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phylogenetics In biology, phylogenetics (; from Greek φυλή/ φῦλον [] "tribe, clan, race", and wikt:γενετικός, γενετικός [] "origin, source, birth") is the study of the evolutionary history and relationships among or within groups ...
, the crown group or crown assemblage is a collection of
species In biology, a species is the basic unit of classification and a taxonomic rank of an organism, as well as a unit of biodiversity. A species is often defined as the largest group of organisms in which any two individuals of the appropriat ...
composed of the living representatives of the collection, the most recent common ancestor of the collection, and all descendants of the most recent common ancestor. It is thus a way of defining a
clade A clade (), also known as a monophyletic group or natural group, is a group of organisms that are monophyletic – that is, composed of a common ancestor and all its lineal descendants – on a phylogenetic tree. Rather than the English ter ...
, a group consisting of a species and all its extant or
extinct Extinction is the termination of a kind of organism or of a group of kinds (taxon), usually a species. The moment of extinction is generally considered to be the death of the last individual of the species, although the capacity to breed and ...
descendants. For example, Neornithes (birds) can be defined as a crown group, which includes the most recent common ancestor of all modern birds, and all of its extant or extinct descendants. The concept was developed by
Willi Hennig Emil Hans Willi Hennig (20 April 1913 – 5 November 1976) was a German biologist and zoologist who is considered the founder of phylogenetic systematics, otherwise known as cladistics. In 1945 as a prisoner of war, Hennig began work on his th ...
, the formulator of phylogenetic systematics, as a way of classifying living organisms relative to their extinct relatives in his "Die Stammesgeschichte der Insekten", and the "crown" and "stem" group terminology was coined by R. P. S. Jefferies in 1979. Though formulated in the 1970s, the term was not commonly used until its reintroduction in 2000 by
Graham Budd Graham Edward Budd is a British palaeontologist. He is Professor and head of palaeobiology at Uppsala University. Budd's research focuses on the Cambrian explosion and on the evolution and development, anatomy, and patterns of diversification ...
and
Sören Jensen Sören is a municipality in the district of Rendsburg-Eckernförde Rendsburg-Eckernförde (; da, Rendsborg-Egernførde) is a district in Schleswig-Holstein, Germany. It is bounded by (from the east and clockwise) the city of Kiel, the district ...
.


Contents of the crown group

It is not necessary for a species to have living descendants in order for it to be included in the crown group. Extinct side branches on the
family tree A family tree, also called a genealogy or a pedigree chart, is a chart representing family relationships in a conventional tree structure. More detailed family trees, used in medicine and social work, are known as genograms. Representations ...
that are descended from the most recent common ancestor of living members will still be part of a crown group. For example, if we consider the crown-birds (i.e. all extant birds and the rest of the family tree back to their most recent common ancestor), extinct side branches like the
dodo The dodo (''Raphus cucullatus'') is an extinct flightless bird that was endemic to the island of Mauritius, which is east of Madagascar in the Indian Ocean. The dodo's closest genetic relative was the also-extinct Rodrigues solitaire. ...
or
great auk The great auk (''Pinguinus impennis'') is a species of flightless alcid that became extinct in the mid-19th century. It was the only modern species in the genus ''Pinguinus''. It is not closely related to the birds now known as penguins, wh ...
are still descended from the most recent common ancestor of all living
bird Birds are a group of warm-blooded vertebrates constituting the class Aves (), characterised by feathers, toothless beaked jaws, the laying of hard-shelled eggs, a high metabolic rate, a four-chambered heart, and a strong yet lightweig ...
s, so fall within the bird crown group. One very simplified cladogram for birds is shown below: In this diagram, the clade labelled "Neornithes" is the crown group of birds: it includes the most recent common ancestor of all living birds and its descendants, living or not. Although considered to be birds (i.e. members of the clade Aves), ''Archaeopteryx'' and other extinct groups are not included in the crown group, as they fall outside the Neornithes clade, being descended from an earlier ancestor. An alternative definition does not require any members of a crown group to be extant, only to have resulted from a "major cladogenesis event". The first definition forms the basis of this article. Often, the crown group is given the designation "crown-", to separate it from the group as commonly defined. Both
birds Birds are a group of warm-blooded vertebrates constituting the class Aves (), characterised by feathers, toothless beaked jaws, the laying of hard-shelled eggs, a high metabolic rate, a four-chambered heart, and a strong yet lightweigh ...
and mammals are traditionally defined by their traits, and contain fossil members that lived before the last common ancestors of the living groups or, like the mammal '' Haldanodon'', were not descended from that ancestor although they lived later. Crown-Aves and Crown-Mammalia therefore differ slightly in content from the common definition of Aves and Mammalia. This has caused some confusion in the literature.


Other groups under the crown group concept

The cladistic idea of strictly using the topology of the
phylogenetic tree A phylogenetic tree (also phylogeny or evolutionary tree Felsenstein J. (2004). ''Inferring Phylogenies'' Sinauer Associates: Sunderland, MA.) is a branching diagram or a tree showing the evolutionary relationships among various biological spec ...
to define groups necessitates other definitions than crown groups to adequately define commonly discussed fossil groups. Thus, a host of
prefix A prefix is an affix which is placed before the stem of a word. Adding it to the beginning of one word changes it into another word. For example, when the prefix ''un-'' is added to the word ''happy'', it creates the word ''unhappy''. Particul ...
es have been defined to describe various branches of the phylogenetic tree relative to extant organisms.


Pan-group

A pan-group or total group is the crown group and all organisms more closely related to it than to any other extant organisms. In a tree analogy, it is the crown group and all branches back to (but not including) the split with the closest branch to have living members. The Pan-Aves thus contain the living birds and all (fossil) organisms more closely related to birds than to
crocodilian Crocodilia (or Crocodylia, both ) is an order of mostly large, predatory, semiaquatic reptiles, known as crocodilians. They first appeared 95 million years ago in the Late Cretaceous period (Cenomanian stage) and are the closest livin ...
s (their closest living relatives). The phylogenetic lineage leading back from Neornithes to the point where it merges with the crocodilian lineage, along with all side branches, constitutes pan-birds. In addition to non-crown group primitive birds like ''Archaeopteryx'', '' Hesperornis'' and '' Confuciusornis'', therefore, pan-group birds would include all
dinosaur Dinosaurs are a diverse group of reptiles of the clade Dinosauria. They first appeared during the Triassic period, between 243 and 233.23 million years ago (mya), although the exact origin and timing of the evolution of dinosaurs is t ...
s and
pterosaur Pterosaurs (; from Greek ''pteron'' and ''sauros'', meaning "wing lizard") is an extinct clade of flying reptiles in the order, Pterosauria. They existed during most of the Mesozoic: from the Late Triassic to the end of the Cretaceous (228 ...
s as well as an assortment of non-crocodilian animals like '' Marasuchus''. Pan-Mammalia consists of all mammals and their fossil ancestors back to the phylogenetic split from the remaining
amniotes Amniotes are a clade of tetrapod vertebrates that comprises sauropsids (including all reptiles and birds, and extinct parareptiles and non-avian dinosaurs) and synapsids (including pelycosaurs and therapsids such as mammals). They are dis ...
(the
Sauropsida Sauropsida ("lizard faces") is a clade of amniotes, broadly equivalent to the class Reptilia. Sauropsida is the sister taxon to Synapsida, the other clade of amniotes which includes mammals as its only modern representatives. Although early sy ...
). Pan-Mammalia is thus an alternative name for Synapsida.


Stem groups

A stem group is a
paraphyletic In taxonomy, a group is paraphyletic if it consists of the group's last common ancestor and most of its descendants, excluding a few monophyletic subgroups. The group is said to be paraphyletic ''with respect to'' the excluded subgroups. In ...
assemblage composed of the members of a pan-group or total group, above, ''minus'' the crown group itself (and therefore minus all living members of the pan-group). This leaves primitive relatives of the crown groups, back along the phylogenetic line to (but not including) the last common ancestor of the crown group and their nearest living relatives. It follows from the definition that all members of a stem group are extinct. The "stem group" is the most used and most important of the concepts linked to crown groups, as it offers a means to reify and name paraphyletic assemblages of fossils that otherwise do not fit into systematics based on living organisms. While often attributed to Jefferies (1979), Willmann (2003) traced the origin of the stem group concept to German systematist Othniel Abel (1914) , and it was discussed and diagrammed in English as early as 1933 by A. S. Romer. Alternatively, the term "stem group" is sometimes used in a wider sense to cover any members of the traditional taxon falling outside the crown group. Permian synapsids like ''
Dimetrodon ''Dimetrodon'' ( or ,) meaning "two measures of teeth,” is an extinct genus of non-mammalian synapsid that lived during the Cisuralian (Early Permian), around 295–272 million years ago (Mya). It is a member of the family Sphenacodont ...
'' or '' Anteosaurus'' are stem mammals in the wider sense but not in the narrower one. Often, an (extinct) grouping is identified as belonging together. Later, it may be realized other (extant) groupings actually emerged within such grouping, rendering them a stem grouping. Cladistically, the new groups should then be added the group, as paraphyletic groupings are not natural. In any case, stem groupings with living descendants should not be viewed as a cohesive group, but their tree should be further resolved to reveal the full bifurcating phylogeny.


Examples of stem groups (in the wider sense)

Stem birds perhaps constitute the most cited example of a stem group, as the phylogeny of this group is fairly well known. The following cladogram, based on Benton (2005), illustrates the concept: The crown group here is Neornithes, all modern bird lineages back to their last common ancestor. The closest living relatives of birds are
crocodilian Crocodilia (or Crocodylia, both ) is an order of mostly large, predatory, semiaquatic reptiles, known as crocodilians. They first appeared 95 million years ago in the Late Cretaceous period (Cenomanian stage) and are the closest livin ...
s. If we follow the phylogenetic lineage leading to Neornithes to the left, the line itself and all side branches belong to the stem birds until the lineage merges with that of the crocodilians. In addition to non-crown group primitive birds like ''
Archaeopteryx ''Archaeopteryx'' (; ), sometimes referred to by its German name, "" ( ''Primeval Bird''), is a genus of bird-like dinosaurs. The name derives from the ancient Greek (''archaīos''), meaning "ancient", and (''ptéryx''), meaning "feather" ...
'', '' Hesperornis'' and '' Confuciusornis'', stem group birds include the
dinosaurs Dinosaurs are a diverse group of reptiles of the clade Dinosauria. They first appeared during the Triassic period, between 243 and 233.23 million years ago (mya), although the exact origin and timing of the evolution of dinosaurs is the ...
and the pterosaurs. The last common ancestor of birds and crocodilians—the first crown group archosaur—was neither bird nor crocodilian and possessed none of the features unique to either. As the bird stem group evolved, distinctive bird features such as feathers and hollow bones appeared. Finally, at the base of the crown group, all traits common to extant birds were present. Under the widely used total-group perspective, the Crocodylomorpha would become synonymous with the Crocodilia, and the Avemetatarsalia would become synonymous with the birds, and the above tree could be summarized as An advantage of this approach is that declaring Theropoda to be birds (or Pan-aves) is more specific than declaring it to be a member of the Archosauria, which would not exclude it from the Crocodilia branch. Basal branch names such as Avemetatarsalia are usually more obscure. However, not so advantageous are the facts that "Pan-Aves" and "Aves" are not the same group, the circumscription of the concept of "Pan-Aves" (synonymous with Avemetatarsalia) is only evident by examination of the above tree, and calling both groups "birds" is ambiguous. Stem mammals are those in the lineage leading to living mammals, together with side branches, from the divergence of the lineage from the Sauropsida to the last common ancestor of the living mammals. This group includes the synapsids as well as mammaliaforms like the morganucodonts and the docodonts; the latter groups have traditionally and anatomically been considered mammals even though they fall outside the crown group mammals. Romer, A.S. (1966): Vertebrate Paleontology. University of Chicago Press, Chicago; 3rd edition Stem tetrapods are the animals belonging to the lineage leading to
tetrapod Tetrapods (; ) are four-limbed vertebrate animals constituting the superclass Tetrapoda (). It includes extant and extinct amphibians, sauropsids ( reptiles, including dinosaurs and therefore birds) and synapsids ( pelycosaurs, extinct t ...
s from their divergence from the
lungfish Lungfish are freshwater vertebrates belonging to the order Dipnoi. Lungfish are best known for retaining ancestral characteristics within the Osteichthyes, including the ability to breathe air, and ancestral structures within Sarcopterygii, i ...
, our nearest relatives among the fishes. In addition to a series of lobe-finned fishes, they also include some of the early labyrinthodonts. Exactly what labyrinthodonts are in the stem group tetrapods rather than the corresponding crown group is uncertain, as the phylogeny of early tetrapods is not well understood. This example shows that crown and stem group definitions are of limited value when there is no consensus phylogeny. Stem arthropods constitute a group that has seen attention in connection with the Burgess Shale fauna. Several of the finds, including the enigmatic '' Opabinia'' and ''
Anomalocaris ''Anomalocaris'' ("unlike other shrimp", or "abnormal shrimp") is an extinct genus of radiodont, an order of early-diverging stem-group arthropods. The first fossils of ''Anomalocaris'' were discovered in the ''Ogygopsis'' Shale of the Stephen F ...
'' have some, though not all, features associated with
arthropod Arthropods (, (gen. ποδός)) are invertebrate animals with an exoskeleton, a segmented body, and paired jointed appendages. Arthropods form the phylum Arthropoda. They are distinguished by their jointed limbs and cuticle made of chiti ...
s, and are thus considered stem arthropods. The sorting of the Burgess Shale fauna into various stem groups finally enabled phylogenetic sorting of this enigmatic assemblage and also allowed for identifying
velvet worms Onychophora (from grc, ονυχής, , "claws"; and , , "to carry"), commonly known as velvet worms (due to their velvety texture and somewhat wormlike appearance) or more ambiguously as peripatus (after the first described genus, '' Peripatus ...
as the closest living relatives of arthropods. Stem priapulids are other early Cambrian to middle Cambrian faunas, appearing in Chengjiang to Burgess Shale. The genus '' Ottoia'' has more or less the same build as modern priapulids, but phylogenetic analysis indicates that it falls outside the crown group, making it a stem priapulid.


Plesion-group

The name ''plesion'' has a long history in biological systematics, and plesion group has acquired several meanings over the years. One use is as "nearby group" (plesion means ''close to'' in Greek), i.e. sister group to a given
taxon In biology, a taxon ( back-formation from '' taxonomy''; plural taxa) is a group of one or more populations of an organism or organisms seen by taxonomists to form a unit. Although neither is required, a taxon is usually known by a particular n ...
, whether that group is a crown group or not. The term may also mean a group, possibly
paraphyletic In taxonomy, a group is paraphyletic if it consists of the group's last common ancestor and most of its descendants, excluding a few monophyletic subgroups. The group is said to be paraphyletic ''with respect to'' the excluded subgroups. In ...
, defined by primitive traits (i.e. symplesiomorphies). It is generally taken to mean a side branch splitting off earlier on the phylogenetic tree than the group in question.


Palaeontological significance of stem and crown groups

Placing
fossil A fossil (from Classical Latin , ) is any preserved remains, impression, or trace of any once-living thing from a past geological age. Examples include bones, shells, exoskeletons, stone imprints of animals or microbes, objects preserved ...
s in their right order in a stem group allows the order of these acquisitions to be established, and thus the ecological and functional setting of the evolution of the major features of the group in question. Stem groups thus offer a route to integrate unique palaeontological data into questions of the evolution of living organisms. Furthermore, they show that fossils that were considered to lie in their own separate group because they did not show all the diagnostic features of a living clade, can nevertheless be related to it by lying in its stem group. Such fossils have been of particular importance in considering the origins of the tetrapods, mammals, and
animal Animals are multicellular, eukaryotic organisms in the biological kingdom Animalia. With few exceptions, animals consume organic material, breathe oxygen, are able to move, can reproduce sexually, and go through an ontogenetic stage ...
s. The application of the stem group concept also influenced the interpretation of the organisms of the Burgess shale. Their classification in stem groups to extant phyla, rather than in phyla of their own, is thought by some to make the Cambrian explosion easier to understand without invoking unusual evolutionary mechanisms; however, application of the stem group concept does nothing to ameliorate the difficulties that phylogenetic telescoping poses to evolutionary theorists attempting to understand both macroevolutionary change and the abrupt character of the Cambrian explosion. Overemphasis on the stem group concept threatens to delay or obscure proper recognition of new higher taxa.


Stem groups in systematics

As originally proposed by Karl-Ernst Lauterbach, stem groups should be given the prefix "stem" (i.e. Stem-Aves, Stem-Arthropoda), however the crown group should have no prefix. The latter has not been universally accepted for known groups. A number of paleontologists have opted to apply this approach anyway.Gauthier, J., and de Queiroz, K. (2001). "Feathered dinosaurs, flying dinosaurs, crown dinosaurs, and the name Aves." Pp. 7-41 in ''New perspectives on the origin and early evolution of birds: proceedings of the International Symposium in Honor of John H. Ostrom'' (J. A. Gauthier and L. F. Gall, eds.). Peabody Museum of Natural History, Yale University, New Haven, Connecticut, U.S.A.


References


Further reading

* * {{Phylogenetics Phylogenetics Evolutionary biology