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:



#Evolution of gene expression networks by integration of new genes;

#Phenotypic effects and functions of new genes;

#Evolutionary analysis of gene interactions with new genes;

#Copy number variation within Drosophila populations;

#Evolution of sex chromosomes and sex-related genes;

#Genes and Genomes in plants: high origination rate of chimeric genes in the grass family.



Our scientific 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).



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.

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

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

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, Rosa Farias DD, 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. Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza. Nat Genet. 2018 02; 50(2):285-296.
PMID: 29358651

View All Publications

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