BMC Biology最新文献

{"title":"The demic expansion of Yangshao culture inferred from ancient human genomes.","authors":"Lei Sun, Hao Ma, Rui Wang, Zhijiang Wu, Limin Qiu, Haodong Chen, Chuan-Chao Wang","doi":"10.1186/s12915-025-02286-9","DOIUrl":"10.1186/s12915-025-02286-9","url":null,"abstract":"<p><strong>Background: </strong>Originating from the middle Yellow River, Yangshao culture is one of the most influential archaeological cultures in Neolithic China. It has long been debated whether there was a genetic substructure between the core Yangshao sites and those representing regional variants of the Yangshao culture, such as the Qinwangzhai culture. The excavated human remains from the burials at the Zhanmatun site, which belonged to the Qinwangzhai culture, present ideal material for inferring the population dynamics accompanying the cultural expansion.</p><p><strong>Results: </strong>In this study, we analyzed genome-wide data from 12 human remains obtained from the Zhanmatun site. The results indicated that Zhanmatun individuals were genetically homogeneous with all published Yangshao culture-related individuals from the core region of Yangshao and its periphery as well as Late Dawenkou culture-related Xixiahou people in the east, with no tracts of genetic influence from Neolithic Southern East Asian in the south.</p><p><strong>Conclusions: </strong>Our findings support a demic diffusion model for Yangshao culture expansion, where human migration, rather than mere cultural diffusion, played a dominant role in spreading Yangshao-related ancestry across northern China.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":"23 1","pages":"186"},"PeriodicalIF":4.4,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12218936/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144539061","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Ophiocordyceps sinensis-induced changes in Thitarodes xiaojinensis: from intestinal barrier destruction, microbiome dysbiosis to immune responses at the molecular level.","authors":"Xiu-Wen Bao, Qing-He Wang, Ting Li, Yong Li, Zhi-Ying Bian, Si-Jing Liu, Li-Ying He, Shu-Qi Niu, Jin-Lin Guo","doi":"10.1186/s12915-025-02277-w","DOIUrl":"10.1186/s12915-025-02277-w","url":null,"abstract":"<p><strong>Background: </strong>The entomopathogenic fungus (EPF) Ophiocordyceps sinensis has a long-term coexistence with its host insect, Thitarodes xiaojinensis, making it a unique model for host-pathogen interactions. Hemolymph, a critical component in insects, plays an essential role in maintaining both nutritional and immune homeostasis. However, the mechanism of the host's immune response remains unclear when O. sinensis proliferates in the hemolymph.</p><p><strong>Results: </strong>O. sinensis caused damage to the insect's intestinal barrier, facilitating the translocation of gut bacteria into the hemocoel. Subsequently, the presence of O. sinensis and opportunistic pathogenic bacteria from the gut disrupted the homeostasis of the hemolymph microbiota, resulting in an increase in bacterial diversity. This disruption triggered a series of physiological responses in the host, including elevated levels of endocrine hormones specifically 20-hydroxyecdysone (20E) and juvenile hormone 3 (JH3). Additionally, there was an enhancement of antioxidant capacity, as indicated by increased total antioxidant capacity and glutathione S-transferase activity, along with the production of antimicrobial peptides (AMPs) as part of the immune defense. Notably, the rise in 20E levels during O. sinensis infection might have significantly contributed to the increased production of AMPs.</p><p><strong>Conclusions: </strong>O. sinensis infection significantly alters T. xiaojinensis physiology. Humoral immunity in infected hosts is primarily in response to hemolymph microbial homeostasis due to intestinal translocation. Among them, 20E upregulates AMP-related genes, suggesting a key immune strategy for managing microbial imbalances while tolerating fungal pathogens.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":"23 1","pages":"183"},"PeriodicalIF":4.4,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12220380/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144538972","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"AmpHGT: expanding prediction of antimicrobial activity in peptides containing non-canonical amino acids using multi-view constrained heterogeneous graph transformer.","authors":"Yongcheng He, Xu Song, Hongping Wan, Xinghong Zhao","doi":"10.1186/s12915-025-02253-4","DOIUrl":"10.1186/s12915-025-02253-4","url":null,"abstract":"<p><strong>Background: </strong>Antimicrobial peptide (AMP) prediction has been extensively studied in recent years. However, many existing models do not fully leverage the intrinsic chemical structures of AMPs, such as atomic composition and sidechain group characteristics. Instead, these models often focus on letter composition, positional encodings, and pre-defined chemical-physical descriptors. The incorporation of non-canonical amino acids, which enhance peptide stability and reduce toxicity, is getting more attention in peptide design. Despite this, they are overlooked in predictive studies, as traditional deciphering methods and single-letter representation systems are inadequate for this task. Even though some efforts have been made to expand current alphabets, these approaches remain insufficient, impeding the development of novel AMPs.</p><p><strong>Results: </strong>A novel deep learning model, termed AmpHGT, was developed based on heterogeneous graphs' representation of peptides. AmpHGT demonstrates competitive performance against current methods on canonical amino acid benchmarks. Notably, AmpHGT is capable of efficiently classifying antimicrobial peptides with non-canonical amino acids, addressing the limitations of traditional feature extraction methods. In addition, this model is adaptable to handling different conformations, sidechains, and backbones (e.g., α, β, γ), demonstrating its potential to enhance the screening and discovery of AMPs containing non-canonical amino acids.</p><p><strong>Conclusions: </strong>Our study suggests that AmpHGT is reliable for antimicrobial peptide classification task. It may serve as an efficient primary filter for evaluating thousands of mined peptides and provides a good foundation for future studies aimed at producing peptide antibiotics containing non-canonical amino acids.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":"23 1","pages":"184"},"PeriodicalIF":4.4,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12217533/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144539025","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Astaxanthin prevents postovulatory oocyte aging by targeting TNFR2 and inhibiting the TNF signaling pathway.","authors":"Xin Wen, Zhe Han, Qi Yang, Ke-Song Shi, Dui Sun, Xiao-Jie Zhang, Cheng-Guang Liang","doi":"10.1186/s12915-025-02292-x","DOIUrl":"10.1186/s12915-025-02292-x","url":null,"abstract":"<p><strong>Background: </strong>MII oocytes undergo time-dependent aging after ovulation, which is closely associated with impaired fertilization potential, poor embryo quality, and an increased risk of miscarriage. The apoptosis of cumulus cells and their secretion of TNF-α are identified as the primary contributors to postovulatory oocyte aging.</p><p><strong>Results: </strong>In this study, we demonstrated that astaxanthin supplementation in culture medium effectively prevents postovulatory oocyte aging and extends oocyte lifespan in vitro. Importantly, this protective effect does not operate through the inhibition of cumulus cell apoptosis or TNF-α release. Notably, astaxanthin selectively binds to TNFR2 in oocytes, thereby preventing TNFR2 from interacting with TNF-α and inhibiting the activation of the TNF signaling pathway within oocytes. Furthermore, oocytes cultured with astaxanthin exhibit enhanced potential for early embryonic development and significantly increased IVF-ET litter size compared to controls.</p><p><strong>Conclusions: </strong>Our findings, based on a mouse model, provide valuable insights into the potential clinical application of astaxanthin in mitigating post-ovulatory oocyte aging.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":"23 1","pages":"176"},"PeriodicalIF":4.4,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12210564/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144539028","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Avian interferon regulatory factor (IRF) family reunion: IRF3 and IRF9 found.","authors":"Lenka Ungrová, Josef Geryk, Marina Kohn, Dana Kučerová, Veronika Krchlíková, Tomáš Hron, Vladimír Pečenka, Petr Pajer, Eliška Gáliková, Ľubomíra Pecnová, Bernd Kaspers, Jiří Hejnar, Jiří Nehyba, Daniel Elleder","doi":"10.1186/s12915-025-02261-4","DOIUrl":"10.1186/s12915-025-02261-4","url":null,"abstract":"<p><strong>Background: </strong>Interferon regulatory factors (IRFs) are a family of transcription factors with important functions in immunity. The genomes of most vertebrates encode ten IRF genes. IRF3 and IRF9 have key roles in interferon (IFN) induction and signaling. Most of our knowledge about the IFN pathways originates from the study of the mammalian IFN system, and the description of the corresponding avian components is not as complete. Both IRF3 and IRF9 were considered missing from the chicken genome and from the genomes of other avian species.</p><p><strong>Results: </strong>Here we describe multiple avian IRF3 and IRF9 genes, all with difficult GC-rich sequence context that prevented their earlier characterization. IRF3 orthologs are narrowly distributed and are present in the avian infraclass Palaeognathae. In contrast, IRF9 orthologs were found in most avian species, with the exception of the order Galliformes. In about half of the avian orders, IRF9 was located in noncanonical chromosomal positions, indicating past translocations. Phylogenetic analysis confirmed the correct orthology of all newly described IRFs. We further performed experiments using duck IRF9, confirming its role in the IFN pathway. IRF9 knockout in duck fibroblasts decreases the induction of IFN-stimulated genes (ISGs). Full induction of ISGs in duck cells requires both an intact IRF9 and a canonical IFN-stimulated response element. Lastly, intact IRF9 is needed for IFN-mediated protection of duck cells against the vesicular stomatitis virus-induced cytopathicity.</p><p><strong>Conclusions: </strong>The identification of avian IRFs fills an important gap in our understanding of avian immunology and brings new questions related to the evolution of the IRF family.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":"23 1","pages":"180"},"PeriodicalIF":4.4,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12220609/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144539029","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Epigenetic silencing and genome dynamics determine the fate of giant virus endogenizations in Acanthamoeba.","authors":"Cédric Blais, Morgan J Colp, Luke A Sarre, Alex de Mendoza, John M Archibald","doi":"10.1186/s12915-025-02280-1","DOIUrl":"10.1186/s12915-025-02280-1","url":null,"abstract":"<p><strong>Background: </strong>Endogenized giant viruses are emerging as major contributors to the genome evolution of microbial eukaryotes, with both degraded and fully functional latent viruses being found integrated in diverse lineages. The mechanisms that determine the fate of viral integrants are poorly understood, however. Acanthamoeba is a unicellular eukaryote known for undergoing lateral gene transfer (LGT) with viruses. Here we have leveraged chromosome-scale assemblies of two strains of Acanthamoeba, Neff and C3, to investigate the genomic mechanisms that mediate the fate of viral integrations in eukaryotic genomes.</p><p><strong>Results: </strong>Viral integrations in the C3 and Neff genomes are largely non-overlapping and disproportionately found in sub-telomeric regions. Multiple partial copies of these insertions are found throughout the Neff genome, but they are not expressed, do not obviously encode functions associated with their own mobility, and are colonized by host mobile elements. Viral regions are hypermethylated and highly condensed, suggesting that the expression of recently acquired viral DNA is suppressed in heterochromatic regions.</p><p><strong>Conclusions: </strong>We propose a model for the trajectory of viral sequences in Acanthamoeba: (i) integration of DNA from giant viruses, (ii) epigenetic suppression of the viral DNAs, allowing them to persist in the genome, and (iii) deterioration of viral genomes by point mutation, mobile element colonization, and intra- and inter-chromosomal recombination. Viral integrations in Acanthamoeba spp. are transient and may not have long-lasting effects on the fitness of the amoeba. Our work highlights the importance of host genome dynamics and epigenetic silencing for understanding the evolution of endogenized viral elements.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":"23 1","pages":"171"},"PeriodicalIF":4.4,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12210455/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144539046","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Single-cell transcriptomics and time-series metabolite profiling reveal the spatiotemporal regulation of flavonoid biosynthesis genes and phytohormone homeostasis by PAP1 in Arabidopsis.","authors":"Bingxu Zhang, Thomas Ka Yam Lam, Linheng Chen, Chen Zhang, Liping Zhu, Hailei Zhang, Pengxi Wang, Jianing Wang, Zongwei Cai, Yiji Xia","doi":"10.1186/s12915-025-02297-6","DOIUrl":"10.1186/s12915-025-02297-6","url":null,"abstract":"<p><strong>Background: </strong>Understanding the spatiotemporal regulation of specialized metabolism in plants is critical for advancing both basic plant biology and biotechnological applications. PRODUCTION OF ANTHOCYANIN PIGMENT 1 (PAP1) is a well-known transcription factor that plays a key regulatory role in the biosynthesis pathway of plant flavonoids. Similar to other secondary metabolites, flavonoid biosynthesis displays cell heterogeneity. However, the cell-specific regulation network of the flavonoid biosynthetic pathway remains unclear.</p><p><strong>Results: </strong>In this study, we utilized single-cell RNA sequencing (scRNA-seq) and time-series metabolite profiling to investigate the regulation of flavonoid biosynthesis and phytohormone homeostasis in Arabidopsis thaliana by PAP1. By comparing single-cell transcriptomes of the pap1-D mutant and wild-type plant leaves, we constructed a cell-type-specific atlas of gene expression and high-resolution dynamics of metabolites across developmental stages. Our findings reveal that PAP1 overexpression induces distinct spatiotemporal regulation of phenylpropanoid pathway genes in different cell types and widespread upregulation of glycosylation processes. Metabolomic profiling validated these transcriptional patterns and showed significant changes of metabolites in phenylalanine metabolic processes as pap1-D leaf matures. Additionally, PAP1 overexpression leads to significant changes in phytohormone levels, particularly jasmonate and salicylate, indicating complex crosstalk between flavonoid biosynthesis and hormone homeostasis.</p><p><strong>Conclusions: </strong>This integrated multi-omics approach provides unprecedented insights into the cell-specific regulatory networks controlling specialized metabolism and establishes a valuable framework for optimizing metabolic engineering strategies to enhance the production of bioactive plant compounds.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":"23 1","pages":"191"},"PeriodicalIF":4.4,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12220432/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144539058","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Adaptation of Diqing Tibetan pigs to hypoxic and cold environments through extramedullary hematopoiesis and uncoupled thermogenesis in the liver.","authors":"Xinpeng Li, Xinxing Dong, Shuhong Zhao, Yunlong Ma, Siqi Jin, Chunlu Zhou, Yi Lan, Shuyuan Luo, Bin Ni, Hongjiang Wei, Dawei Yan","doi":"10.1186/s12915-025-02281-0","DOIUrl":"10.1186/s12915-025-02281-0","url":null,"abstract":"<p><strong>Background: </strong>Tibetan pigs, which have long inhabited the Qinghai-Tibet Plateau at elevations exceeding 3000 m, serve as an ideal model for studying adaptation to extreme high-altitude environments. The multifunctionality of the liver (hematopoiesis, metabolism, detoxification) plays a crucial role in the adaptation of Tibetan pigs to hypoxic and cold environments, yet the specific mechanisms remain unclear.</p><p><strong>Results: </strong>This study employed single-nucleus RNA sequencing to profile and conduct bioinformatic analyses on the liver tissues of Diqing Tibetan pigs across 5 developmental stages (embryonic day 25, embryonic day 55, day of birth, development to 30 days, and development to 90 days). The goal was to identify and investigate key cell types and the regulatory mechanisms of core gene expression that facilitate adaptation to hypoxia and cold. In the fetal liver, various subpopulations of erythrocytes were detected. Analysis of these subpopulations allowed for the construction of a cellular development trajectory from proliferative erythrocytes to division erythrocytes to denucleating erythrocytes, revealing that key transcription factors (JUNB and MAFF) and functional genes (HBP1 and PPP2CB) play significant roles in erythrocyte enucleation. Furthermore, the presence of hematopoietic stem cells in the postnatal liver was observed, with identification of subpopulations exhibiting myeloid differentiation tendencies. These cells continuously support hematopoiesis and facilitate new blood vessel formation, thereby increasing red blood cell counts to aid in the adaptation of Diqing Tibetan pigs to hypoxic conditions. Additionally, a class of hepatocytes capable of converting metabolic energy into heat through uncoupling processes was identified, which assists in the adaptation to the cold environments of the plateau.</p><p><strong>Conclusions: </strong>In summary, our study provides new scientific perspectives on the adaptation mechanisms of high-altitude animals to extreme environments.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":"23 1","pages":"181"},"PeriodicalIF":4.4,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12218016/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144539023","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Rotifers in space: transcriptomic response of the bdelloid rotifer Adineta vaga aboard the International Space Station.","authors":"Victoria C Moris, Lucie Bruneau, Jérémy Berthe, Richard Coos, Bjorn Baselet, Anne-Catherine Heuskin, Nicol Caplin, René Demets, Jutta Krause, Lobke Zuijderduijn, Alexandra Tortora, Magdalena Herova, Sébastien Penninckx, Luca Parmitano, Kevin Tabury, Sarah Baatout, Karine Van Doninck, Boris Hespeels","doi":"10.1186/s12915-025-02272-1","DOIUrl":"10.1186/s12915-025-02272-1","url":null,"abstract":"<p><strong>Background: </strong>The biological effects of spaceflight remain incompletely understood, even in humans (Homo sapiens), and are largely unexplored in non-traditional models such as bdelloid rotifers.</p><p><strong>Results: </strong>This study analyzes the transcriptomic changes experienced by Adineta vaga, a bdelloid rotifer aboard the International Space Station (ISS), using RNA sequencing. The aim was to investigate the overall effect of spaceflight in Low Earth Orbit (LEO) on these organisms. To this end, new hardware was developed to enable autonomous culturing of rotifers with minimal astronaut intervention. The study revealed significant transcriptomic changes, with 18.61% of genes showing differential expression in response to microgravity and radiation. These changes included upregulation of genes involved in protein synthesis, RNA metabolic processes, and DNA repair. Notably, the study also found a significant enrichment of foreign genes (Horizontal Gene Transfers: HGTs) among the genes that were either over- or under-expressed during spaceflight, suggesting that HGTs play a role in bdelloids' adaptability to new and potentially atypical environments.</p><p><strong>Conclusions: </strong>This research not only enhances our understanding of how organisms respond to microgravity but also proposes A. vaga as a valuable model for future studies in space biology.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":"23 1","pages":"182"},"PeriodicalIF":4.4,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12220480/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144538974","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Ancient genomes in Southwest China revealed genetic interactions among diverse populations in the historical period.","authors":"Wen Wan, Huangzhen Huang, Changguo Hu, Xinglong Zhang, Qingting Zhou, Meiqing Yang, Jianxin Guo, Mingxia Xie, Kongyang Zhu, Xiaomin Yang, Hao Ma, Rui Wang, Jing Zhao, Le Tao, Haifeng He, Qun Zhang, Li Jin, Bisu Zhou, Jiang Huang, Chuan-Chao Wang","doi":"10.1186/s12915-025-02299-4","DOIUrl":"10.1186/s12915-025-02299-4","url":null,"abstract":"<p><strong>Background: </strong>Southwest China has been pivotal for agricultural spread, ethnic formation, and cultural diffusion. However, the genetic diversity and population structure of this area remain insufficiently explored, especially during the historical period.</p><p><strong>Results: </strong>Here, we report genome-wide data of eight ancient individuals from the Songshan site in Guizhou dating back to the Song and Ming Dynasty. Our results reveal that most Songshan individuals are closely related to the Yellow River Basin farmers, while also showing significant genetic influences from southern East Asia, including affinities with ancients in Guangxi, coastal Fujian, and Southeast Asia. Additionally, some Songshan individuals displayed a high genetic affinity with local Hmong-Mien populations.</p><p><strong>Conclusions: </strong>These findings underscore the complexity of genetic interactions and population movements during the historical period, providing new insights into the genetic landscape and ethnic formation processes in Southwest China.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":"23 1","pages":"174"},"PeriodicalIF":4.4,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12211951/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144539027","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}