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Table of contents
- Materials and Methods
- Or Not 2B Comics : Awkward Moments in Animal Dating 2
- Let’s flip the script on DTF
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We did not attempt to accommodate the uncertainty in the dating of the fossil beds, since this is likely to be negligible compared to the other sources of error in the analysis. To find an appropriate prior for the substitution rate the base rate of the clock in the calibrated analyses, we first ran uncalibrated strict-clock analyses with three different priors on tree height, namely exponential distributions with means of 0.
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The posterior distribution on tree height was almost invariant across these prior settings, with the median ranging from 0. In deriving the base rate of the clock, we used the posterior distribution from the Exp 1. The outgroups in our analysis included a broad sample across Holometabola and some hemimetabolous Neoptera; therefore, reasonable estimates of the minimum and mean age of the tree might be the ages of Katerinka , the oldest fossil neopteran Prokop and Nel , and Rhyniognatha , the oldest insect Engel and Grimaldi To assess the sensitivity of node age estimates to calibration settings, we also used a more restrictive and a less restrictive prior on the root calibration A and the Holometabola calibration B.
To obtain these priors, we doubled and halved the respective intervals between the minimum and mean of the offset-exponential distributions Table 3. To validate the implementation of the relaxed-clock models, the tree prior for total-evidence dating, and other aspects of the Bayesian MCMC machinery, we ran a number of tests that are available in the public SVN repository of MrBayes https: The tests included runs on simulated data to verify that we could retrieve parameter values correctly, and runs without data to check that we obtained reasonable samples from the prior distribution.
We show an example from one of the latter tests here Fig. In this test, we used a data set consisting of either four extant terminals Fig. In both cases, we could retrieve the tree probabilities Fig. Extensive simulations were used to validate the MCMC algorithms. Here we show a simple example: The age of the tree root was fixed to 1. Both tree probabilities a and c and branch length distributions b and d; only part shown in d closely match analytically derived values. The results shown are for the strict-clock model; similar results were obtained under all relaxed-clock models.
To generate samples from the posteriors, we used four independent runs of four parallel chains each MrBayes command blocks for all analyses are provided as Supplementary Material. The initial heating coefficient was set to 0. We used random starting trees, and sampled parameters and trees every generations. Convergence was assessed by the built-in diagnostics of MrBayes 3. We also examined trace plots of likelihoods, chain swap frequencies, and parameter samples for evidence of non-stationarity or poor mixing. The diagnostic criteria were met for all parameters in all analyses except as noted below for the CPP model.
Bayes factors were used to choose among relaxed-clock models. They were calculated from estimates of the marginal likelihoods obtained using the stepping stone sampling approach Xie et al. Our implementation estimates model likelihood by going from posterior to prior or in the reverse direction. It supports multiple-run convergence diagnostics, implements both initial and stepwise burn-in, and uses Metropolis coupling to enhance mixing during the entire procedure.
The consensus tree obtained in an initial nonclock analysis of the combined extant data set Fig. Most of the basal nodes received maximal support from the combined data set, posterior probability PP of 1. Regions of uncertain resolution mainly include Tenthredinidae and Apocrita; the latter was very sparsely sampled. Additionally, the relationships at the base of Unicalcarida remain uncertain, especially whether Xiphydria is the sister to Vespina or to Siricidae.
The nonclock tree also shows that the rate of molecular evolution varies considerably between hymenopteran lineages, most conspicuously exemplified by the very short branches leading to extant Xyeloidea Fig. The Xyeloidea form the sister group of all other extant Hymenoptera in our analysis; previous studies have always placed the two constituent lineages, the Xyelinae and Macroxyelinae, at the very base of the hymenopteran tree, but variously as: The Xyeloidea have apparently retained many primitive characters found in the oldest known hymenopteran fossils Rasnitsyn Our results show that the Xyeloidea are characterized by low evolutionary rates both in morphological and molecular characters.
The choice of clock model and rooting method had a large impact on tree topology Fig.
Materials and Methods
The nonclock topology Fig. Imposing a strict clock drastically changed the topology, most importantly by shuffling the outgroups and rerooting the hymenopteran tree on the branch separating the Vespina from other hymenopterans Fig. Constraining the Holometabola to be monophyletic, to help structure outgroups according to the received wisdom, did not reverse the unorthodox rooting of the hymenopteran tree Fig. Unconstrained relaxed-clock models similarly resulted in an unorthodox topology Fig. All subsequent analyses used relaxed-clock models with the Holometabola constrained to be monophyletic.
Clock model and rooting assumption had a large effect on tree topology.
Or Not 2B Comics : Awkward Moments in Animal Dating 2
When a clock was not assumed, the morphological a , molecular not shown , and combined morphological and molecular b trees were virtually congruent and agreed well with previous studies. The widths of clades are proportional to their representation in our data set, not to their true diversity. Only extant taxa were included in the analyses shown here. To select the best relaxed-clock model, we performed Bayes factor comparisons.
Let’s flip the script on DTF
Because the dating approach could influence the results, we performed the comparisons separately on the uncalibrated, node-calibrated, and total-evidence-calibrated data sets. Model likelihoods were computed using the stepping-stone algorithm Xie et al. Four independent analyses were performed on each data set.
The results differed across data sets. For the total-evidence data set, we had some difficulties with convergence among the four independent stepping-stone analyses. The scatter among estimates was about 10 to 15 log likelihood units except for TK02, see below , whereas it was around 5 log likelihood units for the other data sets.
However, the results do suggest that inclusion of the fossils changed the performance of the models. Examining the uncalibrated trees estimated by the different relaxed-clock models Fig. The IGR model allows the changes in substitution rates on adjacent basal branches to be quite extreme, accounting for most of the rate variation in the whole tree Fig.
In some cases, rates are strongly decelerated on one branch and accelerated on its sister branch, for example, in the most basal xyelid branch and in the ancestor of all other Hymenoptera.
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The autocorrelated CPP and TK02 models have a smoothing effect, such that the rate changes occur more slowly and over a larger part of the basal tree Fig. The result is that the time duration of many basal branches is extended. For the uncalibrated analyses in general, the choice of relaxed-clock model had only a small effect on the estimates of effective branch lengths but often a profound effect on the estimated time lengths of the branches Fig.
Different relaxed-clock models result in different relative divergence time estimates uncalibrated trees. The letters denote the branches examined in plots c—f, respectively. For the relaxed-clock models, we plotted both the time length in expected substitutions per site at the base rate of the clock and the corresponding effective branch length, which equals the time length times the rate estimated for that branch see labels in Fig.
Note that effective branch lengths tend to be very similar to nonclock branch lengths, while time length distributions vary more across relaxed-clock models and tend to be less precise. In the dated analyses, the extension of the basal branches resulted in the autocorrelated models implying the existence of considerably longer, unsampled ghost lineages than the IGR model, suggesting that the IGR model fits the fossil record better.
Despite the fact that our tree model did not account for fossil sampling and thus did not penalize long ghost lineages, inclusion of the fossils in the analysis nevertheless tipped the model comparison in favor of the IGR model, as mentioned above, giving additional support for the idea that the IGR model agrees better with the fossil data. For these reasons, and because it also appears to us that it is more important to capture the apparently drastic rate changes among basal hymenopteran branches than it is to exactly model the rate autocorrelation in the rest of the tree, we focus on the IGR results in the following.
Presumably, the rate variation in our data set would have been described more accurately by a relaxed-clock model allowing the degree of rate autocorrelation to change across the tree, unlike the models we explored. When fossils were included as terminals in the total-evidence analysis, the consensus tree was highly unresolved Fig.
The fossils that jump around in the tree mask any potential resolution among extant taxa in the consensus tree. When the consensus tree was calculated from the same tree sample after the fossil taxa were removed, the relationships among extant taxa were highly resolved and corresponded to the relationships obtained when analyzing extant taxa alone. Majority-rule consensus tree from a total-evidence analysis including all fossils IGR model.
The tree is poorly resolved, which reflects the uncertainty in fossil placement. The underlying consensus tree of extant taxa is virtually identical to trees obtained in analyses without fossils see Figs. Grey-scale boxes indicate the percentage of morphological characters that were coded for each taxon, showing the incompleteness of the fossils.
Values above branches represent PPs. The uncertainty concerning the phylogenetic placement varied considerably among the fossils. While some of the better preserved fossils could be assigned with high PP to a specific branch of the tree of extant taxa e. In some cases, this was apparently due to poor preservation e.