People

Manyuan Long, PhD

//// Since my doctoral study in California in the early 1990s, I have been focusing on the study of a new and major scientific problem: How does a gene originate and evolve? The approaches I have developed and are being used to investigate the new gene problem include theoretical, computational, and molecular experimental approaches. We are currently exploring following scientific issues:



#Phenotypic effects and functions of new genes;

#Evolution of gene essentiality in development;

#Evolutionary analysis of gene interactions with new genes;

#Sex selection and sexual conflict on new genes:

#De novo gene origination.



//// Our scientific works have been recorded in ~200 publications of research reports, commentaries, reviews, interviews and popular science articles with numerous reports of news media. 110 research articles are selected below. Most of their pdf files can be found in the lab website. Besides, five books and monographs were also published:



2021. How Do New Genes Originate and Evolve? Genes. With E. Beltran

2020. Walter Gilbert: Selected Works. 614 pages. World Scientific, Singapore. With W. Gilbert.

2019. Evolution of Genes and Genomes. 174 pages. Science China Life Science. With B. Shen

2010. Darwin’s Heritage Today. 385 pages. Higher Education Press. With H. Gu and Z. Zhou

2003. Origin and Evolution of New Gene Functions. Volume 10, Contemporary Issues in Genetics and Evolution. 202 pages. Kluwer Academic Publishers. The Netherlands.



//// Our works have generated scientific and societal impacts:



## Scientific impacts:



#The American Association for the Advancement of Science (AAAS) summarized my contribution when conferring me with a fellow honor (2014 AAAS Fellow) as “You are being honored: For distinguished contributions to the fields of molecular evolution and genetics, particularly for starting and leading the area of new gene evolution using experimental and computational genomics and molecular biology”.



#Our discovers have helped shape the new chapters and sections about new gene evolution in major textbooks pf evolutionary biology (e.g. Douglas Futuyma, 2009 and 2005, Evolution, Sinauer, Massachusetts; Michael Lynch, 2007, The Origins of Genome Architecture, Sinauer, Massachesetts; Wen-Hsiung Li, 1997, Molecular Evolution, Sinauer, Massachusetts; Roderic Page and Edward Holmes, 1998, Molecular Evolution. Blackwell Science London). Nature published a News Feature to highlight our discovery of a large number of de novo genes in Oryza (Levy, 2019. Genes from the Junkyard. Nature 574: 314-316).



## Societal impacts:



#New York Times, Washington Times, Chicago Tribune, Sacramento Bee, The Huffington Post, La Vanguardia, the New Scientist, the Scientist, Discover, La Recherche, Wen Hui Bao, and other news media in US, Europe, East Asia reported in various languages his scientific discovers and commentaries.



#Our research results summarized in a Nature Rev Genet article (Manyuan Long et al, 2003) were cited as major evidence for a successful defense of Amendment I to the United States Constitution in the nationally concerned case of Kitzmiller et al. vs. Dover Area School District in Pennsylvania in 2005.



#American Scientist published a feature popular science article by us to discuss de novo gene origination (Mortola and Long, 2021. New Genes Born to Junk. May-June Issue.) Quanta magazine published two interviews with me to discuss de novo gene origination and evolution of gene essentiality (Callier, 2020. Where do new genes come from. April 9. Callier, 2020. Scientists Find Vital Genes Evolving in Genome’s Junkyard. November 16.)

Sichuan Agricultural University
Sichuan
B.A. and M.S. - Crop Plants and Genetics
2015

Harvard University
Cambridge Massachusetts
Postdoctoral Fellow - Gene evolution and molecular biology
1997

University of California at Davis
California
M.S. and Ph.D. - Genetics and Evolution
1992

A zebrafish-specific chimeric gene evolved essential developmental functions: discussion of conceptual significance.
Long M. A zebrafish-specific chimeric gene evolved essential developmental functions: discussion of conceptual significance. Sci China Life Sci. 2021 May; 64(5):840-842.
PMID: 33580430

Evolutionary Dynamics of Abundant 7-bp Satellites in the Genome of Drosophila virilis.
Flynn JM, Long M, Wing RA, Clark AG. Evolutionary Dynamics of Abundant 7-bp Satellites in the Genome of Drosophila virilis. Mol Biol Evol. 2020 05 01; 37(5):1362-1375.
PMID: 31960929

Rapid Evolution of Gained Essential Developmental Functions of a Young Gene via Interactions with Other Essential Genes.
Lee YCG, Ventura IM, Rice GR, Chen DY, Colmenares SU, Long M. Rapid Evolution of Gained Essential Developmental Functions of a Young Gene via Interactions with Other Essential Genes. Mol Biol Evol. 2019 10 01; 36(10):2212-2226.
PMID: 31187122

Evolution of genes and genomes: an emerging paradigm in life science.
Long M, Shen B. Evolution of genes and genomes: an emerging paradigm in life science. Sci China Life Sci. 2019 04; 62(4):435-436.
PMID: 30929192

Topological evolution of coexpression networks by new gene integration maintains the hierarchical and modular structures in human ancestors.
Zu J, Gu Y, Li Y, Li C, Zhang W, Zhang YE, Lee U, Zhang L, Long M. Topological evolution of coexpression networks by new gene integration maintains the hierarchical and modular structures in human ancestors. Sci China Life Sci. 2019 Apr; 62(4):594-608.
PMID: 30919280

Origination and evolution of orphan genes and de novo genes in the genome of Caenorhabditis elegans.
Zhang W, Gao Y, Long M, Shen B. Origination and evolution of orphan genes and de novo genes in the genome of Caenorhabditis elegans. Sci China Life Sci. 2019 Apr; 62(4):579-593.
PMID: 30919281

GenTree, an integrated resource for analyzing the evolution and function of primate-specific coding genes.
Shao Y, Chen C, Shen H, He BZ, Yu D, Jiang S, Zhao S, Gao Z, Zhu Z, Chen X, Fu Y, Chen H, Gao G, Long M, Zhang YE. GenTree, an integrated resource for analyzing the evolution and function of primate-specific coding genes. Genome Res. 2019 04; 29(4):682-696.
PMID: 30862647

Rapid evolution of protein diversity by de novo origination in Oryza.
Zhang L, Ren Y, Yang T, Li G, Chen J, Gschwend AR, Yu Y, Hou G, Zi J, Zhou R, Wen B, Zhang J, Chougule K, Wang M, Copetti D, Peng Z, Zhang C, Zhang Y, Ouyang Y, Wing RA, Liu S, Long M. Rapid evolution of protein diversity by de novo origination in Oryza. Nat Ecol Evol. 2019 04; 3(4):679-690.
PMID: 30858588

Publisher Correction: Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza.
Stein JC, Yu Y, Copetti D, Zwickl DJ, Zhang L, Zhang C, Chougule K, Gao D, Iwata A, Goicoechea JL, Wei S, Wang J, Liao Y, Wang M, Jacquemin J, Becker C, Kudrna D, Zhang J, Londono CEM, Song X, Lee S, Sanchez P, Zuccolo A, Ammiraju JSS, Talag J, Danowitz A, Rivera LF, Gschwend AR, Noutsos C, Wu CC, Kao SM, Zeng JW, Wei FJ, Zhao Q, Feng Q, El Baidouri M, Carpentier MC, Lasserre E, Cooke R, da Rosa Farias D, da Maia LC, Dos Santos RS, Nyberg KG, McNally KL, Mauleon R, Alexandrov N, Schmutz J, Flowers D, Fan C, Weigel D, Jena KK, Wicker T, Chen M, Han B, Henry R, Hsing YC, Kurata N, de Oliveira AC, Panaud O, Jackson SA, Machado CA, Sanderson MJ, Long M, Ware D, Wing RA. Publisher Correction: Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza. Nat Genet. 2018 11; 50(11):1618.
PMID: 30291357

Gene duplicates resolving sexual conflict rapidly evolved essential gametogenesis functions.
VanKuren NW, Long M. Gene duplicates resolving sexual conflict rapidly evolved essential gametogenesis functions. Nat Ecol Evol. 2018 04; 2(4):705-712.
PMID: 29459709

View All Publications

Distinguished Investigator Award, Senior Award
The University of Chicago, Division of Biological Sciences
2020

15 Studies That Challenged Medical Dogma in 2019
Medscape
2019

AAAS Fellow
the American Association for the Advancement of Science
2014

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

CAREER Award
National Science Foundation
2003

Packard Fellow for Science & Engineering
Davis & Lucile Packard Foundation
1999

Allen Marr Prize
The University of California at Davis
1993