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Manyuan Long

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American evolutionary biologist, guggenheim fellow

In this Chinese name, the family name is Long.

Manyuan Long
Known forNew gene evolution
AwardsJohn Simon Guggenheim Memorial Fellowship for Natural Sciences, US and Canada
David & Lucille Packard Fellowship for Science and Engineering (1998)
Scientific career
FieldsGenetics and Evolution
InstitutionsUniversity of Chicago (1997)

Harvard University (1992)
University of California, Davis (1992)

Sichuan Agricultural University (1985)
Thesis The Origin and Evolutionary Mechanism of New Genes  (1992)
Doctoral advisorCharles Langley

Manyuan Long (simplified Chinese: 龙漫远; traditional Chinese: 龍漫遠; pinyin: Lóng Mànyuǎn) is a China-born American evolutionary biologist and geneticist. Long pioneered the studies of origination and evolution of new genes and received many awards including the John Simon Guggenheim Memorial Fellowship for Natural Sciences, US and Canada and the Ray Wu Award.

The Long lab website is https://manyuanlonglab.uchicago.edu/

Early life and education

Manyuan Long was born and grew up in a family of an ethnic minority group from the mountainous area of southwestern China, the Miao (also called Hmong). In the late stage of the political turmoil of the Cultural Revolution, after middle school, Long was exiled as "Sent-down youth" to a poor mountainous area in southern Sichuan.

Long studied in Sichuan Agricultural university and earned a baccalaureate in agronomy in 1982 and a master's degree in plant genetics and breeding in 1985, mentored by Zhiren Gao, a population geneticist trained by C.C. LI. In 1987, Long was admitted into the genetics graduate program at the University of California, Davis, where Long earned M.S. in genetics supervised by John Gillespie and a PhD in genetics mentored by Charles Langley in 1992. Long worked as postdoctoral fellow in Harvard University to research molecular biology and population genetics with Walter Gilbert and Richard Lewontin.

Career and research

Academic career

Long worked as assistant professor in 1997, associate professor with tenure in 2003, full professor with tenure in 2005, in department of Ecology and Evolution at the University of Chicago. Long serves as the Edna K. Papazian Distinguished Service Professor since 2011.

New gene origination

Concept and approach

Long proposed and defined the concept of the "evolutionary new genes" or simply called "new genes" in early 1990s, different from the conventional belief that genes and their functions are stationary in evolution.

Long studies on the problem of new genes, or the origin of genes, since Long's doctoral research, by molecular biological experiments and computational analyses. To avoid inefficiency brought by multiple evolutionary events in ancient genes, Long chose to study new genes that recently originated in less than one to a few tens of million years, which turned to be a productive approach.

The first ever known new gene

In 1993, Long published the scientific problem of new gene evolution while researching a gene called Jingwei, the first ever known new gene. Long did postdoctoral research work for four and a half years, investigating the evolution of gene structures while continuing research on Jingwei.

New genes everywhere with patterns

Long and coworkers have investigated molecular mechanisms, rates, and patterns of new gene origination in species ranging from fruit flies to insects, humans, vertebrates, and plants. These analyses revealed the patterns of gene origination, for example, the rapid evolution of essential gene functions in fruit flies, gene traffics between the X chromosomes and autosomes, the out of testis expression evolution in fruit flies, and also in vertebrates and increasing structural complexity of new genes in evolution. Long's major research interests and contributions include the essentiality of new genes, de novo gene origination, and new genes resolving sexual conflict. His research activities also cover the phenotypic innovation of new genes and the expression network of new genes.

Scientific impact

Long and coworkers' findings on new gene evolution were noted as examples in Nature Education library and the textbooks, for example Evolution, Molecular Evolution: a Phylogenetic Approach, and the Princeton Guide to Evolution. One of Long and coworkers' findings, de novo genes are far more commonly than previously thought, was rated as one of "15 studies that challenged medical dogma in 2019" (medscape).

Publication

Long and his teams have published 180 research reports, reviews, commentaries and popular science articles on origination and evolution of new genes with their newly derived functions and phenotypes.

The history of science

Long collaborated with Walter Gilbert to investigate and record important discoveries as molecular biology began to emerge as a field, driven by research in the labs of Walter Gilbert and other scientific pioneers of the era. Long oversaw the editing and publication of the book Walter Gilbert: Selected Works. Long and two scholars (Hongya Gu and Zhonghe Zhou) published another book, entitled Darwin’s Heritage Today, regarding the history and impact of evolutionary biology research defined by Darwin since the publication of his work, On the Origin of Species, in 1859.

Social impact

The new gene studies summarized by Long were presented in the case of Kitzmiller v. Dover Area School District and elsewhere in defense of the First Amendment to U.S. Constitution and the evolutionary biology.

Awards and honors

1993 – Allen Marr Prize for the best Ph.D. thesis research in University of California, Davis, USA

1998 – David & Lucille Packard Fellowship for Science and Engineering

2003 – CAREER Award National Science Foundation

2011 – Inaugural Edna K Papazian Distinguished Service Professor The University of Chicago

2013 – Honorary Visiting professor, the National Institute of Genetics, Mishima, Japan.

2014 – Fellow, the American Association for the Advancement of Science

2019 – 15 Studies That Challenged Medical Dogma in 2019 Medscape

2020 – The Distinguished Investigator Award in Biology, University of Chicago, USA

2022 – The John Simon Guggenheim Memorial Fellowship for Natural Sciences (Biology), USA & Canada

2022 – The Ray Wu Award, USA.

References

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  8. Levy, Adam (2019-10-16). "How evolution builds genes from scratch". Nature. 574 (7778): 314–316. Bibcode:2019Natur.574..314L. doi:10.1038/d41586-019-03061-x. PMID 31619796. S2CID 204707405.
  9. Mortola, Emily; Long, Manyuan (2021-05-01). "Turning Junk into Us: How Genes Are Born". American Scientist. 109 (3): 174–182.
  10. 哈赛 (September 2014). 未来光锥 (in Chinese). Beijing: 清华大学出版社. ISBN 9787302362142.
  11. ^ Long, Manyuan; Langley, Charles H. (1993-04-02). "Natural Selection and the Origin of jingwei , a Chimeric Processed Functional Gene in Drosophila". Science. 260 (5104): 91–95. Bibcode:1993Sci...260...91L. doi:10.1126/science.7682012. ISSN 0036-8075. PMID 7682012.
  12. De Souza, Sandro J.; Long, Manyuan; Gilbert, Walter (June 1996). "Introns and gene evolution". Genes to Cells. 1 (6): 493–505. doi:10.1046/j.1365-2443.1996.d01-264.x. ISSN 1356-9597. PMID 9078380. S2CID 2229831.
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  14. ^ Long, Manyuan (1992). The origin and evolutionary mechanism of new genes. University of California, Davis.
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  19. ^ Long, Manyuan; VanKuren, Nicholas W.; Chen, Sidi; Vibranovski, Maria D. (2013). "New Gene Evolution: Little Did We Know". Annual Review of Genetics. 47: 307–333. doi:10.1146/annurev-genet-111212-133301. ISSN 0066-4197. PMC 4281893. PMID 24050177.
  20. ^ Emerson, J. J.; Kaessmann, Henrik; Betrán, Esther; Long, Manyuan (2004-01-23). "Extensive Gene Traffic on the Mammalian X Chromosome". Science. 303 (5657): 537–540. Bibcode:2004Sci...303..537E. doi:10.1126/science.1090042. ISSN 0036-8075. PMID 14739461. S2CID 41158232.
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  24. ^ Betrán, Esther; Thornton, Kevin; Long, Manyuan (2002-11-12). "Retroposed New Genes Out of the X in Drosophila". Genome Research. 12 (12): 1854–1859. doi:10.1101/gr.604902. ISSN 1088-9051. PMC 187566. PMID 12466289.
  25. ^ Xia, Shengqian; VanKuren, Nicholas W.; Chen, Chunyan; Zhang, Li; Kemkemer, Clause; Shao, Yi; Jia, Hangxing; Lee, UnJin; Advani, Alexander S.; Gschwend, Andrea; Vibranovski, Maria D.; Chen, Sidi; Zhang, Yong E.; Long, Manyuan (2021-07-09). "Genomic analyses of new genes and their phenotypic effects reveal rapid evolution of essential functions in Drosophila development". PLOS Genetics. 17 (7): e1009654. doi:10.1371/journal.pgen.1009654. ISSN 1553-7404. PMC 8270118. PMID 34242211.
  26. Xia, Shengqian; Ventura, Iuri M.; Blaha, Andreas; Sgromo, Annamaria; Han, Shuaibo; Izaurralde, Elisa; Long, Manyuan (2021-08-27). "Rapid gene evolution in an ancient post-transcriptional and translational regulatory system compensates for meiotic X chromosomal inactivation". doi:10.1101/2021.08.25.457683. Retrieved 2022-11-27. {{cite journal}}: Cite journal requires |journal= (help)
  27. Miller, Duncan; Chen, Jianhai; Liang, Jiangtao; Betrán, Esther; Long, Manyuan; Sharakhov, Igor V. (2022-05-28). "Retrogene Duplication and Expression Patterns Shaped by the Evolution of Sex Chromosomes in Malaria Mosquitoes". Genes. 13 (6): 968. doi:10.3390/genes13060968. ISSN 2073-4425. PMC 9222922. PMID 35741730.
  28. Zhang, Li; Park, Jonathan J; Dong, Matthew B; Arsala, Deanna; Xia, Shengqian; Chen, Jianhai; Sosa, Dylan; Atlas, Jared E; Long, Manyuan; Chen, Sidi (May 2023). "Human Gene Age Dating Reveals an Early and Rapid Evolutionary Construction of the Adaptive Immune System". Genome Biology and Evolution. 15 (5). doi:10.1093/gbe/evad081. ISSN 1759-6653. PMC 10210621. PMID 37170918.
  29. Shao, Yi; Chen, Chunyan; Shen, Hao; He, Bin Z.; Yu, Daqi; Jiang, Shuai; Zhao, Shilei; Gao, Zhiqiang; Zhu, Zhenglin; Chen, Xi; Fu, Yan; Chen, Hua; Gao, Ge; Long, Manyuan; Zhang, Yong E. (2019-03-12). "GenTree, an integrated resource for analyzing the evolution and function of primate-specific coding genes". Genome Research. 29 (4): 682–696. doi:10.1101/gr.238733.118. ISSN 1088-9051. PMC 6442393. PMID 30862647.
  30. ^ Zhang, Li; Ren, Yan; Yang, Tao; Li, Guangwei; Chen, Jianhai; Gschwend, Andrea R.; Yu, Yeisoo; Hou, Guixue; Zi, Jin; Zhou, Ruo; Wen, Bo; Zhang, Jianwei; Chougule, Kapeel; Wang, Muhua; Copetti, Dario (April 2019). "Rapid evolution of protein diversity by de novo origination in Oryza". Nature Ecology & Evolution. 3 (4): 679–690. doi:10.1038/s41559-019-0822-5. ISSN 2397-334X. PMID 30858588. S2CID 73728579.
  31. Jin, Guihua; Ma, Peng-Fei; Wu, Xiaopei; Gu, Lianfeng; Long, Manyuan; Zhang, Chengjun; Li, De-Zhu (2021-09-28). "New Genes Interacted With Recent Whole-Genome Duplicates in the Fast Stem Growth of Bamboos". Molecular Biology and Evolution. 38 (12): 5752–5768. doi:10.1093/molbev/msab288. ISSN 1537-1719. PMC 8662795. PMID 34581782.
  32. Huang, Yuan; Chen, Jiahui; Dong, Chuan; Sosa, Dylan; Xia, Shengqian; Ouyang, Yidan; Fan, Chuanzhu; Li, Dezhu; Mortola, Emily (2021-04-06). "Species-specific gene duplication inArabidopsis thalianaevolved novel phenotypic effects on morphological traits under strong positive selection". doi:10.1101/2021.04.05.438504. Retrieved 2022-11-27. {{cite journal}}: Cite journal requires |journal= (help)
  33. ^ Chen, Sidi; Zhang, Yong E.; Long, Manyuan (2010-12-17). "New Genes in Drosophila Quickly Become Essential". Science. 330 (6011): 1682–1685. Bibcode:2010Sci...330.1682C. doi:10.1126/science.1196380. ISSN 0036-8075. PMC 7211344. PMID 21164016.
  34. Vibranovski, Maria D.; Zhang, Yong; Long, Manyuan (2009-05-01). "General gene movement off the X chromosome in the Drosophila genus". Genome Research. 19 (5): 897–903. doi:10.1101/gr.088609.108. ISSN 1088-9051. PMC 2675978. PMID 19251740.
  35. Dai, Hongzheng; Yoshimatsu, Toshio F.; Long, Manyuan (2006-12-30). "Retrogene movement within- and between-chromosomes in the evolution of Drosophila genomes". Gene. Evolutionary Genomics. 385: 96–102. doi:10.1016/j.gene.2006.04.033. ISSN 0378-1119. PMID 17101240.
  36. Vinckenbosch, Nicolas; Dupanloup, Isabelle; Kaessmann, Henrik (2006-02-21). "Evolutionary fate of retroposed gene copies in the human genome". Proceedings of the National Academy of Sciences. 103 (9): 3220–3225. Bibcode:2006PNAS..103.3220V. doi:10.1073/pnas.0511307103. ISSN 0027-8424. PMC 1413932. PMID 16492757.
  37. Kaessmann, Henrik; Vinckenbosch, Nicolas; Long, Manyuan (2009). "RNA-based gene duplication: mechanistic and evolutionary insights". Nature Reviews. Genetics. 10 (1): 19–31. doi:10.1038/nrg2487. ISSN 1471-0064. PMC 3690669. PMID 19030023.
  38. VanKuren, Nicholas W.; Long, Manyuan (2018-02-19). "Gene duplicates resolving sexual conflict rapidly evolved essential gametogenesis functions". Nature Ecology & Evolution. 2 (4): 705–712. doi:10.1038/s41559-018-0471-0. ISSN 2397-334X. PMC 5866764. PMID 29459709.
  39. Gallach, Miguel; Betrán, Esther (May 2011). "Intralocus sexual conflict resolved through gene duplication". Trends in Ecology & Evolution. 26 (5): 222–228. doi:10.1016/j.tree.2011.02.004. ISSN 0169-5347. PMC 3090214. PMID 21397976.
  40. Perry, Jennifer C. (April 2018). "Duplication resolves conflict". Nature Ecology & Evolution. 2 (4): 597–598. doi:10.1038/s41559-018-0493-7. ISSN 2397-334X. PMID 29459705. S2CID 3402243.
  41. Zhang, Yong E.; Landback, Patrick; Vibranovski, Maria D.; Long, Manyuan (2011-10-18). "Accelerated Recruitment of New Brain Development Genes into the Human Genome". PLOS Biology. 9 (10): e1001179. doi:10.1371/journal.pbio.1001179. ISSN 1545-7885. PMC 3196496. PMID 22028629.
  42. Zhang, Yong E.; Landback, Patrick; Vibranovski, Maria; Long, Manyuan (2012-09-24). "New genes expressed in human brains: Implications for annotating evolving genomes". BioEssays. 34 (11): 982–991. doi:10.1002/bies.201200008. ISSN 0265-9247. PMID 23001763. S2CID 40744028.
  43. Zhang, Wenyu; Landback, Patrick; Gschwend, Andrea R.; Shen, Bairong; Long, Manyuan (2015-10-01). "New genes drive the evolution of gene interaction networks in the human and mouse genomes". Genome Biology. 16 (1): 202. doi:10.1186/s13059-015-0772-4. ISSN 1474-760X. PMC 4590697. PMID 26424194.
  44. Chen, Sidi; Ni, Xiaochun; Krinsky, Benjamin H; Zhang, Yong E; Vibranovski, Maria D; White, Kevin P; Long, Manyuan (2012-04-27). "Reshaping of global gene expression networks and sex-biased gene expression by integration of a young gene". The EMBO Journal. 31 (12): 2798–2809. doi:10.1038/emboj.2012.108. ISSN 0261-4189. PMC 3380208. PMID 22543869.
  45. Wang, W.; Zhang, J.; Alvarez, C.; Llopart, A.; Long, M. (2000). "The origin of the Jingwei gene and the complex modular structure of its parental gene, yellow emperor, in Drosophila melanogaster". Molecular Biology and Evolution. 17 (9): 1294–1301. doi:10.1093/oxfordjournals.molbev.a026413. ISSN 0737-4038. PMID 10958846.
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