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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 evolutionary rates for subsetsof genes specifically expressed in certain tissues; boxes in blueand red denote significantly reduced and increasedvalues, respectively. Whiskers were drawn as implemented in theR-function boxplot (see Materials andMethods).
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evu157-F2: Boxplots of evolutionary rates for subsetsof genes specifically expressed in certain tissues; boxes in blueand red denote significantly reduced and increasedvalues, respectively. Whiskers were drawn as implemented in theR-function boxplot (see Materials andMethods).

Mentions: We have shown that the rate of molecular evolution varies substantially inpasserine birds across the genome. It is, however, unclear whether genes withissue-specific expression also have different ω’s. To answer thisquestion, we extracted tissue-specific genes for the eight tissues included inthe transcriptome sequencing, and compared their ω values (fig. 2). The median ω value forgenes specifically expressed in the brain is 0.051, which is significantly lowerthan the genome-wide median of 0.1 (Mann–Whitney U test[MWU], P = 0.005) and the median value of othertissue-specific genes (MWU, P = 0.021). This could beexplained by the theory put forward by Drummond and Wilke (2008, see Introduction). In contrast,testis/ovary-specific genes have significantly increased evolutionary rates whencompared with other tissue-specific genes (MWU, P =0.027), consistent with the intra- and interspecific arms race theory.Interestingly, genes specifically expressed in the heart had the highest medianω = 0.129, which is comparable to that of the testis/ovary-specificgenes (MWU, P = 0.15). This is different from humanswhose heart-specific genes have significantly lower median ω (0.07) thantestis-specific genes (0.103) (Winter etal. 2004). The cause of this difference is unclear and warrantsinvestigation in future. Fig.2.—


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 evolutionary rates for subsetsof genes specifically expressed in certain tissues; boxes in blueand red denote significantly reduced and increasedvalues, respectively. Whiskers were drawn as implemented in theR-function boxplot (see Materials andMethods).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

evu157-F2: Boxplots of evolutionary rates for subsetsof genes specifically expressed in certain tissues; boxes in blueand red denote significantly reduced and increasedvalues, respectively. Whiskers were drawn as implemented in theR-function boxplot (see Materials andMethods).
Mentions: We have shown that the rate of molecular evolution varies substantially inpasserine birds across the genome. It is, however, unclear whether genes withissue-specific expression also have different ω’s. To answer thisquestion, we extracted tissue-specific genes for the eight tissues included inthe transcriptome sequencing, and compared their ω values (fig. 2). The median ω value forgenes specifically expressed in the brain is 0.051, which is significantly lowerthan the genome-wide median of 0.1 (Mann–Whitney U test[MWU], P = 0.005) and the median value of othertissue-specific genes (MWU, P = 0.021). This could beexplained by the theory put forward by Drummond and Wilke (2008, see Introduction). In contrast,testis/ovary-specific genes have significantly increased evolutionary rates whencompared with other tissue-specific genes (MWU, P =0.027), consistent with the intra- and interspecific arms race theory.Interestingly, genes specifically expressed in the heart had the highest medianω = 0.129, which is comparable to that of the testis/ovary-specificgenes (MWU, P = 0.15). This is different from humanswhose heart-specific genes have significantly lower median ω (0.07) thantestis-specific genes (0.103) (Winter etal. 2004). The cause of this difference is unclear and warrantsinvestigation in future. Fig.2.—

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