J Syst Evol ›› 2013, Vol. 51 ›› Issue (3): 365-369.

• Research Articles •

### A note on gene pleiotropy estimation from phylogenetic analysis of protein sequences

1,2Wen‐Hai CHEN 1Zhi‐Xi SU* 1,3Xun GU*

1. 1(School of Life Sciences and Center for Evolutionary Biology, Fudan University, Shanghai 200433, China)
2(College of Mathematics & Information Science, Wenzhou University, Wenzhou, Zhejiang 325035, China)
3(Department of Genetics, Development and Cell Biology Iowa State University, Ames, IA 50011, USA)
• Received:2012-04-05 Published:2013-05-21

Abstract: Recently, several statistical methods have been independently proposed for estimating the degree (n) of gene pleiotropy (i.e. the capacity of a gene to affect many phenotypes) without knowing measurable phenotypic traits. However, the theoretical limitation of these approaches has not been well demonstrated. In this short note, we show that our previous method based on the phylogeny of protein sequences is, in fact, an effective estimate of a parameter that can be written symbolically as K = min(n,r), where r is the rank of mutations at an amino acid site. Hence, understanding of r is crucial for appropriate interpretation of the estimated K, denoted by Ke (the effective gene pleiotropy). Indeed, when protein sequence alignment is used to estimate effective gene pleiotropy (Ke) by this method, Ke can be interpreted as an effective estimate of n when n ≤ 20, as long as the phylogeny is sufficiently large. If n > 20, Ke → 20, although the true n could be much higher.