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Highly variable recombinational landscape modulates efficacy of natural selection in birds.

Gossmann TI, Santure AW, Sheldon BC, Slate J, Zeng K - Genome Biol Evol (2014)

Bottom Line: We investigated whether a special feature of avian genomes, the highly variable recombinational landscape, modulates the efficacy of natural selection through the effects of Hill-Robertson interference, which predicts that selection should be more effective in removing deleterious mutations and incorporating beneficial mutations in high-recombination regions than in low-recombination regions.Furthermore, more compact genes (i.e., those with fewer/shorter introns or shorter proteins) evolve faster than less compact ones.In sum, our results demonstrate that transcriptome sequencing is a powerful method to answer fundamental questions about genome evolution in nonmodel organisms.

View Article: PubMed Central - PubMed

Affiliation: Department of Animal and Plant Sciences, University of Sheffield, United Kingdom toni.gossmann@googlemail.com k.zeng@sheffield.ac.uk.

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Boxplots of (a) GC content at 3rd positions (GC3),(b) expression specificity τ,(c) ds, and(d) dn for subsetsof genes according to their chromosomal positions. Whiskers aredrawn as implemented in the R-function box plot (see Materials andMethods). ,,.
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evu157-F4: Boxplots of (a) GC content at 3rd positions (GC3),(b) expression specificity τ,(c) ds, and(d) dn for subsetsof genes according to their chromosomal positions. Whiskers aredrawn as implemented in the R-function box plot (see Materials andMethods). ,,.

Mentions: There is evidence that GC content is not at statistical equilibrium in multipleavian lineages and that GC-biased gene conversion (gBGC) may have contributed tothis (Webster et al. 2006; Nabholz et al. 2011; Mugal et al. 2013). However, ourresults should also be robust to variation in GC content and the action gBGC,which can upwardly bias estimates of ω and lead to false detection oftargets of positive selection (reviewed by Duret and Galtier 2009). First, we used the sitemodels in PAML, which analyzed substitution patterns over the entirephylogenetic tree in the search of positively selected genes. A recent analysishas shown that results produced by this approach are unlikely to be affected bygBGC (Ratnakumar et al. 2010).Second, if substitutions of slightly deleterious mutations were driven by gBGC(Galtier et al. 2009), weexpect this effect to be stronger in regions with higher recombination rates andGC content, which are often used as proxies of the intensity of gBGC (Duret and Galtier 2009). Contrary tothis prediction, in regions with reduced recombination, where ω is higher,GC content is lower (figs. 3 and4a), andevidence of relaxed constraints on nonsynonymous sites also comes from theseregions (fig. 4d).Fig. 4.—


Highly variable recombinational landscape modulates efficacy of natural selection in birds.

Gossmann TI, Santure AW, Sheldon BC, Slate J, Zeng K - Genome Biol Evol (2014)

Boxplots of (a) GC content at 3rd positions (GC3),(b) expression specificity τ,(c) ds, and(d) dn for subsetsof genes according to their chromosomal positions. Whiskers aredrawn as implemented in the R-function box plot (see Materials andMethods). ,,.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4231635&req=5

evu157-F4: Boxplots of (a) GC content at 3rd positions (GC3),(b) expression specificity τ,(c) ds, and(d) dn for subsetsof genes according to their chromosomal positions. Whiskers aredrawn as implemented in the R-function box plot (see Materials andMethods). ,,.
Mentions: There is evidence that GC content is not at statistical equilibrium in multipleavian lineages and that GC-biased gene conversion (gBGC) may have contributed tothis (Webster et al. 2006; Nabholz et al. 2011; Mugal et al. 2013). However, ourresults should also be robust to variation in GC content and the action gBGC,which can upwardly bias estimates of ω and lead to false detection oftargets of positive selection (reviewed by Duret and Galtier 2009). First, we used the sitemodels in PAML, which analyzed substitution patterns over the entirephylogenetic tree in the search of positively selected genes. A recent analysishas shown that results produced by this approach are unlikely to be affected bygBGC (Ratnakumar et al. 2010).Second, if substitutions of slightly deleterious mutations were driven by gBGC(Galtier et al. 2009), weexpect this effect to be stronger in regions with higher recombination rates andGC content, which are often used as proxies of the intensity of gBGC (Duret and Galtier 2009). Contrary tothis prediction, in regions with reduced recombination, where ω is higher,GC content is lower (figs. 3 and4a), andevidence of relaxed constraints on nonsynonymous sites also comes from theseregions (fig. 4d).Fig. 4.—

Bottom Line: We investigated whether a special feature of avian genomes, the highly variable recombinational landscape, modulates the efficacy of natural selection through the effects of Hill-Robertson interference, which predicts that selection should be more effective in removing deleterious mutations and incorporating beneficial mutations in high-recombination regions than in low-recombination regions.Furthermore, more compact genes (i.e., those with fewer/shorter introns or shorter proteins) evolve faster than less compact ones.In sum, our results demonstrate that transcriptome sequencing is a powerful method to answer fundamental questions about genome evolution in nonmodel organisms.

View Article: PubMed Central - PubMed

Affiliation: Department of Animal and Plant Sciences, University of Sheffield, United Kingdom toni.gossmann@googlemail.com k.zeng@sheffield.ac.uk.

Show MeSH