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Phylogenomics is extremely powerful but introduces new challenges as no agreement exists on “standards” for data selection, curation and tree inference. We use jawed vertebrates (Gnathostomata) as model to address these issues. Despite considerable efforts in resolving their evolutionary history and macroevolution, few studies have included a full phylogenetic diversity of gnathostomes and some relationships remain controversial. We tested a novel bioinformatic pipeline to assemble large and accurate phylogenomic datasets from RNA sequencing and find this phylotranscriptomic approach successful and highly cost-effective. Increased sequencing effort up to ca. 10Gbp allows recovering more genes, but shallower sequencing (1.5Gbp) is sufficient to obtain thousands of full-length orthologous transcripts. We reconstruct a robust and strongly supported timetree of jawed vertebrates using 7,189 nuclear genes from 100 taxa, including 23 new transcriptomes from previously unsampled key species. Gene jackknifing of genomic data corroborates the robustness of our tree and allows calculating genome-wide divergence times by overcoming gene sampling bias. Mitochondrial genomes prove insufficient to resolve the deepest relationships because of limited signal and among-lineage rate heterogeneity. Our analyses emphasize the importance of large curated nuclear datasets to increase the accuracy of phylogenomics and provide a reference framework for the evolutionary history of jawed vertebrates.

Most non-tetrapod vertebrates develop mineralized extra-oral elements within the integument. Known collectively as the integumentary skeleton, these elements represent the structurally diverse skin-bound contribution to the dermal skeleton. In this review we begin by summarizing what is known about the histological diversity of the four main groups of integumentary skeletal tissues: hypermineralized (capping) tissues; dentine; plywood-like tissues; and bone. For most modern taxa, the integumentary skeleton has undergone widespread reduction and modification often rendering the homology and relationships of these elements confused and uncertain. Fundamentally, however, all integumentary skeletal elements are derived (alone or in combination) from only two types of cell condensations: odontogenic and osteogenic condensations. We review the origin and diversification of the integumentary skeleton in aquatic non-tetrapods (including stem gnathostomes), focusing on tissues derived from odontogenic (hypermineralized tissues, dentines and elasmodine) and osteogenic (bone tissues) cell condensations. The novelty of our new scenario of integumentary skeletal evolution resides in the demonstration that elasmodine, the main component of elasmoid scales, is odontogenic in origin. Based on available data we propose that elasmodine is a form of lamellar dentine. Given its widespread distribution in non-tetrapod lineages we further propose that elasmodine is a very ancient tissue in vertebrates and predict that it will be found in ancestral rhombic scales and cosmoid scales.

In the first part of this paper we review current knowledge regarding fish scales, focusing on elasmoid scales, the only type found in two model species, the zebrafish and the medaka. After reviewing the structure of scales and their evolutionary origin, we describe the formation of the squamation pattern. The regularity of this process suggests a pre-patterning of the skin before scale initiation. We then summarise the dynamics of scale development on the basis of morphological observations. In the absence of molecular data, these observations support the existence of genetic cascades involved in the control of scale development. In the second part of this paper, we illustrate the potential that scale development offers as a model to study organogenesis mediated by epithelial-mesenchymal interactions. Using the zebrafish (Danio rerio), we have combined alizarin red staining, light and transmission electron microscopy and in situ hybridisation using an anti-sense RNA probe for the sonic hedgehog (

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Although often overlooked, the integument of many tetrapods is reinforced by a morphologically and structurally diverse assemblage of skeletal elements. These elements are widely understood to be derivatives of the once all-encompassing dermal skeleton of stem-gnathostomes but most details of their evolution and development remain confused and uncertain. Herein we re-evaluate the tetrapod integumentary skeleton by integrating comparative developmental and tissue structure data. Three types of tetrapod integumentary elements are recognized: (1) osteoderms, common to representatives of most major taxonomic lineages; (2) dermal scales, unique to gymnophionans; and (3) the lamina calcarea, an enigmatic tissue found only in some anurans. As presently understood, all are derivatives of the ancestral cosmoid scale and all originate from scleroblastic neural crest cells. Osteoderms are plesiomorphic for tetrapods but demonstrate considerable lineage-specific variability in size, shape, and tissue structure and composition. While metaplastic ossification often plays a role in osteoderm development, it is not the exclusive mode of skeletogenesis. All osteoderms share a common origin within the dermis (at or adjacent to the stratum superficiale) and are composed primarily (but not exclusively) of osseous tissue. These data support the notion that all osteoderms are derivatives of a neural crest-derived osteogenic cell population (with possible matrix contributions from the overlying epidermis) and share a deep homology associated with the skeletogenic competence of the dermis. Gymnophionan dermal scales are structurally similar to the elasmoid scales of most teleosts and are not comparable with osteoderms. Whereas details of development are lacking, it is hypothesized that dermal scales are derivatives of an odontogenic neural crest cell population and that skeletogenesis is comparable with the formation of elasmoid scales. Little is known about the lamina calcarea. It is proposed that this tissue layer is also odontogenic in origin, but clearly further study is necessary. Although not homologous as organs, all elements of the integumentary skeleton share a basic and essential relationship with the integument, connecting them with the ancestral rhombic scale.

Osteichthyan and chondrichthyan fish present an astonishing diversity of skeletal and dental tissues that are often difficult to classify into the standard textbook categories of bone, cartilage, dentine and enamel. To address the question of how the tissues of the dermal skeleton evolved from the ancestral situation and gave rise to the diversity actually encountered, we review previous data on the development of a number of dermal skeletal elements (odontodes, teeth and dermal denticles, cranial dermal bones, postcranial dermal plates and scutes, elasmoid and ganoid scales, and fin rays). A comparison of developmental stages at the tissue level usually allows us to identify skeletogenic cell populations as either odontogenic or osteogenic on the basis of the place of formation of their dermal papillae and of the way of deposition of their tissues. Our studies support the evolutionary affinities (1) between odontodes, teeth and denticles, (2) between the ganoid scales of polypterids and the elasmoid scales of teleosts, and (3) to a lesser degree between the different bony elements. There is now ample evidence to ascertain that the tissues of the elasmoid scale are derived from dental and not from bony tissues. This review demonstrates the advantage that can be taken from developmental studies, at the tissue level, to infer evolutionary relationships within the dermal skeleton in chondrichthyans and osteichthyans.

The evolutionary links that exist between odontodes and organs that are phylogenetically related to them (teeth and scales) suggest the use of comparative approaches to study these structures. Part one of this review briefly introduces current ideas on how the pattern of odontodes and odontode‐derived tissues has been established during evolution to yield the diversity of odontode‐related organs currently observed in nature in the cranial and postcranial skeleton. This introductory survey is used to highlight aspects of the developmental processes underlying the formation of some of these organs and the resemblance their development bears to odontogenesis. Part two provides a concise survey of the diversity of tooth structure in the different classes of extant vertebrates, in particular with reference to enamel/enameloid and dentine structure, and tooth attachment. Against this background, the current state of knowledge is reviewed with regard to developmental mechanisms involved in non‐mammalian odontogenesis. Common structure and similarities in development demonstrate that teeth and odontode derivatives should not be considered subjects of separate lines of research. On the contrary, results acquired in one of these fields are relevant to the other and may disclose model species that are relevant to studies on mammalian odontogenesis.