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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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Related in: MedlinePlus

The mean substitution rate estimates for MSV and SSRV are between 2.0 × 10-4 and 3.5 × 10-4 subs/site/year. For the six-year MSV-B and MSV-F and the 32-year SSRV evolution experiments, substitution rate estimates made using a range of demographic and molecular clock models are presented. Whereas black squares indicate the most probable substitution rates, vertical bars indicate the 95% highest probability density of the substitution rate estimates. Red squares indicate rates estimated using the best fit demographic and clock models (determined using Bayes factor tests; Additional file 1). Stars indicates the models that returned the highest likelihood. When more than one red square is shown for a particular dataset this indicates that neither demographic model provided better support for the data. For purposes of comparison, previous estimates of substitution rates are presented (in the grey area) for both MSV (full genome sequences sampled during shorter term evolution experiments lasting between 2 months and 5 years; [9,22] from individual plants) and the begomoviruses, TYLCV (full genome sequences sampled from nature over 19 years [4]), East African cassava mosaic virus (EACMV, full genome sequences sampled from nature over 8 years [5]), Tomato yellow leaf curl China virus (TYLCCV, partial genome sequences sampled over 1 to 2 months from individual plants [6]) and TYLCV (full genome sequences sampled over 1 month from individual plants[8]).
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Figure 2: The mean substitution rate estimates for MSV and SSRV are between 2.0 × 10-4 and 3.5 × 10-4 subs/site/year. For the six-year MSV-B and MSV-F and the 32-year SSRV evolution experiments, substitution rate estimates made using a range of demographic and molecular clock models are presented. Whereas black squares indicate the most probable substitution rates, vertical bars indicate the 95% highest probability density of the substitution rate estimates. Red squares indicate rates estimated using the best fit demographic and clock models (determined using Bayes factor tests; Additional file 1). Stars indicates the models that returned the highest likelihood. When more than one red square is shown for a particular dataset this indicates that neither demographic model provided better support for the data. For purposes of comparison, previous estimates of substitution rates are presented (in the grey area) for both MSV (full genome sequences sampled during shorter term evolution experiments lasting between 2 months and 5 years; [9,22] from individual plants) and the begomoviruses, TYLCV (full genome sequences sampled from nature over 19 years [4]), East African cassava mosaic virus (EACMV, full genome sequences sampled from nature over 8 years [5]), Tomato yellow leaf curl China virus (TYLCCV, partial genome sequences sampled over 1 to 2 months from individual plants [6]) and TYLCV (full genome sequences sampled over 1 month from individual plants[8]).

Mentions: The Bayesian coalescent based methods implemented in the computer program BEAST[29] are ideally suited to inferring nucleotide substitution rates from temporally structured datasets such as ours. Applying these methods we estimated mean substitution rates of approximately 3.5 × 10-4, 2.0 × 10-4 and 2.1 × 10-4 sub/site/year over the duration of the SSRV, MSV-F and MSV-B experiments, respectively (Figure 2). These estimates were reasonably consistent irrespective of the molecular clock or demographic models used. All had overlapping 95% highest probability density (HPD) intervals within the range of 7.22 × 10-5 (observed with the MSV-F dataset using a relaxed clock + Bayesian skyline plot model) to 6.77 × 10-4 subs/site/year (observed with the SSRV dataset using a relaxed clock + Bayesian skyline plot model; Figure 2).


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 mean substitution rate estimates for MSV and SSRV are between 2.0 × 10-4 and 3.5 × 10-4 subs/site/year. For the six-year MSV-B and MSV-F and the 32-year SSRV evolution experiments, substitution rate estimates made using a range of demographic and molecular clock models are presented. Whereas black squares indicate the most probable substitution rates, vertical bars indicate the 95% highest probability density of the substitution rate estimates. Red squares indicate rates estimated using the best fit demographic and clock models (determined using Bayes factor tests; Additional file 1). Stars indicates the models that returned the highest likelihood. When more than one red square is shown for a particular dataset this indicates that neither demographic model provided better support for the data. For purposes of comparison, previous estimates of substitution rates are presented (in the grey area) for both MSV (full genome sequences sampled during shorter term evolution experiments lasting between 2 months and 5 years; [9,22] from individual plants) and the begomoviruses, TYLCV (full genome sequences sampled from nature over 19 years [4]), East African cassava mosaic virus (EACMV, full genome sequences sampled from nature over 8 years [5]), Tomato yellow leaf curl China virus (TYLCCV, partial genome sequences sampled over 1 to 2 months from individual plants [6]) and TYLCV (full genome sequences sampled over 1 month from individual plants[8]).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: The mean substitution rate estimates for MSV and SSRV are between 2.0 × 10-4 and 3.5 × 10-4 subs/site/year. For the six-year MSV-B and MSV-F and the 32-year SSRV evolution experiments, substitution rate estimates made using a range of demographic and molecular clock models are presented. Whereas black squares indicate the most probable substitution rates, vertical bars indicate the 95% highest probability density of the substitution rate estimates. Red squares indicate rates estimated using the best fit demographic and clock models (determined using Bayes factor tests; Additional file 1). Stars indicates the models that returned the highest likelihood. When more than one red square is shown for a particular dataset this indicates that neither demographic model provided better support for the data. For purposes of comparison, previous estimates of substitution rates are presented (in the grey area) for both MSV (full genome sequences sampled during shorter term evolution experiments lasting between 2 months and 5 years; [9,22] from individual plants) and the begomoviruses, TYLCV (full genome sequences sampled from nature over 19 years [4]), East African cassava mosaic virus (EACMV, full genome sequences sampled from nature over 8 years [5]), Tomato yellow leaf curl China virus (TYLCCV, partial genome sequences sampled over 1 to 2 months from individual plants [6]) and TYLCV (full genome sequences sampled over 1 month from individual plants[8]).
Mentions: The Bayesian coalescent based methods implemented in the computer program BEAST[29] are ideally suited to inferring nucleotide substitution rates from temporally structured datasets such as ours. Applying these methods we estimated mean substitution rates of approximately 3.5 × 10-4, 2.0 × 10-4 and 2.1 × 10-4 sub/site/year over the duration of the SSRV, MSV-F and MSV-B experiments, respectively (Figure 2). These estimates were reasonably consistent irrespective of the molecular clock or demographic models used. All had overlapping 95% highest probability density (HPD) intervals within the range of 7.22 × 10-5 (observed with the MSV-F dataset using a relaxed clock + Bayesian skyline plot model) to 6.77 × 10-4 subs/site/year (observed with the SSRV dataset using a relaxed clock + Bayesian skyline plot model; Figure 2).

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