Taking the modern ice-fishing practices at Chagan Lake as a point of departure, this study examines the ice-fishing procedures, tool assemblages, fishing techniques, fish-luring practices, and related ritual activities employed by the Khitan during the spring nabo period of the Liao Dynasty (916–1125 CE). The analysis relies on both historical texts and archaeological evidence, and places these traditional fishing practices in dialogue with contemporary ice-fishing activities at Chagan Lake in order to explore patterns of similarity, transformation, and possible historical resonance. While ice-fishing is a widespread practice in cold regions and likely predates the Liao Dynasty in Northeast Asia, the findings indicate that the ritual practices, fishing techniques, ecological principles and the celebration of the “first catch” preserved in the ice-fishing tradition of Chagan Lake may be understood as reflecting partial correspondence and selective reinterpretations, rather than as evidence of continuity in a strict historical case. Meanwhile, notable differences in fishing environment, techniques, and operational organisation between the Liao period and the present suggest that these practices have undergone substantial transformation instead of simple transmission. This case illustrates how a seasonal fishing system developed within an empire established by a nomadic polity in northern China can be reinterpreted and recontextualised as a form of contemporary living heritage. Its transformation reflects the combined influence of socio-economic conditions, technological innovation, and political authority in Khitan society. By presenting an exploratory and integrative archaeological perspective on fishing technology, this investigation elucidates the multifaceted nature of Khitan ice-fishing practices a millennium ago and highlights the ways in which elements of traditional ecological knowledge may be selectively preserved, adapted, or reconfigured, together with their long-standing social significance in Northeast Asia. We also examine cases of ice-fishing from cold regions such as Finland, the United States and Canada. Cross-cultural comparisons show that ice-fishing techniques are widespread in high-latitude, cold environments and display clear adaptive features.

Chloroplast genomes, once considered highly conserved, have been shown to exhibit significant structural variations, though the underlying mechanisms remain unclear. In this study, we investigated the chloroplast genome structure of eight populations comprising 76 individuals of Paphiopedilum barbigerum, P. helenae, and P. vejvarutianum. By using chloroplast genome sequences and 15,924 nuclear SNP loci, we conducted analyses and validations of chloroplast genome structural recombination and natural hybridization. Our key findings include the following: (1) Structural variations in the chloroplast genomes were found to be stable and heritable across populations. (2) In P. barbigerum, populations exhibiting structural variation contained an unidentified insertion sequence in the SSC region, which was associated with a significant reduction in GC content within this region. (3) The presence of non-LTR retrotransposons suggests their potential role in the expansion and contraction of the IR region in Paphiopedilum, with this chloroplast variation potentially linked to natural hybridization events. (4) The incongruent phylogenetic relationships, gene flow and gene introgression among P. barbigerum, P. helenae, and P. vejvarutianum point to a history of hybridization within these species. Our study proposes that both transposon activity and hybridization play crucial roles in driving chloroplast structural variations. For the first time, the structural variations of chloroplasts have been linked to transposons and natural hybridization, breaking the traditional stereotype of chloroplasts being highly conserved. This discovery enhances our understanding of how natural hybridization contributes to species formation and provides a basis for exploring the evolutionary mechanisms of chloroplast genomes.

Musk deer (Moschus), the sole genus in the family Moschidae, are critically endangered and face an uncertain future due to the limited understanding of their taxonomy, evolutionary history, genetic load, and adaptive evolution. These knowledge gaps hinder conservation efforts at crucial stages. Here, we conducted a comprehensive conservation genomic analysis by sequencing eight M. anhuiensis genomes and integrating public data from 15 M. berezovskii individuals. Phylogenomic and population genomic analyses confirmed that M. anhuiensis is a distinct phylogenetic species that diverged approximately 260 thousand years ago (kya). Both species experienced severe population bottlenecks, subsequently exhibiting marked genetic divergence. Over the past 200 kya, M. berezovskii has undergone multiple admixture events and bottlenecks, whereas M. anhuiensis has steadily declined and maintained a small, stable population. Anthropogenic activities have intensified these pressures, leading to sharp declines in both species. Notably, M. anhuiensis has accumulated homozygous deleterious mutations, thereby heightening its extinction risk. Moreover, selective sweep analysis revealed 32 positively selected genes, including olfactory receptor genes (OLF3 and OR6B1), which are essential for foraging, reproduction, and social interactions; the proliferation-related gene (PDGFRA), which responds to environmental changes and injury; and the thermoregulation gene (CDH13), which helps maintain body temperature stability in extreme conditions. These findings shed light on the speciation and evolutionary history of musk deer, offering crucial insights into their local adaptations and vulnerabilities. This work provides a foundation for targeted conservation efforts to avert extinction and safeguard biodiversity.

Phylogenetic networks (Web of Life) depict the intricate evolutionary dynamics of organisms more accurately than simple bifurcating trees (Tree of Life), because processes such as hybridization and polyploidy connect lineages through reticulation. However, most existing workflows still examine evolutionary mechanisms separately. To provide an integrated view, we studied the bellflower tribe (Campanuleae), a lineage with a well‑documented reticulate past, and developed Ortho2Web, a workflow that teases apart hybridization and polyploidization within a single analytical framework. Ortho2Web employs multiple strategies to reduce the impact of non-biological factors, including (1) integrating multi-source genomic data to minimize sampling gaps, (2) generating complementary datasets to quantify phylogenetic signals, and (3) using tree-based orthology inference methods to mitigate the effects of paralogs. It then focused on clarifying the roles of biological factors, such as incomplete lineage sorting (ILS), hybridization/gene flow, and polyploidization. When applied to Campanuleae, the workflow produced a robust phylogenetic backbone and showed that early diversification was driven by interacting hybridization and allopolyploidization, while ILS contributed only marginally. By integrating diverse data sources and analytical approaches in a modular, scalable framework, Ortho2Web offers a practical platform for inferring web-like phylogenies and elucidating the mechanisms of reticulate evolution. The Ortho2Web workflow is freely available at: https://github.com/PhyloAI/Ortho2Web .

The genus Pseudo-nitzschia within Bacillariophyta (diatoms) is best known for its rich collection of toxigenic harmful algal bloom (HAB) species capable of producing the neurotoxin domoic acid (DA), which causes amnesic shellfish poisoning (ASP) in humans. Molecular markers such as 18S rDNA, ITS1, and ITS2 have been applied to facilitate Pseudo-nitzschia species identification because morphology-based methods often could not adequately distinguish different species due to their morphological similarities and plasticity. In this study, we constructed mitochondrial genomes (mtDNAs) for 11 Pseudo-nitzschia species and assessed their utility as "super-barcodes" for species identification and evolutionary analysis. These mtDNAs exhibited conserved genome structures despite variability in repeat regions. A potential tatA-tatC gene fusion event was observed in a single Pseudonitzschia species P. brasiliana. We also observed intron variability in cox1 genes. Phylogenetic analyses of mtDNAs, chloroplast genomes (cpDNAs), and nuclear ribosomal DNA (nrDNA) arrays revealed consistent results, supporting the closely related but distinct clustering of the genera Fragilariopsis and Pseudo-nitzschia. We further designed a high-resolution molecular marker tatA for species identification based on the comparative analysis of these mtDNAs, which could be used to track Pseudo-nitzschia diversity. These findings offer new genome resources and new insights into the genetic evolution and classification of Pseudo-nitzschia, underscoring the need for continued research in this field.

In this study, we aimed to evaluate the effect of dietary supplementation with edible mushroom (Pleurotus ostreatus)-derived polysaccharides on microcystin leucine-arginine (MC-LR)-induced skin damage in Pelophylax nigromaculatus tadpoles. Tadpoles were exposed to 1 μg/L daily MC-LR, with or without 5.0 g/kg of dietary P. ostreatus polysaccharides, for 30 days. P. ostreatus polysaccharide supplementation significantly increased the dermal collagen fibrils, increased tight junction protein gene expression, decreased the amount of MC-LR accumulation in skin tissues, attenuated oxidative stress, downregulated apoptosis-associated gene transcription, decreased eosinophil numbers, and downregulated transcription of inflammation-related genes (e.g. TLR4, NF-κB, and TNF-α). The composition of the skin commensal microbiota of MC-LR-exposed tadpoles supplemented with P. ostreatus polysaccharides was similar to that of the no-treatment control group. Lipopolysaccharide (LPS) content was positively correlated with the abundance of Gram-negative bacteria, including Chryseobacterium and Thauera. Therefore, P. ostreatus polysaccharides may alleviate MC-LR-induced skin barrier damage in tadpoles in two ways: 1) attenuation of oxidative stress-mediated apoptosis mediated by increased glutathione (GSH) content and total superoxide dismutase activity; and 2) alteration of the skin commensal microbiota composition to attenuate the LPS/Toll-like receptor 4 inflammatory pathway response. Furthermore, P. ostreatus polysaccharides may increase skin GSH synthesis by promoting glycine production via the gut microbiota and may restore the MC-LR-damaged skin resistance to pathogenic bacteria by increasing antimicrobial peptide transcripts and lysozyme activity. This study highlights for the first time the potential application of P. ostreatus polysaccharides, an ecologically active substance, in mitigating the skin damage induced by MC-LR exposure, and may provide new insights for its further development in aquaculture.

This study addresses the longstanding absence of a comprehensive phylogenetic backbone for the apple tribe Maleae, a deficiency attributed to limited taxon and marker sampling. We conducted an extensive taxon sampling, incorporating 563 plastomes from a diverse range of 370 species encompassing 26 presently recognized genera. Employing a range of phylogenetic inference methods, including RAxML and IQ-TREE2 for Maximum Likelihood (ML) analyses, we established a robust phylogenetic framework for the Maleae tribe. Our phylogenomic investigations provided compelling support for three major clades within Maleae. By integrating nuclear phylogenetic data with morphological and chromosomal evidence, we propose an updated infra-tribal taxonomic system, comprising subtribe Malinae Reveal, subtribe Lindleyinae Reveal, and subtribe Vauqueliniinae B.B.Liu (subtr. nov.). Plastid phylogenetic analysis also confirmed the monophyly of most genera, except for Amelanchier, Malus, Sorbus sensu lato, and Stranvaesia. In addition, we present a comprehensive taxonomic synopsis of Photinia and its morphological allies in the Old World, recognizing 27 species and ten varieties within Photinia, three species and two varieties within Stranvaesia, and two species and three varieties within Weniomeles. Furthermore, we also lectotypified 12 names and made two new combinations, Photiniamicrophylla (J.E.Vidal) B.B.Liu and Weniomelesatropurpurea (P.L.Chiu ex Z.H.Chen & X.F.Jin) B.B.Liu.

Aim: Genetic diversity is crucial for species adaptability. Understanding the mechanisms behind its formation and maintenance is essential for effective conservation. Recent studies have demonstrated that despite experiencing severe population bottlenecks, Muntiacus reevesi retains high genetic diversity and continues its northward migration, indicative of ongoing adaptive evolution. However, our comprehension of this phenomenon remains incomplete. The objective of this study is to explore the mechanisms underlying the formation of high genetic diversity and the genomic characteristics associated with local adaptation, using M. reevesi as a case study. Location: Southern China. Methods: We analysed resequencing data from 62 genomes and identified 29,124,081 high-quality single-nucleotide polymorphisms (SNPs). We used population genetics, demographic history, population differentiation, gene flow analysis software, and genotype-environment association (GEA) models to assess the factors that have contributed to high genetic diversity and environmental adaptability in the historical climate and geographical context. Results: The study identified that during Pleistocene climatic fluctuations, M. reevesi diverged into eastern (DB and WJW populations) and western lineages (WL, BA, and QL populations), all displayed high genetic diversity. Historically, M. reevesi maintained large effective populations, but contemporary human-induced threats have led to a significant decline. Population differentiation models suggest distinct expansion pathways for eastern and western lineages, resulting in population admixture, with mountain corridors facilitating gene flow and maintaining high genetic diversity. Additionally, environmental-genotype analysis revealed local adaptation in the QL-BA population, highlighting candidate adaptive genes (ME3 and PRKG1) potentially linked to cold adaptation and foraging behaviour. Conclusion: This study enhances our understanding of the mechanisms behind the high genetic diversity and environmental adaptability of M. reevesi, offering insights into how bottleneck populations maintain diversity, crucial for biogeographic research and conservation strategies for similar species.

The beet webworm, Loxostege sticticalis, is a typical migratory pest. Although miRNAs participate in many physiological functions, little is known about the functions of miRNAs in olfactory regulation. In this study, 1120 (869 known and 251 novel) miRNAs were identified in the antennae of L. sticticalis by using high-throughput sequencing technology. Among the known miRNAs, 189 from 49 families were insect-specific, indicating that these miRNAs might play unique roles in insects. Furthermore, based on the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses, we found that 3647 and 1393 miRNAs were associated with localization and the regulation of localization, respectively, and 80 miRNAs were enriched in the neuroactive ligand–receptor interaction pathway. These miRNAs might be involved in the olfactory system of L. sticticalis. Notably, qRT-PCR showed that most of the tested miRNAs presented similar expression patterns compared with the RNA-seq data and that miR-87-3, novel-miR-78, and novel-miR-142 were significantly differentially expressed in the antennae of males and females. In addition, 21 miRNAs were predicted to target 23 olfactory genes, including 10 odorant-binding proteins (OBPs), 3 chemosensory proteins (CSPs), 4 odorant receptors (ORs), 1 ionotropic receptor (IR), and 5 gustatory receptors (GRs). The olfactory-related miRNAs exhibited low-abundance transcripts, except undef-miR-55 and undef-miR-523, and gender-biased expression was not observed for olfactory-related miRNAs. Our findings provide an overview of the potential miRNAs involved in olfactory regulation, which may provide important information on the function of miRNAs in the insect olfactory system.

Treutlera is hitherto a monotypic genus of the tribe Marsdenieae in the family Apocynaceae, comprising the single rare-known species T. insignis known from Bhutan, India, and Nepal. Recent phylogenetic studies have resulted in great changes in the generic classification of Marsdenieae, yet left the unsampled Treutlera on an unclear generic status. Here we report its new occurrences in southeastern Xizang, China and test the generic status for the first time by using molecular evidence. Phylogenetic analysis highly supported the position of Treutlera embedded within the Marsdenia oreophila subclade which is separated from the Marsdenia s.s. subclade. Because of the internal relationships poorly resolved within the M. oreophila subclade and less-known morphological variations, Treutlera as the earliest generic name available for this subclade should be recognized and is tentatively kept monospecific with a conical and raised style-head; the probable expansion of Treutlera to include those species with long-rostrate or hemispherical and exserted style-heads from the M. oreophila subclade and even the unsampled Sinomarsdenia with included styles needs future studies to confirm. Based on all available materials, we update the morphological description of T. insignis concerning the much variable flower colors and some errors in previous descriptions. A lectotype is newly designated for T. insignis from the mixed original material. A distribution map and color photos from field and with detailed floral dissection are provided.

Phylogenetic studies in the phylogenomics era have demonstrated that reticulate evolution greatly impedes the accuracy of phylogenetic inference, and consequently can obscure taxonomic treatments. However, the sys-tematics community lacks a broadly applicable strategy for taxonomic delimitation in groups characterized by pervasive reticulate evolution. The red-fruit genus, Stranvaesia, provides an ideal model to examine the influence of reticulation on generic circumscription, particularly where hybridization and allopolyploidy dominate the evolutionary history. In this study, we conducted phylogenomic analyses integrating data from hundreds of single-copy nuclear (SCN) genes and plastomes, and interrogated nuclear paralogs to clarify the inter/intra-generic relationship of Stranvaesia and its allies in the framework of Maleae. Analyses of phylogenomic discord and phylogenetic networks showed that allopolyploidization and introgression promoted the origin and diversification of the Stranvaesia clade, a conclusion further bolstered by cytonuclear and gene tree discordance. With a well-inferred phylogenetic backbone, we propose an updated generic delimitation of Stranvaesia and introduce a new genus, Weniomeles. This new genus is distinguished by its purple-black fruits, thorns trunk and/ or branches, and a distinctive fruit core anatomy characterized by multilocular separated by a layer of sclereids and a cluster of sclereids at the top of the locules. Through this study, we highlight a broadly-applicable workflow that underscores the significance of reticulate evolution analyses in shaping taxonomic revisions from phylogenomic data.

In this comprehensive study, we conducted extensive taxon sampling and performed phylogenomic analyses based on plastome and nuclear ribosomal DNA (nrDNA) datasets. We employed multiple inference methods, including concatenated and coalescent-based strategies, to generate an accurate phylogeny of the woody Rosaceae genus Pourthiaea . The nrDNA phylogeny of Pourthiaea strongly supported three major clades, which were consistent with morphology. However, the plastid tree provided an alternative phylogenetic topology, indicating cytonuclear discordance. Frequent hybridizations between and among the species of Pourthiaea could explain the cytonuclear discordance. Considering the evidence from morphology and phylogenomic data, we propose a new infrageneric classification for Pourthiaea , consisting of three sections: P. sect. Pourthiaea , P. sect. Amphidoxae B.B.Liu, and P. sect. Impressivenae B.B.Liu.

Phylogenetic networks, rather than purely bifurcating trees, more accurately depict the intricate evolutionary dynamics of most lineages, especially those characterized by extensive hybridization and allopolyploidization events. However, the challenges of achieving complete taxon sampling, and limited financial resources for studying non-model plant lineages, have hindered comprehensive and robust estimation of phylogenetic backbones with guidance from networks. The bellflower tribe, Campanuleae, characterized by a reticulate evolutionary history, serves as an ideal model to investigate how to diagnose nested ancient reticulation events. Here, by integrating multiple genomic data sources and a range of phylogenetic inference methods, we produced a robust phylogenetic backbone for the tribe Campanuleae. Our investigation of reticulate evolution indicates that hybridization and allopolyploidization were instrumental in shaping the diversity of the bellflower tribe, particularly during the initial diversification of the subtribe Phytematinae. Additionally, we ascertained that conflicting topologies resulting from distinct genomic datasets and inference methodologies significantly impact downstream estimates of divergence dating, ancestral area construction, and diversification rates. This study offers a universally relevant framework for deciphering how to use network-based phylogenetic structures using various genomic sources and inference methods. [Campanulaceae, Campanuleae, Cytonuclear discordance, paralog, phylogenomics, reticulate evolution]

Microcystin-LR (MC-LR) is widely present in waters around the world, but its potential toxic effects and mechanisms on amphibian gills remain unknown. In the present study, tadpoles (Lithobates catesbeianus) were exposed to environmentally realistic concentrations of 0.5, 2 μg/L MC-LR, and 0 μg/L MC-LR (Control) for 30 days with the objective to unveil the impairment of gill health. The lysozyme was downregulated, while pattern recognition receptors and complement and adaptive immune processes were upregulated and the ability of gill supernatant to inhibit pathogenic bacteria decreased in the 0.5 and 2 μg/L MC-LR groups. The transcriptions of epithelial barrier components (e.g., CLDN1) were significantly decreased in MC-LR-exposed gills, while the gill content of lipopolysaccharide (LPS) endotoxins and the transcriptions of downstream responsive genes (e.g., TLR4 and NF-κB) were concurrently increased. In addition, the number of eosinophils and the expression of pro-inflammatory cytokines (e.g., IL-1β and TNF-α) were increased. These results imply that exposure of tadpoles to low environmentally concentrations of MC-LR leads to inflammation, increased permeability, and a reduced ability to inhibit pathogenic bacteria. The epithelial cells of inner gill filaments increased and transcriptions of hypoxic stress genes (e.g., HIF-1α, FLT1, and SERPINE1) were upregulated within the exposed group. As a consequence, exposure to MC-LR may lead to hypoxic stress. MC-LR exposure also drove gill microbiota to a dysbiosis. The relative abundance of Elizabethkingia was positively correlated with content of LPS and transcriptions of NF-κB and TNF-α. Overall, this study presents the first evidence about the pronounced impacts of MC-LR exposure on gills of amphibians, highlighting the susceptibility of early developing tadpoles to the environmental risks of MC-LR.

Lycoris longifolia, a new species from China, was described and illustrated here. Our phylogenomic evidence based on whole plastomes strongly supported the separate phylogenetic position of this new species, and morphologically it could also be distinguished by its long leaves with a distinct purplish-red midrib on the abaxial surface.

Background: Chimarrogale leander is a species of the family Soricidae and is mainly distributed in southern China. Methods: Here, a complete mitochondrial genome for C. leander was assembled via high-throughput sequencing technology. Results The results showed that the complete mitogenome of C. leander is 17,357 bp and includes 13 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and one control region. The nucleotide composition is A: 33.1%, T: 31.5%, C: 22.5% and G: 12.9%. Through the phylogenetic analysis of complete mitochondrial genome, it is found that C. leander has a close genetic relationship with Nectogale elegans. Conclusions: The new mitogenome will hopefully prove useful for systematic analyses of genus Chimarrogale .

Background: Chimarrogale leander is a species of the family Soricidae and is mainly distributed in southern China. Methods: Here, a complete mitochondrial genome for C. leander was assembled via high-throughput sequencing technology. Results The results showed that the complete mitogenome of C. leander is 17,357 bp and includes 13 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and one control region. The nucleotide composition is A: 33.1%, T: 31.5%, C: 22.5% and G: 12.9%. Through the phylogenetic analysis of complete mitochondrial genome, it is found that C. leander has a close genetic relationship with Nectogale elegans. Conclusions: The new mitogenome will hopefully prove useful for systematic analyses of genus Chimarrogale.