Postdoctoral Fellow
Reconstructing the timing of divergence events is critical for testing evolutionary hypotheses. This project will explore large-scale patterns of disparity between temporal information provided by the fossil record and molecular divergence dating. Synthesis will be achieved via re-use of results mined from the bioinformatics resource TimeTree and the Paleobiology Database. Preliminary results indicate that a critical mass of divergence estimates exist to serve as a catalyst for meta-analysis. Pilot analyses of Aves and Insecta confirm a substantial gap between molecular estimates and fossil appearances, with molecular dates averaging 2.33 times fossil age. Partial reconciliation of this gap (reducing ratio to 1.66) can be achieved by accounting for first fossil appearances of sister taxa and constructing confidence intervals that realistically model distributions of fossils through time. Unexpected patterns suggestive of biases in branch length estimation warrant further investigation. Consistently greater disparity exists between fossil and molecular dates for shallow versus deep nodes, and for dates from mitochondrial versus nuclear genes. In order to determine whether these patterns are general, meta-analysis of data from ~300 clades spanning 6 major groups is proposed. Objectives include: (1) Establishing baseline estimates of disparity and modeling the proportion expected from gaps in the fossil record, (2) testing hypotheses of bias related to fossil preservation and branch-length reconstruction artifacts by comparing disparity for stem and crown divergences, and (3) testing for consistent biases related to data type (mitochondrial, nuclear, mixed) and calibration regime (e.g., position of calibrated nodes relative to dated nodes).
Large scale patterns of disparity between the fossil record and divergence dating analyses
| PI(s): | Daniel Ksepka |
| Start Date: | 1-Jan-2013 |
| End Date: | 31-Dec-2014 |
| Keywords: | systematics, paleontology, phylogenetics, meta-analysis, molecular biology |
Reconstructing the timing of divergence events is critical for testing evolutionary hypotheses. This project will explore large-scale patterns of disparity between temporal information provided by the fossil record and molecular divergence dating. Synthesis will be achieved via re-use of results mined from the bioinformatics resource TimeTree and the Paleobiology Database. Preliminary results indicate that a critical mass of divergence estimates exist to serve as a catalyst for meta-analysis. Pilot analyses of Aves and Insecta confirm a substantial gap between molecular estimates and fossil appearances, with molecular dates averaging 2.33 times fossil age. Partial reconciliation of this gap (reducing ratio to 1.66) can be achieved by accounting for first fossil appearances of sister taxa and constructing confidence intervals that realistically model distributions of fossils through time. Unexpected patterns suggestive of biases in branch length estimation warrant further investigation. Consistently greater disparity exists between fossil and molecular dates for shallow versus deep nodes, and for dates from mitochondrial versus nuclear genes. In order to determine whether these patterns are general, meta-analysis of data from ~300 clades spanning 6 major groups is proposed. Objectives include: (1) Establishing baseline estimates of disparity and modeling the proportion expected from gaps in the fossil record, (2) testing hypotheses of bias related to fossil preservation and branch-length reconstruction artifacts by comparing disparity for stem and crown divergences, and (3) testing for consistent biases related to data type (mitochondrial, nuclear, mixed) and calibration regime (e.g., position of calibrated nodes relative to dated nodes).Related products
Publications- Avian diversification patterns across the K-Pg boundary: influence of calibrations, datasets and model misspecification Ksepka, D.T. and M.J. Phillips. IN REVIEW. Avian diversification patterns across the K-Pg boundary: influence of calibrations, datasets and model misspecification. Annals of the Missouri Botanical Garden (invited contribution to systematics symposium volume).
- Flying rocks and flying clocks: disparity in fossil and molecular dates for birds Ksepka, D.T., J.L. Ware and K.S. Lamm. 2014. Flying rocks and flying clocks: disparity in fossil and molecular dates for birds. Proceedings of the Royal Society B 281: 20140677.
- 2013. Hummingbird ancestor reveals evolution of its unique flight. Discover Magazine.
- 2013. Fossil illuminates ancestry of swifts and hummingbirds. Science News.
- 2013. Fly like a hummingbird, glide like a swift. Science Magazine.
- 2013. Bird fossil sheds light on how swift and hummingbird flight came to be. Eurekalert.
- 2013. Uncovering Africa's oldest known penguins. Eurekalert
- 2013. Penguin fossils discovered in Africa called oldest specimens on continent. Huffington Post
- 2013. Oldest fossils yet of African penguins found. NBC News
- 2013. Found: Africa's oldest penguins. Scientific American
- 2013. Found: Africa's oldest penguins. Discovery
- 2013. Africa's oldest known penguins are SEVEN MILLION years old: Amazing discovery shows boiling continent had four species but they were wiped out by changing sea levels. UK Daily Mail
