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Albuminoid genes: evolving at the interface of dispensability and selection.

Mozzi A, Forni D, Cagliani R, Pozzoli U, Vertemara J, Bresolin N, Sironi M - Genome Biol Evol (2014)

Bottom Line: Population genetic analysis revealed that GC was also the target of locally exerted selective pressure, which drove the frequency increase of different haplotypes in distinct human populations.A search for known variants that modulate GC and 25-hydroxyvitamin D concentrations revealed linkage disequilibrium with positively selected variants, although European and Asian major GC haplotypes carry alleles with reported opposite effect on GC concentration.Data herein indicate that albumin, an extremely abundant housekeeping protein, was the target of pervasive and episodic selection in mammals, whereas GC represented a selection target during the recent evolution of human populations.

View Article: PubMed Central - PubMed

Affiliation: Bioinformatics, Scientific Institute IRCCS E.MEDEA, Bosisio Parini, Italy manuela.sironi@bp.lnf.it.

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Branch-site analysis of positive selection. Branch lengths are scaled to the expected number of substitutions per nucleotide, and branch colors indicate the strength of selection (ω). Red, positive selection (ω > 5); blue, purifying selection (ω = 0); gray, neutral evolution (ω = 1). The proportion of each color represents the fraction of the sequence undergoing the corresponding positive class of selection. Thick branches indicate statistical support for evolution under episodic diversifying selection as determined by BS-REL. Red dots denote branches that were also detected to be under selection using the PAML branch-site models.
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evu235-F1: Branch-site analysis of positive selection. Branch lengths are scaled to the expected number of substitutions per nucleotide, and branch colors indicate the strength of selection (ω). Red, positive selection (ω > 5); blue, purifying selection (ω = 0); gray, neutral evolution (ω = 1). The proportion of each color represents the fraction of the sequence undergoing the corresponding positive class of selection. Thick branches indicate statistical support for evolution under episodic diversifying selection as determined by BS-REL. Red dots denote branches that were also detected to be under selection using the PAML branch-site models.

Mentions: We also explored possible variations in selective pressure among lineages. To this aim, we tested whether models that allow dN/dS to vary along branches had significant better fit to the ALB data than models that assume one same dN/dS across the entire phylogeny (Yang and Nielsen 1998). Because this hypothesis was verified, we used the BS-REL method (Kosakovsky Pond et al. 2011) to analyze selection along specific lineages. Branches identified by BS-REL were cross-validated using codeml (branch-site LRT models) (Zhang et al. 2005) with FDR correction, as suggested (Anisimova and Yang 2007). Sites positively selected along specific branches were identified through BEB analysis (Zhang et al. 2005) (table 3). This method is sensitive but has low power, thus BEB may fail to identify branch-specific sites even when the LRT is significant (Zhang et al. 2005). Because MEME was specifically developed to detect episodic positive selection, only sites identified by both MEME and BEB were considered (table 3). Several lineages showed statistically supported evidence of positive selection (fig. 1), and positively selected residues were identified for the Lemuriformes (residues 316 and 513), squirrel (residue 142), and manatee (residue 588) branches (table 3).Fig. 1.—


Albuminoid genes: evolving at the interface of dispensability and selection.

Mozzi A, Forni D, Cagliani R, Pozzoli U, Vertemara J, Bresolin N, Sironi M - Genome Biol Evol (2014)

Branch-site analysis of positive selection. Branch lengths are scaled to the expected number of substitutions per nucleotide, and branch colors indicate the strength of selection (ω). Red, positive selection (ω > 5); blue, purifying selection (ω = 0); gray, neutral evolution (ω = 1). The proportion of each color represents the fraction of the sequence undergoing the corresponding positive class of selection. Thick branches indicate statistical support for evolution under episodic diversifying selection as determined by BS-REL. Red dots denote branches that were also detected to be under selection using the PAML branch-site models.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4255767&req=5

evu235-F1: Branch-site analysis of positive selection. Branch lengths are scaled to the expected number of substitutions per nucleotide, and branch colors indicate the strength of selection (ω). Red, positive selection (ω > 5); blue, purifying selection (ω = 0); gray, neutral evolution (ω = 1). The proportion of each color represents the fraction of the sequence undergoing the corresponding positive class of selection. Thick branches indicate statistical support for evolution under episodic diversifying selection as determined by BS-REL. Red dots denote branches that were also detected to be under selection using the PAML branch-site models.
Mentions: We also explored possible variations in selective pressure among lineages. To this aim, we tested whether models that allow dN/dS to vary along branches had significant better fit to the ALB data than models that assume one same dN/dS across the entire phylogeny (Yang and Nielsen 1998). Because this hypothesis was verified, we used the BS-REL method (Kosakovsky Pond et al. 2011) to analyze selection along specific lineages. Branches identified by BS-REL were cross-validated using codeml (branch-site LRT models) (Zhang et al. 2005) with FDR correction, as suggested (Anisimova and Yang 2007). Sites positively selected along specific branches were identified through BEB analysis (Zhang et al. 2005) (table 3). This method is sensitive but has low power, thus BEB may fail to identify branch-specific sites even when the LRT is significant (Zhang et al. 2005). Because MEME was specifically developed to detect episodic positive selection, only sites identified by both MEME and BEB were considered (table 3). Several lineages showed statistically supported evidence of positive selection (fig. 1), and positively selected residues were identified for the Lemuriformes (residues 316 and 513), squirrel (residue 142), and manatee (residue 588) branches (table 3).Fig. 1.—

Bottom Line: Population genetic analysis revealed that GC was also the target of locally exerted selective pressure, which drove the frequency increase of different haplotypes in distinct human populations.A search for known variants that modulate GC and 25-hydroxyvitamin D concentrations revealed linkage disequilibrium with positively selected variants, although European and Asian major GC haplotypes carry alleles with reported opposite effect on GC concentration.Data herein indicate that albumin, an extremely abundant housekeeping protein, was the target of pervasive and episodic selection in mammals, whereas GC represented a selection target during the recent evolution of human populations.

View Article: PubMed Central - PubMed

Affiliation: Bioinformatics, Scientific Institute IRCCS E.MEDEA, Bosisio Parini, Italy manuela.sironi@bp.lnf.it.

Show MeSH