new methods for controlling mites based on the knowledge of their ecology, behavior, and silk gene genetics. Full article

Monitoring water supply requires, among other quality indicators, the identification of the cyanobacteria community and taking into account their potential impact in terms of water quality. In this work, cyanobacteria strains were isolated from the Cheffia Reservoir and identified based on morphological features, the 16S rRNA gene, phylogenetic analysis, and toxin production by polymerase chain reaction PCR screening of the genes involved in the biosynthesis of cyanotoxins (mcyA, mcyE, sxtA, sxtG, sxtI, cyrJ, and anaC). Thirteen strains representing six different genera: Aphanothece, Microcystis, Geitlerinema, Lyngbya, Microcoleus, and Pseudanabaena were obtained. The results demonstrated the importance of morphological features in determining the genus or the species when incongruence between the morphological and phylogenetic analysis occurs and only the utility of the 16S rRNA gene in determining higher taxonomic levels. The phylogenetic analysis confirmed the polyphyly of cyanobacteria for the Microcystis and Oscillatoriales genera. Unexpectedly, Aphanothece sp. CR 11 had the genetic potential to produce microcystins. Our study gives new insight into species with picoplanktonic (or small) cell size and potentially toxic genotypes in this ecosystem. Thus, conventional water treatment methods in this ecosystem have to be adapted, indicating the requirement for pre-treatment methods that can effectively eliminate picocyanobacteria while preserving cell integrity to prevent toxin release. Full article

Rubus L. (Rosaceae, Rosoideae) contains around 700 species distributed on all continents except Antarctica, with the highest species diversity in temperate to subtropical regions of the northern hemisphere. The taxonomy of Rubus is challenging due to the frequency of polyploidy, hybridization and apomixis. Previous studies mostly sampled sparsely and used limited DNA sequence data. The evolutionary relationships between infrageneric taxa, therefore, remain to be further clarified. In the present study, genotyping by sequencing (GBS) reduced-representation genome sequencing data from 186 accessions representing 65 species, 1 subspecies and 17 varieties of Rubus, with emphasis on diploid species, were used to infer a phylogeny using maximum likelihood and maximum parsimony methods. The major results were as follows: (1) we confirmed or reconfirmed the polyphyly or paraphyly of some traditionally circumscribed subgenera, sections and subsections; (2) 19 well-supported clades, which differed from one another on molecular, morphological and geographical grounds, were identified for the species sampled; (3) characteristics such as plants with dense bristles or not, leaves leathery or papyraceous, number of carpels, instead of inflorescences paniculate or not, aggregate fruits and leaves abaxially tomentose or not, may be of some use in classifying taxa whose drupelets are united into a thimble-shaped aggregate fruit that falls in its entirety from the dry receptacle; and (4) a preliminary classification scheme of diploid species of Rubus is proposed based on our results combined with those from previous phylogenetic analyses. Full article

The recent molecular phylogenetic study of the families Aongstroemiaceae and Dicranellaceae, which resolved the genera Aongstroemia and Dicranella as polyphyletic, indicated the need for changes in their circumscription and provided new morphological evidence to support the formal description of newly recognized lineages. Following up on these results, the present study adds another molecular marker, the highly informative trnK–psbA region, to a subset of previously analyzed taxa and presents molecular data from newly analyzed austral representatives of Dicranella and collections of Dicranella-like plants from North Asia. The molecular data are linked with morphological traits, particularly the leaf shape, tuber morphology, and capsule and peristome characters. Based on this multi-proxy evidence, we propose three new families (Dicranellopsidaceae, Rhizogemmaceae, and Ruficaulaceae) and six new genera (Bryopalisotia, Calcidicranella, Dicranellopsis, Protoaongstroemia, Rhizogemma, and Ruficaulis) to accommodate the described species according to the revealed phylogenetic affinities. Additionally, we amend the circumscriptions of the families Aongstroemiaceae and Dicranellaceae, as well as the genera Aongstroemia and Dicranella. In addition to the monotypic Protoaongstroemia that contains the newly described dicranelloid plant with a 2–3-layered distal leaf portion from Pacific Russia, P. sachalinensis, Dicranella thermalis is described for a D. heteromalla-like plant from the same region. Fourteen new combinations, including one new status change, are proposed. Full article

The Astragalus subgenus Hypoglottis Bunge, which consists of several sections, is one of the taxonomically most complicated groups in the genus. The Astragalus section Stereothrix Bunge belongs to this subgenus and is a significant element of the Irano-Turanian floristic region. A molecular phylogenetic analysis of this section and its closely related taxa using nuclear ribosomal DNA internal transcribed spacers (ITS) and external transcribed spacer (ETS) regions as well as plastid matK sequences were conducted. Parsimony analyses and Bayesian phylogenetic inference revealed that the section is not monophyletic in its current form, as some taxa belonging to closely related sections such as Hypoglottidei DC. and the Malacothrix Bunge group within the sect. Stereothrix render it paraphyletic. Moreover, species groups belonging to sect. Stereothrix are placed in different clades within the phylogenetic tree of subgenus Hypoglottis, which indicates polyphyly, i.e., multiple independent origins of taxa placed in the sect. Stereothrix. Molecular dating of the group estimated an age of 3.62 (1.73–5.62) My for this assemblage with the major diversification events happening during the last 2 My. Many species groups separated only within the last 0.5 to 1 My. Based on morphological and molecular data, we discuss the phylogenetic relationships of the groups and synonymy of species. In addition, the included taxa of sect. Hypoglottidei are not monophyletic and include species belonging to sects. Hololeuce, Koelziana, Malacothrix, Onobrychoideae, and Ornithodpodium group within the sect. Stereothrix taxa. We conclude that only an analysis including all groups and nearly all species of the sections within the Hypoglottis clade can finally result in an new evolutionary-based system for these taxa. Full article