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Advanced Search Abstract Phylogenies are usually dated by calibrating interior nodes against Ronquist total evidence dating services fossil record. This relies on indirect methods that, in the worst case, misrepresent the fossil information. Here, we contrast such node dating with an approach that includes fossils along with the extant taxa in a Bayesian total-evidence analysis. As a test case, we focus on the early radiation of the Hymenoptera, mostly documented by poorly preserved impression fossils that are difficult to place phylogenetically. Specifically, we compare node dating using nine calibration points derived from the fossil record with total-evidence dating based on morphological characters scored for 45 fossil complete and 68 extant taxa.
Because it is difficult to model speciation, extinction, sampling, and fossil preservation realistically, we develop a simple uniform prior for clock trees with fossils, and we use relaxed clock models to accommodate rate variation across the tree. Despite considerable uncertainty in the placement of most fossils, we find that they contribute significantly to the estimation of divergence times in the total-evidence analysis. In particular, the posterior distributions on divergence times are less sensitive to prior assumptions and tend to be more precise than in node dating. 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 Ronquist total evidence dating services the fossil placement.
Methodological and empirical advances now allow time trees to be estimated more accurately than ever before. At the same time, biologists have discovered that the relative timing of different events provides crucial information in the study of many evolutionary phenomena. Originally, phylogenies were dated by assuming a constant molecular clock, the rate of which could be estimated by reference to the fossil record Zuckerkandl and Pauling Since then, divergence time estimation has become much more sophisticated. In our study, the 3 fossils that were used to calibrate nodes were not used to date the tips of the tree; we were thus able to combine node-dating and tip-dating, using different sets of fossils, in a novel approach.
Two methods were used to test hypotheses. Bayes factors were also used to compare rival hypotheses. A Bayes factor is the ratio of the marginal likelihoods of 2 models, which is used to measure support for one hypothesis over the other. We used 2ln BF10 as the test statistic [Kass and Raftery, ; Brown and Lemmon, ], which is calculated as the difference of the natural logs of the 2 marginal likelihoods of model hypothesis 1 and model 0, times 2. A positive value indicates evidence in favor of model 1; a negative value indicates the reverse. Following Kass and Raftery , we interpret the magnitude of the test statistic as: Bayes factors have advantages over other methods such as likelihood-ratio tests or the Aikake Information Criterion.
Because they integrate over multiple parameters, it is not necessary to account for numbers of parameters in hypothesis testing. Furthermore, an arbitrary number of non-nested models can be compared, as opposed to likelihood-ratio tests, which are applied to nested models [Lepage et al. In Bayesian phylogenetic analysis, marginal likelihoods are often estimated from the post-burn-in samples using the harmonic mean. However, the harmonic mean was shown to be a poor estimator of marginal likelihood, so we used the stepping stone method [Xie et al. The alpha parameter was set to 0. Four replicate runs of million generations were used for the DNA and combined datasets and million for Morph and Morph-Fossil datasets.
In some analyses, partial backbone constraints were used on extant taxa only MrBayesallowing the fossils to attach to the tree on any branch, regardless of the constraint. The Pipa-Hymenochirus partial constraint forced Pipa, Hymenochirus and Pseudhymenochirus to form a clade. Each analysis was run under both constraints. Results The details of the analyses are summarized in tables 3 and 4 and figures 3 and 4, and we report only the highlights here. Analysis of the Morph dataset extant taxa with parsimony and Bayesian analyses yielded a better score for the PipHym tree under both tests, but the differences were not significant B1 and B2.
Numbers above the branches are parsimony bootstrap proportions, below are posterior probabilities. The white circles indicate nodes that were constrained. The subtree is scaled so that its root Pipidae is at the same level as Pipidae in the complete tree. Parsimony analysis of the Morph-Fossil dataset fig. Similarly, the MrBayes analysis fig. The parsimony tree topology is identical to this one. Names of extant taxa are shown in bold. The numbers below the branches are the posterior probabilities. The scale is number of changes per unit branch length.
Effects of Clock Analyses on Topology: Node-Dating The results of the relaxed-clock analyses are presented in columns of table 3 and figure 4. Addition of 3 fossil calibrations very strongly supported the same result A4.
Ronquistt In contrast, analysis of the Morph dataset with or without these calibrations provided either positive but non-significant support B3 for the PipHym tree or no substantial support dvidence either hypothesis B4. The clock analysis Rknquist the DNA-Morph data without evodence calibrations C3 did not significantly favor either tree, although there is positive support for the XenHym datijg. The incorporation servicee 3 fossil Ronqyist, however, yielded strong support for the XenHym tree C4. In general, the use of fossil calibrations strengthened the evidence for Roonquist XenHym model Rpnquist analyses in which Gotal data were included.
This corresponds to analyses D6 and E6 in table 3 Ronquist total evidence dating services the light green and light orange bars in figure 4. The Xen-Hym topology is very strongly supported. Ronquist total evidence dating services shape and limits of the exponential calibration prior are shown for Anura. Eviednce of node calibrations increased the support for eviednce XenHym tree E6. Dxting both topologies the datijg calibrations greatly xervices the evidence for the more complex model. Datimg, in both analyses support for most nodes is weak fig. Within this subclade the relationships among fossils under the 2 analyses are similar, but weakly supported. The second subclade, which is weakly to moderately supported, includes Pipa, Hymenochirini and their fossil relatives.
In turn, Pipa is fating sister-group of this clade. Overall, these results echo those of previous parsimony analyses [e. Effects of Clock Analyses on Node Ages Figure 4 and table 4 summarize the various analyses across a nested service of selected nodes. For each node, the results rvidence analyses of the 5 datasets are presented in pairs identified by dark and light shades of the Ronquiist color; the first of each pair dark colors does not include node-dating. For each named node, analysis results of the 5 datasets are presented in pairs of horizontal bars distinguished by dark and light shades of the same color. The first of each pair dark does not include node-dating; the second light incorporates node calibrations from 3 fossils table 2.
The vertical black bars indicate median ages. The inset shows the position of the named nodes on a tree derived from extant taxa only. These do not include fossils and so were not analyzed by tip-dating table 4. The fourth and fifth analyses contrast tip-dating with combined tip- and node-dating for the Morph-Fossil and DNA-Morph-Fossil datasets. In almost all cases, the credible intervals are larger in analyses in which the node calibrations are not used compare each darker bar with its lighter partner. In the first 3 datasets red, blue and purplethe median age is older in the analysis lacking internal calibrations.
The 2 datasets green and orange in which tip-dating was used present a different picture. One striking feature fig. This results from the narrowness of the prior distribution Palaeobiogeography As has been found in previous parsimony analyses, the clades of Pipidae do not sort cleanly between South America and Africa fig. No formal quantitative biogeographic analysis was performed here, but distributional discordance is apparent. Regardless of whether the XenHym or PipHym topology is favored, certain relationships are consistently recovered. In either case, the closest relative of Pipa is an African taxon. The Morph dataset alone did not support either tree significantly although it favored the PipHym treebut inclusion of fossils in the Morph matrix tipped support to significantly favor the PipHym tree.
This suggests that more data help resolve the tree, although the result cannot be attributed to adding extinct taxa per se. The combined 3-dataset analysis supported neither topology. In this case, the non-clock analysis of all data did not provide a clear answer, and the DNA data did not overwhelm the morphological-fossil data. However, Bewick et al. This result is particularly notable because their matrix, which is remarkably complete, contains the largest number of characters relevant to this question: Given that the Hedtke et al. Or, the paucity of taxa and long branches are causing the tree to root in the wrong place. However, no significant improvement was seen by incorporating node calibrations into the analysis of the Morph data B3, B4 table 3.
The analysis of the Morph-Fossil matrix, which included tip-dating, strongly favored the PipHym tree D5. However, the parsimony and non-clock Bayesian analyses also strongly favored the PipHym tree D1, D2so the addition of tip-dating seems to have not added to the discriminatory power of the Bayes factor tests for this dataset. Interestingly, the addition of node calibrations reduced the level of discrimination between the 2 topologies D5, D6. The uniform tree prior does not have any parameters. The ages of fossils were updated from O'Leary et al. We did not associate the age estimates with any uncertainty, assuming that this would be a negligible source of error in our analyses, and we take our results to confirm this assumption at least with respect to our main conclusions.
However, the uncertainty of age estimates may clearly be important in many contexts [ 6 ]. First, we increased the prior probability of a low extinction rate by using a Beta 1, prior instead of a flat prior for the turnover, r. Second, we increased the prior probability of a high fossilization rate by using a Beta ,1 prior instead of a flat prior for the fossil sampling probability, f. Finally, we explored the effects of assuming a rapid net diversification rate, d, by fixing it to 0. All analyses were run both with fossils under the FBD model, and without fossils under the corresponding BD model.
We first allowed the diversification process to vary across time by using a skyline FBD model [ 25 ] with three intervals: FBD parameters were estimated separately for each of these intervals, using the standard priors Exp 10 for d and Beta 1,1 for r and f. Second, we decoupled the relaxed clocks for morphology and molecules, allowing morphological and molecular rates to have different trajectories across the tree.
Moreover, many of the more powerful preserved fossils are sold from the staff from the outset because their asian cannot be discussed with other country. The co can be ran into 2 scenarios:.
The code is now part of the latest MrBayes release. To tptal topological convergence when fossils are included, we added a couple of topology moves that specifically target Ronquisg subtrees but that are, otherwise, identical to existing topology moves. For each model, we ran four independent analyses, each using four Metropolis-coupled chains. When fossils were included in the analysis, tree samples were summarized both with fossils included and with fossils first pruned away from all tree samples. Data files and MrBayes run files for all analyses are provided in the totzl supplementary material. All tree figures were drawn using FigTree [ 27 ]. The morphological evidence sprinkles the afrotherian taxa across the tree, and even if we disregard the Afrotheria, the Euarchontoglires and Laurasiatheria remain intermixed.
Among the Laurasiatheria, the pangolin Manis occupies a basal position in the tree together with Xenarthra anteaters, sloths and armadillos. Furthermore, primates and their relatives Euarchonta group with bats Chiroptera rather than with Glires rodents and lagomorphssplitting the Euarchontoglires in two. Figure 1. Phylogenetic signal in the dataset. Note that the morphological tree c has longer branches and is more poorly supported than the molecular tree bindicating weak and potentially misleading phylogenetic signal owing to morphological convergence. The morphological tree is also strongly in conflict with monophyly of the four placental superorders indicated by coloured bars.
The placement of fossils and absolute branch times are determined in one joint inference rather than in separate analyses. The combination of clock models and substitution models for molecular and morphological data and a model of the process that generates dated phylogenetic trees with fossils comprises a full probabilistic model that generates all data used in the analysis.
This approach can utilize all available fossils as individual data points. In contrast, the node calibration method only directly incorporates the age of the oldest fossil of a given clade, typically as a hard minimum for the clade age. The overall fossil record of the clade can be indirectly incorporated as the basis for choosing a hard or soft maximum or to justify the shape of a prior distribution, however, individual fossils aside from the oldest will not contribute directly except perhaps if they are used to generate a confidence interval.
Although total-evidence dating overcomes limitations of other methods that use fossil evidence to date phylogenies, some aspects of the method still need to be improved Arcila et al. One improvement is using better tree prior models.
Services Ronquist total evidence dating
Previous attempts at total-evidence dating analyses have used datiing, Yule, or birth—death tree priors that do not model the fossil sampling process and do not allow direct ancestors among the sample e. However, evidenve probability of ancestor—descendant pairs among fossil and extant samples is not negligible Foote Moreover, ancestor—descendant pairs need to be considered when incomplete and nonidentified specimens are included in the analyses because such specimens might belong to the same single lineages as other better preserved fossils. A good choice of the tree prior model is important for dating methods due to the limited amount of fossil data. Dos Reis and Yang and Zhu et al.