title: Ancient hybridization and genomic stabilization in a swordtail fish.
abstract: A rapidly increasing body of work is revealing that the genomes of distinct species often exhibit hybrid ancestry, presumably due to postspeciation hybridization between closely related species. Despite the growing number of documented cases, we still know relatively little about how genomes evolve and stabilize following hybridization, and to what extent hybridization is functionally relevant. Here, we examine the case of Xiphophorus nezahualcoyotl, a teleost fish whose genome exhibits significant hybrid ancestry. We show that hybridization was relatively ancient and is unlikely to be ongoing. Strikingly, the genome of X. nezahualcoyotl has largely stabilized following hybridization, distinguishing it from examples such as human-Neanderthal hybridization. Hybridization-derived regions are remarkably distinct from other regions of the genome, tending to be enriched in genomic regions with reduced constraint. These results suggest that selection has played a role in removing hybrid ancestry from certain functionally important regions. Combined with findings in other systems, our results raise many questions about the process of genomic stabilization and the role of selection in shaping patterns of hybrid ancestry in the genome.
authors.affiliation: Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, 08544, USA.|Centro de Investigaciones Científicas de las Huastecas "Aguazarca", 16 de Septiembre 392, Calnali, Hidalgo, 43230, Mexico.
authors.forename: Molly
authors.initials: M
authors.lastname: Schumer
authors.affiliation: Centro de Investigaciones Científicas de las Huastecas "Aguazarca", 16 de Septiembre 392, Calnali, Hidalgo, 43230, Mexico.|Department of Biology, Texas A&M University, TAMU, College Station, TX, 77843, USA.|Max Planck Institute for the Biology of Aging, D-50931, Cologne, Germany.
authors.forename: Rongfeng
authors.initials: R
authors.lastname: Cui
authors.affiliation: Centro de Investigaciones Científicas de las Huastecas "Aguazarca", 16 de Septiembre 392, Calnali, Hidalgo, 43230, Mexico.|Department of Biology, Texas A&M University, TAMU, College Station, TX, 77843, USA.
authors.forename: Daniel L
authors.initials: DL
authors.lastname: Powell
authors.affiliation: Centro de Investigaciones Científicas de las Huastecas "Aguazarca", 16 de Septiembre 392, Calnali, Hidalgo, 43230, Mexico.|Department of Biology, Texas A&M University, TAMU, College Station, TX, 77843, USA.
authors.forename: Gil G
authors.initials: GG
authors.lastname: Rosenthal
authors.affiliation: Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, 08544, USA.|Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, 08544, USA.
authors.forename: Peter
authors.initials: P
authors.lastname: Andolfatto
mesh_terms: D000818:Animals; D005075:Biological Evolution; D003532:Cyprinodontiformes / Q000145:classification / Q000235:genetics*; D016678:Genome; D023281:Genomics; D006824:Hybridization, Genetic; D010802:Phylogeny; D017422:Sequence Analysis, DNA
keywords: divergence; genomic stabilization; hybridization; whole-genome sequencing