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Long, Manyuan
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overview 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.
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Academic Article Intron-exon structures of eukaryotic model organisms.
Academic Article Origin of sphinx, a young chimeric RNA gene in Drosophila melanogaster.
Academic Article Rapid divergence of gene duplicates on the Drosophila melanogaster X chromosome.
Academic Article The origin of the Jingwei gene and the complex modular structure of its parental gene, yellow emperor, in Drosophila melanogaster.
Academic Article A new function evolved from gene fusion.
Academic Article Evolution of novel genes.
Academic Article Testing the "proto-splice sites" model of intron origin: evidence from analysis of intron phase correlations.
Academic Article Evolution of the phosphoglycerate mutase processed gene in human and chimpanzee revealing the origin of a new primate gene.
Academic Article Origin of new genes: evidence from experimental and computational analyses.
Academic Article Retroposed new genes out of the X in Drosophila.
Academic Article Dntf-2r, a young Drosophila retroposed gene with specific male expression under positive Darwinian selection.
Academic Article Nucleotide variation and recombination along the fourth chromosome in Drosophila simulans.
Academic Article Intron presence-absence polymorphism in Drosophila driven by positive Darwinian selection.
Academic Article Expansion of genome coding regions by acquisition of new genes.
Academic Article Sex chromosomes and male functions: where do new genes go?
Academic Article Excess of amino acid substitutions relative to polymorphism between X-linked duplications in Drosophila melanogaster.
Academic Article Duplication-degeneration as a mechanism of gene fission and the origin of new genes in Drosophila species.
Academic Article The evolution of courtship behaviors through the origination of a new gene in Drosophila.
Academic Article Extensive gene traffic on the mammalian X chromosome.
Academic Article Evolving protein functional diversity in new genes of Drosophila.
Academic Article Origination of chimeric genes through DNA-level recombination.
Academic Article RNA-based gene duplication: mechanistic and evolutionary insights.
Academic Article Translational effects of differential codon usage among intragenic domains of new genes in Drosophila.
Academic Article Natural selection shapes genome-wide patterns of copy-number polymorphism in Drosophila melanogaster.
Academic Article Recombination yet inefficient selection along the Drosophila melanogaster subgroup's fourth chromosome.
Academic Article Detection of intergenic non-coding RNAs expressed in the main developmental stages in Drosophila melanogaster.
Academic Article Retrogene movement within- and between-chromosomes in the evolution of Drosophila genomes.
Academic Article A new retroposed gene in Drosophila heterochromatin detected by microarray-based comparative genomic hybridization.
Academic Article High rate of chimeric gene origination by retroposition in plant genomes.
Academic Article Age-dependent chromosomal distribution of male-biased genes in Drosophila.
Academic Article Tight junction-associated MARVEL proteins marveld3, tricellulin, and occludin have distinct but overlapping functions.
Academic Article Origins of new male germ-line functions from X-derived autosomal retrogenes in the mouse.
Academic Article A cautionary note for retrocopy identification: DNA-based duplication of intron-containing genes significantly contributes to the origination of single exon genes.
Academic Article General gene movement off the X chromosome in the Drosophila genus.
Academic Article Positive selection for the male functionality of a co-retroposed gene in the hominoids.
Academic Article Evolution of genes and genomes on the Drosophila phylogeny.
Academic Article Deficiency of X-linked inverted duplicates with male-biased expression and the underlying evolutionary mechanisms in the Drosophila genome.
Academic Article Repetitive element-mediated recombination as a mechanism for new gene origination in Drosophila.
Academic Article Adaptive evolution of the insulin two-gene system in mouse.
Academic Article Evolutionary patterns of RNA-based duplication in non-mammalian chordates.
Academic Article Adaptive evolution and the birth of CTCF binding sites in the Drosophila genome.
Academic Article Stage-specific expression profiling of Drosophila spermatogenesis suggests that meiotic sex chromosome inactivation drives genomic relocation of testis-expressed genes.
Academic Article Retrogenes moved out of the z chromosome in the silkworm.
Academic Article The subtelomere of Oryza sativa chromosome 3 short arm as a hot bed of new gene origination in rice.
Academic Article Mutational bias shaping fly copy number variation: implications for genome evolution.
Academic Article Direct evidence for postmeiotic transcription during Drosophila melanogaster spermatogenesis.
Academic Article The rapid generation of chimerical genes expanding protein diversity in zebrafish.
Academic Article Highly tissue specific expression of Sphinx supports its male courtship related role in Drosophila melanogaster.
Academic Article Re-analysis of the larval testis data on meiotic sex chromosome inactivation revealed evidence for tissue-specific gene expression related to the drosophila X chromosome.
Academic Article Drosophila duplication hotspots are associated with late-replicating regions of the genome.
Academic Article New genes in Drosophila quickly become essential.
Academic Article Extensive structural renovation of retrogenes in the evolution of the Populus genome.
Academic Article Accelerated recruitment of new brain development genes into the human genome.
Academic Article Origin of new genes and source for N-terminal domain of the chimerical gene, jingwei, in Drosophila.
Academic Article Gene duplication and evolution.
Academic Article Nucleotide variation along the Drosophila melanogaster fourth chromosome.
Academic Article Origination of an X-linked testes chimeric gene by illegitimate recombination in Drosophila.
Academic Article Recurrent tandem gene duplication gave rise to functionally divergent genes in Drosophila.
Academic Article Evolution of enzymatic activities of testis-specific short-chain dehydrogenase/reductase in Drosophila.
Academic Article Reshaping of global gene expression networks and sex-biased gene expression by integration of a young gene.
Academic Article Frequent recent origination of brain genes shaped the evolution of foraging behavior in Drosophila.
Academic Article Dynamic programming procedure for searching optimal models to estimate substitution rates based on the maximum-likelihood method.
Academic Article A rice gene of de novo origin negatively regulates pathogen-induced defense response.
Academic Article Roles of young serine-endopeptidase genes in survival and reproduction revealed rapid evolution of phenotypic effects at adult stages.
Academic Article Segmental dataset and whole body expression data do not support the hypothesis that non-random movement is an intrinsic property of Drosophila retrogenes.
Academic Article gKaKs: the pipeline for genome-level Ka/Ks calculation.
Academic Article High occurrence of functional new chimeric genes in survey of rice chromosome 3 short arm genome sequences.
Academic Article New genes contribute to genetic and phenotypic novelties in human evolution.
Academic Article The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication.
Academic Article New gene evolution: little did we know.
Academic Article New genes as drivers of phenotypic evolution.
Academic Article Evolution of gene structural complexity: an alternative-splicing-based model accounts for intron-containing retrogenes.
Academic Article New genes important for development.
Academic Article A long-term demasculinization of X-linked intergenic noncoding RNAs in Drosophila melanogaster.
Academic Article New genes drive the evolution of gene interaction networks in the human and mouse genomes.
Academic Article LTR-mediated retroposition as a mechanism of RNA-based duplication in metazoans.
Academic Article Expressed Structurally Stable Inverted Duplicates in Mammalian Genomes as Functional Noncoding Elements.
Academic Article Genetic Architecture of Natural Variation Underlying Adult Foraging Behavior That Is Essential for Survival of Drosophila melanogaster.
Award or Honor Receipt Allen Marr Prize
Award or Honor Receipt David & Lucile Packard Fellow for Science & Engineering
Award or Honor Receipt Inaugural Edna K Papazian Distinguished Service Professor
Academic Article Publisher Correction: Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza.
Academic Article Gene duplicates resolving sexual conflict rapidly evolved essential gametogenesis functions.
Academic Article Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza.
Academic Article GenTree, an integrated resource for analyzing the evolution and function of primate-specific coding genes.
Academic Article Rapid evolution of protein diversity by de novo origination in Oryza.
Academic Article Origination and evolution of orphan genes and de novo genes in the genome of Caenorhabditis elegans.
Academic Article Topological evolution of coexpression networks by new gene integration maintains the hierarchical and modular structures in human ancestors.
Academic Article Evolution of genes and genomes: an emerging paradigm in life science.
Academic Article Rapid Evolution of Gained Essential Developmental Functions of a Young Gene via Interactions with Other Essential Genes.
Academic Article Evolutionary Dynamics of Abundant 7-bp Satellites in the Genome of Drosophila virilis.
Academic Article A zebrafish-specific chimeric gene evolved essential developmental functions: discussion of conceptual significance.
Award or Honor Receipt 15 Studies That Challenged Medical Dogma in 2019
Award or Honor Receipt Distinguished Investigator Award, Senior Award
Academic Article Exon shuffling and the origin of the mitochondrial targeting function in plant cytochrome c1 precursor.
Academic Article Origin of genes.
Academic Article Natural selection and the origin of jingwei, a chimeric processed functional gene in Drosophila.
Academic Article Intron phase correlations and the evolution of the intron/exon structure of genes.
Academic Article The yeast splice site revisited: new exon consensus from genomic analysis.
Academic Article Generation of a widespread Drosophila inversion by a transposable element.
Academic Article Toward a resolution of the introns early/late debate: only phase zero introns are correlated with the structure of ancient proteins.
Academic Article Relationship between "proto-splice sites" and intron phases: evidence from dicodon analysis.
Academic Article Evolution of the intron-exon structure of eukaryotic genes.
Academic Article Introns and gene evolution.
Academic Article Codon usage divergence of homologous vertebrate genes and codon usage clock.
Academic Article Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution.
Academic Article Genomic analyses of new genes and their phenotypic effects reveal rapid evolution of essential functions in Drosophila development.
Academic Article New Genes Interacted With Recent Whole-Genome Duplicates in the Fast Stem Growth of Bamboos.
Academic Article Rapid Gene Evolution in an Ancient Post-transcriptional and Translational Regulatory System Compensates for Meiotic X Chromosomal Inactivation.
Academic Article Species-specific partial gene duplication in Arabidopsis thaliana evolved novel phenotypic effects on morphological traits under strong positive selection.
Academic Article Rapid Cis-Trans Coevolution Driven by a Novel Gene Retroposed from a Eukaryotic Conserved CCR4-NOT Component in Drosophila.
Academic Article Retrogene Duplication and Expression Patterns Shaped by the Evolution of Sex Chromosomes in Malaria Mosquitoes.
Award or Honor Receipt John Simon Guggenheim Memorial Fellowship for Natural Sciences
Academic Article Evolution and maintenance of phenotypic plasticity.
Concept Domestication
Concept Inbreeding Depression
Concept CCCTC-Binding Factor
Concept MARVEL Domain Containing 2 Protein
Concept Occludin
Concept Fatty Acid Synthases
Academic Article Evolutionarily new genes in humans with disease phenotypes reveal functional enrichment patterns shaped by adaptive innovation and sexual selection.
Academic Article Sexual conflict drive in the rapid evolution of new gametogenesis genes.
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