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Gnathostome phylogenomics utilizing lungfish EST sequences.

Hallström, Björn LU and Janke, Axel LU (2009) In Molecular Biology and Evolution 26(2). p.463-471
Abstract
The relationship between the Chondrichthyes (cartilaginous fishes), the Actinopterygii (ray-finned fishes) and the piscine Sarcopterygii (lobe-finned fishes), and how the Tetrapoda (four-limbed terrestrial vertebrates) are related to these has been a contentious issue for more than a century. A general consensus about the relationship of these vertebrate clades has gradually emerged among morphologists, but no molecular study has yet provided conclusive evidence for any specific hypothesis. In order to examine these relationships on the basis of more extensive sequence data we have produced almost 1,000,000 base pairs of expressed sequence tags (ESTs) from the African marbled lungfish, Protopterus aethiopicus. This new data set yielded 771... (More)
The relationship between the Chondrichthyes (cartilaginous fishes), the Actinopterygii (ray-finned fishes) and the piscine Sarcopterygii (lobe-finned fishes), and how the Tetrapoda (four-limbed terrestrial vertebrates) are related to these has been a contentious issue for more than a century. A general consensus about the relationship of these vertebrate clades has gradually emerged among morphologists, but no molecular study has yet provided conclusive evidence for any specific hypothesis. In order to examine these relationships on the basis of more extensive sequence data we have produced almost 1,000,000 base pairs of expressed sequence tags (ESTs) from the African marbled lungfish, Protopterus aethiopicus. This new data set yielded 771 transcribed nuclear sequences that had not been previously described. The lungfish EST sequences were combined with EST data from two cartilaginous fishes and whole genome data from an agnathan, four ray-finned fishes and four tetrapods. Phylogenomic analysis of these data yielded, for the first time, significant maximum likelihood support for a traditional gnathostome tree with a split between the Chondrichthyes and remaining (bone) gnathostomes. Also the sister group relationship between Dipnoi (lungfishes) and Tetrapoda received conclusive support. Previously proposed hypotheses, such as the monophyly of fishes, could be rejected significantly. The divergence time between lungfishes and tetrapods was estimated to 382-390 million years ago by the current data set and six calibration points. (Less)
Please use this url to cite or link to this publication:
author
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
expressed sequence tags, molecular dating, phylogenomics, Sarcopterygii, tetrapods, vertebrate evolution
in
Molecular Biology and Evolution
volume
26
issue
2
pages
463 - 471
publisher
Oxford University Press
external identifiers
  • wos:000262525700021
  • scopus:58449118344
ISSN
0737-4038
DOI
10.1093/molbev/msn271
language
English
LU publication?
yes
id
b64186cd-5097-4d76-9133-ddc508122001 (old id 1271162)
date added to LUP
2009-02-02 12:44:22
date last changed
2017-05-28 03:31:24
@article{b64186cd-5097-4d76-9133-ddc508122001,
  abstract     = {The relationship between the Chondrichthyes (cartilaginous fishes), the Actinopterygii (ray-finned fishes) and the piscine Sarcopterygii (lobe-finned fishes), and how the Tetrapoda (four-limbed terrestrial vertebrates) are related to these has been a contentious issue for more than a century. A general consensus about the relationship of these vertebrate clades has gradually emerged among morphologists, but no molecular study has yet provided conclusive evidence for any specific hypothesis. In order to examine these relationships on the basis of more extensive sequence data we have produced almost 1,000,000 base pairs of expressed sequence tags (ESTs) from the African marbled lungfish, Protopterus aethiopicus. This new data set yielded 771 transcribed nuclear sequences that had not been previously described. The lungfish EST sequences were combined with EST data from two cartilaginous fishes and whole genome data from an agnathan, four ray-finned fishes and four tetrapods. Phylogenomic analysis of these data yielded, for the first time, significant maximum likelihood support for a traditional gnathostome tree with a split between the Chondrichthyes and remaining (bone) gnathostomes. Also the sister group relationship between Dipnoi (lungfishes) and Tetrapoda received conclusive support. Previously proposed hypotheses, such as the monophyly of fishes, could be rejected significantly. The divergence time between lungfishes and tetrapods was estimated to 382-390 million years ago by the current data set and six calibration points.},
  author       = {Hallström, Björn and Janke, Axel},
  issn         = {0737-4038},
  keyword      = {expressed sequence tags,molecular dating,phylogenomics,Sarcopterygii,tetrapods,vertebrate evolution},
  language     = {eng},
  number       = {2},
  pages        = {463--471},
  publisher    = {Oxford University Press},
  series       = {Molecular Biology and Evolution},
  title        = {Gnathostome phylogenomics utilizing lungfish EST sequences.},
  url          = {http://dx.doi.org/10.1093/molbev/msn271},
  volume       = {26},
  year         = {2009},
}