Putative Allopolyploid Evolution of the Tetraploid X. laevis

<div><p>Daggers indicate extinct diploid ancestors or genes. Nodes 1 and 2 correspond with the divergence and union, respectively, of two diploid genomes, and Node 3 marks the diversification of <i>Xenopus</i> tetraploids.</p><p>(A) A reticulate phylogeny with ploidy in parentheses.</p><p>(B) Nuclear genealogy assuming no recombination and no gene conversion between alleles at different paralogous loci (α and β). The dashed portion of the paralogous lineages evolved independently in different diploid ancestors.</p></div

A Non-Exhaustive Diagram Relating Various Models for the Fate of Duplicate Genes

<p>Citations that either propose mechanisms or discuss them: Clark 1994 [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020056#pgen-0020056-b100" target="_blank">100</a>]; Ferris and Whitt 1979 [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020056#pgen-0020056-b101" target="_blank">101</a>]; Force et al. 1999 [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020056#pgen-0020056-b017" target="_blank">17</a>]; Gibson and Spring 1998 [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020056#pgen-0020056-b074" target="_blank">74</a>]; Goodman et al. 1987 [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020056#pgen-0020056-b102" target="_blank">102</a>]; Gu et al. 2003 [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020056#pgen-0020056-b006" target="_blank">6</a>]; Hughes 1994 [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020056#pgen-0020056-b042" target="_blank">42</a>]; Jensen 1976 [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020056#pgen-0020056-b103" target="_blank">103</a>]; Kondrashov et al. 2002 [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020056#pgen-0020056-b019" target="_blank">19</a>]; Li 1980 [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020056#pgen-0020056-b104" target="_blank">104</a>];Li et al. 1982 [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020056#pgen-0020056-b105" target="_blank">105</a>]; Lynch and Conery 2000 [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020056#pgen-0020056-b001" target="_blank">1</a>]; Lynch and Conery 2003 [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020056#pgen-0020056-b106" target="_blank">106</a>]; Lynch and Force 2000 [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020056#pgen-0020056-b002" target="_blank">2</a>]; Ohno 1973 [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020056#pgen-0020056-b107" target="_blank">107</a>]; Ohta 1987 [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020056#pgen-0020056-b108" target="_blank">108</a>]; Piatigorsky and Wistow 1991 [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020056#pgen-0020056-b109" target="_blank">109</a>]; Rodin and Riggs 2003 [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020056#pgen-0020056-b110" target="_blank">110</a>]).; Sidow 1996 [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020056#pgen-0020056-b111" target="_blank">111</a>]; Stoltzfus 1999 [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020056#pgen-0020056-b060" target="_blank">60</a>]; Takahata and Maruyama 1979 [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020056#pgen-0020056-b112" target="_blank">112</a>]; Wagner 1999 [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020056#pgen-0020056-b053" target="_blank">53</a>]; Wagner 2000 [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020056#pgen-0020056-b113" target="_blank">113</a>]; and Zhang et al. 1998 [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020056#pgen-0020056-b068" target="_blank">68</a>].</p

The Observed Relationship between <i>ka/ks</i> and <i>ks</i>

<p>The observed relationship between <i>ka/ks</i> and <i>ks</i> corresponds with simulations that predict a negative relationship under neutral or near-neutral evolution of synonymous substitutions because of stochastic sampling of synonymous substitutions at in slowly evolving or young genes [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020056#pgen-0020056-b061" target="_blank">61</a>]. The plot shows the average <i>ka/ks</i> ratio on each branch of 290 genealogies versus average <i>ks</i> of bins of 50 lineages ranked by <i>ks</i> of each one. The last bin has only 20 lineages. Bars indicate the standard deviation of each bin.</p

Assignment of Putative Retention Mechanisms Based on Molecular Changes in the Coding Region

<div><p>We assigned a retention mechanism to paralogs based on the results of three analyses. The first one compared a model with no change in the <i>ka/ks</i> ratio after duplication (Model A in which the <i>ka/ks</i> ratio on all branches is indicated by R0) to a model with a higher <i>ka/ks</i> ratio after duplication (Model B with <i>ka/ks</i> ratio R1 > R0). The second one compared a model with no difference in the nonsynonymous substitution rate (Model B, in which R0 and R1 are nonsynonymous rates on each branch) to a model with different rates of nonsynonymous substitution in each paralog (Model C in which R0, R1, and R2 are nonsynonymous rates on each branch), with the stipulation that the paralog with the higher nonsynonymous rate also have a higher <i>ka/ks</i> ratio than the slower paralog and a higher <i>ka/ks</i> ratio than the diploid lineage. The third analysis tested for complementarity of amino acid substitution in each paralog.</p><p>In the table in the figure, a minus sign (−) indicates either no significant difference between the models or no significant complementarity of nonsynonymous substitutions. A plus sign (+) indicates a significant improvement in likelihood of the more parameterized model or significant complementarity of nonsynonymous substitution. An asterisk (*) denotes the caveat that an increased substitution ratio could stem from relaxed purifying selection and therefore be a consequence of rather than a cause for retention.</p></div

The <i>ka/ks</i> Ratio of Genes with No Significant Difference before and after Tetraploidization

<p>The <i>ka/ks</i> ratio is often slightly higher in the paralogs (above the dashed line), even though this average is not significantly higher than the diploid lineage. Only ratios from genes with no significant difference are shown (226 out of 292 genes). A dashed line indicates an equal <i>ka/ks</i> ratio before and after duplication.</p

Nonsynonymous Substitutions in Each X. laevis Paralog (α and β) and the Diploid Lineage in Representative Genes

<p>Substitutions in the diploid lineage (d) occurred on the thick branches in the rooted topologies to the left of each locus. (A) <i>liver-type arginase,</i> (B) <i>fibroblast growth factor receptor</i> (FGFR), (C) <i>embryonic fibroblast growth factor</i> (EFGF), and (D) <i>FTZ-F1–related orphan receptor</i>. In (A) a gap indicates a single amino acid deletion, an arrow above the paralog indicates a single amino acid insertion, and this paralog is shortened due to an early stop codon. In (B) three red boxes and a blue box indicate three immunoglobulin domains and a tyrosine kinase domain. In (C) arrows below the paralog indicate predicted cleavage sites in each paralog [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020056#pgen-0020056-b079" target="_blank">79</a>]. In (D) yellow, green, and two lighter blue boxes indicate the DNA-binding C-domain, FTZ-F1 box, and DNA binding domain regions II and III [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020056#pgen-0020056-b080" target="_blank">80</a>].</p

Probability Distribution of the Difference in the Number of Substitutions in Concatenated Paralogs (“Superparalogs”)

<div><p>Analysis was performed on concatenated data from (A) nonsynonymous substitutions of paralogs identified by the likelihood analysis as having asymmetric rates of evolution, (B) synonymous substitutions of these paralogs, (C) nonsynonymous substitutions of the other paralogs that were not identified as having asymmetric rates and (D) synonymous substitutions of these paralogs.</p><p>Black circles are the expected Skellam distributions, gray dots are d_SP distributions from ten example simulations (out of 1,000 total), and white circles are the observed distribution of superparalog differences.</p></div

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-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-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