Toward a Neutral Evolutionary Model of Gene Expression

Overview

Journal Genetics

Publisher Oxford University Press

Specialty Genetics

Date 2005 Apr 19

PMID 15834146

Citations 45

Authors

Philipp Khaitovich

Svante Paabo

Gunter Weiss

Affiliations

Soon will be listed here.

Abstract

We introduce a stochastic model that describes neutral changes of gene expression over evolutionary time as a compound Poisson process where evolutionary events cause changes of expression level according to a given probability distribution. The model produces simple estimators for model parameters and allows discrimination between symmetric and asymmetric distributions of evolutionary expression changes along an evolutionary lineage. Furthermore, we introduce two measures, the skewness of expression difference distributions and relative difference of evolutionary branch lengths, which are used to quantify deviation from clock-like behavior of gene expression distances. Model-based analyses of gene expression profiles in primate liver and brain samples yield the following results: (1) The majority of gene expression changes are consistent with a neutral model of evolution; (2) along evolutionary lineages, upward changes in expression are less frequent but of greater average magnitude than downward changes; and (3) the skewness measure and the relative branch length difference confirm that an acceleration of gene expression evolution occurred on the human lineage in brain but not in liver. We discuss the latter result with respect to a neutral model of transcriptome evolution and show that a small number of genes expressed in brain can account for the observed data.

Citing Articles

On the Decoupling of Evolutionary Changes in mRNA and Protein Levels.

Jiang D, Cope A, Zhang J, Pennell M Mol Biol Evol. 2023; 40(8).

PMID: 37498582 PMC: 10411491. DOI: 10.1093/molbev/msad169.

Decoupling of evolutionary changes in mRNA and protein levels.

Jiang D, Cope A, Zhang J, Pennell M bioRxiv. 2023; .

PMID: 37066157 PMC: 10104238. DOI: 10.1101/2023.04.08.536110.

Transposable elements orchestrate subgenome-convergent and -divergent transcription in common wheat.

Zhang Y, Li Z, Liu J, Zhang Y, Ye L, Peng Y Nat Commun. 2022; 13(1):6940.

PMID: 36376315 PMC: 9663577. DOI: 10.1038/s41467-022-34290-w.

Stochastic Modeling of Gene Expression Evolution Uncovers Tissue- and Sex-Specific Properties of Expression Evolution in the Genus.

Pal S, Oliver B, Przytycka T J Comput Biol. 2022; 30(1):21-40.

PMID: 36037023 PMC: 9917317. DOI: 10.1089/cmb.2022.0121.

Layered evolution of gene expression in "superfast" muscles for courtship.

Pease J, Driver R, de la Cerda D, Day L, Lindsay W, Schlinger B Proc Natl Acad Sci U S A. 2022; 119(14):e2119671119.

PMID: 35363565 PMC: 9168950. DOI: 10.1073/pnas.2119671119.

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