4 research outputs found
Convergent evolution of gene expression in two high-toothed stickleback populations
<div><p>Changes in developmental gene regulatory networks enable evolved changes in morphology. These changes can be in <i>cis</i> regulatory elements that act in an allele-specific manner, or changes to the overall <i>trans</i> regulatory environment that interacts with <i>cis</i> regulatory sequences. Here we address several questions about the evolution of gene expression accompanying a convergently evolved constructive morphological trait, increases in tooth number in two independently derived freshwater populations of threespine stickleback fish (<i>Gasterosteus aculeatus</i>). Are convergently evolved <i>cis</i> and/or <i>trans</i> changes in gene expression associated with convergently evolved morphological evolution? Do <i>cis</i> or <i>trans</i> regulatory changes contribute more to gene expression changes accompanying an evolved morphological gain trait? Transcriptome data from dental tissue of ancestral low-toothed and two independently derived high-toothed stickleback populations revealed significantly shared gene expression changes that have convergently evolved in the two high-toothed populations. Comparing <i>cis</i> and <i>trans</i> regulatory changes using phased gene expression data from F1 hybrids, we found that <i>trans</i> regulatory changes were predominant and more likely to be shared among both high-toothed populations. In contrast, while <i>cis</i> regulatory changes have evolved in both high-toothed populations, overall these changes were distinct and not shared among high-toothed populations. Together these data suggest that a convergently evolved trait can occur through genetically distinct regulatory changes that converge on similar <i>trans</i> regulatory environments.</p></div
<i>Trans</i> changes are more likely to be shared across populations.
<p>(A) Genes with significantly different evolved expression in both freshwater populations relative to marine fish, showing significantly correlated changes in gene expression in PAXB<sub>FW</sub> and CERC<sub>FW</sub> dental tissue. (B) Freshwater dental tissue had a significant but small number of shared <i>cis</i>-regulatory changes. (C) Freshwater dental tissue showed significantly correlated changes in <i>trans</i> expression changes. A-C show genes with significant expression changes between populations and quantifiable (i.e. genes with transcripts containing a polymorphic SNP covered by at least 20 reads) <i>cis</i>-regulatory changes in both populations. Density (color) was estimated with a Gaussian kernal density estimator. (D-F) Bar graphs show the number of genes with shared or divergent expression patterns from the above panels. (G-I) Similar to (A-C), but showing only genes in the BiteCode gene set.</p
Evolved changes in <i>cis</i>-regulation.
<p>(A) Cartoon showing the two different regulatory changes detectable by our F1 hybrid system. Both genes 1 and 2 show an evolved increase of expression in freshwater fish, but the freshwater allele of gene 1 but not gene 2 is expressed more highly in F1 hybrids. Therefore, gene 1 has evolved its increased gene expression through <i>cis</i>-regulatory changes, while gene 2 was modulated by <i>trans</i> regulatory changes. (B) Density plot showing the measured <i>cis</i>-regulatory changes. Neither population displayed a significant allelic bias, as measured by a Wilcoxon signed-rank test. (C-D) Gene expression changes in both parental and hybrid dental tissue–genes are color-coded based on the role of <i>cis</i> and/or <i>trans</i> change in PAXB<sub>FW</sub> (C) or CERC<sub>FW</sub> (D) dental tissue. Dashed line indicates the first principal component axis.</p
<i>Trans</i> changes predominate evolved dental gene expression changes.
<p>(A-B) Proportion of differentially expressed genes displaying opposing and concordant <i>cis</i> and <i>trans</i> changes in PAXB<sub>FW</sub> (A) or CERC<sub>FW</sub> (B) dental tissue. Genes whose expression differences were mostly explained by <i>cis</i> changes tended to be more concordant (<i>P</i> = 5.0e-17, 0.002 for PAXB<sub>FW</sub> and CERC<sub>FW</sub>, respectively) than those mostly explained by <i>trans</i> changes. (C) Density of the relative percentage of gene expression differences which are explained by <i>cis</i> changes in PAXB<sub>FW</sub> and CERC<sub>FW</sub> dental tissue. (D) Cumulative percentage of percentage of gene expression due to <i>cis</i> changes. Genes in CERC<sub>FW</sub> samples display a higher percentage <i>cis</i> change than genes in PAXB<sub>FW</sub> samples (<i>P</i> = 1.25e-22, Mann-Whitney U test).</p