Genomic divergence between nine- and three-spined sticklebacks

Peer reviewe

The odds of duplicate gene persistence after polyploidization

Background: Gene duplication is an important biological phenomenon associated with genomic redundancy,degeneration, specialization, innovation, and speciation. After duplication, both copies continue functioning when natural selection favors duplicated protein function or expression, or when mutations make them functionally distinct before one copy is silenced. Results: Here we quantify the degree to which genetic parameters related to gene expression, molecular evolution, and gene structure in a diploid frog - Silurana tropicalis - influence the odds of functional persistence of orthologous duplicate genes in a closely related tetraploid species - Xenopus laevis. Using public databases and 454 pyrosequencing, we obtained genetic and expression data from S. tropicalis orthologs of 3,387 X. laevis paralogs and 4,746 X. laevis singletons - the most comprehensive dataset for African clawed frogs yet analyzed. Using logistic regression, we demonstrate that the most important predictors of the odds of duplicate gene persistence in the tetraploid species are the total gene expression level and evenness of expression across tissues and development in the diploid species. Slow protein evolution and information density (fewer exons, shorter introns) in the diploid are also positively correlated with duplicate gene persistence in the tetraploid. Conclusions: Our findings suggest that a combination of factors contribute to duplicate gene persistence following whole genome duplication, but that the total expression level and evenness of expression across tissues and through development before duplication are most important. We speculate that these parameters are useful predictors of duplicate gene longevity after whole genome duplication in other taxa

Extensive Copy-Number Variation of Young Genes across Stickleback Populations

MM received funding from the Max Planck innovation funds for this project. PGDF was supported by a Marie Curie European Reintegration Grant (proposal nr 270891). CE was supported by German Science Foundation grants (DFG, EI 841/4-1 and EI 841/6-1). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Duplicate gene evolution and expression in the wake of vertebrate allopolyploidization

Abstract Background 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. Results 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. Conclusion 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.</p

Duplicate gene evolution and expression in the wake of vertebrate allopolyploidization

BACKGROUND: 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. RESULTS: 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. CONCLUSION: 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

Duplicate gene evolution and expression in the wake of vertebrate allopolyploidization-2

Ofiles (white bars) and between paralogous expression profiles (black bars). Ninety percent of the non-paralogous expression profiles have a Pearson correlation coefficient that is greater than -0.861 but less than 0.865. The Pearson correlation coefficients of 62% of the paralogous expression profiles are less than 0.865, and 0.3% of them are less than -0.861.<p><b>Copyright information:</b></p><p>Taken from "Duplicate gene evolution and expression in the wake of vertebrate allopolyploidization"</p><p>http://www.biomedcentral.com/1471-2148/8/43</p><p>BMC Evolutionary Biology 2008;8():43-43.</p><p>Published online 8 Feb 2008</p><p>PMCID:PMC2275784.</p><p></p

Duplicate gene evolution and expression in the wake of vertebrate allopolyploidization-0

) Regression of Ka/Ks versus Ks in the early and later stages indicates that selection (relaxed purifying + positive) is not more common in the early stage of duplicate gene evolution (blue dots) than the later stage (red dots). The Y-intercept of these regression lines was set to zero and Ka/Ks ratios greater 2 (including undefined ratios) were given a value of 2. In (A) and (B), a dashed line indicates the neutral expectation. Fragments with Ka/Ks > 2 are, on average, half of the size of those with Ka/Ks < 2. Ka/Ks ratios above 2 may therefore be attributable in part to stochastic variance in Ks [43].<p><b>Copyright information:</b></p><p>Taken from "Duplicate gene evolution and expression in the wake of vertebrate allopolyploidization"</p><p>http://www.biomedcentral.com/1471-2148/8/43</p><p>BMC Evolutionary Biology 2008;8():43-43.</p><p>Published online 8 Feb 2008</p><p>PMCID:PMC2275784.</p><p></p

Duplicate gene evolution and expression in the wake of vertebrate allopolyploidization-1

Ction of expression and three probe specificities were compared that are labeled low, medium, and high (see Methods). We report paralogous profiles whose presence/absence scores in all five treatments were identical in the medium and high specificity analysis (shaded in gray on the left of each chart). 1789 and 1462 genes had consistent present/absent expression profiles in the medium and high specificity analyses using the standard and conservative thresholds. These sets of genes included 841 and 632 paralogous pairs, respectively. The tables on the right compare paralogous profiles by tabulating whether they are both present and absent in the same treatments (identical), the expression profile of one overlaps entirely with the other (overlap), or paralogs in which each duplicate has a unique component (distinct).<p><b>Copyright information:</b></p><p>Taken from "Duplicate gene evolution and expression in the wake of vertebrate allopolyploidization"</p><p>http://www.biomedcentral.com/1471-2148/8/43</p><p>BMC Evolutionary Biology 2008;8():43-43.</p><p>Published online 8 Feb 2008</p><p>PMCID:PMC2275784.</p><p></p