Chapter

Molecular Phylogenetics and Phylogeography

James L. Patton, David G. Huckaby and Sergio Ticul Álvarez-Castañeda

in The Evolutionary History and a Systematic Revision of Woodrats of the Neotoma lepida Group

Published by University of California Press

Published in print April 2008 | ISBN: 9780520098664
Published online March 2012 | e-ISBN: 9780520942592 | DOI: http://dx.doi.org/10.1525/california/9780520098664.003.0003
Molecular Phylogenetics and Phylogeography

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The hypothesis of the monopoly members of the Neotoma lepida group with respect to other species in the genus Neotoma is examined in this chapter. Once monophyly is established, the degree of geographic structure at the molecular level is addressed. All molecular data are fully concordant with respect to the monophyly of the complex as well as in the major elements of internal clade structure. Plots of p-distances versus K2-p distances are linear for both first and second positions, and only slightly curvilinear for third positions, with deviations only present at the highest degrees of divergence. Hence, saturation is not a major factor in any comparison among sequences, including those of the Neotoma lepida group as well as the nine outgroup species used in phylogenetic analyses. As a result, the maximum parsimony phylogenetic analysis includes equal weighting for base substitutions at each codon position. Bayesian analyses incorporated separate partitions for each codon position.

Keywords: monophyly; clade; phylogenetic; codon; Bayesian

Chapter.  7168 words.  Illustrated.

Subjects: Zoology and Animal Sciences

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