Alternative nodal assignments (a, b, or c) for the six fossils listed in Table 1 Germany, Belgium, Dorofeev, , , ; Collinson and Pingen, ; Dyjor Molecular clock calibrations and Metazoan divergence dates. J. Mol. Evol.
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Belgium tightens measures: bubbles shrink, bars close early. Molko has been open about his use of recreational drugs: in a interview with Kerrang! Molko admitted in that many of his initial excesses were due to his mental health issues; he was officially diagnosed with major depressive disorder in his late twenties. Molko uses a variety of guitars. For amplification he used a Marshall LM. His amplifier was a Fender Twin Reverb. In , he signed an endorsement contract to use Orange amps. From Wikipedia, the free encyclopedia.
For the 16th-century Jewish Messiah claimant, see Solomon Molcho. Retrieved 6 September Archived from the original on 25 January Retrieved 20 September May Archived from the original on 16 October Archived from the original on 25 July Archived from the original on 19 January Digital Spy. In the study presented here, we expand the fossil cross-validation approach to evaluate whether alternative assignments of available fossils to different calibration nodes produce calibration sets with different levels of internal consistency.
Whereas the key idea of the method devised by Near and Sanderson was to eliminate individual fossils that had already been unequivocally assigned to single calibration points in a multicalibration set, the key idea of our approach is to compare the internal consistencies among entire calibration sets formed by multiple fossils that can be attached to alternative calibration points.
Earlier molecular dating results Conti et al.
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Given the controversial nature of calibration, the contradictory calibration procedures previously applied to date the Crypteroniaceae phylogeny, and the availability of multiple fossils in Myrtales, this group of taxa provides an ideal case study to investigate problems of fossil nodal assignment, at the same time attempting to refine the age estimates that are central to the biogeographic history of Crypteroniaceae.
MrBayes majority-rule consensus tree with maximum likelihood branch lengths optimized in estbranches , based on the nucleotide data set. Maximum likelihood bootstrap support values and Bayesian clade credibility values are reported above and below the branches, respectively. General distribution ranges of the focus groups are reported to the right of the tree, as are the infrafamilial ranks relevant to fossil nodal assignments. Alternative nodal assignments a , b , or c for the six fossils listed in Table 1 numbers 1 to 6 are labeled on the tree.
Outgroup taxa are indicated by an asterisk. To calibrate the Crypteroniaceae phylogeny we use six fossils Table 1. Based on the morphological traits preserved in the fossils, five out of the six fossils can each be assigned to two or three different nodes in the phylogeny Fig. In total, 72 different combinations of six calibration points are possible, each combination forming a calibration set. Here, we employ an expanded molecular data set and the six fossils to address the following questions: 1 How can the fossil cross-validation procedure be used to assign a fossil to a calibration point that is most internally consistent with the other points in a calibration set?
In other words, which fossil assignments produce the calibration sets that are most internally consistent?
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The general goal of our paper is to stir discussion and foster further investigation on the under-studied problem of uncertainty in fossil nodal assignment. Fossils used in this study with corresponding ages, locations, and references. Sampling was expanded from published studies Conti et al. In total, new sequences were generated for this study.
Almost complete taxon sampling was achieved for Crypteroniaceae seven of 12 species; Mentink and Baas, ; Pereira and Wong, ; Pereira, , Alzateaceae one of one species; Graham, , Rhynchocalycaceae one of one species; Johnson and Briggs, , Penaeaceae 19 of 23 species, plus four subspecies of Penaea cneorum ; Dahlgren and Thorne, ; Dahlgren and van Wyk, , and Oliniaceae five of eight species; Sebola and Balkwill, ; Tobe and Raven, The five missing species of Crypteroniaceae, Axinandra alata, A. DNA extractions from dried vouchers were unsuccessful, because all herbarium specimens of these taxa were treated with ethanol after collection.
The four missing Penaeaceae, Stylapterus barbatus , S. Phylogenies were rooted using representatives of Lythraceae, i.
Introduction
DNA was extracted as described in Rutschmann et al. Primers from Zurawski et al. PCR and sequencing procedures followed the protocols described in Rutschmann et al. The software Sequencher 4. Rbc L, nr26S, and nr18S sequences were readily aligned by eye, whereas ndh F and rpl intron sequences were first aligned using Clustal X 1.
Plastid rbc L, ndh F, and rpl intron and nuclear nr18S, nr26S partitions were first analyzed separately results not shown. Model selection for each partition was performed in MrAIC 1. Tree topology and model parameters for each data set were estimated simultaneously using MrBayes version 3. For each data set, MCMC runs were repeated twice. The first trees were discarded as burn-in after checking for stationarity on the log-likelihood curves. The remaining trees were used to construct one Bayesian consensus tree and to calculate clade credibility values Fig.
In addition to the Bayesian clade credibility values see Fig. Branch lengths see Fig. All dating analyses described below were performed with multidivtime Kishino et al. For the present study, it was important that multidivtime allows for multiple calibration windows in our case six calibration points and different substitution parameters for each data partition in our case five different partitions.
The value for bigtime was chosen in order to reflect the estimated age of the oldest eudicot pollen Doyle and Donoghue, The age of the eudicots about My is one of the firmest dates from the fossil record because of the numerous reports of fossil tricolpate pollen, with no tricolpate pollen appearing before this time. We performed each analysis at least twice with different initial conditions and checked the output sample files to assure convergence of the Markov chain by using the program Tracer 1.
Briefly, six fossils were chosen, five of which could be attached to alternative calibrations nodes, for a total of 72 possible calibration sets. To evaluate whether some of the 72 calibration sets were more internally consistent than others, we implemented the fossil cross-validation procedure of Near and Sanderson and Near et al.
Whereas these authors developed the method to identify possibly inconsistent points in a single calibration set, we expanded their approach to compare the internal consistencies of different calibration sets generated by alternative nodal assignments of multiple fossils. Therefore, for each of the 72 calibration sets in our case study, we performed the following steps:.
We fixed one out of the six calibration points and estimated the ages of the remaining five unconstrained nodes. For each unconstrained node, we then calculated the difference D i between its estimated and its fossil age. The procedure described above steps 1 to 3 was then repeated 5 times, each time by fixing a different calibration point.
Characteristics of the 72 different calibration sets, each consisting of six calibration points: Average squared deviation s see Fig. The three sets with the highest level of corrected calibration-set consistency are shaded in light grey, whereas the three sets with the lowest corrected consistency are shaded in dark grey see Fig. Note that fossil 2 could be assigned to only one node in our phylogeny node 2. By using this procedure iteratively, we obtained s values for all 72 calibration sets. High values of s would indicate that one or more calibration points in a set are inconsistent with the others, suggesting that the corresponding fossils were erroneously assigned to the respective nodes, whereas low s values would characterize calibration sets with high internal consistency.
In order to account for possible effects related to the molecular dating method in our case multidivtime , the cross-validation experiments were repeated by using penalized likelihood Sanderson, implemented in r 8 s Sanderson, ; data not shown. Because the fossil cross-validation procedure might be influenced by the position of the calibration points relative to each other Near et al.
For each calibration set, the total nodal distance was calculated by adding all pairwise nodal distances between each fixed calibration node and each of the five unconstrained nodes step 1 of the fossil cross-validation; see above and then summing up over all calibrations step 4 of the fossil cross-validation.
This calculation of total nodal distance thus reflects the goal of the present study; i. Correlation significance was tested by using the F -test statistic under a linear regression model in R R Development Core Team, Because the 72 calibration sets differed in their degree of correlation between average squared deviation s and nodal distance Fig. Correlation between the average squared deviation s and nodal distance among calibration points for each calibration set see Table 2.
R represents Pearson's correlation coefficient. Calibration sets 1, 9, 5 and 50, 66, 58 represent the sets with the lowest and highest s values, respectively. Calibration sets 18, 10, 11 and 33, 41, 25 circled show the s values that deviate the most below and above the regression line, respectively.
Histogram representing the percent deviation of s from the regression line of Figure 2 for all 72 calibration sets. These sets are associated with the highest level of corrected calibration-set consistency. These sets are associated with the lowest level of corrected calibration-set consistency. In order to check whether there is a relationship between the corrected calibration-set consistency and the precision of the dating estimates for the node of interest node X; see Fig.
Correlation significance was then tested with an F -test statistic under a linear regression model in R. Correlation between corrected calibration-set consistency expressed as percent deviation of s from the regression line with nodal distance; see Fig. The three calibration sets 18, 10, and 11 produced lower standard deviations for the age of node X than the three calibration sets 33, 41, and The MrBayes majority-rule consensus tree, including maximum likelihood branch lengths optimized in estbranches , maximum likelihood bootstrap support values estimated in BootPHYML 3.
The tree topology is congruent with published phylogenies Conti et al.