Despite several phylogeographic studies had provided evidence to support the existence of glacial refugia of cool‐temperate deciduous trees in northeast China, the species used in these studies were limited by the species ranges, which could not exclude the possibility that northern populations were the colonists from southern refugial populations during the last glacial maximum (LGM). Here, we estimated the nucleotide variation inPopulus davidiana, a widespread species distributed in Eurasia. Three groups in northeast, central, and southwest China were constructed according to the simulation results from SAMOVA, composition of chloroplast haplotypes and structure results. We revealed that the northeast China had endemic haplotypes, the haplotypes and nucleotide diversity in northern regions were not lower than that in southern China, and this species has not experienced population expansion base on the estimation of Bayesian skyline plots. Ecological niche modeling (ENM) indicated that the northeast China had a high suitability score during the last glacial maximum. The combined evidence clearly demonstrated that northeastern and southwestern refugia were maintained across the current distributional range ofP. davidianaduring the LGM. The genetic differentiation between these two refugia might be mainly caused by differences of climate among these areas. The phylogeographic analyses of a widely distributedP. davidianaprovided robust evidence to clarify the issue of refugia in northeast China, and these results are of great importance for understanding the influence of Quaternary glaciations on the distribution and evolution of species in East Asia.

Hybridization and introgression have resulted in reticulate evolution within the genusPopulus. Consequently, the origin and evolutionary history of some hybrids has become blurred.P.hopeiensisandP.tomentosaare endemic to China, and there is still controversy about their origin. We employ phylogeny, Bayesian estimation of admixture, and approximate Bayesian computation to investigate their origin with 10 nuclear DNA and 6 cpDNA regions. The combined evidences firmly support the hypothesis that they are hybrids and dominated by F₁s.P.hopeiensiswas generated via hybridization between the paternal speciesP.albaand maternal speciesP.davidiana. Surprisingly,P.tomentosawas divided into two genetic types with different maternal parents.P.adenopodahybridized withP.albadirectly to generate the first genetic type (mb1) and hybridized withP.davidianafollowed byP.albato generate the second (mb2). In both genetic types,P.albaacted as the male parent. The maternal parent wasP.adenopodaandP.davidianafor mb1 and mb2, respectively. Hybridization not only generated these hybrids but also resulted in a unidirectional gene flow fromP.davidianatoP.adenopoda. ThePopulusspecies have maintained a delicate balance between their genetic integrity and gene exchange.

Global climate change has increased concerns regarding biodiversity loss. However, many key conservation issues still required further research, including demographic history, deleterious mutation load, adaptive evolution, and putative introgression. Here we generated the first chromosome-level genome of the endangered Chinese hazelnut, Corylus chinensis, and compared the genomic signatures with its sympatric widespread C. kwechowensis–C. yunnanensis complex. We found large genome rearrangements across all Corylus species and identified species-specific expanded gene families that may be involved in adaptation. Population genomics revealed that both C. chinensis and the C. kwechowensis–C. yunnanensis complex had diverged into two genetic lineages, forming a consistent pattern of southwestern-northern differentiation. Population size of the narrow southwestern lineages of both species have decreased continuously since the late Miocene, whereas the widespread northern lineages have remained stable (C. chinensis) or have even recovered from population bottlenecks (C. kwechowensis–C. yunnanensis complex) during the Quaternary. Compared with C. kwechowensis–C. yunnanensis complex, C. chinensis showed significantly lower genomic diversity and higher inbreeding level. However, C. chinensis carried significantly fewer deleterious mutations than C. kwechowensis–C. yunnanensis complex, as more effective purging selection reduced the accumulation of homozygous variants. We also detected signals of positive selection and adaptive introgression in different lineages, which facilitated the accumulation of favorable variants and formation of local adaptation. Hence, both types of selection and exogenous introgression could have mitigated inbreeding and facilitated survival and persistence of C. chinensis. Overall, our study provides critical insights into lineage differentiation, local adaptation, and the potential for future recovery of endangered trees.

The olive tree (Olea europaea L.) is the most iconic fruit crop of the Mediterranean Basin. Since the plant was introduced to China in the 1960s, the summer rain climate makes it susceptible to pathogens, leading to some olive diseases. Olea europaea L. subsp. cuspidata is natively distributed in the Yunnan province of China. It has a smaller fruit size, lower oil content, and higher resistance compared to subsp. europaea, which makes subsp. cuspidata a critical germplasm resource to be investigated. Here, a high-quality genome of subsp. cuspidata with 1.38 Gb in size was assembled and anchored onto 23 pseudochromosomes with a mounting rate of 85.57%. It represents 96.6% completeness [benchmarking universal single-copy orthologs (BUSCO)] with a contig N50 of 14.72 Mb and a scaffold N50 of 52.68 Mb, which shows a significant improvement compared with other olive genomes assembled. The evaluation of the genome assembly showed that 92.31% of resequencing reads and an average of 96.52% of assembled transcripts could be aligned to the assembled genome. We found that a positively selected gene, evm.model.Chr16.1133, was shared with the results of transcriptome analysis. This gene belongs to the susceptible gene and negatively regulates the disease resistance process. Furthermore, we identified the Cercospora genus which causes the leaf spot disease in the infected leaves. The high-quality chromosome-level genomic information presented here may facilitate the conservation and utilization of germplasm resources of this subspecies and provide an essential genetic basis for further research into the differences in oil content and resistance between subsp. cuspidata and europaea.

Populus adenopoda, an endemic tree species in China with considerable ecological and industrial value, is threatened by climate change-induced habitat loss. Understanding its spatial response is critical for conservation. This study employed the MaxEnt model with 181 occurrence records and seven environmental variables to project its current and future suitable habitats under multiple climate scenarios (SSP126, SSP245, SSP370, SSP585 for the 2050s and 2090s). The model exhibited high predictive performance (AUC = 0.947 and TSS = 0.817). Annual precipitation and the minimum temperature of the coldest month were the dominant factors shaping its distribution. Currently, the total suitable habitat spans approximately 228.19 × 10⁴ km², predominantly in subtropical China. Future projections consistently revealed a stark degradation of highly suitable habitat, with losses of up to 78.81% under SSP585 by the 2090s, partially offset by an expansion of low-suitability areas. A pronounced northwestward shift of the habitat centroid indicates a potential migration toward higher elevations. These results provide a critical scientific foundation for developing climate-adaptive conservation strategies, including identifying priority areas and planning assisted migration, to ensure the long-term sustainability of P. adenopoda.