American Journal of Botany 91 10 1656 1665 2004 MOLECULAR EVIDENCE ON PLANT DIVERGENCE TIMES1 MICHAEL J SANDERSON 2 5 JEFFREY L THORNE 3 NIKLAS WIKSTRO M 4 AND KA RE BREMER4 Section of Evolution and Ecology University of California Davis California 95616 USA 3Bioinformatics Research Center North Carolina State University Campus Box 7566 Raleigh North Carolina 27695 USA and 4Department of Systematic Botany Evolutionary Biology Centre Uppsala University Norbyva gen 18D SE 752 36 Uppsala Sweden 2 Estimation of divergence times from sequence data has become increasingly feasible in recent years Conflicts between fossil evidence and molecular dates have sparked the development of new methods for inferring divergence times further encouraging these efforts In this paper available methods for estimating divergence times are reviewed especially those geared toward handling the widespread variation in rates of molecular evolution observed among lineages The assumptions strengths and weaknesses of local clock Bayesian and rate smoothing methods are described The rapidly growing literature applying these methods to key divergence times in plant evolutionary history is also reviewed These include the crown group ages of green plants land plants seed plants angiosperms and major subclades of angiosperms Finally attempts to infer divergence times are described in the context of two very different temporal settings recent adaptive radiations and much more ancient biogeographic patterns Key words adaptive radiation biogeography divergence time molecular clock phylogeny rates Molecular sequence data have been used to estimate divergence times in plants for thirty years often with controversial results For example early studies aimed at the abominable mystery of angiosperm origins undertaken assuming a strict molecular clock reported ages two to four times older than the first Early Cretaceous angiosperm fossils Ramshaw et al 1972 Martin et al 1989 However the broader molecular evolution community did not turn its attention to resolving conflicts between molecules and fossils until the publication of similarly surprising findings about the age of metazoans birds and mammals Doolittle et al 1996 Hedges et al 1996 Wray et al 1996 Although Doolittle et al 1996 obtained paleontologically reasonable dates for the metazoan radiation their study was overshadowed by the findings of Wray et al 1996 which estimated that the crown group radiation of metazoans lay deep in the Precambrian perhaps twice as ancient as implied by Cambrian fossils In another provocative paper Hedges et al 1996 estimated the age of orders of mammals and birds to be much older than that suggested by the fossil evidence These studies and numerous subsequent analyses at similar taxonomic scales Ayala et al 1998 Lee 1999 Wang et al 1999 Benton and Ayala 2003 spurred great interest in estimating divergence times from sequence data Among the consequences has been an increased appreciation for the role of fossil evidence Lee 1999 Smith and Peterson 2002 development of new methodologies that impose less restrictive assumptions on the molecular substitution process Takezaki et al 1995 Sanderson 1997 2002 Rambaut and Bromham 1998 Thorne et al 1998 Huelsenbeck et al 2000 Thorne and Kishino 2002 and development of new techniques to bring large quantities of heterogeneous sequence data to bear on a single problem Nei et al 2001 Several recent reviews cover these issues from these different perspectives Sanderson 1998 Arbogast et al 2002 Smith and Peterson 2002 Bromham and Penny 2003 Benton and Ayala 2003 However renewed enthusiasm has been tempered somewhat by a realization that inference methods are still far from per1 5 Manuscript received 30 December 2003 revision accepted 24 June 2004 E mail mjsanderson ucdavis edu fect Methods clearly need improvement when they produce conflicting answers to the same question Although dramatic conflicts between ages based on sequence divergences vs fossils may have raised the most concerns about the use of molecular data to estimate ages other lines of evidence have also raised questions These include conflicting estimates derived from different data sets such as different taxon samples Sanderson and Doyle 2001 sequence samples Heckman et al 2001 and sequence partitions Sanderson and Doyle 2001 Yang and Yoder 2003 conflicts between dates estimated using different calibration points Soltis et al 2002 and conflicts between different inference methods themselves applied to precisely the same data The rapidly increasing number of case studies in plants promises to provide useful insights to sort through these conflicts and help improve methodology In this paper we examine the interplay between methodology and data and review how new methods have shed light on the timing of important events in plant evolution METHODOLOGICAL ISSUES When using molecular sequence data to estimate divergence times one key problem is how to disentangle times from evolutionary rates The expected divergence between homologous sequences is determined by the time since common ancestry and the rate at which differences have been accumulating Although they provide information about the products of rates and times sequence data do not by themselves allow rates and times to be disentangled This explains why all such studies supply one or the other of these pieces of information as external assumptions either calibration times e g fossils or other events in Earth history or canonical rates e g the legendary vertebrate mitochondrial rate of 2 sequence divergence per million years Klicka and Zink 1997 Methods assuming a clock Inferring divergence times with a known topology and a molecular clock is relatively straightforward Calibration points based on fossil evidence can dictate the time duration of a branch and molecular sequence data can provide information about its length A branch length divided by its time duration yields the average evolutionary rate on the branch Under the assumption of a clock rates in one part of the tree derived from solid paleontological or biogeographical evidence permit dating of nodes in other parts of the tree that lack paleontological evidence Because the number of interior nodes on a rooted tree is guaranteed to be 1656 October 2004 SANDERSON ET AL PLANT DIVERGENCE TIMES less than the number of branches the clock assumption together with calibration points allow branch length information to be converted
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