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What Fraction of Duplicates Observed in Recently Sequenced Genomes Is Segregating and Destined to Fail to Fix?

Teufel AI, Masel J, Liberles DA - Genome Biol Evol (2015)

Bottom Line: To date, mechanistic models for duplicate gene retention only account for the mutation-driven nonfunctionalization process.Here, a neutral model for the distribution of synonymous substitutions in duplicated genes which are segregating and expected to never fix in a population is introduced.The model has been validated on simulated data and subsequent analysis with the model on genomic data from human and mouse shows that conclusions about the underlying mechanisms for duplicate gene retention can be sensitive to consideration of population genetic processes.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Biology, University of Wyoming Center for Computational Genetics and Genomics and Department of Biology, Temple University.

No MeSH data available.


The age distribution of M. musculus duplicate pairs interval of size ΔdS = 0.001 and scaled for duplicates with dS < 0.01 and in intervals of ΔdS = 0.01 for older duplicates from Lynch and Conery (2000) is shown. The red “x” denotes the median points of bins and the black line is the fit from the model best supported by AIC.
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evv139-F4: The age distribution of M. musculus duplicate pairs interval of size ΔdS = 0.001 and scaled for duplicates with dS < 0.01 and in intervals of ΔdS = 0.01 for older duplicates from Lynch and Conery (2000) is shown. The red “x” denotes the median points of bins and the black line is the fit from the model best supported by AIC.

Mentions: Applying the approach outlined above to data presented in Lynch and Conery (2000) for dS < 0.3 and including duplicates with dS < 0.01, the average numbers of silent nucleotide sites in the H. sapiens and M. musculus data sets are estimated to initially be 335 and 334, respectively. The age distribution of duplicate pairs was computed as counts as described in Materials and Methods. Figures 3 and 4 illustrate the distribution of dS values in Lynch and Conery’s (2000) duplicate pairs, and how many of those pairs likely represent duplications that have not and will not become fixed, based on . Figure 5 shows the corrected number of duplicates, where the expected amount of transiently segregating variation has been subtracted out for H. sapiens and M. musculus.Fig. 3.—


What Fraction of Duplicates Observed in Recently Sequenced Genomes Is Segregating and Destined to Fail to Fix?

Teufel AI, Masel J, Liberles DA - Genome Biol Evol (2015)

The age distribution of M. musculus duplicate pairs interval of size ΔdS = 0.001 and scaled for duplicates with dS < 0.01 and in intervals of ΔdS = 0.01 for older duplicates from Lynch and Conery (2000) is shown. The red “x” denotes the median points of bins and the black line is the fit from the model best supported by AIC.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4558857&req=5

evv139-F4: The age distribution of M. musculus duplicate pairs interval of size ΔdS = 0.001 and scaled for duplicates with dS < 0.01 and in intervals of ΔdS = 0.01 for older duplicates from Lynch and Conery (2000) is shown. The red “x” denotes the median points of bins and the black line is the fit from the model best supported by AIC.
Mentions: Applying the approach outlined above to data presented in Lynch and Conery (2000) for dS < 0.3 and including duplicates with dS < 0.01, the average numbers of silent nucleotide sites in the H. sapiens and M. musculus data sets are estimated to initially be 335 and 334, respectively. The age distribution of duplicate pairs was computed as counts as described in Materials and Methods. Figures 3 and 4 illustrate the distribution of dS values in Lynch and Conery’s (2000) duplicate pairs, and how many of those pairs likely represent duplications that have not and will not become fixed, based on . Figure 5 shows the corrected number of duplicates, where the expected amount of transiently segregating variation has been subtracted out for H. sapiens and M. musculus.Fig. 3.—

Bottom Line: To date, mechanistic models for duplicate gene retention only account for the mutation-driven nonfunctionalization process.Here, a neutral model for the distribution of synonymous substitutions in duplicated genes which are segregating and expected to never fix in a population is introduced.The model has been validated on simulated data and subsequent analysis with the model on genomic data from human and mouse shows that conclusions about the underlying mechanisms for duplicate gene retention can be sensitive to consideration of population genetic processes.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Biology, University of Wyoming Center for Computational Genetics and Genomics and Department of Biology, Temple University.

No MeSH data available.