Biology subjects

Liu, Y.-C.

Publications and source records attributed to Liu, Y.-C..

At least 19 recordsLinked to original sources

bioRxiv2026

Immunogen selection and prior immunity shape antibody breadth following immunisation with avian H5 hemagglutinin

Avian influenza A viruses pose a persistent zoonotic threat to humans owing to their expanding host range and high case fatality rates. In particular, viruses from the 2.3.4.4b clade of the H5 subtype have now been detected in over 60 mammalian species, raising serious pandemic concerns. Understanding immune recognition of the H5 hemagglutinin (HA) is therefore critical for effective vaccine design and pandemic preparedness. To understand the breadth of cross-recognition induced by different H5 strains, we selected genetically diverse H5 human isolates from 2003-2023 and assessed neutralising antibody responses elicited by adjuvanted recombinant HA protein-based vaccines in C57BL/6 mice. Neutralisation activity of sera was determined against seven H5 HA variants using pseudotyped viruses and a PR8-reassortant virus in micro-neutralisation assays. Our results showed a wide variety of cross-strain neutralisation across H5 HA antigen variants. The conventional vaccine strain A/Indonesia/05/2005 displayed narrow activity against emerging clade 2.3.4.4b viruses, whereas ancestral variants exhibited cross-neutralisation profiles showing a diversity of breath but with limited potency. Polyvalent H5 HA formulations and nanoparticle-displayed H5 HA platforms substantially broadened cross-neutralisation against diverse H5 strains. To examine the impact of pre-existing immunity on H5 vaccine immunogenicity in mouse models, mice were primed with either seasonal influenza infection or quadrivalent influenza vaccine (QIV) prior to H5 HA immunisation. QIV pre-vaccination, but not prior influenza infection, enhanced subsequent neutralizing responses towards A/Fujian-Sanyuan/21099/2017 (clade 2.3.4.4b) H5. Collectively, our results demonstrate that immunogen selection and prior immunity shape antibody breadth following immunisation with avian A(H5) hemagglutinin.

immunology↗

bioRxiv2026

High culturable diversity and climate-associated seasonal dynamics of Saccharomycotina yeasts in subtropical forest leaf litter

Forest-associated Saccharomycotina occur at low relative abundance, limiting inference about their diversity and dynamics. We sampled leaf litter weekly for 47 weeks across a subtropical forest in northern Taiwan. Enrichment, isolation and ITS sequencing recovered 687 isolates, including 613 Saccharomycotina representing 56 described species and 77 putatively novel operational taxonomic units. Rarefaction indicated unsampled culturable diversity. Among litter traps, community dissimilarity was high and dominated by taxon replacement, but neither topography nor geographic distance was associated with composition, and turnover matched randomised expectations. Richness peaked during warm, wet periods and declined in winter, and minimum temperature showed the strongest statistical association. Composition was associated with maximum temperature, minimum relative humidity, precipitation and solar radiation. Selected isolates' thermal optima covaried with collection-week temperatures, and two October Magnusiomyces magnusii isolates had higher optima than four winter isolates. Together, these findings reveal substantial culturable diversity and seasonal community restructuring consistent with temperature-related filtering.

microbiology↗

bioRxiv2026

Reprogramming Dedifferentiation Regulatory Networks Preserves Human Chondrocyte Phenotypes

Chondrocyte-based cartilage repair strategies such as autologous chondrocyte implantation (ACI) require extensive in vitro expansion to obtain clinically relevant cell numbers. However, this expansion step progressively drives chondrocyte dedifferentiation, reducing matrix-forming capacity and contributing to variable repair outcomes. To better understand this process, we used single-nucleus multiome profiling (snRNA-Seq + snATAC-Seq) to define the transcriptional and chromatin accessibility programs underlying human chondrocyte dedifferentiation during expansion. Multiome integration across passages revealed a continuous dedifferentiation trajectory accompanied by coordinated remodeling of gene expression and chromatin accessibility, identifying chromatin destabilization as an early regulatory event during phenotype loss. Guided by these regulatory signatures, we screened available small-molecule inhibitors targeting candidate pathways and found that Fludarabine most consistently preserved chondrocyte identity during early expansion. Fludarabine was associated with suppression of STAT1-related programs and early stabilization of the chromatin landscape prior to broader transcriptional recovery. Functionally, treated cells demonstrated enhanced matrix-forming capacity in chondrogenic pellet culture and significantly increased nascent protein synthesis in 3D hydrogel culture, with biosynthetic output approaching unexpanded controls by day 21. Together, these findings identify chromatin stability as a key regulatory determinant of expansion-associated chondrocyte dedifferentiation and establish a pharmacologic strategy to preserve chondrocyte functional potency during cell manufacturing for cartilage repair.

bioengineering↗

bioRxiv2026

A haploid wild yeast resource for exploring the natural ecology of Saccharomyces cerevisiae

Saccharomyces cerevisiae predominantly exists as diploid cells in nature, a life-cycle feature that limits classical genetic analyses of wild populations. Here, we establish a stable haploid strain collection derived from 33 diverse Taiwanese S. cerevisiae isolates through targeted disruption of the HO endonuclease gene. This resource spans predomesticated Asian wild lineages and enables systematic analyses of mating compatibility, reproductive isolation, and ecological trait variation. Although all pairwise hybridizations formed zygotes, many produced low spore viabilities, revealing strong postzygotic barriers. Genome analyses show that reduced hybrid fertility is primarily associated with chromosomal inversions and inter-chromosomal rearrangements rather than sequence divergence, indicating that structural variation maintains lineage separation despite geographic coexistence. Phenotypic profiling uncovered marked ecological differentiation, with the most diverged TW1 lineage favoring cooler growth conditions and a naturally occurring hybrid exhibiting heterosis with expanded thermal tolerance. While most wild strains grew poorly on maltose, two anthropogenically associated strains displayed enhanced maltose utilization linked to functional MAL regulatory alleles and maltose-specific transporters. Together, these findings demonstrate how structural genomic variation and metabolic gene divergence drive ecological and reproductive divergence in wild S. cerevisiae and establish this haploid collection as a platform for studying yeast evolution in nature.

genetics↗

bioRxiv2025

Dynamic evolution of AT-rich isochores shapes the genome of an intertidal fungus Annulohypoxylon annulatoides

Marine and coastal fungi experience intense environmental variability, yet the genomic mechanisms enabling filamentous fungi to tolerate such conditions remain unclear. From 56 fungal isolates collected along the Lailai rocky shore in northern Taiwan, we selected Annulohypoxylon annulatoides for deeper investigation due to its prevalence and distinctive stress response. Phenotypic assays revealed that this strain exhibits distinct growth and recovery dynamics under salinity, temperature, and UV stress compared to conspecific strains isolated from tree bark. To investigate the genomic basis of its adaptation, we generated a high-quality 41.8 Mbp de novo genome assembly with 11,529 predicted proteins. Across Hypoxylaceae genomes, we identified variably sized and dispersed AT-rich isochores, which in A. annulatoides were enriched in repeats and displayed low gene density. Despite differences in AT content, core gene content and Pfam domain profiles remained conserved. These AT-rich isochores exhibit several sequence and structural features consistent with scaffold/matrix attachment regions (S/MARs), raising the possibility that they influence higher-order genome organisation. Comparative analyses suggest they arose through independent repeat insertions or via ancestral repeat amplifications. Together, our findings point to a role for AT-rich isochores in shaping genome architecture and potentially mediating stress-responsive regulation, supporting the broader environmental flexibility observed in Hypoxylaceae, including adaptation to dynamic coastal habitats.

genomics↗

bioRxiv2025

Mechanical Cues Regulate Estrogen and Progesterone-Induced Nascent ECM Deposition by Human Endometrial Stromal Cells

The endometrium, the mucosal lining of the uterus, is a highly regenerative tissue that undergoes cyclic remodeling guided by tightly regulated levels of estrogen and progesterone. Stromal cells are embedded within the connective tissue of the endometrium and contribute to the rapidly changing extracellular matrix (ECM). With hormone exposure, endometrial stromal cells undergo decidualization, which alters their morphology and protein secretion. While an increase in tissue modulus is associated with gynecological diseases, the relationship between mechanical properties, hormone exposure, and ECM deposition remains poorly understood. Here, we investigated how both stiffness and hormones regulate ECM deposition by human endometrial stromal cells during decidualization. Using metabolic labeling with sugar analogs and click chemistry, we measure newly secreted ECM proteins deposited by endometrial stromal cells during decidualization. Additionally, we study the nascent ECM in response to different mechanical properties using hyaluronic acid hydrogels. To increase throughput and reproducibility, we designed an automated ImageJ-based workflow for unbiased quantification of nascent ECM deposition. Our results demonstrate that hormones induce decidualization, characterized by F-actin stress fiber formation and prolactin secretion. In addition, we show that decidualization on hydrogels is characterized by an increase in nascent ECM deposition which depends on the initial hydrogel modulus. In contrast, endometrial stromal cells on glass show little change in nascent ECM deposition during hormone exposure. Collectively, these findings demonstrate that both mechanical and biochemical cues regulate ECM deposition during endometrial remodeling. These observations may provide new insights towards future studies addressing the mechanisms of ECM remodeling in gynecological diseases.

bioengineering↗

bioRxiv2025

Memory T and B cells with recognition of avian influenza hemagglutinins are poorly responsive to existing seasonal influenza vaccines

Immunisation remains the most cost-effective mechanism to combat global influenza infection and is widely employed against seasonal influenza viruses. Zoonotic transmission of avian influenza A viruses represents a significant threat to human health given the lack of population level immunity, which could translate into an influenza pandemic. Therefore, there is a need to better understand pre-existing human immunity against avian influenza strains. as highlighted by the recent rapid, global spread of avian H5Nx clade 2.3.4.4b variants. Here, we sought to quantify the frequencies and specificities of B cells recognising avian hemagglutinin (HA) within unexposed adults, and to characterise the ability of seasonal immunisation to boost cross-reactive immune responses to H5Nx strains, including from clade 2.3.4.4b. Low but detectable serum antibody titres against H5 and H7 avian influenza HA were observed in donors. The frequency of memory B cells with cross-reactive recognition of H5 and H7 HA was low and 2-5 fold lower than populations of seasonal H1N1 and H3N2 HA-specific B cells. Boosting of B cell responses against H5Nx clade 2.3.4.4b HA following seasonal immunisation were sporadic with only 3 out of 19 individuals showing an increased population of probe-positive cells. Cross-reactive B cells generally expressed immunoglobulins drawn from variable heavy chain genes associated with recognition of the HA stem (VH6-1, VH1-69, VH1-18). CD4+ T cell responses towards H5 HA were also weakly boosted with little to no increase in circulating T follicular helper cell populations. These findings highlight the need for avian influenza-specific vaccine products to bolster immunity in human populations, with consideration for use in pre-pandemic preparedness to expand baseline frequencies of avian influenza-specific memory B and T lymphocytes.

immunology↗

bioRxiv2024

METCAM/MUC18 plays a tumor promoter role in the development of nasopharyngeal carcinoma type III

Our previous studies by testing the effects of huMETCAM/MUC18 over-expression on the tumorigenesis of the NPC-TW01 cell line supports the notion that huMETCAM/MUC18 plays a tumor suppressor role in the development of nasopharyngeal carcinoma (NPC) type I. However, it is not clear if this notion also holds true for another NPC cell line, NPC-TW04, which was established from NPC type III. For this purpose, we further investigated the effects of huMETCAM/MUC18 over-expression in the NPC-TW04 cell line on their in vitro cellular behaviors and in vivo tumorigenesis in athymic nude mice. First, the G418-resistant clones were obtained after transfection of the huMETCAM/MUC18 cDNA into the NPC-TW04 cell line. Then, one NPC-TW04 clone, which expressed a high level of huMETCAM/MUC18, and one empty vector (control) clone were used for testing effects of huMETCAM/MUC18 over-expression on their in vitro behaviors (intrinsic growth rate, motility, and invasiveness, and growth on three-dimensional basement membrane) and in vivo tumorigenesis (via subcutaneous injection) in the athymic nude mice. Time course of tumor proliferation and final tumor volumes/weights were determined. Tumor sections were used for histology and immunohistochemistry (IHC) analyses. Tumor lysates were used to determine levels of huMETCAM/MUC18 and various downstream key effectors. We found that over-expression of huMETCAM/MUC18 increased in vitro motility and invasiveness, induced the invasive growth in the 3D basement membrane culture assay, and increased in vivo tumorigenicity of NPC-TW04 cell line. The expression levels of downstream effectors, such as an anti-apoptosis index, proliferation index, an index of metabolic switch to aerobic glycolysis, angiogenesis indexes and survival pathway index, were increased, whereas the pro-apoptosis index decreased in the tumors. Thus, contrary to the role of huMETCAM/MUC18 in the NPC-TW01 cells, huMETCAM/MUC18 over-expression in the NPC-TW04 cells increased epithelial-to-mesenchymal transition and also in vitro invasive growth and in vivo tumorigenesis, suggesting that it plays a tumor promoter role in the development of NPC type III by reducing apoptosis and increasing anti-apoptosis, angiogenesis, proliferation and metabolic switch to aerobic glycolysis.

cancer biology↗

bioRxiv2024

Spatiotemporal dynamics and assembly process differ in fungal communities across contiguous habitats in tropical forests

BackgroundThe variation in fungal community composition within a single habitat space has been extensively studied in forest ecosystems. However, the spatial and temporal distribution of fungi across contiguous habitats, particularly at a local scale and in tropical regions, remains underexplored. In this study, we examined the fungal community composition across multiple habitats proximal to each other over two seasons in seven Fagaceae species in Taiwanese broadleaf forests. We tested how local spatial scale and habitat influence community assembly. ResultsUsing a metabarcoding approach, we sequenced ITS3/ITS4 amplicons from 864 samples collected from four distinct habitats--leaves, twigs, litter, and soil. We identified 11,600 fungal amplicon sequence variants (ASVs), with community composition differing significantly between habitats proximal to each other. Phyllosphere (leaves and twigs) fungi exhibited higher diversity compared to soil. Habitat type and long-term precipitation emerged as the most influential factors driving fungal diversity and composition, with a clear distance-decay relationship observed in leaf and twig but not in soil. Random forest analysis accurately classified habitats based on ASVs relative abundances, with strong predictors were mostly endemic ASVs prevalent in soil. Misclassified samples were due to secondary contact of fungi between adjacent habitats. Co-occurrence network analysis revealed more complex and deterministic networks in leaf and twig habitats, while soil was driven by stochastic processes and contained most endemic ASVs. A Cladosporium sp. emerged as a keystone species, maintaining network stability across forests. ConclusionThis study reveals how local spatial variation and habitat shape distinct fungal communities in tropical forests, with deterministic processes dominating in some habitats and stochasticity playing a key role in others. We show local fungal taxa were strong habitat predictors and drivers of community cohesion. These findings highlight the importance of studying coexisting habitats to gain a deeper understanding of fungal biogeography and ecosystem function.

ecology↗

bioRxiv2024

Novel naphthyridones targeting Pannexin 1 for colitis management

Pannexin 1 (PANX1) forms cell-surface channels capable of releasing signaling metabolites for diverse patho-physiological processes. While inhibiting dysregulated PANX1 is proposed as a therapeutic strategy for many pathological conditions, including inflammatory bowel disease (IBD), low efficacy or poor specificity of classical PANX1 inhibitors introduces uncertainty for their applications in basic and translational research. Here, we performed hit-to-lead optimization and identified a naphthyridone, compound 12, as a new PANX1 inhibitor with an IC50 of 0.73 M that does not affect pannexin-homologous LRRC8/SWELL1 channels. Using structure-activity relationship analysis, mutagenesis, cell thermal shift assays, and molecular docking, we revealed that compound 12 directly engages PANX1 Trp74 residue. Using a dextran sodium sulfate mouse model of IBD, we found that compound 12 markedly reduced colitis severity, highlighting new PANX1 inhibitors as a proof-of-concept treatment for IBD. These data describe the mechanism of action for a new PANX1 inhibitor, identify the binding site for future drug design, and present a targeted strategy for treating IBD. TeaserA specific PANX1 inhibitor presents a proof-of-concept treatment for inflammatory bowel disease.

molecular biology↗

bioRxiv2024

Dynamic positioning of a TFIIE-related winged-helix domain in RNA polymerase elongation complex III underpins its multi-functionality

The tandem-winged-helix (tWH) domain of RNA polymerase III (Pol III) Rpc34 subunit is a multi-function hub in Pol III apparatus while the structure basis remains elusive. To probe tWH in Pol III elongation complex (EC), we engineered an azide-bearing unnatural amino acid into tWH and implemented a thiol-capping scheme to enable strain- promoted click reaction for selective dye labeling to suit single-molecule Forster resonance energy transfer (smFRET). Our discrete smFRET results and nano-positioning analysis reveal multiple docking sites of Rpc34 WH2 on Pol III EC with characteristic dwell-times, reflecting promiscuous and weak interactions underpinning tWHs multi-functionality. The docking sites include one overlapping with that during initiation and others on transcription bubble and downstream DNA, previously unreported. This work provides mechanistic insights into Pol III transcription re-initiation and elongation, with useful bio-orthogonal strategies for studying structural dynamics of large native protein complexes.

biophysics↗

bioRxiv2024

No Reliable Evidence Supports the Presence of Javan Tigers - Data Issues Related to the DNA Analysis of a Recent Hair Sample

A paper recently published in Oryx by Wirdateti et al. (2024) suggests that the extinct Javan tiger may still survive on the Island of Java, Indonesia, based on mtDNA analysis of a single hair collected from a claimed tiger encounter site. After carefully re-analyzing the data presented in Wirdateti et al. (2024), we conclude that there is little support for the authors statements. Importantly, the sequences of the putative tiger hair and museum Javan tiger specimens generated by the authors are not from tiger cytoplasmic mitochondrial DNA but more likely the nuclear copies of mitochondrial DNA. In addition, the high mismatches found between the two "Javan tiger" sequences generated by the authors is unusual for homologous sequences that are both from tigers and hence indicative of data unreliability. Yet, too few details regarding the quality control were provided in Wirdateti et al. (2024) to rule out the possibility of contamination introduced during the data production process. In conclusion, it is inappropriate to use these unreliable sequences presented in Wirdateti et al. (2024) to infer the existence of the Javan tiger.

zoology↗

bioRxiv2024

A mediating framework in resting-state connectivity between the medial prefrontal cortex and anterior cingulate in mild cognitive impairment

Mild cognitive impairment (MCI) is recognized as the prodromal phase of dementia, a condition that can be either maintained or reversed through timely medical interventions to prevent cognitive decline. Considerable studies using functional magnetic resonance imaging (fMRI) have indicated that altered activity in the medial prefrontal cortex (mPFC) serves as an indicator of various cognitive stages of aging. However, the impacts of intrinsic functional connectivity in the mPFC as a mediator on cognitive performance in individuals with and without MCI have not been fully understood. In this study, we recruited 42 MCI patients and 57 healthy controls, assessing their cognitive abilities and functional brain connectivity patterns through neuropsychological evaluations and resting-state fMRI, respectively. The MCI patients exhibited poorer performance on multiple neuropsychological tests compared to the healthy controls. At the neural level, functional connectivity between the mPFC and the anterior cingulate cortex (ACC) was significantly weaker in the MCI group and correlated with multiple neuropsychological test scores. The result of the mediation analysis further demonstrated that functional connectivity between the mPFC and ACC notably mediated the relationship between the MCI and semantic working memory. These findings suggest that altered mPFC-ACC connectivity may have a plausible causal influence on cognitive decline and provide implications for early identifications of neurodegenerative diseases and precise monitoring of disease progression.

neuroscience↗

bioRxiv2024

scGND: Graph neural diffusion model enhances single-cell RNA-seq analysis

Single-cell sequencing technologies have played a pivotal role in advancing biomedical research over the last decade. With the evolution of deep learning, a variety of models based on deep neural networks have been developed to improve the precision of single-cell RNA sequencing (scRNA-seq) analysis from multiple angles. However, deep learning models currently used in scRNA-seq analysis frequently suffer from a lack of interpretability. In this study, we present a novel physics-informed graph generative model, termed Single Cell Graph Neural Diffusion (scGND). This model is founded on solid mathematical concepts and provides enhanced interpretability. Unlike methods that focus solely on gene expression in individual cells, scGND concentrates on the cell-cell interaction graph, incorporating two key physical concepts: local and global equilibrium. We show that achieving a balance between local and global equilibrium significantly improves the geometric properties of the graph, aiding in the extraction of inherent biological insights from the cell-cell interaction graph at multiple scales. The effectiveness of scGND has been proven through benchmark tests involving five independent scRNA-seq datasets from various tissues and species. scGND consistently achieves better or comparable results comparing with several established competitors in both clustering and trajectory analysis. scGND represents a comprehensive generative model based on cell graph diffusion, demonstrating considerable promise for both theoretical and practical applications in scRNA-seq data analysis.

bioinformatics↗

bioRxiv2023

An acidophilic fungus is integral to prey digestion in a carnivorous plant

Carnivorous plant leaves, such as those of the spoon-leaved sundew Drosera spatulata, secrete mucilage which hosts microorganisms potentially aiding in prey digestion. We characterised the mucilage microbial communities and identified the acidophilic fungus Acrodontium crateriforme as the ecologically dominant species. The fungus grows and sporulates on sundew glands as its preferred acidic environment. We show that the A. crateriforme has a reduced genome similar to that of other symbiotic fungi. Based on the transcriptomes when encountering prey insects, we revealed a high degree of genes co-option in each species during fungus-plant coexistence and digestion. Expression patterns of the holobiont during digestion further revealed synergistic effects in several gene families including fungal aspartic and sedolisin peptidases, facilitating the digestion of sundews prey, as well as transporters and dose-dependent responses in plant genes involved in jasmonate signalling pathway. This study establishes that botanical carnivory is defined by multidimensional adaptations correlated with interspecies interactions.

microbiology↗

bioRxiv2023

Efficient estimation for large-scale linkage disequilibrium patterns of the human genome

In this study, we proposed an efficient algorithm (X-LD) for estimating LD patterns for a genomic grid, which can be of inter-chromosomal scale or of small segments. Compared with conventional methods, the proposed method was significantly faster, dropped from [O] (nm2) to [O] (n2m)--n the sample size and m the number of SNPs, and consequently we were permitted to explore in depth unknown or reveal long-anticipated LD features of the human genome. Having applied the algorithm for 1000 Genome Project (1KG), we found: I) The extended LD, driven by population structure, was universally existed, and the strength of inter-chromosomal LD was about 10% of their respective intra-chromosomal LD in relatively homogeneous cohorts, such as FIN and to nearly 56% in admixed cohort, such as ASW. II) After splitting each chromosome into upmost more than a half million grids, we elucidated the LD of the HLA region was nearly 42 folders higher than chromosome 6 in CEU and 11.58 in ASW; on chromosome 11, we observed that the LD of its centromere was nearly 94.05 folders higher than chromosome 11 in YRI and 42.73 in ASW. III) We uncovered the long-anticipated inversely proportional linear relationship between the length of a chromosome and the strength of chromosomal LD, and their Pearsons correlation was on average over 0.80 for 26 1KG cohorts. However, this linear norm was so far perturbed by chromosome 11 given its more completely sequenced centromere region. Uniquely chromosome 8 of ASW was found most deviated from the linear norm than any other autosomes. The proposed algorithm has been realized in C++ (called X-LD) and available at https://github.com/gc5k/gear2, and can be applied to explore LD features in any sequenced populations.

evolutionary biology↗

bioRxiv2023

Single worm long read sequencing reveals genome diversity in free-living nematodes

Obtaining sufficient genetic material from a limited biological source is currently the primary operational bottleneck in studies investigating biodiversity and genome evolution. In this study, we employed multiple displacement amplification (MDA) and Smartseq2 to amplify nanograms of genomic DNA and mRNA, respectively from individual Caenorhabditis elegans. Although reduced genome coverage was observed in repetitive regions, we produced assemblies covering 98% of the reference genome using long-read sequences generated with Oxford Nanopore Technologies (ONT). Annotation with the sequenced transcriptome coupled with the available assembly revealed that gene predictions were more accurate, complete and contained far fewer false positives than de novo transcriptome assembly approaches. We sampled and sequenced the genomes and transcriptomes of 13 nematodes from Dorylaimia, Enoplia, and early-branching species in Chromadoria. These free-living species had larger genome sizes, ranging from 147-792 Mb, compared to those of the parasitic lifestyle. Nine mitogenomes were fully assembled and displaying a complete lack of synteny to other species. Phylogenomic analyses based on the new annotations revealed strong support for Enoplia as sister to the rest of Nematoda. Our result demonstrates the robustness of MDA in combination with ONT, paving the way for the study of genome diversity in the phylum Nematoda and beyond.

genomics↗

bioRxiv2022

Ancient DNA Reveals China as a Historical Genetic Melting Pot in Tiger Evolution

The contrast between the tigers (Panthera tigris) 2-3 My age and extant tigers coalescence approximately 110,000 years ago suggests an ancient demographic bottleneck. Here we collected over 60 extinct specimens across mainland Asia and generated whole genome sequences from a 10,600-year-old Russian Far East (RFE) specimen (RUSA21, 8{xi} coverage), 14 South China tigers (0.1-12{xi}), three Caspian tigers (4-8{xi}), plus 17 new mitogenomes. RUSA21 clustered within modern Northeast Asian phylogroups and partially derived from an extinct Late Pleistocene lineage. While some 8,000-10,000-year-old RFE mitogenomes are basal to all tigers, one 2,000-year-old specimen resembles present Amur tigers. The Caspian tiger likely dispersed from an ancestral Northeast Asian population and experienced gene flow from southern Bengal tigers. Lastly, genome-wide monophyly supported the South China tiger as a distinct subspecies, albeit with mitochondrial paraphyly, hence resolving its longstanding taxonomic controversy. The distribution of mitochondrial haplogroups corroborated by biogeographical modeling suggested Southwest China was a Late Pleistocene refugium for a relic basal lineage. As suitable habitat returned, Eastern China became a genetic melting pot to foster divergent lineages to merge into South China tigers and other subsequent northern subspecies to develop. Genomic information retrieved from ancient tigers hence sheds light on the species full evolutionary history leading to nine modern subspecies and resolves the natural history of surviving tigers.

evolutionary biology↗