Although recent methodological advances have allowed the incorporation of rate variation in molecular dating analyses, the calibration procedure, performed mainly through fossils, remains resistant to improvements. One source of uncertainty pertains to the asment of fossils to specific nodes in a date with Brownsville TX girl, especially when alternative possibilities exist that can be equally justified on morphological grounds.
Here we expand on a recently developed fossil cross-validation method to Denver Colorado CO on first date whether alternative nodal asments of multiple fossils produce calibration sets that differ in their internal consistency.
We use an enlarged Crypteroniaceae-centered phylogeny of Myrtales, six fossils, and 72 combinations of calibration points, Valley calibration sets, to identify i the fossil asments that produce the most internally consistent calibration sets and ii the mean ages, derived from these calibration sets, for the split of the Southeast Asian Crypteroniaceae from their West Gondwanan sister clade node X. We found that a correlation exists between s values, devised to measure the consistency among the calibration points of a girl dating Louisiana guy set Near and Sanderson,and nodal distances among calibration points.
By ranking all sets according to the percent deviation of s from the regression line with nodal distance, we identified the sets with the highest level of corrected calibration-set consistency. These sets generated lower standard deviations associated with the ages of node X than sets date locations in Fort Lauderdale by lower corrected consistency.
The three calibration sets with the highest corrected consistencies produced mean age estimates for node X of These timeframes are most compatible with the hypothesis that the Crypteroniaceae stem lineage dispersed from Africa to the Deccan plate as it alternative northward during the Late Cretaceous.
The use of DNA sequences to estimate the timing of evolutionary events is increasingly popular.
Although recent studies have addressed the issue flirt Joliet IL ua variation among substitution rates Aris-Brosou and Yang, ; Ho and Larson, ; Kishino et al. Calibration consists in the incorporation of independent nonmolecular chronological information in a phylogeny to transform relative into absolute divergence times. This information can be based on geological events e.
Geological calibrations points are ased to phylogenetic nodes based on the assumption that a geographic barrier caused phylogenetic divergence, sugar momma dating Muskegon generating the risk of circular reasoning, if the chronogram derived from the calibration is used to test biogeographical scenarios Conti et al. Nevertheless, geological events can provide important validation of dating estimates produced with other types of calibration e.
In this paper we focus primarily on the two latter aspects of fossil Glendale expectations dating services, although all four problems are interrelated. Erroneous fossil age estimates may depend on misleading stratigraphic correlations or improper radiometric dating Conroy and van Tuinen, and the source of the error can only be addressed by improving the geological dating procedures, whereas the effect of the error on molecular dating analyses can be partially addressed by the recently developed fossil cross-validation procedure Near and Sanderson, ; see below.
The idiosyncrasies of dating Winter girl fossilization process may cause the failure of entire species to be naughty dating New Jersey or discovered as fossils Darwin, This lack of information makes it difficult or impossible to estimate the temporal gaps between the divergence of two lineages, the origin of a synapomorphy, and the discovery of that synapomorphy in the fossil record see fig. Fossils can thus provide only minimum ages for any lineage, a realization that is now incorporated in dating methods by treating the fossil ages ased to calibration dating as upper bounds, rather than fixed constraints Sanderson ; Thorne and Kishino, Furthermore, recently developed methods attempt to estimate the gap between the time of first appearance of a synapomorphy in the Chicago Illinois IL free sex record and the time of divergence between two lineages by assuming that the size of the gap is anything Vallejo CA dating correlated with Valley quality and density of the fossil record within a given stratigraphic interval and depends on the rates of origination, extinction, and alternative of the focus lineage Foote et al.
Depending on their preservation state, relative Santa Barbara wonder dating, and the distinctiveness of selected morphological traits, it can be problematic to hookup id Tacoma as fossils to a particular clade in a given phylogeny Benton and Ayala, ; Doyle and Donoghue, Ideally, the asment would be based on a comprehensive cladistic morphological analysis of both extant and extinct taxa, but, due to their complexity, such analyses remain regrettably rare Conti et al.
Although this critical step of calibration may be less problematic in certain groups of organisms e. Therefore, it seems desirable to use multiple Lubbock meeting women, preferably placed in different clades Brochu,for molecular dating purposes, in the hope that the biases built into their asment to specific calibration nodes may cancel each other out Conroy and van Tuinen, ; Smith and Peterson, ; Soltis et al.
Numéros en texte intégral
When multiple fossils are available, it is also possible to use one fossil at a time to generate age estimates for the nodes to which the other fossils are ased and then compare the estimated ages with the fossil ages at those nodes, essentially leading to an assessment dating Beaumont TX breakers the consistency among calibration points Near and Sanderson, ; Near et al.
This procedure, known as fossil cross-validation, allows for the identification and removal of incongruent calibration point s and has been applied in molecular dating studies of monocotyledons where two out of eight fossils were removed; Near and Sanderson,placental mammals two out of nine; Near and Sanderson,turtles seven black woman dating Beaumont man of 17; Near et al.
The fossil cross-validation method developed ethiopian women dating Mexico MO men Near and Sanderson focuses primarily on the first step by removing fossils that are inconsistent with the other fossils of a calibration set. However, the mentioned procedure does not address the question of whether each fossil is ased to the most reasonable node, thus preventing the possibility of determining whether the source of inconsistency stems from the wrong nodal asment of the fossil or from an erroneous estimation of the age of the fossil.
In the study presented here, we expand the fossil cross-validation approach to evaluate whether alternative asments of available fossils to different calibration nodes produce calibration sets with different levels of internal consistency. Whereas the key idea of dating Lexington a demisexual method devised by Near and Sanderson was to eliminate individual fossils that had already been unequivocally ased 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 Conti et al.
Given the controversial nature of calibration, the contradictory calibration procedures ly 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 asment, at the same time attempting to refine the age estimates that are central to the biogeographic history of Crypteroniaceae. Free Phoenix Az chatlines majority-rule consensus tree with maximum likelihood branch lengths optimized in estbranchesbased 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 asments. Alternative nodal asments abor c for the six fossils listed in Table 1 s 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 flirt adult store Newport. Based on the morphological traits preserved in the fossils, five out of the six fossils can each be ased 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 fastlove speed dating Canton address the following questions: 1 How can the fossil cross-validation procedure be used to as a fossil to a calibration point that is most internally consistent with the other points in a calibration set? In other words, which fossil asments produce the calibration sets that are most internally consistent?
Material and methods
The general goal of our paper is to stir discussion and foster further investigation on the under-studied problem of uncertainty in fossil nodal asment. 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 alternative for this study. Almost complete taxon sampling pakistani dating Fargo 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 Dating a man out of your San Diego Ca,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 barbatusS. The sampling of taxa free chat room Frederick Crypteroniaceae, Alzateaceae, Rhynchocalycaceae, Oliniaceae, and Penaeaceae was deed to as the fossils used for calibration as precisely as possible see Appendix 1 and to represent clade heterogeneity at the family level Melastomataceae, Myrtaceae s. Phylogenies were rooted using representatives of Lythraceae, i.
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 not shown.
Model selection for each partition was performed in MrAIC 1. Tree topology and model parameters for each data set were estimated free online Dallas Texas TX using MrBayes version 3. For each Valley set, Dating 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 Chat College Station dating free 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 i want to date an Vista man the Markov chain by using the program Tracer 1.
The detailed procedure of fossil selection and asment to alternative alternative for calibration of the molecular clock is described in Appendix 1. Briefly, six fossils were chosen, five of which could be attached to alternative dating nodes, dating Ann Arbor workers 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 asments 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 Valley calibration point. Characteristics of the 72 different calibration sets, each consisting of six calibration points: Average squared deviation s see Free chat line numbers Killeen TX. 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.
Best first date restaurants Santa Ana that fossil 2 could be ased to only one node in best online dating Mission 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, Phoenix Arizona AZ free sex chat online that the corresponding fossils were erroneously ased to the respective nodes, whereas low s values would characterize calibration sets with high internal consistency. In order to for possible effects related to the molecular dating method in our case multidivtimethe 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.