Title

Evaluating phylogenetic informativeness and data-type usage for new protein-coding genes across Vertebrata

Document Type

Journal article

Source Publication

Molecular Phylogenetics and Evolution

Publication Date

11-2011

Volume

61

Issue

2

First Page

300

Last Page

307

Publisher

Academic Press

Keywords

EST, cDNA, Marker development, Tetrapoda, Amniota, Amphibia, Mammalia, Reptilia, Aves, Theria hypothesis, Marsupionta hypothesis

Abstract

As a resource for vertebrate phylogenetics, we developed 75 new protein-coding genes using a combination of expressed sequence tags (ESTs) available in Genbank, and targeted amplification of complementary DNA (cDNA). In addition, we performed three additional analyses in order to assess the utility of our approach. First, we profiled the phylogenetic informativeness of these new markers using the online program PhyDesign. Next, we compared the utility of four different data-types used in phylogenetics: nucleotides (NUCL), amino acids (AA), 1st and 2nd codon positions only (N12), and modified sequences to account for codon degeneracy (DEGEN1; Regier et al., 2010). Lastly, we use these new markers to construct a vertebrate phylogeny and address the uncertain relationship between higher-level mammal groups: monotremes, marsupials, and placentals. Our results show that phylogenetic informativeness of the 75 new markers varies, both in the amount of phylogenetic signal and optimal timescale. When comparing the four data-types, we find that the NUCL data-type, due to the high level of phylogenetic signal, performs the best across all divergence times. The remaining three data-types (AA, N12, DEGEN1) are less subject to homoplasy, but have greatly reduced levels of phylogenetic signal relative to NUCL. Our phylogenetic inference supports the Theria hypothesis of mammalian relationships, with marsupials and placentals being sister groups.

DOI

10.1016/j.ympev.2011.06.016

Print ISSN

10557903

E-ISSN

10959513

Publisher Statement

Copyright © 2012 Institute for Scientific Information. Access to external full text or publisher's version may require subscription.

Full-text Version

Publisher’s Version

Recommended Citation

Fong, J.J. & Fujita, M.K. (2011). Evaluating phylogenetic informativeness and data-type usage for new protein-coding genes across Vertebrata. Molecular Phylogenetics and Evolution, 61(2), 300–307. doi: 10.1016/j.ympev.2011.06.016