Biological Group
In biology, taxonomy (from Ancient Greek τάξις (taxis) 'arrangement', and -νομία (-nomia) 'method') is the scientific study of naming, defining (circumscribing) and classifying groups of biological organisms based on shared characteristics. Organisms are grouped into taxa (singular: taxon) and these groups are given a taxonomic rank; groups of a given rank can be aggregated to form a more inclusive group of higher rank, thus creating a taxonomic hierarchy. The principal ranks in modern use are domain, kingdom, phylum (division is sometimes used in botany in place of phylum), class, order, family, genus, and species. The Swedish botanist Carl Linnaeus is regarded as the founder of the current system of taxonomy, as he developed a ranked system known as Linnaean taxonomy for categorizing organisms and binomial nomenclature for naming organisms.
biological group
With advances in the theory, data and analytical technology of biological systematics, the Linnaean system has transformed into a system of modern biological classification intended to reflect the evolutionary relationships among organisms, both living and extinct.
The exact definition of taxonomy varies from source to source, but the core of the discipline remains: the conception, naming, and classification of groups of organisms.[1] As points of reference, recent definitions of taxonomy are presented below:
The varied definitions either place taxonomy as a sub-area of systematics (definition 2), invert that relationship (definition 6), or appear to consider the two terms synonymous. There is some disagreement as to whether biological nomenclature is considered a part of taxonomy (definitions 1 and 2), or a part of systematics outside taxonomy.[8] For example, definition 6 is paired with the following definition of systematics that places nomenclature outside taxonomy:[6]
... there is an increasing desire amongst taxonomists to consider their problems from wider viewpoints, to investigate the possibilities of closer co-operation with their cytological, ecological and genetics colleagues and to acknowledge that some revision or expansion, perhaps of a drastic nature, of their aims and methods, may be desirable ... Turrill (1935) has suggested that while accepting the older invaluable taxonomy, based on structure, and conveniently designated "alpha", it is possible to glimpse a far-distant taxonomy built upon as wide a basis of morphological and physiological facts as possible, and one in which "place is found for all observational and experimental data relating, even if indirectly, to the constitution, subdivision, origin, and behaviour of species and other taxonomic groups". Ideals can, it may be said, never be completely realized. They have, however, a great value of acting as permanent stimulants, and if we have some, even vague, ideal of an "omega" taxonomy we may progress a little way down the Greek alphabet. Some of us please ourselves by thinking we are now groping in a "beta" taxonomy.[20]
An understanding of the biological meaning of variation and of the evolutionary origin of groups of related species is even more important for the second stage of taxonomic activity, the sorting of species into groups of relatives ("taxa") and their arrangement in a hierarchy of higher categories. This activity is what the term classification denotes; it is also referred to as "beta taxonomy".
How species should be defined in a particular group of organisms gives rise to practical and theoretical problems that are referred to as the species problem. The scientific work of deciding how to define species has been called microtaxonomy.[24][25][18][unreliable source?] By extension, macrotaxonomy is the study of groups at the higher taxonomic ranks subgenus and above.[18]
A pattern of groups nested within groups was specified by Linnaeus' classifications of plants and animals, and these patterns began to be represented as dendrograms of the animal and plant kingdoms toward the end of the 18th century, well before Charles Darwin's On the Origin of Species was published.[32] The pattern of the "Natural System" did not entail a generating process, such as evolution, but may have implied it, inspiring early transmutationist thinkers. Among early works exploring the idea of a transmutation of species were Erasmus Darwin's (Charles Darwin's grandfather's) 1796 Zoönomia and Jean-Baptiste Lamarck's Philosophie Zoologique of 1809.[18] The idea was popularized in the Anglophone world by the speculative but widely read Vestiges of the Natural History of Creation, published anonymously by Robert Chambers in 1844.[47]
With Darwin's theory, a general acceptance quickly appeared that a classification should reflect the Darwinian principle of common descent.[48] Tree of life representations became popular in scientific works, with known fossil groups incorporated. One of the first modern groups tied to fossil ancestors was birds.[citation needed] Using the then newly discovered fossils of Archaeopteryx and Hesperornis, Thomas Henry Huxley pronounced that they had evolved from dinosaurs, a group formally named by Richard Owen in 1842.[49][50] The resulting description, that of dinosaurs "giving rise to" or being "the ancestors of" birds, is the essential hallmark of evolutionary taxonomic thinking. As more and more fossil groups were found and recognized in the late 19th and early 20th centuries, palaeontologists worked to understand the history of animals through the ages by linking together known groups.[51] With the modern evolutionary synthesis of the early 1940s, an essentially modern understanding of the evolution of the major groups was in place. As evolutionary taxonomy is based on Linnaean taxonomic ranks, the two terms are largely interchangeable in modern use.[52]
The cladistic method has emerged since the 1960s.[48] In 1958, Julian Huxley used the term clade.[18] Later, in 1960, Cain and Harrison introduced the term cladistic.[18] The salient feature is arranging taxa in a hierarchical evolutionary tree, with the desideratum that all named taxa are monophyletic.[48] A taxon is called monophyletic if it includes all the descendants of an ancestral form.[53][54] Groups that have descendant groups removed from them are termed paraphyletic,[53] while groups representing more than one branch from the tree of life are called polyphyletic.[53][54] Monophyletic groups are recognized and diagnosed on the basis of synapomorphies, shared derived character states.[55]
Domains are a relatively new grouping. First proposed in 1977, Carl Woese's three-domain system was not generally accepted until later.[60] One main characteristic of the three-domain method is the separation of Archaea and Bacteria, previously grouped into the single kingdom Bacteria (a kingdom also sometimes called Monera),[59] with the Eukaryota for all organisms whose cells contain a nucleus.[61] A small number of scientists include a sixth kingdom, Archaea, but do not accept the domain method.[59]
Thomas Cavalier-Smith, who published extensively on the classification of protists, in 2002[62] proposed that the Neomura, the clade that groups together the Archaea and Eucarya, would have evolved from Bacteria, more precisely from Actinomycetota. His 2004 classification treated the archaeobacteria as part of a subkingdom of the kingdom Bacteria, i.e., he rejected the three-domain system entirely.[63] Stefan Luketa in 2012 proposed a five "dominion" system, adding Prionobiota (acellular and without nucleic acid) and Virusobiota (acellular but with nucleic acid) to the traditional three domains.[64]
Partial classifications exist for many individual groups of organisms and are revised and replaced as new information becomes available; however, comprehensive, published treatments of most or all life are rarer; recent examples are that of Adl et al., 2012 and 2019,[72][73] which covers eukaryotes only with an emphasis on protists, and Ruggiero et al., 2015,[74] covering both eukaryotes and prokaryotes to the rank of Order, although both exclude fossil representatives.[74] A separate compilation (Ruggiero, 2014)[75] covers extant taxa to the rank of Family. Other, database-driven treatments include the Encyclopedia of Life, the Global Biodiversity Information Facility, the NCBI taxonomy database, the Interim Register of Marine and Nonmarine Genera, the Open Tree of Life, and the Catalogue of Life. The Paleobiology Database is a resource for fossils.
Translating genetic findings into therapeutics remains an unsolved challenge, partly because in 93% of cases, disease-associated common variants do not disrupt proteins directly, but instead alter their genomic control elements. Our group develops and uses epigenomic maps of regulatory elements, and cellular circuits linking them to their regulators and target genes, in order to understand how human genetic variation contributes to disease and cancer. We have developed resources and methods for studying how genetic variation impacts gene expression, regualtory region activity, cellular phenotypes, and ultimately human disease. We have applied these methods to obesity, Alzheimer's disease, cardiovascular traits, psychiatric disorders, and cancer, resulting in multiple insights. In addition to dissecting these circuits, we have used gene manilations and genome editing to reverse the phenotypic signatures of disease from risk and non-risk individuals, paving the way for genomics-based therapeutics.
Our group uncovered the mechanism of action of the FTO locus, which confers the strongest known genetic effect on obesity. We found two new master regulators of me-tabolism, IRX3 and IRX5, which are located up to 1.2 million nucleotides away from the causal variant rs1421085 in a super-enhancer active in preadipocytes, and dictating whether maturing cells will become lipid-storing white adipocytes, or calorie-burning beige adipocytes through the process of thermogenesis. We are currently seeking to understand the global interplay of transcriptional and epigenomic alterations induced by obesity across multiple tissues, and how exercised muscle helps combat them through within-tissue and across-tissue cellular interactions inferred from multi-tissue multi-omic single-cell profiling of transcriptional, epigenomic, and metabolomic alterations in the obesity-exercise axis. 041b061a72