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Experimental evidence indicating that mastreviruses probably did not co-diverge with their hosts.

Harkins GW, Delport W, Duffy S, Wood N, Monjane AL, Owor BE, Donaldson L, Saumtally S, Triton G, Briddon RW, Shepherd DN, Rybicki EP, Martin DP, Varsani A - Virol. J. (2009)

Bottom Line: This "co-divergence hypothesis" requires that long-term mastrevirus substitution rates be at least 100,000-fold lower than their basal mutation rates and 10,000-fold lower than their observable short-term substitution rates.We further show that mutation biases are similar for different geminivirus genera, suggesting that mutational processes that drive high basal mutation rates are conserved across the family.The absence of strong negative selection signals within our evolution experiments and the uniformly high geminivirus substitution rates that we and others have reported suggest that mastreviruses cannot have co-diverged with their hosts.

View Article: PubMed Central - HTML - PubMed

Affiliation: South African National Bioinformatics Institute, University of the Western Cape, Cape Town, South Africa. gordon@sanbi.ac.za

ABSTRACT

Background: Despite the demonstration that geminiviruses, like many other single stranded DNA viruses, are evolving at rates similar to those of RNA viruses, a recent study has suggested that grass-infecting species in the genus Mastrevirus may have co-diverged with their hosts over millions of years. This "co-divergence hypothesis" requires that long-term mastrevirus substitution rates be at least 100,000-fold lower than their basal mutation rates and 10,000-fold lower than their observable short-term substitution rates. The credibility of this hypothesis, therefore, hinges on the testable claim that negative selection during mastrevirus evolution is so potent that it effectively purges 99.999% of all mutations that occur.

Results: We have conducted long-term evolution experiments lasting between 6 and 32 years, where we have determined substitution rates of between 2 and 3 x 10(-4) substitutions/site/year for the mastreviruses Maize streak virus (MSV) and Sugarcane streak Réunion virus (SSRV). We further show that mutation biases are similar for different geminivirus genera, suggesting that mutational processes that drive high basal mutation rates are conserved across the family. Rather than displaying signs of extremely severe negative selection as implied by the co-divergence hypothesis, our evolution experiments indicate that MSV and SSRV are predominantly evolving under neutral genetic drift.

Conclusion: The absence of strong negative selection signals within our evolution experiments and the uniformly high geminivirus substitution rates that we and others have reported suggest that mastreviruses cannot have co-diverged with their hosts.

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The maximum clade credibility phylogenetic tree recovered under one of the best-fit models (exponential growth strict-clock) identified using BEAST Almost identical results were obtained under the constant population size strict-clock model (available from the authors on request). The best fit model indicates that: (1) the sugarcane-to-Coix SSRV transmission event that initiated the experiment, which actually occurred in 1976, was estimated to have occurred in 1971 (95% highest clade credibility interval = 1962–1979, indicated by the red posterior probability distribution beneath the tree) and (2) the date of the three-way 1984 sugarcane virus population split was estimated to have occurred in 1985 (95% highest probability density = 1980 – 1989 indicated by the blue posterior probability distribution for the tMRCA situated beneath the tree). Thus, applying the estimated SSRV substitution rate quite accurately recovers the dates of two important events in the 32-year long SSRV evolution experiment.
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Figure 3: The maximum clade credibility phylogenetic tree recovered under one of the best-fit models (exponential growth strict-clock) identified using BEAST Almost identical results were obtained under the constant population size strict-clock model (available from the authors on request). The best fit model indicates that: (1) the sugarcane-to-Coix SSRV transmission event that initiated the experiment, which actually occurred in 1976, was estimated to have occurred in 1971 (95% highest clade credibility interval = 1962–1979, indicated by the red posterior probability distribution beneath the tree) and (2) the date of the three-way 1984 sugarcane virus population split was estimated to have occurred in 1985 (95% highest probability density = 1980 – 1989 indicated by the blue posterior probability distribution for the tMRCA situated beneath the tree). Thus, applying the estimated SSRV substitution rate quite accurately recovers the dates of two important events in the 32-year long SSRV evolution experiment.

Mentions: Importantly, the structure of the SSRV experiment allowed us to verify the accuracy of our SSRV nucleotide substitution rate estimate. Firstly, we knew that the date associated with root node separating the 2008 Coix samples from the 1989, 1991, 1997 and 2008 sugarcane samples was 1976 – the year in which viruses were transmitted from sugarcane to Coix. Secondly, we knew that in 1984 two lineages represented by the 1991 and 1997 sugarcane samples were split from the lineage represented by the 1989 and 2008 samples (Figure 3).


Experimental evidence indicating that mastreviruses probably did not co-diverge with their hosts.

Harkins GW, Delport W, Duffy S, Wood N, Monjane AL, Owor BE, Donaldson L, Saumtally S, Triton G, Briddon RW, Shepherd DN, Rybicki EP, Martin DP, Varsani A - Virol. J. (2009)

The maximum clade credibility phylogenetic tree recovered under one of the best-fit models (exponential growth strict-clock) identified using BEAST Almost identical results were obtained under the constant population size strict-clock model (available from the authors on request). The best fit model indicates that: (1) the sugarcane-to-Coix SSRV transmission event that initiated the experiment, which actually occurred in 1976, was estimated to have occurred in 1971 (95% highest clade credibility interval = 1962–1979, indicated by the red posterior probability distribution beneath the tree) and (2) the date of the three-way 1984 sugarcane virus population split was estimated to have occurred in 1985 (95% highest probability density = 1980 – 1989 indicated by the blue posterior probability distribution for the tMRCA situated beneath the tree). Thus, applying the estimated SSRV substitution rate quite accurately recovers the dates of two important events in the 32-year long SSRV evolution experiment.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2719613&req=5

Figure 3: The maximum clade credibility phylogenetic tree recovered under one of the best-fit models (exponential growth strict-clock) identified using BEAST Almost identical results were obtained under the constant population size strict-clock model (available from the authors on request). The best fit model indicates that: (1) the sugarcane-to-Coix SSRV transmission event that initiated the experiment, which actually occurred in 1976, was estimated to have occurred in 1971 (95% highest clade credibility interval = 1962–1979, indicated by the red posterior probability distribution beneath the tree) and (2) the date of the three-way 1984 sugarcane virus population split was estimated to have occurred in 1985 (95% highest probability density = 1980 – 1989 indicated by the blue posterior probability distribution for the tMRCA situated beneath the tree). Thus, applying the estimated SSRV substitution rate quite accurately recovers the dates of two important events in the 32-year long SSRV evolution experiment.
Mentions: Importantly, the structure of the SSRV experiment allowed us to verify the accuracy of our SSRV nucleotide substitution rate estimate. Firstly, we knew that the date associated with root node separating the 2008 Coix samples from the 1989, 1991, 1997 and 2008 sugarcane samples was 1976 – the year in which viruses were transmitted from sugarcane to Coix. Secondly, we knew that in 1984 two lineages represented by the 1991 and 1997 sugarcane samples were split from the lineage represented by the 1989 and 2008 samples (Figure 3).

Bottom Line: This "co-divergence hypothesis" requires that long-term mastrevirus substitution rates be at least 100,000-fold lower than their basal mutation rates and 10,000-fold lower than their observable short-term substitution rates.We further show that mutation biases are similar for different geminivirus genera, suggesting that mutational processes that drive high basal mutation rates are conserved across the family.The absence of strong negative selection signals within our evolution experiments and the uniformly high geminivirus substitution rates that we and others have reported suggest that mastreviruses cannot have co-diverged with their hosts.

View Article: PubMed Central - HTML - PubMed

Affiliation: South African National Bioinformatics Institute, University of the Western Cape, Cape Town, South Africa. gordon@sanbi.ac.za

ABSTRACT

Background: Despite the demonstration that geminiviruses, like many other single stranded DNA viruses, are evolving at rates similar to those of RNA viruses, a recent study has suggested that grass-infecting species in the genus Mastrevirus may have co-diverged with their hosts over millions of years. This "co-divergence hypothesis" requires that long-term mastrevirus substitution rates be at least 100,000-fold lower than their basal mutation rates and 10,000-fold lower than their observable short-term substitution rates. The credibility of this hypothesis, therefore, hinges on the testable claim that negative selection during mastrevirus evolution is so potent that it effectively purges 99.999% of all mutations that occur.

Results: We have conducted long-term evolution experiments lasting between 6 and 32 years, where we have determined substitution rates of between 2 and 3 x 10(-4) substitutions/site/year for the mastreviruses Maize streak virus (MSV) and Sugarcane streak Réunion virus (SSRV). We further show that mutation biases are similar for different geminivirus genera, suggesting that mutational processes that drive high basal mutation rates are conserved across the family. Rather than displaying signs of extremely severe negative selection as implied by the co-divergence hypothesis, our evolution experiments indicate that MSV and SSRV are predominantly evolving under neutral genetic drift.

Conclusion: The absence of strong negative selection signals within our evolution experiments and the uniformly high geminivirus substitution rates that we and others have reported suggest that mastreviruses cannot have co-diverged with their hosts.

Show MeSH
Related in: MedlinePlus