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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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Influences of individual calibration points on node ages. Mean molecular divergence dates, ± 1 standard deviation, for the major lineages estimated using different combinations of fossil calibrations. Divergence dates were calculated using: all four fossil calibrations; all excluding the teiid Cnemidophorus tigris and the amphisbaenian Rhineura floridana; all except R. floridana; and all except C. tigris. Evolutionary splits are Teiidae-Amphisbaenia (circle), Amphisbaenia-Lacertidae (star), Gallotinae-Lacertinae (triangle), and Lacertini-Eremiadini (square).
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Figure 5: Influences of individual calibration points on node ages. Mean molecular divergence dates, ± 1 standard deviation, for the major lineages estimated using different combinations of fossil calibrations. Divergence dates were calculated using: all four fossil calibrations; all excluding the teiid Cnemidophorus tigris and the amphisbaenian Rhineura floridana; all except R. floridana; and all except C. tigris. Evolutionary splits are Teiidae-Amphisbaenia (circle), Amphisbaenia-Lacertidae (star), Gallotinae-Lacertinae (triangle), and Lacertini-Eremiadini (square).

Mentions: Three analyses were run under the ULN model each excluding one or more fossil priors. In almost all cases, estimated divergence dates were older and had larger standard deviations than when all calibrations were used (Figure 5). The largest changes occurred when both the amphisbaenian and teiid calibrations were removed. With the exception of the most recent split (Mesalina guttulata/Mesalina rubropunctata), divergence estimates became significantly older and standard deviations expanded by 5–20 My. Excluding the amphisbaenian calibration caused posterior ranges to increase by up to 30 My. Age increases were most strongly evident at the origins of the major lineages. Removing the teiid calibration alone had the least effect on posterior estimates, with a maximum increase of 2 My at all nodes (except for the Teiidae-Amphisbaenia split itself, which increased by almost 15 My).


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)

Influences of individual calibration points on node ages. Mean molecular divergence dates, ± 1 standard deviation, for the major lineages estimated using different combinations of fossil calibrations. Divergence dates were calculated using: all four fossil calibrations; all excluding the teiid Cnemidophorus tigris and the amphisbaenian Rhineura floridana; all except R. floridana; and all except C. tigris. Evolutionary splits are Teiidae-Amphisbaenia (circle), Amphisbaenia-Lacertidae (star), Gallotinae-Lacertinae (triangle), and Lacertini-Eremiadini (square).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 5: Influences of individual calibration points on node ages. Mean molecular divergence dates, ± 1 standard deviation, for the major lineages estimated using different combinations of fossil calibrations. Divergence dates were calculated using: all four fossil calibrations; all excluding the teiid Cnemidophorus tigris and the amphisbaenian Rhineura floridana; all except R. floridana; and all except C. tigris. Evolutionary splits are Teiidae-Amphisbaenia (circle), Amphisbaenia-Lacertidae (star), Gallotinae-Lacertinae (triangle), and Lacertini-Eremiadini (square).
Mentions: Three analyses were run under the ULN model each excluding one or more fossil priors. In almost all cases, estimated divergence dates were older and had larger standard deviations than when all calibrations were used (Figure 5). The largest changes occurred when both the amphisbaenian and teiid calibrations were removed. With the exception of the most recent split (Mesalina guttulata/Mesalina rubropunctata), divergence estimates became significantly older and standard deviations expanded by 5–20 My. Excluding the amphisbaenian calibration caused posterior ranges to increase by up to 30 My. Age increases were most strongly evident at the origins of the major lineages. Removing the teiid calibration alone had the least effect on posterior estimates, with a maximum increase of 2 My at all nodes (except for the Teiidae-Amphisbaenia split itself, which increased by almost 15 My).

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
Related in: MedlinePlus