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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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Posterior distributions for key node dates under different models. Posterior distributions (shaded curves) and 95% highest posterior density intervals (solid lines) for the MRCA of the subgenera Drosophila and Sophophora (panel a), and the MRCA of Drosophila melanogaster and D. simulans (panel b), under five different models. Model "Mu" (yellow) uses an experimental estimate of the mutation rate, models "A1" and "A2" (green) use a Hawaiian calibration with small effective population size (i.e., instant coalescence), and models "C1" and "C2" (red) use a Hawaiian calibration with coalescence in an effective population size of Ne = 106 (see main text for details).
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mss150-F3: Posterior distributions for key node dates under different models. Posterior distributions (shaded curves) and 95% highest posterior density intervals (solid lines) for the MRCA of the subgenera Drosophila and Sophophora (panel a), and the MRCA of Drosophila melanogaster and D. simulans (panel b), under five different models. Model "Mu" (yellow) uses an experimental estimate of the mutation rate, models "A1" and "A2" (green) use a Hawaiian calibration with small effective population size (i.e., instant coalescence), and models "C1" and "C2" (red) use a Hawaiian calibration with coalescence in an effective population size of Ne = 106 (see main text for details).

Mentions: The substitution rates at third-codon positions estimated using Hawaiian Drosophila allow us to estimate divergence dates of the 12 species of Drosophila with published genomes (table 3). In these analyses, we estimated gene coalescent dates, so these will be older than speciation dates. Using 50 genes with low codon-usage bias from the published Drosophila genomes and assuming the colonization-on-emergence model for Hawai’i (and that Hawaiian flies have extremely small population sizes: model A1), we find the posterior means for the MRCA of D. melanogaster and D. simulans to be 4.2 (1.8–7.1) Ma (fig. 3 and table 3; model A1). This increases to 6.3 (4.3–8.6) Ma if Hawaiian population sizes are large (fig. 3 and table 3; model C1). The corresponding dates for the MRCA of the subgenera Drosophila and Sophophora are 103 (47–170) Ma and 154 (120–193) Ma (fig. 3 and table 3). Dates of the other main divergences are listed in table 3, and a tree calibrated with model A1 is illustrated in figure 4.Fig. 3.


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)

Posterior distributions for key node dates under different models. Posterior distributions (shaded curves) and 95% highest posterior density intervals (solid lines) for the MRCA of the subgenera Drosophila and Sophophora (panel a), and the MRCA of Drosophila melanogaster and D. simulans (panel b), under five different models. Model "Mu" (yellow) uses an experimental estimate of the mutation rate, models "A1" and "A2" (green) use a Hawaiian calibration with small effective population size (i.e., instant coalescence), and models "C1" and "C2" (red) use a Hawaiian calibration with coalescence in an effective population size of Ne = 106 (see main text for details).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

mss150-F3: Posterior distributions for key node dates under different models. Posterior distributions (shaded curves) and 95% highest posterior density intervals (solid lines) for the MRCA of the subgenera Drosophila and Sophophora (panel a), and the MRCA of Drosophila melanogaster and D. simulans (panel b), under five different models. Model "Mu" (yellow) uses an experimental estimate of the mutation rate, models "A1" and "A2" (green) use a Hawaiian calibration with small effective population size (i.e., instant coalescence), and models "C1" and "C2" (red) use a Hawaiian calibration with coalescence in an effective population size of Ne = 106 (see main text for details).
Mentions: The substitution rates at third-codon positions estimated using Hawaiian Drosophila allow us to estimate divergence dates of the 12 species of Drosophila with published genomes (table 3). In these analyses, we estimated gene coalescent dates, so these will be older than speciation dates. Using 50 genes with low codon-usage bias from the published Drosophila genomes and assuming the colonization-on-emergence model for Hawai’i (and that Hawaiian flies have extremely small population sizes: model A1), we find the posterior means for the MRCA of D. melanogaster and D. simulans to be 4.2 (1.8–7.1) Ma (fig. 3 and table 3; model A1). This increases to 6.3 (4.3–8.6) Ma if Hawaiian population sizes are large (fig. 3 and table 3; model C1). The corresponding dates for the MRCA of the subgenera Drosophila and Sophophora are 103 (47–170) Ma and 154 (120–193) Ma (fig. 3 and table 3). Dates of the other main divergences are listed in table 3, and a tree calibrated with model A1 is illustrated in figure 4.Fig. 3.

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