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A lineage outside the focal group used to inform rooting and character polarity. An extant outgroup is not an unchanged ancestor.

The terms describe contrasting palatal architectures; their literal “old” and “new” implications do not establish which architecture was ancestral. A palaeognathous palate has extensive bracing of the palatal apparatus against the skull base, involving the vomer, pterygoid bone, palatine bone and prominent basipterygoid processes. In a neognathous palate, reduced bracing and a more mobile pterygoid–palatine connection permit greater relative movement. These are arrangements of joints and contacts, not simply differences in lower-jaw shape. The distinction concerns the structural basis of cranial kinesis, movement within the skull beyond ordinary opening of the lower jaw.^[ref]

Living Palaeognathae, including ostriches and tinamous, and living Neognathae, including landfowl, waterfowl and other birds, form the deepest two surviving branches of crown Aves. Historically, the heavily braced condition was commonly interpreted as retention of a primitive nonavian configuration, followed by evolution of a more mobile palate in Neognathae. That interpretation combined resemblance to outgroups with the misleading intuition that a lineage branching early must preserve the ancestral anatomy. A sister lineage has had just as much time to change; its living members are not ancestors of the other branch.

The difficulty is establishing character polarity when delicate palatal elements are absent, crushed or wrongly identified in fossils near the crown divergence. Comparisons of the vomer across living and extinct birds documented meaningful differences in contact geometry but also substantial variation and repeated reduction. The 2019 analysis by Han Hu and colleagues emphasized how incomplete contacts restrict inferences about extinct cranial kinesis. A single robust-looking element cannot establish an immobile skull, and one potentially mobile joint cannot establish the full range of movement. Constraints elsewhere in the kinetic chain remain relevant.^[ref]

The Ichthyornis material described in 2018 helped separate components of the supposedly modern avian head. Three-dimensionally preserved skull elements combined a small beak at the jaw tips and retained teeth with a reconstructed kinetic apparatus, while other cranial regions remained markedly dinosaurian. Thus tooth loss, beak expansion and acquisition of a mobile feeding apparatus did not form one indivisible evolutionary event. This example of mosaic evolution also weakens the argument that a toothed stem bird must have a fully rigid, palaeognath-like palate. Its importance is the combination of characters, rather than an inference that every modern kinetic mechanism was already identical.^[ref]

The strongest recent change came from Janavis finalidens, a toothed bird from approximately 66.7 million years ago, described in 2022. micro-computed tomography exposed a well-preserved pterygoid bone within the specimen. Its articular construction and comparative shape resemble those of Galloanserae, supporting a mobile pterygoid–palatine connection. The animal was recovered outside the living-bird crown group, close to Ichthyornis, rather than inside Neognathae. Consequently, anatomy previously treated as a neognath innovation occurred on an earlier branch. On that reconstruction, mobility evolved before crown Aves, and the tightly integrated palaeognathous palate is a subsequent specialization of the palaeognath lineage.^[ref]

The inference is best understood by separating observation, placement and reconstruction. The observation is the morphology of a fossil pterygoid bone. Its placement outside crown Aves comes from a wider analysis of phylogenetic characters using phylogenetics. The inference that the crown ancestor had a relatively mobile palate combines those findings with distributions of phylogenetic characters in living groups. None alone proves the entire history. Convergence in the fossil lineage remains a logical alternative; it would require a different pattern of character acquisition from ancestral mobility followed by increased bracing. Distinguishing these alternatives requires additional palatal characters and fossil sampling, not the age of the specimen alone. A 66.7-million-year-old stem bird need not predate the crown ancestor chronologically: stem and crown lineages can coexist.

Functional and developmental caution also matters. fossils generally lack ligaments, muscles and direct measurements of movement. Comparative joint geometry can support potential mobility, but cannot yield exact excursions or feeding performance without further assumptions. The palaeognathous palate should not be reduced to total skull immobility, nor every neognathous palate to one uniform kinetic mechanism. The defensible revision is that important neognath-like palatal features originated before the living-bird crown split, making palaeognath specializations a plausible derived condition. The two living clades remain valid; what changes is the inferred history of the anatomical states used to describe them.

Living cartilaginous fishes are specialized descendants, not a surviving anatomical stage before the origin of bony vertebrates. fossil discoveries have shifted several apparently “bony-fish” features toward the ancestry of all living jawed vertebrates. Their absence in living Chondrichthyes can consequently represent character loss, while other shark features remain ancestral or are new specializations. The change is a revision of character polarity, not a claim that every aspect of shark anatomy is reduced.

A simple comparison of living sharks with Osteichthyes can suggest a one-way sequence: an ancestor with a cartilaginous internal skeleton, followed by origin of extensive bone on the bony-vertebrate branch. That inference is insecure because the two living sister lineages can both have changed, and living jawless outgroups can also have lost structures. The fossil record samples extinct combinations near the relevant divergences. To determine whether a structure is a gain or loss, one must place those combinations on a rooted phylogenetic tree and distinguish anatomical absence from poor preservation.

The early gnathostome problem involves four familiar assemblages: placoderms, acanthodians, Chondrichthyes and Osteichthyes. Treating all four as separate complete clades can conceal transitions occurring along the stems of surviving groups. In particular, many newer analyses place acanthodians as successive branches on the chondrichthyan stem. Their name “spiny sharks” is not itself evidence for that placement; cranial, scale, fin and other characters must support it. If this topology is correct, the large difference between living sharks and early armoured jawed fishes includes a history of reduction within the cartilaginous-fish lineage.

The 2012 redescription of the Acanthodes braincase illustrates why anatomical interpretation and tree position must be kept separate. It revealed a mixture of conditions previously assigned to different living groups and argued for shark-like aspects of the last common ancestor of modern jawed vertebrates. Its analysis still placed Acanthodes on the osteichthyan stem, rather than treating every acanthodian as a stem chondrichthyan. Thus a resemblance initially interpreted as an osteichthyan specialization could instead be an ancestral feature retained in more than one lineage. Later hypotheses should not be projected retrospectively onto that study.^[ref]

Entelognathus primordialis, described in 2013 from the Silurian of China, supplied a particularly important association: an armoured placoderm-like body and skull with large marginal jaw bones identifiable as premaxilla, maxilla and dentary. Such bones had been treated as characteristic innovations of Osteichthyes. Placement of this animal near the top of the jawed-vertebrate stem, together with recovery of acanthodians on the chondrichthyan stem, instead supported a macromeric, extensively ossified dermal ancestor. On that reconstruction, the small-scale-dominated covering and absence of those large jaw bones in living Chondrichthyes reflect reduction and reorganization rather than simple retention of a primitively unossified condition.^[ref]

Janusiscus schultzei, described in 2015 from the Early Devonian, reinforced the point using a different anatomical region. Its combination of a bony dermal skull roof and informative internal cranial conditions supported a position outside crown gnathostomes. Braincase anatomy therefore did not align neatly with the traditional picture of a primitive shark head versus a derived bony-fish head. Together, these fossils move apparently osteichthyan-like states closer to the common ancestry of both surviving groups. Their significance comes from character combinations and placement, not from choosing whichever living animal looks most similar.^[ref]

A separate question concerns internal skeletal tissue. dermal bone, perichondral bone, endochondral bone and calcified cartilage must not be conflated. endochondral bone forms during replacement of a cartilaginous template; perichondral bone forms around it; calcified cartilage remains a different tissue despite being mineralized. Therefore a bony dermal skull roof alone cannot establish endochondral ossification in the same animal.

The 2020 description of Minjinia turgenensis, from the Early Devonian of Mongolia, addressed that distinction. micro-computed tomography revealed extensive internal trabecular tissue in the braincase, interpreted as endochondral bone, rather than just an external bony shell. Its recovery close to the crown divergence permits endochondral ossification to be reconstructed before the separation of Chondrichthyes and Osteichthyes, followed by loss or marked suppression along the chondrichthyan lineage. This conclusion depends on identification of the tissue and the animal's position; the absence of a more complete skeleton and uncertainty among early jawed-vertebrate trees constrain how strongly it can be generalized.^[ref]

The resulting inference is conditional but testable. If well-supported stem relatives and the bony-vertebrate branch possess a particular homologous tissue, while living cartilaginous fishes lack it, an ancestral presence followed by loss can fit better than several independent origins. Moving a crucial fossil to another branch, changing a tissue identification or allowing different transition rates can change the ancestral reconstruction. maximum parsimony is useful but is not proof that losses and gains have equal biological probability. Character coding should record unknown preservation as unknown, rather than use an unobserved delicate feature as evidence of absence.

The major revision is from a ladder of increasing ossification to a branching history of gains, retention and losses. It concerns particular tissues and anatomical elements: reduction of large dermal bones need not coincide exactly with loss of endochondral ossification. fossils reveal that apparently simple modern anatomy can be secondarily simplified, and that major living-group differences may reflect transformations on both sides of a divergence. Continued uncertainty over placoderm relationships and individual tissue homologies defines the comparisons still needed; it does not restore living sharks as unchanged proxies for the jawed-vertebrate ancestor.

The two classical anatomical hypotheses are derivation from gill arches and differentiation of continuous lateral fin folds. Developmental co-option supplies an additional explanation for shared patterning mechanisms. The histories of the shoulder support, appendage blade and developmental programme need not be identical. Evaluating them separately allows evidence that initially appears contradictory to describe different components of the same evolutionary transition.

The gill-arch hypothesis of paired fin origins, associated with Carl Gegenbaur, proposes transformation of a posterior branchial apparatus into a girdle and projecting appendage skeleton. In living cartilaginous fishes, branchial rays project from the gill skeleton, inviting comparison with skeletal supports extending from a pectoral girdle. The historical archipterygium interpretation treated these as evidence for a gill-to-fin transformation. Positional similarity alone is insufficient: the relevant branchial construction must be ancestral, and a plausible transformation must explain both the supporting girdle and distal fin.

Developmental experiments provide stronger evidence for shared mechanisms than simple adult resemblance. Work on the little skate, Leucoraja erinacea, showed interactions among Sonic hedgehog, FGF signalling and retinoic acid in branchial-ray outgrowth and patterning, resembling regulatory interactions in paired appendages. The crucial inference is reuse of a spatial patterning system; expression of the same molecule by itself would be weaker evidence. Functional perturbation helps distinguish an active requirement from a coincidental expression domain.^[ref]

A 2016 study used timed inhibition of Hedgehog signalling with cyclopamine, lineage labelling and measurements of cell proliferation in skate embryos. Earlier inhibition disrupted branchial-ray polarity, while later inhibition reduced their production or expansion. EdU labeling provided a proxy for proliferative activity through new dNA synthesis, and labelled precursor positions related early arch territories to later cartilage. Solvent-treated controls are necessary because handling and drug vehicle can alter development; stage matching and general growth measurements are needed to distinguish pattern-specific effects from generalized retardation. These results support parallel roles for the signal in axial organization and progenitor expansion. They do not alone demonstrate that an ancestral gill arch physically moved to become a fin.^[ref]

The fossil argument for a pharyngeal contribution was strengthened before this examination by the 2023 analysis of Kolymaspis sibirica. computed tomography and comparative anatomy identified a craniothoracic relationship interpreted as connecting the shoulder to a posterior, sixth branchial arch. This provides evidence for the origin of a component of the pectoral girdle, rather than a complete fossil sequence converting branchial rays into the entire free fin. Homology of the articulation and the reconstruction of the head–trunk boundary remain important assumptions. A pharyngeal contribution to the girdle does not require a wholly pharyngeal origin for every appendicular tissue.^[ref]

The lateral fin-fold hypothesis proposes that the two localized pairs of fins arose through differentiation and regional restriction of continuous bilateral folds along the body wall. It predicts possible precursors extending through intervening pectoral and pelvic regions, with increased regional differentiation and locomotor control later. It does not require an ancestral animal to possess fully developed pectoral and pelvic girdles throughout the fold. A persistent developmental field capable of forming appendages could be evolutionarily restricted even if a continuous fold is not retained in living embryos.

The 2022 description of the jawless galeaspid Tujiaaspis vividus supplied a striking fossil comparison. Articulated specimens preserve continuous paired ventrolateral fins extending from the branchial region toward the tail. They occur outside the group of osteostracans and jawed vertebrates in the reported tree. Models using computational fluid dynamics indicated that the lateral surfaces could provide passive lift. This supports an evolutionary stage with extended lateral appendages before differentiation of localized, actively controlled pectoral fins; it does not prove powered swimming by the folds or show that the fossil itself was a direct ancestor. Surface reconstruction, swimming conditions and the assumed body geometry constrain the functional model.^[ref]

Other jawless stem relatives sharpen the proposed sequence. osteostracans have differentiated pectoral fins without an equivalent localized pelvic pair; jawed vertebrates subsequently include both. This distribution argues against assuming simultaneous origin of the two appendage pairs. In a fin-fold interpretation, anterior differentiation can precede restriction of the remaining competent body-wall region to a pelvic position. fossils supporting that sequence still have to distinguish flexible fins from rigid body-armour extensions and demonstrate their relation to the enclosing skeleton.

The median-fin co-option hypothesis addresses where the developmental machinery came from. median fins are evolutionarily older than the paired appendages. Comparative work on shark and lamprey embryos found that median-fin development uses aspects of the appendage-patterning toolkit, including regional Hox gene expression and boundary-associated regulation. In sharks, the median-fin skeleton develops largely from paraxial mesoderm, whereas paired appendage mesenchyme has major contributions from lateral plate mesoderm. Similar patterning despite different tissue sources supports redeployment of an older regulatory programme. It does not imply that a dorsal fin literally split and migrated down the body wall.^[ref]

This is the distinction between deep homology of mechanisms and a claim of whole-organ biological homology. Shared regulation could reflect inherited serial homology, recruitment of the same programme to a novel site, or a mixture of both. Testing alternatives requires spatial and temporal perturbations, embryonic lineage tracing, comparison across jawless and jawed outgroups, and fossil evidence locating the relevant structures. Tissue origins are informative but can change during evolution; neither a shared gene nor a different germ-layer contribution is a self-sufficient verdict.

The strongest synthesis is component-based: fossil lateral fins support a body-wall appendage precursor; developmental comparisons support recruitment of an older fin-patterning programme; and developmental plus 2023 fossil evidence supports a pharyngeal contribution to the shoulder. The remaining problem is to establish how those components were assembled and when regional pectoral and pelvic control evolved. This synthesis retains the testable content of the classical hypotheses without treating either a complete gill-to-fin conversion or a literal universal fin fold as already demonstrated.