A molecular phylogeny based on rDNA analysis dating from 2005 suggests that salamanders and caecilians are more closely related to each other than they are to frogs and that the divergence of the three groups took place in the Paleozoic or early Mesozoic before the breakup of the supercontinent Pangaea and soon after their divergence from the lobe-finned fish.

Other ways of classifying the vertebrates have been devised, particularly with emphasis on the phylogeny on early amphibians and reptiles.

A. M. Khazen, on the one hand, states that " ontogeny is obliged to repeat the main stages of phylogeny.

But the current understanding of Passeroidea phylogeny is better reflected in keeping the fundamental nine-primaried oscine clades as distinct families.

The phylogeny depicted below is based on seven different sources.

As we know it in 2009, the phylogeny of Malpighiales is, at its deepest level, an unresolved polytomy of 16 clades.

The theory of recapitulation, also called the biogenetic law or embryological parallelism — and often expressed as " ontogeny recapitulates phylogeny "— is a biological hypothesis that in developing from embryo to adult, animals go through stages resembling or representing successive stages in the evolution of their remote ancestors.

Ontogeny is the growth ( size change ) and development ( shape change ) of an individual organism ; phylogeny is the evolutionary history of a species.

For example, the peculiar development of the works by modernist composer Arnold Schoenberg ( here an " ontogeny ") is generalized in many histories into a " phylogeny " – a historical development (" evolution ") of Western Music toward atonal styles of which Schoenberg is a representative.

The result of phylogenetic studies is a hypothesis about the evolutionary history of taxonomic groups: their phylogeny.

In biology, phenetics (), also known as taximetrics, is an attempt to classify organisms based on overall similarity, usually in morphology or other observable traits, regardless of their phylogeny or evolutionary relation.

The phylogeny shown below is based on the one published by Shuguang Jian and coauthors in 2008.

Approaching the egg cell is a rather complex, multistep process of chemotaxis guided by different chemical substances / stimuli on individual levels of phylogeny.

The Tree of Life Web Project is an ongoing Internet project containing information about phylogeny and biodiversity, produced by biologists from around the world.

Generally, if a structure pre-dates another structure in evolutionary terms, then it often appears earlier than the second in an embryo ; this general observation is sometimes summarized by the phrase " ontogeny recapitulates phylogeny ".

Phylogenetic classification is based solely on phylogeny.

( This is an instance of correlation between ontogeny and phylogeny.

However, the phylogeny of the great white is still in dispute.

Using a parsimony criterion is only one of several methods to infer a phylogeny from molecular data ; maximum likelihood and Bayesian inference, which incorporate explicit models of sequence evolution, are non-Hennigian ways to evaluate sequence data.

With a faulty outgroup or character set, no method of evaluation is likely to produce a phylogeny representing the evolutionary reality.

in 2009 noted that " The deep phylogeny of eukaryotes is an extremely difficult and controversial problem.

", there appears to be a consensus that the 2005 six supergroup model does not reflect the true phylogeny of the eukaryotes and hence how they should be classified, although there is no agreement as to the model which should replace it.

Ernst Haeckel ( 1866 ), in his endeavour to produce a synthesis of Darwin's theory with Lamarckism and Naturphilosophie, proposed that " ontogeny recapitulates phylogeny ," that is, the development of the embryo of every species ( ontogeny ) fully repeats the evolutionary development of that species ( phylogeny ), in Geoffroy's linear model rather than Darwin's idea of branching evolution.

Molecular studies, however, have shown that the Cetacea descend from the Artiodactyl ancestors, although the precise phylogeny within the order remains uncertain.

As of 2005, the taxonomy and phylogeny for the specimens are still uncertain, although most paleoanthropologists consider them related to Homo erectus in some way.

While studies of molecular phylogeny has caused substantial reclassifications, it is uncertain whether this new scheme will be widely adopted.

When analyzing " supertrees " ( datasets incorporating as many taxa of a suspected clade as possible ), it may become unavoidable to introduce character definitions that are imprecise, as otherwise the characters might not apply at all to a large number of taxa ; to continue with the " wings " example, the presence of wings would hardly be a useful character if attempting a phylogeny of all Metazoa, as most of these don't have wings at all.

It has to be borne in mind that any typological system has heuristic value as a convenience for description, and need not reflect phylogeny: each category ( term ) may include representatives of many distantly related taxa, each of which may well have close relatives that are in another category ( term ) or that are not migratory and thus fall completely outside the typology.

Ostracods are grouped together based on gross morphology, but the group may not be monophyletic ; their molecular phylogeny remains ambiguous.

There is a very high probability that the family may be sister to Velloziaceae but similarities with Zingiberaceae family ( which is a part of a whole different order-Zingiberales ) do not exclude the chance for a different phylogeny.

Origin and phylogeny has been obtained by Antonio Arnaiz-Villena et al .. Estrildinae may have originated in India and dispersed thereafter ( towards Africa and Pacific Ocean habitats ).

Origin and phylogeny has been obtained by Antonio Arnaiz-Villena et al .. Estrildinae may have originated in India and dispersed thereafter ( towards Africa and Pacific Ocean habitats ).

Baldwin gives the following case involving cooperation: " Animals may be kept alive let us say in a given environment by social cooperation only ; these transmit this social type of variation to posterity ; thus social adaptation sets the direction of physical phylogeny and physical heredity is determined in part by this factor " ( Baldwin, 1896, p. 553 ).

However, based on the presence of unusually long leg feathers in various feathered dinosaurs, Archaeopteryx, and some modern birds such as raptors, as well as the discovery of further dinosaur with long primary feathers on their feet ( such as Pedopenna ), the authors argued that the current body of evidence, both from morphology and phylogeny, suggests that bird flight did shift at some point from shared limb dominance to front-limb dominance, and that all modern birds may have evolved from four-winged ancestors, or at least ancestors with unusually long leg feathers relative to the modern configuration.

Although excluding characters or taxa may appear to improve resolution, the resulting tree is based on less data, and is therefore a less reliable estimate of the phylogeny ( unless the characters or taxa are non informative, see safe taxonomic reduction ).

The systematics and phylogeny of gomphotheres are unclear and the group might in fact be paraphyletic — i. e., may not include all known descendants of their common ancestor.

Although this indicates that the Pseudorthoceratidae may be in need of revision, it also shows the value of embryonic shell morphology in understanding orthocerid phylogeny.

Pseudotermination is extreme form of pseudoextinction, when lineage may continue in form of new species of frequently difficult to predict phylogeny.

A phylogeny showing when gill slits may have arisen.

Specifically, Tai – Kadai and Sino-Tibetan could possibly both belong to the Austronesian language family ( not to be confused with Austroasiatic ) due to a scattering of cognates between their ancestral forms, and there is also some, albeit much more tenuous, evidence to suggest that Austroasiatic should also be included, however his views are but one among competing hypotheses about the phylogeny of these languages, see the Sino-Austronesian languages article for some further detail.

Within biology, ontogeny pertains to the developmental history of an organism within its own lifetime, as distinct from phylogeny, which refers to the evolutionary history of species.

The low effective population size and rapid mutation rate ( in animals ) makes mtDNA useful for assessing genetic relationships of individuals or groups within a species and also for identifying and quantifying the phylogeny ( evolutionary relationships ; see phylogenetics ) among different species, provided they are not too distantly related.

In their phylogeny, Tucker and Tenorio noted the close relationship of the cone species within the various clades, corresponding to their proposed families and genera ; this also corresponded to the results of prior molecular studies by Puillandre et al.

Some experts are however still holding ( in 2011 ) to the traditional classification system and place all species in a single family, Conidae, within the Linnean genus Conus, waiting for a more complete molecular phylogeny of the family to be published.

" Debate within the scientific community regarding this issue continues, and additional molecular phylogeny studies are being carried out in an attempt to clarify the issue.

in 1993, and prior to 2011 a large number of diverse genera were included within the family Conidae, however as a result of molecular phylogeny studies in 2011 many of these genera which were in the family Conidae ( commonly known as turrids ) have been moved back to the Turridae or placed in new families within the superfamily Conoidea.

It was formerly classified within the now-obsolete order Lycoperdales, as the type genus which, following a restructuring of fungal taxonomy brought about by molecular phylogeny, has been split.

Comparison of ribosomal RNA genes has provided a phylogeny of known strains within Chlamydiae.

A study of the phylogeny of some Hieraaetus species and other eagles indicated that they were nested within the Aquila clade of eagles, resulting in their repositioning.

demonstrated that L. monocytogenes is a distinct taxon within the Lactobacillus-Bacillus branch of the bacterial phylogeny constructed by Woese.

Ankylosaur phylogeny is a contentious topic, with several mutually exclusive analyses presented in recent years, so the exact position of Ankylosaurus within Ankylosauridae is unknown.

In the old view of metazoan phylogeny, the lophophorates were placed within the Deuterostomia.

A molecular phylogeny of the family was published in 2007, greatly clarifying relationships within the family.

It was formerly classified within the now-obsolete order Lycoperdales, which, following a restructuring of fungal taxonomy brought about by molecular phylogeny, has been split ; the puffballs, Calvatia spp.