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Prolonged decay of molecular rate estimates for metazoan mitochondrial DNA.

Molak M, Ho SY - PeerJ (2015)

Bottom Line: We found evidence of time-dependent rates in both coding and non-coding mitochondrial markers, in every group of animals that we studied.This indicates that, over long time frames, purifying selection gives way to mutational saturation as the main driver of time-dependent biases in rate estimates.The results of our study stress the importance of accounting for time-dependent biases in estimating mitochondrial rates regardless of the timescale over which they are inferred.

View Article: PubMed Central - HTML - PubMed

Affiliation: School of Biological Sciences, University of Sydney , Sydney , Australia ; Museum and Institute of Zoology, Polish Academy of Sciences , Warsaw , Poland.

ABSTRACT
Evolutionary timescales can be estimated from genetic data using the molecular clock, often calibrated by fossil or geological evidence. However, estimates of molecular rates in mitochondrial DNA appear to scale negatively with the age of the clock calibration. Although such a pattern has been observed in a limited range of data sets, it has not been studied on a large scale in metazoans. In addition, there is uncertainty over the temporal extent of the time-dependent pattern in rate estimates. Here we present a meta-analysis of 239 rate estimates from metazoans, representing a range of timescales and taxonomic groups. We found evidence of time-dependent rates in both coding and non-coding mitochondrial markers, in every group of animals that we studied. The negative relationship between the estimated rate and time persisted across a much wider range of calibration times than previously suggested. This indicates that, over long time frames, purifying selection gives way to mutational saturation as the main driver of time-dependent biases in rate estimates. The results of our study stress the importance of accounting for time-dependent biases in estimating mitochondrial rates regardless of the timescale over which they are inferred.

No MeSH data available.


Related in: MedlinePlus

Linear regressions of log-transformed rate estimates against log-transformed calibration times used for their estimation for different taxonomic groups (insects (A), reptiles (D), birds (B, E), and mammals (C, F)) and mitochondrial marker types (coding (A–D) and non-coding (E, F)).There were insufficient data for regression analyses of non-coding markers in reptiles and insects.
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fig-2: Linear regressions of log-transformed rate estimates against log-transformed calibration times used for their estimation for different taxonomic groups (insects (A), reptiles (D), birds (B, E), and mammals (C, F)) and mitochondrial marker types (coding (A–D) and non-coding (E, F)).There were insufficient data for regression analyses of non-coding markers in reptiles and insects.

Mentions: We found significant negative relationships between mitochondrial rate estimates and calibration ages in our separate analyses of coding and non-coding markers in mammals, birds, reptiles, and insects (Fig. 2 and Table S3). However, there were too few data points from non-coding markers for reptiles (2 data points) and insects (0 data points) to allow regression analysis. We also found support for time-dependent rates in our intraspecific analysis of mitochondrial sequence data from humans (Fig. S1 and Table S3), corroborating results previously obtained from a smaller data set (Henn et al., 2009).


Prolonged decay of molecular rate estimates for metazoan mitochondrial DNA.

Molak M, Ho SY - PeerJ (2015)

Linear regressions of log-transformed rate estimates against log-transformed calibration times used for their estimation for different taxonomic groups (insects (A), reptiles (D), birds (B, E), and mammals (C, F)) and mitochondrial marker types (coding (A–D) and non-coding (E, F)).There were insufficient data for regression analyses of non-coding markers in reptiles and insects.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4358697&req=5

fig-2: Linear regressions of log-transformed rate estimates against log-transformed calibration times used for their estimation for different taxonomic groups (insects (A), reptiles (D), birds (B, E), and mammals (C, F)) and mitochondrial marker types (coding (A–D) and non-coding (E, F)).There were insufficient data for regression analyses of non-coding markers in reptiles and insects.
Mentions: We found significant negative relationships between mitochondrial rate estimates and calibration ages in our separate analyses of coding and non-coding markers in mammals, birds, reptiles, and insects (Fig. 2 and Table S3). However, there were too few data points from non-coding markers for reptiles (2 data points) and insects (0 data points) to allow regression analysis. We also found support for time-dependent rates in our intraspecific analysis of mitochondrial sequence data from humans (Fig. S1 and Table S3), corroborating results previously obtained from a smaller data set (Henn et al., 2009).

Bottom Line: We found evidence of time-dependent rates in both coding and non-coding mitochondrial markers, in every group of animals that we studied.This indicates that, over long time frames, purifying selection gives way to mutational saturation as the main driver of time-dependent biases in rate estimates.The results of our study stress the importance of accounting for time-dependent biases in estimating mitochondrial rates regardless of the timescale over which they are inferred.

View Article: PubMed Central - HTML - PubMed

Affiliation: School of Biological Sciences, University of Sydney , Sydney , Australia ; Museum and Institute of Zoology, Polish Academy of Sciences , Warsaw , Poland.

ABSTRACT
Evolutionary timescales can be estimated from genetic data using the molecular clock, often calibrated by fossil or geological evidence. However, estimates of molecular rates in mitochondrial DNA appear to scale negatively with the age of the clock calibration. Although such a pattern has been observed in a limited range of data sets, it has not been studied on a large scale in metazoans. In addition, there is uncertainty over the temporal extent of the time-dependent pattern in rate estimates. Here we present a meta-analysis of 239 rate estimates from metazoans, representing a range of timescales and taxonomic groups. We found evidence of time-dependent rates in both coding and non-coding mitochondrial markers, in every group of animals that we studied. The negative relationship between the estimated rate and time persisted across a much wider range of calibration times than previously suggested. This indicates that, over long time frames, purifying selection gives way to mutational saturation as the main driver of time-dependent biases in rate estimates. The results of our study stress the importance of accounting for time-dependent biases in estimating mitochondrial rates regardless of the timescale over which they are inferred.

No MeSH data available.


Related in: MedlinePlus