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Open Access Open Badges Research article

Duplicate gene evolution and expression in the wake of vertebrate allopolyploidization

Frédéric JJ Chain1, Dora Ilieva2 and Ben J Evans1*

Author Affiliations

1 Center for Environmental Genomics, Department of Biology, Life Sciences Building Room 328 McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada

2 Michael DeGroote School of Medicine – 5045, McMaster University, 1200 Main Street West, Hamilton ON L8N 3Z5, Canada

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BMC Evolutionary Biology 2008, 8:43  doi:10.1186/1471-2148-8-43

Published: 8 February 2008



The mechanism by which duplicate genes originate – whether by duplication of a whole genome or of a genomic segment – influences their genetic fates. To study events that trigger duplicate gene persistence after whole genome duplication in vertebrates, we have analyzed molecular evolution and expression of hundreds of persistent duplicate gene pairs in allopolyploid clawed frogs (Xenopus and Silurana). We collected comparative data that allowed us to tease apart the molecular events that occurred soon after duplication from those that occurred later on. We also quantified expression profile divergence of hundreds of paralogs during development and in different tissues.


Our analyses indicate that persistent duplicates generated by allopolyploidization are subjected to strong purifying selection soon after duplication. The level of purifying selection is relaxed compared to a singleton ortholog, but not significantly variable over a period spanning about 40 million years. Despite persistent functional constraints, however, analysis of paralogous expression profiles indicates that quantitative aspects of their expression diverged substantially during this period.


These results offer clues into how vertebrate transcriptomes are sculpted in the wake of whole genome duplication (WGD), such as those that occurred in our early ancestors. That functional constraints were relaxed relative to a singleton ortholog but not significantly different in the early compared to the later stage of duplicate gene evolution suggests that the timescale for a return to pre-duplication levels is drawn out over tens of millions of years – beyond the age of these tetraploid species. Quantitative expression divergence can occur soon after WGD and with a magnitude that is not correlated with the rate of protein sequence divergence. On a coarse scale, quantitative expression divergence appears to be more prevalent than spatial and temporal expression divergence, and also faster or more frequent than other processes that operate at the protein level, such as some types of neofunctionalization.