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Dodge TO, Kim BY, Baczenas JJ, Banerjee SM, Gunn TR, Donny AE, Given LA, Rice AR, Haase Cox SK, Weinstein ML, Cross R, Moran BM, Haber K, Haghani NB, Machin Kairuz JA, Gellert HR, Du K, Aguillon SM, Tudor MS, Gutiérrez-Rodríguez C, Rios-Cardenas O, Morris MR, Schartl M, Powell DL, Schumer M. Structural genomic variation and behavioral interactions underpin a balanced sexual mimicry polymorphism. Curr Biol 2024; 34:4662-4676.e9. [PMID: 39326413 DOI: 10.1016/j.cub.2024.08.053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 07/15/2024] [Accepted: 08/29/2024] [Indexed: 09/28/2024]
Abstract
How phenotypic diversity originates and persists within populations are classic puzzles in evolutionary biology. While balanced polymorphisms segregate within many species, it remains rare for both the genetic basis and the selective forces to be known, leading to an incomplete understanding of many classes of traits under balancing selection. Here, we uncover the genetic architecture of a balanced sexual mimicry polymorphism and identify behavioral mechanisms that may be involved in its maintenance in the swordtail fish Xiphophorus birchmanni. We find that ∼40% of X. birchmanni males develop a "false gravid spot," a melanic pigmentation pattern that mimics the "pregnancy spot" associated with sexual maturity in female live-bearing fish. Using genome-wide association mapping, we detect a single intergenic region associated with variation in the false gravid spot phenotype, which is upstream of kitlga, a melanophore patterning gene. By performing long-read sequencing within and across populations, we identify complex structural rearrangements between alternate alleles at this locus. The false gravid spot haplotype drives increased allele-specific expression of kitlga, which provides a mechanistic explanation for the increased melanophore abundance that causes the spot. By studying social interactions in the laboratory and in nature, we find that males with the false gravid spot experience less aggression; however, they also receive increased attention from other males and are disdained by females. These behavioral interactions may contribute to the maintenance of this phenotypic polymorphism in natural populations. We speculate that structural variants affecting gene regulation may be an underappreciated driver of balanced polymorphisms across diverse species.
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Affiliation(s)
- Tristram O Dodge
- Department of Biology, Stanford University, 327 Campus Drive, Stanford, CA 94305, USA; Centro de Investigaciones Científicas de las Huastecas "Aguazarca" A.C., 16 de Septiembre, 392 Barrio Aguazarca, Calnali, Hidalgo 43240, México.
| | - Bernard Y Kim
- Department of Biology, Stanford University, 327 Campus Drive, Stanford, CA 94305, USA
| | - John J Baczenas
- Department of Biology, Stanford University, 327 Campus Drive, Stanford, CA 94305, USA
| | - Shreya M Banerjee
- Department of Biology, Stanford University, 327 Campus Drive, Stanford, CA 94305, USA; Centro de Investigaciones Científicas de las Huastecas "Aguazarca" A.C., 16 de Septiembre, 392 Barrio Aguazarca, Calnali, Hidalgo 43240, México; Center for Population Biology and Department of Evolution and Ecology, University of California, Davis, 475 Storer Mall, Davis, CA 95616, USA
| | - Theresa R Gunn
- Department of Biology, Stanford University, 327 Campus Drive, Stanford, CA 94305, USA; Centro de Investigaciones Científicas de las Huastecas "Aguazarca" A.C., 16 de Septiembre, 392 Barrio Aguazarca, Calnali, Hidalgo 43240, México
| | - Alex E Donny
- Department of Biology, Stanford University, 327 Campus Drive, Stanford, CA 94305, USA; Centro de Investigaciones Científicas de las Huastecas "Aguazarca" A.C., 16 de Septiembre, 392 Barrio Aguazarca, Calnali, Hidalgo 43240, México
| | - Lyle A Given
- Department of Biology, Stanford University, 327 Campus Drive, Stanford, CA 94305, USA
| | - Andreas R Rice
- Department of Biology, Stanford University, 327 Campus Drive, Stanford, CA 94305, USA
| | - Sophia K Haase Cox
- Department of Biology, Stanford University, 327 Campus Drive, Stanford, CA 94305, USA
| | - M Luke Weinstein
- Department of Biological Sciences, Ohio University, 7 Depot St., Athens, OH 45701, USA
| | - Ryan Cross
- Department of Biological Sciences, Ohio University, 7 Depot St., Athens, OH 45701, USA
| | - Benjamin M Moran
- Department of Biology, Stanford University, 327 Campus Drive, Stanford, CA 94305, USA; Centro de Investigaciones Científicas de las Huastecas "Aguazarca" A.C., 16 de Septiembre, 392 Barrio Aguazarca, Calnali, Hidalgo 43240, México
| | - Kate Haber
- Department of Biology, Stanford University, 327 Campus Drive, Stanford, CA 94305, USA; Berkeley High School, 1980 Allston Way, Berkeley, CA 94704, USA
| | - Nadia B Haghani
- Department of Biology, Stanford University, 327 Campus Drive, Stanford, CA 94305, USA; Centro de Investigaciones Científicas de las Huastecas "Aguazarca" A.C., 16 de Septiembre, 392 Barrio Aguazarca, Calnali, Hidalgo 43240, México
| | | | - Hannah R Gellert
- Department of Biology, Stanford University, 327 Campus Drive, Stanford, CA 94305, USA
| | - Kang Du
- Xiphophorus Genetic Stock Center, Texas State University, San Marcos, 601 University Drive, San Marcos, TX 78666, USA
| | - Stepfanie M Aguillon
- Department of Biology, Stanford University, 327 Campus Drive, Stanford, CA 94305, USA; Centro de Investigaciones Científicas de las Huastecas "Aguazarca" A.C., 16 de Septiembre, 392 Barrio Aguazarca, Calnali, Hidalgo 43240, México; Department of Ecology and Evolutionary Biology, University of California, Los Angeles, 612 Charles E. Young Drive South, Los Angeles, CA 90095, USA
| | - M Scarlett Tudor
- Cooperative Extension and Aquaculture Research Institute, University of Maine, 33 Salmon Farm Road, Franklin, ME 04634, USA
| | - Carla Gutiérrez-Rodríguez
- Red de Biología Evolutiva, Instituto de Ecología, A.C., Carretera antigua a Coatepec 351, Col. El Haya, Xalapa, Veracruz 91073, México
| | - Oscar Rios-Cardenas
- Red de Biología Evolutiva, Instituto de Ecología, A.C., Carretera antigua a Coatepec 351, Col. El Haya, Xalapa, Veracruz 91073, México
| | - Molly R Morris
- Department of Biological Sciences, Ohio University, 7 Depot St., Athens, OH 45701, USA
| | - Manfred Schartl
- Xiphophorus Genetic Stock Center, Texas State University, San Marcos, 601 University Drive, San Marcos, TX 78666, USA; Developmental Biochemistry, Biocenter, University of Würzburg, Am Hubland, 97074 Wuerzburg, Germany
| | - Daniel L Powell
- Department of Biology, Stanford University, 327 Campus Drive, Stanford, CA 94305, USA; Centro de Investigaciones Científicas de las Huastecas "Aguazarca" A.C., 16 de Septiembre, 392 Barrio Aguazarca, Calnali, Hidalgo 43240, México; Department of Biology, Louisiana State University, 202 Life Science Building, Baton Rouge, LA 70803, USA
| | - Molly Schumer
- Department of Biology, Stanford University, 327 Campus Drive, Stanford, CA 94305, USA; Centro de Investigaciones Científicas de las Huastecas "Aguazarca" A.C., 16 de Septiembre, 392 Barrio Aguazarca, Calnali, Hidalgo 43240, México; Howard Hughes Medical Institute, 327 Campus Drive, Stanford, CA 94305, USA.
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Soria E, Lu Q, Boswell W, Du K, Xing Y, Boswell M, Weldon KS, Lai Z, Savage M, Schartl M, Lu Y. Segregation Between an Ornamental and a Disease Driver Gene Provides Insights Into Pigment Cell Regulation. Pigment Cell Melanoma Res 2024. [PMID: 39289030 DOI: 10.1111/pcmr.13196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 07/18/2024] [Accepted: 08/19/2024] [Indexed: 09/19/2024]
Abstract
Genetic interactions are adaptive within a species. Hybridization can disrupt such species-specific genetic interactions and creates novel interactions that alter the hybrid progeny overall fitness. Hybrid incompatibility, which refers to degenerative genetic interactions that decrease the overall hybrid survival and sterility, is one of the results from combining two diverged genomes in hybrids. The discovery of spontaneous lethal tumorigenesis and underlying genetic interactions in select hybrids between diverged Xiphophorus species showed that lethal pathological process can result from degenerative genetic interactions. Such genetic interactions leading to lethal phenotype are thought to shield gene flow between diverged species. However, hybrids between certain Xiphophorus species do not develop such tumors. Here we report the identification of a locus residing in the genome of one Xiphophorus species that represses an oncogene from a different species. Our finding provides insights into normal and pathological pigment cell development, regulation and a molecular mechanism in hybrid incompatibility.
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Affiliation(s)
- Erika Soria
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, Texas, USA
| | | | - Will Boswell
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, Texas, USA
| | - Kang Du
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, Texas, USA
| | - Yanting Xing
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, Texas, USA
| | - Mikki Boswell
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, Texas, USA
| | - Korri S Weldon
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, Texas, USA
| | - Zhao Lai
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, Texas, USA
- Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, Texas, USA
| | - Markita Savage
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, Texas, USA
| | - Manfred Schartl
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, Texas, USA
- Developmental Biochemistry, Biocenter, University of Würzburg, Würzburg, Germany
- Research Department for Limnology, University of Innsbruck, Mondsee, Austria
| | - Yuan Lu
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, Texas, USA
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Du K, Ricci JMB, Lu Y, Garcia-Olazabal M, Walter RB, Warren WC, Dodge TO, Schumer M, Park H, Meyer A, Schartl M. Phylogenomic analyses of all species of swordtail fishes (genus Xiphophorus) show that hybridization preceded speciation. Nat Commun 2024; 15:6609. [PMID: 39098897 PMCID: PMC11298535 DOI: 10.1038/s41467-024-50852-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Accepted: 07/16/2024] [Indexed: 08/06/2024] Open
Abstract
Hybridization has been recognized to play important roles in evolution, however studies of the genetic consequence are still lagging behind in vertebrates due to the lack of appropriate experimental systems. Fish of the genus Xiphophorus are proposed to have evolved with multiple ancient and ongoing hybridization events. They have served as an informative research model in evolutionary biology and in biomedical research on human disease for more than a century. Here, we provide the complete genomic resource including annotations for all described 26 Xiphophorus species and three undescribed taxa and resolve all uncertain phylogenetic relationships. We investigate the molecular evolution of genes related to cancers such as melanoma and for the genetic control of puberty timing, focusing on genes that are predicted to be involved in pre-and postzygotic isolation and thus affect hybridization. We discovered dramatic size-variation of some gene families. These persisted despite reticulate evolution, rapid speciation and short divergence time. Finally, we clarify the hybridization history in the entire genus settling disputed hybridization history of two Southern swordtails. Our comparative genomic analyses revealed hybridization ancestries that are manifested in the mosaic fused genomes and show that hybridization often preceded speciation.
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Affiliation(s)
- Kang Du
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, Texas, TX, USA
| | | | - Yuan Lu
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, Texas, TX, USA
| | - Mateo Garcia-Olazabal
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, Texas, TX, USA
| | - Ronald B Walter
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, Texas, TX, USA
| | - Wesley C Warren
- Department of Animal Sciences, Department of Surgery, Institute for Data Science and Informatics, University of Missouri, Bond Life Sciences Center, Columbia, MI, USA
| | - Tristram O Dodge
- Department of Biology & Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Molly Schumer
- Department of Biology & Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Hyun Park
- Division of Biotechnology, College of Life Science and Biotechnology, Korea University, Seoul, Republic of Korea
| | - Axel Meyer
- Department of Biology, University of Konstanz, Konstanz, Germany.
| | - Manfred Schartl
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, Texas, TX, USA.
- Developmental Biochemistry, Biocenter, University of Wuerzburg, Am Hubland, Wuerzburg, Germany.
- Research Department for Limnology, University of Innsbruck, Mondsee, Austria.
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Münch L, Helmprobst F, Volff JN, Chalopin D, Schartl M, Kneitz S. Transposable Element Expression Profiles in Premalignant Pigment Cell Lesions and Melanoma of Xiphophorus. Genes (Basel) 2024; 15:620. [PMID: 38790249 PMCID: PMC11121471 DOI: 10.3390/genes15050620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 05/03/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024] Open
Abstract
Transposable elements (TEs) are characterized by their ability to change their genomic position. Through insertion or recombination leading to deletions and other chromosomal aberrations, they can cause genetic instability. The extent to which they thereby exert regulatory influence on cellular functions is unclear. To better characterize TEs in processes such as carcinogenesis, we used the well-established Xiphophorus melanoma model. By transcriptome sequencing, we show that an increasing total number in transposons correlates with progression of malignancy in melanoma samples from Xiphophorus interspecific hybrids. Further, by comparing the presence of TEs in the parental genomes of Xiphophorus maculatus and Xiphophorus hellerii, we could show that even in closely related species, genomic location and spectrum of TEs are considerably different.
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Affiliation(s)
- Luca Münch
- Neurology Asklepios Klinik Barmbek, Rübenkamp 220, 22307 Hamburg, Germany;
| | - Frederik Helmprobst
- Institute of Neuropathology, Philipps-University Marburg, 35037 Marburg, Germany;
| | | | | | - Manfred Schartl
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 786666, USA
- Developmental Biochemistry, University of Würzburg, 97974 Würzburg, Germany
| | - Susanne Kneitz
- Biochemistry and Cell Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany;
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