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 - Genetics and Evolution
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
Bryophytes hold a larger gene family space than vascular plants.
Bryophytes hold a larger gene family space than vascular plants. Nat Genet. 2025 Oct; 57(10):2562-2569.
PMID: 40983756
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. Genome Res. 2025 Mar 18; 35(3):379-392.
PMID: 39952680
Publisher Correction: Functional innovation through new genes as a general evolutionary process.
Publisher Correction: Functional innovation through new genes as a general evolutionary process. Nat Genet. 2025 Mar; 57(3):764.
PMID: 39920270
Subcellular Enrichment Patterns of New Genes in Drosophila Evolution.
Subcellular Enrichment Patterns of New Genes in Drosophila Evolution. Mol Biol Evol. 2025 Feb 03; 42(2).
PMID: 39920336
Functional innovation through new genes as a general evolutionary process.
Functional innovation through new genes as a general evolutionary process. Nat Genet. 2025 Feb; 57(2):295-309.
PMID: 39875578
The three-dimensional genome drives the evolution of asymmetric gene duplicates via enhancer capture-divergence.
The three-dimensional genome drives the evolution of asymmetric gene duplicates via enhancer capture-divergence. Sci Adv. 2024 Dec 20; 10(51):eadn6625.
PMID: 39693425
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. 2024 Sep 04.
PMID: 38045239
The Rapid Evolution of De Novo Proteins in Structure and Complex.
The Rapid Evolution of De Novo Proteins in Structure and Complex. Genome Biol Evol. 2024 06 04; 16(6).
PMID: 38753069
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 Jun-Jul; 159-160:27-37.
PMID: 38309142
High-Quality Genome Assemblies Reveal Evolutionary Dynamics of Repetitive DNA and Structural Rearrangements in the Drosophila virilis Subgroup.
High-Quality Genome Assemblies Reveal Evolutionary Dynamics of Repetitive DNA and Structural Rearrangements in the Drosophila virilis Subgroup. Genome Biol Evol. 2024 01 05; 16(1).
PMID: 38159044
Fellow des Wissenschaftskolleg zu Berlin (the Institute for Advanced Study in Berlin)
IAS founded by German, Switzerland and Berlin Governments, supervised by Ernst Reuter Foundation
2026
The Sigma Xi Member
The Scientific Research Honor Society
2024
Ray Wu Award
the Ray Wu Society / international Chinese Biological Investigator Society, Ithaca
2022
John Simon Guggenheim Memorial Fellowship in 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