全球气候变化增加了对生物多样性丧失的担忧。然而,许多关键的保护问题仍需进一步研究,包括人口统计历史,有害的突变负荷,适应性进化,和推定的内向。在这里,我们产生了濒危的中国榛子的第一个染色体水平基因组,中国珊瑚,并将基因组特征与其同胞广泛分布的C.kwechowensis-C.进行了比较。云南情结。我们发现了所有Corylus物种的大型基因组重排,并确定了可能参与适应的物种特异性扩展基因家族。种群基因组学表明,中国金丝雀和中国金丝雀。云南复合体分为两个遗传谱系,形成一致的西南-北方分化模式。自上新世晚期以来,这两个物种的西南狭窄谱系的种群规模一直在减少,而广泛的北方血统保持稳定(C.中国)或甚至已经从人口瓶颈中恢复过来(C.kwechowensis-C.云南复合体)在第四纪。与C.kwechowensis-C.比较云南情结,C.chinensis显示出明显较低的基因组多样性和较高的近交水平。然而,C.chinensis携带的有害突变明显少于C.kwechowensis-C.云南情结,因为更有效的清除选择减少了纯合变体的积累。我们还在不同谱系中检测到正向选择和适应性基因渗入的信号,这促进了有利变体的积累和局部适应的形成。因此,两种类型的选择和外源基因渗入都可能减轻近亲繁殖,并促进了C.chinensis的生存和持久性。总的来说,我们的研究提供了对谱系分化的关键见解,本地适应,以及未来恢复濒危树木的潜力。
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.