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The Scientific World Journal
Volume 2012, Article ID 479824, 5 pages
http://dx.doi.org/10.1100/2012/479824
Research Article

Some Problems in Proving the Existence of the Universal Common Ancestor of Life on Earth

1School of Life Sciences, Fudan University, Shanghai 200433, China
2Department of Statistical Modeling, Institute of Statistical Mathematics, Tokyo 190-8562, Japan

Received 31 October 2011; Accepted 8 December 2011

Academic Editor: Yidong Bai

Copyright © 2012 Takahiro Yonezawa and Masami Hasegawa. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

Although overwhelming circumstantial evidence supports the existence of the universal common ancestor of all extant life on Earth, it is still an open question whether the universal common ancestor existed or not. Theobald (Nature 465, 219–222 (2010)) recently challenged this problem with a formal statistical test applied to aligned sequences of conservative proteins sampled from all domains of life and concluded that the universal common ancestor hypothesis holds. However, we point out that there is a fundamental flaw in Theobald's method which used aligned sequences. We show that the alignment gives a strong bias for the common ancestor hypothesis, and we provide an example that Theobald's method supports a common ancestor hypothesis for two apparently unrelated families of protein-encoding sequences (cytb and nd2 of mitochondria). This arouses suspicion about the effectiveness of the “formal” test.