Phylogenetic analysis shows that Neolithic slate plaques from the Southwestern Iberian Peninsula are not genealogical recording systems

Phylogenetic Analysis Shows That Neolithic Slate Plaques from the Southwestern Iberian Peninsula Are Not Genealogical Recording Systems Daniel Garcı ´a Rivero 1 , Michael J. O’Brien 2 * 1Department of Prehistory and Archaeology, University of Seville, Seville, Spain, 2Department of Anthropology, University of Missouri, Columbia, Missouri, United States of America Abstract Prehistoric material culture proposed to be symbolic in nature has been the object of considerable archaeological work from diverse theoretical perspectives, yet rarely are methodological tools used to test the interpretations. The lack of testing is often justified by invoking the opinion that the slippery nature of past human symbolism cannot easily be tackled by the scientific method. One such case, from the southwestern Iberian Peninsula, involves engraved stone plaques from megalithic funerary monuments dating ca. 3,500–2,750 B.C. (calibrated age). One widely accepted proposal is that the plaques are ancient mnemonic devices that record genealogies. The analysis reported here demonstrates that this is not the case, even when the most supportive data and techniques are used. Rather, we suspect there was a common ideological background to the use of plaques that overlay the southwestern Iberian Peninsula, with little or no geographic patterning. This would entail a cultural system in which plaque design was based on a fundamental core idea, with a number of mutable and variable elements surrounding it. Citation: Garcı ´a Rivero D, O’Brien MJ (2014) Phylogenetic Analysis Shows That Neolithic Slate Plaques from the Southwestern Iberian Peninsula Are Not Genealogical Recording Systems. PLoS ONE 9(2): e88296. doi:10.1371/journal.pone.0088296 Editor: John P. Hart, New York State Museum, United States of America Received August 5, 2013; Accepted December 27, 2013; Published February 18, 2014 Copyright: ß2014 Garcı ´a Rivero, O’Brien. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: The authors have no support or funding to report. Competing Interests: The authors have declared that no competing interests exist. * E-mail: [email protected] Introduction Prehistoric engraved plaques dating ca. 3,500–2,750 B.C. (calibrated age) (Table 1) are found in archaeological sites across the southwestern Iberian Peninsula. The plaques are thin slabs, usually of slate or schist but in some cases of sandstone, that vary in shape from rectangular to trapezoidal. Size is highly variable, but most specimens range in length from 10 cm to 20 cm and have maximum widths in the 5–10-cm range (Fig. 1). In addition to geometric, anthropomorphic, or zoomorphic designs engraved on one face, most specimens have one or two drilled holes at one end, through which, it has been proposed [1], [2], strings were passed so they could be worn. The majority of plaques have come from burial sites (,200), in some cases resting directly on or to the side of human skeletons [2]. Plaques are usually associated with undecorated pottery, flint blades, and other chipped and polished stone tools with no clear evidence of wear [2]. Interpretations of the intended function(s) of the stone plaques extend back to the last quarter of the nineteenth century and include Na kind of ideographic writing system [3]; Nprestige objects [1], [4], [5]; Nsymbolic items used by groups within a social hierarchy [6], [7]; Nheraldic objects [8], [9]; Namulets or cult objects [10], [11], perhaps used in superstitious activities [12]; Napotropaic images of the deceased to ward off evil [13]; Nidols [14]–[16], perhaps related to the devotion of specific divine figures [17]–[21]; and Nsymbolic expressions related to different specific geographical regions and units of cultural identity [22], [23]. More recently, Katina Lillios combined two of those functions—ideographic writing and heraldic items—hypothesizing that the majority of the plaques codify genealogical information [2], [24]–[27], whereas others perhaps were relics or specific expressions of several individuals [28], [29]. She proposed that decorative motifs on the lower portion of the plaque—the end opposite the hole (Fig. 2)—identify individual descent groups and that the number of decorative ‘‘registers’’—the horizontal rows of triangles shown on the specimen in Fig. 2—indicates the generational distance between the deceased and the founding ancestor of his or her lineage. For example, a plaque containing two rows of triangles would connote ‘‘a person two generations removed from a founding ancestor [of the ‘triangle’ lineage]…. The increase in register [row] numbers suggests gradual demic diffusion away from a core ‘ancestral’ area over time’’ ([2], p. 149). Thus plaques with a higher number of rows should be later that those with fewer rows. And, just as with the concentric circles that radiate out from a pebble thrown in a pond, the number of rows should increase with distance from the original center of plaque development, as groups moved outward, carrying the plaquemaking tradition with them. PLOS ONE | www.plosone.org 1 February 2014 | Volume 9 | Issue 2 | e88296 Lillios created a sequence of types based on expected chronological changes in various features of the plaques, with emphasis on decorative motifs on the lower portion of the plaque. She anchored the sequence with plaques containing vertical bands, herringbone designs, or checkerboard patterning (Fig. 1), followed by plaques with zigzag decoration, followed by plaques with chevrons and triangles. Her reasoning was that many of the examples with vertical bands, herringbone designs, and checkerboard patterning appeared to come from the E ´vora district of southern Portugal, which many Iberian archaeologists consider to be the original heartland of Late Neolithic peoples responsible for the megalithic tombs in which many of the plaques have been found [10], [30], [31]. So her reasoning went, as those peoples moved out from E ´vora, the plaques they made became increasingly younger in age, ending with triangle designs. Lillios ([2], pp. 157–158) states that she used both the ‘‘proxy method of ordering the plaques’’ as well as phyletic seriation [32] to ‘‘propose a tentative chronological sequencing’’ of plaques, but she presents no data that would allow us to examine the strength of the sequence. A few comments are in order. First, her ‘‘proxy method’’ is based on using row number as a chronological proxy (fewer rows early, more rows later) and then placing the plaques in sequence based on the number of rows they contain. This method, however, assumes that row number is actually a measure of elapsed time, which is what Lillios was trying to establish in the first place. Thus, any results are tautological. We return to this point later. Second, Lillios did not test the sequence either stratigraphically or against radiometric dates. Admittedly, there are only a small number of published radiocarbon dates available (Table 1), but as we discuss later, they, together with published stratigraphic information, are clear indicators that Lillios’s sequence is suspect. Despite these problems, Lillios’s hypothesis has gained considerable weight among archaeologists working on the Iberian Peninsula ([33], [34]; but see [21]). To test her hypothesis, we turned to an evolutionary model—cladogenetic, or branching, evolution—that reflects the nature of evolutionary change, whether in organisms or material culture [35]–[37]. Instead of collapsing all change into a single line of ancestry, as in the model underlying phyletic seriation, the cladogenetic model recognizes that ancestry is bushy, or tree-like. As we detail below, we designed a series of phylogenetic exercises—similar to protocols used on other archaeological materials [36], [38], [39]—to maximize the expectations of Lillios’s hypothesis. This meant that we weighted every experimental protocol and analytical decision in favor of her hypothesis, our rationale being that if we tried every way possible to meet the expectations but could not, then the hypothesis should be rethought. In summary, our analysis did not support Lillios’s hypothesis that the plaques are genealogical mnemonic recording systems. We should say that her hypothesis is not supported in its current form, meaning that it is her proposed sequence of plaque designs that is unsupported. Our analysis does not negate the possibility that the plaques served as mnemonic devices or some other function tied to ‘‘external symbolic storage’’ [40], [41]. Whatever their purpose, it appears there was a common ideological background to the use of plaques that overlay the southwestern Iberian Peninsula—a cultural system in which plaque design was based on a fundamental core tradition, similar to Swadesh’s [42] ‘‘morphological kernel’’ of a language [43], [44], with a number of mutable and variable elements surrounding it. Table 1. Available radiocarbon dates directly associated with plaques. Site and District 1 Sample Date RCYBP Date BC Cal Date BC 2 (1 sigma) Plaque (Esprit Number) Reference Gruta da Lapa do Fumo (Set) ICEN-240 4420645 BP 2470645 BC 3101–3000 BC 658 [82] Covas das Lapas I (Lei) ICEN-463 4550660 BP 2600660 BC 3238–3108 BC 1103 [20] Gruta 2 da Marmota (San) OxA-5535 4605655 BP 2655655 BC 3509–3426 BC Unknown [82] Gruta da Lapa do Bugio (Set) OxA-5507 44206110 BP 24706110 BC 3119–2919 BC Unknown [82] Anta da Bola da Cera (Port) ICEN-66 4360650 BP 2410650 BC 3023–2909 BC Unknown [81] Sala nu1 (Bej) ICEN-448 41406110 BP 21906110 BC 2876–2618 BC Unknown [82] Anta de STAM-3 (Evo) Beta-166422 4270640 BP 2320640 BC 2917–2877 BC 650 [82] Olival da Pega 2b (Evo) ICEN-957 4130660 BP 2180660 BC 2763–2620 BC 137, 492, and 515 [82] Olival da Pega 2b (Evo) ICEN-955 42906100 BP 23406100 BC 3034–2856 BC 137, 492, and 515 [82] Olival da Pega 2b (Evo) ICEN-956 4180680 BP 2230680 BC 2817–2664 BC 137, 492, and 515 [82] Anta 4 de Coureleiros (Port) ICEN-976 42406150 BP 22906150 BC 3022–2617 BC Unknown [81] Pe ´da Erra (San) ICEN-587 4220645 BP 2270645 BC 2808–2755 BC Unknown [82] Anta da Horta (Port) Beta-194313 4480640 BP 2530640 BC 3332–3214 BC [81] Figs. 138 (above) and 147 (below) [81] Anta da Horta (Port) Beta-194312 4270650 BP 2320650 BC 2928–2866 BC [81] Figs. 136–149 [81] Gruta Praia das Mac¸a ˜s (Lis) OxA-5509 4410675 BP 2460675 BC 3107–2916 BC Unknown [82] Gruta Praia das Mac¸a ˜s (Lis) OxA-5510 4395660 BP 2445660 BC 3096–2916 BC Unknown [82] 1 See Fig. 4 for district locations. 2 Calibrations are made in software Calib 7.0 based on IntCal 13 data sets. doi:10.1371/journal.pone.0088296.t001 Neolithic Plaques Are Not Recording Systems PLOS ONE | www.plosone.org 2 February 2014 | Volume 9 | Issue 2 | e88296 Materials Our data were derived from the online Esprit (Engraved Stone Plaque Registry and Inquiry Tool) database (http://research2.its. uiowa.edu/iberian/index.php) created by Lillios and collaborators [45]. It contains information on over 1400 plaques. Although some archaeologists [46] have claimed that the data set does not contain the total number of excavated plaques, which is likely, we have no reason to think that it is not representative of the variation in decoration that existed across the southwestern Iberian Peninsula. Because of inconsistencies in how plaque types have been created by the authors of and contributors to Esprit—not an unusual occurrence in archaeologywe used paradigmatic classification to define analytical classes [35], [47]. In paradigmatic classification, the investigator specifies a priori the characters and character states that are of analytical interest, and each specimen is then classified by linking the state of each character. Any character state can combine with any of the states of the other characters to create a class (taxon). Key to Lillios’s hypothesis is the character ‘‘base decorative motif’’ (DM), but five other characters are also proposed to have chronological significance: ‘‘structure (ST),’’ ‘‘tattoo straps (TT),’’ ‘‘necklace (NK),’’ ‘‘head motif (H),’’ and ‘‘number of registers (rows).’’ We excluded the last character because, if we use Lillios’s reasoning, it is not an independent variable. As we mentioned above, to her, rows of engraved lines tell us about the use life of a plaque, not its chronological age. To use our earlier example, a plaque with two rows signifies two generations, whereas a plaque with five rows signifies five generations. The first plaque could have been made many centuries before the second one but did not record as many generations before it was placed in the ground. Fig. 3 shows the possible discrete states of each of the five characters used. By excluding specimens that were broken, showed evidence of re-engraving, or were not illustrated in the online database, we ended up with a population of 735 plaques. We judged the population to be too large to analyze because of the number of unique classes involved (see below), so we reduced it to 349 specimens using a 5% error and a 99% confidence interval (http:// www.med.unne.edu.ar/biblioteca/calculos/calculadora.htm). Those 349 specimens were spread across 81 classes. Table 2 lists the number of specimens by class and Esprit database identification number [45]. For the latter we used the first specimen listed in the database as the class representative. For example, class 1 contains 15 specimens that are identical in terms of character states. We list only one specimen identification number for that class instead of all 15. Table 3 reorders the data in Table 2 to show the number of duplicate cases across the sample. For example, the first row of the table shows that 36 classes contain only one specimen (there are zero duplicate specimens in those 36 classes). The second-to-last row shows that there is one class that contains 27 specimens (one plus 26 duplicates). We can see from Table 2 that that 27-specimen class is class 3. Because the tree-building computer program we used—PAUP* 4.0 [48] (see below)—could not accommodate that number of classes, we took a weighted random sample (with replacement [SPSS v. 20]) from the 81-class sample to create 4 samples of 20 classes each. (The weight of each class was determined by the number of specimens in it.) Table 4 lists the classes in each sample and their character states; Fig. 4 shows the distribution of classes geographically. Method Phylogenetic reconstruction is the main method used in biology to construct testable hypotheses of ancestor–descendant relationships [49]–[52]. It has also begun to see wide usage in archaeology [37–39], [53–58] and other studies of material culture [59]–[67]. As Riede ([58] p. 799) points, cultural phylogenetics has advantages over traditional typological approaches in that a given phylogeny constitutes a quantitative hypothesis of the historical relatedness among the chosen units of analysis…. Such hypotheses can then be evaluated statistically and in relation to external datasets, such as stratigraphic, geographical or radiocarbon dating information. While a phylogenetic quantification of material culture relations alone can reveal important new insights in its own right, phylogenies can also be used in additional comparative analyses. Figure 1. Engraved plaques from the Iberian Peninsula. a, Valencina de la Concepcio ´n, Sevilla, Spain (Museo Arqueolo ´gico de Sevilla [MAS]); b, S. Geraldo, Montemor-o-Novo, E ´vora, Portugal (Museo Nacional de Arqueologia de Portugal [MNAP]); c, Monsaraz, Reguengos de Monsaraz, E ´vora (MNAP); d, Mora, E ´vora (MNAP); e, Jabugo, Aracena, Huelva, Spain (MAS); f, Ciborro, Monte-o-Novo, E ´vora (MNAP); g, Marva ˜o, Portalegre, Portugal (MNAP); h, Estremoz, E ´vora (MNAP); and I, Pavia, Mora, E ´vora (MNAP). doi:10.1371/journal.pone.0088296.g001 Neolithic Plaques Are Not Recording Systems PLOS ONE | www.plosone.org 3 February 2014 | Volume 9 | Issue 2 | e88296 Phylogenetics is based on a model of descent with modification in which new taxa arise from the bifurcation of existing ones. Phylogenetic relationships are defined in terms of relative recency of common ancestry: Two taxa are deemed to be more closely related to one another than either is to a third taxon if they share a common ancestor that is not also shared by the third taxon. The evidence for exclusive common ancestry is the sharing of evolutionarily novel, or derived, character states, termed synapomorphies. Various methods have been used for phylogenetic inference, each based on different models and each having its own strengths and weaknesses [68]–[72]. The one we used, maximum parsimony, is based on a model that seeks to identify the least number of evolutionary steps required to arrange the taxonomic units under study. In simplest form, the method consists of four steps: 1. Generation of a data matrix that shows the states of the characters exhibited by each taxon. 2. Establishment of direction (polarity) of evolutionary change among the states of each character. One method for doing this is outgroup analysis [73], which entails examining a close relative of the study group. When a character occurs in two states among the study group, but only one of the states is found in the outgroup, the principle of parsimony is invoked (see above), and the state found only in the study group is deemed to be evolutionarily novel with respect to the outgroup state. 3. Construction of a branching diagram of relationships for each character by joining the two most derived taxa—those at the branch tips of a tree—and then successively connecting each of the other taxa according to how derived they are. Ideally, the distribution of character states among the taxa will be such that all the character trees imply relationships among the taxa that are congruent with one another. Normally, however, a number of the character trees will suggest relationships that are incompatible—a phenomenon known as homoplasy.This problem is overcome through the fourth step: 4. Construction of an ensemble tree that is consistent with the largest number of characters and therefore requires the smallest number of homoplasies to account for the distribution of character states among the taxa. We refer to such a tree as the ‘‘most parsimonious’’ solution. Parsimony trees are evaluated on the basis of the minimum number of character-state changes required to create them, without assuming a priori a specific distribution of trait changes. This compensates for the process pathways, biases, and random variation that characterize ‘‘cultural transmission’’ [74]–[76]. It is worth underscoring that trees are hypothetical statements of relatedness, ‘‘given the model and parameters used’’ ([68] p. 189), not irrefutable statements of precise phylogenetic relationships. Numerous techniques are available for measuring the goodness of fit between a data set and a given tree, with the consistency index (CI), the retention index (RI), and the rescaled consistency index (RC) being the most commonly used. The CI measures the relative amount of homoplasy in a data set but is dependent on the Figure 2. Characters used in the analysis and abbreviations: Decorative Motif (DM), Structure (ST), Traps/Tattoo (TT), Necklace (NK), and Head (H). Terms in parentheses are particular character states for this example (see Fig. 3). After [31]. doi:10.1371/journal.pone.0088296.g002 Neolithic Plaques Are Not Recording Systems PLOS ONE | www.plosone.org 4 February 2014 | Volume 9 | Issue 2 | e88296 number of taxa. Thus, the expected CI for a given tree must be assessed relative to the number of taxa used in the analysis [77]. The RI measures the number of similarities in a data set that are retained as homologies in relation to a given tree. It is insensitive to both the presence of derived character states that are present in only a single taxon and the number of characters or taxa employed. Thus, it can be compared among studies. The rescaled consistency index (RC) is the product of the consistency index and the retention index. Indices range from zero, which indicates a lack of fit between a tree and the data set used to generate it, to 1.0, which represents a perfect fit. Our phylogenetic analysis consisted of four exercises (Table 5), each of which was carried out on each of the four samples listed in Table 4. Each exercise searched for the best-supported tree using the same tree-building methods and character/character-state parameters (Table 4). We used the ‘‘parsimony heuristic search’’ in PAUP*. All searches were carried out using the stepwise-addition strategy for the addition of classes, with a simple addition sequence and keeping only one tree at every step; the tree bisection and reconnection method, with the branch-swapping algorithm in relation to the tree rearrangements; and a maximum set of 100 for the initial trees. The following scores were extracted from all searches: number of trees, length of trees, consistency index (CI), retention index (RI), and rescaled consistency index (RC). We generated three kinds of consensus trees—strict, semi-strict, and majority-rule—to reconcile different outcomes. We also generated bootstrap trees using the following parameters: 100 bootstrap replicates; simple weighting; randomly starting seed; parsimony Figure 3. Character states used in the analysis. doi:10.1371/journal.pone.0088296.g003 Neolithic Plaques Are Not Recording Systems PLOS ONE | www.plosone.org 5 February 2014 | Volume 9 | Issue 2 | e88296 optimality criterion; and 500 saved trees in each bootstrap replicate step. Certain characters can be hypothesized as being more important than others in determining phylogenetic relationships, and thus more analytical weight can be placed on them. As mentioned, our goal was to stack the deck in favor of Lillios’s hypothesis, in which character DM plays a crucial role, so for exercises 2 and 4 (Table 5), we assigned it a weight of 2, whereas characters ST, TT, NK and H were each assigned a weight of 1. Character states can also be ordered, which means there are defined pathways that a character transformation can take [78]. Thus, for example, it may be the case that evolutionary ‘‘laws’’ dictate that an organism can lose or gain only one toe at a time. It could move from five toes to four toes, or vice versa, but never from five to three or from two to four. The character ‘‘number of toes,’’ then, is said to have ordered character states. In reality, an Table 2. Distribution of specimens across the 81 classes. Class Esprit Identification Number of Specimens 11 15 22 1 33 27 48 5 512 2 613 6 714 23 815 3 11 18 4 12 19 1 13 23 17 14 29 22 15 30 5 16 31 3 18 33 2 20 35 1 21 36 10 24 44 6 25 45 1 26 46 8 32 53 24 39 61 2 41 63 5 42 64 6 44 66 7 45 68 9 50 75 5 56 85 3 59 89 4 91 157 10 94 160 18 96 163 4 97 164 3 107 175 5 111 180 1 114 183 3 138 226 4 146 236 4 150 241 11 151 243 3 155 253 2 161 259 2 169 268 1 174 275 5 177 279 1 180 282 1 189 296 1 211 321 1 219 332 2 Table 2. Cont. Class Esprit Identification Number of Specimens 222 335 1 225 340 2 244 365 1 249 370 3 271 405 1 304 466 2 313 479 2 321 489 1 328 499 1 330 501 1 342 513 3 344 515 1 355 536 1 361 544 1 401 612 1 415 637 1 420 650 2 432 676 1 438 700 1 442 709 1 478 836 1 483 844 1 497 861 1 498 862 1 616 1074 1 618 1076 1 623 1084 1 638 1109 1 660 1165 1 670 1178 1 681 1191 1 690 1221 1 doi:10.1371/journal.pone.0088296.t002 Neolithic Plaques Are Not Recording Systems PLOS ONE | www.plosone.org 6 February 2014 | Volume 9 | Issue 2 | e88296 ordered transformation series is a hypothesis about a particular pathway because rarely will we know absolutely what is possible in nature. Lillios’s hypothesis assumes that the lower portion of the plaques, containing character DM, represents lineage affiliations, whereas the number of rows represents the generations back to the founding ancestor of the lineage [2], [24], [25]. With respect to character DM, Lillios suggests that plaques with checkerboard (DM 4 ) and herringbone (DM 6 ) designs are ancestral to plaques with other decorative designs, given that the former are more limited to her suspected core area of plaque manufacture and use (the E ´vora district of southern Portugal). For exercises 3 and 4 (Table 5), we assigned costs to changes that violated the order of character states indicated by Lillios’s hypothesis. As shown in Fig. 5, transformations from supposed ancestral character states to derived states—say, from herringbone (DM 6 ) to zigzag (DM 3 )—have the lowest cost (1), meaning that they have evolved in the manner Lillios suggested. At the other end of the spectrum, a transformation from a derived state to the original ancestral state—say, from triangle (DM 2 ) to herringbone (DM 6 ) or from unipartite (ST 0 ) to bipartite (ST 2 )—has a cost of 3. Any transformation between a derived state and one immediately preceding it (an intermediate state)—say, from triangles (DM 2 )to zigzag (DM 3 )—has a cost of 2, as does any transformation between derived states of character H. Here, Lillios proposed that the inverted triangular head (H 1 ) was immediately ancestral to all three other states (H 0 ,H 2 , and H 3 ), meaning she identified no intermediate states between the ancestral state and the three derived states. We find it difficult to believe, however, that there are no intermediate states and view the situation as a polytomy— an unresolved (nondichotomous) branching episode. If so, there are more possible reversals than there are nonreversals and thus we gave all changes among H 0 ,H 2 , and H 3 a cost of 2 [79]. If anything, this move stacked the deck even further in favor of Lillios’s hypothesis, given that the best two trees (see below) both contained ordered character states. We did not order characters TT and NK because Lillios’s hypothesis is unclear as to their chronological ordering. Two exercises were carried out with outgroups (ROOT in Table 5) and two without outgroups (UNRT in Table 5). We used classes 21, 59, 146, and 618 as outgroups because they display all or most of the presumed ancestral states in Lillios’s hypothesis— again, a deliberate decision to maximize polarity in favor of the hypothesis. In summary, exercise 1 used unweighted characters, unordered character states, and unrooted trees; exercise 2 used weighted characters, unordered character states, and unrooted trees; exercise 3 used unweighted characters, ordered character states, and rooted trees; and exercise 4 used weighted characters, ordered character states, and rooted trees (Table 5). Results Table 6 presents the following scores for each heuristic search: number of most-parsimonious trees returned, branch length of trees, consistency index (CI), retention index (RI), and rescaled consistency index (RC). The number of most-parsimonious trees obtained in the exercises is high, running into the tens of thousands. The CI, RI, and RC show strong differences among the exercises. In particular, the CI decreases dramatically between exercises 1 and 2, with a mean of 0.56, and exercises 3 and 4, with a mean of 0.16. The RI, however, decreases from 0.65 to only 0.52. The RC indicates the same trend as the CI: Exercises 1 and 2 have a mean of 0.36, whereas exercises 3 and 4 have a mean of 0.08. Table 3. Frequency and percentage of classes that have multiple specimens. Number of Multiple Specimens Frequency Percentage of 349 Specimens Cumulative Percentage of 349 Specimens 0 36 10.3 10.3 1 10 5.7 16.0 2 8 6.9 22.9 3 5 5.7 28.6 4 6 8.6 37.2 5 3 5.1 42.3 6 1 2.0 44.3 7 1 2.3 46.6 8 1 2.6 49.2 9 2 5.7 54.9 10 1 3.1 58.0 14 1 4.3 62.3 16 1 4.9 67.2 17 1 5.1 72.3 21 1 6.3 78.6 22 1 6.6 85.2 23 1 6.9 92.1 26 1 7.7 99.8 Total 81 99.8 doi:10.1371/journal.pone.0088296.t003 Neolithic Plaques Are Not Recording Systems PLOS ONE | www.plosone.org 7 February 2014 | Volume 9 | Issue 2 | e88296 The RI scores from all the exercises indicate that the data set has some consistency and phylogenetic structure. The sharp contrast observed for CI and RC values between the first two and the last two exercises indicates a significant difference related to the methodological parameters applied, specifically the switch from parameter US (unordered states) to parameter OS (orderedstates). In contrast, parameter WC, which implements different weights for a couple of characters, has no influence on the values. Table 4. Data matrix for the four samples. Class ID 1 DM 2 ST 3 TT 4 NK 5 H 6 Sample 1 2 Evo 7 212211 6Evo1332011 12Evo1922012 13Evo2322111 14Evo2932111 15Evo3052201 18Evo3330002 26Evo4650000 32Evo5322101 59Evo8942101 94 Lis 160 2 2 0 0 1 96 Far 163 2 2 0 1 1 107 Lis 175 5 2 0 0 1 169 Port 268 5 2 0 1 2 222 Port 335 2 1 3 0 1 342 Set 513 1 2 1 1 1 415 Port 637 6 0 0 1 1 420 Evo 650 2 0 0 0 2 478 Cac 836 1 0 0 0 3 497 Evo 861 3 1 4 0 1 Sample 2 4 Evo 7 832401 8Evo1512201 12Evo1922012 21Evo3642201 26Evo4650000 32Evo5322101 39Evo6122301 114 Lis 183 3 1 2 0 1 138 Lis 226 3 2 0 0 0 177 Port 279 2 1 0 0 0 222 Port 335 2 1 3 0 1 321 Bad 489 3 2 2 0 0 401 Evo 612 5 1 1 1 1 415 Port 637 6 0 0 1 1 442 Port 709 2 1 0 1 2 483 Set 844 3 2 1 0 0 616 Evo 1074 3 2 0 0 1 618 Evo 1076 6 2 1 0 1 660 Set 1165 3 1 1 1 1 681 Bad 1191 2 2 2 1 1 Sample 3 1 Evo 7 132101 12Evo1922012 14Evo2932111 15Evo3052201 16Evo3130011 21Evo3642201 Table 4. Cont. Class ID 1 DM 2 ST 3 TT 4 NK 5 H 6 24 Evo 44 2 2 0 0 2 25 Evo 45 6 1 0 0 1 32 Evo 53 2 2 1 0 1 45 Evo 68 5 2 1 0 1 138 Lis 226 3 2 0 0 0 146 Evo 236 6 2 1 1 1 177 Port 279 2 1 0 0 0 189 Evo 296 2 1 0 1 1 304 San 466 5 2 0 0 2 321 Bad 489 3 2 2 0 0 344 Evo 515 1 2 3 0 1 361 Evo 544 3 2 0 2 2 438 Cac 700 2 2 1 0 0 442 Port 709 2 1 0 1 2 Sample 4 3 Evo 7 322201 4 Evo 8 3 2 4 0 1 11 Evo 18 2 0 0 0 1 13 Evo 23 2 2 1 1 1 14 Evo 29 3 2 1 1 1 16 Evo 31 3 0 0 1 1 24 Evo 44 2 2 0 0 2 32 Evo 53 2 2 1 0 1 96 Far 163 2 2 0 1 1 146 Evo 236 6 2 1 1 1 151 Bej 243 3 0 0 0 0 174 Port 275 5 2 0 0 0 177 Port 279 2 1 0 0 0 249 Evo 370 1 0 0 0 0 342 Set 513 1 2 1 1 1 415 Port 637 6 0 0 1 1 432 Lei 676 3 1 2 1 1 438 Cac 700 2 2 1 0 0 498 Evo 862 1 2 0 1 1 618 Evo 1076 6 2 1 0 1 1 ID = specimen number in the ESPRIT database [45]. 2 DM = decorative motif. 3 ST = structure. 4 TT = tattoo straps. 5 NK = neck. 6 H = head. 7 Abbreviations to the right of the class numbers refer to the geographic provinces shown in Fig. 5. doi:10.1371/journal.pone.0088296.t004 Neolithic Plaques Are Not Recording Systems PLOS ONE | www.plosone.org 8 February 2014 | Volume 9 | Issue 2 | e88296 This indicates that the suspected order of character states in the hypothesis is inaccurate. We next created four trees per exercise and sample—three consensus trees (strict, semistrict, and 50% majority rule) and a bootstrap tree (Table 5). The result was 64 trees (1664). We then reduced the number of trees to two in order to focus on those that best fit the expectations of Lillios’s hypothesis (Table 6). Those two trees come from exercise 2 (sample 3)—termed the ‘‘2/3 tree’’ (Fig. 6)—and exercise 4 (sample 2)—the ‘‘4/2 tree’’ (Fig. 7). Both are 50% majority-rule trees [80]; the 2/3 tree was unrooted, and the 4/2 tree was rooted. When PAUP* creates rooted trees, it sets polarity—the direction of character-state change—using outgroups selected by the analyst. The 4/2 tree (Fig. 7) was rooted using class 21 (Table 5), the class in the sample that displayed the highest number of presumed ancestral states in Lillios’s hypothesis. When PAUP* creates unrooted trees, its default is to start with the first taxon in the input list and build from there. PAUP* constructed the 2/3 tree using class 1 as a starting point. After examining the tree, however, we went a step further in favoring the hypothesis. We swapped class 146 for class 1 because it is another class that displays all or most of the presumed ancestral states in Lillios’s hypothesis. The CI, RI, and CR remained unaffected. In general, the two trees have large sections that exhibit poor structural and topological resolution. Both have some large polytomies (unresolved branches) close to their roots. In the 2/3 tree (Fig. 6), the basal branching episode creates class 25, but it also creates nine unresolved branches (class 14 through class 361). The 4/2 tree (Fig. 7) has a basal polytomy, five branches of which (class 4 through class 8) are completely unresolved. Both trees also exhibit sections where relationships are more resolved. The 2/3 tree (Fig. 6), for example, contains a seven-class clade, shown in red, with considerable branching structure. The 4/2 tree (Fig. 7) also contains a seven-class clade, shown in green, that contains two smaller, multiclass clades. Given the overall lack of deep structure, it is not surprising that no character is free of homoplasy. In the 2/3 tree (Fig. 6), only 9 of the 32 character-state changes are nonhomoplastic, and only 4 of Figure 4. Distribution map of the four data sets. Sample 1: red; sample 2: green; sample 3: blue; and sample 4: pink. Gray numbers reference plaques that belong to more than one sample. The names of Portuguese districts are Leiria (Lei), Lisboa (Lis), Setu ´bal (Set), Beja (Bej), Faro (Far), E ´vora (Evo), and Portalegre (Port), and the Spanish provinces are Ca ´ceres (Cac) and Badajoz (Bad). doi:10.1371/journal.pone.0088296.g004 Neolithic Plaques Are Not Recording Systems PLOS ONE | www.plosone.org 9 February 2014 | Volume 9 | Issue 2 | e88296 Figure 9. Fifty-percent majority-rule consensus tree from exercise 4, sample 2 (the 4/2 tree) showing character-state changes states according to the assumed polarities for characters DM, ST, and H. Changes of states for characters TT and NK do not appear here because Lillios’s hypothesis makes no assumptions about polarity. Numbers at nodes are bootstrap values. doi:10.1371/journal.pone.0088296.g009 Neolithic Plaques Are Not Recording Systems PLOS ONE | www.plosone.org 16 February 2014 | Volume 9 | Issue 2 | e88296 whether they served the purpose(s) assigned to them. Certainly the available stratigraphic evidence and radiocarbon dates do not impart clear chronological structure to the plaques, which is yet another strike against Lillios’s hypothesis that they served as genealogical mnemonic recording systems. Acknowledgments We thank the Consejerı ´a de Innovacio´n, Ciencia y Empresa de la Junta de Andalucı ´a, the Departamento de Prehistoria y Arqueologı ´adela Universidad de Sevilla, the Centre for the Evolution of Cultural Diversity, University College London, Jose´ L. Escacena Carrasco, Stephen Shennan, Ruth Taylor, Gabriel Gutie´rrez Pozo, Herna´n J. Muscio, Felix Riede, John Hart, and several anonymous reviewers. The latter greatly improved the presentation of the argument. We also thank Katina Lillios, who, while not agreeing with our conclusions, made helpful suggestions on improving the manuscript. Author Contributions Conceived and designed the experiments: DGR MJO. Performed the experiments: DGR MJO. Analyzed the data: DGR MJO. Contributed reagents/materials/analysis tools: DGR MJO. Wrote the paper: MJO DGR. References 1. Cartailhac E (1886) Les ages pre´historiques de l’Espagne et du Portugal. Paris: Reinwald. 2. 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