In spite of the markedly different composition of data sets, our results show congruence across all analyses for age estimates of basal nodes that are well constrained with respect to fossil calibrations e. By contrast, derived nodes that lack fossil calibrations e. Total evidence dating consistently produced older median ages than node dating for ingroup nodes, due to the nested placement of multiple Palaeozoic fossils.
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Our analyses support basal diversification of Opiliones in the Ordovician-Devonian period, corroborating the inferred ancient origins of this arthropod order, and underscore the importance of diversity discovery—both paleontological and neontological—in evolutionary inference. Dating molecular phylogenies has the power to provide an evolutionary framework for a group in question, beyond inference of relationships alone Benton, ; Wang et al.
Therefore, dating phylogenies has become a standard practice in phylogenetic, biogeographic, ecological, and other evolutionary studies Pisani et al. The effects of both practices are just beginning to be evaluated Wood et al. Another key issue is incorporation of uncertainty into calibrations Ho and Phillips, , as recently demonstrated in an analysis of the biogeographically iconic trees of the genus Nothofagus Sauquet et al.
Consequently, recent studies have evaluated a range of dating techniques and calibrations to better test biogeographic hypotheses Mao et al. A separate concern for molecular dating is confidence in the adequacy of taxonomic sampling, which affects topological accuracy as well as precision of molecular divergence times. Particularly for hyper-diverse clades, such as arthropods or flowering plants, continually accruing knowledge of biodiversity results in periodic amendments to systematics and phylogeny.
One such taxon is the arachnid order Opiliones harvestmen or daddy-long-legs, among other common names; Figure 1 , one of the best-studied arthropod groups in terms of molecular phylogenetics, and more recently, the timing of cladogenesis Giribet et al. In contrast to many terrestrial arthropod orders, Opiliones is a group with a Palaeozoic fossil record, and for which morphological matrices coding these fossils are available Giribet and Dunlop, ; Garwood et al. Modern-looking members of the suborders Eupnoi and Dyspnoi were already present in the Carboniferous Garwood et al.
Furthermore, a specimen previously placed in Eupnoi is known from the Devonian Rhynie Cherts Dunlop et al.
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This fossil, Eophalangium sheari , has been used in recent studies to constraint the age of Eupnoi or Palpatores in previous dated phylogenies Giribet et al. The recent discovery of a new Opiliones fossil in the Carboniferous Montceau-les-Mines Garwood et al.
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Node dating of a taxon dataset in that study suggested a very different scenario for the timing of subordinal diversification Garwood et al. Summary tree of the phylogenetic relationships of the extant Opiliones families. Unranked clades are indicated to facilitate discourse.
In addition to the discovery of the extinct sister group of Cyphophthalmi Garwood et al. This parallels the identification of Synthetonychiidae, a relictual family endemic to New Zealand, as the sister group of the remaining Laniatores Giribet et al. Thus, discoveries of fossils and new, refined phylogenetic hypotheses in the last five years necessitate further reevaluation of Opiliones diversification and divergence time estimation. We thus tested both the placement of fossils and the newly discovered extant lineages in a single analysis.
We separately conducted node dating on this data set after culling fossil taxa, to examine the effect of treating fossils as terminals. To approach node dating with a modern data set, we amassed a phylogenomic data set of 24, amino acid sites for 14 species of Opiliones, sampling all extant suborders. In this way, we approached comparative molecular dating of basal harvestman phylogeny using different data sources and approaches to assess congruence of divergence time estimates.
An existing morphological matrix of unordered characters recently analyzed by the authors Garwood et al. To this matrix, we added exemplars of Pettalidae Pettalus thwaitesi , Caddidae Caddo pepperella , Acrosopilionidae Acropsopilio neozealandiae , Austropsopilio altus , and Caddella croeseri , and a new lineage of Phalangioidea not ascribed to a family Hesperopilio magnificus , thus improving sampling of basally branching lineages in Cyphophthalmi, Eupnoi, and Dyspnoi, respectively. Synthetonychiidae, the sister lineage of the remaining Laniatores, could not be included in this matrix, as a previously sequenced species was small and was entirely consumed in previous DNA extractions Sharma and Giribet, The modified matrix was This morphological matrix was combined with molecular sequence data from five genes, totaling 3, aligned nucleotide positions sequence data previously published; Giribet et al.
The combined alignment is provided as supplementary material. We also changed outgroup sampling in this matrix, replacing the troglomorphic scorpion Belisarius xambeui with the more representative Pandinus imperator both exemplars of Iurida. This was done to reduce ambiguity in optimization of characters pertaining to eyes, as almost all scorpions bear multiple pairs of eyes, with a few exceptional troglomorphic species like B. This is pertinent to the placement of the harvestman fossil Hastocularis argus , the only Opiliones interpreted to bear two sets of eyes Garwood et al.
The final matrix included four outgroup terminals, 41 extant harvestman terminals five Cyphophthalmi, eleven Laniatores, eleven Eupnoi, and fourteen Dyspnoi , and six extinct harvestman terminals four Palaeozoic, two Mesozoic. Priors of calibration points used in the analyses are provided in Table 1. Total evidence dating made use of the independent gamma rates model. Limulus polyphemus Xiphosura was used to root the tree. For molecular sequence data, we excluded third codon positions of the genes cytochrome c oxidase subunit I and histone H3 in order to retain conserved sites only.
A one-parameter Markov model Lewis, was applied to the morphological data. Analyses followed the methods deployed for a hymenopteran data set by Ronquist et al. In summary, we compared branch lengths from non-clock and uncalibrated strict clock analyses, and used the slope of the variance as the median for an exponential hyperprior for variance increase. A prior for the substitution rate was obtained by dividing the median tree height from uncalibrated strict clock analyses with an estimated age of the Xiphosura-Arachnida split.
We used Myr as an approximation of the latter, as inferred from the early fossil record of Euchelicerata reviewed by Dunlop, The standard deviation of the lognormal was also chosen following the method of Ronquist et al. Uncertainty in the ages of fossils was disregarded, as it was considered negligible with respect to other sources of error and the scale of geological time spanned by Opiliones.
To bound the root age of the tree and maintain consistency with the fossil record, a uniform prior of — Ma was applied to the divergence of Arachnida Dunlop, ; Garwood et al. Convergence diagnostics were assessed using Tracer ver. To compare the effects of total evidence dating versus node dating on the combined data set, the combined data matrix from the total evidence analysis was analyzed with fossils removed.
Partitioning and models applied to the morphological and molecular data sets, as well as independent gamma rates model priors, were as specified in the total evidence analysis. A uniform prior of — Ma was applied to the divergence of Arachnida Dunlop, ; Garwood et al.
Based upon the placements of Palaeozoic harvestman fossils in the total evidence topology, three node calibrations were applied as exponential prior distributions, thus permitting node ages only to exceed a given minimum age constraint. The age of Opiliones was constrained with an offset lower bound of Ma and a mean of Ma, reflecting the age of E. Both Eupnoi and Dyspnoi calibration priors consisted of exponential distributions with an offset of Ma and mean of Ma, reflecting the ages of Ameticos scolos and Macrogyion cronus. Transcriptomic data for several species of Opiliones were analyzed previously as part of a broader investigation of arachnid relationships Sharma et al.
Retained ingroup taxa consisted of all 14 Opiliones transcriptomes sequenced to date two Cyphophthalmi, six Laniatores, three Eupnoi, three Dyspnoi.
Subsequent to reducing indel-containing sites with GBlocks v. Divergence times based on this alignment were inferred using PhyloBayes v. A constraint tree was provided, based on analyses of the original data set Sharma et al. Limulus polyphemus was used to root the tree as in other analyses. The split between Xiphosura and Arachnida was again constrained with a uniform prior of — Ma. As PhyloBayes can implement soft bounds, we constrained the floor of Opiliones as Ma based on the age of the oldest fossil, E.
The ceilings of these four nodes were not bounded. Four runs were conducted under each model for 14,—19, cycles. For all runs, cycles were discarded as burnin. Bayesian inference analysis of the total evidence data set recovered a consensus tree topology supporting previous understanding of Opiliones relationships Figure 2. Uncalibrated total evidence tree topology.
Colors in tree correspond to suborders purple: Fossil taxa indicated in red lettering. Major recent amendments to Opiliones systematics are indicated in yellow highlights: Asterisks indicate posterior probabilities of 1. Fossil placements within the tree topology were consistent with the total evidence analysis of Garwood et al. This result indicates that the analysis of Garwood et al. By contrast, the placements of Ameticos scolos and Macrogyion cronus within Dyspnoi and Eupnoi, respectively, were not supported as in the previous analysis of Garwood et al. For this reason, the inclusion of Macrogyion cronus in Phalangioidea was enforced as a topological constraint in the total evidence dating analysis.
So You Want to Make a Time-Calibrated Phylogenetic Tree
Similarly, the placement of Mesobunus dunlopi was constrained with respect to the remaining Sclerosomatidae, due to the unambiguous and observable genitalic morphology of this fossil Giribet et al. Total evidence dating under an independent gamma rates model recovered a chronogram with significant variance in estimated divergence times for derived nodes Figure 3. Colors in branches correspond to suborders, as in Figure 2. Node dating using the combined data matrix with fossils removed recovered a chronogram with consistently smaller median age estimates for all represented nodes, with respect to the total evidence dating Figure 3.
Asymmetrical a posteriori distributions of divergence times for crown Eupnoi and crown Dyspnoi indicate that the priors were informative in the analysis. Two models were explored for molecular dating: Due to the significance of Opiliones for studies of biogeography, several authors have employed molecular dating to analyse harvestman data sets under a variety of approaches e.
Consecutive efforts have improved upon previous counterparts, mostly through incorporation of newly discovered fossils and updated hypotheses concerning their placement Garwood et al. As an example, the oldest fossil harvestman, E. Another study, also conducting node dating, treated E. Therefore, Hedin et al. The discovery of the basally branching placement of Acropsopilionidae as sister group of the remaining Dyspnoi Groh and Giribet, also necessitates complete reevaluation of the actual MRCA of the extant dyspnoids.
The present study constitutes the first effort to analyze molecular dating in Opiliones treating all well-characterized fossil species as terminals, which has been argued to be philosophically and methodologically superior to node dating e. The appeal of total evidence dating stems from the consideration that the point of divergence for a given fossil along a branch can be explicitly parameterized through phylogenetic treatment of a morphological data set.
Original Research ARTICLE
While results of both approaches rely upon confident placement of fossils in a phylogeny—either a priori node dating or during the dating analysis total evidence dating —total evidence dating provides the singular advantage of obviating guesswork and bet-hedging with regard to fossil placement, which typically manifests as multiple analyses using alternative placements of calibration points, with often mutually exclusive alternatives e.
Total evidence dating also enables informative use of all well-known fossils; in typical node dating analyses, only the oldest fossil corresponding to an extant clade is employed for calibration, whereas younger fossils of the constituent clade will be ignored Ronquist et al. We observed that total evidence dating consistently recovered older ages than commonly used node dating methods, regardless of data set size or inclusion of morphological data Figures 3 and 4 ; Table 2.
This result is both intuitive and plausible; node dating approaches are limited in that they treat the age of the oldest fossil member of a clade as equivalent to the crown age of that clade. In practice, discovering the actual MRCA of a given clade in the fossil record is both highly improbable and epistemologically indefensible. Due to the incompleteness of the fossil record and well-documented artifacts associated with determining the stratigraphic range of taxa e. Moreover, if the oldest fossil taxon of a given clade nests within that clade, and is not in fact situated along the branch subtending the clade, the inferred MRCA age of the clade will be even greater.
In our data set, this phenomenon occurs throughout the Opiliones tree topology. Eophalangium sheari , the oldest harvestman fossil, is part of a clade sister to Cyphophthalmi as in Garwood et al. Ameticos scolos and Macrogyion cronus , previously treated as either stem or crown group members of Dyspnoi and Eupnoi, respectively Hedin et al. Finally, Halitherses grimaldii , treated as the oldest crown group member of the superfamily Troguloidea Hedin et al.
The consequence of these fossil placements is uniformly older ages for nodes in the total evidence dating analysis in comparison to node dating analyses Figures 3 — 5. The best way to format your data is therefore to set up an excel spreadsheet like this: Use getMRCA to find the node number for whichever age you want to record, and stick your age into that row in Excel.
I like to use RStudio for working with R. You need to do a few things at the beginning of a new session with R:. So, you can check to make sure the names of the ranges and tree line up correctly using. We are now ready to use the paleotree function to time-calibrate those trees! It looks like this in the official documentation:. Hopefully you now have a nice set of time-calibrated trees stored in tree1! You can now save these to your hard drive using.
You can open this file up in Mesquite or figtree if you want to manipulate it there rather than in R, or you can use these trees in other R functions. Going over your data carefully will reduce a lot of errors, but sometimes these can be hard to spot. Bucky Gates has helpfully created a little bit of code to help find errors in your range data and has graciously allowed me to share it here — download the R file HERE and open it up in R to check it out. Alright folks, spot any errors in this tutorial? Huge gigantic thanks for this post go to Bucky Gates, David Bapst, and especially my sister Jessica Arbour who is a total whiz at R and a cool scientist go check out her papers!
The right side shows the exposed bone, but the left side shows the preserved horny sheath impression, and all around it are scale impressions! Hi there, I was just wondering if you know a way to summarize the stochastic trees you obtain in this analysis. So, regarding the use of the dating methods available in timePaleoPhy e. Rather, I think you should consider the likely range of estimates for similar groups with similar fossil records. Cesan, it depends on what you want. You can get all the ages for the nodes for a tree sample with dateNodes, but it will be like drinking from a fire hose with good reason.
As for the topology alone goes. It may be better to use the sample of dated trees directly for your question of interest e. You are commenting using your WordPress. You are commenting using your Twitter account. You are commenting using your Facebook account. Notify me of new comments via email. What do you need to make a time tree in paleotree? Information about the ages of the taxa in your tree.
I had a tree with lots of extant mammals and like 2 fossil taxa; to make the time-calibration make more sense, I needed some ages for deeper splits in the mammal tree, like the split between marsupials and placentals, the split between euarchontoglires and laurasiatheres, etc.