Local adaptation sustains genetic differentiation between two varieties of Chinese walnut (Juglans cathayensis) despite extensive hybridization in subtropical China

doi:10.1016/j.pld.2026.03.005

Plant Diversity ›› 2026, Vol. 48 ›› Issue (04): 734-746.DOI: 10.1016/j.pld.2026.03.005

• Articles • Previous Articles Next Articles

Local adaptation sustains genetic differentiation between two varieties of Chinese walnut (Juglans cathayensis) despite extensive hybridization in subtropical China

Wan Hu^a, Caixia Han^a, Li Li^a, Chunhua Zang^b, Runzi Li^b, Hong Nie^a, Jianbo Nie^a, Yong Shi^a, Chen Feng^a, Jie Zhang^a, Yixuan Kou^c, Zhiyong Zhang^c, Dengmei Fan^b, Danqi Li^a

a. Jiangxi Provincial Key Laboratory of Ex Situ Plant Conservation and Utilization, Lushan Botanical Garden, Jiangxi Province and Chinese Academy of Sciences, Jiujiang 332900, China;
b. Laboratory of Subtropical Biodiversity, College of Forestry, Jiangxi Agricultural University, Nanchang 330045, China;
c. Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin 541004, China

Received:2025-11-03 Revised:2026-03-02 Accepted:2026-03-06 Online:2026-03-12 Published:2026-07-25
Contact: Zhiyong Zhang,E-mail:pinus-rubus@163.com;Dengmei Fan,E-mail:dmf.625@163.com;Danqi Li,E-mail:lidq@lsbg.cn
Supported by:
We gratefully thank Dr. Rengang Zhang from the Kunming Institute of Botany, Chinese Academy of Sciences, for his valuable assistance with data analysis. We are grateful to the handling editor and the two anonymous reviewers for their constructive comments and suggestions on our manuscript. This work was financially supported by the National Natural Science Foundation of China (grant numbers 32460063 and 41961009), the Innovation Leading Talent Program in Jiangxi Province (JXSQ2023101107), the National Key R&D Program of China (2024YFF1307405) and the Key R&D Program of Jiangxi Province (20252BCF320039).

Local adaptation sustains genetic differentiation between two varieties of Chinese walnut (Juglans cathayensis) despite extensive hybridization in subtropical China

Wan Hu^a, Caixia Han^a, Li Li^a, Chunhua Zang^b, Runzi Li^b, Hong Nie^a, Jianbo Nie^a, Yong Shi^a, Chen Feng^a, Jie Zhang^a, Yixuan Kou^c, Zhiyong Zhang^c, Dengmei Fan^b, Danqi Li^a

a. Jiangxi Provincial Key Laboratory of Ex Situ Plant Conservation and Utilization, Lushan Botanical Garden, Jiangxi Province and Chinese Academy of Sciences, Jiujiang 332900, China;
b. Laboratory of Subtropical Biodiversity, College of Forestry, Jiangxi Agricultural University, Nanchang 330045, China;
c. Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin 541004, China

通讯作者: Zhiyong Zhang,E-mail:pinus-rubus@163.com;Dengmei Fan,E-mail:dmf.625@163.com;Danqi Li,E-mail:lidq@lsbg.cn
基金资助:
We gratefully thank Dr. Rengang Zhang from the Kunming Institute of Botany, Chinese Academy of Sciences, for his valuable assistance with data analysis. We are grateful to the handling editor and the two anonymous reviewers for their constructive comments and suggestions on our manuscript. This work was financially supported by the National Natural Science Foundation of China (grant numbers 32460063 and 41961009), the Innovation Leading Talent Program in Jiangxi Province (JXSQ2023101107), the National Key R&D Program of China (2024YFF1307405) and the Key R&D Program of Jiangxi Province (20252BCF320039).

Abstract

Abstract: Understanding how natural selection sustains genetic differentiation despite ongoing hybridization remains a central question in evolutionary biology. Here, we integrated range-wide whole-genome resequencing data and ecological niche modeling to elucidate the evolutionary history, local adaptation, and hybridization patterns of Juglans cathayensis, a walnut species widely distributed across subtropical China. Our analyses revealed that Chinese walnut comprised two genetic clusters corresponding to its two recognized varieties, which were further subdivided into three lineages: the East lineage, consisting exclusively of J. cathayensis var. formosana individuals; and the West and Admixed lineages, comprising genetically pure and admixed individuals of J. cathayensis var. cathayensis, respectively. The admixed populations formed a hybrid zone in the ecotone between the East and West lineages. Divergence between the East and West lineages dates to the Middle Pliocene, with persistent bidirectional gene flow until the mid-Pleistocene, likely driven by long-term local adaptation to niche differences between eastern and western China. Genomic regions of differentiation may result from divergent selection under gene flow and divergent sorting of ancient polymorphisms. Moreover, we identified positively selected genes and environment-associated loci involved in ecological adaptation, underscoring their role in promoting intraspecific differentiation. Bayesian genomic cline analysis detected limited introgression of adaptive loci in the hybrid zone, suggesting that natural selection sustains divergence in genomic regions associated with local adaptation, while neutral loci are homogenized through hybridization. Together, these findings provide novel insights into the evolutionary mechanisms shaping plant diversity in subtropical China, a region recognized as an evolutionary cradle.

Key words: Local adaptation, Genetic differentiation, Hybrid zone, Juglans cathayensis, Subtropical China

摘要： Understanding how natural selection sustains genetic differentiation despite ongoing hybridization remains a central question in evolutionary biology. Here, we integrated range-wide whole-genome resequencing data and ecological niche modeling to elucidate the evolutionary history, local adaptation, and hybridization patterns of Juglans cathayensis, a walnut species widely distributed across subtropical China. Our analyses revealed that Chinese walnut comprised two genetic clusters corresponding to its two recognized varieties, which were further subdivided into three lineages: the East lineage, consisting exclusively of J. cathayensis var. formosana individuals; and the West and Admixed lineages, comprising genetically pure and admixed individuals of J. cathayensis var. cathayensis, respectively. The admixed populations formed a hybrid zone in the ecotone between the East and West lineages. Divergence between the East and West lineages dates to the Middle Pliocene, with persistent bidirectional gene flow until the mid-Pleistocene, likely driven by long-term local adaptation to niche differences between eastern and western China. Genomic regions of differentiation may result from divergent selection under gene flow and divergent sorting of ancient polymorphisms. Moreover, we identified positively selected genes and environment-associated loci involved in ecological adaptation, underscoring their role in promoting intraspecific differentiation. Bayesian genomic cline analysis detected limited introgression of adaptive loci in the hybrid zone, suggesting that natural selection sustains divergence in genomic regions associated with local adaptation, while neutral loci are homogenized through hybridization. Together, these findings provide novel insights into the evolutionary mechanisms shaping plant diversity in subtropical China, a region recognized as an evolutionary cradle.

关键词: Local adaptation, Genetic differentiation, Hybrid zone, Juglans cathayensis, Subtropical China

Wan Hu, Caixia Han, Li Li, Chunhua Zang, Runzi Li, Hong Nie, Jianbo Nie, Yong Shi, Chen Feng, Jie Zhang, Yixuan Kou, Zhiyong Zhang, Dengmei Fan, Danqi Li. Local adaptation sustains genetic differentiation between two varieties of Chinese walnut (Juglans cathayensis) despite extensive hybridization in subtropical China[J]. Plant Diversity, 2026, 48(04): 734-746.

References

[1] Abbott, R., Albach, D., Ansell, S., et al., 2013. Hybridization and speciation. J. Evol. Biol. 26, 229-246. http://doi.org/10.1111/j.1420-9101.2012.02599.x.
[2] Abbott, R.J., 2017. Plant speciation across environmental gradients and the occurrence and nature of hybrid zones. J. Syst. Evol. 55, 238-258. http://doi.org/10.1111/jse.12267.
[3] Alexander, D.H., Lange, K., 2011. Enhancements to the ADMIXTURE algorithm for individual ancestry estimation. BMC Bioinf. 12, 246. http://doi.org/10.1186/1471-2105-12-246.
[4] An, Z., John, E.K., Warren, L.P., et al., 2001. Evolution of Asian monsoons and phased uplift of the Himalaya-Tibetan plateau since Late Miocene times. Nature 411, 62-66. http://doi.org/10.1038/35075035.
[5] Ao, H., Rohling, E.J., Li, X., et al., 2023. Northern hemisphere ice sheet expansion intensified Asian aridification and the winter monsoon across the mid-Pleistocene transition. Commun. Earth Environ. 4, 36. http://doi.org/10.1038/s43247-023-00686-9.
[6] Bai, W.N., Wang, W.T., Zhang, D.Y., 2014. Contrasts between the phylogeographic patterns of chloroplast and nuclear DNA highlight a role for pollen-mediated gene flow in preventing population divergence in an East Asian temperate tree. Mol. Phylogenet. Evol. 81, 37-48. http://doi.org/10.1016/j.ympev.2014.08.024.
[7] Bai, W.N., Wang, W.T., Zhang, D.Y., 2016. Phylogeographic breaks within Asian butternuts indicate the existence of a phytogeographic divide in East Asia. New Phytol. 209, 1757-1772. http://doi.org/10.1111/nph.13711.
[8] Barraclough, T.G., 2024. Does selection favour the maintenance of porous species boundaries? J. Evol. Biol. 37, 616-627. http://doi.org/10.1093/jeb/voae030.
[9] Bartrina, I., Otto, E., Strnad, M., et al., 2011. Cytokinin regulates the activity of reproductive meristems, flower organ size, ovule formation, and thus seed yield in Arabidopsis thaliana. Plant Cell 23, 69-80. http://doi.org/10.1105/tpc.110.079079.
[10] Bernard, A., Lheureux, F., Dirlewanger, E., 2018. Walnut: past and future of genetic improvement. Tree Genet. Genomes 14, 1. http://doi.org/10.1007/s11295-017-1214-0.
[11] Bock, D.G., Cai, Z., Elphinstone, C., et al., 2023. Genomics of plant speciation. Plant Commun. 4, 100599. http://doi.org/10.1016/j.xplc.2023.100599.
[12] Borthakur, D., Busov, V., Cao, X.H., et al., 2022. Current status and trends in forest genomics. For. Res. 2, 11. http://doi.org/10.48130/fr-2022-0011.
[13] Bourgeois, Y.X.C., Warren, B.H., 2021. An overview of current population genomics methods for the analysis of whole-genome resequencing data in eukaryotes. Mol. Ecol. 30, 6036-6071. http://doi.org/10.1111/mec.15989.
[14] Browning, S.R., Browning, B.L., 2007. Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. Am. J. Hum. Genet. 81, 1084-1097. http://doi.org/10.1086/521987.
[15] Campbell, Q., Bedford, J.A., Yu, Y., et al., 2025. Agricultural landscape genomics to increase crop resilience. Plant Commun. 6, 101260. http://doi.org/10.1016/j.xplc.2025.101260.
[16] Cantalapiedra, C.P., Hernandez-Plaza, A., Letunic, I., et al., 2021. eggNOG-mapper v2: Functional annotation, orthology assignments, and domain prediction at the metagenomic scale. Mol. Biol. Evol. 38, 5825-5829. http://doi.org/10.1093/molbev/msab293.
[17] Cao, Y., Almeida-Silva, F., Zhang, W.P., et al., 2023. Genomic insights into adaptation to karst limestone and incipient speciation in East Asian Platycarya spp. (Juglandaceae). Mol. Biol. Evol. 40, msad121. http://doi.org/10.1093/molbev/msad121.
[18] Capblancq, T., Forester, B.R., 2021. Redundancy analysis: A Swiss Army Knife for landscape genomics. Methods Ecol. Evol. 12, 2298-2309. http://doi.org/10.1111/2041-210X.13722.
[19] Chen, H., Patterson, N., Reich, D., 2010. Population differentiation as a test for selective sweeps. Genome Res. 20, 393-402. http://doi.org/10.1101/gr.100545.109.
[20] Chen, S., Zhou, Y., Chen, Y., et al., 2018. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34, i884-i890. http://doi.org/10.1093/bioinformatics/bty560.
[21] Coyne, J.A., Orr, H.A., 2004. Speciation. Sunderland, MA: Sinauer Associates.
[22] Dai, X., Xiang, S., Zhang, Y., et al., 2024. Genomic evidence for evolutionary history and local adaptation of two endemic apricots: Prunus hongpingensis and P. zhengheensis. Hortic. Res. 11, uhad215. http://doi.org/10.1093/hr/uhad215.
[23] Danecek, P., Auton, A., Abecasis, G., et al., 2011. The variant call format and VCFtools. Bioinformatics 27, 2156-2158. http://doi.org/10.1093/bioinformatics/btr330.
[24] Dang, M., Zhou, H.J., Ye, H., et al., 2025. Reconstructing evolutionary history of Chinese walnuts (Juglans). J. Syst. Evol. 63, 612-628. http://doi.org/10.1111/jse.13153.
[25] Dixon, P., 2003. VEGAN, a package of R functions for community ecology. J. Veg. Sci. 14, 927-930. http://doi.org/10.1111/j.1654-1103.2003.tb02228.x.
[26] Doyle, J.J., Doyle, J.L., 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bull. 19, 11-15.
[27] Excoffier, L., Dupanloup, I., Huerta-Sanchez, E., et al., 2013. Robust demographic inference from genomic and SNP data. PLoS Genet. 9, e1003905. http://doi.org/10.1371/journal.pgen.1003905.
[28] Fairfax, K.C., Landeryou, T., Rabone, M., et al., 2022. Genome-wide insights into adaptive hybridisation across the Schistosoma haematobium group in West and Central Africa. PLoS Negl. Trop. Dis. 16, e0010088. http://doi.org/10.1371/journal.pntd.0010088.
[29] Feng, J., Dan, X., Cui, Y., et al., 2024. Integrating evolutionary genomics of forest trees to inform future tree breeding amid rapid climate change. Plant Commun. 5, 101044. http://doi.org/10.1016/j.xplc.2024.101044.
[30] Filipe, J.C., Rymer, P.D., Byrne, M., et al., 2022. Signatures of natural selection in a foundation tree along Mediterranean climatic gradients. Mol. Ecol. 31, 1735-1752. http://doi.org/10.1111/mec.16351.
[31] Forester, B.R., Lasky, J.R., Wagner, H.H., et al., 2018. Comparing methods for detecting multilocus adaptation with multivariate genotype-environment associations. Mol. Ecol. 27, 2215-2233. http://doi.org/10.1111/mec.14584.
[32] Fouet, C., Kamdem, C., Gamez, S., et al., 2017. Genomic insights into adaptive divergence and speciation among malaria vectors of the Anopheles nili group. Evol. Appl. 10, 897-906. http://doi.org/10.1111/eva.12492.
[33] Frankel, L.E., Ane, C., 2023. Summary tests of introgression are highly sensitive to rate variation across lineages. Syst. Biol. 72, 1357-1369. https://doi.org/10.1093/sysbio/syad056.
[34] Freedman, A.H., Harrigan, R.J., Zhen, Y., et al., 2023. Evidence for ecotone speciation across an African rainforest-savanna gradient. Mol. Ecol. 32, 2287-2300. http://doi.org/10.1111/mec.16867.
[35] Frichot, E., Francois, O., 2015. LEA: An R package for landscape and ecological association studies. Methods Ecol. Evol. 6, 925-929. http://doi.org/10.1111/2041-210X.12382.
[36] Gao, F., Ming, C., Hu, W., et al., 2016. New software for the fast estimation of population recombination rates (FastEPRR) in the genomic era. G3-Genes Genom. Genet. 6, 1563-1571. http://doi.org/10.1534/g3.116.028233.
[37] Gao, J., Liu, Z.L., Zhao, W., et al., 2021. Combined genotype and phenotype analyses reveal patterns of genomic adaptation to local environments in the subtropical oak Quercus acutissima. J. Syst. Evol. 59, 541-556. http://doi.org/10.1111/jse.12568.
[38] Geng, F.D., Lei, M.F., Zhang, N.Y., et al., 2024. Demographic complexity within walnut species provides insights into the heterogeneity of geological and climatic fluctuations in East Asia. J. Syst. Evol. 62, 1037-1053. http://doi.org/10.1111/jse.13061.
[39] Gompert, Z., Alex Buerkle, C., 2010. introgress: a software package for mapping components of isolation in hybrids. Mol. Ecol. Resour. 10, 378-384. http://doi.org/10.1111/j.1755-0998.2009.02733.x.
[40] Gompert, Z., Buerkle, C.A., 2011. Bayesian estimation of genomic clines. Mol. Ecol. 20, 2111-2127. http://doi.org/10.1111/j.1365-294X.2011.05074.x.
[41] Gompert, Z., Buerkle, C.A., 2012. bgc: Software for Bayesian estimation of genomic clines. Mol. Ecol. Resour. 12, 1168-1176. http://doi.org/10.1111/1755-0998.12009.x.
[42] Gompert, Z., Mandeville, E.G., Buerkle, C.A., 2017. Analysis of population genomic data from hybird zones. Annu. Rev. Ecol. Evol. S. 48, 207-229. http://doi.org/10.1146/annurev-ecolsys-110316-022652.
[43] Goudet, J., 2005. hierfstat, a package for R to compute and test hierarchical F-statistics. Mol. Ecol. Notes 5, 184-186. http://doi.org/10.1111/j.1471-8286.2004.00828.x.
[44] Guo, J.F., Zhao, W., Andersson, B., et al., 2023a. Genomic clines across the species boundary between a hybrid pine and its progenitor in the eastern Tibetan Plateau. Plant Commun. 4, 100574. http://doi.org/10.1016/j.xplc.2023.100574.
[45] Guo, W., Yang, Y., Zhang, X., et al., 2023b. Genomic divergence between two sister Medicago species triggered by the quaternary climatic oscillations on the Qinghai-Tibet plateau and northern China. Mol. Ecol. 32, 3118-3132. http://doi.org/10.1111/mec.16925.
[46] Gutenkunst, R.N., Hernandez, R.D., Williamson, S.H., et al., 2009. Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data. PLoS Genet. 5, e1000695. http://doi.org/10.1371/journal.pgen.1000695.
[47] Han, F., Lamichhaney, S., Grant, B.R., et al., 2017. Gene flow, ancient polymorphism, and ecological adaptation shape the genomic landscape of divergence among Darwin’s finches. Genome Res. 27, 1004-1015. http://doi.org/10.1101/gr.212522.116.
[48] He, W., Zhao, S., Liu, X., et al., 2013. ReSeqTools: an integrated toolkit for large-scale next-generation sequencing based resequencing analysis. Genet. Mol. Res. 12, 6275-6283. http://doi.org/10.4238/2013.December.4.15.
[49] Hewitt, G., 2000. The genetic legacy of the Quaternary ice ages. Nature 405, 907-913. http://doi.org/10.1038/35016000.
[50] Hornikova, M., Lanier, H.C., Markova, S., et al., 2024. Genetic admixture drives climate adaptation in the bank vole. Commun. Biol. 7, 863. http://doi.org/10.1038/s42003-024-06549-z.
[51] Hou, J., Liu, M., Yang, K., et al., 2025. Genetic variation for adaptive evolution in response to changed environments in plants. J. Integr. Plant Biol. 67, 2265-2293. http://doi.org/10.1111/jipb.13961.
[52] Hu, H., Yang, Y., Li, A., et al., 2022. Genomic divergence of Stellera chamaejasme through local selection across the Qinghai-Tibet plateau and northern China. Mol. Ecol. 31, 4782-4796. http://doi.org/10.1111/mec.16622.
[53] Hu, W., Qiu, Q., Liang, H., et al., 2025. Speciation and hybridization of Enkianthus quinqueflorus and E. serrulatus (Ericaceae) across a tropical-subtropical transitional zone in South China. Bot. J. Linn. Soc. 209, 173-185. http://doi.org/10.1093/botlinnean/boaf013.
[54] Jiang, Q., Shen, Y., Wu, L., et al., 2025. Genomic signatures of local adaptation to precipitation and solar radiation in kiwifruit. Plant Divers. 47, 733-745. http://doi.org/10.1016/j.pld.2025.02.003.
[55] Jing, Z.Y., Zhang, R.G., Liu, Y., et al., 2025. Genomic insights into the evolutionary history and conservation of the living fossil Tetracentron sinense. Plant Divers. 47, 759-771. http://doi.org/10.1016/j.pld.2025.05.008.
[56] Johannesson, K., Faria, R., Le Moan, A., et al., 2024. Diverse pathways to speciation revealed by marine snails. Trends Genet. 40, 337-351. http://doi.org/10.1016/j.tig.2024.01.002.
[57] Kakioka, R., Kume, M., Ishikawa, A., et al., 2021. Genetic basis for variation in the number of cephalic pores in a hybrid zone between closely related species of goby, Gymnogobius breunigii and Gymnogobius castaneus. Bot. J. Linn. Soc. 133, 143-154. http://doi.org/10.1093/biolinnean/blab033.
[58] Ke, F., Vasseur, L., Yi, H., et al., 2022. Gene flow, linked selection, and divergent sorting of ancient polymorphism shape genomic divergence landscape in a group of edaphic specialists. Mol. Ecol. 31, 104-118. http://doi.org/10.1111/mec.16226.
[59] Koch, M., Lemke, R., Heise, K.P., et al., 2003. Characterization of gamma-tocopherol methyltransferases from Capsicum annuum L and Arabidopsis thaliana. Eur. J. Biochem. 270, 84-92. http://doi.org/10.1046/j.1432-1033.2003.03364.x.
[60] Kou, Y., Zhang, L., Fan, D., et al., 2020. Evolutionary history of a relict conifer, Pseudotaxus chienii (Taxaceae), in south-east China during the late Neogene: old lineage, young populations. Ann. Bot. 125, 105-117. http://doi.org/10.1093/aob/mcz153.
[61] Kuang, K.Z., Lu, A.M., 1979. In: Kuang, K.Z., Li, P.C. (Eds.). In: Flora Reipublicae Popularis Sinicae, 21. Institutum Academiae Science Press, Beijing, pp. 6–44.
[62] Letunic, I., Bork, P., 2024. Interactive Tree of Life (iTOL) v6: recent updates to the phylogenetic tree display and annotation tool. Nucleic Acids Res. 52, W78-W82. http://doi.org/10.1093/nar/gkae268.
[63] Li, C., Zheng, L., Wang, X., et al., 2019. Comprehensive expression analysis of Arabidopsis GA2-oxidase genes and their functional insights. Plant Sci. 285, 1-13. http://doi.org/10.1016/j.plantsci.2019.04.023.
[64] Li, D., Jiang, L., He, W., et al., 2024a. Allopatric speciation and secondary sympatry of Fagus longipetiolata and F. lucida (Fagaceae) in subtropical China. Bot. J. Linn. Soc. 205, 403-415. http://doi.org/10.1093/botlinnean/boad077.
[65] Li, H., Durbin, R., 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754-1760. http://doi.org/10.1093/bioinformatics/btp324.
[66] Li, H., Durbin, R., 2011. Inference of human population history from individual whole-genome sequences. Nature 475, 493-496. http://doi.org/10.1038/nature10231.
[67] Li, H., Handsaker, B., Wysoker, A., et al., 2009. The sequence alignment/map format and SAMtools. Bioinformatics 25, 2078-2079. http://doi.org/10.1093/bioinformatics/btp352.
[68] Li, W., Ma, M., Feng, Y., et al., 2015. EIN2-directed translational regulation of ethylene signaling in Arabidopsis. Cell 163, 670-683. http://doi.org/10.1016/j.cell.2015.09.037.
[69] Li, X., Cai, K., Zhang, Q., et al., 2022. The Manchurian walnut genome: insights into juglone and lipid biosynthesis. GigaScience 11, giac057. http://doi.org/10.1093/gigascience/giac057.
[70] Li, Y.R., Fritsch, P.W., Zhao, G.G., et al., 2024b. Population differentiation and dynamics of five pioneer species of Gaultheria from the secondary forests in subtropical China. BMC Plant Biol. 24, 506. http://doi.org/10.1186/s12870-024-05189-z.
[71] Liu, A., Geraldes, A., Taylor, E.B., 2024. Historical and contemporary processes driving the origin and structure of an admixed population within a contact zone between subspecies of a north temperate diadromous fish. Mol. Ecol. 33, e17459. http://doi.org/10.1111/mec.17459.
[72] Liu, M.L., Shang, Q.H., Cheng, Y.J., et al., 2023. Drivers of intraspecific differentiation of an alpine cold-tolerant herb, Notopterygium oviforme: Roles of isolation by distance and ecological factors. J. Syst. Evol. 61, 383-398. http://doi.org/10.1111/jse.12844.
[73] Liu, X., Yu, F., 2023. New insights into the functions and regulations of MAP215/MOR1 and katanin, two conserved microtubule-associated proteins in Arabidopsis. Plant Signaling Behav. 18, 2171360. http://doi.org/10.1080/15592324.2023.2171360.
[74] Lopez-Pujol, J., Zhang, F.M., Sun, H.Q., et al., 2011. Mountains of southern China as “plant museums” and “plant cradles”: evolutionary and conservation insights. Mt. Res. Dev. 31, 261-269. http://doi.org/10.1659/mrd-journal-d-11-00058.1.
[75] Ma, T., Wang, K., Hu, Q., et al., 2018. Ancient polymorphisms and divergence hitchhiking contribute to genomic islands of divergence within a poplar species complex. Proc. Natl. Acad. Sci. U.S.A. 115, E236-E243. http://doi.org/10.1073/pnas.1713288114.
[76] Malinsky, M., Matschiner, M., Svardal, H., 2021. Dsuite - Fast D-statistics and related admixture evidence from VCF files. Mol. Ecol. Resour. 21, 584-595. http://doi.org/10.1111/1755-0998.13265.
[77] Marczak, M., Ciesla, A., Janicki, M., et al., 2025. The HECT ubiquitin-protein ligases UPL1 and UPL2 are involved in degradation of Arabidopsis thaliana ACC synthase 7. Physiol. Plant. 177, e70030. http://doi.org/10.1111/ppl.70030.
[78] Martin, B.T., Chafin, T.K., Douglas, M.R., et al., 2021. ClineHelpR: an R package for genomic cline outlier detection and visualization. BMC Bioinf. 22, 501. http://doi.org/10.1186/s12859-021-04423-x.
[79] McCready, K., Victoria, S., Kim, M., 2020. The importance of TOR kinase in plant development. Front. Plant Sci. 11, 16. http://doi.org/10.3389/fpls.2020.00016.
[80] McKenna, A., Hanna, M., Banks, E., et al., 2010. The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297-1303. http://doi.org/10.1101/gr.107524.110.
[81] Meek, M.H., Beever, E.A., Barbosa, S., et al., 2023. Understanding local adaptation to prepare populations for climate change. BioScience 73, 36-47. http://doi.org/10.1093/biosci/biac101.
[82] Meier, J.I., Sousa, V.C., Marques, D.A., et al., 2017. Demographic modelling with whole-genome data reveals parallel origin of similar Pundamilia cichlid species after hybridization. Mol. Ecol. 26, 123-141. https://doi.org/10.1111/mec.13838.
[83] Menon, M., Bagley, J.C., Friedline, C.J., et al., 2018. The role of hybridization during ecological divergence of southwestern white pine (Pinus strobiformis) and limber pine (P. flexilis). Mol. Ecol. 27, 1245-1260. http://doi.org/10.1111/mec.14505.
[84] Mi, X., Feng, G., Hu, Y., et al., 2021. The global significance of biodiversity science in China: an overview. Natl. Sci. Rev. 8, nwab032. http://doi.org/10.1093/nsr/nwab032.
[85] Miura, K., Nozawa, R., 2014. Overexpression of SIZ1 enhances tolerance to cold and salt stresses and attenuates response to abscisic acid in Arabidopsis thaliana. Plant Biotechnol. 31, 167-172. http://doi.org/10.5511/plantbiotechnology.14.0109a.
[86] Monnet, F., Postel, Z., Touzet, P., et al., 2025. Rapid establishment of species barriers in plants compared with that in animals. Science 389, 1147-1150. http://doi.org/doi:10.1126/science.adl2356.
[87] Nazareno, A.G., Bemmels, J.B., Dick, C.W., et al., 2017. Minimum sample sizes for population genomics: an empirical study from an Amazonian plant species. Mol. Ecol. Resour. 17, 1136-1147. http://doi:10.1111/1755-0998.12654.
[88] Nielsen, R., Wakeley, J., 2001. Distinguishing migration from isolation: a Markov Chain Monte Carlo approach. Genetics 158, 885-896. http://doi.org/10.1093/genetics/158.2.885.
[89] Noor, M.A., Bennett, S.M., 2009. Islands of speciation or mirages in the desert? Examining the role of restricted recombination in maintaining species. Heredity 103, 439-444. http://doi.org/10.1038/hdy.2009.151.
[90] Phillips, S.J., Anderson, R.P., Schapire, R.E., 2006. Maximum entropy modeling of species geographic distributions. Ecol. Modell. 190, 231-259. http://doi.org/10.1016/j.ecolmodel.2005.03.026.
[91] Pickrell, J.K., Pritchard, J.K., 2012. Inference of population splits and mixtures from genome-wide allele frequency data. PLoS Genet. 8, e1002967. http://doi.org/10.1371/journal.pgen.1002967.
[92] Price, M.N., Dehal, P.S., Arkin, A.P., 2010. FastTree 2-approximately maximum-likelihood trees for large alignments. PloS One 5, e9490. http://doi.org/10.1371/journal.pone.0009490.
[93] Purcell, S., Neale, B., Todd-Brown, K., et al., 2007. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 81, 559-575. http://doi.org/10.1086/519795.
[94] Qian, H., Ricklefs, R.E., 2000. Large-scale processes and the Asian bias in species diversity of temperate plant. Nature 407, 180-182. http://doi.org/10.1038/35025052.
[95] Qiu, Y.X., Fu, C.X., Comes, H.P., 2011. Plant molecular phylogeography in China and adjacent regions: Tracing the genetic imprints of Quaternary climate and environmental change in the world’s most diverse temperate flora. Mol. Phylogenet. Evol. 59, 225-244. http://doi.org/10.1016/j.ympev.2011.01.012.
[96] Qureshi, M.K., Radeva, V., Genkov, T., et al., 2011. Isolation and characterization of Arabidopsis mutants with enhanced tolerance to oxidative stress. Acta Physiol. Plant. 33, 375-382. http://doi.org/10.1007/s11738-010-0556-0.
[97] R Core Team, 2021. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria.
[98] Ravinet, M., Faria, R., Butlin, R.K., et al., 2017. Interpreting the genomic landscape of speciation: a road map for finding barriers to gene flow. J. Evol. Biol. 30, 1450-1477. http://doi.org/10.1111/jeb.13047.
[99] Rehman, H.M., Nawaz, M.A., Shah, Z.H., et al., 2018. Comparative genomic and transcriptomic analyses of Family-1 UDP glycosyltransferase in three Brassica species and Arabidopsis indicates stress-responsive regulation. Sci. Rep. 8, 1875. http://doi.org/10.1038/s41598-018-19535-3.
[100] Ren, Y., Zhang, L., Yang, X., et al., 2024. Cryptic divergences and repeated hybridizations within the endangered “living fossil” dove tree (Davidia involucrata) revealed by whole genome resequencing. Plant Divers. 46, 169-180. http://doi.org/10.1016/j.pld.2024.02.004.
[101] Rolan-Alvarez, E., Johannesson, K., Erlandsson, J., 1997. The maintenance of a cline in the marine snail Littorina saxatilis: the role of home site advantage and hybrid fitness. Evolution 51, 1838-1847. http://doi.org/10.1111/j.1558-5646.1997.tb05107.x.
[102] Ryan, S.F., Fontaine, M.C., Scriber, J.M., et al., 2017. Patterns of divergence across the geographic and genomic landscape of a butterfly hybrid zone associated with a climatic gradient. Mol. Ecol. 26, 4725-4742. http://doi.org/10.1111/mec.14236.
[103] Sang, Y., Long, Z., Dan, X., et al., 2022. Genomic insights into local adaptation and future climate-induced vulnerability of a keystone forest tree in East Asia. Nat. Commun. 13, 6541. http://doi.org/10.1038/s41467-022-34206-8.
[104] Shi, Y., Zhou, B.F., Liang, Y.Y., et al., 2024. Linked selection and recombination rate generate both shared and lineage-specific genomic islands of divergence in two independent Quercus species pairs. J. Syst. Evol. 62, 505-519. http://doi.org/10.1111/jse.13008.
[105] Stankowski, S., Shipilina, D., Westram, A.M., 2021. Hybrid zones. eLS 2, 1-12. http://doi.org/10.1002/9780470015902.a0029355.
[106] Sun, Y., Hu, H., Huang, H., et al., 2014. Chloroplast diversity and population differentiation of Castanopsis fargesii (Fagaceae): a dominant tree species in evergreen broad-leaved forest of subtropical China. Tree Genet. Genomes 10, 1531-1539. http://doi.org/10.1007/s11295-014-0776-3.
[107] Sun, Y., Surget-Groba, Y., Gao, S., 2016. Divergence maintained by climatic selection despite recurrent gene flow: a case study of Castanopsis carlesii (Fagaceae). Mol. Ecol. 25, 4580-4592. http://doi.org/10.1111/mec.13764.
[108] Sung, C.J., Bell, K.L., Nice, C.C., et al., 2018. Integrating Bayesian genomic cline analyses and association mapping of morphological and ecological traits to dissect reproductive isolation and introgression in a Louisiana Iris hybrid zone. Mol. Ecol. 27, 959-978. http://doi.org/10.1111/mec.14481.
[109] Terhorst, J., Kamm, J.A., Song, Y.S., 2017. Robust and scalable inference of population history from hundreds of unphased whole genomes. Nat. Genet. 49, 303-309. http://doi.org/10.1038/ng.3748.
[110] Wait, D.R., Penalba, J.V., Taylor, S., et al., 2025. Suture zones, speciation, and evolution. Evolution 79, 329-341. http://doi.org/10.1093/evolut/qpae184.
[111] Wang, H., Liu, C., Ren, Y., et al., 2019a. An RNA-binding protein MUG13.4 interacts with AtAGO2 to modulate salinity tolerance in Arabidopsis. Plant Sci. 288, 110218. http://doi.org/10.1016/j.plantsci.2019.110218.
[112] Wang, H., Lu, H., Zhao, L., et al., 2019b. Asian monsoon rainfall variation during the Pliocene forced by global temperature change. Nat. Commun. 10, 5272. http://doi.org/10.1038/s41467-019-13338-4.
[113] Wang, X.H., Kent, M., Fang, X.F., 2007. Evergreen broad-leaved forest in Eastern China: Its ecology and conservation and the importance of resprouting in forest restoration. For. Ecol. Manage. 245, 76-87. http://doi.org/10.1016/j.foreco.2007.03.043.
[114] Warren, D.L., Glor, R.E., Turelli, M., 2008. Environmental niche equivalency versus conservatism: quantitative approaches to niche evolution. Evolution 62, 2868-2883. http://doi.org/10.1111/j.1558-5646.2008.00482.x.
[115] Warren, D.L., Glor, R.E., Turelli, M., 2010. ENMTools: a toolbox for comparative studies of environmental niche models. Ecography 33, 607-611. http://doi.org/10.1111/j.1600-0587.2009.06142.x.
[116] White, N.J., Butlin, R.K., 2021. Multidimensional divergent selection, local adaptation, and speciation. Evolution 75, 2167-2178. http://doi.org/10.1111/evo.14312.
[117] Wiens, B.J., Colella, J.P., 2025. That’s not a hybrid: how to distinguish patterns of admixture and isolation by distance. Mol. Ecol. Resour. 25, e14039. http://doi.org/10.1111/1755-0998.14039.
[118] Willing, E.M., Dreyer, C., van Oosterhout, C., 2012. Estimates of genetic differentiation measured by FST do not necessarily require large sample sizes when using many SNP markers. PLoS One 7, e42649. http://doi:10.1371/journal.pone.0042649.
[119] Wu, T., Hu, E., Xu, S., et al., 2021. clusterProfiler 4.0: A universal enrichment tool for interpreting omics data. Innovation 2, 100141. http://doi.org/10.1016/j.xinn.2021.100141.
[120] Wu, Y., Linan, A.G., Hoban, S., et al., 2024. Divergent ecological selection maintains species boundaries despite gene flow in a rare endemic tree, Quercus acerifolia (maple-leaf oak). J. Hered. 115, 575-587. http://doi.org/10.1093/jhered/esae033.
[121] Xu, W.Q., Ren, C.Q., Zhang, X.Y., et al., 2024. Genome sequences and population genomics reveal climatic adaptation and genomic divergence between two closely related sweetgum species. Plant J. 118, 1372-1387. http://doi.org/10.1111/tpj.16675.
[122] Yang, R., 2018. Study of temporal and spatial expression and subcellular location of AGD class I subfamily in Arabidopsis thaliana. Master Dissertations. Harbin Institute of Technology, Harbin.
[123] Yang, Y., Guo, Y., 2018. Unraveling salt stress signaling in plants. J. Integr. Plant Biol. 60, 796-804. http://doi.org/10.1111/jipb.12689.
[124] Yuan, S., Shi, Y., Zhou, B.F., et al., 2023. Genomic vulnerability to climate change in Quercus acutissima, a dominant tree species in East Asian deciduous forests. Mol. Ecol. 32, 1639-1655. http://doi.org/10.1111/mec.16843.
[125] Yuan, X., Wang, H., Cai, J., et al., 2019. NAC transcription factors in plant immunity. Phytopathol. Res. 1, 3. http://doi.org/10.1186/s42483-018-0008-0.
[126] Yuan, Y., Feng, Y., Wang, J., et al., 2025. Integrative taxonomy for species delimitation: a case study in two widely accepted yet morphologically confounding Rosa species within Sect. Pimpinellifoliae (Rosaceae). Mol. Ecol. 34, e17779. http://doi.org/10.1111/mec.17779.
[127] Zhang, B.W., Xu, L.L., Li, N., et al., 2019a. Phylogenomics reveals an ancient hybrid origin of the persian walnut. Mol. Biol. Evol. 36, 2451-2461. http://doi.org/10.1093/molbev/msz112.
[128] Zhang, C., Dong, S.S., Xu, J.Y., et al., 2019b. PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format files. Bioinformatics 35, 1786-1788. http://doi.org/10.1093/bioinformatics/bty875.
[129] Zhang, W.P., Cao, L., Lin, X.R., et al., 2022. Dead-end hybridization in walnut trees revealed by large-scale genomic sequence data. Mol. Biol. Evol. 39, msab308. http://doi.org/10.1093/molbev/msab308.
[130] Zhang, X., Guo, R., Shen, R., et al., 2023. The genomic and epigenetic footprint of local adaptation to variable climates in kiwifruit. Hortic. Res. 10, uhad031. http://doi.org/10.1093/hr/uhad031.
[131] Zhang, X.W., Li, Y., Zhang, Q., et al., 2018. Ancient east-west divergence, recent admixture, and multiple marginal refugia shape genetic structure of a widespread oak species (Quercus acutissima) in China. Tree Genet. Genomes 14, 88. http://doi.org/10.1007/s11295-018-1302-9.
[132] Zhou, Z., Han, M., Hou, M., et al., 2017. Comparative study of the leaf transcriptomes and ionoms of Juglans regia and its wild relative species Juglans cathayensis. Acta Physiol. Plant. 39, 224. http://doi.org/10.1007/s11738-017-2504-8.
[133] Zhu, B.S., Zhu, Y.X., Zhang, Y.F., et al., 2022. Ethylene activates the EIN2-EIN3/EIL1 signaling pathway in tapetum and disturbs anther development in Arabidopsis. Cells 11, 3177. http://doi.org/10.3390/cells11193177.
[134] Zhu, H., Tan, Y., 2024. The origin of evergreen broad-leaved forests in East Asia from the evidence of floristic elements. Plants 13, 1106. http://doi.org/10.3390/plants13081106.
[135] Zhuang, X., Chung, K.P., Cui, Y., et al., 2017. ATG9 regulates autophagosome progression from the endoplasmic reticulum in Arabidopsis. Proc. Natl. Acad. Sci. U.S.A. 114, E426-E435. http://doi.org/10.1073/pnas.1616299114.
[136] Zou, Y., Yang, W., Zhang, R., et al., 2024. Signatures of local adaptation and maladaptation to future climate in wild Zizania latifolia. Commun. Biol. 7, 1313. http://doi.org/10.1038/s42003-024-07036-1.

Local adaptation sustains genetic differentiation between two varieties of Chinese walnut (Juglans cathayensis) despite extensive hybridization in subtropical China

Local adaptation sustains genetic differentiation between two varieties of Chinese walnut (Juglans cathayensis) despite extensive hybridization in subtropical China

PDF (PC)

Knowledge

Abstract

Cite this article

share this article

References

Related Articles 15

Recommended Articles

Metrics

Comments

[1]	Chichi Zhao, Lei Huang, Huijun Wang, Xinwei Xu. The Tianshan Mountains as a biogeographic barrier driving North-South divergence and local adaptation in Typha laxmannii [J]. Plant Diversity, 2026, 48(04): 720-733.
[2]	May Zin Win, Shuang-Xiu Xu, Shu-Yang Gao, Jing-Xia Liu, Zu-Chang Xu, Cen Guo, Yun-Long Liu, Peng-Fei Ma, De-Zhu Li. Resequencing of 284 genomes reveals evolutionary history and hotspot of genetic diversity of the giant bamboos [J]. Plant Diversity, 2026, 48(03): 460-473.
[3]	Hum Kala Rana, Santosh Kumar Rana, Jacob B. Landis, Hang Sun, Dong Luo. Decoding the genomic basis of adaptive capacity and vulnerability in the high-altitude Saussurea obvallata complex [J]. Plant Diversity, 2026, 48(03): 474-486.
[4]	Wei Zheng, Li-Jun Yan, Kevin S. Burgess, Richard I. Milne, Han-Tao Qin, Shao-Lin Tan, Ya-Huang Luo, Jia-Yun Zou, Zhi-Qiong Mo, Michael Möller, Chao-Nan Fu, Lian-Ming Gao. Comparative analysis of multiple hybrid zones of Rhododendron × duclouxii uncovered different potential evolutionary outcomes [J]. Plant Diversity, 2025, 47(06): 944-955.
[5]	Zhao-Yang Jing (景昭阳), Ren-Gang Zhang (张仁纲), Yang Liu (刘阳), Ke-Guang Cheng (程可光), De-Tuan Liu (刘德团), Heng Shu (舒恒), Jiali Kong (孔佳莉), Zhong-Hua Liu (刘忠华), Yong-Peng Ma (马永鹏), Ping-Li Liu (刘平丽). Genomic insights into the evolutionary history and conservation of the living fossil Tetracentron sinense [J]. Plant Diversity, 2025, 47(05): 759-771.
[6]	Quan Jiang, Yufang Shen, Lianhai Wu, Zhengwang Jiang, Xiaohong Yao. Genomic signatures of local adaptation to precipitation and solar radiation in kiwifruit [J]. Plant Diversity, 2025, 47(05): 733-745.
[7]	Zhi-Li Zhou (周知里), Tial C. Ling, Jian-Li Zhao (赵建立), Xin-Zhi Wang (王欣之), Lin-Lin Wang (王林林), Li Li (李莉), Wen-Jing Wang (王雯婧), Dong-Rui Jia (贾东瑞), Zhi-Kun Wu (吴之坤), Xu-Dong Sun (孙旭东), Yong-Ping Yang (杨永平), Yuan-Wen Duan (段元文). Parallel loss of anthocyanins triggers the incipient sympatric speciation in an alpine ginger [J]. Plant Diversity, 2025, 47(03): 429-439.
[8]	Yufeng Xu, Chenyang Xue, Xuezhi Wang, Lin Meng, Ying Gao, Mengyang Yu, Lin Geng, Meini Shao, Bo Qu. Morphological adaptation strategy of invasive plant Ambrosia trifida seed distributed along rivers is closely related to soil nutrients [J]. Plant Diversity, 2025, 47(03): 499-510.
[9]	Zhen Yang, Lisong Liang, Weibo Xiang, Lujun Wang, Qinghua Ma, Zhaoshan Wang. Conservation genomics provides insights into genetic resilience and adaptation of the endangered Chinese hazelnut, Corylus chinensis [J]. Plant Diversity, 2024, 46(03): 294-308.
[10]	Peng-Cheng Fu, Qiao-Qiao Guo, Di Chang, Qing-Bo Gao, Shan-Shan Sun. Cryptic diversity and rampant hybridization in annual gentians on the Qinghai-Tibet Plateau revealed by population genomic analysis [J]. Plant Diversity, 2024, 46(02): 194-205.
[11]	HUANG Jia-Lin, LI Shu-Yun, HU Hong. ISSR and SRAP Markers Reveal Genetic Diversity and Population Structure of an Endangered Slipper Orchid, Paphiopedilum micranthum (Orchidaceae) [J]. Plant Diversity, 2014, 36(02): 209-218.
[12]	YUAN JuHong, HU MianHao, XIA Bing. Genetic Diversity of Wild Lycoris radiata (Amaryllidaceae) from China Revealed by SRAP [J]. Plant Diversity, 2010, 32(03): 255-262.
[13]	ZHAO Nian-Xi , GAO Yu-Bao, WANG Jin-Long. An Analysis of Genetic Differentiation and Distribution of RAPD Polymorphism in Stipa grandis (Gramineae) Populations [J]. Plant Diversity, 2008, 30(05): 557-564.
[14]	WANG Shu-Li ^,, LI Qiao-Ming. Population Genetic Diversity of Bombax malabaricum(Bombacaceae) in China [J]. Plant Diversity, 2007, 29(05): 529-536.
[15]	WANG Jin-Feng^, , Chiaki kuroda , GONG Xun. Assessment of Genetic Variation and Differentiation of Ligularia tongolensis (Compositae) Detected by ISSRs [J]. Plant Diversity, 2007, 29(05): 537-542.