Histo-icalBiology, 1996, Vol 12,pp I 1I-157 © 1996 OPA (Overseas Publishers Association) Reprints available directly from the publisher Amsterdam B V Published in The Netherlands Photocopying available by license only By Harwood Academic Publishers GmbH Printed in Malaysia TESTING THE QUALITY OF THE FOSSIL RECORD BY GROUPS AND BY MAJOR HABITATS

MICHAEL J BENTON and REBECCA HITCHIN

Department of Geology, University of Bristol, Bristol, B 58 IRJ, United Kingdom

(Received February 9 1996; in final form March 25, 1996)

The evolution of life is a form of history and, as Karl Popper pointed out, that makes much of palaeontology and evolutionary biology metaphysical and not scientific, since direct testing is not possible: history cannot be re-run However, it is possible to cross-compare three sources of data on phylogeny stratigraphic, cladistic, and molecular Three metrics for comparing cladograms with stratigraphic information allow cross-testing of () the order of branching with the stratigraphic order of fossils, and of (2) the relative amount of cladistically-implied gap in proportion to known fossil record. Results of the metrics, based upon a data set of 376 cladograms, show that there are statistically significant differences in the results for echinoderms, fishes, and tetrapods Matching of rank- order data on stratigraphic age of first appearances and branching points in cladograms, using Spearman Rank Correlation (SRC), is poorer than reported before, with only 148 of the 376 cladograms tested (39 %) showing statistically significant matching Tests of the relative amount of cladistically-implied gap, using the Relative Completeness Index (RCI), indicated excellent results, with 288 of the cladograms tested (77 %) having records more than 50% complete. Assessment of the Stratigraphic Consistency Index (SCI), the relative number of nodes i a cladogram having younger taxa located above them than immediately below them showed that 79 % of cladograms tested scored over 0 500 This indicates that node order was generally consistent with stratigraphic order of first finds, contrary to the findings of the rather cruder SRC metric. Group-by-group results were variable SRC results, based on significances of age-clade rank order equivalence, were best for tetrapods, moderate for echinoderms, and worst for fishes Best RCI values were for fishes, and poorer for tetrapods and echinoderms SCI values were best for echinoderms, poorer for tetrapods, and poorest for fishes Arbitrary scoring of the three metrics suggests provisionally that the echinoderms and tetrapods have a better fossil record than fishes. Comparison of marine groups (echinoderms + fishes) versus continental groups (tetrapods) showed that many more continental cladograms (50 %) showed significant SRC matching of age and clade order than marine cladograms (25 %) Continental cladograms also yielded higher SCI values, with 87 % achieving values equal to, or higher than, 0 5, while for marine cladograms, the value was 72 % Marine cladograms, on the other hand, scored better for relative completeness, with 79% showing RCI values greater than 50 %, compared to 74 % for continental cladograms The aggregate results suggest that continental cladograms are better than marine cladograms by two metrics (SRC, SCI) to one (RCI).

KEY WORDS: Cladistics, phylogeny, stratigraphy, evolution, Popper, fossil record.

INTRODUCTION

Fossil data offer unique information on evolution, giving the only evidence for the existence of groups that are now extinct, and providing precise data on the order of events in phylogeny Two serious problems with the fossil record have been identified, however, and these must be tackled before palaeontological data can be used

III 112 M J BENTON AND R HITCHIN seamlessly in combination with information on living organisms These problems are that ( 1) studies of the history of life may be viewed as non-scientific, as metaphysical (Popper, 1960, 1972, 1976), and that (2) the fossil record is clearly incomplete, but that incompleteness cannot be quantified against an absolute knowledge of the true pattern of the history of life. A potential resolution of these two issues is presented here It is proposed that large parts of Darwinian evolution can be cast in a way that is falsifiable, and phylogeny reconstruction, the methods used to discover the true shape of the history of life, offer means of mutual cross-falsification, a solution to the dilemma that Popper highlighted. The mutual cross-testing approach also offers the opportunity of finding measures of the completeness of the fossil record, in part and in whole.

POPPER, EVOLUTION, AND METAPHYSICS

Popper (1960, 1972, 1976) charged that the historical sciences, such as the study of the history of life, are metaphysics and not science This is a serious challenge, and potentially damaging to the acceptance of conclusions from large parts of evolutionary biology and palaeontology (Platnick and Gaffney, 1977, 1978 a, 1978 b; Halstead, 1980). Popper based his conclusion on his discovery (Popper, 1959, 1965) of a clear operational demarcation between science and metaphysics: in his terms, scientific theories are capable of falsification, while metaphysical propositions are not. Popper did not use the word 'metaphysics' in a pejorative sense, although many before him and after him have done so, sometimes equating metaphysics with mumbo-jumbo or pseudo-science Indeed, Popper argued very clearly that a theory in metaphysics is not testable, but that does not mean that it is wrong Indeed, in the history of many subjects, what was once metaphysics may become science when the tools or insights become available to design adequate tests that offer the possibility of falsification. Popper considered the nature of Darwinian evolution in various of his writings, but came to the firm conclusion, through a series of his works in which he considered the correct method for studying and analysing history, that evolution is more metaphysics than science Popper ( 1976, p 172) compared the natural theological explanation that nature is perfect because God created it that way, with Darwinian evolution: "Now to the degree that Darwinism creates the same impression, it is not much better than the theistic view of adaptation; it is therefore important to show that Darwinism is not a scientific theory, but metaphysical But its value for science as a metaphysical research programme is very great, especially if it is admitted that it may be criticized, and improved upon " Popper argued that Darwinism was metaphysics, and not science, for two reasons, ( 1) the theory is not testable, and indeed is almost tautological, and (2) the evolution of life happened once, and it is impossible to generalise law-like statements from a single set of events Darwinian evolution is untestable, Popper ( 1976) argued, because it cannot make predictions about what might happen on another planet where life originates The key tenets of Darwinism, natural selection, diversification, and adaptation in a sense simply describe what has happened, and is happening, but these phenomena cannot be framed in a precise way that permits of their falsification. Popper repeats the favourite argument of Creationists that adaptation is virtually a tautologous proposition: adaptation and fitness are defined as survival value, and they can be measured by actual success in survival, but such a definition is virtually untestable The second criticism of evolution was that life has evolved once only, so far as we know, and cannot be tested Hence, the scientist, used to applying the TESTING THE QUALITY OF THE FOSSIL RECORD 113 experimental hypothesis-testing approach is powerless How can a scientific study of phylogeny be instituted if it is impossible to re-run evolutionary history many times, altering variables on each run so that the fundamental principles may be determined? Put another way, and still applying the Popperian method of science, how can evolution be falsified? What single test could be imagined? lThis critique, in simple form, is beloved of creationists, who use it to deny that evolution is scientific l The usual riposte, convincing, but not overwhelming, is that evolution is a complex amalgam of numerous hypotheses, any one of which may be tested, and many of which have been tested repeatedly by evolutionary ecologists, geneticists, palaeobiologists, and systematists. It is important first to divide evolution into two main propositions: ( 1) the assertion that life has evolved (literally 'unrolled') during the course of geological time; and, (2) that evolution has occurred by natural selection As Platnick and Gaffney (1978 a), Patterson (1978), and others have argued, the first proposition probably offers most difficulty Natural selection can be subjected to test in a variety of ways, some of them in the form of short-term laboratory experiments, others by longer-term natural experiments, but all of these are, and have been, repeatable time and time again, with different organisms, and in different settings There is no need to get sucked into the Creationists' tautology'argument, as Popper did (see Ridley, 1993, chapter 3 for an excellent overview). The first proposition, not original to Darwin, simply that life has evolved, from simple to complex organisms, from low to high diversity, and over a long period of time, is at first sight harder to tackle, for the reasons given by Popper Patterson (1978, pp 145-147) accepted Popper's description of evolution as a pattern as metaphysical, while Platnick and Gaffney (1978 a) argued that infinite numbers of testable (i e scientific propositions may be made in the field of systematics (the study of evolution as pattern) These testable propositions may be at the lowest level, such as: 'there are only three species of great ape in Africa' Every new great ape specimen that is examined provides a potential falsifier, in that it may represent an additional species, or perhaps an intermediate between two already-named species, or it may possess a suite of character states that overthrow the current most parsimonious cladogram of the taxa (Platnick and Gaffney, 1978 b) Indeed, every cladogram, molecular tree, or fossil sequence is hypothetical, the best possible conclusion at the time, generally based on a variety of available information Each new discovery can falsify all or part of any such proposed phylogenetic pattern, providing of course that the pattern has been discovered according to a rigorous and repeatable technique This excludes all phylogenies that are based on intuition: these are metaphysical propositions, incapable of falsification. The suggestion that cladograms, and indeed any phylogenetic tree produced by a defined and repeatable methodology, are potentially falsifiable, and hence scientific in a Popperian sense, may provide one resolution of the dilemma of the evolutionist This use of Popperian falsificationism is, however, rather trivial in comparison with his original intention, which was in regard to universal laws of physics (Rieppel, 1988, pp 13-14) Individual phylogenetic hypotheses have no general law-like properties, and they cannot make predictions about broader issues Science in general, and evolutionary biology in particular, must be founded on falsifiable hypotheses, but there is more to it Competing hypotheses may survive in parallel, each capable of explaining a large body of observations, and neither capable of decisive falsification by a single critical experiment This is as true of the attempt to discover phylogeny as for most other areas of science For much-studied groups, like the placental mammals, there are numerous current competing hypotheses of relationship, based on a variety of 114 M 1 BENTON AND R HITCHIN morphological and molecular evidence, and the decisive test has yet to be discovered. Clearly only one of the published cladograms, or perhaps none of them, is actually correct, and each of the trees is potentially falsifiable, but the debate now hinges on interpretation of specific characters, debates about the relative importance of different evolutionary transitions, and disputes over analytical algorithms In one of his later statements on the question, nonetheless, Popper ( 1980) stated that palaeontology and evolutionary history 'have in my opinion scientific character: their hypotheses can in many cases be tested' lhis italicsl Perhaps he had taken account of the methodological revolution in the study of evolution, particularly since the 1970 s Since then, the methods of cladistics and molecular phylogeny reconstruction have been formulated and debated, and the use of computers has provided testing techniques that were not dreamt of in 1970 Is the justification for the pattern of evolution as science to be based on the chopping up of the history of life into numerous falsifiable phylogenies, or is there a larger test? It might indeed be possible to find a single test, or at least a single kind of test, of evolution J B S Haldane hinted at this when he said that he would give up his belief in evolution if someone found a fossil rabbit in the Precambrian (Ridley, 1993, p 56) Patterson (1982) extended Haldane's suggestion, and couched it in cladistic terminology He argued that cladistic phylogenies could test evolution, since they were composed independently of evolutionary theory Patterson ( 1982) was instrumental in demonstrating that cladistics as a method is a geometrical system for developing a shortest bifurcating tree linking many taxa, and based on a data matrix consisting of presence/ absence data In practice, there is no reference to evolution in the process of building a cladogram (Platnick, 1979 ; Eldredge and Cracraft, 1980 ; Nelson and Platnick, 1981 ; Forey et al , 1992) At times, it has been suggested that fossils should be used as the arbiters of character polarity and tree rooting However, in current cladistic practice, fossils and living taxa are treated as equal terminal taxa, and there is no reference to stratigraphy in determining the polarity (primitive or derived state of a character) Equally, tree rooting is carried out by reference to close outgroups of the taxa under study, and the outgroup(s) may be extant or extinct taxa. Fossil taxa are chosen for tree rooting simply when their position in phylogeny, and their character combinations, prove to be most suitable Again, there is no input of stratigraphic data in determining the shape of the tree (Smith, 1994 ; Benton, 1995). Molecular phylogenies, whether based on protein or nucleic acid sequences, are produced in a way that is independent of stratigraphy, and indeed of cladistic analysis of morphological, physiological, and ecological characters. If it is correct that the stratigraphic order of fossils, the cladistic analysis of phenotypic characters, and molecular phylogeny reconstruction, are all substantially independent of each other, then it can be argued (Benton, 1995) that these three approaches to discovering phylogeny may be cross-tested in order to determine whether they all give the same picture of history Tests so far (Norell and Novacek, 1992 a, b; Benton and Storrs, 1994, 1996 ; Benton, 1995 ; Benton and Simms, 1995) show that they do These tests have, however, been rather small-scale, being based on samples of 24 (Norell and Novacek, 1992 a), 33 (Norell and Novacek, 1992 b), 74 (Benton and Storrs, 1994), and 63 (Benton and Simms, 1995), which were then submitted to statistical testing The purpose of this paper is to present a larger data set of tested cladograms, to apply a wider range of tests to them, and to test broad-scale aspects of the quality of the fossil record in two ways, (1) by taxa, and (2) by major habitats. TESTING THE QUALITY OF THE FOSSIL RECORD 115

DATA

Our sample of tested cladograms (Appendix) amounts to 376 ( 58 cladograms of echinoderms, 144 cladograms of fishes, and 174 cladograms of tetrapods) Outline data sets of some of these tested cladograms have already been published: tetrapods by Benton and Storrs ( 1994, 1996) and echinoderms by Benton and Simms ( 1995). The fish data are new, and they have been compiled by R H The new listing of tested tetrapod cladograms is much greater than the previously published set. Our samples of tested cladograms are comprehensive in different ways First, they are a larger sample of published cladograms than previously assembled Second, the regime for selection of cladograms for test is more comprehensive than before The list of cladograms of echinoderms that are tested here, and in Benton and Simms ( 1995), consists of all cladograms and molecular trees that we could find, published up to the end of 1994 The list of cladograms of fishes presented here likewise consists of every tree we could find, published up to the middle of 1995, but excluding about half the total which either (1) consisted only of extant forms with no fossil record, or, much more rarely, (2) were composed only of low-level taxa, species and genera, where the fossil record is not good enough to discriminate dates of origin of each terminal taxon In both cases, the samples represent a cull from all leading palaeontological and biological journals and conference proceedings, but we have probably missed a further 25 % or more of the available trees. In the case of tetrapods, there are probably several thousand published cladograms and molecular trees The present sample of 174 consists solely of cladograms (no molecular trees), and it was generalised from the listing presented by Benton and Storrs ( 1994, 1996) by including every cladogram from a random sample of multi-author compilations (Benton, 188 ; Estes and Pregill, 1988 ; Prothero and Schoch, 1989 ; Weishampel et al , 1990 ; Schultze and Trueb, 1991) plus every cladogram from volumes 13 to 15 (3) of Journal of Vertebrate Paleontology (1993-1995) This latter data set expands the array of previously tested cladograms of tetrapods (Norell and Novacek, 1992 a, b; Benton and Storrs, 1994, 1996) from a core set of well-tested cladograms, generally at high taxonomic level (typically families), to include a truer representative cross-section of published cladograms, including alternative less-parsimonious trees, reworked representations of pre-cladistic phylogenies, cladograms based on terminal taxa of low taxonomic level (e g genera instead of families), and cladograms based solely on modern taxa in groups with poor to virtually non-existent fossil records. Cladograms based on four or fewer terminal taxa were excluded from the tetrapod test list. The present data set (Appendix) differs in two further important ways from the previously published parts of the listing (Benton and Storrs, 1994, 1996 ; Benton and Simms, 1995) First, all cladograms are subjected to three metrics of matching with stratigraphic data, the SRC and RCI techniques, and the SCI technique (see below). Second, the RCI metric is applied to the entire unadjusted cladogram, whereas in previous publications (Benton and Storrs, 1994, 1996 ; Benton and Simms, 1995), we had applied the RCI metric to the collapsed pectinate cladogram that is required for the SRC test The SCI metric is also applied to the full uncollapsed cladogram. In the first comparisons of results shown in Figures 2 and 6, all sampled cladograms are included In the second set of comparisons (Figs 3-5, 7-9), where Kolmogorov- Smirnov tests are applied, the samples were modified in two ways lThe Kolmogorov- Smirnov test is a non-parametric test which compares the mean, the variance, and the overall shape of two distributions, and assesses whether one could have been sampled at random from the other l First, all cladograms with four terminal taxa were 116 M J BENTON AND R HITCHIN excluded (9 for echinoderms, 36 for fishes, and none for tetrapods) in order to make the comparisons more equivalent This left 49 echinoderm cladograms, 108 fish cladograms, and 174 tetrapod cladograms in the sample Second, the sample sizes were adjusted to equal 49, the sample size for echinoderms, so that the Kolmogorov- Smimov test would not simply detect differences in sample size This was achieved by multiplying all frequency values for fish and tetrapod cladograms by 49/109 and 49/174 respectively, which preserved the shape, the mean, and the variance of the frequency polygon.

TESTING EVOLUTION

In our analyses, we adopt a census approach, in which we consider large samples of cladograms, in an attempt to determine broad-scale aspects of the quality of the fossil record, and the quality of cladograms Values for individual cladograms are not considered in detail, merely the aggregate of a typical sample of available cladograms. We have, therefore, adopted a variety of metrics that lend themselves to this approach These metrics, and others, may also be applied to tests of particular cladograms A number of tests for comparing phylogenies have been proposed. These metrics concentrate on one or other of two aspects of the history of life, ( 1) the order of branching points or nodes, and (2) the relative completeness of the record. The testing techniques will be presented first.

Order The simplest test of the order of branching points is to apply a Spearman Rank Correlation (SRC) test to two lists of numbers representing the order of first fossils in the rocks (stratigraphic or age data) and the order of branching points in a cladogram or molecular tree Cladistic rank is determined by counting the sequence of primary nodes in a cladogram (Figure 1A) In many cases, published cladograms do not conform to a simple pectinate (comb-like) pattern in which all terminal taxa are simple side branches of a single main stem Frequently, there are more complex topologies in which some branches subdivide further (Figure IA), or some nodes may be partially unresolved, and give rise to more than one branch In these cases, the cladogram is reduced to a pectinate form (Figure 1B), and groups of taxa that meet the main axis at the same point are combined and treated as a single unit The stratigraphic sequence of clade appearance is assessed from the earliest known fossil representative of sister groups (Figure IC) In our studies, we use the Fossil Record 2 (Benton, 1993) as our sole source of stratigraphic data for the dates of origin of families and suprafamilial taxa Some of the tested cladograms include individual genera, and their dates of origin are generally determined from internal data within the paper that presented the cladogram under test. Spearman Rank Correlation is an appropriate nonparametric test for comparing any two lists of numbers that indicate rank orders A parametric approach, such as the use of regression lines, would be inappropriate since there are no independent and dependent variables, the values do not come from a normally distributed population of points, and outlying points do not affect the others The SRC test was used previously in testing clade and age rank data by Norell and Novacek (1992 a, b), Benton and Storrs ( 1994, 1996), Benton (1994, 1995), and Benton and Simms (1995). A second metric that compares stratigraphic order of oldest fossils in each lineage, with the order of nodes implied by a cladogram, is the Stratigraphic Consistency Index TESTING THE QUALITY OF THE FOSSIL RECORD 117

(SCI) of Huelsenbeck ( 1994) This statistic was proposed as a means of testing among equally parsimonious solutions to a single phylogeny, and the aim was to test each solution against the currently known stratigraphic order of minimum geological dates of nodes (based on the maximum age of one or other sister group above each node). The SCI is calculated by scrutinising each node in an unadjusted cladogram (Figure ID) The nodes are most conveniently numbered from the most derived ends of the cladogram, backwards to the deepest node which receives the highest number. Each node is then compared to the one immediately below it in the cladogram, and it is scored for stratigraphic consistency A node is said to be consistent if the node immediately below is older, or of precisely the same age, according to fossil evidence (Figure 1E; nodes 2, 3, 4, 6) The node is inconsistent if the node below is younger, according to fossil evidence (Figure E; nodes 1, 5, 7) The ratio of consistent nodes

taxon taxon A C D E F GH I A B C D E F GH I 6 5 nd2 1

yj$ N ode number A U - taxon A-D E F-G H I taxon \ \ \ 4 A B C D E F G H I

B clade rank time 21

~6 J 4 ~l 5

time E minimum age of nodes

clade rank 1 2 3 4 4 stratigraphic rank 1 2 4 5 3 C Figure I Methods for assessing the quality of the fossil record, by comparing branching order in cladograms with stratigraphic data (A-E), and by comparing the relative amount of gap and known record (E) For comparisons of clade order and age order, cladistic rank is determined by counting the sequence of primary nodes in a cladogram (A) In cases of non-pectinate cladograms (A), the cladogram is reduced to pectinate form (B), and groups of taxa that meet the main axis at the same point are combined and treated as a single unit The stratigraphic sequence of clade appearance is assessed from the earliest known fossil representative of sister groups, and clade rank and stratigraphic rank may then be compared (C) For comparisons of the proportions of minimum implied gap (MIG) and known stratigraphic ranges, using the Relative Completeness Index (RCI), the whole cladogram is used (E) MIG (diagonal rule) is the difference between the age of the first representative of a lineage and that of its sister, as oldest known fossils of sister groups are rarely of the same age Stratigraphic consistency is assessed (D, E) as a comparison of the ratio of nodes that are younger than, or of equal age to, the node immediately below (consistent), compared to those that are apparently older (inconsistent) The Stratigraphic Consistency Index (SCI) is assessed on the full cladogram (D, E). 118 M J BENTON AND R HITCHIN to total nodes is the SCI (here, the SCI value is 4/7 = 0 571), and it can range from 0 (all nodes inconsistent) to I (all nodes consistent with the order of dating of nodes). In representing some results, we have chosen an SCI value of 0 5 to distinguish those cladograms in which most of the nodes are inconsistent (SCI < 0 5) from those in which most nodes are consistent (SCI > 0 5) If the number of terminal taxa in a cladogram is n, the number of nodes is n-I, and the number of testable nodes is n-2, since the basal node in a cladogram (Figure E, node 8) cannot be tested by the SCI The tests presented here are the first substantial application of the SCI statistic to a large number of cladograms.

Relative Completeness We proposed a statistic, the Relative Completeness Index (Benton, 1994 ; Benton and Storrs, 1994, 1996), or RCI, which gives a measure of the relative amount of stratigraphic gap implied by a cladogram in relation to the amount of stratigraphic range that is currently known from fossils The amount of gap is quantified as the Minimum Implied Gap (MIG, Figure IC, diagonal shading), the difference between the age of the first representative of a lineage and that of its sister Sister taxa, by definition, originated at a single time, represented by a node in a cladogram, but the oldest known fossils of sister groups are rarely of the same age The mean age-difference of all nodes in a cladogram is a rough indicator of the relative quality of any particular fossil record. MIG is a minimum estimate of stratigraphic gap, as the true age of lineage divergence may lie well before the oldest known fossil The RCI metric does not provide a precise test of the absolute quality of a cladogram and the relevant fossil record: such a test would also use confidence intervals at the ends of ranges, based on known distributions of fossil specimens (Marshall, 1990, 1994 ; Wagner, 1995). The relative completeness of a fossil record may then be assessed by comparing the proportion of known range (standard range length, SRL) to ghost range (MIG), in the form of the relative completeness index (RCI), defined as: (MIG) RCI = ( I Y(SR ) ) x 100 %.

Values of the RCI range from O% (MIG = SRL) to 100 % (MIG = 0) Negative values also occur when MIG > SRL In representing some of the results, we have selected an RCI value of 50 % as an arbitrary marker separating those cladograms in which there is more known stratigraphic range than MIG (RCI > 50 %) from those in which the duration of total MIG is greater than the total known ranges (RCI < 50%) As with the SRC and SCI measures, a single standard source of stratigraphic information (Benton, 1993) has been used throughout our work.

RESULTS

We present the main results of our comparative tests here Further details of the tests on fish cladograms, and on comparisons of the effectiveness of the tests, will be published elsewhere (Benton and Hitchin, 1996 ; Hitchin and Benton, 1996). TESTING THE QUALITY OF THE FOSSIL RECORD 119

Goodness of Fit of Cladistic and Stratigraphic Data Most cladograms in our sample fail the SRC test of matching between the rank order of age and clade data (Figure 2) For echinoderms, only 23 out of 58 cladograms (40 %) show statistically significant (P < 0 05) matching of clade rank and age rank data For fishes, the figure is 37 out of 144 cladograms ( 26%), and for tetrapods, 87 out of 174 cladograms (50 %) The results for all cladograms in the test sample is that 148 out of 376 showed significant SRC values (39 %). The sample of cladograms shows better results for the measure of completeness, RCI (Figure 2) For all three groups, many more cladograms have RCI values greater than 50 %, than values less than 50 % In all cases, the difference between the two categories is statistically significant by a comparison of error bars based on an approximation formula for errors based on a binomial probability distribution (Raup, 1991) The results for RCI values greater than 50% are 41 out of 58 cladograms (71 %) for echinoderms, 119 out of 144 cladograms ( 83%) for fishes, and 128 out of 174 cladograms (74 %) for tetrapods The proportion of cladograms that had RCI values in excess of 50 % was 77 % In other words, 288 of the 376 cladograms tested have more than twice as much of their ranges represented by fossils than represented

Echinoderms Fishes Tetrapods nn 1 rn I ' i- uu80 N = 17 n = 144 *~~~""60 40 20

A*r 0 I- :Io~ Not sinif Significant Notsignif Significant Not signif Sinificant

100 i i 100 ' v OA ID I n-t ,rnX = _ a U ILX%1-l ' 60 u mean= 60 o 40 623 40 . 20 20 0 O < O 5 > OS < O5 >= O S n < 05 > as

I.0 g 1nn O inn I L'L I nn- S I~~- ~~~~~~~~~~~~ mean = 'wt Rn A AA 80 ' Sc71 IxanuJJ I uv 60 ' 60 ' 60- 40' 0.78 40 40 ' sow 20 20 20- 0' X"* 0 I; 0 < 0 5 >= OS < O5 >= 0 5 < 0 5 >= 5 Category Category Figure 2 Summary of the metrics for comparison of cladogram data and stratigraphic age data Metrics indicated are Spearman Rank Correlation (SRC) of age and clade data, the Relative Completeness Index (RCI), based on comparisons of known and implied stratigraphic ranges, and the Stratigraphic Consistency Index (SCI) of nodes in cladograms The metrics have been applied to large samples of cladograms (n, number of cladograms in sample) for echinoderms, fishes, and tetrapods Comparisons are between frequencies of significant and non-significant SRC tests, frequencies of values of the RCI above and below 50 %, and frequencies of values of the SCI above and below 0 5 The differences in values among the three groups are significant, based on comparison of the binomial error bars. 120 M J BENTON AND R HITCHIN by ghost range (cladistically-implied gap) The differences in mean values of RCI for echinoderms (mean, 62 3 %) and fishes (mean, 69 4 %) are modest, but continental tetrapods have a much lower value (mean, 49 8 %), and the reasons will be explored elsewhere (Hitchin and Benton, 1996). The results are similarly favourable for the SCI measure (Figure 2) In these cases, all three sets of cladograms have significantly more than half their nodes showing stratigraphic consistency than inconsistency (significance tested by comparison of binomial error bars) SCI values are greater than, or equal to, 0 5 in 53 out of 58 cladograms (91 %) for echinoderms, 93 out of 144 cladograms (65 %) for fishes, and 152 out of 174 cladograms (87 %) for tetrapods SCI values greater than, or equal to, 0.5 occur in 298 of the sample of 376 cladograms, namely in 79 % of cases The reasons for significantly higher SCI values for echinoderms (mean, 0 78) than fishes (mean, 0 55) and tetrapods (mean, 0 66) are not immediately evident, and they will be explored elsewhere (Hitchin and Benton, 1996).

Comparing Groups The results for the SRC, RCI, and SCI metrics for the three taxonomic groups tested are shown in more detail in Figures 3-5 SRC tests, presented in terms of the frequency of significance intervals for standardised samples of 49 cladograms from each group (Figure 3), differ for the three groups assessed, echinoderms, fishes, and tetrapods, as indicated by a Kolmogorov-Smirnov test The probability of matching in each case is too low (P = 0 778 for matching of fish and echinoderm distributions, and of fish and tetrapod distributions, and P = 0 333 for matching of echinoderm and tetrapod distributions), and hence they are all regarded as different The SRC test for matching of age and clade order suggests that tetrapods have the best results, followed by echinoderms, and then fishes.

:3 ;-1

44

neg not sig P

14

12

10

8

ag 6

4

2

0 -100 -50 O 50 100 RCI value

Figure 4 Frequencies of RCI values for cladograms of echinoderms, fishes, and tetrapods The frequency distributions for each of the three groups differ significantly from each other (Kolmogorov-Smimov test).

The frequency distributions of RCI values, grouped in increments of 10 %, seem broadly comparable (Figure 4) However, Kolmogorov-Smirnov tests indicate that this is not the case The probability of matching of the tetrapod and echinoderm, and the tetrapod and fish, distributions is very low (P = 0 023 for both), while that for matching of the echinoderm and fish distributions is higher (P = 0 749), but not significant The main differences in the distributions are the high number of very low negative RCI values for tetrapod cladograms, and the low number of values in the 90 %+ class Echinoderms show an unusual distribution of RCI values at the high end, with a dip in the 70-80 % class Fishes differ in having high numbers of cladograms in the 90 %+ RCI class These distributions are reflected in the summary distributions (Figure 2 B), where fishes have the lowest number of cladograms (17 %) with RCI values below 50 %, followed by tetrapods (26 %) and echinoderms (29 %), although mean RCI values for fishes and echinoderms are comparable, but much higher than for tetrapods (Figure 2) The values for echinoderms and tetrapods are similar to those noted before, based on smaller data sets (Benton and Simms 1995). The SCI values (Figure 5) also show considerable differences in distribution among the three groups sampled Kolmogorov-Smimov tests show that echinoderm and tetrapod distributions differ from that of fishes, with the probability of matching, P = 0 664, while echinoderm and tetrapod distributions differ even more, with the probability of matching, P = 0 309 The echinoderm distribution shows lower low SCI values and more high values than does the fish distribution More fish cladograms score low SCI values than do cladograms of echinoderms or tetrapods The order of groups, in terms of the proportions of cladograms with SCI values lower than 0 5 is fishes ( 35%), tetrapods (13 %), and echinoderms (9 %) This is confirmed by the mean SCI values (Figure 2). 122 M J BENTON AND R HITCHIN

0 0 2 0 4 0 6 0 8 1 SCI value Figure 5 Frequencies of SCI values for cladograms of echinoderms, fishes, and tetrapods The frequency distributions for each of the three groups differ significantly from each other (Kolmogorov-Smimov test).

Comparing Habitats A comparison of SRC, RCI, and SCI metrics for all marine cladograms and all continental cladograms (Figure 6) yields mixed results The SRC test shows that 87 out of 174 continental cladograms (50 %) have significant matching of age and clade order, while the value for marine groups is only 50 out of 202 cladograms (25 %), much worse than the results for echinoderms alone, as reported by Benton and Simms (1995). The value for the RCI metrics is much more comparable, with 160 of the 202 marine cladograms yielding values higher than 50% (79 %), compared to 128 of 174 continental cladograms (74 %) Mean values confirm that marine cladograms show a lower proportion of implied gaps (mean RCI, 67 3) than do continental cladograms (mean RCI, 49 8) The values for the SCI metric, on the other hand, favour the continental cladograms, where 152 of 174 cladograms had values equal to, or better than, 0 500 (87 %), compared to 146 of the 202 marine cladograms (72 %) Mean values (Figure 6) suggest that continental cladograms (mean SCI, 0 66) perform slightly better than marine cladograms (mean SCI, 0 62) in the SCI metric. These results are confirmed by more detailed examination of the frequency distributions of normalised data sets, containing only cladograms with five or more terminal taxa This gave samples of 157 marine cladograms and 174 continental. Frequency values for the latter data set were multiplied by 157/174 to make the data sets equal in size Continental cladograms indeed show more examples with statistically significant matching of clade and age order (SRC), and a particularly large group in the P < 0 005 category (Figure 7) A Kolmogorov-Smirnov test confirms that the marine and continental distributions differ (matching P = 0 778) Comparison of RCI values for marine and continental cladograms (Figure 8), shows that many more marine cladograms have RCI values in the 90%+ class A Kolmogorov-Smirnov test confirms the difference (matching P = 0 059) Comparison of SCI values (Figure 9) shows that continental cladograms have more high values overall, although marine cladograms have many more SCI values greater than 0 9 A Kolmogorov-Smimov test confirms that the two distributions are different (matching P = 0 664). TESTING THE QUALITY OF THE FOSSIL RECORD 123

Marine Continental

C;OAG{5 e XA ru···e··.Ned ;;; ,.su m dal Not signif Significat

100 - 100oo 1 801 RCI 80 U) 60 ' 60- to mean x = meanx 0 40 ' 67 3 40 = 49 8 20 20 ' 0 _ so il . < O >= 0 5 < 05 0.

. * | inn. 11 V. * I 80 ' f 60 ' mean x 40 ' = O 62 4 20 ' 0o A& < O5 >= O 5 >= 05

Category Figure 6 Summary of the metrics for comparison of cladogram data and stratigraphic age data Comparisons of cladograms of marine (echinoderm + fish) and continental (tetrapod) cladograms according to the SRC, RCI, and SCI metrics The differences in values among the three groups are significant, based on comparison of the binomial error bars Abbreviations as in Figure 2.

10 (

80

U 60 1z 01

w:3 W- 40

20

neg not sig Panimals The differences are significant (Kolmogorov-Smimov test). 124 M J BENTON AND R HITCHIN

-100 -50 O 50 100 RCI value Figure 8 Frequencies of RCI values for cladograms of marine and continental animals The frequency distributions for the two groups differ significantly from each other (Kolmogorov-Smimov test).

0 0 2 0 4 0 6 O 8 1 SCI value Figure 9 Frequencies of SCI values for cladograms of marine and continental animals The frequency distributions for the two groups differ significantly from each other (Kolmogorov-Smimov test).

DISCUSSION

The metrics presented here, based on a large number of cladograms, and three test metrics, confirm earlier findings (Norell and Novacek 1992 a, 1992 b; Benton 1994, 1995 ; Benton and Storrs 1994, 1996 ; Benton and Simms 1995) that there is a good match in phylogenetic data between the the fossil record and cladograms (RCI and SCI metrics) This confirms the reality of reconstructed evolutionary trees, and perhaps acts as a comprehensive test of evolution (Benton 1995). Unlike previous studies, however, the new results show a very poor pass rate for the SRC test ( 39 % of cladograms show significant matching of clade and age order). This finding is a dramatic reversal of the results obtained in previous analyses of smaller data sets Norell and Novacek (1992 a) found that 18 of their 24 test cladograms (75 %) gave statistically significant (P < 0 05) correlations of cladistic branching order TESTING THE QUALITY OF THE FOSSIL RECORD 125 and stratigraphic order Best values were found for mammalian ungulate groups, which are believed qualitatively to have 'good' fossil records and relatively stable well- resolved cladograms The six cases that failed (amniotes, Squamata, hadrosaurs 1, hadrosaurs 2, higher primates, artiodactyls) could not be explained by any single shared characteristic In a slightly expanded study, Norell and Novacek (1992 b) found that 24 of 33 cladograms of tetrapods (73 %) gave statistically significant correlations. Benton and Storrs ( 1994, 1996) found that 41 of their 74 tetrapod cladograms (55 %) showed statistically significant matching, but Benton and Simms (1995) reported the lower pass rate noted here for echinoderm cladograms. The low matching of stratigraphic and cladistic node rank orders in the present study may relate to the nature of the enlarged sample of tested cladograms We include many kinds of cladograms that were excluded from previous studies, for example, cladograms that are less parsimonious alternatives, pre-cladistic phylogenies, cladograms based on lower-category taxa (e g genera), where the likelihood of a mismatch with coarse-scale stratigraphic data is greater than at higher taxonomic levels, and cladograms with fewer terminal taxa On the latter point, Benton and Simms (1995) found that the small echinoderm cladograms, those with four terminal taxa, included a disproportionate number of mismatches If the 9 small cladograms are excluded, 22 of the 49 echinoderm cladograms (45 %) show statistically significant matching of age and clade rank data, an improvement of 5% over the whole set of cladograms For fish cladograms, this measure improves by 8 8 % when 4-taxon cladograms are excluded We explore correlates of pass and fail of the SRC test of rank-order matching elsewhere (Hitchin and Benton, 1996). It is surprising at first that the results of the SRC and SCI metrics apparently differ in their conclusions Whereas only 39 % of cladograms showed statistically significant matching in clade and age data (SRC test), 79% showed a better than 0.5 ratio of consistent to inconsistent nodes (SCI metric) However, the value of 0.5 for the SCI metric is not a measure of statistical significance of fit against a null model of no matching, as for the SRC metric There is a general match between SRC values, and significances of matching, and SCI values for the same cladograms (Hitchin and Benton, 1996) Of the three test statistics, only SRC is dependent on numbers of terminal taxa (n) in test cladograms, while RCI and SCI show no consistent relationship with N (Hitchin and Benton, 1996), so it probably is not necessary to construct tables of significance for the latter two metrics. The comparisons of results from cladograms of echinoderms, fishes, and tetrapods shows that none of the three groups consistently has a better fossil record, or better cladistic resolution, than the others (Table 1) Each of the animal groups under study could be said to have the best fossil record since each is supported by one of the three metrics: tetrapods by SRC, fishes by RCI, and echinoderms by SCI Only one group comes out worst on two of the metrics: fishes have the poorest showing for the SRC and SCI metrics Echinoderms have the worst fossil record according to values of the RCI metric greater than 50 % (although by only a tiny margin), while tetrapods are worst of the three animal groups according to the mean RCI score. The aggregate results (Table 1) suggest, tentatively, that echinoderms and tetrapods have a better fossil record than fishes This 'pecking order', from tetrapods to echinoderms to fishes is based only on a sum of first, second, and third rankings in the SRC, RCI, and SCI metrics, in terms of pass values and mean values (Table 1). If all five metrics in Table I are summed (scoring 3 for a first, 2 for a second, and I for a third), echinoderms score 9, tetrapods 10, and fishes 11 If the means of the two RCI and SCI measures are taken, echinoderms and tetrapods score 5 5, and fishes 7 In both cases, low values indicate best matching of cladograms and fossil 126 M J BENTON AND R HITCHIN

Table I Comparison of the results of tests of the quality of matching between cladograms and stratigraphic data for different groups of animals, and different major habits Animal groups are echinoderms (58 cladograms), fishes (144 cladograms), and tetrapods (174 cladograms), and habitats are marine (echinoderms + fishes) and continental (tetrapods) The metrics are Spearman Rank Correlation (SRC), Relative Completeness Index (RCI), and Stratigraphic Consistency Index (SCI), and summary results here are shown also in figures 2 and 6 The results are given as ranks 1, 2, and 3, where I represents the highest ('best) value of the metric, either as a pass rate (greater than, or equal to, 50% or 0 50) or as a measure of the mean, and 3 is the lowest ('worst') value.

Groups Habitats Test Echinoderms Fishes Tetrapods Marine Continental

SRC 2 3 1 2 1 RCI pass 3 1 2 I 2 mean 2 1 3 1 2 SCI pass 1 3 2 2 1 mean 1 3 2 2 1 records This crude ranking assumes that these metrics are equally valid indicators of fossil record quality, and that they measure independent aspects of fossil record quality (which they do not), and that the dfferences between first, second, and third rankings by each metric are equally large (which they are not) The reasons for the differences in values among the three groups have yet to be investigated fully. The comparisons of cladograms of marine and continental organisms confirm the result of Benton and Simms ( 1995) that neither habitat offers consistently better matching of cladograms and stratigraphy Results of the three metrics show that continental cladograms perform best in two of them, and marine cladograms in one of the metrics This analysis confirms the unexpected result presented by Benton and Simms ( 1995) that marine environments do not necessarily consistently preserve fossils better than continental environments Further investigation of temporal scaling effects and the relative intensity of study of tetrapods, in comparison to echinoderms and fishes, are required.

Acknowledgements We thank the Leverhulme Trust (Individual grants 1988 and Grant F 182/AK) for funding of this work.

References

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