Ancestral State Estimation Research Articles

Evolutionary origins, macroevolutionary dynamics, and climatic niche space of the succulent plant syndrome in the Caryophyllales.

The succulent plant syndrome is defined by the coordination of traits that enhance internal water storage within plant tissues. Although distributed globally in different habitats, succulent plants are thought to have evolved to avoid drought in arid regions, due to trait modifications that decrease tissue water deficits. We evaluated the evolution and the ecological significance of the succulent strategy at a global scale by comparing the climatic niche of species displaying succulence within the Core Caryophyllales with their non-succulent relatives. We assembled and curated a worldwide dataset of 201K georeferenced records belonging to 5447 species within 28 families, and analyzed the climatic niche of species along with their origin and evolutionary trajectories using ecological niche modeling, phylogenetic regression, divergence dates and ancestral state estimation. Results indicate the Core Caryophyllales have inhabited drylands since their origin in the Early Cretaceous. However, the succulent syndrome appeared and diversified during later geologic periods. The climatic niche space of succulents is narrower than non-succulent relatives, but no climate niche separation was detected between groups. Our results support alternative interpretations on the environmental and ecological forces that spurred the origin and diversification of the succulent plant syndrome and the radiation of rich succulent lineages.

Transcriptomic data support phylogenetic congruence and reveal genomic changes associated with the repeated evolution of annualism in aplocheiloid killifishes (Cyprinodontiformes)

Repeated evolution of novel life histories that are correlated with ecological variables offers opportunities to study convergence in genetic, developmental, and metabolic features. Nearly half of the 800 species of Aplocheiloid killifishes, a clade of teleost fishes with a circumtropical distribution, are “annual” or seasonal species that survive in ephemeral bodies of water that desiccate and are unfeasible for growth, reproduction, or survival for weeks to months every year. But the repeated evolution of adaptations that are key features of the annual life history among these fishes remains poorly known without a robust phylogenetic framework. We present a large-scale phylogenomic reconstruction of aplocheiloid killifishes evolution using newly sequenced transcriptomes obtained from a diversity of killifish lineages representing putative independent origins of annualism. Ancestral state estimation shows that developmental dormancy (diapause), a key trait of the killifish annual life cycle, may have originated up to seven times independently among African and South American lineages. To further explore the genetic basis of this unique trait, we measure changes in evolutionary rates among orthologous genes across the killifish tree of life by quantifying codon evolution using dN/dS ratios. We show that some genes have higher dN/dS ratios in lineages leading to species with annual life history. Many of them constitute key developmental genes or nuclear-encoded metabolic genes that control oxidative phosphorylation. Lastly, we compare these genes with higher ω to genes previously associated to developmental dormancy and metabolic shifts in killifishes and other vertebrates, and thereby identify molecular evolutionary signatures of repeated transitions to extreme environments.

Habitat opening fostered diversity: impact of dispersal and habitat‐shifts in the evolutionary history of a speciose afrotropical insect group

The opening of habitats associated with the emergence of C4 grasslands during the Neogene had a massive influence on the evolution of plant and animal communities. Strikingly, the impacts of grassland expansion on species diversification in Africa, where the largest surface of grasslands and savannas in the world is located, are not well understood. To explore the impact of habitat opening, we investigate the evolution of noctuid stemborers, a group of moths mostly associated with open habitats, and whose diversity is centered in the Afrotropics. We generate a dated molecular phylogeny for ca 80% of the known stemborer species, and assess the role of habitat opening on the evolutionary trajectory of the group through a combination of parametric historical biogeography, ancestral character state estimation, life history traits and habitat‐dependent diversification analyses. Our results support an origin of stemborers in Southern and East Africa ca 20 million years ago (Ma), with range expansions linked to the increased availability of open habitats to act as dispersal corridors, and closed habitats acting as potent barriers to dispersal. Early specialization on open habitats was maintained over time, with shifts towards closed habitats being rare and invariably unidirectional. Analyses of life history traits showed that habitat changes involved specific features likely associated with grassland adaptations, such as variations in larval behavior and color. We compare these findings to those previously inferred for an Afrotropical butterfly group that diversified roughly in parallel with the stemborers but distributed predominantly in closed habitats. Remarkably, these two groups show nearly opposite responses in relation to habitat specialization, whether in terms of biogeographical patterns, or in terms of rates of transition between open and closed habitats. We conclude that habitat opening played a major role in the evolutionary history of Afrotropical lineages through dispersal and adaptation linked to habitat shifts.

The evolution of multi-component weapons in the superfamily of leaf-footed bugs.

Sexually selected weapons, such as the antlers of deer, claws of crabs, and tusks of beaked whales, are strikingly diverse across taxa and even within groups of closely related species. Phylogenetic comparative studies have typically taken a simplified approach to investigate the evolution of weapon diversity, examining the gains and losses of entire weapons, major shifts in size or type, or changes in location. Less understood is how individual weapon components evolve and assemble into a complete weapon. We addressed this question by examining weapon evolution in the diverse, multi-component hind-leg and body weapons of leaf-footed bugs, superfamily Coreoidea (Hemiptera: Heteroptera). Male leaf-footed bugs use their morphological weapons to fight for access to mating territories. We used a large multilocus dataset comprised of ultraconserved element loci for 248 species and inferred evolutionary transitions among component states using ancestral state estimation. Our results suggest that weapons added components over time with some evidence of a cyclical evolutionary pattern-gains of components followed by losses and then gains again. Furthermore, our best estimate indicated that certain trait combinations evolved repeatedly across the phylogeny, suggesting that they function together in battle or that they are genetically correlated. This work reveals the remarkable and dynamic evolution of weapon form in the leaf-footed bugs and provides insights into weapon assembly and disassembly over evolutionary time.

Inferring chromatin accessibility during murine hematopoiesis through phylogenetic analysis

ObjectiveDiversification of cell types and changes in epigenetic states during cell differentiation processes are important for understanding development. Recently, phylogenetic analysis using DNA methylation and histone modification information has been shown useful for inferring these processes. The purpose of this study was to examine whether chromatin accessibility data can help infer these processes in murine hematopoiesis.ResultsChromatin accessibility data could partially infer the hematopoietic differentiation hierarchy. Furthermore, based on the ancestral state estimation of internal nodes, the open/closed chromatin states of differentiating progenitor cells could be predicted with a specificity of 0.86–0.99 and sensitivity of 0.29–0.72. These results suggest that the phylogenetic analysis of chromatin accessibility could offer important information on cell differentiation, particularly for organisms from which progenitor cells are difficult to obtain.

Fossilization can mislead analyses of phenotypic disparity.

Analyses of morphological disparity can incorporate living and fossil taxa to facilitate the exploration of how phenotypic variation changes through time. However, taphonomic processes introduce non-random patterns of data loss in fossil data and their impact on perceptions of disparity is unclear. To address this, we characterize how measures of disparity change when simulated and empirical data are degraded through random and structured data loss. We demonstrate that both types of data loss can distort the disparity of clades, and that the magnitude and direction of these changes varies between the most commonly employed distance metrics and disparity indices. The inclusion of extant taxa and exceptionally preserved fossils mitigates these distortions and clarifies the full extent of the data lost, most of which would otherwise go uncharacterized. This facilitates the use of ancestral state estimation and evolutionary simulations to further control for the effects of data loss. Where the addition of such reference taxa is not possible, we urge caution in the extrapolation of general patterns in disparity from datasets that characterize subsets of phenotype, which may represent no more than the traits that they sample.

Dynamic evolution of size and colour in the highly specialized Zodarion ant-eating spiders.

Ecological specialists constitute relevant case studies for understanding the mechanisms, potential and limitations of evolution. The species-rich and strictly myrmecophagous spiders of the genus Zodarion show diversified defence mechanisms, including myrmecomorphy of different ant species and nocturnality. Through Hybridization Capture Using RAD Probes (hyRAD), a phylogenomic technique designed for sequencing poorly preserved specimens, we reconstructed a phylogeny of Zodarion using 52 (approx. a third of the nominal) species that cover its phylogenetic and distributional diversity. We then estimated the evolution of body size and colour, traits that have diversified noticeably and are linked to defence mechanisms, across the group. Our genomic matrix of 300 loci led to a well-supported phylogenetic hypothesis that uncovered two main clades inside Zodarion. Ancestral state estimation revealed the highly dynamic evolution of body size and colour across the group, with multiple transitions and convergences in both traits, which we propose is likely indicative of multiple transitions in ant specialization across the genus. Our study will allow the informed targeted selection of Zodarion taxa of special interest for research into the group's remarkable adaptations to ant specialization. It also exemplifies the utility of hyRAD for phylogenetic studies using museum material.

Recent transposable element bursts are associated with the proximity to genes in a fungal plant pathogen.

The activity of transposable elements (TEs) contributes significantly to pathogen genome evolution. TEs often destabilize genome integrity but may also confer adaptive variation in pathogenicity or resistance traits. De-repression of epigenetically silenced TEs often initiates bursts of transposition activity that may be counteracted by purifying selection and genome defenses. However, how these forces interact to determine the expansion routes of TEs within a pathogen species remains largely unknown. Here, we analyzed a set of 19 telomere-to-telomere genomes of the fungal wheat pathogen Zymoseptoria tritici. Phylogenetic reconstruction and ancestral state estimates of individual TE families revealed that TEs have undergone distinct activation and repression periods resulting in highly uneven copy numbers between genomes of the same species. Most TEs are clustered in gene poor niches, indicating strong purifying selection against insertions near coding sequences, or as a consequence of insertion site preferences. TE families with high copy numbers have low sequence divergence and strong signatures of defense mechanisms (i.e., RIP). In contrast, small non-autonomous TEs (i.e., MITEs) are less impacted by defense mechanisms and are often located in close proximity to genes. Individual TE families have experienced multiple distinct burst events that generated many nearly identical copies. We found that a Copia element burst was initiated from recent copies inserted substantially closer to genes compared to older copies. Overall, TE bursts tended to initiate from copies in GC-rich niches that escaped inactivation by genomic defenses. Our work shows how specific genomic environments features provide triggers for TE proliferation in pathogen genomes.

Phylogeny, biogeography, and character evolution of the genus Sophora s.l. (Fabaceae, Papilionoideae)

The papilionoid legume genus Sophora (Fabaceae) exhibits a worldwide distribution, but a phylogenetic framework to understand the evolution of this group is lacking to date. Previous studies have demonstrated that Sophora is not monophyletic and might include Ammodendron, Ammothamnus, and Echinosophora, but the relationships among these four genera (defined as Sophora s.l.) are unclear. Here we used a nuclear DNA dataset (ETS, ITS, SQD1) and a plastid DNA dataset (matK, rbcL, rpl32-trnL, trnL-F) of 654 accession sequences to reconstruct the phylogenetic relationships, estimate the divergence times and ancestral range of Sophora s.l., and infer the evolution of chromosome number and morphological characteristics. Our major aim was to reconstruct phylogenetic relationships to test monophyly and elucidate relationships within the genus. Our results indicated that Ammodendron, Ammothamnus, and Echinosophora are embedded within Sophora s.s. and that nine well-supported clades can be recognized within comprise Sophora s.l. Ancestral character state estimation revealed that the most recent common ancestor of Sophora s.l. was a deciduous shrub that lacks rhizome spines and has unwinged legumes. Divergence times estimation and ancestral area reconstruction showed that Sophora s.l. originated in Central Asia and/or adjacent Southeast China in the early Oligocene (ca. 31 Mya) and dispersed from these regions into East and South Asia’s adjacent areas and North America via the Bering land bridge. The analyses also supported a South American origin for S. sect. Edwardsia, which experienced rapid radiation with its major lineages diversifying over a relatively narrow timescale (8 Mya).

Illuminating the evolution of bioluminescence in sharks

AbstractThe evolutionary context in which shark bioluminescence originated is poorly understood, despite it being critical to uncovering influential factors in the evolutionary history and diversity of living chondrichthyans as well as the mechanisms of deep‐water colonization by vertebrates. This study provides the first joint reconstruction of the habitats, lifestyles, and occurrence of bioluminescence in the evolution of squalomorph sharks using ancestral state estimation analysis to resolve the timing of deep‐sea colonization, the evolutionary origin of bioluminescence and the ancestral ecologies of this group. The results suggest that most squalomorphs originated in neritic environments from where they colonized deep waters on several independent occasions during the Late Jurassic and Early Cretaceous, predating most of the previous estimates of the timing of this event. The colonization of the deep sea took place via the benthic zone, in contrast to the view that an intermediate mesopelagic stage occurred during this ecological transition. Finally, the analyses accounting for uncertainty of the presence of bioluminescence strongly support that this trait evolved only once among sharks in a bathydemersal ancestor. This study reveals that shark bioluminescence evolved in a complex scenario that combines elements of several previous proposals, and enriches our perspective on the sequence of events that characterized the vertebrate conquest of the deep sea.

The origin of modern patterns of continental diversity in Mauritiinae palms: the Neotropical museum and the Afrotropical graveyard.

While the latitudinal diversity gradient has received much attention, biodiversity and species richness also vary between continents across similar latitudes. Fossil information can be used to understand the evolutionary mechanisms that generated such variation between continents of similar latitudes. We integrated fossil data into a phylogenetic analysis of the Mauritiinae palms, whose extant diversity is restricted to the Neotropics, but extended across Africa and India during most of the Cenozoic. Mauritiinae diverged from its sister lineage Raphiinae ca 106 Ma. Using ancestral state estimation and a lineage through time analysis, we found that diversity arose globally during the late Cretaceous and Palaeocene across South America, Africa and India. The Palaeocene-Eocene transition (ca 56 Ma) marked the end of global Mauritiinae expansion, and the beginning of their decline in both Africa and India. Mauritiinae disappeared from the Indian subcontinent and Africa at the end of the Eocene and the Miocene, respectively. By contrast, Neotropical diversity steadily increased over the last 80 Myr. Taken together, our results suggest that the Neotropics functioned as a continental-scale refuge for Mauritiinae palms, where lineages survived and diversified while global climatic changes that drastically reduced rainforests led to their demise on other continents.

Evolution of the rostral scale and mimicry in the genusXenodonBoie, 1826 (Serpentes: Dipsadidae: Xenodontinae)

AbstractSnakes are a stimulating life form from an evolutionary perspective. Despite the basic morphological body shape (limbless, with a tubular body), these vertebrates are extremely diverse. The Neotropical region is one of the most diverse regions for snakes in the world, with >650 known species. Within this great diversity, the genus Xenodon includes 12 species with interesting adaptations to terrestrial and semi-fossorial habitats. Members of this genus are mostly diurnal and terrestrial, feed mainly on anurans and exhibit Batesian mimicry of venomous snakes of the genera Bothrops or Micrurus. Here, through phylogenetic analysis and ancestral state estimation, we explore the evolution of the rostral scale and mimicry within the genus Xenodon. Our results suggest that the ancestral lineage of Xenodon had a rounded rostral scale and exhibited Bothrops mimicry. The evolution of the rostral scale in Xenodon might be related to abiotic factors, as an adaptation for open and forested habitats, and mimicry is likely to be related to biotic factors, as a defensive strategy resembling those of venomous snakes.

Chronogram or phylogram for ancestral state estimation? Model‐fit statistics indicate the branch lengths underlying a binary character's evolution

AbstractModern methods of ancestral state estimation (ASE) incorporate branch length information, and it has been demonstrated that ASEs are more accurate when conducted on the branch lengths most correlated with a character's evolution; however, a reliable method for choosing between alternate branch length sets for discrete characters has not yet been proposed.In this study, we simulate paired chronograms and phylograms, and generate binary characters that evolve in correlation with one of these. We then investigate (a) the effect of alternate branch lengths on ASE error and (b) whether phylogenetic signal statistics and/or model‐fit statistic can be used to select the branch lengths most correlated with a binary character.In agreement with previous studies, we find that ASEs are more accurate when conducted on the branch lengths most correlated with the character. Phylogenetic signal statistics show limited utility for selecting the correct branch lengths, but model‐fit statistics are found to be more accurate, with the correct branch lengths generally returning greater model‐fit (lower AICc and BIC values). Using this method to choose between alternate branch length sets is more accurate when tree and character properties are more favourable for model optimization, and when shape differences between alternate phylogenies are greater.Our results indicate that researchers conducting ASEs on discrete characters should carefully consider which branch lengths are appropriate, and, in the absence of other evidence, we suggest estimating model‐fit values over alternate branch length sets and evolutionary models and choosing the branch length/model combination that returns better model‐fit.

A case of cooperative breeding in the European Starling, Sturnus vulgaris.

Cooperative breeding, where individuals other than the parents help to raise offspring, occurs in only ~9% of bird species. Although many starlings (Sturnidae) are cooperative breeders, the European starling (Sturnus vulgaris) has rarely been observed exhibiting this behavior. Only two other records exist, one of which was limited to a juvenile giving food to chicks that had already been collected by a parent (and hence providing limited help). Herein, we report a case of cooperative breeding by a juvenile European starling, which represents the second with any evidence of the juvenile collecting food independently and the first to document the extent of such help in the form of feeding rates. Over a period of at least 3 days, a juvenile starling assisted two parents to feed their second brood of the year, and it fed the chicks at the same rate as the adults (~3.5 feeds per hour). In considering potential explanations for this behavior, we conducted an ancestral state estimation of cooperative breeding across starlings and were able to eliminate the possibility that this is a rarely expressed behavior inherited from cooperatively breeding ancestors. Instead, we propose that our observations point to a behavioral innovation, which may be in response to environmental change such as climate change (which has previously been associated with cooperative breeding). Researchers working on birds should be alert to such behavior to determine whether this apparently new breeding strategy will increase as a potential adaptation to environmental change.

Phylogenomics of Bony-Tongue Fishes (Osteoglossomorpha) Shed Light on the Craniofacial Evolution and Biogeography of the Weakly Electric Clade (Mormyridae).

Bonytongues (Osteoglossomorpha) constitute an ancient clade of teleost fishes distributed in freshwater habitats throughout the world. The group includes well-known species such as arowanas, featherbacks, pirarucus, and the weakly electric fishes in the family Mormyridae. Their disjunct distribution, extreme morphologies, and electrolocating capabilities (Gymnarchidae and Mormyridae) have attracted much scientific interest, but a comprehensive phylogenetic framework for comparative analysis is missing, especially for the species-rich family Mormyridae. Of particular interest are disparate craniofacial morphologies among mormyrids which might constitute an exceptional model system to study convergent evolution. We present a phylogenomic analysis based on 546 exons of 179 species (out of 260), 28 out of 29 genera, and all six families of extant bonytongues. Based on a recent reassessment of the fossil record of osteoglossomorphs, we inferred dates of divergence among transcontinental clades and the major groups. The estimated ages of divergence among extant taxa (e.g., Osteoglossomorpha, Osteoglossiformes, and Mormyroidea) are older than previous reports, but most of the divergence dates obtained for clades on separate continents are too young to be explained by simple vicariance hypotheses. Biogeographic analysis of mormyrids indicates that their high species diversity in the Congo Basin is a consequence of range reductions of previously widespread ancestors and that the highest diversity of craniofacial morphologies among mormyrids originated in this basin. Special emphasis on a taxon-rich representation for mormyrids revealed pervasive misalignment between our phylogenomic results and mormyrid taxonomy due to repeated instances of convergence for extreme craniofacial morphologies. Estimation of ancestral phenotypes revealed contingent evolution of snout elongation and unique projections from the lower jaw to form the distinctive Schnauzenorgan. Synthesis of comparative analyses suggests that the remarkable craniofacial morphologies of mormyrids evolved convergently due to niche partitioning, likely enabled by interactions between their exclusive morphological and electrosensory adaptations. [Africa; ancestral state estimation; diversity; exon capture; freshwater fishes; Phylogenomics.].

The accessory neural arch: development, morphology, and systematic distribution

The accessory neural arch is an oddly distributed character present in several non-acanthomorph teleostean taxa. Its homology was often implied but never satisfyingly tested. In this study, we attended this pending problem. We analyzed the morphology, development, and systematic distribution of the accessory neural arch in teleosts. Using a comprehensive taxon sampling of cleared and stained specimens, we evaluated if the accessory neural arch fulfils existing homology criteria. We then combined these data with recent genetic phylogenies and ancestral character state estimation to reconstruct the evolutionary history of the accessory neural arch. While its gross morphology and development fit homology criteria, results from ancestral character state estimations suggest multiple independent evolutions within teleosts. Although the accessory neural arch cannot be homologous between several teleostean taxa, the concept of parallelism may explain the presence of such a similar character in a variety of non-acanthomorph teleostean taxa.

Comparative Mitogenomics of Fungal Species in Stachybotryaceae Provides Evolutionary Insights into Hypocreales.

Stachybotrys chartarum is one of the world’s ten most feared fungi within the family Stachybotryaceae, although to date, not a single mitogenome has been documented for Stachybotryaceae. Herein, six mitogenomes of four different species in Stachybotryaceae are newly reported. The S. chartarum mitogenome was 30.7 kb in length and contained two introns (one each in rnl and cox1). A comparison of the mitogenomes of three different individuals of S. chartarum showed few nucleotide variations and conservation of gene content/order and intron insertion. A comparison of the mitogenomes of four different Stachybotryaceae species (Memnoniella echinata, Myrothecium inundatum, S. chartarum, and S. chlorohalonata), however, revealed variations in intron insertion, gene order/content, and nad2/nad3 joining pattern. Further investigations on all Hypocreales species with available mitogenomes showed greater variabilities in gene order (six patterns) and nad2/nad3 joining pattern (five patterns) although a dominant pattern always existed in each case. Ancestral state estimation showed that in each case the dominant pattern was always more ancestral than those rare patterns. Phylogenetic analyses based on mitochondrion-encoded genes supported the placement of Stachybotryaceae in Hypocreales. The crown age of Stachybotryaceae was estimated to be approximately the Early Cretaceous (141–142 Mya). This study greatly promotes our understanding of the evolution of fungal species in Hypocreales.

Evolutionary patterns of host type and chasmothecial appendage morphology in obligate plant parasites belonging to Cystotheceae (powdery mildew, Erysiphaceae)

ABSTRACT The chasmothecial appendages of Erysiphaceae are considered to function in the overwintering strategy and evolve morphologically in line with transitions of different host type. However, the evolutionary patterns and relationships of these traits have not yet been verified using statistical models based on phylogenetic information. We aimed to clarify the evolutionary process of host type and appendage morphology in Cystotheceae using phylogenetic comparative methods (PCMs) and to evaluate the evolutionary relationship of these traits. The ancestral state estimation of host types showed that the deciduous type is the most ancestral in Cystotheceae, and the herb or evergreen types evolved secondarily four times and twice, respectively. Branched- or circinate-type appendages were estimated to be the most ancestral, and the mycelioid and rudimentary types evolved secondarily thrice and once, respectively. The results of the random forest analysis showed that the host type was predictable from the phylogeny and appendage morphology. The ancestral state estimation suggested that simultaneous transitions of the host type and appendage morphology occurred at several ancestral nodes. These results suggest some functional relationships between host type and appendage morphology, but there was no statistical support for an overall trend in evolutionary dependence between these traits. Our results demonstrate the utility of PCMs in the study of trait evolution in Cystotheceae, which can be applied to a broader phylogeny of powdery mildews to elucidate the evolutionary relationship and functional causality of phenotypic traits.

Find the food first: An omnivorous sensory morphotype predates biomechanical specialization for plant based diets in phyllostomid bats.

The role of mechanical morphologies in the exploitation of novel niche space is well characterized; however, the role of sensory structures in unlocking new niches is less clear. Here, we investigate the relationship between the evolution of sensory structures and diet during the radiation of noctilionoid bats. With a broad range of foraging ecologies and a well-supported phylogeny, noctilionoids constitute an ideal group for studying this relationship. We used diffusible iodine-based contrast enhanced computed tomography scans of 44 noctilionoid species to analyze relationships between the relative volumes of three sensory structures (olfactory bulbs, orbits, and cochleae) and diet. We found a positive relationship between frugivory and both olfactory and orbit size. However, we also found a negative relationship between nectarivory and cochlea size. Ancestral state estimates suggest that larger orbits and olfactory bulbs were present in the common ancestor of family Phyllostomidae, but not in other noctilionoid. This constellation of traits indicates a shift toward omnivory at the base of Phyllostomidae, predating their radiation into an exceptionally broad range of dietary niches. This is consistent with a scenario in which changes in sensory systems associated with foraging and feeding set the stage for subsequent morphological modification and diversification.

Acanthodian dental development and the origin of gnathostome dentitions.

Chondrichthyan dentitions are conventionally interpreted to reflect the ancestral gnathostome condition but interpretations of osteichthyan dental evolution in this light have proved unsuccessful, perhaps because chondrichthyan dentitions are equally specialized, or else evolved independently. Ischnacanthid acanthodians are stem-Chondrichthyes; as phylogenetic intermediates of osteichthyans and crown-chondrichthyans, the nature of their enigmatic dentition may inform homology and the ancestral gnathostome condition. Here we show that ischnacanthid marginal dentitions were statodont, composed of multicuspidate teeth added in distally diverging rows and through proximal superpositional replacement, while their symphyseal tooth whorls are comparable to chondrichthyan and osteichthyan counterparts. Ancestral state estimation indicates the presence of oral tubercles on the jaws of the gnathostome crown-ancestor; tooth whorls or tooth rows evolved independently in placoderms, osteichthyans, ischnacanthids, other acanthodians and crown-chondrichthyans. Crown-chondrichthyan dentitions are derived relative to the gnathostome crown-ancestor, which possessed a simple dentition and lacked a permanent dental lamina, which evolved independently in Chondrichthyes and Osteichthyes.