Manyuan Long - US grants

The questions to be asked center on the molecular evolutionary mechanisms that create initial gene structures and control subsequent evolution. The objectives of this research are: (1) to understand molecular evolutionary relationships among the new genes in the jgw (jinwei)-ynd(yande) gene system by characterizing their gene structures and flanking sequences in D. teisseiri, D, yakuba, and D melanogaster, using various methods of molecular analysis (2) to determine when the two mosiac genes, ynd and ymp(yellow- emperor) originated,by determining their phylogenetic distribution using molecular phylogenetic techniques (3) to determine the roles of various evolutionary forces governing the early stages of new genes, by analyzing molecular evolution and population genetics of jgw, ynd, and ymp (4) in order to look for the correspondence between the newly evolved function and the fast sequence evolution of jgw as revealed by previous analysis of molecular population genetics, the biochemical functions of the jgw proteins at three stages: the ancestral jgw when first created, the evolved ancestral jgw before speciation, and the modern jgw genes will be investigated. The two ancestral jgw sequences are inferred by evolutionary analysis and they will be made by site-direced mutagenesis.

The long-term goal of this research is to elucidate how new genes with novel functions originate, a fundamentally important problem of gene evolution. Studying the origin of a gene in detail requires the discovery of a young gene, since the early evolution of old genes has often been obscured by later evolutionary processes. The recently identified jingwei-yande gene system in Drosophila contains several genes only 2.5 to 30 million years old jingwei (jgw) originated as an Adh retrosequence that recruited several additional exons, while yande (ynd) evolved through exon recombination with yellow-emperor (ymp). Therefore, these young genes, with other related genes in the gene system that evolved recently in gene structure and copy number, provide an excellent opportunity to examine early processes in the origin of new genes.

In this project, Dr. Long investigates the rates and patterns of new gene origination in the model organism Drosophila (the fruit fly) by using experimental and computational genomic analysis in research and teaching. Previous investigations have revealed a number of young genes with peculiar evolutionary features, which include the rapid emergence of novel expression patterns, accelerated rates of evolution, and an asymmetrical distribution of new gene donor sequences within the Drosophila genome. This project initiates a large-scale effort to explore gene originations via recent (within 10 million years) retroposition events in Drosophila genomes. (1) The investigator will measure the rate of new gene origination via retroposition by undertaking a genomic screen of recently evolved genes in the D. melanogaster subgroup species using an approach integrating genomic analysis and molecular evolution. He will identify recently retroposed genes in the D. melanogaster genome by means of genomic hybridization experiments and computational analysis of D. melanogaster genome sequences. (2) He recently observed in his laboratory the first pattern of new gene origination, asymmetric retroposition. New autosomal genes that retroposed from X-linked parental genes are more common than are new X-linked genes that retroposed from autosomal parental genes. (3) He will investigate divergence in function of new genes by examining their tissue-specific expression patterns using DNA microarrays and other RNA analysis techniques. (4) He will train young researchers at different levels, including undergraduates, graduates, and postdoctoral fellows, to meet the urgent needs in the field. He will enhance the education of undergraduates at selected small midwestern colleges by giving lectures on evolutionary genomics at the colleges and providing summer research projects in his laboratory to two students from these schools each year.

These studies will add significantly to the understanding of one of the most basic phenomena of biology: how do new genes and coding portions of genomes evolve? Not only does this work promise to enhance our knowledge base, the large number of new genes identified will also provide a valuable resource for the further study of evolutionary genomics. Furthermore, this project will train young scientists, including undergraduates, in the broad issues of evolutionary genomics

[unreadable] DESCRIPTION (provided by applicant): The objective of this research is to systematically study new genes in the Drosophila melanogaster subgroup and to investigate the tempo and mode of new gene originations. We will focus on the new chimerical genes created by RNA-involved retroposition that often evolve novel functions associated with the mosaic gene structures. To meet these objectives, the following four-prong integrated approaches will be pursued using the D. melanogaster subgroup as our model taxa. (1) Detection of New Genes by Genomic Analyses: Taking advantage of the known divergence times within the subgroup (0.5-12 million years (mys)), new gene detection will be based upon an interdisciplinary approach that integrates computational and experimental genomic analyses. Our computational analyses will utilize available genome sequences and work in conjunction with Fluorescence In Situ Hybridization with multiple species genomes (MFISH) and Comparative Genomic Hybridization (CGH) using DMA microarrays. These analyses will detect and provide new gene candidates on the genome-wide scale. (2) Inference of the Functionality of the New Genes: To infer functionality for these new genes we will examine the molecular evolutionary and transcriptional constraints of each new gene and their temporal-spatial expression patterns. Molecular evolution and population genetic analyses will be also conducted to detect adaptive evolution of new functional genes. (3) Analysis of phylogenetic Distribution of New Gene Originations: We will map all detected origination events of new genes on the phylogenetic tree of the melanogaster subgroup species. We will estimate the rate of new gene origination and its variation along branches of the phylogeny, using related statistical analyses including maximum likelihood approach. (4) Sex Chromosome-dependence of the Origination of New Genes: Taking advantage of the young ages of the identified new genes (between 0.5 and 12 mys), we will investigate whether or not the male gene traffic that we observed in ancient retrogene samples is an on- going process by analyzing the chromosomal location distribution of new genes and their parental genes. The results from these four categories of studies will generate the first phylogenetic distribution of new genes and provide the fresh-insight into the rates and patterns of new gene originations in genomes. [unreadable] [unreadable] [unreadable]

To understand the evolutionary diversification of animals, the applicants will investigate the variation of phenotypes and their genetic basis in multiple species of fruitflies in the genus Drosophila. The connection to diverse phenotypic features has been mapped to protein-coding changes, cis-regulatory changes and lineage-specific genes. The applicants' recent discoveries showed that many young genes played essential roles in organism development. This research will (1) investigate the reproductive contribution of young genes using the evolutionary genetic analysis and gene silencing techniques, (2) detect their interactions with other genes in the genome using the gene-chip based techniques of experimental genomics, and (3) study their roles in the species divergence by comparative analysis of related species. These efforts will advance the understanding of fundamental problems of gene evolution and phenotypic evolution.

These studies will bring conceptual innovations in the understanding of biological systems. The applicants will also create new data and share with the public. Furthermore, the applicants will train undergraduate students, visiting students from other schools and different disciplines, to encourage more talented undergraduates to enter graduate schools and nurture cross-disciplinary investigation. The applicants will purposely initiate more collaborate with multiple research groups in various institutions both nationally and internationally. The knowledge on gene origination is important to the understanding of human evolution. The proposed project will be of general interest to the broad audience including scientists and non-scientists and the discoveries from this project will play a role in scientific education for the general public.

DESCRIPTION (provided by applicant): Although energy homeostasis is central in feeding behavior, the decision to eat is not merely a question of hunger. In a natural environment in which food is often scarce, evaluating the benefit of gaining food over the energy cost or risk in seeking and acquiring food, and the decision to either seek food or stay put and conserve energy is essential for survival. However, the genetic and molecular basis of food-seeking decision-making behaviors, and their functional significance in fitness are poorly understood. We propose a bottom-up approach: starting from well-defined behaviors that are essential for food-seeking decision-making in Drosophila, taking advantage of its rich genetic tools and genomic resources. Moreover, flies are ideal for viability studies to examine the relations between genetic variations, differences in decision- making and differences in fitness under different environmental conditions. We have already taken the critical step and designed novel assays. We will optimize the following assays for quantitative analysis in this application. Decision-making in choosing between 1) small free reward or large reward that requires work; 2) small reward or large reward with a relatively low probability in its availability; 3) small reward or large reward that is paired with potential risks of getting noxious food; and 4) immediate small reward or delayed large reward. We will take advantage of natural variation in genetics and behaviors between different D. melanogaster populations living in African. We will establish 200 recombinant inbred strains derived from original African strains with extreme behavioral phenotypes for each decision-making behavior. We will perform QTL mapping and identify QTLs that contribute to the variations in food-seeking decision-making and fitness. We will then use RNAi transgenic lines to identify specific genes and variants responsible for the above behavioral variations. Although the most likely immediate clinical relevance of our study is obesity, it will have a much broader impact on neuroeconomics, the genetic basis of behavior in general, evolution and ecology.

Sexual selection is a major driver of evolution, often resulting in drastically different characteristics between males and females. Recently it has become clear that gene duplication is also a powerful contributor to evolutionary diversification. This research seeks to understand how young gene duplicates evolve sex-specific essential functions under sexually antagonistic selection. Males and females, while sharing most of their DNA, satisfy different functional requirements for reproduction and survival. Sexual selection on traits with a shared genetic basis can have opposing effects in the two sexes, causing sexual conflict (SC) that may reduce fitness until the conflict is resolved by new genetic changes. This project addresses the hypothesis that gene duplication is an effective mechanism to resolve sexual conflict, using the fruit fly as a convenient model organism. In pursuing these aims, postdocs, graduates, undergraduates and high school students will be trained in molecular and evolutionary biology. The project will also partner with the Illinois Mathematics and Science Academy to involve diverse high school students in the research through lectures and summer internships.

This project focuses on a pair of recently duplicated genes (Apl and Arts) in Drosophila that have opposing fitness effects in the two sexes. The functional evolution in the protein sequences will be characterized to understand the role of protein divergence in mitigation of sexual conflict. The ancestral gene from which Apl and Arts were derived will then be computationally reconstructed and experimentally synthesized. A series of engineered Drosophila strains will then be created using gene editing technology, with different versions of the synthesized ancestral gene replacing the wildtype gene locus which harbors Apl and Arts. Divergence in expression of constructs with different regulatory regions will reveal their role in mitigating sexual conflict. The generality of the duplication-mediated SC resolution model will be tested by examining a score of recent gene duplicates with sex complementary expression patterns using gene knockout and rescue analyses.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.