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Estimating divergence dates and substitution rates in the Drosophila phylogeny.

Obbard DJ, Maclennan J, Kim KW, Rambaut A, O'Grady PM, Jiggins FM - Mol. Biol. Evol. (2012)

Bottom Line: Surprisingly, our estimate for the date for the most recent common ancestor of the genus Drosophila based on mutation rate (25-40 Ma) is closer to being compatible with independent fossil-derived dates (20-50 Ma) than are most of the Hawaiian-calibration models and also has smaller uncertainty.Potential problems with the Hawaiian calibration may arise from systematic variation in the molecular clock due to the long generation time of Hawaiian Drosophila compared with other Drosophila and/or uncertainty in linking island formation dates with colonization dates.As either source of error will bias estimates of divergence time, we suggest mutation rate estimates be used until better models are available.

View Article: PubMed Central - PubMed

Affiliation: Institute of Evolutionary Biology, and Centre for Infection Immunity and Evolution, University of Edinburgh, Edinburgh, United Kingdom. darren.obbard@ed.ac.uk

ABSTRACT
An absolute timescale for evolution is essential if we are to associate evolutionary phenomena, such as adaptation or speciation, with potential causes, such as geological activity or climatic change. Timescales in most phylogenetic studies use geologically dated fossils or phylogeographic events as calibration points, but more recently, it has also become possible to use experimentally derived estimates of the mutation rate as a proxy for substitution rates. The large radiation of drosophilid taxa endemic to the Hawaiian islands has provided multiple calibration points for the Drosophila phylogeny, thanks to the "conveyor belt" process by which this archipelago forms and is colonized by species. However, published date estimates for key nodes in the Drosophila phylogeny vary widely, and many are based on simplistic models of colonization and coalescence or on estimates of island age that are not current. In this study, we use new sequence data from seven species of Hawaiian Drosophila to examine a range of explicit coalescent models and estimate substitution rates. We use these rates, along with a published experimentally determined mutation rate, to date key events in drosophilid evolution. Surprisingly, our estimate for the date for the most recent common ancestor of the genus Drosophila based on mutation rate (25-40 Ma) is closer to being compatible with independent fossil-derived dates (20-50 Ma) than are most of the Hawaiian-calibration models and also has smaller uncertainty. We find that Hawaiian-calibrated dates are extremely sensitive to model choice and give rise to point estimates that range between 26 and 192 Ma, depending on the details of the model. Potential problems with the Hawaiian calibration may arise from systematic variation in the molecular clock due to the long generation time of Hawaiian Drosophila compared with other Drosophila and/or uncertainty in linking island formation dates with colonization dates. As either source of error will bias estimates of divergence time, we suggest mutation rate estimates be used until better models are available.

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A time-scaled phylogeny of the melanogaster subgroup. Two alternatively calibrated phylogenetic trees for the melanogaster subgroup, inferred from 36 loci. Trees were inferred under an uncorrelated log-normal relaxed clock, and the topology presented is the maximum clade-credibility tree with node dates scaled to the posterior median. The 95% highest posterior density intervals (in blue) are shown for each node, and reflect uncertainty both in the rate estimate used to calibrate the tree and sampling error associated with the data. Nodes with less than 100% posterior support are labeled. The alternative time calibrations (mutation rate vs. Hawai’i) are the same as those used in figure 4 (see main text). Note that the inferred topology of the D. simulans complex differs between the two data sets. Species name abbreviations are given in figure 4.
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mss150-F5: A time-scaled phylogeny of the melanogaster subgroup. Two alternatively calibrated phylogenetic trees for the melanogaster subgroup, inferred from 36 loci. Trees were inferred under an uncorrelated log-normal relaxed clock, and the topology presented is the maximum clade-credibility tree with node dates scaled to the posterior median. The 95% highest posterior density intervals (in blue) are shown for each node, and reflect uncertainty both in the rate estimate used to calibrate the tree and sampling error associated with the data. Nodes with less than 100% posterior support are labeled. The alternative time calibrations (mutation rate vs. Hawai’i) are the same as those used in figure 4 (see main text). Note that the inferred topology of the D. simulans complex differs between the two data sets. Species name abbreviations are given in figure 4.

Mentions: To obtain divergence dates within the melanogaster subgroup, we used the experimentally estimated mutation rate together with the data set of 36 loci (fig. 5 and supplementary table S4, Supplementary Material online). When all loci were constrained to follow the same inferred topology, we estimated the MRCA of D. melanogaster and D. simulans to be 1.4 (1.1–1.8) Ma, the MRCA of D. erecta and D. yakuba to be 2.7 (2.2–3.3) Ma, and the MRCA of the melanogaster subgroup to be 3.4 (2.7–4.1) Ma. These estimates are very similar to those derived from the 12-genome data set (compare figs. 4 and 5). In general, the mutation rate calibration results in dates that are considerably more recent than the Hawaiian dates (although some of the Hawaiian dates are inferred with extremely low precision; tables 3 and 4).Fig. 5.


Estimating divergence dates and substitution rates in the Drosophila phylogeny.

Obbard DJ, Maclennan J, Kim KW, Rambaut A, O'Grady PM, Jiggins FM - Mol. Biol. Evol. (2012)

A time-scaled phylogeny of the melanogaster subgroup. Two alternatively calibrated phylogenetic trees for the melanogaster subgroup, inferred from 36 loci. Trees were inferred under an uncorrelated log-normal relaxed clock, and the topology presented is the maximum clade-credibility tree with node dates scaled to the posterior median. The 95% highest posterior density intervals (in blue) are shown for each node, and reflect uncertainty both in the rate estimate used to calibrate the tree and sampling error associated with the data. Nodes with less than 100% posterior support are labeled. The alternative time calibrations (mutation rate vs. Hawai’i) are the same as those used in figure 4 (see main text). Note that the inferred topology of the D. simulans complex differs between the two data sets. Species name abbreviations are given in figure 4.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3472498&req=5

mss150-F5: A time-scaled phylogeny of the melanogaster subgroup. Two alternatively calibrated phylogenetic trees for the melanogaster subgroup, inferred from 36 loci. Trees were inferred under an uncorrelated log-normal relaxed clock, and the topology presented is the maximum clade-credibility tree with node dates scaled to the posterior median. The 95% highest posterior density intervals (in blue) are shown for each node, and reflect uncertainty both in the rate estimate used to calibrate the tree and sampling error associated with the data. Nodes with less than 100% posterior support are labeled. The alternative time calibrations (mutation rate vs. Hawai’i) are the same as those used in figure 4 (see main text). Note that the inferred topology of the D. simulans complex differs between the two data sets. Species name abbreviations are given in figure 4.
Mentions: To obtain divergence dates within the melanogaster subgroup, we used the experimentally estimated mutation rate together with the data set of 36 loci (fig. 5 and supplementary table S4, Supplementary Material online). When all loci were constrained to follow the same inferred topology, we estimated the MRCA of D. melanogaster and D. simulans to be 1.4 (1.1–1.8) Ma, the MRCA of D. erecta and D. yakuba to be 2.7 (2.2–3.3) Ma, and the MRCA of the melanogaster subgroup to be 3.4 (2.7–4.1) Ma. These estimates are very similar to those derived from the 12-genome data set (compare figs. 4 and 5). In general, the mutation rate calibration results in dates that are considerably more recent than the Hawaiian dates (although some of the Hawaiian dates are inferred with extremely low precision; tables 3 and 4).Fig. 5.

Bottom Line: Surprisingly, our estimate for the date for the most recent common ancestor of the genus Drosophila based on mutation rate (25-40 Ma) is closer to being compatible with independent fossil-derived dates (20-50 Ma) than are most of the Hawaiian-calibration models and also has smaller uncertainty.Potential problems with the Hawaiian calibration may arise from systematic variation in the molecular clock due to the long generation time of Hawaiian Drosophila compared with other Drosophila and/or uncertainty in linking island formation dates with colonization dates.As either source of error will bias estimates of divergence time, we suggest mutation rate estimates be used until better models are available.

View Article: PubMed Central - PubMed

Affiliation: Institute of Evolutionary Biology, and Centre for Infection Immunity and Evolution, University of Edinburgh, Edinburgh, United Kingdom. darren.obbard@ed.ac.uk

ABSTRACT
An absolute timescale for evolution is essential if we are to associate evolutionary phenomena, such as adaptation or speciation, with potential causes, such as geological activity or climatic change. Timescales in most phylogenetic studies use geologically dated fossils or phylogeographic events as calibration points, but more recently, it has also become possible to use experimentally derived estimates of the mutation rate as a proxy for substitution rates. The large radiation of drosophilid taxa endemic to the Hawaiian islands has provided multiple calibration points for the Drosophila phylogeny, thanks to the "conveyor belt" process by which this archipelago forms and is colonized by species. However, published date estimates for key nodes in the Drosophila phylogeny vary widely, and many are based on simplistic models of colonization and coalescence or on estimates of island age that are not current. In this study, we use new sequence data from seven species of Hawaiian Drosophila to examine a range of explicit coalescent models and estimate substitution rates. We use these rates, along with a published experimentally determined mutation rate, to date key events in drosophilid evolution. Surprisingly, our estimate for the date for the most recent common ancestor of the genus Drosophila based on mutation rate (25-40 Ma) is closer to being compatible with independent fossil-derived dates (20-50 Ma) than are most of the Hawaiian-calibration models and also has smaller uncertainty. We find that Hawaiian-calibrated dates are extremely sensitive to model choice and give rise to point estimates that range between 26 and 192 Ma, depending on the details of the model. Potential problems with the Hawaiian calibration may arise from systematic variation in the molecular clock due to the long generation time of Hawaiian Drosophila compared with other Drosophila and/or uncertainty in linking island formation dates with colonization dates. As either source of error will bias estimates of divergence time, we suggest mutation rate estimates be used until better models are available.

Show MeSH