Search Results (275)

Hainania Koller (Teleostei, Cypriniformes, Xenocyprididae) is known as a monotypic genus of sharpbelly fish that is endemic to Hainan Island, China. We describe Ha. minzhengi sp. nov., the second species of Hainania collected from Guangdong, based on morphology and molecular evidence. Phylogenetic relationships were inferred based on the mitochondrial cytochrome b (Cyt b) gene and cytochrome oxidase subunit 1 (COI) gene, by maximum likelihood and Bayesian methods and different partitioning schemes. Our result supports the sister group relationship between Ha. serrata and Ha. minzhengi sp. nov., but the monophyly of Pseudohemiculter or Hemiculterella was not recovered. A diagnostic key to Chinese species of Hainania and Pseudohemiculter is provided. Full article

Background/Objectives: Scutiger ningshanensis (Fang, 1985) is an endemic Chinese amphibian species within the genus Scutiger (Megophryidae). Despite its ecological significance, its mitochondrial genome architecture and evolutionary relationships remain poorly understood. Given the high structural variability in Megophryidae mitogenomes and unresolved phylogenetic patterns in Scutiger, this study aims to (1) characterize the complete mitogenome of S. ningshanensis, (2) analyze its molecular evolution, and (3) clarify its phylogenetic position and divergence history within Megophryidae. Methods: The complete mitochondrial genome was sequenced and annotated, followed by analyses of nucleotide composition, codon usage bias, and selection pressures (Ka/Ks ratios). Secondary structures of rRNAs and tRNAs were predicted, and phylogenetic relationships were reconstructed using maximum likelihood and Bayesian methods. Divergence times were estimated using molecular clock analysis. Results: The mitogenome of S. ningshanensis is 17,282 bp long, encoding 13 protein-coding genes (PCGs), 22 tRNAs, 2 rRNAs, and a control region, with a notable AT bias (61.05%) with nucleotide compositions of T (32.51%), C (24.64%), G (14.3%), and A (28.54%). All tRNAs exhibited cloverleaf structures except trnS1, which lacked a DHU stem. Phylogenetic analysis confirmed the monophyly of Scutiger, forming a sister clade to Oreolalax and Leptobrachium, and that S. ningshanensis and S. liubanensis are sister species with a close evolutionary relationship. Positive selection was detected in Atp8 (Ka/Ks > 1), suggesting adaptation to plateau environments, while other PCGs underwent purifying selection (Ka/Ks < 1). Divergence time estimation placed the origin of Megophryidae at~47.97 MYA (Eocene), with S. ningshanensis diverging~32.67 MYA (Oligocene). Conclusions: This study provides the first comprehensive mitogenomic characterization of S. ningshanensis, revealing its evolutionary adaptations and phylogenetic placement. The findings enhance our understanding of Megophryidae’s diversification and offer a genomic foundation for future taxonomic and conservation studies. Full article

Diptera comprises more than 154,000 described species, representing approximately 10–12% of insects. Members have successfully colonized all continents and a wide range of habitats. However, higher-level phylogenetic relationships within Diptera have remained ambiguous. Mitochondrial genomes (mitogenomes) have been used as valuable molecular markers for resolving phylogenetic issues. To explore the effect of such markers in solving the higher-level phylogenetic relationship of Diptera, we sequenced and annotated the mitogenomes of 25 species, combined with 180 mitogenomes from 33 superfamilies of dipteran insects to conduct a phylogenetic analysis based on the PCGsrRNA and PCGs12rRNA datasets using IQ-TREE under the partition model. The phylogenetic analysis failed to recover the monophyly of the two suborders Nematocera and Brachycera. Two of six infraorders within the Nematocera—Tipulomorpha and Ptychopteromorpha—were monophyletic. The ancestral Deuterophlebiidae were a strongly supported sister group of all remaining Diptera, but Anisopodidae, as the closest relative of Brachycera, received only weak support. Three of four infraorders within Branchycera—Tabanomorpha, Xylophagomorpha, and Stratiomyomorpha—were, respectively, supported as a monophyletic clade, except Muscomorpha due to the strong long-branch attraction between Cecidomyiidae and Nycteribiidae. The inferred infraordinal relationships followed the topology Tabanomorpha + (Xylophagomorpha + (Stratiomyomorpha + Muscomorpha)). However, the proposed topology lacks strong statistical support, suggesting alternative relationships remain plausible. Based on mitogenome data alone, we infer that Diptera originated earlier than the Late Triassic at 223.43 Mya (95% highest posterior density [HPD] 166.60–272.02 Mya) and the earliest brachyeran Diptera originated in the mid-Jurassic (171.61 Mya). Full article

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

Rhododendron purdomii Rehder & E. H. Wilson (Ericaceae) is a threatened ornamental and medicinal shrub or small tree species primarily distributed in the Qinling-Daba Mountains of Central China. To facilitate its conservation and utilization, the complete chloroplast genome of Rh. purdomii was sequenced, assembled, and characterized. The cp genome exhibited a typical quadripartite structure with a total length of 208,062 bp, comprising a large single copy (LSC) region of 110,618 bp, a small single copy (SSC) region of 2606 bp, and two inverted repeat (IR) regions of 47,419 bp each. The overall GC content was 35.81%. The genome contained 146 genes, including 96 protein-coding genes, 42 transfer RNA genes, and 8 ribosomal RNA genes. Structure analysis identified 67,354 codons, 96 long repetitive sequences, and 171 simple sequence repeats. Comparative genomic analysis across Rhododendron species revealed hypervariable coding regions (accD, rps9) and non-coding regions (trnK-UUU-ycf3, trnI-CAU-rpoB, trnT-GGU-accD, rpoA-psbL, rpl20-trnC-GCA, trnI-CAU-rrn16, and trnI-CAU-rps16), which may serve as potential molecular markers for genetic identification. Phylogenetic reconstruction confirmed the monophyly of Rhododendron species and highlighted a close relationship between Rh. purdomii and Rh. henanense subsp. lingbaoense. These results provide essential genomic resources for advancing taxonomic, evolutionary, conservation, and breeding studies of Rh. purdomii and other species within the genus Rhododendron. Full article

Salvia, a medicinally and economically important genus, is widely used in traditional medicine, agriculture, and horticulture. This study compares the chloroplast genomes of eight East Asian Salvia species to assess genetic diversity, structural features, and evolutionary relationships. Complete chloroplast genomes were sequenced, annotated, and analyzed for gene content, codon usage, and repetitive sequences. Phylogenetic relationships were reconstructed using Maximum Likelihood, Maximum Parsimony and Bayesian inference. The genomes exhibited a conserved quadripartite structure (151,081–152,678 bp, GC content 37.9–38.1%), containing 114 unique genes with consistent arrangement. Codon usage favored A/T endings, with leucine (Leu) most frequent and cysteine (Cys) least. We identified 281 long sequence repeats (LSRs) and 345 simple sequence repeats (SSRs), mostly in non-coding regions. Comparative analysis revealed five hypervariable regions (trnH-psbA, rbcL-accD, petA-psbJ, rpl32-trnL, ycf1) as potential molecular markers. Phylogenetic analysis confirmed the monophyly of East Asian Salvia, dividing them into five clades, with Sect. Sonchifoliae basal. While G1, G3, and G8 were monophyletic, G5 and G6 were paraphyletic, and the G7-G8 relationship challenged traditional classifications. The genomic evidence provides crucial insights for resolving long-standing taxonomic uncertainties and refining the classification system of Salvia. These findings suggest a complex evolutionary history involving hybridization and incomplete lineage sorting, providing valuable genomic insights for Salvia phylogeny, taxonomy, and conservation. Full article

The nocturnal, flightless camel crickets (Rhaphidophoridae) have a global distribution and are believed to have originated prior to the breakup of Pangea. We investigated the phylogeny and the timing of the radiation of East Asian species with mitogenomic data. Initially we analyzed a large taxon dataset (n = 117) using available partial mitochondrial and nuclear DNA sequences to confirm the monophyly of subfamilies and current taxonomy. Our findings support the monophyly of each genus within the subfamily Aemodogryllinae, with a minor inconsistency between taxonomy and phylogeny resolved by resurrection of the genus Gymnaeta Adelung. Fossil-calibrated molecular clock analysis used 11,124 bp alignment of 13 complete mitochondrial protein-coding genes for 20 species of Rhaphidophoridae, with a focus on the neglected Rhaphidophorinae and Aemodogryllinae lineages. Divergence time estimates suggest that the most recent common ancestor of the family lived during the Early Jurassic (189 Mya ± 23 Mya) before Pangea broke into the supercontinents or possibly during the early stage of breakup when Gondwana and Laurasia were still connected by land. The two subfamilies, Rhaphidophorinae and Aemodogryllinae, that overlap in Asia are estimated to have diverged 138 Mya ± 17 Mya, well before the Late Cretaceous northern connection between America and Asia (the Bering Land Bridge). Thus, our extended sampling of species from East Asia and Oceania refutes the importance of continental drift in the evolution of this wingless orthopteran family. Full article

In China, Anostostomatidae is represented by a single tribe, Anabropsini; two genera; and 33 species. Although extensive research has been conducted on Anabropsini, the monophyly of this tribe within Anostostomatidae remains unverified. Furthermore, the phylogenetic relationships within Anabropsis remain under debate. To address these gaps, we sequenced and annotated the mitochondrial genomes of five Anabropsini species to investigate their mitochondrial characteristics and phylogenetic positions and clarify the relationships among Anabropsis subgenera. The total mitochondrial length of the five species ranged from 15,985 bp to 16,423 bp and contained 13 protein-coding genes, 22 tRNAs, 2 rRNAs, and 1 control region. A grouped analysis of selection pressure on Anabropsis revealed that the Ka/Ks values for alate and apterous forms are not significantly different, suggesting that using wing length alone as the basis for dividing subgenera within Anabropsis may be unreliable. Tertiary structure modeling of proteins showed that the variable sites were concentrated in α-helix regions. Phylogenetic trees were reconstructed using the Bayesian inference and maximum likelihood methods and were based on two better datasets, namely, PCG123 (all codon positions of the PCGs) and PCG123 + 2R (all codon positions of PCGs, 12SrRNA, and 16SrRNA). The results indicate that the Chinese Anabropsini is paraphyletic, whereas Anabropsis is monophyletic, with a stable subgeneric topology. Full article

Phylogenetic relationships within the subtribe Arethusinae (Arethuseae: Epidendroideae: Orchidaceae) remain unresolved, with particular uncertainty surrounding the phylogenetic positions of Anthogonium gracile and Eleorchis japonica. The monophyly of this subtribe remains contentious, making it one of the challenging taxa in Orchidaceae phylogenetics. In this study, we sequenced and analyzed the complete plastome sequences of A. gracile and E. japonica for the first time, aiming to elucidate their plastome characteristics and phylogenetic relationships. Both plastomes exhibited a conserved quadripartite structure, with 158,358 bp in A. gracile and 152,432 bp in E. japonica, and GC contents of 37.1% and 37.3%, respectively. Comparative analyses revealed strong structural conservation, but notable gene losses: E. japonica lacked seven ndh genes (ndhC/D/F/G/H/I/K), whereas A. gracile retained a complete ndh gene set. Repetitive sequence analysis identified an abundance of simple sequence repeats (68 and 77), tandem repeats (43 and 30), and long repeats (35 and 40). Codon usage displayed a bias toward the A/U termination, with leucine and isoleucine being the most frequent. Selection pressure analysis indicated that 68 protein-coding genes underwent purifying selection (Ka/Ks < 1), suggesting evolutionary conservation of plastome protein-coding genes. Nucleotide diversity analysis highlighted six hypervariable regions (rps8-rpl14, rps16-trnQ^UUG, psbB-psbT, trnT^UGU-trnL^UAA, trnF^GAA-ndhJ, and ycf1), suggesting their potential as molecular markers. Phylogenomic reconstruction, using complete plastome sequences, (ML, MP, and BI) indicated that Arethusinae was non-monophyletic. A. gracile formed a sister relationship with Mengzia foliosa and E. japonica, whereas Arundina graminifolia exhibited a sister relationship with Coelogyninae members. These results shed new light on the plastome characteristics and phylogenetic relationships of Arethusinae. Full article

Insect mitochondrial genomes are vital to understanding evolutionary relationships and identifying species. This study focused on Microtendipes (Chironomidae), a genus with unresolved phylogenetic positioning and cryptic species challenges. We sequenced and analyzed eight mitogenomes from five Microtendipes species, integrating 23 published Chironominae mitogenomes to reconstruct phylogenies using Maximum Likelihood and Bayesian Inference. The mitogenomes exhibited conserved gene arrangements but variable control region lengths (338–1266 bp) and high AT content (94.14–96.42% in control regions). Our results show that Microtendipes species may be a separate group within the subfamily, while also supporting the monophyly of the Harnischia, Polypedilum, and Chironomus complexes. The monophyly of Microtendipes bimaculus was weakly supported, which may demonstrate the presence of two potential cryptic species. Notably, larval morphology-based species groupings conflicted with the molecular data, suggesting that classifications derived from larval morphological traits may be unreliable. This study advances the evolutionary understanding of Chironomidae and underscores the limitations of single-gene barcodes in species-rich genera. Full article

Diptera is one of the most ecologically significant and species-rich insect orders, but there are still unresolved phylogenetic relationships among its basal lineages, particularly within the infraorder Blephariceromorpha, due to limited molecular data. To address this gap, this study employs two parallel genomic approaches: mitochondrial genomes and nuclear genomic analysis, covering 64 families and over 100 species of Diptera and their outgroups, to elucidate these phylogenetic relationships. Our results strongly support the monophyly of each constituent family (Blephariceridae, Deuterophlebiidae, and Nymphomyiidae), yet they reject the monophyly of Blephariceromorpha. Crucially, we found that Deuterophlebiidae and Nymphomyiidae form a sister group representing the basal-most lineage of Diptera, whereas Blephariceridae is positioned within Psychodomorpha. This indicates that the similar larval habitats and morphological traits shared between Blephariceridae and the Nymphomyiidae + Deuterophlebiidae clade are the result of convergent evolution. By resolving long-standing debates on the relationships within Blephariceromorpha and the basal lineages of Diptera, this study provides new insights into the evolutionary history of Diptera, especially within the suborder Nematocera. Full article

Absidia is the most species-rich genus within the family Cunninghamellaceae, with its members commonly isolated from diverse substrates, particularly rhizosphere soil. In this study, four novel Absidia species, A. irregularis sp. nov., A. multiformis sp. nov., A. ovoidospora sp. nov., and A. verticilliformis sp. nov., were discovered from soil samples collected in southern and southwestern China, using integrated morphological and molecular analyses. Phylogenetic analyses based on concatenated ITS, SSU, LSU, Act, and TEF1α sequence data reconstructed trees that strongly supported the monophyly of each of these four new taxa. Key diagnostic features include A. irregularis (closely related to A. oblongispora) exhibiting irregular colony morphology, A. multiformis (sister to A. heterospora) demonstrating polymorphic sporangiospores, A. ovoidospora (forming a clade with A. panacisoli and A. abundans) producing distinctive ovoid sporangiospores, and A. verticilliformis (next to A. edaphica) displaying verticillately branched sporangiophores. Each novel species is formally described with comprehensive documentation, including morphological descriptions, illustrations, Fungal Names registration identifiers, designated type specimens, etymological explanations, maximum growth temperatures, and taxonomic comparisons. This work constitutes the sixth instalment in a series investigating early-diverging fungal diversity in China aiming to enhance our understanding of the diversity of fungi in tropical and subtropical ecosystems in Asia. In this paper, the known species of Absidia are expanded to 71. Full article

Trogopterus xanthipes (Sciuridae, Rodentia) is a medium-sized flying squirrel species in the monotypic genus Trogopterus, and is endemic to China. It is distinguishable from other squirrels by the long black hairs on the inner and outer sides at the base of the ears and numerous ridges on the crowns of the upper and lower cheek teeth. Mitogenomes have been widely used in phylogenetic studies. We described T. xanthipes morphological features and successfully sequenced its mitogenome for the first time. The T. xanthipes mitogenome was conserved in number and order of genes. We analyzed codon usage patterns, evolutionary mutation rates, K2P distance, and genetic diversity of protein-coding genes. We reconstructed the phylogeny of Sciuridae (94 species and 21 genera in 4 subfamilies). All phylogenetic trees shared the same topologies and consistently supported the monophyly of Sciuridae, and the supported subfamilies relationship as follows: ((Xerinae + Callosciurinae) + Sciurinae) + Ratufinae. The relationship within the Sciurinae clade was ((Glaucomys + Hylopetes) + ((Trogopterus+Pteromys) + Petaurista) + Sciurus). The relationship within the Callosciurinae clade was Exilisciurus + ((Tamiops + Dremomys) + ((Lariscus+Sundasciurus) + Callosciurus)). The relationship within the Xerinae clade was Sciurotamias + (Tamias + (Callospermophilus + (Marmota + (Spermophilus + (Urocitellus + (Ictidomys + Cynomys)))))). The phylogenetic position among different subfamilies of Sciuridae was consistently recovered with high support across different datasets (PCGRNA and PCG12RNA) and supported the monophyletic lineage of each genus of Sciuridae. Trogopterus xanthipes was sister species to Pteromys volans. Species within the genus formed different minor clades, suggesting relatively high interspecific divergences. The tribe Pteromyini was sister taxon of the tribe Sciurini, which was not supported by the traditional division of Sciuridae into subfamilies Pteromyinae and Sciurinae. Hence, our data supported a division of the Sciuridae into five subfamilies. Full article

Lepidostomatidae is a relatively large family of the infraorder Plenitentoria (Integripalpia), comprising four fossil genera and seven extant genera. Lepidostomatid adults exhibit pronounced sexual dimorphism and have thus been referred to as the ‘cabinet of curiosities’ within Trichoptera. However, only five annotated mitogenomes of Lepidostoma have been recorded in the GeneBank database, and some of these mitogenomes are incomplete. To better understand the structure of mitogenome and phylogenetic relationships of Lepidostomatidae, we present mitogenomes of 13 Lepidostoma species and one Paraphlegopteryx species for the first time. We combined these new mitogenomes with previously published data for a comparative analysis. The results showed that the structure of mitogenome was relatively conserved, the nucleotide composition was significantly AT biased, and the control region showed the highest A + T content. Evolutionary rate analysis showed that all protein-coding genes underwent purification selection. The phylogenetic relationships supported the monophyly of Lepidostomatidae and restored the taxonomic positions of the two subfamilies. Meanwhile, two monophyletic branches (Lepidostoma ferox branch and Lepidostoma hirtum branch) within the genus Lepidostoma were also strongly supported. These findings significantly advance our understanding of the mitogenome and phylogeny of Lepidostomatidae. Full article

In order to examine the phylogeny and evolutionary history of the subfamily Notodontinae (Noctuoidea: Notodontidae), a molecular systematic study was conducted, mainly based on mitochondrial protein-coding genes (PCGs) generated by high-throughput sequencing, including 57 species belonging to 37 genera, together with 64 other species within Notodontidae and 14 outgroups, with the dataset comprising 10,980 bp of nucleotide sequences. An individual dataset of orthologous genes (OGs) comprising 589 loci (919,493 bp in total) was utilized as a supporting analysis for the result from the mitochodrial dataset. In this study, the monophyly of Notodontinae was well supported, with the internal clades consisting of three tribes—Stauropini, Notodontini, and Fentoniini—and supporting evidence found in the male genital characteristics. Furthermore, Neodrymoniaini Kobayashi, 2016 syn. nov. was synonymized with Fentoniini Matsumura, 1929. Divergence time estimation for Notodontinae, conducted using phylogenetic results across five fossil calibration points, suggested that Notodontinae originated around 22.71 Ma, and the most recent common ancestor of Stauropini and Fentoniini diverged between 24.44 and 20.23 Ma, followed by the emergence of Stauropini between 23.83 and 19.53 Ma. Then, Notodontini diverged around 23.60–19.10 Ma, with the youngest tribe, Fentoniini, dividing in 21.70–16.63 Ma. In summary, this study provided a robust foundation for classification within the terminal clades of Notodontidae and laid the groundwork for further research on phylogenetic relationships across the whole family. Full article