Phylogenomic Analysis of Fundulidae (Teleostei: Cyprinodotiformes) using RNA-Sequencing Data


Fishes of the New World cyprinodontiform family Fundulidae display a wide variety of tolerance to environmental conditions, making them a valuable model system for comparative, evolutionary, and environmental studies. Despite numerous attempts to resolve the phylogenetic relationships of family Fundulidae, the basal structure of the phylogeny remains unresolved. The lack of a robust and fully resolved phylogeny for family Fundulidae and its most speciose genus Fundulus is an impediment to future research. This study utilized novel RNA-sequencing data for phylogenetic inference among16 members of Fundulidae to better refine the basal nodes of the family and confront long-standing questions regarding (1) the monophyletic status of genus Fundulus, and validity of the Lucania and recently synonymized Adinia genera; (2) the relationship of the west coast endemic Fundulus parvipinnis and F. lima to other Fundulus species; and (3) the validity of subgeneric classifications. In addition, previously published nuclear gene sequences for 32 Fundulidae species were re-analyzed in combination with novel RNA-sequencing data. Maximum likelihood and Bayesian analyses generated identical phylogenies with strong statistical support at nearly all nodes, demonstrating the utility of RNA-sequencing data in constructing robust phylogenies not achievable by previous methods. While many past hypothesized evolutionary relationships for Fundulidae were reinforced, several alternative relationships are hypothesized at basal nodes resulting in a re-analysis of the deeper structure of family Fundulidae. These results reveal family Fundulidae as a paraphyletic grouping of members of genus Fundulus and Lucania and supports the previous synonymy of genus Adinia with genus Fundulus.


Biological Sciences


National Institutes of Health (U.S.)
National Science Foundation (U.S.)
Southern Illinois University Edwardsville


This work used the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley, supported by NIH S10 Instrumentation Grants S10RR029668 and S10RR027303. This work used the Extreme Science and Engineering Discovery Environment (XSEDE, National Science Foundation grant number ACI-1053575) and the CC*DNI Networking Infrastrucutre (National Science Foundation grant number ACI-1541435). Research was supported by funding from the National Science Foundation (DEB-1265282 and ROA supplement DEB-1314561 to AW, and DEB-1556778 to DDD). This effort was also supported by Southern Illinois University Edwardsville (SIUE) which designated research funds to purchase hardware and provide technical support.

Keywords and Phrases

Fundulidae; Fundulus; Phylogenetics; Phylogenomics; RNA-Seq

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Article - Journal

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© 2018 Elsevier, All rights reserved.

Publication Date

01 Apr 2018

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