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Open Access Highly Accessed Research article

Subfunctionalization reduces the fitness cost of gene duplication in humans by buffering dosage imbalances

Ariel Fernández123*, Yun-Huei Tzeng4 and Sze-Bi Hsu5

Author Affiliations

1 Instituto Argentino de Matemática “Alberto P. Calderón”, CONICET (National Research Council of Argentina), Buenos Aires, 1083, Argentina

2 Department of Computer Science, The University of Chicago, Chicago, IL 60637, USA

3 Morgridge Institute for Research, Madison, WI 73715, USA

4 Graduate Institute of Biostatistics, China Medical University, Taichung 40402, Taiwan

5 Department of Mathematics and National Center for Theoretical Science, National Tsing-Hua University, Hsinchu 300, Taiwan

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BMC Genomics 2011, 12:604  doi:10.1186/1471-2164-12-604

Published: 14 December 2011

Abstract

Background

Driven essentially by random genetic drift, subfunctionalization has been identified as a possible non-adaptive mechanism for the retention of duplicate genes in small-population species, where widespread deleterious mutations are likely to cause complementary loss of subfunctions across gene copies. Through subfunctionalization, duplicates become indispensable to maintain the functional requirements of the ancestral locus. Yet, gene duplication produces a dosage imbalance in the encoded proteins and thus, as investigated in this paper, subfunctionalization must be subject to the selective forces arising from the fitness bottleneck introduced by the duplication event.

Results

We show that, while arising from random drift, subfunctionalization must be inescapably subject to selective forces, since the diversification of expression patterns across paralogs mitigates duplication-related dosage imbalances in the concentrations of encoded proteins. Dosage imbalance effects become paramount when proteins rely on obligatory associations to maintain their structural integrity, and are expected to be weaker when protein complexation is ephemeral or adventitious. To establish the buffering effect of subfunctionalization on selection pressure, we determine the packing quality of encoded proteins, an established indicator of dosage sensitivity, and correlate this parameter with the extent of paralog segregation in humans, using species with larger population -and more efficient selection- as controls.

Conclusions

Recognizing the role of subfunctionalization as a dosage-imbalance buffer in gene duplication events enabled us to reconcile its mechanistic nonadaptive origin with its adaptive role as an enabler of the evolution of genetic redundancy. This constructive role was established in this paper by proving the following assertion: If subfunctionalization is indeed adaptive, its effect on paralog segregation should scale with the dosage sensitivity of the duplicated genes. Thus, subfunctionalization becomes adaptive in response to the selection forces arising from the fitness bottleneck imposed by gene duplication.