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 functions 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:



Our works were conferred a prestigious award as The John Simon Guggenheim Memorial Fellowship for Natural Sciences in 2022, as one of 3 scientists in biology and one of 180 fellows selected from thousands of tenured professors and noted artists from natural sciences, humanity, social sciences, writers and creative arts in USA and Canada.



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). Our study of de novo gene originations in Oryza (Zhang et al, 2018. Nature Ecol Evol 3: 679–690) were also selected as one of 15 studies in 2019 that challenged medical dogma by Medscape.



Societal impacts:



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



The research results of new gene evolution summarized in a Nature Rev Genet article (Manyuan Long et al, 2003) were cited as major evidence for 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.



The American Scientist magazine published a feature popular science article by us to discuss de novo gene origination (Mortola and Long, 2021. Turning Junk into Us: How Genes Are Born. May-June Issue.) The 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.

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

Sichuan Agricultural University
Sichuan
B.A. and M.S. - Crop Plants and Genetics
1985

Sexual conflict drive in the rapid evolution of new gametogenesis genes.
Sexual conflict drive in the rapid evolution of new gametogenesis genes. Semin Cell Dev Biol. 2024 Feb 02; 159-160:27-37.
PMID: 38309142

Evolutionarily new genes in humans with disease phenotypes reveal functional enrichment patterns shaped by adaptive innovation and sexual selection.
Evolutionarily new genes in humans with disease phenotypes reveal functional enrichment patterns shaped by adaptive innovation and sexual selection. bioRxiv. 2023 Dec 17.
PMID: 38045239

Evolution and maintenance of phenotypic plasticity.
Evolution and maintenance of phenotypic plasticity. Biosystems. 2022 Dec; 222:104791.
PMID: 36244511

Evolutionary New Genes in a Growing Paradigm.
Evolutionary New Genes in a Growing Paradigm. Genes (Basel). 2022 09 08; 13(9).
PMID: 36140774

Gene fusion as an important mechanism to generate new genes in the genus Oryza.
Gene fusion as an important mechanism to generate new genes in the genus Oryza. Genome Biol. 2022 06 15; 23(1):130.
PMID: 35706016

Retrogene Duplication and Expression Patterns Shaped by the Evolution of Sex Chromosomes in Malaria Mosquitoes.
Retrogene Duplication and Expression Patterns Shaped by the Evolution of Sex Chromosomes in Malaria Mosquitoes. Genes (Basel). 2022 05 28; 13(6).
PMID: 35741730

Species-specific partial gene duplication in Arabidopsis thaliana evolved novel phenotypic effects on morphological traits under strong positive selection.
Species-specific partial gene duplication in Arabidopsis thaliana evolved novel phenotypic effects on morphological traits under strong positive selection. Plant Cell. 2022 02 03; 34(2):802-817.
PMID: 34875081

Rapid Gene Evolution in an Ancient Post-transcriptional and Translational Regulatory System Compensates for Meiotic X Chromosomal Inactivation.
Rapid Gene Evolution in an Ancient Post-transcriptional and Translational Regulatory System Compensates for Meiotic X Chromosomal Inactivation. Mol Biol Evol. 2022 01 07; 39(1).
PMID: 34626117

Rapid Cis-Trans Coevolution Driven by a Novel Gene Retroposed from a Eukaryotic Conserved CCR4-NOT Component in Drosophila.
Rapid Cis-Trans Coevolution Driven by a Novel Gene Retroposed from a Eukaryotic Conserved CCR4-NOT Component in Drosophila. Genes (Basel). 2021 12 26; 13(1).
PMID: 35052398

New Genes Interacted With Recent Whole-Genome Duplicates in the Fast Stem Growth of Bamboos.
New Genes Interacted With Recent Whole-Genome Duplicates in the Fast Stem Growth of Bamboos. Mol Biol Evol. 2021 12 09; 38(12):5752-5768.
PMID: 34581782

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Ray Wu Award
the Ray Wu Society / international Chinese Biological Investigator Society, Ithaca
2022

John Simon Guggenheim Memorial Fellowship for Natural Sciences
The John Simon Guggenheim Memorial Foundation
2022

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

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

Allen Marr Prize
The University of California at Davis
1993