Codex @codex  0

Used here for the crown group of birds: the last common ancestor of living palaeognaths and neognaths and all descendants. Broader historical definitions also occur and should be stated explicitly.

The clade comprising the last common ancestor of a stated set of living lineages and all its descendants. An older fossil closely related to that group may instead belong to its stem group.

For a crown-based usage, a member of the clade comprising the last common ancestor of living monotremes and therians and all its descendants. hair and lactation characterize living members, but recognition of many early fossils depends on jaw and dental characters.

A member of the living marsupial crown group, including all descendants of its last common ancestor. marsupials include several independently specialized feeding and locomotor lineages.

A definition selecting the smallest clade containing specified internal reference taxa: their last common ancestor and every descendant. The specifiers need not be living.

A node-based name selects a common ancestor from included reference taxa; a branch-based name selects a lineage by including one reference and excluding another. Both designate a clade, so both include every descendant of the selected ancestor. The distinction concerns the rule locating that ancestor, not whether descendants are included. Neither requires its members to share a particular modern appearance.^[ref]

For a node-based clade definition, choose internal phylogenetic specifiers $A$ and $B$. Let $m(A,B)$ be their last common ancestor, and let $D(v)$ include ancestor $v$ and all its descendants. Then the named group isIt is the smallest clade containing both references. For a branch-based clade definition, choose an internal reference $A$ and an external reference $Z$. The named group is the largest clade containing $A$ but excluding $Z$: organisms sharing a more recent common ancestor with $A$ than with $Z$. On a rooted phylogenetic tree, this selects the $A$-side lineage after its separation from the lineage containing $Z$. These are also called minimum-clade definitions and maximum-clade definitions. The names describe inclusion constraints, not distances measured from branch lengths.^[ref]

An informative avian node example is crown Aves, here anchored to living ostrich and sparrow lineages. Their last common ancestor is the ancestor of living Palaeognathae and Neognathae; the name includes that ancestor and all descendants, including extinct descendants within either branch. An informative branch example is Panaves, the avian total group: the largest clade including living birds but excluding living crocodilians. With standard archosaur relationships it includes Aves, extinct avian stem relatives, nonavian dinosaurs and pterosaurs. The external reference is decisive: the definition asks which side of the bird–crocodilian split an organism occupies, not whether it flies. These crown and total usages were distinguished explicitly in the avian nomenclatural analysis by Jacques A. Gauthier and Kevin de Queiroz.^[ref]

Consider a simplified cladogram in which the crocodilian lineage separates first, followed on the avian side by pterosaurs, successive nonavian dinosaur branches, Archaeopteryx, other extinct avian branches and finally the living-bird crown divergence. Archaeopteryx belongs to Panaves but lies outside crown Aves. A fossil on the palaeognath branch after the palaeognath–neognath divergence belongs to both. A crocodilian belongs to neither. Finding a still earlier bird-line fossil would extend the known fossil history of Panaves without automatically changing the age or known membership of crown Aves. This example is schematic: it illustrates how definitions operate and is not a claim that any sampled fossil is the direct ancestor of another.

Two distinctions prevent mistakes. First, a node-based clade definition need not define a crown group: internal references can be extinct, as in a deliberately broader Archaeopteryx-inclusive node definition. Likewise, a branch-based clade definition need not define an entire total group; using a nonavian theropod dinosaur as the excluded reference selects a much narrower avian-lineage branch than excluding crocodilians. Second, a stem group is not synonymous with the branch-defined total group. The total includes the crown; the stem alone excludes it and normally forms a succession of extinct branches.

The definition must therefore accompany an ambiguous name. Historical uses of Aves have included the living-bird crown and more inclusive fossil assemblages; Avialae has also received differing definitions. Discovery of feathers in a nonavian theropod dinosaur changes the inferred distribution of a phylogenetic character, but does not by itself place the animal inside crown Aves. Conversely, loss of flight does not remove a crown descendant from its clade. A name supplies an ancestry rule; anatomical and molecular evidence supply the tree on which that rule is applied. Uncertain fossil placement produces uncertain membership even when the definition is precise.

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.

Living great apes are indispensable comparative evidence, but none is a preserved version of the Pan–Homo last common ancestor. The ancestor was a population with its own combination of traits, and every living descendant has subsequently evolved. A defensible reconstruction is therefore a set of trait-specific hypotheses constrained by phylogenetics, functional comparison and fossils.

The comparison starts with relationships. Homo and Pan are closest living sister lineages; Pan contains chimpanzees and bonobos. Gorilla provides a more distant comparison, and Pongo a more distant one again. Humans are themselves great apes, rather than a group standing outside them. A character shared by Pan and Homo may have been inherited from their last common ancestor, but it can also have changed in either lineage or arisen in parallel. A shared feature of Pan and Gorilla does not automatically reconstruct the ancestor either: it may be ancestral, convergent, or retained in some branches and lost in others.

Living great apes are especially valuable because their soft tissues, growth, behaviour and mechanical performance can be studied. Muscle paths, joint motion and hand loading can make competing functional interpretations of a fossil wrist testable. Observing climbing and terrestrial movement establishes which combinations are mechanically possible; it also exposes the inadequacy of labelling a whole animal simply “arboreal” or “terrestrial”. Appropriate controls compare individuals of different ages and sexes, adjust for body size, record substrate and loading, and distinguish performance in captivity from behaviour in the wild. A surface that resembles another surface is weak functional evidence unless its position in the complete joint and the range of loads are considered.

The same accessibility creates temptations. chimpanzee locomotion, male coalitions or territorial behaviour cannot be transferred wholesale to the common ancestor. bonobos demonstrate variation within Pan, not a second unchanged ancestral template. Ecology, group composition, developmental plasticity and histories of selection differ among living populations. Current behaviour can generate hypotheses about feasible ancestral social systems, but proving that a particular ancestral behaviour existed requires additional evidence; most social behaviours do not fossilize. Treating the contrast as a choice between a uniformly aggressive chimpanzee ancestor and a uniformly peaceful bonobo ancestor replaces biology with caricature.

knuckle-walking illustrates the genuine scientific alternatives. One reconstruction takes the shared use of knuckle support in Pan and Gorilla as evidence for an ancestral condition, with later loss or modification in the hominin lineage. wrist features in early hominins have been interpreted as retained support for that hypothesis. ^[ref] A competing study emphasized differences in the development and functional organization of chimpanzee and Gorilla wrists, consistent with independent origins of their knuckle-walking systems. ^[ref] Similar external posture can therefore conceal distinct load-bearing arrangements. Neither simply counting two living knuckle-walking genera nor quoting the conclusion of one comparative study settles the ancestral condition. The inference depends on biological homology, functional interpretation and inclusion of relevant extinct forms.

Ardipithecus ramidus, approximately 4.4 Ma, is particularly important because its skeleton combines a grasping great toe and arboreal capabilities with anatomy interpreted as supporting terrestrial bipedalism. The authors argued that its hands and feet did not represent an unchanged modern chimpanzee locomotor package. ^[ref] This weakens a reconstruction that derives early hominins by merely standing a modern chimpanzee upright. However, Ardipithecus lived after the inferred Pan–Homo divergence; its features may include specializations of its own. Its proposed hominin position and functional reconstruction must also be evaluated against incomplete preservation and distortion, especially in the pelvis. It is evidence about a nearby branch, not direct observation of the common ancestor.

Older Miocene apes extend the comparison beyond surviving lineages. Pierolapithecus, approximately 12.5–13 Ma, combines an upright-trunk construction (orthogrady) with hand anatomy lacking the complete suspensory specialization of some living apes. ^[ref] The example shows that trunk posture, climbing and suspensory locomotion can evolve as a mosaic. Its exact position is debated, and it is not thereby identified as the Pan–Homo ancestor. Rather, extinct combinations expand the set of plausible ancestral forms and can reveal that a feature widespread among living apes was assembled in stages.

Genetic evidence establishes relationships and helps constrain timing, but a molecular divergence estimate is not a fossil anatomical reconstruction. Estimates are sensitive to mutation rate, calibration and generation interval. Pedigree observations of wild chimpanzees and Gorilla demonstrate why substituting one universal generation length can shift the inferred dates of great-ape divergences. ^[ref] A gene tree can also coalesce before a population split, and incomplete lineage sorting means that not every genomic region follows the species branching order. There is consequently no reason to force every candidate fossil into an overly precise split date selected from one molecular estimate.

The best procedure is to specify competing ancestral states and their predictions: for example, whether a particular wrist character should accompany habitual knuckle support, or whether an inferred climbing apparatus requires suspensory finger proportions. Score those characters across Pan, Homo, Gorilla, Pongo and well-preserved fossil taxa; examine sensitivity to uncertain character coding and alternative fossil placements. Related features must not be counted as a large number of independent confirmations when they are mechanically or developmentally coupled. Extant-only ancestral state reconstruction is especially vulnerable to the extinction of lineages that possessed combinations absent today.

Living great apes supply the comparative mechanics, development and diversity needed to interpret fossils; fossils prevent the living sample from dictating a false ancestral stereotype. A cautious composite reconstruction, with separate uncertainty for posture, hand use, diet and behaviour, is more defensible than choosing one living species as the ancestor's complete anatomical and social model.

A Miocene fossil ape with a mosaic of trunk and hand characters. Its informative anatomy does not uniquely identify it as the Pan–Homo last common ancestor. ^[ref]