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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.
Paraphyly is a taxonomic term describing a grouping that consists of the grouping's last common ancestor and most of its descendants, but excludes one or more subgroups. The grouping is said to be paraphyletic with respect to the excluded subgroups. In contrast, a monophyletic grouping includes a common ancestor and all of its descendants.
In biology, taxonomy is the scientific study of naming, defining (circumscribing) and classifying groups of biological organisms based on shared characteristics. Organisms are grouped into taxa 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, 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.
Monocotyledons, commonly referred to as monocots, are grass and grass-like flowering plants (angiosperms), the seeds of which typically contain only one embryonic leaf, or cotyledon. They constitute one of the major groups into which the flowering plants have traditionally been divided; the rest of the flowering plants have two cotyledons and are classified as dicotyledons, or dicots.
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.
Molecular phylogenetics is the branch of phylogeny that analyzes genetic, hereditary molecular differences, predominantly in DNA sequences, to gain information on an organism's evolutionary relationships. From these analyses, it is possible to determine the processes by which diversity among species has been achieved. The result of a molecular phylogenetic analysis is expressed in a phylogenetic tree. Molecular phylogenetics is one aspect of molecular systematics, a broader term that also includes the use of molecular data in taxonomy and biogeography.
In biology, a taxon is a group of one or more populations of an organism or organisms seen by taxonomists to form a unit. Although neither is required, a taxon is usually known by a particular name and given a particular ranking, especially if and when it is accepted or becomes established. It is very common, however, for taxonomists to remain at odds over what belongs to a taxon and the criteria used for inclusion, especially in the context of rank-based ("Linnaean") nomenclature. If a taxon is given a formal scientific name, its use is then governed by one of the nomenclature codes specifying which scientific name is correct for a particular grouping.
Phylogenesis is the biological process by which a taxon appears. The science that studies these processes is called phylogenetics.
The Angiosperm Phylogeny Group (APG) is an informal international group of systematic botanists who collaborate to establish a consensus on the taxonomy of flowering plants (angiosperms) that reflects new knowledge about plant relationships discovered through phylogenetic studies.
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, an apomorphy is a novel character or character state that has evolved from its ancestral form. A synapomorphy is an apomorphy shared by two or more taxa and is therefore hypothesized to have evolved in their most recent common ancestor. In cladistics, synapomorphy implies homology.
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.
Tetanurae is a clade that includes most theropod dinosaurs, including megalosauroids, allosauroids, tyrannosauroids, ornithomimosaurs, compsognathids and maniraptorans. Tetanurans are defined as all theropods more closely related to modern birds than to Ceratosaurus and contain the majority of predatory dinosaur diversity. Tetanurae likely diverged from its sister group, Ceratosauria, during the late Triassic. Tetanurae first appeared in the fossil record by the Early Jurassic about 190 mya and by the Middle Jurassic had become globally distributed.
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.
In phylogenetics, a sister group or sister taxon, also called an adelphotaxon, comprises the closest relative(s) of another given unit in an evolutionary tree.
A grade is a taxon united by a level of morphological or physiological complexity. The term was coined by British biologist Julian Huxley, to contrast with clade, a strictly phylogenetic unit.
Drepanosaurs are a group of extinct reptiles that lived between the Carnian and Rhaetian stages of the late Triassic Period, approximately between 230 and 210 million years ago. The various species of drepanosaurid were characterized by specialized grasping limbs and often prehensile tails, adaptions for arboreal (tree-dwelling) and fossorial (digging) lifestyles, with some having also been suggested to be aquatic. Fossils of drepanosaurs have been found in Arizona, New Mexico, New Jersey, Utah, England, and northern Italy. The name is taken from the family's namesake genus Drepanosaurus, which means "sickle lizard," a reference to their strongly curved claws.
Phylogenetic nomenclature is a method of nomenclature for taxa in biology that uses phylogenetic definitions for taxon names as explained below. This contrasts with the traditional approach, in which taxon names are defined by a type, which can be a specimen or a taxon of lower rank, and a description in words. Phylogenetic nomenclature is currently regulated by the International Code of Phylogenetic Nomenclature (PhyloCode).
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.
References
- ↑ Bock, W.J. (1994), "Foreword on organization of information in HBW", in del Hoyo, Josep; Elliott, Andrew; Sargatal, Jordi & Bock, Walter Joseph (eds.), Handbook of Birds of the World , Barcelona: Lynx Edicions, ISBN 978-84-87334-15-3
- ↑ Mayr, Ernst & Bock, W.J. (2002), "Classifications and other ordering systems" (PDF), J. Zool. Syst. Evol. Research, 40 (4): 169–194, doi:10.1046/j.1439-0469.2002.00211.x , retrieved 2011-01-05
- ↑ Porter, Diane (2007), The ABCs of Field Guides , retrieved 2011-01-05
- ↑ Brush, A.H. (1992), "Reviews (A Complete Checklist of the Birds of the World)" (PDF), Auk, 109 (2): 404–405, retrieved 2011-01-05