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Integration of Bayesian molecular clock methods and fossil-based soft bounds reveals early Cenozoic origin of African lacertid lizards.

Hipsley CA, Himmelmann L, Metzler D, Müller J - BMC Evol. Biol. (2009)

Bottom Line: We also test the reliability of our proposed calibrations by exploring effects of individual priors on posterior estimates.Our findings indicate much earlier origins for these clades than previously reported, and we discuss our results in light of paleogeographic trends during the Cenozoic.Our results emphasize the sensitivity of molecular divergence dates to fossil calibrations, and support the use of combined molecular data sets and multiple, well-spaced dates from the fossil record as minimum node constraints.

View Article: PubMed Central - HTML - PubMed

Affiliation: Museum für Naturkunde - Leibniz-Institut für Evolutions- und Biodiversitätsforschung an der Humboldt-Universität zu Berlin, Invalidenstr, 43, 10115 Berlin, Germany. Christy.Hipsley@mfn-berlin.de

ABSTRACT

Background: Although current molecular clock methods offer greater flexibility in modelling evolutionary events, calibration of the clock with dates from the fossil record is still problematic for many groups. Here we implement several new approaches in molecular dating to estimate the evolutionary ages of Lacertidae, an Old World family of lizards with a poor fossil record and uncertain phylogeny. Four different models of rate variation are tested in a new program for Bayesian phylogenetic analysis called TreeTime, based on a combination of mitochondrial and nuclear gene sequences. We incorporate paleontological uncertainty into divergence estimates by expressing multiple calibration dates as a range of probabilistic distributions. We also test the reliability of our proposed calibrations by exploring effects of individual priors on posterior estimates.

Results: According to the most reliable model, as indicated by Bayes factor comparison, modern lacertids arose shortly after the K/T transition and entered Africa about 45 million years ago, with the majority of their African radiation occurring in the Eocene and Oligocene. Our findings indicate much earlier origins for these clades than previously reported, and we discuss our results in light of paleogeographic trends during the Cenozoic.

Conclusion: This study represents the first attempt to estimate evolutionary ages of a specific group of reptiles exhibiting uncertain phylogenetic relationships, molecular rate variation and a poor fossil record. Our results emphasize the sensitivity of molecular divergence dates to fossil calibrations, and support the use of combined molecular data sets and multiple, well-spaced dates from the fossil record as minimum node constraints. The bioinformatics program used here, TreeTime, is publicly available, and we recommend its use for molecular dating of taxa faced with similar challenges.

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Comparison of divergence dates estimated in the Bayesian programs TreeTime and BEAST. Mean molecular divergence dates, in millions of years, estimated under the ULN relaxed molecular clock model with a 10% prior probability distribution in TreeTime plotted against dates estimated in BEAST for all nodes in the Additional file 1. The solid line indicates a 1:1 relationship between the two values.
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Figure 3: Comparison of divergence dates estimated in the Bayesian programs TreeTime and BEAST. Mean molecular divergence dates, in millions of years, estimated under the ULN relaxed molecular clock model with a 10% prior probability distribution in TreeTime plotted against dates estimated in BEAST for all nodes in the Additional file 1. The solid line indicates a 1:1 relationship between the two values.

Mentions: The BEAST analysis of the combined data resulted in a tree topology identical to TreeTime, except for the loss of the Archaeolacerta/Zootoca sister group. Molecular dates were younger in BEAST for all but one node (Figure 3; Additional file 1, node 19), but still all fall within the 95% confidence intervals produced in TreeTime. The most significant differences occur at the major lacertid splits (Additional file 1, nodes 4, 5 and 6), where divergences occur approximately 10 My later. These changes are most likely attributed to differences in model parameters and not performance of the programs themselves. The prior distribution on branching times used in BEAST, the Yule Process, has a tendency to pull divergence dates towards the tips of the tree when basal internodes are short but terminal branches are long. This influence can be even stronger when rates vary inside the tree, as is most likely the case in Lacertidae. In TreeTime, prior information on branching times is applied only to calibrated nodes, and every allocation of branching times for remaining nodes in the tree is equally likely. Because of these differences in program settings, we refer only to the age estimates given by TreeTime for our discussion.


Integration of Bayesian molecular clock methods and fossil-based soft bounds reveals early Cenozoic origin of African lacertid lizards.

Hipsley CA, Himmelmann L, Metzler D, Müller J - BMC Evol. Biol. (2009)

Comparison of divergence dates estimated in the Bayesian programs TreeTime and BEAST. Mean molecular divergence dates, in millions of years, estimated under the ULN relaxed molecular clock model with a 10% prior probability distribution in TreeTime plotted against dates estimated in BEAST for all nodes in the Additional file 1. The solid line indicates a 1:1 relationship between the two values.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2719621&req=5

Figure 3: Comparison of divergence dates estimated in the Bayesian programs TreeTime and BEAST. Mean molecular divergence dates, in millions of years, estimated under the ULN relaxed molecular clock model with a 10% prior probability distribution in TreeTime plotted against dates estimated in BEAST for all nodes in the Additional file 1. The solid line indicates a 1:1 relationship between the two values.
Mentions: The BEAST analysis of the combined data resulted in a tree topology identical to TreeTime, except for the loss of the Archaeolacerta/Zootoca sister group. Molecular dates were younger in BEAST for all but one node (Figure 3; Additional file 1, node 19), but still all fall within the 95% confidence intervals produced in TreeTime. The most significant differences occur at the major lacertid splits (Additional file 1, nodes 4, 5 and 6), where divergences occur approximately 10 My later. These changes are most likely attributed to differences in model parameters and not performance of the programs themselves. The prior distribution on branching times used in BEAST, the Yule Process, has a tendency to pull divergence dates towards the tips of the tree when basal internodes are short but terminal branches are long. This influence can be even stronger when rates vary inside the tree, as is most likely the case in Lacertidae. In TreeTime, prior information on branching times is applied only to calibrated nodes, and every allocation of branching times for remaining nodes in the tree is equally likely. Because of these differences in program settings, we refer only to the age estimates given by TreeTime for our discussion.

Bottom Line: We also test the reliability of our proposed calibrations by exploring effects of individual priors on posterior estimates.Our findings indicate much earlier origins for these clades than previously reported, and we discuss our results in light of paleogeographic trends during the Cenozoic.Our results emphasize the sensitivity of molecular divergence dates to fossil calibrations, and support the use of combined molecular data sets and multiple, well-spaced dates from the fossil record as minimum node constraints.

View Article: PubMed Central - HTML - PubMed

Affiliation: Museum für Naturkunde - Leibniz-Institut für Evolutions- und Biodiversitätsforschung an der Humboldt-Universität zu Berlin, Invalidenstr, 43, 10115 Berlin, Germany. Christy.Hipsley@mfn-berlin.de

ABSTRACT

Background: Although current molecular clock methods offer greater flexibility in modelling evolutionary events, calibration of the clock with dates from the fossil record is still problematic for many groups. Here we implement several new approaches in molecular dating to estimate the evolutionary ages of Lacertidae, an Old World family of lizards with a poor fossil record and uncertain phylogeny. Four different models of rate variation are tested in a new program for Bayesian phylogenetic analysis called TreeTime, based on a combination of mitochondrial and nuclear gene sequences. We incorporate paleontological uncertainty into divergence estimates by expressing multiple calibration dates as a range of probabilistic distributions. We also test the reliability of our proposed calibrations by exploring effects of individual priors on posterior estimates.

Results: According to the most reliable model, as indicated by Bayes factor comparison, modern lacertids arose shortly after the K/T transition and entered Africa about 45 million years ago, with the majority of their African radiation occurring in the Eocene and Oligocene. Our findings indicate much earlier origins for these clades than previously reported, and we discuss our results in light of paleogeographic trends during the Cenozoic.

Conclusion: This study represents the first attempt to estimate evolutionary ages of a specific group of reptiles exhibiting uncertain phylogenetic relationships, molecular rate variation and a poor fossil record. Our results emphasize the sensitivity of molecular divergence dates to fossil calibrations, and support the use of combined molecular data sets and multiple, well-spaced dates from the fossil record as minimum node constraints. The bioinformatics program used here, TreeTime, is publicly available, and we recommend its use for molecular dating of taxa faced with similar challenges.

Show MeSH