Phylogenomic analyses of all species of swordtail fishes (genus Xiphophorus) show that hybridization preceded speciation

Kang Du, Juliana Morena Bonita Ricci, Yuan Lu, Mateo Garcia-Olazabal, Ronald B. Walter, Wesley C. Warren, Tristram O. Dodge, Molly Schumer, Hyun Park, Axel Meyer () and Manfred Schartl ()
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Kang Du: Texas State University, San Marcos
Juliana Morena Bonita Ricci: Texas State University, San Marcos
Yuan Lu: Texas State University, San Marcos
Mateo Garcia-Olazabal: Texas State University, San Marcos
Ronald B. Walter: Texas State University, San Marcos
Wesley C. Warren: University of Missouri, Bond Life Sciences Center
Tristram O. Dodge: Stanford University
Molly Schumer: Stanford University
Hyun Park: Korea University
Axel Meyer: University of Konstanz
Manfred Schartl: Texas State University, San Marcos

Nature Communications, 2024, vol. 15, issue 1, 1-15

Abstract: 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.

Date: 2024
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DOI: 10.1038/s41467-024-50852-6

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