The Manyuan Long Laboratory

Research

We are currently exploring the following scientific issues:

  1. Phenotypic effects and functions of new genes
  2. Evolution of gene essentiality in development
  3. Evolutionary analysis of gene interactions with new genes
  4. Sex selection and sexual conflict on new genes
  5. De novo gene origination

An interesting problem in evolutionary biology is how genes with novel functions originate. The research in my laboratory focuses on this problem, although we are also interested in other issues of molecular evolution. Interest in evolutionary novelties can be traced back to the time of Darwin. However, studies of the origin and evolution of genes with new functions have only recently become possible and attracted increasing attention.

Although conceptual revolution is always what we wish to pursue, the available molecular techniques and rapidly expanded genome data from many organisms mean that searching for and characterizing new genes is no longer a formidable technical obstacle. Molecular and evolutionary studies have provided powerful analytical tools for the detection of the processes and mechanisms that underlie the origin of new genes. Two levels of questions about this process can be defined. First, at the level of individual new genes, what are the initial molecular mechanisms that generate new gene structures? Once a new gene arises in an individual genome in a natural population, how does it spread throughout an entire species to become fixed? And, how does the young gene subsequently evolve? Second, at the level of the genome, how often do new genes originate? If new gene formation is not a rare event, are there any patterns that underlie the process? And, what evolutionary and genetic mechanisms govern any such patterns?

 I believe that an efficient approach to these questions is to examine young genes because their early processes of origination are directly observable. Pursuit of these problems requires an integrated approach incorporating molecular, genomic and population analyses. My lab applies such an approach to our studies. Using experimental and computational genomic analysis, we identified numerous new genes in Drosophila and mammalian genomes. Using molecular analysis, we revealed some important molecular evolutionary mechanisms responsible for their current gene structures. By evolutionary genetic analysis, we observed a significant role of the adaptive evolution in the determination of the fate of those new genes. Interesting patterns are observed associated with these new genes. We saw, we came, and we found.


Credit: Nik Spencer/Nature

Scientific Impacts
  • Our scientific discoveries on new gene evolution led to Manyuan receiving a prestigious award in 2022: the “John Simon Guggenheim Memorial Fellowship for Nature Sciences (Biology).” Manyuan was one of three awardees in the area of biology in the U.S. and Canada. The Guggenheim Foundation has awarded fellowships annually since 1925 to professionals who have demonstrated exceptional ability by publishing a significant body of work in the fields of natural sciences, social sciences, humanities, and the creative arts, excluding the performing arts.
  • 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 of 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 scientific works have been recorded in ~200 publications of research reports, commentaries, reviews, interviews, and popular science articles with numerous reports of news media.We have also published five books and monographs:

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.

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, and East Asia reported our scientific discoveries and commentaries in multiple languages
  • 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 the 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.)
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