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. It is closely related to numerical taxonomy which is concerned with the use of numerical methods for taxonomic classification. Many people contributed to the development of phenetics, but the most influential were Peter Sneath and Robert R. Sokal. Their books are still primary references for this sub-discipline, although now out of print.
Ungulates are members of the diverse clade Euungulata which primarily consists of large mammals with hooves. Once part of the clade "Ungulata" along with the clade Paenungulata, "Ungulata" has since been determined to be a polyphyletic and thereby invalid clade based on molecular data. As a result, true ungulates had since been reclassified to the newer clade Euungulata in 2001 within the clade Laurasiatheria while Paenungulata has been reclassified to a distant clade Afrotheria. Living ungulates are divided into two orders: Perissodactyla including equines, rhinoceroses, and tapirs; and Artiodactyla including cattle, antelope, pigs, giraffes, camels, sheep, deer, and hippopotamuses, among others. Cetaceans such as whales, dolphins, and porpoises are also classified as artiodactyls, although they do not have hooves. Most terrestrial ungulates use the hoofed tips of their toes to support their body weight while standing or moving. Two other orders of ungulates, Notoungulata and Litopterna, both native to South America, became extinct at the end of the Pleistocene, around 12,000 years ago.
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, so many differing evolutionary trees can be consistent with the same 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.
A phylogenetic tree, phylogeny or evolutionary tree is a graphical representation which shows the evolutionary history between a set of species or taxa during a specific time. In other words, it is a branching diagram or a tree showing the evolutionary relationships among various biological species or other entities based upon similarities and differences in their physical or genetic characteristics. In evolutionary biology, all life on Earth is theoretically part of a single phylogenetic tree, indicating common ancestry. Phylogenetics is the study of phylogenetic trees. The main challenge is to find a phylogenetic tree representing optimal evolutionary ancestry between a set of species or taxa. Computational phylogenetics focuses on the algorithms involved in finding optimal phylogenetic tree in the phylogenetic landscape.
Baleen is a filter-feeding system inside the mouths of baleen whales. To use baleen, the whale first opens its mouth underwater to take in water. The whale then pushes the water out, and animals such as krill are filtered by the baleen and remain as a food source for the whale. Baleen is similar to bristles and consists of keratin, the same substance found in human fingernails, skin and hair. Baleen is a skin derivative. Some whales, such as the bowhead whale, have longer baleen than others. Other whales, such as the gray whale, only use one side of their baleen. These baleen bristles are arranged in plates across the upper jaw of whales.
Tylopoda is a suborder of terrestrial herbivorous even-toed ungulates belonging to the order Artiodactyla. They are found in the wild in their native ranges of South America and Asia, while Australian feral camels are introduced. The group has a long fossil history in North America and Eurasia. Tylopoda appeared during the Eocene around 50 million years ago.
Neobalaenidae is a family of baleen whales including the extant pygmy right whale. Although traditionally considered related to balaenids, recent studies by Fordyce and Marx (2013) and Ludovic Dutoit and colleagues (2023) have recovered the living pygmy right whale as a member of Cetotheriidae, making it the only extant cetotheriid. Not all authors agree with this placement.
Phylogenesis is the biological process by which a taxon appears. The science that studies these processes is called phylogenetics.
In phylogenetics and computational phylogenetics, maximum parsimony is an optimality criterion under which the phylogenetic tree that minimizes the total number of character-state changes. 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. Some of the basic ideas behind maximum parsimony were presented by James S. Farris in 1970 and Walter M. Fitch in 1971.
In biology, a substitution model, also called models of DNA sequence evolution, are Markov models that describe changes over evolutionary time. These models describe evolutionary changes in macromolecules represented as sequence of symbols. Substitution models are used to calculate the likelihood of phylogenetic trees using multiple sequence alignment data. Thus, substitution models are central to maximum likelihood estimation of phylogeny as well as Bayesian inference in phylogeny. Estimates of evolutionary distances are typically calculated using substitution models. Substitution models are also central to phylogenetic invariants because they are necessary to predict site pattern frequencies given a tree topology. Substitution models are also necessary to simulate sequence data for a group of organisms related by a specific tree.
Laurasiatheria is a superorder of placental mammals that groups together true insectivores (eulipotyphlans), bats (chiropterans), carnivorans, pangolins (pholidotes), even-toed ungulates (artiodactyls), odd-toed ungulates (perissodactyls), and all their extinct relatives. From systematics and phylogenetic perspectives, it is subdivided into order Eulipotyphla and clade Scrotifera. It is a sister group to Euarchontoglires with which it forms the magnorder Boreoeutheria. Laurasiatheria was discovered on the basis of the similar gene sequences shared by the mammals belonging to it; no anatomical features have yet been found that unite the group, although a few have been suggested such as a small coracoid process, a simplified hindgut and allantoic vessels that are large to moderate in size. The Laurasiatheria clade is based on DNA sequence analyses and retrotransposon presence/absence data. The superorder originated on the northern supercontinent of Laurasia, after it split from Gondwana when Pangaea broke up. Its last common ancestor is supposed to have lived between ca. 76 to 90 million years ago.
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.
Phenomics is the systematic study of traits that make up a phenotype. It was coined by UC Berkeley and LBNL scientist Steven A. Garan. As such, it is a transdisciplinary area of research that involves biology, data sciences, engineering and other fields. Phenomics is concerned with the measurement of the phenotype where a phenome is a set of traits that can be produced by a given organism over the course of development and in response to genetic mutation and environmental influences. It is also important to remember that an organisms phenotype changes with time. The relationship between phenotype and genotype enables researchers to understand and study pleiotropy. Phenomics concepts are used in functional genomics, pharmaceutical research, metabolic engineering, agricultural research, and increasingly in phylogenetics.
Boreoeutheria is a magnorder of placental mammals that groups together superorders Euarchontoglires and Laurasiatheria. With a few exceptions male animals in the clade have a scrotum, an ancestral feature of the clade. The sub-clade Scrotifera was named after this feature.
Janjucetus is an extinct genus of cetacean, and a basal baleen whale (Mysticeti), from the Late Oligocene around 25 million years ago (mya) off southeast Australia, containing one species J. hunderi. Unlike modern mysticetes, it possessed large teeth for gripping and shredding prey, and lacked baleen, and so was likely to have been a predator that captured large single prey animals rather than filter feeding. However, its teeth may have interlocked, much like those of the modern-day filter-feeding crabeater seal, which would have allowed some filter-feeding behavior. Its hunting behaviour was probably similar to the modern-day leopard seal, probably eating large fish. Like baleen whales, Janjucetus could not echolocate; however, it did have unusually large eyes, and so probably had an acute sense of vision. The only specimen was found on the Jan Juc beach, where the remains of the extinct whales Mammalodon, Prosqualodon and Waipatia have also been discovered.
The Cetruminantia are a clade made up of the Cetancodontamorpha and their closest living relatives, the Ruminantia.
Aetiocetus is a genus of extinct basal mysticete, or baleen whale that lived 33.9 to 23.03 million years ago, in the Oligocene in the North Pacific ocean, around Japan, Mexico, and Oregon, U.S. It was first described by Douglas Emlong in 1966 and currently contains known four species, A. cotylalveus, A. polydentatus, A. tomitai, and A. weltoni. These whales are remarkable for their retention of teeth and presence of nutrient foramina, indicating that they possessed baleen. Thus, Aetiocetus represents the transition from teeth to baleen in Oligocene mysticetes. Baleen is a highly derived character, or synapomorphy, of mysticetes, and is a keratinous structure that grows from the palate, or roof of the mouth, of the whale. The presence of baleen is inferred from the fossil record in the skull of Aetiocetus. Aetiocetus is known from both sides of the Pacific Ocean: it was first documented in Oregon, United States, but it is also known from Japan and Mexico. The genus is currently constrained to the Northern hemisphere and has little value in biostratigraphic studies of the Oligocene due to its limited occurrences across the Pacific.
Artiofabula is a clade made up of the Suina and the Cetruminantia. The clade was found in molecular phylogenetic analyses and contradicted traditional relationships based on morphological analyses.
Nancy B. Simmons is an American zoologist, mammalogist, professor, and author. Specializing in bats, Simmons has conducted extensive research on the morphology and evolutionary history of numerous bat species. She is also the curator-in-charge of the Department of Mammalogy at the American Museum of Natural History and a professor at the Richard Gilder Graduate School.
