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Benton2009chap04.Pdf Calibrating and constraining molecular clocks Michael J. Bentona,*, Philip C. J. Donoghuea, and molecules (e.g., 1, 2). It is no longer a question of which Robert J. Asherb is better than the other, or how far one can go with one aDepartment of Earth Sciences, University of Bristol, Bristol BS8 1RJ, or the other source of data. It is evident that both fossils UK; bDepartment of Zoology, University of Cambridge, Downing and molecules have great strengths, but in recognizing Street, Cambridge CB2 3EJ, UK the weaknesses of each source of data, a realistic plan *To whom correspondence should be addressed (Mike.Benton@ for collaboration between paleontologists and molecular bristol.ac.uk) biologists can be proposed (3, 4). In this chapter we review the key qualities of the fossil Abstract record in a semi-historical account that provides explana- tions and key references. We then outline a framework In dating phylogenetic trees, it is important to work to the for collaboration in dating the tree of life. Finally, we pre- strengths of paleontology and molecular phylogeny esti- sent further, documented, evidence of key fossil-based mation. Minimum constraints on calibrations (i.e., oldest data for dating. fossils in a crown clade) may be calculated with some pre- cision and may be treated as hard bounds, while maximum constraints are soft bounds that may be represented most The key attributes of the fossil record honestly by probability distributions that refl ect the distri- Fossils occur in temporal order bution of fossiliferous rocks around the time in question, It seems self-evident that older rocks lie at the bottom of but allow a small probability of truly ancient dates as well. the pile, and younger rocks in successive layers on top. We present detailed documentation of 63 key calibration And yet, it was only when Nicholas Steno (1638–1686) in dates, with thorough evidence and error expressions, for a 1669 enunciated this as the law of superposition of strata wide range of organisms. (5) that observers took the point. Fossils were known in Steno’s day, but they were seen as rather random in occur- For well over 200 years, natural scientists have used fos- rence and not linked to any pattern reP ecting the history of sils with varying degrees of conA dence to date the evo- life. By the 1790s, when scientists had A nally accepted the lution of life. 7 e A eld has advanced dramatically in the idea of extinction, Georges Cuvier (1769–1832) in France last few years, and it would be useful now to review some and William Smith (1769–1839) in England showed that of the key issues and to suggest an outline of a modus assemblages of fossils occur in successive rock strata and operandi for the future. that the sequence of rocks and of fossils reP ects some In explaining the role of fossils in establishing times- aspects of the history of the Earth and of life. In more cales, it is useful to review the historical sequence in recent times, this conclusion has been conA rmed by the which key observations were made. Much of this early observation that temporally older vertebrate fossils tend history predates the 1960s concept of the molecular to occupy cladistically more basal nodes (cf. 6). clock; but the way in which fossils should be used today depends crucially on those earlier geological and paleon- tological observations. In presenting these observations Fossils and fossil assemblages are characteristic in a logical sequence, we highlight what can and cannot of units of past time be done with fossils, and link this to the relative strengths Cuvier and Smith also noted the predictability of some and weaknesses of molecular data. 7 e value of carrying aspects of the fossil record, in particular the totality of out this survey now is that it is not framed in the old and fossils that had been collected. SpeciA cally, they noted rather worn narrative of a “conP ict” between fossils and that particular fossils, or assemblages of fossils, appeared M. Benton, P. C. J. Donoghue, and R. J. Asher. Calibrating and constraining molecular clocks. Pp. 35–86 in e Timetree of Life, S. B. Hedges and S. Kumar, Eds. (Oxford University Press, 2009). HHedges.indbedges.indb 3355 11/28/2009/28/2009 11:24:49:24:49 PPMM 36 THE TIMETREE OF LIFE to characterize particular rock units and to occur in the Australia about 1840 showed he was right. Since 1840, same order every time they were seen. 7 is observation the international geologic timescale has not been sub- was used practically by geologists to correlate rock units stantially revised, but some major time units have been from place to place, to name them (e.g., “Carboniferous,” added, most notably the Ediacaran in 2004 (9). “Lias,” “Old Red Sandstone”) and to match stratigraphic units on the A rst geological maps. 7 e principle is fun- damental to modern biostratigraphy and lies behind The order of fossils matches the pattern of the the practical search for new sources of oil and gas today. evolution of life However, the practices of biostratigraphy and correl- Although faintly discerned by Smith, Cuvier, and others, ation have evolved substantially, in particular with the the link between deep time and the phylogeny of life development of graphic correlation which facilitates the could not be made without an understanding that life integration of stratigraphic phenomena, including iso- had evolved. Cuvier’s great rival at the Muséum Nationale tope anomalies and geochronologically dated ash layers d’Histoire Naturelle in the 1790s, Jean-Baptiste Lamarck (7), to derive a global composite standard stratigraphy (1744–1829), was the A rst serious proponent of evolution, against which local sections may be compared and the idea that species change through time. His model of correlated (8). evolution was more an escalator than a tree, the great scala naturae, where every species is arrayed along one or more moving walkways from rocks to angels: the Fossils may be included in phylogenies of humans of today were once apes, and the apes of today modern organisms may some day be humans. Many people in the 1830s Cuvier had no sympathy with then-current ideas of evo- accepted the idea of progress, or directionality, in the lution, but he gave the world the science of comparative order of fossils in the rocks, but others, notably Charles anatomy. Whatever the causes, he recognized the preva- Lyell (1797–1875), saw time as a series of cycles rather lence of anatomical similarities in oJ en widely diB erent than a unidirectional arrow, and so sought to deny the organisms, and he realized these indicated closeness of idea of progress from simple to complex through the suc- relationship in some sense. He famously demonstrated cession of fossils in the rocks. his skills in public demonstrations in Paris in the early nineteenth century, by taking a single fossil bone, and reconstructing the whole animal and its biology and There is a tree of life habits in some detail, before an assistant revealed the Charles Darwin (1809–1882) was the A rst to understand whole skeleton. Cuvier never plotted an evolutionary that the evolution of life was not an escalator, nor any tree, but key concepts such as homology arose from his other kind of linear progression, but a branching tree pre-Darwinian comparative anatomy. that links all living and fossil species, and the lines unite backwards in time to the single common ancestor of all life. His A rst branching tree appeared in manuscript There is a single geological timescale that may be notes in 1838; and the sole illustration in the Origin of used as a yardstick of time Species was a branching tree (10). William Smith around 1800 mapped his correlat- able geological units across England, and guessed they extended over Europe. Roderick Murchison (1792–1871) The fossil record is incomplete and others in the 1830s drove these ideas forward, nam- Charles Darwin also spent some time in the Origin of ing the major divisions of geological time, the Paleozoic, Species discussing the “imperfection of the geological Mesozoic, and Cenozoic eras, and the various geological record.” He pointed out that many living organisms periods (Cambrian, Silurian, Devonian, etc.). Murchison have only soJ parts, and so are unlikely to be preserved. hurtled across Europe and Russia in his coach and Others live in environments such as mountainsides or mapped his British units across the Ural Mountains. beaches, where erosion dominates, and sediment does He declared that the new geological eras and periods, not accumulate. He noted the patchiness of geological established in Western Europe (mainly in England and strata, and the fact that intermediate fossil forms are Wales), provided a yardstick of deep time that would work rare. Darwin did, however, predict that intense eB orts worldwide. Initial studies in Africa, North America, and by paleontologists would A ll many of the gaps in the HHedges.indbedges.indb 3366 11/28/2009/28/2009 11:24:50:24:50 PPMM Calibrating the Molecular Clocks 37 record and allow the deeper parts of the tree of life to Deep time may be dated be disentangled. In many cases (e.g., basal tetrapods, 7 roughout the nineteenth century, most scientists synapsids, and diapsids) his prediction has been fantas- accepted that the Earth was very ancient, but there was no tically conA rmed, whereas others remain more di1 cult meaningful way to determine exact dates for any rocks. to document paleontologically. Raup (11) summarized Calculations based on estimates of the rate of cooling of the issue clearly, arguing that there are biases in the fos- the Earth from an initial supposedly molten state gave sil record; for example, the quality of the record must rise to rather short histories of the Earth, measured in diminish as one goes further back in time.
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