Molecular phylogenetics of myliobatiform fishes (Chondrichthyes: Myliobatiformes), with comments on the effects of missing data on parsimony and likelihood

Katherine A. Dunn; John D. McEachran; Rodney L. Honeycutt

doi:10.1016/S1055-7903(02)00442-6

Molecular phylogenetics of myliobatiform fishes (Chondrichthyes: Myliobatiformes), with comments on the effects of missing data on parsimony and likelihood

Katherine A. Dunn, John D. McEachran, Rodney L. Honeycutt

Research output: Contribution to journal › Article › peer-review

58 Citations (Scopus)

Abstract

Mitochondrial DNA sequences from the 12S rRNA gene, four tRNA genes, and a portion of two protein coding genes were used to investigate the relationship of myliobatoid genera. In addition, we conducted an investigation of the sister group to the freshwater stingrays by sampling additional DNA sequences from GenBank. Consequently, two datasets were used to examine myliobatoid relationships. The first consisted of the genes sequenced in this study. The second dataset was compiled by combining the first dataset with cytochrome b sequences from GenBank. The second dataset, however, included a number of missing characters due to differences in sampling. The effect of the missing characters on both maximum parsimony and maximum likelihood analysis was investigated by conducting a simulation study. Results of the simulation study indicated that maximum likelihood was not sensitive to the missing data, whereas the accuracy of maximum parsimony analysis was expected to decrease. Phylogenetic analysis of this group had several areas concordant with morphological studies, however, the analysis also revealed two novel relationships. In addition, placement of two taxa (Gymnura and Himantura) were dependent both on the dataset and analytical method used.

Original language	English
Pages (from-to)	259-270
Number of pages	12
Journal	Molecular Phylogenetics and Evolution
Volume	27
Issue number	2
DOIs	https://doi.org/10.1016/S1055-7903(02)00442-6
Publication status	Published - May 1 2003
Externally published	Yes

Bibliographical note

Funding Information:
Tissue samples were kindly provided by: Janine N. Caira, John F. Morrissey, Edward J. Heist, and Timothy Clarke. Funding was provided by a National Science Foundation Grant (DEB 9615163) to R.L.H., and a grant from the Texas Institute of Oceanography. This paper represents contribution 103 of the Center for Biosystematics and Biodiversity at Texas A&M University. Early versions of this manuscript benefited from review by Joseph P. Bielawski, John R. Gold, and James B. Woolley. I am gratefull to the anonymous referees and Andrew Martin for their comments.

ASJC Scopus Subject Areas

Ecology, Evolution, Behavior and Systematics
Molecular Biology
Genetics

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10.1016/S1055-7903(02)00442-6

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Molecular phylogenetics of myliobatiform fishes (Chondrichthyes: Myliobatiformes), with comments on the effects of missing data on parsimony and likelihood. / Dunn, Katherine A.; McEachran, John D.; Honeycutt, Rodney L.
In: Molecular Phylogenetics and Evolution, Vol. 27, No. 2, 01.05.2003, p. 259-270.

Research output: Contribution to journal › Article › peer-review

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abstract = "Mitochondrial DNA sequences from the 12S rRNA gene, four tRNA genes, and a portion of two protein coding genes were used to investigate the relationship of myliobatoid genera. In addition, we conducted an investigation of the sister group to the freshwater stingrays by sampling additional DNA sequences from GenBank. Consequently, two datasets were used to examine myliobatoid relationships. The first consisted of the genes sequenced in this study. The second dataset was compiled by combining the first dataset with cytochrome b sequences from GenBank. The second dataset, however, included a number of missing characters due to differences in sampling. The effect of the missing characters on both maximum parsimony and maximum likelihood analysis was investigated by conducting a simulation study. Results of the simulation study indicated that maximum likelihood was not sensitive to the missing data, whereas the accuracy of maximum parsimony analysis was expected to decrease. Phylogenetic analysis of this group had several areas concordant with morphological studies, however, the analysis also revealed two novel relationships. In addition, placement of two taxa (Gymnura and Himantura) were dependent both on the dataset and analytical method used.",

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note = "Funding Information: Tissue samples were kindly provided by: Janine N. Caira, John F. Morrissey, Edward J. Heist, and Timothy Clarke. Funding was provided by a National Science Foundation Grant (DEB 9615163) to R.L.H., and a grant from the Texas Institute of Oceanography. This paper represents contribution 103 of the Center for Biosystematics and Biodiversity at Texas A&M University. Early versions of this manuscript benefited from review by Joseph P. Bielawski, John R. Gold, and James B. Woolley. I am gratefull to the anonymous referees and Andrew Martin for their comments. ",

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Molecular phylogenetics of myliobatiform fishes (Chondrichthyes: Myliobatiformes), with comments on the effects of missing data on parsimony and likelihood

Abstract

Bibliographical note

ASJC Scopus Subject Areas

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