ArticleMolecular biology and evolution2015
Phylogeny of zebrafish, a "model species," within Danio, a "model genus".
Article in Molecular biology and evolution, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers, 1 of them a synthesis that pooled it.
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Who cites it
49 citing papers in PubMed, 1 synthesis or guideline pooled it, 100 citations in OpenAlex.
- Shortcomings of Phylogenetic Studies on Recent Radiated Insular Groups: A Meta-Analysis Using Cabo Verde Biodiversity.International journal of molecular sciences · 2019Pooled it
- Zebrafish relatives as models for functional comparative genetics and genomics.Nature reviews. Genetics · 2026Review
- Graded BMP signals modulate yellow and red color in fishes, impacting adult pigment patterns and conspecific shoaling behavior.Current biology : CB · 2026Article
- Graded BMP signals modulate yellow and red color in fishes impacting adult pigment pattern and behavior.bioRxiv : the preprint server for biology · 2025Article
- Genomic and genetic insights into speciation and pigment pattern diversification inbioRxiv : the preprint server for biology · 2025Article
- Establishment and genetic characterization of zebrafish RW line.Scientific reports · 2025Article
- Embryonic Lethality, Juvenile Growth Variation, and Adult Sterility Correlate With Phylogenetic Distance of Danionin Hybrids.Evolution & development · 2025Article
- The hybrid history of zebrafish.G3 (Bethesda, Md.) · 2025Article
- Laboratory and physiological aspects of substitute metazoan models for in vivo pharmacotoxicological analysis.Naunyn-Schmiedeberg's archives of pharmacology · 2025Review
- kcnj13 regulates pigment cell shapes in zebrafish and has diverged by cis-regulatory evolution between Danio species.Development (Cambridge, England) · 2023Article
- Thyroid hormone regulates proximodistal patterning in fin rays.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Population Genomic Evidence for the Diversification ofBiology · 2022Article
- Population Genomics of Wall Lizards Reflects the Dynamic History of the Mediterranean Basin.Molecular biology and evolution · 2022Article
- The Evolution of Feeding Mechanics in the Danioninae, or Why Giant Danios Don't Suck Like Zebrafish.Integrative organismal biology (Oxford, England) · 2022Article
- Conserved germ plasm characteristics across the Danio and Devario lineages.Genesis (New York, N.Y. : 2000) · 2021Article
- Pigment pattern morphospace of Danio fishes: evolutionary diversification and mutational effects.Biology open · 2021Article
- Article
- Integrating Sequence Capture and Restriction Site-Associated DNA Sequencing to Resolve Recent Radiations of Pelagic Seabirds.Systematic biology · 2021Article
- Evolution of pigment cells and patterns: recent insights from teleost fishes.Current opinion in genetics & development · 2021Review
- Parallel ddRAD and Genome Skimming Analyses Reveal a Radiative and Reticulate Evolutionary History of the Temperate Bamboos.Systematic biology · 2021Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Zebrafish (Danio rerio) is an important model for vertebrate development, genomics, physiology, behavior, toxicology, and disease. Additionally, work on numerous Danio species is elucidating evolutionary mechanisms for morphological development. Yet, the relationships of zebrafish and its closest relatives remain unclear possibly due to incomplete lineage sorting, speciation with gene flow, and interspecies hybridization. To clarify these relationships, we first constructed phylogenomic data sets from 30,801 restriction-associated DNA (RAD)-tag loci (483,026 variable positions) with clear orthology to a single location in the sequenced zebrafish genome. We then inferred a well-supported species tree for Danio and tested for gene flow during the diversification of the genus. An approach independent of the sequenced zebrafish genome verified all inferred relationships. Although identification of the sister taxon to zebrafish has been contentious, multiple RAD-tag data sets and several analytical methods provided strong evidence for Danio aesculapii as the most closely related extant zebrafish relative studied to date. Data also displayed patterns consistent with gene flow during speciation and postspeciation introgression in the lineage leading to zebrafish. The incorporation of biogeographic data with phylogenomic analyses put these relationships in a phylogeographic context and supplied additional support for D. aesculapii as the sister species to D. rerio. The clear resolution of this study establishes a framework for investigating the evolutionary biology of Danio and the heterogeneity of genome evolution in the recent history of a model organism within an emerging model genus for genetics, development, and evolution.
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