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Molecular evolution of anthocyanin pigmentation genes following losses of flower color.

Ho WW, Smith SD - BMC Evol. Biol. (2016)

Bottom Line: Phenotypic transitions, such as trait gain or loss, are predicted to carry evolutionary consequences for the genes that control their development.Focusing on the Iochrominae clade (Solanaceae), we examine how repeated losses of floral anthocyanin pigmentation associated with flower color transitions have affected the molecular evolution of three anthocyanin pathway genes (Chi, F3h, and Dfr).Despite the increase, the values for dN/dS in both pigmented and unpigmented lineages were consistent overall with purifying selection acting on these loci.

View Article: PubMed Central - PubMed

Affiliation: Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, USA.

ABSTRACT

Background: Phenotypic transitions, such as trait gain or loss, are predicted to carry evolutionary consequences for the genes that control their development. For example, trait losses can result in molecular decay of the pathways underlying the trait. Focusing on the Iochrominae clade (Solanaceae), we examine how repeated losses of floral anthocyanin pigmentation associated with flower color transitions have affected the molecular evolution of three anthocyanin pathway genes (Chi, F3h, and Dfr).

Results: We recovered intact coding regions for the three genes in all of the lineages that have lost floral pigmentation, suggesting that molecular decay is not associated with these flower color transitions. However, two of the three genes (Chi, F3h) show significantly elevated dN/dS ratios in lineages without floral pigmentation. Maximum likelihood analyses suggest that this increase is due to relaxed constraint on anthocyanin genes in the unpigmented lineages as opposed to positive selection. Despite the increase, the values for dN/dS in both pigmented and unpigmented lineages were consistent overall with purifying selection acting on these loci.

Conclusions: The broad conservation of anthocyanin pathway genes across lineages with and without floral anthocyanins is consistent with the growing consensus that losses of pigmentation are largely achieved by changes in gene expression as opposed to structural mutations. Moreover, this conservation maintains the potential for regain of flower color, and indicates that evolutionary losses of floral pigmentation may be readily reversible.

No MeSH data available.


Related in: MedlinePlus

Patterns of variation in the dN/dS ratio (ω) across genes and between pigmented and unpigmented lineages. The upper panel shows ω values for the single ratio model for each of the three loci (see also Additional file 4: Table S3). * represents a locus with a significantly lower ω value than the other two loci. The lower panel shows ω values for pigmented (dark gray dot) and unpigmented (white dot) lineages under the two-ratio model. * represents cases in which the unpigmented lineages have significantly higher ω values
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Fig3: Patterns of variation in the dN/dS ratio (ω) across genes and between pigmented and unpigmented lineages. The upper panel shows ω values for the single ratio model for each of the three loci (see also Additional file 4: Table S3). * represents a locus with a significantly lower ω value than the other two loci. The lower panel shows ω values for pigmented (dark gray dot) and unpigmented (white dot) lineages under the two-ratio model. * represents cases in which the unpigmented lineages have significantly higher ω values

Mentions: We applied codon-based maximum likelihood methods to characterize patterns of molecular evolution across these loci and test for the effect of pigment loss on selective constraint. Models with a single ratio of nonsynonymous to synonymous substitution rates (dN/dS or ω) for each locus resulted in values between 0.09 and 0.24, suggesting that these loci have predominantly experienced purifying selection (Additional file 3: Table S2a, Fig. 3). Among the three loci, Chi has the highest dN/dS ratio, followed by Dfr and F3h. The values for Chi and Dfr are statistically indistinguishable, while that for F3h is significantly lower (Additional file 4: Table S3, Fig. 3). The range of dN/dS ratios for these genes in our study is similar to that found for anthocyanin transcription factors and other core anthocyanin pathway genes in previous studies [50, 51].Fig. 3


Molecular evolution of anthocyanin pigmentation genes following losses of flower color.

Ho WW, Smith SD - BMC Evol. Biol. (2016)

Patterns of variation in the dN/dS ratio (ω) across genes and between pigmented and unpigmented lineages. The upper panel shows ω values for the single ratio model for each of the three loci (see also Additional file 4: Table S3). * represents a locus with a significantly lower ω value than the other two loci. The lower panel shows ω values for pigmented (dark gray dot) and unpigmented (white dot) lineages under the two-ratio model. * represents cases in which the unpigmented lineages have significantly higher ω values
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4862180&req=5

Fig3: Patterns of variation in the dN/dS ratio (ω) across genes and between pigmented and unpigmented lineages. The upper panel shows ω values for the single ratio model for each of the three loci (see also Additional file 4: Table S3). * represents a locus with a significantly lower ω value than the other two loci. The lower panel shows ω values for pigmented (dark gray dot) and unpigmented (white dot) lineages under the two-ratio model. * represents cases in which the unpigmented lineages have significantly higher ω values
Mentions: We applied codon-based maximum likelihood methods to characterize patterns of molecular evolution across these loci and test for the effect of pigment loss on selective constraint. Models with a single ratio of nonsynonymous to synonymous substitution rates (dN/dS or ω) for each locus resulted in values between 0.09 and 0.24, suggesting that these loci have predominantly experienced purifying selection (Additional file 3: Table S2a, Fig. 3). Among the three loci, Chi has the highest dN/dS ratio, followed by Dfr and F3h. The values for Chi and Dfr are statistically indistinguishable, while that for F3h is significantly lower (Additional file 4: Table S3, Fig. 3). The range of dN/dS ratios for these genes in our study is similar to that found for anthocyanin transcription factors and other core anthocyanin pathway genes in previous studies [50, 51].Fig. 3

Bottom Line: Phenotypic transitions, such as trait gain or loss, are predicted to carry evolutionary consequences for the genes that control their development.Focusing on the Iochrominae clade (Solanaceae), we examine how repeated losses of floral anthocyanin pigmentation associated with flower color transitions have affected the molecular evolution of three anthocyanin pathway genes (Chi, F3h, and Dfr).Despite the increase, the values for dN/dS in both pigmented and unpigmented lineages were consistent overall with purifying selection acting on these loci.

View Article: PubMed Central - PubMed

Affiliation: Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, USA.

ABSTRACT

Background: Phenotypic transitions, such as trait gain or loss, are predicted to carry evolutionary consequences for the genes that control their development. For example, trait losses can result in molecular decay of the pathways underlying the trait. Focusing on the Iochrominae clade (Solanaceae), we examine how repeated losses of floral anthocyanin pigmentation associated with flower color transitions have affected the molecular evolution of three anthocyanin pathway genes (Chi, F3h, and Dfr).

Results: We recovered intact coding regions for the three genes in all of the lineages that have lost floral pigmentation, suggesting that molecular decay is not associated with these flower color transitions. However, two of the three genes (Chi, F3h) show significantly elevated dN/dS ratios in lineages without floral pigmentation. Maximum likelihood analyses suggest that this increase is due to relaxed constraint on anthocyanin genes in the unpigmented lineages as opposed to positive selection. Despite the increase, the values for dN/dS in both pigmented and unpigmented lineages were consistent overall with purifying selection acting on these loci.

Conclusions: The broad conservation of anthocyanin pathway genes across lineages with and without floral anthocyanins is consistent with the growing consensus that losses of pigmentation are largely achieved by changes in gene expression as opposed to structural mutations. Moreover, this conservation maintains the potential for regain of flower color, and indicates that evolutionary losses of floral pigmentation may be readily reversible.

No MeSH data available.


Related in: MedlinePlus