In biology, phylogenetics is the study of the evolutionary history and relationships among or within groups of organisms. These relationships are determined by phylogenetic inference methods that focus on observed heritable traits, such as DNA sequences, protein amino acid sequences, or morphology. The result of such an analysis is a phylogenetic tree—a diagram containing a hypothesis of relationships that reflects the evolutionary history of a group of organisms.
Coelacanths are an ancient group of lobe-finned fish (Sarcopterygii) in the class Actinistia. As sarcopterygians, they are more closely related to lungfish and tetrapods than to ray-finned fish.
Sarcopterygii — sometimes considered synonymous with Crossopterygii — is a taxon of the bony fish known as the lobe-finned fish or sarcopterygians, characterised by prominent muscular buds (lobes) within the fins. This is in contrast to the other clade of bony fish, the Actinopterygii, which have only bony spines supporting the fins.
The molecular clock is a figurative term for a technique that uses the mutation rate of biomolecules to deduce the time in prehistory when two or more life forms diverged. The biomolecular data used for such calculations are usually nucleotide sequences for DNA, RNA, or amino acid sequences for proteins. The benchmarks for determining the mutation rate are often fossil or archaeological dates. The molecular clock was first tested in 1962 on the hemoglobin protein variants of various animals, and is commonly used in molecular evolution to estimate times of speciation or radiation. It is sometimes called a gene clock or an evolutionary clock.
A living fossil is an extant taxon that cosmetically resembles related species known only from the fossil record. To be considered a living fossil, the fossil species must be old relative to the time of origin of the extant clade. Living fossils commonly are of species-poor lineages, but they need not be. While the body plan of a living fossil remains superficially similar, it is never the same species as the remote relatives it resembles, because genetic drift would inevitably change its chromosomal structure.
In paleontology, a Lazarus taxon is a taxon that disappears for one or more periods from the fossil record, only to appear again later. Likewise in conservation biology and ecology, it can refer to species or populations that were thought to be extinct, and are rediscovered. The term Lazarus taxon was coined by Karl W. Flessa and David Jablonski in 1983 and was then expanded by Jablonski in 1986. Paul Wignall and Michael Benton defined Lazarus taxa as, "At times of biotic crisis many taxa go extinct, but others only temporarily disappeared from the fossil record, often for intervals measured in millions of years, before reappearing unchanged". Earlier work also supports the concept though without using the name Lazarus taxon, like work by Christopher R. C. Paul.
Anagenesis is the gradual evolution of a species that continues to exist as an interbreeding population. This contrasts with cladogenesis, which occurs when there is branching or splitting, leading to two or more lineages and resulting in separate species. Anagenesis does not always lead to the formation of a new species from an ancestral species. When speciation does occur as different lineages branch off and cease to interbreed, a core group may continue to be defined as the original species. The evolution of this group, without extinction or species selection, is anagenesis.
Neontology is a part of biology that, in contrast to paleontology, deals with living organisms. It is the study of extant taxa : taxa with members still alive, as opposed to (all) being extinct. For example:
Introgression, also known as introgressive hybridization, in genetics is the transfer of genetic material from one species into the gene pool of another by the repeated backcrossing of an interspecific hybrid with one of its parent species. Introgression is a long-term process, even when artificial; it may take many hybrid generations before significant backcrossing occurs. This process is distinct from most forms of gene flow in that it occurs between two populations of different species, rather than two populations of the same species.
Computational phylogenetics, phylogeny inference, or phylogenetic inference focuses on computational and optimization algorithms, heuristics, and approaches involved in phylogenetic analyses. The goal is to find a phylogenetic tree representing optimal evolutionary ancestry between a set of genes, species, or taxa. Maximum likelihood, parsimony, Bayesian, and minimum evolution are typical optimality criteria used to assess how well a phylogenetic tree topology describes the sequence data. Nearest Neighbour Interchange (NNI), Subtree Prune and Regraft (SPR), and Tree Bisection and Reconnection (TBR), known as tree rearrangements, are deterministic algorithms to search for optimal or the best phylogenetic tree. The space and the landscape of searching for the optimal phylogenetic tree is known as phylogeny search space.
The Signor–Lipps effect is a paleontological principle proposed in 1982 by Philip W. Signor and Jere H. Lipps which states that, since the fossil record of organisms is never complete, neither the first nor the last organism in a given taxon will be recorded as a fossil. The Signor–Lipps effect is often applied specifically to cases of the youngest-known fossils of a taxon failing to represent the last appearance of an organism. The inverse, regarding the oldest-known fossils failing to represent the first appearance of a taxon, is alternatively called the Jaanusson effect after researcher Valdar Jaanusson, or the Sppil–Rongis effect.
In phylogenetics, an autapomorphy is a distinctive feature, known as a derived trait, that is unique to a given taxon. That is, it is found only in one taxon, but not found in any others or outgroup taxa, not even those most closely related to the focal taxon. It can therefore be considered an apomorphy in relation to a single taxon. The word autapomorphy, introduced in 1950 by German entomologist Willi Hennig, is derived from the Greek words αὐτός, autos "self"; ἀπό, apo "away from"; and μορφή, morphḗ = "shape".
In phylogenetics, basal is the direction of the base of a rooted phylogenetic tree or cladogram. The term may be more strictly applied only to nodes adjacent to the root, or more loosely applied to nodes regarded as being close to the root. Note that extant taxa that lie on branches connecting directly to the root are not more closely related to the root than any other extant taxa.
Paraves are a widespread group of theropod dinosaurs that originated in the Middle Jurassic period. In addition to the extinct dromaeosaurids, troodontids, anchiornithids, and possibly the scansoriopterygids, the group also contains the avialans, which include diverse extinct taxa as well as the over 10,000 species of living birds. Basal members of Paraves are well known for the possession of an enlarged claw on the second digit of the foot, which was held off the ground when walking in some species. A number of differing scientific interpretations of the relationships between paravian taxa exist. New fossil discoveries and analyses make the classification of Paraves an active subject of research.
Ambulacraria, or Coelomopora, is a clade of invertebrate phyla that includes echinoderms and hemichordates; a member of this group is called an ambulacrarian. Phylogenetic analysis suggests the echinoderms and hemichordates separated around 533 million years ago. The Ambulacraria are part of the deuterostomes, a clade that also includes the many Chordata, and the few extinct species belonging to the Vetulicolia.
Alligatoroidea is one of three superfamilies of crocodylians, the other two being Crocodyloidea and Gavialoidea. Alligatoroidea evolved in the Late Cretaceous period, and consists of the alligators and caimans, as well as extinct members more closely related to the alligators than the two other groups.
Xiongguanlong is an extinct genus of tyrannosauroid theropod from the Early Cretaceous period of what is now China. The type and only species is X. baimoensis. The generic name comes from Jiayuguan City and the Mandarin word "long" which means dragon. The specific epithet, "baimoensis" is a latinization of the Mandarin word for "white ghost" in reference to one of the geological features of the type locality.
The chimpanzee–human last common ancestor (CHLCA) is the last common ancestor shared by the extant Homo (human) and Pan genera of Hominini. Estimates of the divergence date vary widely from thirteen to five million years ago.
Incomplete lineage sorting, also termed hemiplasy, deep coalescence, retention of ancestral polymorphism, or trans-species polymorphism, describes a phenomenon in population genetics when ancestral gene copies fail to coalesce into a common ancestral copy until deeper than previous speciation events. It is caused by lineage sorting of genetic polymorphisms that were retained across successive nodes in the species tree. In other words, the tree produced by a single gene differs from the population or species level tree, producing a discordant tree. Whatever the mechanism, the result is that a generated species level tree may differ depending on the selected genes used for assessment. This is in contrast to complete lineage sorting, where the tree produced by the gene is the same as the population or species level tree. Both are common results in phylogenetic analysis, although it depends on the gene, organism, and sampling technique.
Strisores, sometimes called nightbirds, is a clade of birds that includes the living families and orders Caprimulgidae, Nyctibiidae (potoos), Steatornithidae (oilbirds), Podargidae (frogmouths), Apodiformes, as well as the Aegotheliformes (owlet-nightjars) whose distinctness was only recently realized. The Apodiformes and the Aegotheliformes form the Daedalornithes.
