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Alexandra Gavryushkina, Tracy A. Heath, Daniel T. The total-evidence approach to divergence time dating uses molecular and morphological data from extant and fossil species to infer phylogenetic relationships, species divergence times, and macroevolutionary parameters in a single coherent framework. Current model-based implementations of this approach lack an appropriate model for the tree describing the diversification and fossilization process and can produce estimates that lead to erroneous conclusions. We address this shortcoming by providing a total-evidence method implemented in a Bayesian framework. This approach uses a mechanistic tree prior to describe the underlying diversification process that generated the tree of extant and fossil taxa.

Some features of the site may not work correctly. DOI: Zhang and T. Stadler and S. Klopfstein and Tracy A. Heath and F. ZhangT. Bayesian total-evidence dating involves the simultaneous analysis of morphological data from the fossil record and morphological and sequence data from recent organisms, and it accommodates the uncertainty in the placement of fossils while dating the phylogenetic tree.

Due to the flexibility of the Bayesian approach, total-evidence dating can also incorporate additional sources of information.

View. Save to Library. Create Alert. Launch Research Feed. Share This Paper. A-Rong Luo, D. Ho Arong Luo, D. Ho Systematic biology Alexandra Gavryushkina, Tracy A. Heath, A. Drummond Systematic biology Figures, Tables, and Topics from this paper.

Figures and Tables. Fields of Study. Citation Type. Has. More Filters. Highly Influenced. However, divergence time estimates are likely to be less robust under more realistic settings, and additional simulations exploring the performance of FBD-based inferences in these cases would be valuable.

In particular, when the fossil sampling is stratigraphic and the fossils are poorly preserved, as is the rule for empirical data sets, the FBD prior might have considerable impact on the divergence-time estimates see Hymenoptera analysis below so that it becomes important to model the fossilization and sampling processes appropriately.

Furthermore, rate variation across the tree can cause both loss of accuracy and problems with inference biases, especially if the rate variation is not properly addressed by a relaxed-clock model.

Finally, under realistic data-poor scenarios, there may also be problems associated with overparameterization overfitting. To investigate the performance of the FBD model in an empirical setting, we reanalyzed a data set on the early radiation of Hymenoptera Ronquist et al. As in Ronquist et al. Parameters of the substitution models and among-site rate variation were unlinked across partitions, and partition-specific rate multipliers were used to account for variation of evolutionary rates across partitions.

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Specifically, a flat Dirichlet prior was used for the relative partition rate multipliers the partition rate multiplier times the proportion of sites in that partition. The relative partition rate multipliers were constrained to sum to 1. Notes: The data include 60 extant and 45 fossil hymenopteran taxa and 8 outgroups.

The estimated fossil ages are given as the midpoint and the time interval of the corresponding geographical stratum. The bounds of the stratum were used as parameters to a uniform prior on the fossil age in the total-evidence dating analyses. In contrast to the previous analysis Ronquist et al. The fossil ages were assigned uniform prior distributions with ranges corresponding to the age ranges of the respective strata Table 3.

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We used both the uniform tree prior Ronquist et al. For the FBD prior, we first assumed constant birth and death rates. For random sampling of extant taxa, the fossil sampling rate was assumed to be constant through time, whereas for diversified sampling, fossil sampling was constant nonzero before the cutoff time x c u t and zero thereafter. The value of x c u t was adjusted during the MCMC so that the cutoff was just after the youngest internal node and the youngest fossil in the FBD tree.

Because all fossils included in our data set were sampled from the Mesozoic Triassic, Jurassic, and Cretaceous and none from younger or older strata, we also used piecewise-constant rates in the FBD prior. For random sampling, the two rate-shifting times were fixed to Ma separating the Permian and the Triassic and 66 Ma separating the Cretaceous and the Paleocene. The birth, death, and sampling rates shift at the same time, so that we inferred three rates each for speciation, extinction, and fossil sampling, respectively.

For diversified sampling, we only used one rate-shifting time for birth and death rates at Ma, because the cutoff time x c u tthe additional shifting time for the fossil sampling rate is very close to or slightly older than 66 Ma see results below. To infer separate birth and death rates after time x c u t would lead to very uncertain estimates, because that time interval by definition consists of single lineages leading to each extant taxon.

The fossil sampling rate after time x c u t is zero by definition. Under this approach, we thus inferred only two rates each for speciation, extinction, and fossil sampling, respectively. We used an Exponential prior for net diversification and a Beta 1, 1 prior for turnover r and fossil sampling proportion s. The sampling probability or sampling proportion for the extant taxa was set to 0.

The holometabolan constraint are enforced to root the tree properly, as the clock model itself is not sufficient to provide the correct rooting for this data Ronquist et al. These settings were chosen by comparing the age of the oldest insect fossil with the root age estimation from uncalibrated clock analyses as discussed in Ronquist et al.

We performed sensitivity analyses to determine the robustness of our estimates to changes in the priors on root age and clock rate see results below. Ronquist et al. To explore whether these differences would be affected by replacing the simplistic uniform tree prior with the more realistic FBD model, we used two relaxed-clock models: the autocorrelated lognormal rates TK02 model Thorne and Kishino with an Exponential 0.

We executed four independent runs in parallel for each analysis, each consisting of four Metropolis-coupled MCMC chains one cold, three heated. The length of each run was initially set to 50 million iterations, but enlarged to million for the piecewise-constant FBD priors to achieve better convergence.

Convergence was assessed by the MrBayes built-in diagnostics: the average standard deviation of split frequencies ASDSF; target value 0.

We also examined trace plots of likelihoods and parameter samples. The MCMC samples from the four parallel runs were then combined.

We first checked the induced tree prior by running the MCMC without data by setting the sequence and morphology data likelihood to 1under the model priors described above with fixed clock rate 0. We also explored a more relaxed Exponential 1 and a more constrained prior Exponential on net diversification d.

It turns out that the induced divergence time priors vary widely under different prior assumptions Table 4. Under the uniform tree model, the mean of the root age in the induced prior is much older thanthe expectation of the root age prior.

Under the FBD model, the induced divergence times vary widely: they are sensitive both to the model details and to the prior for d. In both these cases, the induced prior favors young trees, thus apparently increasing the probability of fossils being ancestors. This phenomenon seems to be coupled with a high net diversification rate in the induced prior, as the expected proportion of ancestral fossils decreased dramatically when the prior was focused on small values of d.

Induced prior distribution on root age t m r c a and age of Hymenoptera. For the full empirical analysis Table 5the intermediate prior on d was used. The full empirical analyses with the sequence and morphology data only used the intermediate Exponential prior on d.

The posterior estimates of root age and age of Hymenoptera in these analyses are summarized in Table 5 for a range of analyses under two kinds of relaxed-clock models IGR and TK02 and two kinds of tree priors uniform and FBD. In the case of the FBD prior, we assumed that sampling of extant taxa was either random or diversified. Posterior distribution on root age t m r c a and age of Hymenoptera. The same pattern was observed in Ronquist et al. The reason for the difference is apparently that the IGR model allows occasional extreme rate changes on adjacent branches, which makes it easier for this model to accommodate the obviously rapid rate shifts close to the root of the hymenopteran tree.

The autocorrelated TK02 model has a rate smoothing effect on adjacent branches, which tends to produce longer trees. As discussed in Ronquist et al. Therefore, we will focus on the IGR model in the following.

Under these conditions, the modeling of the sampling process has a dramatic impact on the inferred divergence times. When extant taxa are assumed to have been sampled at random, the inferred age of Hymenoptera is older than under the uniform prior Ma versus Ma and has a wider HPD interval.

When changing from random to diversified sampling, the age of Hymenoptera becomes younger Manow lying in the Permian. Compared with the random sampling prior, the diversified sampling assumption has the effect of stretching more recent and shrinking more ancestral branches, resulting in younger age estimates near the root of the tree e.

dating, total-evidence dating can easily be applied to rich sets of fossils without fixing any nodes in the tree. It relies on the morphological similarity between a fossil and the reconstructed ancestors in the extant tree in assessing the likely length of any extinct side branch on which the fossil sits. Thus, total-evidence dating explicitly. Jun 15, The total-evidence approach to divergence-time dating uses molecular and morphological data from extant and fossil species to infer phylogenetic relationships, species divergence times, and macroevolutionary parameters in a single coherent framework. Current model-based implementations of this approach lack an appropriate model for the tree describing the diversification . Aug 01, The total-evidence approach to divergence time dating uses molecular and morphological data from extant and fossil species to infer phylogenetic relationships, species divergence times, and macroevolutionary parameters in a single coherent multicoingames.com by:

Finally, we applied the piecewise-constant FBD priors to account for variable rates of fossil sampling. We allowed net diversification d and turnover r to shift at the same time as s at Ma. For random sampling, rand s were allowed to change again at 66 Ma; for diversified sampling, only s changed to zero at the cutoff time of about 70 Ma.

Consequently, all fossils are included in the second time interval. The estimate of Ma is just at the geological time separating the Triassic and Permian. It is slightly older than the age of the oldest hymenopteran fossils, Triassoxyela and Asioxyelawhich are dated to - Ma Fig.

Majority-rule consensus tree, a including all fossils and b including only extant taxa, from total-evidence dating analysis under the piecewise-constant FBD prior with random sampling and under the IGR relaxed-clock model. Node bars indicate HPD intervals of estimated divergence times cf.

Majority-rule consensus tree, a including all fossils and b including only extant taxa, from total-evidence dating analysis under the piecewise-constant FBD prior with diversified sampling and under the IGR relaxed-clock model. We examined the impact of the priors on root age and clock rate, and that of the assumed sampling fraction. In the previous analyses, the prior for the root age was an offset exponential distribution with mean Ma and offset Ma. We halved and doubled the distance from the mean to the minimum to obtain more and less restrictive priors.

The more restrictive root-age prior had an expectation of Ma, and the less restrictive prior an expectation of Ma. The calibration prior for the holometabolan age was also changed so that the expectation was the same as for the root.

The results show that the impact of the root calibration on the divergence-time estimates is rather small Fig. We also used a smaller 0. As shown in Figure 8 b, the posterior age estimates are not sensitive to the variance parameter in the clock-rate prior. The sampling probability of extant taxa was fixed to 0.

Oct 07, Bayesian molecular dating is widely used to study evolutionary timescales. This procedure usually involves phylogenetic analysis of nucleotide sequence data, with fossil-based calibrations applied as age constraints on internal nodes of the tree. An alternative approach is Bayesian total-evidence dating, which involves the joint analysis of molecular data from present-day taxa and Cited by: 3. The total-evidence analysis also shows that four of the seven Hymenoptera calibration points used in node dating are likely to be based on erroneous or doubtful assumptions about the fossil placement. compare total-evidence dating to node dating, and it thus remains unclear how the two approaches perform on the same data set. In this article, we illustrate total-evidence dating and its potential using the early radiation of the Hymenoptera (wasps, ants, bees, and relatives) as a test case. The Hymenoptera are probably the sister group of.

To assess the sensitivity of the results to changes in the assumed sampling fraction, we enlarged and reduced it by an order of magnitude to 0. For random sampling of extant taxa, increasing the sampling probability decreases the posterior ages slightly, whereas it increases the posterior ages considerably for diversified sampling Fig.

Eventually, the age estimates will approach those under complete sampling. These results contrast with our simulations, in which the sampling probability had only a minor effect on the age estimates Table 2Figs. However, the sampling fractions examined in the empirical analyses are several orders of magnitude smaller than those studied in the simulations. The only exception involves the piecewise-constant FBD prior with random sampling under the IGR model, where approximately one-third of the fossils were estimated to be ancestral.

This is the same model where the induced prior puts a high probability on fossils being ancestors Table 4. The consensus trees including all fossils are partially unresolved, regardless of the tree prior Figs.

However, when the fossils are excluded from the sampled trees to compute the consensus, the consensus trees are fully resolved.

Thus, the polytomies are entirely due to uncertainty in the placement of the fossils see also Ronquist et al. This is especially true for the topology parameter. In this article, we examined the importance of incorporating information about speciation, extinction, and sampling of fossil and extant taxa in total-evidence dating.

Clearly, these processes influence our prior beliefs concerning the shape of the tree and the placement of fossils therein.

For instance, if the fossilization rate is high and the extinction rate is low, we expect most fossils to sit on branches leading to extant taxa.

Conversely, if the fossilization rate is low and the extinction rate high, most fossils are instead likely to represent extinct side branches. The sampling of extant taxa also affects our prior expectations concerning the structure of the tree. If extant taxa are chosen randomly instead, the branching events should be more evenly distributed over time.

Our expectations concerning the structure of the tree are also influenced by differences over time in speciation, extinction, and fossilization rates. The proportion of fossils included from a particular time horizon is strongly affected by decisions about fossil sampling, for example, which sites to explore in the search for fossils, and which fossil specimens to select for analysis.

If the fossilization rate itself varies over time, this will cause some strata to be richer in fossils than others and thus better represented in the tree.

Similarly, variations in speciation and extinction rates over time will cause the density of branching events in the observed tree to vary over time. Together, all these phenomena affect the shape and structure of the tree and therefore potentially influence the estimation of divergence times. However, the tree priors used previously in total-evidence dating e.

To explore their influence in total-evidence dating, the recent FBD process is an obvious choice Stadler a ; Heath et al.

The formulation of the FBD model allows us to examine the effects of speciation, extinction and fossilization processes, and to accommodate different sampling strategies. Even though birth-death models like the FBD process have their limitations, they provide a starting point in the search of more realistic tree priors.

In comparing the performance of the FBD model to previous models used in total-evidence dating, it might first seem like an obvious choice to use Bayes-factor tests, a standard Bayesian approach to model choice. Unfortunately, Bayes factors have severe limitations in this context.

First, the models have different parameters and different dimensionality, which means that the outcome of a Bayes-factor test is decided to a large extent by the priors and not necessarily by model performance.

The sensitivity of Bayes-factor tests to priors is illustrated well by the apparent contradictions that may arise in the testing of topology hypotheses Bergsten et al. Second, even if it were possible to find suitable priors for appropriate Bayes-factor tests, it is difficult to estimate the Bayes factors accurately enough to allow reliable comparison of the complex models used in total-evidence dating.

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For instance, Ronquist et al. Despite considerable computational effort, however, the variance in the estimated marginal likelihoods between independent runs of the algorithm was larger than the differences between the models, making it impossible to distinguish them.

A pragmatic approach in these situations is to compare models with respect to their ability to account for the data. The comparison is simplified if we are comparing models defined on the same or similar parameter spaces, which is arguably the case here. At first sight, the FBD model might seem fundamentally different in that it allows fossils to represent both side branches and ancestors of other taxa in the tree, while previous models considered all fossils to be side branches tip fossils.

However, although ancestral fossils appear distinct from tip fossils, it is possible to consider them simply as the boundary case of tip fossils, when the length of the side branch goes to zero.

In fact, we take this approach in our computational machinery, where ancestral fossils in the FBD model sit on side branches with length zero. Viewed in this way, the FBD model just specifies a different prior probability distribution on the same tree space used by the simpler models. Given this similarity between the models, it is relatively straightforward to compare their ability to account for the data.

At one extreme, the data could be so informative that they were able to pull the simpler tree-model priors toward the same posterior obtained under the FBD model. If so, there would only be minor differences in divergence-time estimates between models. In other words, the FBD model would not add much to the analysis except that we might be able to estimate some additional parameters of interest, like the fossilization rate. At the other extreme, the data might carry very little information about the shape of the tree, in which case we would essentially retrieve the prior under each model.

The interesting case occurs when the data fit the FBD model better, but are not informative enough to modify the simple tree model priors toward the posterior observed under the FBD model.

This may result in significant improvements in divergence-time estimation under the FBD model. Our results suggest that this is indeed the case we are facing. In particular, the fact that we observe informative posterior estimates of FBD model parameters indicates that the model is picking up relevant signal in the data, and thus fits the data better than previous tree priors e.

It also suggests that the FBD models examined here are not overparameterized; if they were, the posterior distributions would be more similar to the induced prior distributions.

Our results also show that the specific details of the FBD prior can have a strong influence on divergence-time estimates. Notably, it seems that the most important factor is how the sampling of extant taxa is modeled Table 5.

Under the assumption of random sampling, the FBD model gives results that are older than those of the uniform model. When we accommodate the fact that the sample is diversified, however, the results change substantially.

Under the IGR model, which appears to be the better of the two relaxed-clock models examined here, the estimate of the crown age of Hymenoptera shifts from around Ma to Ma when diversified sampling is accounted for.

Bayesian total-evidence dating involves the simultaneous analysis of morphological data from the fossil record and morphological and sequence data from recent organisms, and it accommodates the uncertainty in the placement of fossils while dating the phylogenetic tree. Due to the flexibility of the Bayesian approach, total-evidence dating can also incorporate additional sources of information.

A similar shift toward younger ages also occurs under the TK02 relaxed-clock model. Beyond the sampling issue, our results confirm that the relaxed-clock model significantly affects the divergence-time estimates. Such rates are not expected to shift very rapidly, and TK02 therefore has difficulties accommodating the apparently rapid shifts in evolutionary rates close to the root of the hymenopteran tree Ronquist et al.

This results in longer branches close to the root of the hymenopteran subtree, and is associated with substantially older divergence time estimates for the crown age of Hymenoptera. IGRfurther strengthening the conclusion that the model does not fit the data well. It is interesting to note that the result under the piecewise-constant FBD model with random sampling and IGR rates suggests that one third of the fossils are ancestors Table 5.

If one third of the fossils were indeed ancestors of extant lineages, then the diversity of Hymenoptera must have been very low during their early diversification and a large fraction of the ancient lineages must have left current descendants, both of which seem unlikely.

The high proportion of inferred ancestors under this particular model is apparently due to a combination of two factors.

First, the model puts considerably more prior probability on fossils being ancestral than any of the other models Table 4.

Second, the scarcity of character data for the fossils is not enough to pull the posterior away from this prior.

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Thus, it is not surprising that the inferred proportion of ancestral fossils is influenced to a large extent by the tree prior. The previous total-evidence dating analysis of the early radiation of Hymenoptera suggested that the extant taxa started to diversify about Ma, almost immediately after splitting off from the remainder of Holometabola in the Carboniferous Ronquist et al.

In contrast, paleontological reconstructions indicated a time lag of at least 75 myr from the origin of the order in the Carboniferous to the first separation of extant lineages in the Triassic Rasnitsyn ; The results under the diversified sampling FBD model Fig.

For instance, Rasnitsyn suggested that crown Tenthredinoidea date back to Ma Ma in our analysisPamphilioidea to Ma Ma in our analysisand Apocrita to Ma Ma in our analysis. Given the obvious gaps in the early fossil record of hymenopterans, with some lineages having sister groups that are absent for myr or more Rasnitsynthe Ma estimate may appear surprisingly close to the age of the oldest known hymenopteran fossils. Is it really plausible that hymenopterans started to diversify only just before we observe the first evidence of their presence in the fossil record?

There is actually some reason to suspect that the age estimates obtained under the diversified FBD process may be biased toward the recent because of imperfections in the model.

Consider that, for mathematical convenience, our model of diversified sampling assumes that the investigator is able to find the sample representing the maximum amount of phylogenetic diversity given the chosen number of tips.

In practice, however, the investigator is likely to miss a few of the oldest splits in the tree, and instead include a few splits that are younger than the ideal cutoff value, perhaps much younger. To investigate whether such a bias could influence our analyses, we tried to reduce the effect by eliminating the speciation-time outliers from the tree. Specifically, we inferred an uncalibrated relaxed-clock tree of extant taxa under the uniform tree prior and IGR model.

The priors for the root age and the substitution rate were unchanged. We first removed nine taxa representing extremely young splits from the tree.

In the latter case, almost all splits expected to be younger than the youngest fossil 83 Ma were eliminated. We then repeated the dating analysis under the piecewise-constant FBD model with diversified sampling. The estimated dates were very similar to those of the original analysis of the complete tree, especially for the deepest splits in the tree Fig.

This indicates that the biasing effect of the strict maximum-diversity assumption is negligible, at least for the older divergence times in the tree. Nevertheless, this may not always be the case, and relaxing the maximum-diversity assumption would appear to be an important area for further improvement of total-evidence dating under the FBD prior; indeed, for any type of dating under a birth-death prior assuming diversified sampling.

Majority-rule consensus tree of extant taxa from total-evidence dating analysis under the IGR model and the piecewise-constant FBD prior with diversified sampling. The tree above has 9 taxa removed from the original data, whereas the tree below has 20 taxa removed, to eliminate young splits that might be inconsistent with the diversified sampling model.

A recent phylogenomic study of insects Misof et al. However, despite the impressive amounts of sequence data, the divergence-time estimates from this phylogenomic study are not necessarily more accurate, and cannot be taken as reliable confirmation of our results. This is because sequence data primarily inform the estimation of evolutionary branch lengths, while the major sources of dating uncertainty stem from the placement of calibration fossils and from the modeling of processes such as fossilization, sampling of recent and fossil taxa, and rate variation across the tree.

Although the diversified FBD analysis presented here addresses all of these sources of uncertainty, the phylogenomic study was based on traditional node dating with narrow calibration priors Misof et al. In addition, the dating of the hymenopteran part of the tree is limited by the sparse sampling of lineages from this order.

For instance, no member of Xyelidae was included in the analysis, even though they are the sister group of all other extant hymenopteran lineages. To further improve dating of the early hymenopteran radiation, it is important to focus on the major remaining sources of uncertainty, and address them in a total-evidence dating framework. More sequence data can help expand the number of extant terminals, increase the precision of evolutionary branch-length estimates, and possibly improve the modeling of speciation, extinction, and rate variation across the tree.

However, much of the dating uncertainty will remain unless we become better at incorporating the information from the fossil record. For instance, a better understanding of morphological evolution in Hymenoptera will help place the fossils with more certainty in the phylogeny of extant taxa. Most importantly, increasing the number of fossils included in the analysis can help elucidate the speciation, extinction, and fossil sampling processes, all of which can contribute strongly to divergence-time estimation.

Our study has only scratched the surface with respect to fossils that could be informative about the early evolution of Hymenoptera, and the same could be said for many other dating studies. Some of the fossils that were not analyzed by us are poorly preserved, but we have shown earlier that even very incomplete fossils can contribute to the precision of divergence-time estimates in a total-evidence dating analysis Ronquist et al. Another possibility for improvement is to incorporate more stratigraphic information in the analysis, such as data on the variation in fossil sampling intensities over time.

For example, the absence of insects that clearly belong to the hymenopteran crown group from strata older than the Triassic is potentially informative about the age of the crown group, yet we have not addressed this simple fact appropriately even in the most sophisticated models we explored here. To do so, we would have had to extend the sampling of fossils to the entire Holometabola and to older strata. With this study, we have shown that expanding the total-evidence analysis to include information about speciation, extinction, fossilization, and sampling can result in further improvements.

In particular, modeling the sampling strategy of extant taxa in a realistic way appears to have a substantial impact on divergence-time estimates. Diversified sampling, which arguably is the rule rather than the exception in dating studies, results in trees with long terminal branches and most speciation times clustered close to the root of the tree. Such trees have low prior probability under most tree priors, including FBD models assuming complete or random sampling.

This is well illustrated by our analyses of the early hymenopteran radiation, where accounting for diversified sampling of extant taxa results in a major shift in the age estimate of Hymenoptera toward more recent times. Interestingly, the new estimates that accommodate the sampling bias remove much of the misfit observed previously between molecular divergence-time estimates and the fossil record.

The diversity-sampled piecewise-constant FBD model on which these results are based provides the best a priori fit to our data, at least among the models examined here, and it shows all the signs of a well-behaved model in inference, including the ability to pick up relevant signal that is not detected by simpler models. Future studies will have to show to what extent this model is equally successful also in other dating analyses. Taken together, this study and that of Ronquist et al.

Neither of them is unique to total-evidence dating; both are equally relevant to node dating.

Bayesian total-evidence dating involves the simultaneous analysis of morphological data from the fossil record and morphological and sequence data from recent organisms, and it accommodates the uncertainty in the placement of fossils while dating the phylogenetic tree. Due to the flexibility of the Bayesian approach, total-evidence dating can Cited by: The total-evidence approach to divergence-time dating uses molecular and morphological data from extant and fossil species to infer phylogenetic relationships, species divergence times, and macroevolutionary parameters in a single coherent framework. Current model-based implementations of this approach lack an appropriate model for the tree describing the diversification and fossilization. This approach to dating can be referred to as tip-dating, combined-evidence or total-evidence dating (Ronquist et al. ; Zhang et al. ; Gavryushkina et al. ) (although it does not technically use all the evidence we could potentially incorporate into our dating analyses).

In our analyses, both these errors have tended to push the estimate of the crown age of Hymenoptera toward older time intervals. However, they could also bias age estimates in the other direction. For instance, even in our analyses, the failure to account for diversified sampling apparently causes many of the younger splits in the hymenopteran tree to be estimated too young compare Figs. Because of these complexities and the many other sources of error involved in divergence-time estimation, we refrain from speculation on how imperfect relaxed-clock models and failure to model sampling biases might have affected previous dating studies.

Regardless of potential problems with past analyses, it is clear that total-evidence dating provides an ideal platform for going forward in exploring and further improving the models used for Bayesian divergence-time estimation. The processes of speciation, extinction, and fossilization are the real-world evolutionary mechanisms that affect present-day diversity and the observation of lineages as fossils through time.

Thus, incorporating parameters that account for these processes is obviously important for epistemological reasons.

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From an empirical perspective, perhaps the most important ct of the total-evidence approach is that it provides a common analytical platform, helping neontologists and paleontologists to include more information from the fossil record in future dating studies.

The FBD priors are implemented in version 3. The commands are listed in the Appendix and in Zhang We are indebted to Alex Rasnitsyn for invaluable help with information on the fossil record of Hymenoptera and to Nicolas Lartillot for detailed discussion on modeling issues related to this article.

We sincerely thank Frank Anderson, Thomas Near, Alex Pyron, and an anonymous reviewer for constructive criticism of the original article and excellent suggestions for improvement. National Center for Biotechnology InformationU.

Syst Biol. Published online Oct Tracy A. Author information Article notes Copyright and License information Disclaimer. This article has been cited by other articles in PMC.

Abstract Bayesian total-evidence dating involves the simultaneous analysis of morphological data from the fossil record and morphological and sequence data from recent organisms, and it accommodates the uncertainty in the placement of fossils while dating the phylogenetic tree.

Keywords: Bayesian phylogenetic inference, birth-death process, MCMC, relaxed clock, total-evidence dating, tree prior. Open in a separate window. Figure 1. Figure 2.

# Total evidence dating

Figure 3. Table 1. Coverage Prob.

For alignments generated from trees in strategy 2 random sampling of extant taxathe following prior parameters were used: Random sampling of extant taxa with probability 0.

Figure 4. Figure 5. Table 2. T otal-evidence dating of hymenoptera To investigate the performance of the FBD model in an empirical setting, we reanalyzed a data set on the early radiation of Hymenoptera Ronquist et al. Table 3. Summary of Hymenoptera data. Taxa Time Ma Number Fossils2 Results We first checked the induced tree prior by running the MCMC without data by setting the sequence and morphology data likelihood to 1under the model priors described above with fixed clock rate 0.

Table 4. Table 5. Figure 6. Figure 7. Figure 8. D iscussion Modeling Fossilization and Sampling In this article, we examined the importance of incorporating information about speciation, extinction, and sampling of fossil and extant taxa in total-evidence dating. Implications for the Age of Hymenoptera The previous total-evidence dating analysis of the early radiation of Hymenoptera suggested that the extant taxa started to diversify about Ma, almost immediately after splitting off from the remainder of Holometabola in the Carboniferous Ronquist et al.

Figure 9.