何子文，男，畢業於中山大學，博士，中山大學生命科學學院教授、博士生導師。
基本介紹
- 中文名：何子文
- 畢業院校：中山大學
- 學位/學歷：博士
- 專業方向：植物學、生物信息學、生態學
- 任職院校：中山大學
研究方向,個人經歷,學術成就,承擔課題,論文專著,
研究方向
進化生物學與生態基因組學
個人經歷
2004.09 — 2008.06 中山大學，生態學專業，獲理學學士學位，中山大學優秀畢業生；
2008.09 — 2013.06 中山大學，生物化學與分子生物學專業，導師施蘇華教授，獲理學博士學位，教育部博士研究生學術新人獎；
2013.08 — 2015.12 中山大學，生命科學學院，博士後，合作導師吳仲義教授；
2016.01 — 2018.12 中山大學，生命科學學院，特聘研究員；
2019.01 — 2024.03 中山大學，生命科學學院，副教授；
2024.04，中山大學，生命科學學院，教授。
學術成就
在物種形成理論和基因組適應性進化研究領域產出了一系列重要成果，在National Science Review、Nature Ecology & Evolution、Nature Communications、Plant Biotechnology Journal、Molecular Biology and Evolution、New Phytologist等國際一流期刊發表研究論文40餘篇。主持省傑出青年項目和國家級項目多個，入選國家重大人才工程。
發表在Nature Ecology & Evolution的研究論文(He et al., 2022)是首個以同資源種團(ecological guild)為研究對象開展的大規模生態基因組學研究，重建了涵蓋全球紅樹物種的系統發育關係，首次界定紅樹植物的27次獨立起源事件，並發現全球氣候變化導致了紅樹物種極低的遺傳多樣性，紅樹植物在海平面快速變化時期經歷了種群規模急劇減少和破碎分化過程。發表在National Science Review的研究論文(He et al., 2019)提出並驗證了一種全新的物種形成理論MIM Model，發現海平面變化導致的間斷性基因流是促進物種形成的一種有效機制，並推動印度-西太平洋區域成為全球生物多樣性熱點區域。此研究成功地挑戰了過去七十年來解釋物種形成的標準模型的地位，獲得國際進化生物學權威認可，被譽為對物種形成研究領域的重要貢獻(Rieseberg, 2019 Natl. Sci. Rev.)。論文被ESI熱點論文和高被引論文資料庫收錄。發表在PLoS Genetics的研究論文(He et al., 2011)，從群體基因組水平解決了學術界長期爭議的模式物種水稻兩個亞種是單起源還是多起源的問題。該成果一經發表就受到廣泛關注，紐約時報、Discover等媒體進行了報導，被Nature、Cell等期刊引用百餘次。
承擔課題
主持國家自然科學基金青年科學基金項目1項和面上項目2項、中國博士後科學基金面上資助和特別資助項目各1項、廣東省基礎與套用基礎研究基金自然科學基金面上項目和傑出青年項目各1項，以主要參與者參加國家重點重大項目3項。
論文專著
Shaohua Xu#, Shao Shao#, Xiao Feng, Sen Li, Lingjie Zhang, Weihong Wu, Min Liu, Miles E. Tracy, Cairong Zhong, Zixiao Guo, Chung-I Wu, Suhua Shi*, Ziwen He*. Adaptation in unstable environments and global gene losses: small but stable gene networks by the May–Wigner theory. Molecular Biology and Evolution, 2024, 41(4):msae059.
Xiao Feng#, Qipian Chen#, Weihong Wu, Jiexin Wang, Guohong Li, Shaohua Xu, Shao Shao, Min Liu, Cairong Zhong, Chung-I Wu, Suhua Shi*, Ziwen He*. Genomic evidence for rediploidization and adaptive evolution following the whole-genome triplication. Nature Communications, 2024, 15:1635.
Weihong Wu#, Xiao Feng#, Nan Wang, Shao Shao, Min Liu, Fa Si, Linhao Chen, Chuanfeng Jin, Shaohua Xu, Zixiao Guo, Cairong Zhong, Suhua Shi, Ziwen He*. Genomic analysis of Nypa fruticans elucidates its intertidal adaptations and early palm evolution. Journal of Integrative Plant Biology, 2024, 66(4):824-843.
Yuan Wang, Yulong Li, Weihong Wu, Shao Shao, Qi Fang, Shaohua Xu, Zixiao Guo, Suhua Shi, Ziwen He*. The evolution history of an allotetraploid mangrove tree analysed with a new tool Allo4D. Plant Biotechnology Journal, 2023, doi:10.1111/pbi.14281.
Xiao Feng, Guohong Li, Weihong Wu, Haomin Lyu, Jiexin Wang, Cong Liu, Cairong Zhong, Suhua Shi*, Ziwen He*. Expansion and adaptive evolution of the WRKY transcription factor family in Avicennia mangrove trees. Marine Life Science & Technology, 2023, 5(2):155-168.
Shaohua Xu, Zixiao Guo, Xiao Feng, Shao Shao, Yuchen Yang, Jianfang Li, Cairong Zhong, Ziwen He*, Suhua Shi*. Where whole-genome duplication is most beneficial: Adaptation of mangroves to a wide salinity range between land and sea. Molecular Ecology, 2023, 32(2):460-475.
Xinfeng Wang#, Ziwen He#*, Zixiao Guo#, Ming Yang, Shaohua Xu, Qipian Chen, Shao Shao, Sen Li, Cairong Zhong, Norman C Duke, Suhua Shi*. Extensive gene flow in secondary sympatry after allopatric speciation. National Science Review, 2022, 9(12):nwac280.
Ning Sun#, Liandong Yang#, Fei Tian#, Honghui Zeng#, Ziwen He*, Kai Zhao*, Cheng Wang, Minghui Meng, Chenguang Feng, Chengchi Fang, Wenqi Lv, Jing Bo, Yongtao Tang, Xiaoni Gan, Zuogang Peng, Yiyu Chen*, Shunping He*. Sympatric or micro-allopatric speciation in a glacial lake? Genomic islands support neither. National Science Review, 2022, 9(12):nwac291.
Ziwen He#, Xiao Feng#, Qipian Chen#, Liangwei Li#, Sen Li, Kai Han, Zixiao Guo, Jiayan Wang, Min Liu, Chengcheng Shi, Shaohua Xu, Shao Shao, Xin Liu, Xiaomeng Mao, Wei Xie, Xinfeng Wang, Rufan Zhang, Guohong Li, Weihong Wu, Zheng Zheng, Cairong Zhong, Norman C. Duke, David E. Boufford, Guangyi Fan, Chung-I Wu, Robert E. Ricklefs, Suhua Shi*. Evolution of coastal forests based on a full set of mangrove genomes. Nature Ecology & Evolution, 2022, 6(6):738-749.
Qipian Chen, Hao Yang, Xiao Feng, Qingjian Chen, Suhua Shi*, Chung-I Wu*, Ziwen He*. Two decades of suspect evidence for adaptive molecular evolution – Negative selection confounding positive selection signals. National Science Review, 2022, 9(5):nwab217.
Xiao Feng#, Guohong Li#, Shaohua Xu, Weihong Wu, Qipian Chen, Shao Shao, Min Liu, Nan Wang, Cairong Zhong, Ziwen He*, Suhua Shi. Genomic insights into molecular adaptation to intertidal environments in the mangrove Aegiceras corniculatum. New Phytologist, 2021, 231:2346-2358.
Shaohua Xu, Jiayan Wang, Zixiao Guo, Ziwen He*, Suhua Shi*. Genomic convergence in the adaptation to extreme environments. Plant Communications, 2020, 1(6):100117.
Xinfeng Wang#, Ziwen He#, Suhua Shi*, Chung-I Wu*. Genes and speciation: is it time to abandon the biological species concept? National Science Review, 2020, 7(8):1387-1397.
Ziwen He#, Shaohua Xu#, Zhang Zhang#, Wuxia Guo, Haomin Lyu, Cairong Zhong, David E Boufford, Norman C Duke, The International Mangrove Consortium, Suhua Shi*. Convergent adaptation of the genomes of woody plants at the land–sea interface. National Science Review, 2020, 7(6):978-993.
Ziwen He#, Shaohua Xu#, Suhua Shi*. Adaptive convergence at the genomic level—prevalent, uncommon or very rare? National Science Review, 2020, 7(6):947-951.
Xiao Feng#, Shaohua Xu#, Jianfang Li#, Yuchen Yang, Qipian Chen, Haomin Lyu, Cairong Zhong, Ziwen He*, Suhua Shi*. Molecular adaptation to salinity fluctuation in tropical intertidal environments of a mangrove tree Sonneratia alba. BMC Plant Biology, 2020, 20:178.
Qingjian Chen, Ziwen He, Ao Lan, Xu Shen, Haijun Wen*, Chung-I Wu*. Molecular evolution in large steps—codon substitutions under positive selection. Molecular Biology and Evolution, 2019, 36(9):1862-1873.
Ziwen He, Xinnian Li, Ming Yang, Xinfeng Wang, Cairong Zhong, Norman C Duke, Chung-I Wu*, Suhua Shi*. Speciation with gene flow via cycles of isolation and migration: Insights from multiple mangrove taxa. National Science Review, 2019, 6(2):275-288.
Zixiao Guo#, Xinnian Li#, Ziwen He#, Yuchen Yang, Wenqing Wang, Cairong Zhong, Anthony J. Greenberg, Chung-I Wu, Norman C. Duke, Suhua Shi*. Extremely low genetic diversity across mangrove taxa reflects past sea level changes and hints at poor future responses. Global Change Biology, 2018, 24(4):1741-1748.
Haomin Lyu#, Xinnian Li#, Zixiao Guo, Ziwen He*, Suhua Shi. De novo assembly and annotation of the Avicennia officinalis L. transcriptome. Marine Genomics, 2018, 39:3-6.
Haomin Lyu, Ziwen He, Chung-I Wu, Suhua Shi*. Convergent adaptive evolution in marginal environments: unloading transposable elements as a common strategy among mangrove genomes, New Phytologist, 2018, 217:428-438.
Shaohua Xu#, Ziwen He#, Zixiao Guo, Zhang Zhang, Gerald J. Wyckoff, Anthony Greenberg, Chung-I Wu*, Suhua Shi*. Genome-wide convergence during evolution of mangroves from woody plants. Molecular Biology and Evolution, 2017, 34(4):1008-1015.
Shaohua Xu#, Ziwen He#, Zhang Zhang#, Zixiao Guo#, Wuxia Guo, Haomin Lyu, Jianfang Li, Ming Yang, Zhenglin Du, Yelin Huang, Renchao Zhou, Cairong Zhong, David E. Boufford, Manuel Lerdau, Chung-I Wu, Norman C. Duke, The International Mangrove Consortium, Suhua Shi*. The origin, diversification and adaptation of a major mangrove clade (Rhizophoreae) revealed by whole-genome sequencing. National Science Review, 2017, 4(5):721-734.
Ming Yang#, Ziwen He#, Yelin Huang, Lu Lu, Yubin Yan, Lan Hong, Hao Shen, Ying Liu, Qiang Guo, Lu Jiang, Yanwu Zhang, Anthony J. Greenberg, Renchao Zhou, Xuejun Ge, Chung‐I Wu*, Suhua Shi*. The emergence of the hyperinvasive vine, Mikania micrantha (Asteraceae), via admixture and founder events inferred from population transcriptomics. Molecular Ecology, 2017, 26(13):3405-3423.
Ming Yang, Ziwen He, Suhua Shi*, Chung-I Wu*. Can genomic data alone tell us whether speciation happened with gene flow? Molecular Ecology, 2017, 26(11):2845-2849.
Zhang Zhang#, Ziwen He#, Shaohua Xu, Xinnian Li, Wuxia Guo, Yuchen Yang, Cairong Zhong, Renchao Zhou*, Suhua Shi*. Transcriptome analyses provide insights into the phylogeny and adaptive evolution of the mangrove fern genus Acrostichum. Scientific Reports, 2016, 6:35634.
Ziwen He#, Zhang Zhang#, Wuxia Guo, Ying Zhang, Renchao Zhou, Suhua Shi*. De novo assembly of coding sequences of the mangrove palm (Nypa fruticans) using RNA-seq and discovery of whole-genome duplications in the ancestor of palms. PLoS One, 2015, 10(12):e0145385.
Ziwen He, Xinnian Li, Shaoping Ling, Yun-Xin Fu, Eric Hungate, Suhua Shi*, Chung-I Wu*. Estimating DNA polymorphism from next generation sequencing data with high error rate by dual sequencing applications. BMC Genomics, 2013, 14(1):535.
Ziwen He#, Weiwei Zhai#, Haijun Wen#, Tian Tang, Yu Wang, Xuemei Lu, Anthony J. Greenberg, Richard R. Hudson, Chung-I Wu*, Suhua Shi*. Two evolutionary histories in the genome of rice: the roles of domestication genes. PLoS Genetics, 2011, 7(6):e1002100.
