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Gene family size conservation is a good indicator of evolutionary rates.

Chen FC, Chen CJ, Li WH, Chuang TJ - Mol. Biol. Evol. (2010)

Bottom Line: In addition, we show that the duplicate genes with family size conservation evolve significantly more slowly than those without family size conservation.Our results thus suggest that the controversy on whether duplicate genes evolve more slowly than singletons can be resolved when family size conservation is taken into consideration.Our results thus point to the importance of family size conservation in the evolution of duplicate genes.

View Article: PubMed Central - PubMed

Affiliation: Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Miaoli County, Taiwan.

ABSTRACT
The evolution of duplicate genes has been a topic of broad interest. Here, we propose that the conservation of gene family size is a good indicator of the rate of sequence evolution and some other biological properties. By comparing the human-chimpanzee-macaque orthologous gene families with and without family size conservation, we demonstrate that genes with family size conservation evolve more slowly than those without family size conservation. Our results further demonstrate that both family expansion and contraction events may accelerate gene evolution, resulting in elevated evolutionary rates in the genes without family size conservation. In addition, we show that the duplicate genes with family size conservation evolve significantly more slowly than those without family size conservation. Interestingly, the median evolutionary rate of singletons falls in between those of the above two types of duplicate gene families. Our results thus suggest that the controversy on whether duplicate genes evolve more slowly than singletons can be resolved when family size conservation is taken into consideration. Furthermore, we also observe that duplicate genes with family size conservation have the highest level of gene expression/expression breadth, the highest proportion of essential genes, and the lowest gene compactness, followed by singletons and then by duplicate genes without family size conservation. Such a trend accords well with our observations of evolutionary rates. Our results thus point to the importance of family size conservation in the evolution of duplicate genes.

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Related in: MedlinePlus

Comparisons of median Ka (filled circles), Ks (filled triangles), and Ka/Ks (open diamonds) values of human genes and their closest counterparts in chimpanzee in (A) HS/CS expansion, HS/CS contraction, and H=C=M families; and (B) the C>H>M, all CS expansion (C>H≥M), C>H=M, and H=C=M families. Error bars represent the standard errors.
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fig2: Comparisons of median Ka (filled circles), Ks (filled triangles), and Ka/Ks (open diamonds) values of human genes and their closest counterparts in chimpanzee in (A) HS/CS expansion, HS/CS contraction, and H=C=M families; and (B) the C>H>M, all CS expansion (C>H≥M), C>H=M, and H=C=M families. Error bars represent the standard errors.

Mentions: The next question to ask is whether family size expansion and contraction have different effects on the evolutionary rates of the affected families. Using rhesus macaque as the outgroup species, we can extract from non-H=C=M families the families that have potentially undergone expansion or contraction in human and chimpanzee and classify them into four subgroups (table 3): human-specific (HS) expansion (281 families), HS contraction (91 families), chimpanzee-specific (CS) expansion (87 families), and CS contraction (289 families). The HS/CS expansion and contraction families may have, respectively, experienced net gene gain and loss events in terms of maximum parsimony of evolution. Figure 2A illustrates the median Ka, Ks, and Ka/Ks values between human genes and their chimpanzee counterparts in these four subgroups compared with those of the H=C=M families. We have four observations. First, the median Ka and Ka/Ks values are significantly higher in the HS expansion families than in the CS contraction families, both of which have a larger number of genes in human than in chimpanzee (fig. 2A, both P values < 0.001). A similar trend is also observed in the comparison between the CS expansion and HS contraction families, both of which have a larger family size in chimpanzee than in human (fig. 2A, both P values < 0.05).


Gene family size conservation is a good indicator of evolutionary rates.

Chen FC, Chen CJ, Li WH, Chuang TJ - Mol. Biol. Evol. (2010)

Comparisons of median Ka (filled circles), Ks (filled triangles), and Ka/Ks (open diamonds) values of human genes and their closest counterparts in chimpanzee in (A) HS/CS expansion, HS/CS contraction, and H=C=M families; and (B) the C>H>M, all CS expansion (C>H≥M), C>H=M, and H=C=M families. Error bars represent the standard errors.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2908708&req=5

fig2: Comparisons of median Ka (filled circles), Ks (filled triangles), and Ka/Ks (open diamonds) values of human genes and their closest counterparts in chimpanzee in (A) HS/CS expansion, HS/CS contraction, and H=C=M families; and (B) the C>H>M, all CS expansion (C>H≥M), C>H=M, and H=C=M families. Error bars represent the standard errors.
Mentions: The next question to ask is whether family size expansion and contraction have different effects on the evolutionary rates of the affected families. Using rhesus macaque as the outgroup species, we can extract from non-H=C=M families the families that have potentially undergone expansion or contraction in human and chimpanzee and classify them into four subgroups (table 3): human-specific (HS) expansion (281 families), HS contraction (91 families), chimpanzee-specific (CS) expansion (87 families), and CS contraction (289 families). The HS/CS expansion and contraction families may have, respectively, experienced net gene gain and loss events in terms of maximum parsimony of evolution. Figure 2A illustrates the median Ka, Ks, and Ka/Ks values between human genes and their chimpanzee counterparts in these four subgroups compared with those of the H=C=M families. We have four observations. First, the median Ka and Ka/Ks values are significantly higher in the HS expansion families than in the CS contraction families, both of which have a larger number of genes in human than in chimpanzee (fig. 2A, both P values < 0.001). A similar trend is also observed in the comparison between the CS expansion and HS contraction families, both of which have a larger family size in chimpanzee than in human (fig. 2A, both P values < 0.05).

Bottom Line: In addition, we show that the duplicate genes with family size conservation evolve significantly more slowly than those without family size conservation.Our results thus suggest that the controversy on whether duplicate genes evolve more slowly than singletons can be resolved when family size conservation is taken into consideration.Our results thus point to the importance of family size conservation in the evolution of duplicate genes.

View Article: PubMed Central - PubMed

Affiliation: Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Miaoli County, Taiwan.

ABSTRACT
The evolution of duplicate genes has been a topic of broad interest. Here, we propose that the conservation of gene family size is a good indicator of the rate of sequence evolution and some other biological properties. By comparing the human-chimpanzee-macaque orthologous gene families with and without family size conservation, we demonstrate that genes with family size conservation evolve more slowly than those without family size conservation. Our results further demonstrate that both family expansion and contraction events may accelerate gene evolution, resulting in elevated evolutionary rates in the genes without family size conservation. In addition, we show that the duplicate genes with family size conservation evolve significantly more slowly than those without family size conservation. Interestingly, the median evolutionary rate of singletons falls in between those of the above two types of duplicate gene families. Our results thus suggest that the controversy on whether duplicate genes evolve more slowly than singletons can be resolved when family size conservation is taken into consideration. Furthermore, we also observe that duplicate genes with family size conservation have the highest level of gene expression/expression breadth, the highest proportion of essential genes, and the lowest gene compactness, followed by singletons and then by duplicate genes without family size conservation. Such a trend accords well with our observations of evolutionary rates. Our results thus point to the importance of family size conservation in the evolution of duplicate genes.

Show MeSH
Related in: MedlinePlus