AMMONOIDS ACROSS THE PERMIAN/TRIASSIC BOUNDARY: A CLADISTIC PERSPECTIVE

Abstract:  The rapid diversification of ceratitid ammonoids during the earliest Mesozoic has been taken at face value as an example of explosive radiation following the Permian/Triassic mass extinction. However, the validity of this interpretation has never been tested within a phylogenetic framework. A total evidence cladistic analysis of Mid–Late Permian and Induan (earliest Triassic) ammonoids confirms the monophyly of the Ceratitida. Partitioned phylogenetic analysis of suture line characters vs. shell shape and ornament characters confirms the importance of suture-line characters for resolving the higher taxonomy of ammonoids. When the cladogram is compared with the observed fossil record, the resultant tree implies that the divergence of a number of early Triassic lineages actually occurred during the latest Permian. If these range extensions are taken into account the ammonoid per-genus extinction rate across the Permian/Triassic boundary drops from c. 85 per cent to c. 60 per cent.     

Cladistic analysis of Albian heteromorph ammonites

A computer-based parsimony analysis of Albian heteromorph ammonites from the Tethyan and European faunal provinces is demonstrated. The results indicate that whilst Anisoceratidae, Baculitidae, Scaphitidae and Turrilitidae are monophyletic, Hamitidae is not. Previous studies of ammonite phylogenetics have used the coiling mode, ornamentation of the shell and the suture line as sources of characters. Comparison of the consistency and retention indices of these character suites indicates that whereas ornamentation is relatively consistent within clades, suture line morphology is highly homoplastic. The earliest known Sciponoceras , S. skipperae sp. nov., is described.     

Reconstructing the evolution of umbonal sculptures in the Unionida

‘Umbonal sculptures’ of freshwater mussels (Unionida), which ornament the early ontogenetic shell, have long been used for species identification. Specificity of these sculptures to higher taxonomic levels and their value for phylogenetic reconstruction are still under considerable scientific debate. In particular, the distribution of beak sculpture morphotypes across the unionoid phylogeny and, consequently, evolution of this character remain poorly understood. Based on an examination of 187 taxa, covering five of the six extant unionoid families, this study presents a new model of character evolution of umbonal sculptures in the order. Ten morphotypes were recognized and conceptualized into the cladistic characters sculpture presence and category. Optimization of sculpture presence on two recent hypotheses of palaeoheterodont phylogenetic relationships using the program Mesquite indicates a sculptured common ancestor of the extant Unionida, with multiple losses of the umbonal ornament occurring subsequently within the clade. Reconstruction of changes in sculpture category is ambiguous and demonstrates the need for further research into the evolutionary relationships of freshwater mussels in general and of their early ontogenetic sculptures in particular. Ambiguity is reduced in analyses applying a model with unequal costs of transformation between character states, which was derived from observations on intermediate forms and polymorphisms. These analyses suggest ‘V‐shaped’ or ‘nodulous’ sculpture as the plesiomorphic sculptural category for Unionida. The relatively low levels of homoplasy inferred for V‐shaped, pseudo‐radial and double‐looped sculptures suggest that these types may comprise useful guides to relationships within Unionida. The high degree of homoplasy of W‐shaped, pseudo‐concentric, wrinkled and single‐looped sculptures, on the other hand, renders these sculpture types less fit for such purposes.     

Buckman's Paradox: variability and constraints on ammonoid ornament and shell shape

Buckman's Law of Covariation states that ammonoid shell shape and ornamentation are typically correlated, such that compressed, involute forms have light ornament while more inflated, evolute forms have heavier ornament. Such covariation has been observed in many ammonoid groups, and implies a link between the morphogenesis of shell shape and ornamentation. However, other evidence suggests that while ornament growth is controlled by the genetic‐developmental program of the ammonoid, shell shape is strongly influenced by environmental factors. These differing viewpoints lead to Buckman's Paradox – are ornamentation and shell shape tightly linked, as implied by Buckman's covariation, or is the morphogenesis of ornament controlled genetically, while shell shape is controlled environmentally? To address this issue, the variability of shell shape and rib morphology has been compared for a group of endemic acanthoceratid ammonites from the Cretaceous Western Interior Seaway of North America. If Buckman's Law holds due to a morphogenetic connection between shell shape and ornamentation, we would expect taxa with more variable shell shapes to also show more variable rib features and growth. Morphometric analysis of seven shell shape and two rib characters for the Western Interior acanthoceratids finds no such correlation, suggesting that shell shape and rib growth are controlled by different processes. Indeed, rib growth appears to be more constrained than shell shape, consistent with the view that ornamentation is more tightly controlled by the developmental‐genetic growth program of the ammonoid. These results emphasize the complexity of ammonoid morphogenesis and highlight our limited understanding of the causes underlying Buckman's Law.     

HYBRIDS AND PHYLOGENETIC SYSTEMATICS I. PATTERNS OF CHARACTER EXPRESSION IN HYBRIDS AND THEIR IMPLICATIONS FOR CLADISTIC ANALYSIS

Interspecific hybridization is considered common among plants, but the methods of cladistic systematics produce only divergently branching phylogenetic hypotheses and thus cannot give the correct phylogeny if an analysis includes hybrids. Empirical studies of the impact of known hybrids on phylogenetic analysis are lacking, and are necessary to begin to understand the problems that we face if hybrids are often included in cladistic analysis. Examination of the implications of hybrids for cladistics must begin with patterns of character expression in hybrids. This study includes 17 hybrids and their nine parental taxa that are Central American species of Aphelandra (Acanthaceae), analyzed using a set of 50 morphological characters. The hybrids are overwhelmingly intermediate as quantitatively scored for phylogenetic analysis. They express maternal and paternal, and primitive and derived characters in equal frequencies, showing no evidence of predominant inheritance of derived character states as has been assumed by most cladists who have considered hybrids theoretically. Because of their known genetic constitution, hybrids were useful in homology assessment and ordering character states. The parental character set was generally robust, but some changes were made to reflect the special evidence offered by the hybrids. These hybrids suggest that the inclusion of hybrids in phylogenetic analysis will not lead to unresolved cladograms with rampant homoplasy, as has been predicted by other authors. Instead, the patterns of character inheritance in these hybrids lead to the prediction that a hybrid will be placed by phylogenetic analysis as a basal lineage to the clade that includes its most derived parent, with relatively little effect on homoplasy. These predictions will be evaluated by incorporation of the hybrids in phylogenetic analyses, to be reported in a subsequent paper.     

Thriving at high hydrostatic pressure: the example of ammonoids (extinct cephalopods)

Ammonoids are a group of extinct mollusks belonging to the same class of the living genus Nautilus (cephalopoda). In both Nautili and ammonoids, the (usually planospiral) shell is divided into chambers separated by septa that, during their lifetime, are filled with gas at atmospheric pressure. The intersection of septa with the external shell generates a curve called the suture line, which in living and most fossil Nautili is fairly uncomplicated. In contrast, suture lines of ancient ammonoids were gently curved and during the evolution of the group became highly complex, in some cases so extensively frilled as to be considered as fractal curves. Numerous theories have been put forward to explain the complexity of suture ammonoid lines. Calculations presented here lend support to the hypothesis that complex suture lines aided in counteracting the effect of the external water pressure. Additionally, it is suggested that complex suture lines diminished shell shrinkage caused by water pressure, and thus aided in improving buoyancy. Understanding the reason for complex sutures in ammonoids represents an important issue in paleobiology with potential applications to the problem of the resistance of hollow mechanical structures subjected to high pressure.     

Sutural amplitude of ammonite shells as a paleoenvironmental indicator

The Sutural Amplitude Index (SAI), obtained by measuring the maximum height of sutural elements and the length of the suture pattern on ammonoid shells, provides a useful indicator of relative habitat depth for ammonoids with similar shell morphotypes. A higher SAI indicates greater septal support for the shell wall against implosion under increased hydrostatic pressures in deeper waters. Relating the sutural amplitude indices of ammonites found in a well-studied depositional basin, such as the Cretaceous Western Interior Seaway, to morphotype distributions illustrates the utility of this index in bathymetric interpretations. □ Ammonoidea, sutures, Sutural Amplitude Index, Cretaceous, Greenhorn Cyclothem. Western Interior.     

Is there a justification for differential a priori weighting in coding sequences? A case study from rbcL and Apocynaceae s.l

Functional constraints are often assumed to influence the performance of nucleotide characters in phylogenetic analysis: First and second codon positions and sites of structural importance are considered to show less homoplasy. We investigate the performance of rbcL characters with differential functional constraints in a cladistic analysis of the plant family Apocynaceae s.l. (Sennblad and Bremer, in prep.). Performance is measured as rescaled consistency indices (rc). We show there is no significant difference in performance between parsimony-informative sites constrained by function in the enzyme, and sites that are not. Furthermore, the substitutions in third-codon position performed significantly better than those in first and second. The variation of rc within the different classes was high, however. Consequently, there is no support for routinely applied a priori differential weighting, neither of codon positions, nor of different functional classes from the present analysis of rbcL data in the Apocynaceae s.l.     

Weighting against homoplasy improves phylogenetic analysis of morphological data sets

The problem of character weighting in cladistic analysis is revisited. The finding that, in large molecular data sets, removal of third positions (with more homoplasy) decreases the number of well supported groups has been interpreted by some authors as indicating that weighting methods are unjustified. Two arguments against that interpretation are advanced. Characters that collectively determine few well‐supported groups may be highly reliable when taken individually (as shown by specific examples), so that inferring greater reliability for sets of characters that lead to an increase in jackknife frequencies may not always be warranted. But even if changes in jackknife frequencies can be used to infer reliability, we demonstrate that jackknife frequencies in large molecular data sets are actually improved when downweighting characters according to their homoplasy but using properly rescaled functions (instead of the very strong standard functions, or the extreme of inclusion/exclusion); this further weakens the argument that downweighting homoplastic characters is undesirable. Last, we show that downweighting characters according to their homoplasy (using standard homoplasy‐weighting methods) on 70 morphological data sets (with 50–170 taxa), produces clear increases in jackknife frequencies. The results obtained under homoplasy weighting also appear more stable than results under equal weights: adding either taxa or characters, when weighting against homoplasy, produced results more similar to original analyses (i.e., with larger numbers of groups that continue being supported after addition of taxa or characters), with similar or lower error rates (i.e., proportion of groups recovered that subsequently turn out to be incorrect). Therefore, the same argument that had been advanced against homoplasy weighting in the case of large molecular data sets is an argument in favor of such weighting in the case of morphological data sets. © The Willi Hennig Society 2008.     

Untangling phylogenetic,geometric and ornamental imprints on Early Triassic ammonoid biogeography: a similarity‐distance decay study

Ammonoids are diverse and widespread fossil, externally shelled cephalopods that flourished for more than 300 Myr before their total extinction 65 Ma ago. In spite of two centuries of intensive scientific studies, their mode(s) of life and long‐distance dispersal abilities remain poorly known. Here, we address this by focusing on the latitudinal distribution of Early Triassic (approximately 250 Myr) ammonoids through similarity‐distance decay analyses. We examine and compare rates of similarity‐distance decay between various groups with respect to systematics, shell geometry and ornamentation to untangle phylogenetic, geometric and ornamental imprints on the observed biogeographical pattern. Our data do not support any phylogenetic and shell ornamentation influence, but rather demonstrate the significant effect of (sub‐)adult shell geometry on the similarity–distance decay: most evolute morphs tend to have been more endemic than most involute forms. This contrasts with the classic hypothesis that long‐distance ammonoid dispersal mainly occurred during the earliest planktonic stages, and thus that (sub‐)adult morphological characteristics should not constrain large‐scale biogeographical patterns of ammonoids. Although direct control by Sea Surface Temperature can be discarded, this result may indicate that at least some adult Triassic ammonoid morphs were skilled active swimmers capable of achieving long‐distance migration, as observed for some present‐day coleoid cephalopods. □Ammonoid, dispersal, similarity‐distance decay, morphology, phylogeny, biogeography, Triassic.     

Soft anatomy, diffuse homoplasy, and the relationships of lizards and snakes

Most previous phylogenetic analyses of squamates (‘lizards’ and snakes) employing large character sets have focused on osteology. Soft anatomical traits bearing on this problem have usually been considered in small subsets. Here, a comprehensive phylogenetic analysis of squamate soft anatomy is attempted. 126 informative characters are assessed for 23 squamate lineages, representing snakes, amphisbaenians, dibamids, and all the traditionally recognized ‘families’ of lizards. The traditionally recognized groupings Iguania, Scleroglossa, Gekkota, Scincomorpha, Anguimorpha and Varanoidea are corroborated in this analysis. More controversial taxa are resolved as follows. Xantusiids, amphisbaenians and dibamids cluster with gekkotans, and snakes are strongly allied with anguimorphs in general, and varanids in particular. Nearly all these clades are congruent with those found in a recent comprehensive osteological analysis; the strong support for snake‐varanid relationships found in both studies is particularly notable. This congruence is surprising given that previous studies of soft anatomy tended to give differing and often heterodox results. These previous results can be attributed to overrepresentation of misleading characters in small isolated data sets. Such misleading signals are minimized when data sets are combined. For instance, the snake‐varanid clade is contradicted by many characters, and analyses of particular organ systems therefore give differing results. However, characters that are incongruent with the snake‐varanid clade also disagree with each other (diffuse homoplasy), rather than forming coherent support for some particular alternative clade (concerted homoplasy). In a combined analysis these incongruent but diffuse characters cancel each other out to leave a very strong (and orthodox) phylogenetic signal. These results underscore the view that the raw amount of homoplasy — as revealed by consistency and retention indices — is not the only determinant of phylogenetic signal; the distribution of that homoplasy is also important. Thus, questioning a phylogenetic hypothesis (e.g. the snake‐varanid clade) by identifying numerous conflicting characters is insufficient — the structure of the conflicting characters should be assessed in a rigorous phylogenetic analysis.     

Homoplasy and the early hominid masticatory system: inferences from analyses of extant hominoids and papionins

Early hominid masticatory characters are widely considered to be more prone to homoplasy than characters from other regions of the early hominid skull and therefore less reliable for phylogenetic reconstruction. This hypothesis has important implications for current reconstructions of early hominid phylogeny, but it has never been tested. In this paper we evaluate the likely veracity of the hypothesis using craniometric data from extant primate groups for which reliable consensus molecular phylogenies are available.Datasets representing the extant large-bodied hominoid genera and the extant papionin genera were compiled from standard measurements. The data were adjusted to minimise the confounding effects of body size, and then converted into discrete character states using divergence coding. Each dataset was divided into four regional character groups: (1) palate and upper dentition, (2) mandible and lower dentition, (3) face and (4) cranial vault and base. Thereafter, the regional character groups were analysed using cladistic methods and the resulting phylogenetic hypotheses judged against the consensus molecular phylogenies for the hominoids and papionins.The analyses indicated that the regions dominated by masticatory characters-the palate and upper dentition, and the mandible and lower dentition-are no less reliable for phylogenetic reconstruction than the other regions of the skull. The four regions were equally affected by homoplasy and were, therefore, equally unreliable for phylogenetic reconstruction. This finding challenges the recent suggestion that Paranthropus is polyphyletic, which is based on the assumption that masticatory characters are especially prone to homoplasy. Our finding also suggests that, contrary to current practice, there is no a priori reason to de-emphasise the phylogenetic significance of the masticatory similarities between Homo rudolfensis and the australopiths. The corollary of this is that H. rudolfensis is unlikely to be a member of the Homo clade and should therefore be allocated to another genus.     

Phylogenetic analysis of phenotypic characters of Tunicata supports basal Appendicularia and monophyletic Ascidiacea

With approximately 3000 marine species, Tunicata represents the most disparate subtaxon of Chordata. Molecular phylogenetic studies support Tunicata as sister taxon to Craniota, rendering it pivotal to understanding craniate evolution. Although successively more molecular data have become available to resolve internal tunicate phylogenetic relationships, phenotypic data have not been utilized consistently. Herein these shortcomings are addressed by cladistically analyzing 117 phenotypic characters for 49 tunicate species comprising all higher tunicate taxa, and five craniate and cephalochordate outgroup species. In addition, a combined analysis of the phenotypic characters with 18S rDNA-sequence data is performed in 32 OTUs. The analysis of the combined data is congruent with published molecular analyses. Successively up-weighting phenotypic characters indicates that phenotypic data contribute disproportionally more to the resulting phylogenetic hypothesis. The strict consensus tree from the analysis of the phenotypic characters as well as the single most parsimonious tree found in the analysis of the combined dataset recover monophyletic Appendicularia as sister taxon to the remaining tunicate taxa. Thus, both datasets support the hypothesis that the last common ancestor of Tunicata was free-living and that ascidian sessility is a derived trait within Tunicata. “Thaliacea” is found to be paraphyletic with Pyrosomatida as sister taxon to monophyletic Ascidiacea and the relationship between Doliolida and Salpida is unresolved in the analysis of morphological characters; however, the analysis of the combined data reconstructs Thaliacea as monophyletic nested within paraphyletic “Ascidiacea”. Therefore, both datasets differ in the interpretation of the evolution of the complex holoplanktonic life history of thaliacean taxa. According to the phenotypic data, this evolution occurred in the plankton, whereas from the combined dataset a secondary transition into the plankton from a sessile ascidian is inferred. Besides these major differences, both analyses are in accord on many phylogenetic groupings, although both phylogenetic reconstructions invoke a high degree of homoplasy. In conclusion, this study represents the first serious attempt to utilize the potential phylogenetic information present in phenotypic characters to elucidate the inter-relationships of this diverse marine taxon in a consistent cladistic framework.     

On the efficiency of the buoyancy apparatus in ammonoids: evidences from sublethal shell injuries

The five greatest sublethal injuries were selected from a collection of more than 12,000 predominantly Mesozoic injured or otherwise pathological ammonoids. The loss of shell mass from these survived injuries was calculated and compared with comparable tolerances in the recent Nautilus . These ammonoids tolerated a shell loss up to four times greater than in Nautilus . The maximum tolerated shell loss indicates an unexpected buoyancy compensation mechanism. The buoyancy of the selected specimens was calculated. The results show that the buoyancy of all the observed ammonoid shells was positive. In order to maintain neutral buoyancy after injury, these ammonoids had to fill the phragmocone with a volume of mass. Nautilus compensated a maximum mass loss requiring a liquid refill of 3% of the cameral capacity, the ammonoids compensated a maximum of observed mass loss requiring a liquid refill of more than 10% of cameral capacity. The ratio of chamber volume/siphuncular surface area in the ammonoid Lithacoceras is 0.043, indicating that the relative area of the siphuncular epithelium in Lithacoceras is significantly higher when compared with a ratio of 0.12-0.14 in the adult Nautilus . The phragmocone in ammonoids offered the ability of a much more active buoyancy regulation than in Nautilus .     

Phylogeny of the aptychi-possessing Neoammonoidea (Aptychophora nov., Cephalopoda)

The different forms of the aptychi (opercula, homologous with lower jaws) of the Ammonoidea are used for the first time in a phylogenetic analysis of part of the classic Ammonoidea phylogeny. The results indicate that the aptychi-possessing ammonoids form a monophylum for which we propose the informal name Aptychophora nov. Among the Jurassic ammonoids, it is possible to recognize several monophyletic groups. In part, our results support existing superfamilies (e.g. Hildocerataceae, Haplocerataceae) by new synapomorphies. However, the Perisphinctaceae can now be much more clearly differentiated than in the previously established phylogenetic tree. The Upper Cretaceous ammonoid superfamilies cannot be derived from the Haplocerataceae, but are descendants of a 'primitive' perisphinctacean possessing a praestriaptychus. Nor can they be derived from the 'higher' perisphinctaceans (family Perisphinctidae) because that clade is characterized by granulaptychi. The consequence of these results is that the quadrilobate primary suture of the 'Ancyloceratina' must have evolved more than once by reduction from an ancestral quinquelobate primary suture. The Ancyloceratidae have praestraptychi or aptychi types which can be derived from praestriaptychi, whereas the Crioceratitinae have longitudinally striated anaptychi.     

Giant taxon‐character matrices: quality of character constructions remains critical regardless of size

Giant morphological data matrices are increasingly common in cladistic analyses of vertebrate phylogeny, reporting numbers of characters never seen or expected before. However, the concern for size is usually not followed by an equivalent, if any, concern for character construction/selection criteria. Therefore, the question of whether quantity parallels quality for such influential works remains open. Here, we provide the largest compilation known to us of character construction methods and criteria, as derived from previous studies, and from our own de novo conceptualizations. Problematic character constructions inhibit the capacity of phylogenetic analyses to recover meaningful homology hypotheses and thus accurate clade structures. Upon a revision of two of the currently largest morphological datasets used to test squamate phylogeny, more than one‐third of the almost 1000 characters analysed were classified within at least one of our categories of “types” of characters that should be avoided in cladistic investigations. These characters were removed or recoded, and the data matrices re‐analysed, resulting in substantial changes in the sister group relationships for squamates, as compared to the original studies. Our results urge caution against certain types of character choices and constructions, also providing a methodological basis upon which problematic characters might be avoided.     

Nautilus—a poor model for the function and behavior of ammonoids?

Inferences drawn from the biology, function, and behavior of closely related living forms facilitate interpretation of the mode of life of groups known only from the fossil record. The choice of phylogenetically relevant modern 'model organisms' can have critical bearing on the resulting interpretations. The biology and behavior of fossil ammonoids are often interpreted in the light of evidence derived from the study of modern Nautilus . However, examination of the fossil record and cladistic analyses both indicate that coleoids are much more closely related to ammonoids than is Nautilus . Coleoid biology and behavior differ dramatically from the biology and behavior of Nautilus . Thus, the inclusion of coleoids as examples, rather than reliance on Nautilus alone, produces a strikingly different vision of ammonoid biology and suggests that inferences of ammonoid biology and behavior that rely exclusively on Nautilus should be reviewed. Two features related to swimming ability in Nautilus , static stability and large retractor muscles, are much reduced in many ammonoids, leading to the interpretation that ammonoids were poorer swimmers than Nautilus . However, reexamination of the evidence indicates that static stability should not play a role in the swimming of ammonoids with long body chambers. In addition, functional arguments suggest that a coleoid-like swimming mechanism should have evolved prior to the loss of the body chamber in coleoids. Thus, a coleoid-like swimming mechanism is likely to have evolved prior to the separation of ammonoid and coleoid lineages. A mechanism is proposed by which a coleoid swimming mechanism, independent of retractor muscle size, could function in ammonoids with long body chambers.□ Ammonoids, ammonites, evolution, functional morphology , Nautilus, phylogeny .     

Implied weighting and its utility in palaeontological datasets: a study using modelled phylogenetic matrices

Implied weighting, a method for phylogenetic inference that actively seeks to downweight supposed homoplasy, has in recent years begun to be widely utilized in palaeontological datasets. Given the method's purported ability at handling widespread homoplasy/convergence, we investigate the effects of implied weighting on modelled phylogenetic data. We generated 100 character matrices consisting of 55 characters each using a Markov Chain morphology model of evolution based on a known phylogenetic tree. Rates of character evolution in these datasets were variable and generated by pulling from a gamma distribution for each character in the matrix. These matrices were then analysed under equal weighting and four settings of implied weights (k = 1, 3, 5, and 10). Our results show that implied weighting is inconsistent in its ability to retrieve a known phylogenetic tree. Equally weighted analyses are found to generally be more conservative, retrieving higher frequency of polytomies but being less likely to generate erroneous topologies. Implied weighting is found to generally resolve polytomies while also propagating errors, resulting in an increase in both correctly and incorrectly resolved nodes with a tendency towards higher rates of error compared to equal weighting. Our results suggest that equal weights may be a preferable method for parsimony analysis.     

HOMOPLASY AND THE CHOICE AMONG CLADOGRAMS

Abstract Cladistic data are more decisive when the possible trees differ more in tree length. When all the possible dichotomous trees have the same length, no one tree is better supported than the others, and the data are completely undecisive . From a rule for recursively generating undecisive matrices for different numbers of taxa, formulas to calculate consistency, rescaled consistency and retention indices in undecisive matrices are derived. The least decisive matrices are not the matrices with the lowest possible consistency, rescaled consistency or retention indices (on the most parsimonious trees); those statistics do not directly vary with decisiveness. Decisiveness can be measured with a newly proposed statistic, DD = − S )/( − S ) (where S = length of the most parsimonious cladogram, = mean length of all the possible cladograms for the data set and M = observed variation). For any data set, can be calculated exactly with simple formulas; it depends on the types of characters present, and not on their congruence. Despite some recent assertions to the contrary, the consistency index is an appropriate measure of homoplasy (= deviation from hierarchy). The retention index seems more appropriate for comparing the fit of different trees for the same data set.