PUBLICATION
Phylogeny of zebrafish, a 'model species', within Danio, a 'model genus'
- Authors
- McCluskey, B.M., Postlethwait, J.H.
- ID
- ZDB-PUB-141123-1
- Date
- 2015
- Source
- Mol. Biol. Evol. 32(3): 635-52 (Journal)
- Registered Authors
- Postlethwait, John H.
- Keywords
- none
- MeSH Terms
-
- Animals
- Genomics
- Phylogeny
- Sequence Analysis, DNA
- Zebrafish/classification*
- Zebrafish/genetics*
- PubMed
- 25415969 Full text @ Mol. Biol. Evol.
Citation
McCluskey, B.M., Postlethwait, J.H. (2015) Phylogeny of zebrafish, a 'model species', within Danio, a 'model genus'. Mol. Biol. Evol.. 32(3):635-52.
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 datasets from 30,801 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 datasets 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 post-speciation 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.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping