Annals of Botany 104 789 794 2009 doi 10 1093 aob mcp192 available online at www aob oxfordjournals org BOTANICAL BRIEFING Calibrating the Tree of Life fossils molecules and evolutionary timescales Fe lix Forest Jodrell Laboratory Royal Botanic Gardens Kew Richmond Surrey TW9 3DS UK Received 9 April 2009 Returned for revision 11 June 2009 Accepted 9 July 2009 Published electronically 8 August 2009 Background Molecular dating has gained ever increasing interest since the molecular clock hypothesis was proposed in the 1960s Molecular dating provides detailed temporal frameworks for divergence events in phylogenetic trees allowing diverse evolutionary questions to be addressed The key aspect of the molecular clock hypothesis namely that differences in DNA or protein sequence between two species are proportional to the time elapsed since they diverged was soon shown to be untenable Other approaches were proposed to take into account rate heterogeneity among lineages but the calibration process by which relative times are transformed into absolute ages has received little attention until recently New methods have now been proposed to resolve potential sources of error associated with the calibration of phylogenetic trees particularly those involving use of the fossil record Scope and Conclusions The use of the fossil record as a source of independent information in the calibration process is the main focus of this paper other sources of calibration information are also discussed Particularly error prone aspects of fossil calibration are identified such as fossil dating the phylogenetic placement of the fossil and the incompleteness of the fossil record Methods proposed to tackle one or more of these potential error sources are discussed e g fossil cross validation prior distribution of calibration points and confidence intervals on the fossil record In conclusion the fossil record remains the most reliable source of information for the calibration of phylogenetic trees although associated assumptions and potential bias must be taken into account Key words Calibration fossil incompleteness molecular dating rate heterogeneity relaxed molecular clock uncertainty IN T RO DU C T IO N The use of DNA sequences to estimate divergence times on phylogenetic trees molecular dating has gained increasing interest in the field of evolutionary biology in the past decade The abundance of publications on the subject the numerous alternative methods proposed and the often heated debates on various aspects of the discipline demonstrate the interest it generates The molecular clock hypothesis was first proposed by Zuckerkandl and Pauling 1965 they proposed that differences in DNA or protein sequences between two species are proportional to the time elapsed since the divergence from their most recent common ancestor The subsequent inclusion of temporal frameworks in many evolutionary studies has influenced the way results are interpreted and significantly modified the way in which conclusions are drawn from these findings Linking the evolution of particular morphological characters or key ecological innovations to geological climatic or biotic events is much improved in the light of an evolutionary timescale The development of molecular dating tools became particularly valuable to the discipline of historical biogeography it added a temporal gauge to the directionality of events demonstrated by the topology of phylogenetic trees Inferences on observed distribution patterns were rendered significantly more plausible under a temporal framework even if only descriptive Furthermore new methods of biogeographical reconstruction have been developed such as Lagrange which uses a likelihood framework E mail f forest kew org to infer the evolution of geographical ranges and incorporates divergence times as well as constraining the connections between areas to specific times Ree and Smith 2008 The rationale of the molecular clock hypothesis that evolutionary rates are constant was shown to be invalid in the majority of examined cases the clock does not tick regularly The heterogeneity of substitution rates among different lineages in a phylogenetic tree explains this irregularity Britten 1986 and is a result of species specific factors such as generation time metabolic rate effective population size and mutation rates see Rutschmann 2006 The extent of influence of some such factors however remains in dispute e g Whittle and Johnston 2003 Rutschmann 2006 classified the most commonly employed methods for estimating divergence times into three categories depending on how they handle rate heterogeneity namely 1 assuming a global substitution rate standard molecular clock 2 correcting for rate heterogeneity e g by deleting branches or incorporating several rates categories before the dating procedure and 3 incorporating rate heterogeneity i e integrating rate heterogeneity into the dating procedure using rate change models relaxed molecular clock The four most commonly used methods in the literature all fall into the third category these are non parametric rate smoothing NPRS Sanderson 1997 penalized likelihood PL Sanderson 2002 the Bayesian method implemented in the Multidivtime package Thorne et al 1998 and Bayesian evolutionary analysis by sampling trees BEAST Drummond and Rambaut 2007 The first three of these methods assume The Author 2009 Published by Oxford University Press on behalf of the Annals of Botany Company All rights reserved For Permissions please email journals permissions oxfordjournals org 790 Forest Calibrating the Tree of Life rate changes between ancestral and descendant lineages are autocorrelated i e that substitution rates in descendant lineages are to an extent inherited from ancestral lineages these methods differ in the way that rate autocorrelation is handled BEAST does not assume rate autocorrelation instead it samples rates from a distribution Additional flexibility is found in BEAST in its optional tree topology requirement that can incorporate phylogenetic uncertainty and the possibility of assigning distributions to the calibration process a priori see below More details on these methods and several others are available elsewhere Rutschmann 2006 and references therein Two main topics have fuelled the controversy associated with molecular clocks these are how to handle rate heterogeneity and calibration At its outset the field of molecular dating was focused on circumvention of rate
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