Chromosome-level genome assembly of American sweetgum (Liquidambar styraciflua, Altingiaceae).

The deciduous American sweetgum (Liquidambar styraciflua, Altingiaceae) is a popular ornamental and economically valuable tree renowned for its sweet-smelling bark resin, abundant volatile substances, and spectacular fall leaf color. However, the absence of a reference genome hinders thorough investigations into the mechanisms underlying phenotypic variation, secondary metabolite synthesis and adaptation, both in this species and other Liquidambar members. In this study, we sequenced and constructed a chromosome-level assembly of the L. styraciflua genome, covering 662.48 Mb with a scaffold N50 of 39.54 Mb, by integrating PacBio, Illumina and chromosome conformation capture data. We identified 58.83% of the genome sequences as repetitive elements and 25,713 protein-coding genes, 97.28% of which were functionally annotated. The genome sequencing reads, assembly and annotation data have been deposited in publicly available repositories. This high-quality genome assembly provides valuable resources for further evolutionary and functional genomic studies in American sweetgum and other Liquidambar species.

Telomere-to-telomere genome assembly of Eleocharis dulcis and expression profiles during corm development.

Eleocharis dulcis (Burm. f.) Trin. ex Hensch., commonly known as Chinese water chestnut, is a traditional aquatic vegetable in China, and now is widely cultivated throughout the world because of its high nutritional value and unique tastes. Here, we report the assembly of a 493.24 Mb telomere-to-telomere (T2T) genome of E. dulcis accomplished by integrating ONT ultra-long reads, PacBio long reads and Hi-C data. The reference genome was anchored onto 111 gap-free chromosomes, containing 48.31% repeat elements and 33,493 predicted protein-coding genes. Whole genome duplication (WGD) and inter-genomic synteny analyses indicated that chromosome breakage and genome duplication in E. dulcis possibly occurred multiple times during genome evolution after its divergence from a common ancestor with Rhynchospora breviuscula at ca. 35.6 Mya. A comparative time-course transcriptome analysis of corm development revealed different patterns of gene expression between cultivated and wild accessions with the highest number of differentially expressed genes (DEGs, 15,870) at the middle swelling stage and some of the DEGs were significantly enriched for starch metabolic process.

Shared xerophytic genes and their re-use in local adaptation to aridity in the desert plant Gymnocarpos przewalskii.

In order to thrive and survive, plant species need to combine stability in the long term and rapid response to environmental challenges in the short term. The former would be reflected by parallel or convergent adaptation across species, and the latter by pronounced local adaptation among populations of the same species. In the present study, we generated a high-quality genome and re-sequenced 177 individuals for Gymnocarpos przewalskii, an important desert plant species from North-West China, to detect local adaptation. We first focus on ancient adaptation to aridity at the molecular level by comparing the genomic data of 15 species that vary in their ability to withstand aridity. We found that a total of 118 genes were shared across xerophytic species but absent from non-xerophytic species. Of the 65 found in G. przewalskii, 63 were under purifying selection and two under positive selection. We then focused on local adaptation. Up to 20% of the G. przewalskii genome showed signatures of local adaptation to aridity during population divergence. Thirteen of the selected shared xerophytic genes were reused in local adaptation after population differentiation. Hence, only about 20% of the genes shared and specific to xerophytic species and associated with adaptation to aridity were later recruited for local adaptation in G. przewalskii.

Genome sequences and population genomics reveal climatic adaptation and genomic divergence between two closely related sweetgum species.

Understanding the genetic basis of population divergence and adaptation is an important goal in population genetics and evolutionary biology. However, the relative roles of demographic history, gene flow, and/or selective regime in driving genomic divergence, climatic adaptation, and speciation in non-model tree species are not yet fully understood. To address this issue, we generated whole-genome resequencing data of Liquidambar formosana and L. acalycina, which are broadly sympatric but altitudinally segregated in the Tertiary relict forests of subtropical China. We integrated genomic and environmental data to investigate the demographic history, genomic divergence, and climatic adaptation of these two sister species. We inferred a scenario of allopatric species divergence during the late Miocene, followed by secondary contact during the Holocene. We identified multiple genomic islands of elevated divergence that mainly evolved through divergence hitchhiking and recombination rate variation, likely fostered by long-term refugial isolation and recent differential introgression in low-recombination genomic regions. We also found some candidate genes with divergent selection signatures potentially involved in climatic adaptation and reproductive isolation. Our results contribute to a better understanding of how late Tertiary/Quaternary climatic change influenced speciation, genomic divergence, climatic adaptation, and introgressive hybridization in East Asia's Tertiary relict flora. In addition, they should facilitate future evolutionary, conservation genomics, and molecular breeding studies in Liquidambar, a genus of important medicinal and ornamental values.

Genome sequences and population genomics provide insights into the demographic history, inbreeding, and mutation load of two 'living fossil' tree species of Dipteronia.

'Living fossils', that is, ancient lineages of low taxonomic diversity, represent an exceptional evolutionary heritage, yet we know little about how demographic history and deleterious mutation load have affected their long-term survival and extinction risk. We performed whole-genome sequencing and population genomic analyses on Dipteronia sinensis and D. dyeriana, two East Asian Tertiary relict trees. We found large-scale genome reorganizations and identified species-specific genes under positive selection that are likely involved in adaptation. Our demographic analyses suggest that the wider-ranged D. sinensis repeatedly recovered from population bottlenecks over late Tertiary/Quaternary periods of adverse climate conditions, while the population size of the narrow-ranged D. dyeriana steadily decreased since the late Miocene, especially after the Last Glacial Maximum (LGM). We conclude that the efficient purging of deleterious mutations in D. sinensis facilitated its survival and repeated demographic recovery. By contrast, in D. dyeriana, increased genetic drift and reduced selection efficacy, due to recent severe population bottlenecks and a likely preponderance of vegetative propagation, resulted in fixation of strongly deleterious mutations, reduced fitness, and continuous population decline, with likely detrimental consequences for the species' future viability and adaptive potential. Overall, our findings highlight the significant impact of demographic history on levels of accumulation and purging of putatively deleterious mutations that likely determine the long-term survival and extinction risk of Tertiary relict trees.

Pangenome of water caltrop reveals structural variations and asymmetric subgenome divergence after allopolyploidization.

Water caltrop (Trapa spp., Lythraceae) is a traditional but currently underutilized non-cereal crop. Here, we generated chromosome-level genome assemblies for the two diploid progenitors of allotetraploid Trapa. natans (4x, AABB), i.e., diploid T. natans (2x, AA) and Trapa incisa (2x, BB). In conjunction with four published (sub)genomes of Trapa, we used gene-based and graph-based pangenomic approaches and a pangenomic transposable element (TE) library to develop Trapa genomic resources. The pangenome displayed substantial gene-content variation with dispensable and private gene clusters occupying a large proportion (51.95%) of the total cluster sets in the six (sub)genomes. Genotyping of presence-absence variation (PAVs) identified 40 453 PAVs associated with 2570 genes specific to A- or B-lineages, of which 1428 were differentially expressed, and were enriched in organ development process, organic substance metabolic process and response to stimulus. Comparative genome analyses showed that the allotetraploid T. natans underwent asymmetric subgenome divergence, with the B-subgenome being more dominant than the A-subgenome. Multiple factors, including PAVs, asymmetrical amplification of TEs, homeologous exchanges (HEs), and homeolog expression divergence, together affected genome evolution after polyploidization. Overall, this study sheds lights on the genome architecture and evolution of Trapa, and facilitates its functional genomic studies and breeding program.

Molecular phylogeography and historical demography of a widespread herbaceous species from eastern North America, Podophyllum peltatum.

PREMISE: Glacial/interglacial cycles and topographic complexity are both considered to have shaped today's diverse phylogeographic patterns of taxa from unglaciated eastern North America (ENA). However, few studies have focused on the phylogeography and population dynamics of wide-ranging ENA herbaceous species occurring in forest understory habitat. We examined the phylogeographic pattern and evolutionary history of Podophyllum peltatum L., a widely distributed herb inhabiting deciduous forests of ENA. METHODS: Using chloroplast DNA (cpDNA) sequences and nuclear microsatellite loci, we investigated the population structure and genetic diversity of the species. Molecular dating, demographic history analyses, and ecological niche modeling were also performed to illustrate the phylogeographic patterns. RESULTS: Our cpDNA results identified three main groups that are largely congruent with boundaries along the Appalachian Mountains and the Mississippi River, two major geographic barriers in ENA. Populations located to the east of the Appalachians and along the central Appalachians exhibited relatively higher levels of genetic diversity. Extant lineages may have diverged during the late Miocene, and range expansions of different groups may have happened during the Pleistocene glacial/interglacial cycles. CONCLUSIONS: Our findings indicate that geographic barriers may have started to facilitate the population divergence in P. peltatum before the Pleistocene. Persistence in multiple refugia, including areas around the central Appalachians during the Quaternary glacial period, and subsequent expansions under hospitable climatic condition, especially westward expansion, are likely responsible for the species' contemporary genetic structure and phylogeographic pattern.

Chromosome-level reference genome of Tetrastigma hemsleyanum (Vitaceae) provides insights into genomic evolution and the biosynthesis of phenylpropanoids and flavonoids.

Here, we present a high-quality chromosome-scale genome assembly (2.19 Gb) and annotation of Tetrastigma hemsleyanum, a perennial herbaceous liana native to subtropical China with diverse medicinal applications. Approximately 73% of the genome was comprised of transposable elements (TEs), of which long terminal repeat retrotransposons (LTR-RTs) were a predominant group (69% of the genome). The genome size increase of T. hemsleyanum (relative to Vitis species) was mostly due to the proliferation of LTR-RTs. Of the different modes of gene duplication identified, transposed duplication (TRD) and dispersed duplication (DSD) were the predominant ones. Genes, particularly those involved in the phenylpropanoid-flavonoid (PF) pathway and those associated with therapeutic properties and environmental stress resistance, were significantly amplified through recent tandem duplications. We dated the divergence of two intraspecific lineages in Southwest (SW) versus Central-South-East (CSE) China to the late Miocene (approximately 5.2 million years ago). Of those, the former showed more upregulated genes and metabolites. Based on resequencing data of 38 individuals representing both lineages, we identified various candidate genes related to 'response to stimulus' and 'biosynthetic process', including ThFLS11, which is putatively involved in flavonoid accumulation. Overall, this study provides abundant genomic resources for future evolutionary, ecological, and functional genomics studies in T. hemsleyanum and related species.

A Comparative Study of Genetic Responses to Short- and Long-Term Habitat Fragmentation in a Distylous Herb Hedyotis chyrsotricha (Rubiaceae).

The genetic effects of habitat fragmentation are complex and are influenced by both species traits and landscape features. For plants with strong seed or pollen dispersal capabilities, the question of whether the genetic erosion of an isolated population becomes stronger or is counterbalanced by sufficient gene flow across landscapes as the timescales of fragmentation increase has been less studied. In this study, we compared the population structure and genetic diversity of a distylous herb, Hedyotis chyrsotricha (Rubiaceae), in two contrasting island systems of southeast China. Based on RAD-Seq data, our results showed that populations from the artificially created Thousand-Island Lake (TIL) harbored significantly higher levels of genetic diversity than those from the Holocene-dated Zhoushan Archipelago (ZA) (π = 0.247 vs. 0.208, HO = 0.307 vs. 0.256, HE = 0.228 vs. 0.190), while genetic differences between island and mainland populations were significant in neither the TIL region nor the ZA region. A certain level of population substructure was found in TIL populations, and the level of gene flow among TIL populations was also lower than in ZA populations (m = 0.019 vs. 0.027). Overall, our comparative study revealed that genetic erosion has not become much stronger for the island populations of either the TIL or ZA regions. Our results emphasized that the matrix of water in the island system may facilitate the seed (fruit) dispersal of H. chrysotricha, thus maintaining population connectivity and providing ongoing resilience to the effects of habitat fragmentation over thousands of years.

Out of the Himalaya-Hengduan Mountains: Phylogenomics, biogeography and diversification of Polygonatum Mill. (Asparagaceae) in the Northern Hemisphere.

Clarifying the process of formation of diversity hotspots and the biogeographic connection between regions is critical in understanding the impact of environmental changes on organismal evolution. Polygonatum (Asparagaceae) is distributed across the Northern Hemisphere. It displays an uneven distribution, with more than 50% of its species occurring in the Himalaya-Hengduan Mountains (HHM). Here, we generated a time-calibrated phylogeny of Polygonatum, based on whole-plastome data, to reconstruct the genus' biogeographical history and morphological/chromosomal evolution. Our phylogenetic analyses strongly support the monophyly of Polygonatum and its division into three sections (i.e., Verticillata, Sibirica, and Polygonatum). Polygonatum originated from the HHM region during the early-Miocene (c. 20.10 Ma), and began to radiate since the mid-Miocene, driven by the uplift of the Qinghai-Tibet Plateau (QTP), increasingly colder/arid climates following the mid-Miocene Climatic Optimum (MMCO), and intensification of the East Asian winter monsoon. Dispersal from the HHM region to other regions was facilitated by the intensification of East Asian summer monsoon in response to global climatic warming during the MMCO. Decreasing dysploidy accompanied by karyotype change and polyploidization in Polygonatum appears to be associated with its diversification and colonization of new ecological niches. Our results highlight the importance of regional tectonic activities and past climatic changes from the Neogene onwards to the spatial-temporal diversification and distribution patterns of plant lineages with a wide distribution in the Northern Hemisphere. They also contribute to the knowledge of the uneven species richness between East Asia and other regions.

Phylogenomics and diversification drivers of the Eastern Asian - Eastern North American disjunct Podophylloideae.

Evolutionary and biogeographic processes determine species richness patterns of vascular plants between Eastern Asia (EA) and Eastern North America (ENA). However, the strikingly higher species richness of EA relative to ENA remains poorly understood from this perspective. Here, we studied the relative importance of biogeographical, evolutionary and ecological factors underlying differences in species richness between EA and ENA in Podophylloideae (Berberidaceae, Ranunculales; in total 10 spp. in EA vs. 2 spp. in ENA). Based on large-scale transcriptome data, our phylogenomic analyses strongly supported Podophylloideae and its two multi-species genera, i.e. Dysosma (EA) and Diphylleia (EA/ENA), as monophyletic groups. Sinopodophyllum hexandrum (EA) was identified as sister to the remainder of Podophylloideae. Dysosma (7 spp.) was recovered as sister to Podophyllum peltatum (ENA), forming an EA-ENA disjunct pair with a strong bias of species diversity in the EA counterpart. Our biogeographic analyses support the 'out-of-Tibet' hypothesis, suggesting that Podophylloideae started to diversify in the Himalaya-Hengduan Mountains (Mid-Miocene) and migrated eastward (since the Late Miocene) into Central-eastern China, Japan, and ENA (only P. peltatum and Diphylleia cymosa). Overall, we conclude that the striking species diversity anomaly between EA and ENA in Podophylloideae may be explained by a combination of (1) a longer period of time available to accumulate species in EA; and (2) a greater diversification rate in EA, which might have been promoted by greater physiographic and environmental heterogeneity in this region.

Genomic insights into the evolution of Echinochloa species as weed and orphan crop.

As one of the great survivors of the plant kingdom, barnyard grasses (Echinochloa spp.) are the most noxious and common weeds in paddy ecosystems. Meanwhile, at least two Echinochloa species have been domesticated and cultivated as millets. In order to better understand the genomic forces driving the evolution of Echinochloa species toward weed and crop characteristics, we assemble genomes of three Echinochloa species (allohexaploid E. crus-galli and E. colona, and allotetraploid E. oryzicola) and re-sequence 737 accessions of barnyard grasses and millets from 16 rice-producing countries. Phylogenomic and comparative genomic analyses reveal the complex and reticulate evolution in the speciation of Echinochloa polyploids and provide evidence of constrained disease-related gene copy numbers in Echinochloa. A population-level investigation uncovers deep population differentiation for local adaptation, multiple target-site herbicide resistance mutations of barnyard grasses, and limited domestication of barnyard millets. Our results provide genomic insights into the dual roles of Echinochloa species as weeds and crops as well as essential resources for studying plant polyploidization, adaptation, precision weed control and millet improvements.

More opportunities more species: Pleistocene differentiation and northward expansion of an evergreen broad-leaved tree species Machilus thunbergii (Lauraceae) in Southeast China.

BACKGROUND: The broad continuum between tropical and temperate floras in Eastern Asia (EAS) are thought to be one of the main factors responsible for a prominent species diversity anomaly of temperate plants between EAS and eastern North America (ENS). However, how the broad continuum and niche evolution between tropical and temperate floras in EAS contributes to lineage divergence and species diversity remains largely unknown. RESULTS: Population genetic structure, demography, and determinants of genetic structure [i.e., isolation-by-distance (IBD), isolation-by-resistance (IBR), and isolation-by-environment (IBE)] of Machilus thunbergii Sieb. et Zucc. (Lauraceae) were evaluated by examining sequence variation of ten low-copy nuclear genes across 43 populations in southeast China. Climatic niche difference and potential distributions across four periods (Current, mid-Holocene, the last glacial maximum, the last interglacial) of two genetic clusters were determined by niche modelling. North and south clusters of populations in M. thunbergii were revealed and their demarcation line corresponds well with the northern boundary of tropical zone in China of Zhu & Wan. The divergence time between the clusters and demographic expansion of M. thunbergii occurred after the mid-Pleistocene climate transition (MPT, 0.8-1.2 Ma). Migration rates between clusters were asymmetrical, being much greater from north to south than the reverse. Significant effects of IBE, but non-significant effects of IBD and IBR on population genetic divergence were detected. The two clusters have different ecological niches and require different temperature regimes. CONCLUSIONS: The north-south genetic differentiation may be common across the temperate-tropical boundary in southeast China. Divergent selection under different temperature regimes (possibly above and below freezing temperature in winter) could account for this divergence pattern. The broad continuum between tropical and temperate floras in EAS may have provided ample opportunities for tropical plant lineages to acquire freezing tolerance and to colonize the temperate regions during the late-Cenozoic global cooling. Our findings shed deeper insights into the high temperate plant species diversity in EAS.

Genome sequencing and transcriptome analyses provide insights into the origin and domestication of water caltrop (Trapa spp., Lythraceae).

Humans have domesticated diverse species from across the plant kingdom; however, our current understanding of plant domestication is largely founded on major cereal crops. Here, we examine the evolutionary processes and genetic basis underlying the domestication of water caltrop (Trapa spp., Lythraceae), a traditional, yet presently underutilized non-cereal crop that sustained early Chinese agriculturalists. We generated a chromosome-level genome assembly of tetraploid T. natans, and then divided the allotetraploid genome into two subgenomes. Based on resequencing data from 57 accessions, representing cultivated diploid T. natans, wild T. natans (2x and 4x) and diploid T. incisa, we showed that water caltrop was likely first domesticated in the Yangtze River Valley as early as 6300 yr BP, and experienced a second improvement c. 800 years ago. We also provided strong support for an allotetraploid origin of T. natans within the past 230 000-310 000 years. By integrating selective sweep and transcriptome profiling analyses, we identified a number of genes potentially selected and/or differentially expressed during domestication, some of which likely contributed not only to larger fruit sizes but also to a more vigorous root system, facilitating nutrient uptake, environmental stress response and underwater photosynthesis. Our results shed light on the evolutionary and domestication history of water caltrop, one of the earliest domesticated crops in China. This study has implications for genomic-assisted breeding of this presently underutilized aquatic plant, and improves our general understanding of plant domestication.

A new synonym of Polygonatum in China, based on morphological and molecular evidence.

PolygonatumkingianumCollett et Hemsl.var.grandifolium D.M. Liu & W.Z. Zeng (1981), which sprouts twice a year, once in spring and once in autumn, differs from Polygonatumkingianum in leaves, bracts, perianth and filaments. Morphological comparison and molecular phylogeny indicate that it is identical to the newly-published Polygonatumhunanense H.H. Liu & B.Z. Wang (2021). Hence, we propose that P.kingianumvar.grandifolium should be recognised as a new synonym of P.hunanense. In addition, phylogenetic analyses confirmed that P.hunanense is sister to Polygonatumsect.Polygonatum, rather than P.kingianum of Polygonatumsect.Verticillata.

[Investigation on reproductive characteristics of Polygonatum cyrtonema].

The study is aimed to investigate the reproductive biology characteristics of Polygonatum cyrtonema, especially including phenology, flower bud differentiation, flowering timing, floral traits, pollen vigor and stigma receptivity. The results showed that P. cyrtonema forms inflorescence before the leaves spread. In the wild, P. cyrtonema is mainly pollinated by insects such as bumblebees, with a seed setting rate of 65.12%. The seed setting rate of indoor single plant isolation or self-pollination enclosed by parchment paper bag is 0, indicating that it is self-incompatible. In Lin'an city, seedlings begin to emerge from mid-March to early April(the temperature is higher than 7.5 ℃), buds begin to emerge from the end of March to mid-April, and then undergo the full bloom stage from mid-to-late April, and the final flowering stage from the end of April to mid-May. The whole flowering period lasts 36 to 45 days. There are obvious differences in the phenology of different provenances. The flowers come into bloom from the base to the top along the aboveground main axis, which usually contain 4-22 inflorescences with(2-) 4-10(-21) flowers per inflorescence. The flowering pe-riod for a single plant is 26-38 days. The single flower lasts about 20-25 days from budding to opening and withers 2 days after pollination, and then the ovary will gradually expand. If unpollinated, it will continue to bloom for 3-5 days and then wither. Flower development period is significantly related to pollen vigor and stigma remittance. The pollen viability is the highest when the flower is fully opened with anthers gathering on the stigma, and the receptivity is the strongest when the stigma protrudes out of the perianth and secretes mucus. The fruits and seeds ripen in October, and proper shading can ensure the smooth development and maturity of the seeds. This study provides a basis for the hybrid breeding and seed production of P. cyrtonema.

Inferring historical survivals of climate relicts: the effects of climate changes, geography, and population-specific factors on herbaceous hydrangeas.

Climate relicts hold considerable importance because they have resulted from numerous historical changes. However, there are major interspecific variations among the ways by which they survived climate changes. Therefore, investigating the factors and timing that affected population demographics can expand our understanding of how climate relicts responded to historical environmental changes. Here, we examined herbaceous hydrangeas of genus Deinanthe in East Asia, which show limited distributions and a remarkable disjunction between Japan and central China. Chloroplast genome and restriction site-associated DNA sequencing revealed that speciation event occurred in the late Miocene (ca. 7-9 Mya) in response to global climate change. Two lineages apparently remained not branched until the middle Quaternary, and afterwards started to diverge to regional population groups. The narrow endemic species in central China showed lower genetic diversity (He = 0.082), as its population size rapidly decreased during the Holocene due to isolation in montane refugia. Insular populations in the three Japanese islands (He = 0.137-0.160) showed a genetic structure that was inconsistent with sea barriers, indicating that it was shaped in the glacial period when its range retreated to coastal refugia on the exposed sea floor. Demographic modelling by stairway-plot analysis reconstructed variable responses of Japanese populations: some experienced glacial bottlenecks in refugial isolation, while post-glacial range expansion seemingly exerted founder effects on other populations. Overall, this study demonstrated the involvement of not just one, but multiple factors, such as the interplay between climate changes, geography, and other population-specific factors, that determine the demographics of climate relicts.

Genomic insights into historical population dynamics, local adaptation, and climate change vulnerability of the East Asian Tertiary relict Euptelea (Eupteleaceae).

The warm-temperate and subtropical climate zones of East Asia are a hotspot of plant species richness and endemism, including a noticeable number of species-poor Tertiary relict tree genera. However, little is understood about when East Asian Tertiary relict plants diversified, how they responded demographically to past environmental change, and to what extent their current genomic composition (and adaptive capacity) might mitigate the effects of global warming. Here, we obtained genomic (RAD-SNP) data for 171 samples from two extant species of Euptelea in China (24 E. pleiosperma populations) and Japan (11 E. polyandra populations) to elucidate their divergence and demographic histories, genome-wide associations with current environmental variables, and genomic vulnerability to future climate change. Our results indicate that Late Miocene changes in climate and/or sea level promoted species divergence, whereas Late Pliocene uplifting in southwest China likely fostered lineage divergence within E. pleiosperma. Its subsequent range expansion into central/east (CE) China bears genomic signatures of climate-driven selection, yet extant CE populations are predicted to be most vulnerable to future climate change. For E. polyandra, geography was the only significant predictor of genomic variation. Our findings indicate a profound impact of Late Neogene geological and climate change on the evolutionary history of Euptelea, with much stronger signals of local adaptation left in China than in Japan. This study deepens our understanding of the complex evolutionary forces that influence the distribution of genetic variation of Tertiary relict trees, and provides insights into their susceptibility to global change and potential for adaptive responses. Our results lay the groundwork for future conservation and restoration programs for Euptelea.

Genomic insights on the contribution of balancing selection and local adaptation to the long-term survival of a widespread living fossil tree, Cercidiphyllum japonicum.

'Living fossils' are testimonies of long-term sustained ecological success, but how demographic history and natural selection contributed to their survival, resilience, and persistence in the face of Quaternary climate fluctuations remains unclear. To better understand the interplay between demographic history and selection in shaping genomic diversity and evolution of such organisms, we assembled the whole genome of Cercidiphyllum japonicum, a widespread East Asian Tertiary relict tree, and resequenced 99 individuals of C. japonicum and its sister species, Cercidiphyllum magnificum (Central Japan). We dated this speciation event to the mid-Miocene, and the intraspecific lineage divergence of C. japonicum (China vs Japan) to the Early Pliocene. Throughout climatic upheavals of the late Tertiary/Quaternary, population bottlenecks greatly reduced the genetic diversity of C. japonicum. However, this polymorphism loss was likely counteracted by, first, long-term balancing selection at multiple chromosomal and heterozygous gene regions, potentially reflecting overdominance, and, second, selective sweeps at stress response and growth-related genes likely involved in local adaptation. Our findings contribute to a better understanding of how living fossils have survived climatic upheaval and maintained an extensive geographic range; that is, both types of selection could be major factors contributing to the species' survival, resilience, and persistence.