Evolution: Scientific Papers and Data
 

Published Phylogenetic Analyses of Cetacea by Contributors to this Website, with Links to Download the Data Matrices Used in These Studies.

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Montgomery, S.H., J.H. Geisler, M.R. McGowen, C. Fox, L. Marino, and J. Gatesy. 2013 (online early). The evolutionary history of cetacean brain and body size. Evolution. DOI: 10.1111/evo.12197.


Meredith, R.W., J. Gatesy, C.A. Emerling, V.M. York, and M.S. Springer. 2013. Rod monochromacy and the coevolution of cetacean retinal opsin. PLOS Genetics 9(4): e1003432. doi:10.1371/journal.pgen.1003432

A pdf of the paper and datafiles can be downloaded at the PLOS Genetics website and the pdf here as well.

 

Gatesy, J., J. H. Geisler, J. Chang, C. Buell, A. Berta, R. W. Meredith, M.S. Springer, and M.R. McGowen. 2013. A phylogenetic blueprint for a modern whale. Molecular Phylogenetics and Evolution 66(2): 479-506

 
Four data files associated with this paper are available for download: a revised supermatrix for the dataset published by Demere et al. (2008) in nexus format, supermatrix of Geisler et al. (2011) but with character names in file, data file for relationships of extant and extinct artiodactyls in nexus, and the latter file in tnt format. You can view the abstract for this paper and purchase a PDF of the entire paper here.
 
 
Geisler, J.H., Godfrey, S.J., and O. Lambert. 2012. A new genus and species of late Miocene inioid (Cetacea, Odontoceti) from the Meherrin River, North Carolina, U.S.A. Journal of Vertebrate Paleontology 32(1):198-211.
 
Data matrix in tnt is available for download. A pdf of the paper can be purchased here on the webpage of the Journal of Vertebrate Paleontology


Meredith, R.W., J. Gatesy, J. Cheng, and M.S. Springer. 2011. Pseudogenization of the tooth gene enamelysin (MMP20) in the common ancestor of extant baleen whales. Proceedings of the Royal Society B 278:993-1002.
 
Two datasets in nexus format are available here: 1) exon 2 MMP20 sequences  and 2) MMP20 CHR-2 SINE sequences. A PDF of this paper can be downloaded here  or from the Proceedings of the Royal Society B website

Geisler, J.H., M. McGowen, G. Yang, and J. Gatesy. 2011. A supermatrix analysis of genomic, morphological, and paleontological data from crown Cetacea. BMC Evolutionary Biology 11:112.

Data matrix in nexus and tnt formats are available here for download.
A pdf of this paper can be downloaded here or from the BMC Evolutionary Biology homepage
 

 

McGowen, M.R., S.H. Montgomery, C. Clark, and J. Gatesy. 2011 Phylogeny and adaptive evolution of the brain-development gene microcephalin (MCPH1) in cetaceans. BMC Evolutionary Biology 11:98. 

A pdf of this paper can be downloaded from the BMC Evolutionary Biology homepage
 
 

McGowen, M. 2011. Towards the resolution of an explosive radiation—A multilocus phylogeny of oceanic dolphins (Delphinidae). Molecular Phylogenetics and Evolution 60(3):345-357.

Data matrix in MrBayes format (modified nexus format) is available here for download.  You can view the abstract for this paper and purchase a pdf of the entire paper HERE
 
 

McGowen, M., M. Spaulding, and J. Gatesy. 2009. Divergence date estimation and a comprehensive molecular tree of extant cetaceans. Molecular Phylogenetics and Evolution 53:891-906.

Data matrix in nexus format is available here for download. 
You can view the abstract for this paper and purchase a pdf of the entire paper at the following link HERE
 
 

Spaulding, M., M. O'Leary, and J. Gatesy. 2009. Relationships of Cetacea (Artiodactyla) among mammals: Increased taxon sampling alters interpretations of key fossils and character transformations. PLoS One 4(9): e7062.doi:10.1371/journal.pone.0007062.

Data matrix in nexus format is available here for download. 
A pdf of this paper can be downloaded here or from the PLos ONE homepage
 
 

Geisler, J.H., and J.M. Theodor. 2009. Brief Communications Arising: Hippo and Whale Phylogeny. Nature 458: E1-E4. doi:10.1038/nature07776.

Data file in tnt format is available here for download. Also available is a separate file with all most parsimonious trees, a file with the optimum trees for implied weighting with k = 3, and a corrected version of the published appendix.  Full text of the paper can be viewed HERE
 

McGowen, M.R., C. Clark, and J. Gatesy. 2008 The vestigial olfactory receptor subgenome of odontocete whales: phylogenetic congruence between gene-tree reconciliation and supermatrix methods. Systematic Biology 57(4):574-590.

Data file in nexus format with the alignment of olfactory receptor sequences is available here for download, as is the same data concatenated with mtdna and nuclear loci, also in nexus format . You can view the abstract for this paper and purchase a PDF of the entire paper here.
 

Deméré, T., M. McGowen, A. Berta, and J. Gatesy. 2008. Morphological and molecular evidence for a stepwise evolutionary transition from teeth to baleen in mysticete whales. Systematic Biology 57:15-37.

Data matrix in nexus format of the dental genes sequenced for this study is available here for download as well as a nexus version of the supermatrix , which includes morphological and molecular data.  A pdf of the paper is available at no charge HERE
 
 

Geisler, J.H., and M.C. McKenna. 2007. A new species of mesonychian mammal from the early Eocene of Mongolia and its phylogenetic relationships. Acta Palaeontologica Polonica 52(1): 189-212.

Morphological data matrix in nona format associated with this study is available here for download.   A pdf of the paper is available at no charge HERE
 
 

Geisler, J.H., Sanders, A.E., and Z.-X. Luo. 2005. A new protocetid whale (Cetacea: Archaeoceti) from the late middle Eocene of North America. American Museum Novitates 3480: 1-65.

Morphological data matrix in nona format associated with this study is available for here download.  A pdf of the paper can be downloaded here and is available at no charge from HERE
 
 

Geisler, J.H., and A.E. Sanders. 2003. Morphological evidence for the phylogeny of Cetacea. Journal of Mammalian Evolution 10: 23-129.

Morphological data matrix in nona format associated with this study is available here for download.  You can view the abstract for this paper and purchase a pdf of the entire paper HERE
 
 

Geisler, J.H., and M.D. Uhen. 2003. Morphological support for a close relationship between hippo and whales. Journal of Vertebrate Paleontology 23(4): 991-996.

Morphological data matrix in nona format associated with this study is available here for download.  You can purchase a pdf of the entire paper HERE