Three-taxon analysis (or TTS, three-item analysis, 3ia) is a cladistic based method of phylogenetic reconstruction. Introduced by Nelson and Platnick (1991)to reconstruct organisms' phylogeny, this method can also be applied to biogeographic areas. It attempts to reconstruct complex phylogenetic trees by breaking the problem down into simpler chunks. Rather than try to resolve the relationships of all X taxa at once, it considers taxa 3 at a time. It is relatively easy to generate three-taxon statements (3is); that is, statements of the form "A and B are more closely related to one another than to C". Once each group of three taxa has been considered, the method constructs a tree that is consistent with as many three-item statements as possible. Computer program that implement three-taxon analysis is LisBeth (for systematic and biogeographic studies). LisBeth have been freely released. A recent simulation-based study found that Three-taxon analysis yields good power and an error rate intermediate between parsimony with ordered states and parsimony with unordered states.
Cladistics is an approach to biological classification in which organisms are categorized in groups ("clades") based on the most recent common ancestor. Hypothesized relationships are typically based on shared derived characteristics (synapomorphies) that can be traced to the most recent common ancestor and are not present in more distant groups and ancestors. A key feature of a clade is that a common ancestor and all its descendants are part of the clade. Importantly, all descendants stay in their overarching ancestral clade. For example, if within a strict cladistic framework the terms animals, bilateria/worms, fishes/vertebrata, or monkeys/anthropoidea were used, these terms would include humans. Many of these terms are normally used paraphyletically, outside of cladistics, e.g. as a 'grade'. Radiation results in the generation of new subclades by bifurcation, but in practice sexual hybridization may blur very closely related groupings.
In biology, phylogenetics is the study of the evolutionary history and relationships among individuals or groups of organisms. These relationships are discovered through phylogenetic inference methods that evaluate observed heritable traits, such as DNA sequences or morphology under a model of evolution of these traits. The result of these analyses is a phylogeny —a diagrammatic hypothesis about the history of the evolutionary relationships of a group of organisms. The tips of a phylogenetic tree can be living organisms or fossils, and represent the 'end', or the present, in an evolutionary lineage. A phylogenetic tree can be rooted or unrooted. A rooted tree indicates the common ancestor, or ancestral lineage, of the tree. An unrooted tree makes no assumption about the ancestral line, and does not show the origin or "root" of the gene or organism in question. Phylogenetic analyses have become central to understanding biodiversity, evolution, ecology, and genomes.
A cladogram is a diagram used in cladistics to show relations among organisms. A cladogram is not, however, an evolutionary tree because it does not show how ancestors are related to descendants, nor does it show how much they have changed; nevertheless, many evolutionary trees can be inferred from a single cladogram. A cladogram uses lines that branch off in different directions ending at a clade, a group of organisms with a last common ancestor. There are many shapes of cladograms but they all have lines that branch off from other lines. The lines can be traced back to where they branch off. These branching off points represent a hypothetical ancestor which can be inferred to exhibit the traits shared among the terminal taxa above it. This hypothetical ancestor might then provide clues about the order of evolution of various features, adaptation, and other evolutionary narratives about ancestors. Although traditionally such cladograms were generated largely on the basis of morphological characters, DNA and RNA sequencing data and computational phylogenetics are now very commonly used in the generation of cladograms, either on their own or in combination with morphology.
Evolutionary taxonomy, evolutionary systematics or Darwinian classification is a branch of biological classification that seeks to classify organisms using a combination of phylogenetic relationship, progenitor-descendant relationship, and degree of evolutionary change. This type of taxonomy may consider whole taxa rather than single species, so that groups of species can be inferred as giving rise to new groups. The concept found its most well-known form in the modern evolutionary synthesis of the early 1940s.
In cladistics or phylogenetics, an outgroup is a more distantly related group of organisms that serves as a reference group when determining the evolutionary relationships of the ingroup, the set of organisms under study, and is distinct from sociological outgroups. The outgroup is used as a point of comparison for the ingroup and specifically allows for the phylogeny to be rooted. Because the polarity (direction) of character change can be determined only on a rooted phylogeny, the choice of outgroup is essential for understanding the evolution of traits along a phylogeny.
In phylogenetics, maximum parsimony is an optimality criterion under which the phylogenetic tree that minimizes the total number of character-state changes is to be preferred. Under the maximum-parsimony criterion, the optimal tree will minimize the amount of homoplasy. In other words, under this criterion, the shortest possible tree that explains the data is considered best. The principle is akin to Occam's razor, which states that—all else being equal—the simplest hypothesis that explains the data should be selected. Some of the basic ideas behind maximum parsimony were presented by James S. Farris in 1970 and Walter M. Fitch in 1971.
In phylogenetics, long branch attraction (LBA) is a form of systematic error whereby distantly related lineages are incorrectly inferred to be closely related. LBA arises when the amount of molecular or morphological change accumulated within a lineage is sufficient to cause that lineage to appear similar to another long-branched lineage, solely because they have both undergone a large amount of change, rather than because they are related by descent. Such bias is more common when the overall divergence of some taxa results in long branches within a phylogeny. Long branches are often attracted to the base of a phylogenetic tree, because the lineage included to represent an outgroup is often also long-branched. The frequency of true LBA is unclear and often debated, and some authors view it as untestable and therefore irrelevant to empirical phylogenetic inference. Although often viewed as a failing of parsimony-based methodology, LBA could in principle result from a variety of scenarios and be inferred under multiple analytical paradigms.
A sister group or sister taxon is a phylogenetic term denoting the closest relative(s) of another given unit in an evolutionary tree.
Computational phylogenetics is the application of computational algorithms, methods, and programs to phylogenetic analyses. The goal is to assemble a phylogenetic tree representing a hypothesis about the evolutionary ancestry of a set of genes, species, or other taxa. For example, these techniques have been used to explore the family tree of hominid species and the relationships between specific genes shared by many types of organisms. Traditional phylogenetics relies on morphological data obtained by measuring and quantifying the phenotypic properties of representative organisms, while the more recent field of molecular phylogenetics uses nucleotide sequences encoding genes or amino acid sequences encoding proteins as the basis for classification. Many forms of molecular phylogenetics are closely related to and make extensive use of sequence alignment in constructing and refining phylogenetic trees, which are used to classify the evolutionary relationships between homologous genes represented in the genomes of divergent species. The phylogenetic trees constructed by computational methods are unlikely to perfectly reproduce the evolutionary tree that represents the historical relationships between the species being analyzed. The historical species tree may also differ from the historical tree of an individual homologous gene shared by those species.
Ophiacodontidae is an extinct family of early eupelycosaurs from the Carboniferous and Permian. Archaeothyris, and Clepsydrops were among the earliest ophiacodontids, appearing in the Late Carboniferous. Ophiacodontids are among the most basal synapsids, an offshoot of the lineage which includes therapsids and their descendants, the mammals. The group became extinct by the Middle Permian, replaced by anomodonts, theriodonts, and the diapsid reptiles.
Araneoidea is a taxon of araneomorph spiders, termed "araneoids", treated as a superfamily. As with many such groups, its circumscription has varied; in particular some families at one time moved to the Palpimanoidea have more recently been restored to Araneoidea. A 2014 treatment includes 18 families, with the araneoids making up about 26% of the total number of known spider species; a 2016 treatment includes essentially the same taxa, but now divided into 17 families.
Rubeostratilia is an extinct genus of amphibamiform temnospondyl from the early Permian of Texas. It is known from a single skull. This genus was named by Hélène Bourget and Jason S. Anderson in 2011, and the type species is Rubeostratilia texensis. The genus name comes from the Latin translation of 'redbeds' in reference to the Texas redbeds that produced both the holotype and many other early Permian fossils. The species name is for the state of Texas. The holotype and only known specimen was collected in 1941 from the Nocona Formation exposures in Clay County by a Works Projects Administration project that was transferred to the Field Museum of Natural History through an interinstitutional exchange with the Texas Memorial Museum.
Michel Laurin is a Canadian-born French vertebrate paleontologist whose specialities include the emergence of a land-based lifestyle among vertebrates, the evolution of body size and the origin and phylogeny of lissamphibians. He has also made important contributions to the literature on phylogenetic nomenclature.
Wayne Paul Maddison, is a professor and Canada Research Chair at the departments of zoology and botany at the University of British Columbia, and the Scientific Director of the Beaty Biodiversity Museum.
Hypnomys, otherwise known as Balearic giant dormice, is an extinct genus of dormouse, from the family Gliridae. Its species are considered examples of insular gigantism. They first appear in the fossil record during the Early Pliocene, presumably due to the Messinian salinity crisis causing a connection with mainland Europe, and disappear during the Holocene after human arrival on the Balearics. A 2020 mitochondrial DNA analysis found that its closest living relative was Eliomys, from which it diverged around 13.67 million years ago. The dental morphology of the earlier species is more complex than that of Eliomys, suggesting it is derived from Vasseuromys or a similar form, rather than an early diverging lineage within Eliomys. A 2016 study found that H. onicensis could live over 10 years, far longer than related taxa. This genus contains the following species:
Stephanorhinus kirchbergensis, commonly known as Merck's rhinoceros, is an extinct species of rhino known from the Middle to Late Pleistocene of Eurasia. One of the last members of the genus Stephanorhinus, it is considered to be a typical component of the interglacial Palaeoloxodon large faunal assemblage in Europe. It is most closely related to the Woolly rhinoceros and the Sumatran rhinoceros. Across its range it is often sympatric with the narrow nosed rhinoceros S. hemitoechus. It is noted for its very large size, among the largest of Pleistocene rhinoceroses, approaching that of Elasmotherium.
Eucacopinae is an extinct clade of dissorophid temnospondyls. Eucacopines differ from the other main group of dissorophids, the Dissorophinae, in having more lightly built skeletons and more knobby skulls. The subfamily was originally named Cacopinae, but since the name was already established for a group of living microhylid frogs in 1931, the name was changed to Eucacopinae in 2013. Eucacopinae is a stem-based taxon defined as the most inclusive clade containing the species Cacops apsidephorus but not Dissorophus multicinctus, which belongs to Dissorophinae. According to the most recent phylogenetic analyses of Dissorophidae, Eucacopinae includes the basal ("primitive") species Conjunctio multidens and Scapanops neglecta from the southwestern United States and a more derived ("advanced") group including several species of Cacops and the Russian genera Kamacops and Zygosaurus. Derived eucacopines have two rows of bony plates called osteoderms running down their backs, while the more basal eucacopines have only a single row. Dissorophines also have a double row of osteoderms but probably evolved them independently because the most recent common ancestor of the two groups had a single row of osteoderms.
Barasaurus is an extinct genus of owenettid procolophonoid parareptile known from the late Late Permian and early Early Triassic of Madagascar. It contains a single species, Barasaurus besairiei.
Prototherium is a genus of extinct sirenian related to the dugong. It is known from middle (Bartonian) and upper Eocene deposits in Italy and Spain. Type species is P. veronenses