Relaxed Clocks and Inferences of Heterogeneous Patterns of Nucleotide Substitution and Divergence Time Estimates across Whales and Dolphins (Mammalia: Cetacea)
Various nucleotide substitution models have been developed to accommodate among lineage rate heterogeneity, thereby relaxing the assumptions of the strict molecular clock. Recently developed “uncorrelated relaxed clock” and “random local clock” (RLC) models allow decoupling of nucleotide substitutio...
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fthighwire:oai:open-archive.highwire.org:molbiolevol:29/2/721 2023-05-15T18:33:32+02:00 Relaxed Clocks and Inferences of Heterogeneous Patterns of Nucleotide Substitution and Divergence Time Estimates across Whales and Dolphins (Mammalia: Cetacea) Dornburg, Alex Brandley, Matthew C. McGowen, Michael R. Near, Thomas J. 2012-02-01 00:00:00.0 text/html http://mbe.oxfordjournals.org/cgi/content/short/29/2/721 https://doi.org/10.1093/molbev/msr228 en eng Oxford University Press http://mbe.oxfordjournals.org/cgi/content/short/29/2/721 http://dx.doi.org/10.1093/molbev/msr228 Copyright (C) 2012, Society for Molecular Biology and Evolution Research Articles TEXT 2012 fthighwire https://doi.org/10.1093/molbev/msr228 2012-02-04T18:53:43Z Various nucleotide substitution models have been developed to accommodate among lineage rate heterogeneity, thereby relaxing the assumptions of the strict molecular clock. Recently developed “uncorrelated relaxed clock” and “random local clock” (RLC) models allow decoupling of nucleotide substitution rates between descendant lineages and are thus predicted to perform better in the presence of lineage-specific rate heterogeneity. However, it is uncertain how these models perform in the presence of punctuated shifts in substitution rate, especially between closely related clades. Using cetaceans (whales and dolphins) as a case study, we test the performance of these two substitution models in estimating both molecular rates and divergence times in the presence of substantial lineage-specific rate heterogeneity. Our RLC analyses of whole mitochondrial genome alignments find evidence for up to ten clade-specific nucleotide substitution rate shifts in cetaceans. We provide evidence that in the uncorrelated relaxed clock framework, a punctuated shift in the rate of molecular evolution within a subclade results in posterior rate estimates that are either misled or intermediate between the disparate rate classes present in baleen and toothed whales. Using simulations, we demonstrate abrupt changes in rate isolated to one or a few lineages in the phylogeny can mislead rate and age estimation, even when the node of interest is calibrated. We further demonstrate how increasing prior age uncertainty can bias rate and age estimates, even while the 95% highest posterior density around age estimates decreases; in other words, increased precision for an inaccurate estimate. We interpret the use of external calibrations in divergence time studies in light of these results, suggesting that rate shifts at deep time scales may mislead inferences of absolute molecular rates and ages. Text toothed whales HighWire Press (Stanford University) Molecular Biology and Evolution 29 2 721 736 |
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Research Articles Dornburg, Alex Brandley, Matthew C. McGowen, Michael R. Near, Thomas J. Relaxed Clocks and Inferences of Heterogeneous Patterns of Nucleotide Substitution and Divergence Time Estimates across Whales and Dolphins (Mammalia: Cetacea) |
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Research Articles |
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Various nucleotide substitution models have been developed to accommodate among lineage rate heterogeneity, thereby relaxing the assumptions of the strict molecular clock. Recently developed “uncorrelated relaxed clock” and “random local clock” (RLC) models allow decoupling of nucleotide substitution rates between descendant lineages and are thus predicted to perform better in the presence of lineage-specific rate heterogeneity. However, it is uncertain how these models perform in the presence of punctuated shifts in substitution rate, especially between closely related clades. Using cetaceans (whales and dolphins) as a case study, we test the performance of these two substitution models in estimating both molecular rates and divergence times in the presence of substantial lineage-specific rate heterogeneity. Our RLC analyses of whole mitochondrial genome alignments find evidence for up to ten clade-specific nucleotide substitution rate shifts in cetaceans. We provide evidence that in the uncorrelated relaxed clock framework, a punctuated shift in the rate of molecular evolution within a subclade results in posterior rate estimates that are either misled or intermediate between the disparate rate classes present in baleen and toothed whales. Using simulations, we demonstrate abrupt changes in rate isolated to one or a few lineages in the phylogeny can mislead rate and age estimation, even when the node of interest is calibrated. We further demonstrate how increasing prior age uncertainty can bias rate and age estimates, even while the 95% highest posterior density around age estimates decreases; in other words, increased precision for an inaccurate estimate. We interpret the use of external calibrations in divergence time studies in light of these results, suggesting that rate shifts at deep time scales may mislead inferences of absolute molecular rates and ages. |
format |
Text |
author |
Dornburg, Alex Brandley, Matthew C. McGowen, Michael R. Near, Thomas J. |
author_facet |
Dornburg, Alex Brandley, Matthew C. McGowen, Michael R. Near, Thomas J. |
author_sort |
Dornburg, Alex |
title |
Relaxed Clocks and Inferences of Heterogeneous Patterns of Nucleotide Substitution and Divergence Time Estimates across Whales and Dolphins (Mammalia: Cetacea) |
title_short |
Relaxed Clocks and Inferences of Heterogeneous Patterns of Nucleotide Substitution and Divergence Time Estimates across Whales and Dolphins (Mammalia: Cetacea) |
title_full |
Relaxed Clocks and Inferences of Heterogeneous Patterns of Nucleotide Substitution and Divergence Time Estimates across Whales and Dolphins (Mammalia: Cetacea) |
title_fullStr |
Relaxed Clocks and Inferences of Heterogeneous Patterns of Nucleotide Substitution and Divergence Time Estimates across Whales and Dolphins (Mammalia: Cetacea) |
title_full_unstemmed |
Relaxed Clocks and Inferences of Heterogeneous Patterns of Nucleotide Substitution and Divergence Time Estimates across Whales and Dolphins (Mammalia: Cetacea) |
title_sort |
relaxed clocks and inferences of heterogeneous patterns of nucleotide substitution and divergence time estimates across whales and dolphins (mammalia: cetacea) |
publisher |
Oxford University Press |
publishDate |
2012 |
url |
http://mbe.oxfordjournals.org/cgi/content/short/29/2/721 https://doi.org/10.1093/molbev/msr228 |
genre |
toothed whales |
genre_facet |
toothed whales |
op_relation |
http://mbe.oxfordjournals.org/cgi/content/short/29/2/721 http://dx.doi.org/10.1093/molbev/msr228 |
op_rights |
Copyright (C) 2012, Society for Molecular Biology and Evolution |
op_doi |
https://doi.org/10.1093/molbev/msr228 |
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Molecular Biology and Evolution |
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29 |
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2 |
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721 |
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736 |
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1766218166475685888 |