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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 Drosophila. Two alternative calibrations for a phylogenetic tree linking the 12 species of Drosophila for which complete genomes have been published, inferred from 50 one-to-one orthologs with low average codon usage bias. Trees were inferred under an uncorrelated log-normal relaxed clock, and node dates are scaled to the posterior median. The 95% highest posterior density date intervals (in blue) are shown for well-supported nodes 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 left-hand tree is based on 4-fold codons and was inferred by setting the prior distribution for the substitution rate for third positions to be normally distributed with a mean rate equal to a laboratory estimated neutral mutation rate and a variance that reflects the uncertainty in that estimate. The right-hand tree is based on all codons and was inferred by setting the prior distribution for the substitution rate of third positions to be an offset gamma distribution scaled to match the posterior distribution of this parameter inferred from Hawaiian calibration A1 (see main text). Note that the position of D. willistoni relative to the root differs from most previous studies. Given inferred fossil dates for Drosophila and Diptera as a whole, the timescale from Model A1 appears implausibly old (see Discussion). Species abbreviations: Dwil, D. willistoni; Dvir, D. virilis; D moj, D. mojavensis; Dgri, D. grimshawi; Dpse, D. pseudoobscura; Dper, D. persimilis; Dana, D. annanassae; Dmel, D. melanogaster; Dsec, D. sechellia; Dsim, D. simulans; Dere, D. erecta; and Dyak, D yakuba.
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mss150-F4: A time-scaled phylogeny of Drosophila. Two alternative calibrations for a phylogenetic tree linking the 12 species of Drosophila for which complete genomes have been published, inferred from 50 one-to-one orthologs with low average codon usage bias. Trees were inferred under an uncorrelated log-normal relaxed clock, and node dates are scaled to the posterior median. The 95% highest posterior density date intervals (in blue) are shown for well-supported nodes 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 left-hand tree is based on 4-fold codons and was inferred by setting the prior distribution for the substitution rate for third positions to be normally distributed with a mean rate equal to a laboratory estimated neutral mutation rate and a variance that reflects the uncertainty in that estimate. The right-hand tree is based on all codons and was inferred by setting the prior distribution for the substitution rate of third positions to be an offset gamma distribution scaled to match the posterior distribution of this parameter inferred from Hawaiian calibration A1 (see main text). Note that the position of D. willistoni relative to the root differs from most previous studies. Given inferred fossil dates for Drosophila and Diptera as a whole, the timescale from Model A1 appears implausibly old (see Discussion). Species abbreviations: Dwil, D. willistoni; Dvir, D. virilis; D moj, D. mojavensis; Dgri, D. grimshawi; Dpse, D. pseudoobscura; Dper, D. persimilis; Dana, D. annanassae; Dmel, D. melanogaster; Dsec, D. sechellia; Dsim, D. simulans; Dere, D. erecta; and Dyak, D yakuba.

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)

A time-scaled phylogeny of Drosophila. Two alternative calibrations for a phylogenetic tree linking the 12 species of Drosophila for which complete genomes have been published, inferred from 50 one-to-one orthologs with low average codon usage bias. Trees were inferred under an uncorrelated log-normal relaxed clock, and node dates are scaled to the posterior median. The 95% highest posterior density date intervals (in blue) are shown for well-supported nodes 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 left-hand tree is based on 4-fold codons and was inferred by setting the prior distribution for the substitution rate for third positions to be normally distributed with a mean rate equal to a laboratory estimated neutral mutation rate and a variance that reflects the uncertainty in that estimate. The right-hand tree is based on all codons and was inferred by setting the prior distribution for the substitution rate of third positions to be an offset gamma distribution scaled to match the posterior distribution of this parameter inferred from Hawaiian calibration A1 (see main text). Note that the position of D. willistoni relative to the root differs from most previous studies. Given inferred fossil dates for Drosophila and Diptera as a whole, the timescale from Model A1 appears implausibly old (see Discussion). Species abbreviations: Dwil, D. willistoni; Dvir, D. virilis; D moj, D. mojavensis; Dgri, D. grimshawi; Dpse, D. pseudoobscura; Dper, D. persimilis; Dana, D. annanassae; Dmel, D. melanogaster; Dsec, D. sechellia; Dsim, D. simulans; Dere, D. erecta; and Dyak, D yakuba.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

mss150-F4: A time-scaled phylogeny of Drosophila. Two alternative calibrations for a phylogenetic tree linking the 12 species of Drosophila for which complete genomes have been published, inferred from 50 one-to-one orthologs with low average codon usage bias. Trees were inferred under an uncorrelated log-normal relaxed clock, and node dates are scaled to the posterior median. The 95% highest posterior density date intervals (in blue) are shown for well-supported nodes 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 left-hand tree is based on 4-fold codons and was inferred by setting the prior distribution for the substitution rate for third positions to be normally distributed with a mean rate equal to a laboratory estimated neutral mutation rate and a variance that reflects the uncertainty in that estimate. The right-hand tree is based on all codons and was inferred by setting the prior distribution for the substitution rate of third positions to be an offset gamma distribution scaled to match the posterior distribution of this parameter inferred from Hawaiian calibration A1 (see main text). Note that the position of D. willistoni relative to the root differs from most previous studies. Given inferred fossil dates for Drosophila and Diptera as a whole, the timescale from Model A1 appears implausibly old (see Discussion). Species abbreviations: Dwil, D. willistoni; Dvir, D. virilis; D moj, D. mojavensis; Dgri, D. grimshawi; Dpse, D. pseudoobscura; Dper, D. persimilis; Dana, D. annanassae; Dmel, D. melanogaster; Dsec, D. sechellia; Dsim, D. simulans; Dere, D. erecta; and Dyak, D yakuba.
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