The basicranium of dicynodonts (Synapsida) and its use in phylogenetic analysis

Current phylogenetic hypotheses for the dicynodonts conflict, probably because the characters used, especially those of the jaws and facial region, show considerable convergence. Characters of the braincase and basipterygoid articulation of the Late Permian–Middle Triassic dicynodonts Diictodon , Dicynodon , Kingoria, Lystrosaurus , Rechnisaurus , and 14 other genera, may have phylogenetic value. Parsimony analysis and the character compatability permutation test suggest, at the highest possible confidence level, that the data set contains significant hierarchical structure, interpreted as a result of phylogeny. The most parsimonious tree broadly agrees with all recent hypotheses on the relationships among dicynodonts. However, it conflicts with the recent suggestion that Lystrosaurus is part of a clade of Middle–Late Triassic dicynodonts, but supports the basal position of Kingoria . The use of Eodicynodon as an outgroup does not perturb the parsimonious relationship of the included taxa. Topological constraints reveal that phylogenetic hypotheses based only on basicranial characters are not robust. Characters of the basipterygoid articulation and inner braincase have high consistency and retention indices, which suggests that the main evolutionary transformations in the dicynodont basicranium occurred within these structures.     

Testable but not falsifiable?

We are puzzled by a recent comment that suggested that historical hypotheses can be tested but are unfalsifiable. We argue that phylogenetic hypotheses are falsifiable without the aid of a time machine and that they are like any other hypothesis: they are tentative knowledge propositions capable of falsification with character evidence.     

Rejecting "the given" in systematics

How morphology and systematics come together through morphological analysis, homology hypotheses and phylogenetic analysis is a topic of continuing debate. Some contemporary approaches reject biological evaluation of morphological characters and fall back on an atheoretical and putatively objective (but, in fact, phenetic) approach that defers to the test of congruence for homology assessment. We note persistent trends toward an uncritical empiricism (where evidence is believed to be immediately “given” in putatively theory‐free observation) and instrumentalism (where hypotheses of primary homology become mere instruments with little or no empirical foundation for choosing among competing phylogenetic hypotheses). We suggest that this situation is partly a consequence of the fact that the test of congruence and the related concept of total evidence have been inappropriately tied to a Popperian philosophy in modern systematics. Total evidence is a classical principle of inductive inference and does not imply a deductive test of homology. The test of congruence by itself is based philosophically on a coherence theory of truth (coherentism in epistemology), which is unconcerned with empirical foundation. We therefore argue that coherence of character statements (congruence of characters) is a necessary, but not a sufficient, condition to support or refute hypotheses of homology or phylogenetic relationship. There should be at least some causal grounding for homology hypotheses beyond mere congruence. Such causal grounding may be achieved, for example, through empirical investigations of comparative anatomy, developmental biology, functional morphology and secondary structure. © The Willi Hennig Society 2006.     

The Evolution of Integration of Biological Systems: An Evolutionary Perspective through Studies on Cells, Tissues, and Organs

Biologists are integrating studies of morphology, development,physiology,and other disciplines in order to understand howspecies and lineages diversify and cope with their environments.An evolutionary perspective in such studies, including thoseof cells, tissues, and organs, is potentially useful for thestructure and analysis of such problems. Evolutionary biologyis the study of the history of evolution and the elucidationof its mechanisms. Comparative biology is the comparison ofa trait or traits in selected taxa, and may be, but need notbe, evolutionary in approach. A phylogenetic hypothesis is necessaryfor reconstruction of pattern in morphology, ecology, behavior,and other areas. Acquaintance with evolutionary and phylogeneticperspectives can guide selection of taxa for study and opennew approaches to analysis of data. Such an approach is notalways appropriate to problems in biology, but it could be utilizedbeneficially more frequently than is currently practiced. Studiesof cells, tissues, and organs may contribute to the constructionof new phylogenetic hypotheses and to analysis of patterns andmechanisms of change when pursued from an evolutionary perspective     

Parallelism, non-biotic data and phylogeny reconstruction in paleobiology

Webb, G.E. 1994 1015: Parallelism, non-biotic data and phylogeny reconstruction in paleobiology.
Many systematists equate parallelism and convergence. However, whereas convergence is relatively uncommon and easily recognized using divergent characters, parallelism is common but more difficult to recognize because divergent characters are less abundant. Cladists, in particular, equate homeomorphy with convergence and reject parallelism as a distinct concept. Unfortunately, cladistic parsimony analysis may not resolve most parallelism. Therefore, criteria for the a priori recognition and objective evaluation of parallelism are very significant. Non-biotic data (e.g., stratigraphic and geographic distribution) provide independent criteria for the construction of hypotheses of parallelism in cases where taxa (1) were geographically isolated during homeomorphic character-state transformations, (2) occurred with endemic faunas, and (3) evolved in similar environmental conditions as suggested by paleoecological data. Australian lithostrotionoid corals were long considered congeneric with European taxa. However, because of their geographic isolation, occurrence with endemic rugose corals and occurrence in similar depositional environments as European forms, they are now considered a homeomorphic clade, resulting from an extended sequence of parallel character-state transformations. The high degree of parallelism, combined with abundant symplesiomorphic characters, led to erroneous phylogenetic inferences when non-biotic data were excluded from analysis. Cladistics, homeomorphy, lithostrotionoid corals, parallelism, phylogeny .     

Circularity,evolution, systematics … and circularity

Many have argued strongly that incorporation of evolutionary theory into systematics is dangerously circular, while others have maintained that such an integrated approach increases the accuracy of phylogenetic inference. Here, it is demonstrated that such blanket statements regarding exclusion or inclusion of evolutionary principles in systematics fail to distinguish between two very different types of principles. ‘Phylogeny-neutral’ evolutionary principles are those inferred without any recourse to specific phylogenetic hypotheses (e.g. via developmental genetics, biomechanics). In contrast, ‘phylogeny-dependent’ principles are those which can only be inferred on the basis of specific phylogenetic hypotheses (e.g. character associations detected via ‘comparative methods’). Inclusion of phylogeny-neutral principles in systematic studies as a priori assumptions can be justified, since these principles have (often strong) external empirical support from other spheres of investigation. However, inclusion of phylogeny-dependent principles in systematic studies is circular, since such principles have no external empirical support but are themselves derived from systematic studies. Advocating inclusion or exclusion of all (or as many as possible) evolutionary principles from phylogenetic analysis is therefore misguided. Rather, phylogeny-neutral principles are independently supported and can be included, while phylogeny-dependent principles are unjustified assumptions and should be excluded to avoid circularity. However, integration of complex phylogeny-neutral principles in systematics can create operational problems, even though there are no methodological reasons against their inclusion.     

Reconciling gene trees of eastern North American minnows

Most eastern North American cyprinid fishes belong to a clade known as the "open posterior myodome" (OPM) minnows, but phylogenetic relationships within this clade have been difficult to ascertain. Previous attempts to resolve relationships among the generally benthic "chubs" and the more pelagic "shiners", that constitute the majority of OPM minnows, have led to highly discordant phylogenetic hypotheses. To further examine relationships among the OPM minnows, we utilized both a concatenated Bayesian approach and a coalescent-based species tree method to analyze data from six protein coding nuclear loci (Enc1, Ptr, Ryr3, Sh3px3, Tbr1, and Zic1), as well as the mitochondrial locus (Cytb). We focused our analyses on the chub-like genus Phenacobius, a group that has drifted topologically between other benthic chubs and the more pelagic shiners, and also included exemplar taxa from 11 other OPM lineages. Individual gene trees were highly discordant regarding relationships within Phenacobius and across the OPM clade. The concatenated Bayesian analysis and coalescent-based species tree reconstruction recovered slightly different phylogenetic topologies. Additionally, the posterior support values for clades using the coalescent-based approach were consistently lower than the concatenated analysis. However, Phenacobius was resolved as monophyletic and as the sister lineage to Erimystax regardless of the combined data approach taken. Furthermore, Phenacobius+Erimystax was recovered as more closely related to the shiners we examined than to other chubs. Relationships within Phenacobius varied depending on the combined phylogenetic method utilized. Our results highlight the importance of multi-locus, coalescent-based approaches for resolving the phylogeny of diverse clades like the eastern North American OPM minnows.     

Intercontinental community convergence of ecology and morphology in desert lizards

Evolutionary ecologists have long debated the extent to which communities in similar environments but different geographic regions exhibit convergence. On the one hand, if species' adaptations and community structure are determined by environmental features, convergence would be expected. However, if historical contingencies have long-lasting effects convergence would be unlikely. Most studies to date have emphasized the differences between communities in similar environments and little quantitative evidence for convergence exists. The application of comparative phylogenetic methods to ecological studies provides an opportunity to further investigate hypotheses of convergence. We compared the evolutionary patterns of structural ecology and morphology of 42 species of iguanian lizards from deserts of Australia and North America. Using a comparative approach, we found that evolutionary convergence of ecology and morphology occurs both in overall, community-wide patterns and in terms of pairs of highly similar intercontinental pairs of species. This result indicates that in these desert lizards, deterministic adaptive evolution shapes community patterns and overrides the historical contingencies unique to particular lineages.     

Assessing Trait Covariation and Morphological Integration on Phylogenies Using Evolutionary Covariance Matrices

Morphological integration describes the degree to which sets of organismal traits covary with one another. Morphological covariation may be evaluated at various levels of biological organization, but when characterizing such patterns across species at the macroevolutionary level, phylogeny must be taken into account. We outline an analytical procedure based on the evolutionary covariance matrix that allows species-level patterns of morphological integration among structures defined by sets of traits to be evaluated while accounting for the phylogenetic relationships among taxa, providing a flexible and robust complement to related phylogenetic independent contrasts based approaches. Using computer simulations under a Brownian motion model we show that statistical tests based on the approach display appropriate Type I error rates and high statistical power for detecting known levels of integration, and these trends remain consistent for simulations using different numbers of species, and for simulations that differ in the number of trait dimensions. Thus, our procedure provides a useful means of testing hypotheses of morphological integration in a phylogenetic context. We illustrate the utility of this approach by evaluating evolutionary patterns of morphological integration in head shape for a lineage of Plethodon salamanders, and find significant integration between cranial shape and mandible shape. Finally, computer code written in R for implementing the procedure is provided.     

The measurement of test severity, significance tests for resolution, and a unified philosophy of phylogenetic inference

The philosopher Karl Popper described a concept termed degree of corroboration , C , for evaluating and comparing hypotheses according to the results of their tests. C is, fundamentally, a comparison of two likelihoods: p ( e|hb ), the likelihood of the hypothesis ( h ) in conjunction with the background knowledge ( b ), and p ( e|b ), the likelihood of b alone. C is closely related to the likelihood ratio of nested hypotheses. When phylogenetic analysis is interpreted as an attempt to assess C for a phylogenetic tree (the hypothesis, h ), several interpretations have been given for p ( e|b ). Here I describe a new interpretation that equates p ( e|b ) with the probability of the data in the absence of a hypothesis of phylogenetic resolution, that is with the likelihood of an unresolved or polytomous tree. Under this interpretation, C for a fully or partially resolved phylogenetic tree is the likelihood of that tree minus the likelihood of the corresponding unresolved tree. These same two likelihoods can be used in a likelihood ratio test (LRT) to assess the significance of the degree of corroboration of the hypothesis of phylogenetic resolution. This LRT for resolution is closely related to permutation tests for phylogenetic structure in the data, because data that evolved on a true polytomous tree are expected to be phylogenetically randomized. It therefore reconciles the interpretation of the evidence ( e ) as the distribution of character states among taxa (rather than the score of the optimal tree) with the interpretation of permutation tests as methods for assessing C. Likelihood methods are (contrary to the views of some commentators) central to understanding how Popper's C applies to phylogenetic hypotheses, and they form the foundation of a unified and inclusive philosophy of phylogenetic inference.     

Phylogeny of mysticete whales based on mitochondrial and nuclear data

Mysticetes or baleen whales are comprised of four groups: Eschrichtiidae, Neobalaenidae, Balaenidae, and Balaenopteridae. Various phylogenetic hypotheses among these four groups have been proposed. Previous studies have not satisfactorily determined relationships among the four groups with a high degree of confidence. The objective of this study is to determine the relationships among the mysticete whales. Mitochondrial and nuclear DNA were sequenced for phylogenetic analysis. Most species relationships determined using these data were well resolved and congruent. Balaenidae is the most basal group and Neobalaenidae is the second most basal and sister group to the balaenopterid-eschrichtiid clade. In this phylogenetic study, the resolution of Eschrichtiidae with two main lineages of Balaenopteridae was problematic. Some data partitions placed this group within the balaenopterids, and other partitions placed it as a sister taxon to the balaenopterids. An additive likelihood approach was used to determine the most optimal trees. Although it was not found in the combined phylogenetic analyses, the "best" tree found under the additive likelihood approach was one with a monophyletic Balaenopteridae.     

Correlates of species richness in mammals: body size, life history, and ecology

We present the most extensive examination to date of proposed correlates of species richness. We use rigorous phylogenetic comparative techniques, data for 1,692 mammal species in four clades, and multivariate statistics to test four hypotheses about species richness and compare the evidence for each. Overall, we find strong support for the life-history model of diversification. Species richness is significantly correlated with shorter gestation period in the carnivores and large litter size in marsupials. These traits and short interbirth intervals are also associated with species richness in a pooled analysis of all four clades. Additionally, we find some support for the abundance hypotheses in different clades of mammals: abundance correlates positively with species richness in primates but negatively in microchiropterans. Our analyses provide no evidence that mammalian species richness is associated with body size or degree of sexual dimorphism.     

Cranial shape and correlated characters in crocodilian evolution

Crocodilians show a high degree of cranial variation and convergence throughout their 80 million-year fossil record that complicates their phylogenetic reconstruction. Conflicting phylogenetic results from different data partitions and character homoplasies typify crocodilian phylogeny, and differences between molecular and morphological phylogenetic hypotheses are believed to be associated with the slender-snout skull shape of Gavialis gangeticus and Tomistoma schlegelii. Slender-snout skulls are one of five identified eusuchian cranial ecomorph shape categories (ESCs) thought to reflect functional or ecological specialization. This paper tested the effect of transitions among general, blunt and slender ESCs on cranial character-state distributions in phylogeny using the concentrated changes test. In addition, 'tree-free' character compatibility analysis of character independence was conducted on the morphological character matrix to determine if character correlations are observed independent of specific tree topologies. Results suggest cranial ESCs do affect cranial character-state gains in phylogeny. Concentrated changes identify a broad suite of character-state changes that significantly correlate with transitions to slender, general and blunt ESCs on morphological, molecular and combined-data tree topologies, but numbers of correlated characters for each category differ according to topology. Character compatibility analysis results do not mirror the concentrated changes test results and reflect hierarchically distributed support throughout the data. As cranial ESCs affect character-state transitions, it is possible that nonphylogenetic variables could affect inferences of crocodilian phylogeny by affecting cranial morphology.     

Mitochondrial DNA,morphology, and the phylogenetic relationships of Antarctic icefishes (Notothenioidei: Channichthyidae)

The Channichthyidae is a lineage of 16 species in the Notothenioidei, a clade of fishes that dominate Antarctic near-shore marine ecosystems with respect to both diversity and biomass. Among four published studies investigating channichthyid phylogeny, no two have produced the same tree topology, and no published study has investigated the degree of phylogenetic incongruence between existing molecular and morphological datasets. In this investigation we present an analysis of channichthyid phylogeny using complete gene sequences from two mitochondrial genes (ND2 and 16S) sampled from all recognized species in the clade. In addition, we have scored all 58 unique morphological characters used in three previous analyses of channichthyid phylogenetic relationships. Data partitions were analyzed separately to assess the amount of phylogenetic resolution provided by each dataset, and phylogenetic incongruence among data partitions was investigated using incongruence length difference (ILD) tests. We utilized a parsimony-based version of the Shimodaira-Hasegawa test to determine if alternative tree topologies are significantly different from trees resulting from maximum parsimony analysis of the combined partition dataset. Our results demonstrate that the greatest phylogenetic resolution is achieved when all molecular and morphological data partitions are combined into a single maximum parsimony analysis. Also, marginal to insignificant incongruence was detected among data partitions using the ILD. Maximum parsimony analysis of all data partitions combined results in a single tree, and is a unique hypothesis of phylogenetic relationships in the Channichthyidae. In particular, this hypothesis resolves the phylogenetic relationships of at least two species (Channichthys rhinoceratus and Chaenocephalus aceratus), for which there was no consensus among the previous phylogenetic hypotheses. The combined data partition dataset provides substantial statistical power to discriminate among alternative hypotheses of channichthyid relationships. These findings suggest the optimal strategy for investigating the phylogenetic relationships of channichthyids is one that uses all available phylogenetic data in analyses of combined data partitions.     

Phylogenetic analysis, structural evolution and functional divergence of the 12-oxo-phytodienoate acid reductase gene family in plants

Background

Whenever different data sets arrive at conflicting phylogenetic hypotheses, only testable causal explanations of sources of errors in at least one of the data sets allow us to critically choose among the conflicting hypotheses of relationships. The large (28S) and small (18S) subunit rRNAs are among the most popular markers for studies of deep phylogenies. However, some nodes supported by this data are suspected of being artifacts caused by peculiarities of the evolution of these molecules. Arthropod phylogeny is an especially controversial subject dotted with conflicting hypotheses which are dependent on data set and method of reconstruction. We assume that phylogenetic analyses based on these genes can be improved further i) by enlarging the taxon sample and ii) employing more realistic models of sequence evolution incorporating non-stationary substitution processes and iii) considering covariation and pairing of sites in rRNA-genes.

Results

We analyzed a large set of arthropod sequences, applied new tools for quality control of data prior to tree reconstruction, and increased the biological realism of substitution models. Although the split-decomposition network indicated a high noise content in the data set, our measures were able to both improve the analyses and give causal explanations for some incongruities mentioned from analyses of rRNA sequences. However, misleading effects did not completely disappear.

Conclusion

Analyses of data sets that result in ambiguous phylogenetic hypotheses demand for methods, which do not only filter stochastic noise, but likewise allow to differentiate phylogenetic signal from systematic biases. Such methods can only rely on our findings regarding the evolution of the analyzed data. Analyses on independent data sets then are crucial to test the plausibility of the results. Our approach can easily be extended to genomic data, as well, whereby layers of quality assessment are set up applicable to phylogenetic reconstructions in general.     

Mosaics of convergences and noise in morphological phylogenies: what's in a viverrid-like carnivoran?

Adaptive convergence in morphological characters has not been thoroughly investigated, and the processes by which phylogenetic relationships may be misled by morphological convergence remains unclear. We undertook a case study on the morphological evolution of viverrid-like feliformians (Nandinia, Cryptoprocta, Fossa, Eupleres, Prionodon) and built the largest morphological matrix concerning the suborder Feliformia to date. A total of 349 characters grouped into four anatomical partitions were used for all species of Viverridae and viverrid-like taxa plus representatives of the Felidae, Hyaenidae, Herpestidae, and one Malagasy mongoose. Recent molecular phylogenetic analyses suggest that viverrid-like morphotypes appeared independently at least three times during feliformian evolution. We thus used a synthetic molecular tree to assess morphological evolutionary patterns characterizing the viverrid-like taxa. We examined phylogenetic signal, convergence and noise in morphological characters using (a) tree-length distribution (g1), (b) partitioned Bremer support, (c) RI values and their distribution, (d) respective contributions of diagnostic synapomorphies at the nodes for each partition, (e) patterns of shared convergences among viverrid-like taxa and other feliformian lineages, (f) tree-length differences among alternative hypotheses, and (g) the successive removal of convergent character states from the original matrix. In addition, the lability of complex morphological structures was assessed by mapping them onto the synthetic molecular tree. The unconstrained morphological analysis yielded phylogenetic groupings that closely reflected traditional classification. The use of a synthetic molecular tree (constraint) combined with our thorough morphological investigations revealed the mosaics of convergences likely to have contributed to part of the historical uncertainty over viverrid classification. It also showed that complex morphological structures could be subjected to reversible evolutionary trends. The morphological matrix proved useful in characterizing several feliformian clades with diagnostic synapomorphies. These results support the removal from the traditionally held Viverridae of several viverrid-like taxa into three distinct families: Nandiniidae (Nandinia), Prionodontidae (Prionodon), and the newly defined Eupleridae (including Cryptoprocta, Fossa, Eupleres plus all "mongoose-like" Malagasy taxa). No clearly "phylogenetically misleading" data subsets could be identified, and the great majority of morphological convergences appeared to be nonadaptive. The multiple approaches used in this study revealed that the most disruptive element with regards to morphological phylogenetic reconstruction was noise, which blured the expression of phylogenetic signal. This study demonstrates the crucial need to consider independent (molecular) phylogenies in order to produce reliable evolutionary hypotheses and should promote a new approach to the definition of morphological characters in mammals. [Constrained analysis; convergence; evolutionary scenario; Feliformia; morphology; noise; phylogenetic signal; phylogeny; Viverridae.].     

The problem of characters susceptible to parallel evolution in phylogenetic analysis: a reply to Marquès and Gnaspini (2001) with emphasis on cave life phenotypic evolution

Marquès and Gnaspini [Cladistics 17 (2001) 371–381] analyzed the problem of the phylogenetic treatment of characters submitted to parallel evolution. Their proposal aimed at preserving the potential phylogenetic significance of supposedly homoplastic characters and considering them for phylogeny reconstruction. As an example, they used the troglobiomorphic features of animals restricted to caves; according to their preliminary hypothesis of homoplasy, troglobitic animals would exhibit a particular phenotype, referred to as troglobiomorphic, which they would acquire under similar selective pressures from the subterranean environment. We examined Marquès and Gnaspini's approach not from the point of view of its technical flaws, but from the point of view of the authors’ basic assertions on the treatment of troglobiomorphic characters and more generally the inclusion/exclusion/transformation of characters prior to phylogenetic analysis. In the present paper, we argue that this approach is invalidated by the repeated use of ad hoc hypotheses, which are supported neither by an existing phylogenetic pattern nor by available data. We consequently contest the adequateness of this approach with a cladistic analysis of historical questions.     

The utility of AFLPs for supporting mitochondrial DNA phylogeographical analyses in the Taiwanese bamboo viper, Trimeresurus stejnegeri

An amplified fragment length polymorphism (AFLP) assay was performed on individuals representing discrete haplotypes from two genetically distinct mtDNA lineages of the bamboo viper, Trimeresurus stejnegeri (Schmidt), within Taiwan. AFLP (525 polymorphic markers from five primer pairs) and mtDNA genetic distances were highly correlated and an analysis of molecular variance, and a Bayesian approach similarly partitioned estimates of genetic similarity according to the mtDNA phylogeographical pattern. These results are discussed in relation to biogeographical hypotheses, comparative rates of mtDNA molecular evolution, and in the identification of evolutionary significant units of Taiwanese T. stejnegeri. In spite of the high degree of congruence between the genetic datasets, the AFLP phylogenetic analysis did not support the mtDNA tree, suggesting that no contemporary barriers to gene flow exist between individuals from the two mtDNA lineages.     

Causes of plant diversification in the Cape biodiversity hotspot of South Africa

The Cape region of South Africa is one of the most remarkable hotspots of biodiversity with a flora comprising more than 9000 plant species, almost 70% of which are endemic, within an area of only ± 90,000 km2. Much of the diversity is due to an exceptionally large contribution of just a few clades that radiated substantially within this region, but little is known about the causes of these radiations. Here, we present a comprehensive analysis of plant diversification, using near complete species-level phylogenies of four major Cape clades (more than 470 species): the genus Protea, a tribe of legumes (Podalyrieae) and two speciose genera within the iris family (Babiana and Moraea), representing three of the seven largest plant families in this biodiversity hotspot. Combining these molecular phylogenetic data with ecological and biogeographical information, we tested key hypotheses that have been proposed to explain the radiation of the Cape flora. Our results show that the radiations started throughout the Oligocene and Miocene and that net diversification rates have remained constant through time at globally moderate rates. Furthermore, using sister-species comparisons to assess the impact of different factors on speciation, we identified soil type shifts as the most important cause of speciation in Babiana, Moraea, and Protea, whereas shifts in fire-survival strategy is the most important factor for Podalyrieae. Contrary to previous findings in other groups, such as orchids, pollination syndromes show a high degree of phylogenetic conservatism, including groups with a large number of specialized pollination syndromes like Moraea. We conclude that the combination of complex environmental conditions together with relative climatic stability promoted high speciation and/or low extinction rates as the most likely scenario leading to present-day patterns of hyperdiversity in the Cape.     

Teeth before jaws? Comparative analysis of the structure and development of the external and internal scales in the extinct jawless vertebrate Loganellia scotica

Traditional hypotheses posit that teeth evolved from dermal scales, through the expansion of odontogenetically competent ectoderm into the mouth of jawless vertebrates. The discovery of tooth‐like scales inside thelodonts, an extinct group of jawless vertebrates, led to the alternative hypothesis that teeth evolved from endodermal derivatives and that there exists a fundamental developmental and phylogenetic distinction between oral/pharyngeal and external odontodes. We set out a test of this latter hypothesis, examining the development of scales of the thelodont Loganellia scotica using synchrotron radiation X‐ray tomographic microscopy (SRXTM). We reveal that the internal scales are organized into fused patches and rows, a key distinction from the discrete dermal scales. The pattern of growth of oral scale patches is polarized, but not along a particular vector, whereas pharyngeal scale rows grew along a vector. Our test of the phylogenetic distribution of oral and pharyngeal scales and teeth in vertebrates indicates that odontodes are first expressed in an external position. Internal scales, where present, are always located near to external orifices; the sequential development of pharyngeal scales in Loganellia is peculiar among thelodonts and other stem gnathostomes. It represents a convergence on, rather than the establishment of, the developmental pattern underpinning tooth replacement in jawed vertebrates. The available evidence suggests that internal odontodes evolved through the expansion of odontogenic competence from external to internal epithelia.