WHEN CLOCKS (AND COMMUNITIES) COLLIDE: ESTIMATING DIVERGENCE TIME FROM MOLECULES AND THE FOSSIL RECORD

time was the domain of paleontology.Origination time could be assessed only through referenceto ﬁrst appearance data in the rock record. This changed almostfrom the beginnings of modern molecular biology, when it wasrealized that molecules could be used to calculate divergencetimes between living species. Early studies relied on immunolog-ical distance information, and the underlying rationale was sim-ple: because evolution involves changes to the genetic code, andbecause these changes accumulate over time, we should expectthe number of accumulated changes (the molecular distance) be-tween living taxa to increase as their time of divergence becomesolder (Zuckerkandl and Pauling, 1962). By inferring a rate ofevolution of the genetic code, we can place absolute time esti-mates on divergence points.Unfortunately, temporal estimates from molecules did not al-ways coincide with ﬁrst appearance data from the fossil record.This ﬁrst became apparent with the divergence between humansand living great apes. Based on presumed relationships betweenfossil and living primates at the time, paleontologists put the hu-man-ape split at roughly 20 million years (Simons, 1961; Pilbeam,1968). Protein clock studies, and later sequence-based analyses,suggested a much more recent divergence within the past 10 mil-lion years (Sarich and Wilson, 1967; Hasegawa et al., 1985).The outcome of this particular conﬂict colored the nature ofthe debate for many years. New fossil discoveries eventually putthe human-chimp split much closer to the molecular estimate(Fleagle, 1998). This became the standard textbook example ofthe molecule-fossil rift, and it seemed to lend credence to claimsthat molecular approaches were somehow more reliable thanthose restricted to paleontology. Throughout the 1980s and up tothe present, it was not uncommon to see published claims thatmolecular data were inherently superior to morphology and fossilsin phylogeny reconstruction and divergence time estimation (e.g.,Sibley and Ahlquist, 1987; Goodman, 1989; Hedges and Sibley,1994; Givnish and Sytsma, 1997; Douady et al., 2002)—eventhough molecules and morphology usually support very similarresults.Several other temporal conﬂicts have come to the surface overthe past 10 years. The most prominent involve the origin of livingmammalian and avian ‘‘orders.’’ Most ﬁrst appear as fossils inthe latest Cretaceous or Paleogene, but are predicted to have muchlonger roots in the Mesozoic from molecular evidence (Cooperand Penny, 1997; Bromham et al., 1999a; Foote et al., 1999; vanTuinen et al., 2000; Archibald and Duetschman, 2001; Springeret al., 2003). Similarly, the origin of metazoan phyla, most ofwhich ﬁrst appear during the ‘‘Cambrian Explosion’’ 550 ma butwhich are estimated to have originated as much as 1.5 billionyears ago on the basis of mitochondrial data (Wray et al., 1996;Bromham, 2003; Budd, 2003). Other conﬂicts have received lessattention but remain no less perplexing, such as the origin ofangiosperms (Doyle, 1998; Wikstro¨m et al., 2001) and gavialoidcrocodylians (Brochu, 1997; Harshman et al., 2003). These haveremained robust to improved data sets and techniques—the morewe look at fossils, molecules, or algorithms, the stronger the dis-parity seems to grow.What causes these conﬂicts? We believe part of the problemcontinues to be a lack of interaction between proponents of fossil-based and molecule-based dating approaches. This is unfortunate,because the centralization of these conﬂicts and a lack of dialoguemask the basic fact that molecules and fossils often support thesame answer, and in some cases, the answers are different becausethe questions are different (even if we fail to recognize the dif-ference). And both approaches must ultimately refer to the fossilrecord.We organized a symposium at the Sixth North American Pa-leontological Convention entitled ‘‘When Clocks Collide: Cali-brating Lineage Divergences from Fossils and Molecules.’’ Itbrought experts together from a wide range of disciplines, spe-cialists on a large array of taxonomic problems, and proponentsof a diversity of methods to discuss these issues and try to reacha level of understanding of the sources of the conﬂict and addresssome possible solutions. Attendees of that symposium were treat-ed to some remarkable talks and post-talk exchanges. Not sur-prisingly (to us), very little blood was drawn—the ﬁelds of pa-leontology and molecular systematics are beginning to integrate,as they should.Ours was not the only such event in recent years (e.g., Hadly,2003). The number of papers and funded research programs in-volving the collaboration between molecular biologists and mor-phologists is growing. This is remarkable considering the lack ofdialogue in the years since Colin Patterson (1987) edited Mole-cules and Morphology in Evolution: Conﬂict or Compromise? Weare seeing the synthesis our ﬁeld has needed for so long.We here expand on our point that miscommunication is as im-portant as real data conﬂict in these debates. It is written from apaleontologist’s perspective, and is perhaps slanted against mis-interpretations of the paleontological literature by neontologists.Paleontologists may feel beleaguered when revised fossil infor-mation overturns long-held beliefs and conforms to a molecularestimate, but the unease is misplaced; in many cases, fossils andmolecules have never been in conﬂict. The conﬂict is a matter ofinterpretation, and as long as competing hypotheses are not com-pletely understood, the magnitude of the ‘‘conﬂict’’ will be ex-aggerated. As seen in the papers in this issue, we still have a longway to go to resolve some of the inconsistencies between sourcesof information—but an integrative approach holds the greatestpromise in achieving the one goal of understanding the historyof life as thoroughly as possible.