Dating the fossil record pdf. A Total-Evidence Approach to Dating with Fossils, Applied to the Early Radiation of the Hymenoptera.



Dating the fossil record pdf

Dating the fossil record pdf

Fredrik Ronquist and Seraina Klopfstein contributed equally to this article. This relies on indirect methods that, in the worst case, misrepresent the fossil information. Here, wecontrast such node dating with an approach that includes fossils along with the extant taxa in a Bayesian 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 about 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.

The calibration of the trees has also improved considerably. Instead of relying on a single-point estimate of the clock rate, it is now common to use multiple calibration points derived from the fossil record, each of which is associated with a probability distribution summarizing the available information Yang and Rannala Increasingly, such complex data sets are being analyzed with Bayesian methods, which provide a unifying framework for accommodating multiple sources of uncertainty.

To avoid constraining the tree, one can attach the calibration information to the most recent common ancestor of some named terminal taxa instead. Second, node dating only extracts calibration information from the oldest fossil assigned to a particular group, as younger fossils from the same group do not provide any additional information on the minimum age of the calibrated node.

Moreover, many at New Copenhagen University on October 23, http: For node dating, one thus often ends up discarding most of the information preserved in the fossil record but see Marshall Third, the raw data from the fossil record—the ages of the fossils and their morphology—must be translated into appropriate probability distributions for the ages of the calibrated nodes, a process that is not straightforward Parham et al.

Even if the phylogenetic position of a fossil can be determined beyond any reasonable doubt, it is likely to sit on a side branch of some unknown length rather than directly on the calibration node itself.

Thus, the fossil only provides a minimum age, and it remains unclear how the information available in the morphological characters about the period between the calibration point and the formation of the fossil can be translated into a probability distribution for the age of the calibrated node.

Another possibility is to use cross- validation techniques to identify and remove inconsistent calibration nodes Near et al. Nevertheless, node dating still relies heavily on indirect ad hoc translation of the fossil record into appropriate calibration points. Several studies have analyzed fossil and recent taxa together, using combined morphological and molecular data, to study the placement of the fossils and their impact on the topology estimates for the recent taxa Lee et al.

However, these studies were not intended to result in calibrated trees, or if they were, they only used the inferred placements of the fossils to inform a classical node-dating approach. Although the fossil placement and minimum calibration constraints on the tree were thus improved, these approaches could not avoid the largely arbitrary assignment of a probability distribution to the calibration points. It uses morphological data to infer fossil placement, like some previous studies, but it also calibrates the tree at the same time.

It relies on the morphological similarity between a fossil and the reconstructed ancestors in the extant tree in assessing the likely length of any extinct side branch on which the fossil sits. Thus, total-evidence dating explicitly incorporates and exposes the data used to indirectly derive calibration points in the node dating approach, while integrating over the associated uncertainties.

However, his study considered a relatively small data set only one gene with poor overlap between morphological and molecular data only eight taxa coded for both. Moreover, the fossils sampled for his analysis mostly clustered outside of the extant taxa of the ingroup, reducing the power of the approach in inferring ingroup divergence times.

Last but not least, he did not directly compare total-evidence dating to node dating, and it thus remains unclear how the two approaches perform on the same data set.

In this article, we illustrate total-evidence dating and its potential using the early radiation of the Hymenoptera wasps, ants, bees, and relatives as a test case. The Hymenoptera are probably the sister group of all other extant holometabolous insects Beutel et al. The fossil sample consists of 45 taxa spanning the entire Hymenoptera tree and includes the oldest known representatives of all major lineages.

Importantly, we provide a rigorous mathematical foundation for total-evidence analysis by explicitly formulating a prior model for clock trees with fossils. We also contrast the results obtained from total-evidence dating with estimates derived under traditional node dating, allowing detailed comparison of the two approaches.

Finally, we make all Bayesian analytical techniques developed for this study available in the recently released software package MrBayes 3.

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Fossil Record Mystery



Dating the fossil record pdf

Fredrik Ronquist and Seraina Klopfstein contributed equally to this article. This relies on indirect methods that, in the worst case, misrepresent the fossil information. Here, wecontrast such node dating with an approach that includes fossils along with the extant taxa in a Bayesian 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 about 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.

The calibration of the trees has also improved considerably. Instead of relying on a single-point estimate of the clock rate, it is now common to use multiple calibration points derived from the fossil record, each of which is associated with a probability distribution summarizing the available information Yang and Rannala Increasingly, such complex data sets are being analyzed with Bayesian methods, which provide a unifying framework for accommodating multiple sources of uncertainty.

To avoid constraining the tree, one can attach the calibration information to the most recent common ancestor of some named terminal taxa instead. Second, node dating only extracts calibration information from the oldest fossil assigned to a particular group, as younger fossils from the same group do not provide any additional information on the minimum age of the calibrated node. Moreover, many at New Copenhagen University on October 23, http: For node dating, one thus often ends up discarding most of the information preserved in the fossil record but see Marshall Third, the raw data from the fossil record—the ages of the fossils and their morphology—must be translated into appropriate probability distributions for the ages of the calibrated nodes, a process that is not straightforward Parham et al.

Even if the phylogenetic position of a fossil can be determined beyond any reasonable doubt, it is likely to sit on a side branch of some unknown length rather than directly on the calibration node itself. Thus, the fossil only provides a minimum age, and it remains unclear how the information available in the morphological characters about the period between the calibration point and the formation of the fossil can be translated into a probability distribution for the age of the calibrated node.

Another possibility is to use cross- validation techniques to identify and remove inconsistent calibration nodes Near et al. Nevertheless, node dating still relies heavily on indirect ad hoc translation of the fossil record into appropriate calibration points. Several studies have analyzed fossil and recent taxa together, using combined morphological and molecular data, to study the placement of the fossils and their impact on the topology estimates for the recent taxa Lee et al.

However, these studies were not intended to result in calibrated trees, or if they were, they only used the inferred placements of the fossils to inform a classical node-dating approach. Although the fossil placement and minimum calibration constraints on the tree were thus improved, these approaches could not avoid the largely arbitrary assignment of a probability distribution to the calibration points. It uses morphological data to infer fossil placement, like some previous studies, but it also calibrates the tree at the same time.

It relies on the morphological similarity between a fossil and the reconstructed ancestors in the extant tree in assessing the likely length of any extinct side branch on which the fossil sits.

Thus, total-evidence dating explicitly incorporates and exposes the data used to indirectly derive calibration points in the node dating approach, while integrating over the associated uncertainties.

However, his study considered a relatively small data set only one gene with poor overlap between morphological and molecular data only eight taxa coded for both. Moreover, the fossils sampled for his analysis mostly clustered outside of the extant taxa of the ingroup, reducing the power of the approach in inferring ingroup divergence times. Last but not least, he did not directly compare total-evidence dating to node dating, and it thus remains unclear how the two approaches perform on the same data set.

In this article, we illustrate total-evidence dating and its potential using the early radiation of the Hymenoptera wasps, ants, bees, and relatives as a test case.

The Hymenoptera are probably the sister group of all other extant holometabolous insects Beutel et al. The fossil sample consists of 45 taxa spanning the entire Hymenoptera tree and includes the oldest known representatives of all major lineages. Importantly, we provide a rigorous mathematical foundation for total-evidence analysis by explicitly formulating a prior model for clock trees with fossils.

We also contrast the results obtained from total-evidence dating with estimates derived under traditional node dating, allowing detailed comparison of the two approaches. Finally, we make all Bayesian analytical techniques developed for this study available in the recently released software package MrBayes 3.

Dating the fossil record pdf

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