Literature DB >> 15486700

Error in estimation of rate and time inferred from the early amniote fossil record and avian molecular clocks.

Marcel van Tuinen1, Elizabeth A Hadly.   

Abstract

The best reconstructions of the history of life will use both molecular time estimates and fossil data. Errors in molecular rate estimation typically are unaccounted for and no attempts have been made to quantify this uncertainty comprehensively. Here, focus is primarily on fossil calibration error because this error is least well understood and nearly universally disregarded. Our quantification of errors in the synapsid-diapsid calibration illustrates that although some error can derive from geological dating of sedimentary rocks, the absence of good stem fossils makes phylogenetic error the most critical. We therefore propose the use of calibration ages that are based on the first undisputed synapsid and diapsid. This approach yields minimum age estimates and standard errors of 306.1 +/- 8.5 MYR for the divergence leading to birds and mammals. Because this upper bound overlaps with the recent use of 310 MYR, we do not support the notion that several metazoan divergence times are significantly overestimated because of serious miscalibration (sensuLee 1999). However, the propagation of relevant errors reduces the statistical significance of the pre-K-T boundary diversification of many bird lineages despite retaining similar point time estimates. Our results demand renewed investigation into suitable loci and fossil calibrations for constructing evolutionary timescales.

Mesh:

Year:  2004        PMID: 15486700     DOI: 10.1007/s00239-004-2624-9

Source DB:  PubMed          Journal:  J Mol Evol        ISSN: 0022-2844            Impact factor:   2.395


  33 in total

1.  Molecular clock calibrations and metazoan divergence dates.

Authors:  M S Lee
Journal:  J Mol Evol       Date:  1999-09       Impact factor: 2.395

2.  Skeletons of terrestrial cetaceans and the relationship of whales to artiodactyls.

Authors:  J G Thewissen; E M Williams; L J Roe; S T Hussain
Journal:  Nature       Date:  2001-09-20       Impact factor: 49.962

3.  Genomic clocks and evolutionary timescales.

Authors:  S Blair Hedges; Sudhir Kumar
Journal:  Trends Genet       Date:  2003-04       Impact factor: 11.639

Review 4.  The origin and evolution of model organisms.

Authors:  S Blair Hedges
Journal:  Nat Rev Genet       Date:  2002-11       Impact factor: 53.242

5.  Petrolacosaurus, the oldest known diapsid reptile.

Authors:  R R Reisz
Journal:  Science       Date:  1977-06-03       Impact factor: 47.728

6.  Body size effects and rates of cytochrome b evolution in tube-nosed seabirds.

Authors:  G B Nunn; S E Stanley
Journal:  Mol Biol Evol       Date:  1998-10       Impact factor: 16.240

7.  Continental breakup and the ordinal diversification of birds and mammals.

Authors:  S B Hedges; P H Parker; C G Sibley; S Kumar
Journal:  Nature       Date:  1996-05-16       Impact factor: 49.962

8.  Determining divergence times of the major kingdoms of living organisms with a protein clock.

Authors:  R F Doolittle; D F Feng; S Tsang; G Cho; E Little
Journal:  Science       Date:  1996-01-26       Impact factor: 47.728

9.  Mutation rates in mammalian genomes.

Authors:  Sudhir Kumar; Sankar Subramanian
Journal:  Proc Natl Acad Sci U S A       Date:  2002-01-15       Impact factor: 11.205

10.  The complete mitochondrial genome of Alligator mississippiensis and the separation between recent archosauria (birds and crocodiles).

Authors:  A Janke; U Arnason
Journal:  Mol Biol Evol       Date:  1997-12       Impact factor: 16.240

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  11 in total

1.  Characterization of MHC class II genes from an ancient reptile lineage, Sphenodon (tuatara).

Authors:  Hilary C Miller; Katherine Belov; Charles H Daugherty
Journal:  Immunogenetics       Date:  2005-10-29       Impact factor: 2.846

Review 2.  Variability in sex-determining mechanisms influences genome complexity in reptilia.

Authors:  D E Janes; C L Organ; S V Edwards
Journal:  Cytogenet Genome Res       Date:  2010-03-04       Impact factor: 1.636

Review 3.  On the age of eukaryotes: evaluating evidence from fossils and molecular clocks.

Authors:  Laura Eme; Susan C Sharpe; Matthew W Brown; Andrew J Roger
Journal:  Cold Spring Harb Perspect Biol       Date:  2014-08-01       Impact factor: 10.005

4.  Genomic V exons from whole genome shotgun data in reptiles.

Authors:  D N Olivieri; B von Haeften; C Sánchez-Espinel; J Faro; F Gambón-Deza
Journal:  Immunogenetics       Date:  2014-06-04       Impact factor: 2.846

5.  Higher-order phylogeny of modern birds (Theropoda, Aves: Neornithes) based on comparative anatomy. II. Analysis and discussion.

Authors:  Bradley C Livezey; Richard L Zusi
Journal:  Zool J Linn Soc       Date:  2007-01-01       Impact factor: 3.286

6.  A genetic and cytogenetic map for the duck (Anas platyrhynchos).

Authors:  Yinhua Huang; Yonghui Zhao; Chris S Haley; Shengqiang Hu; Jinping Hao; Changxin Wu; Ning Li
Journal:  Genetics       Date:  2006-03-01       Impact factor: 4.562

7.  Best practices for justifying fossil calibrations.

Authors:  James F Parham; Philip C J Donoghue; Christopher J Bell; Tyler D Calway; Jason J Head; Patricia A Holroyd; Jun G Inoue; Randall B Irmis; Walter G Joyce; Daniel T Ksepka; José S L Patané; Nathan D Smith; James E Tarver; Marcel van Tuinen; Ziheng Yang; Kenneth D Angielczyk; Jenny M Greenwood; Christy A Hipsley; Louis Jacobs; Peter J Makovicky; Johannes Müller; Krister T Smith; Jessica M Theodor; Rachel C M Warnock; Michael J Benton
Journal:  Syst Biol       Date:  2011-11-21       Impact factor: 15.683

8.  Potential for bias and low precision in molecular divergence time estimation of the Canopy of Life: an example from aquatic bird families.

Authors:  Marcel van Tuinen; Christopher R Torres
Journal:  Front Genet       Date:  2015-06-08       Impact factor: 4.599

9.  DNA and morphology unite two species and 10 million year old fossils.

Authors:  Simon F K Hills; James S Crampton; Steven A Trewick; Mary Morgan-Richards
Journal:  PLoS One       Date:  2012-12-20       Impact factor: 3.240

10.  Postembryonic Nephrogenesis and Persistence of Six2-Expressing Nephron Progenitor Cells in the Reptilian Kidney.

Authors:  Troy Camarata; Alexis Howard; Ruth M Elsey; Sarah Raza; Alice O'Connor; Brian Beatty; Jack Conrad; Nikos Solounias; Priscilla Chow; Saima Mukta; Aleksandr Vasilyev
Journal:  PLoS One       Date:  2016-05-04       Impact factor: 3.240

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