SpeciesIn biology, a species (: species) is often defined as the largest group of organisms in which any two individuals of the appropriate sexes or mating types can produce fertile offspring, typically by sexual reproduction. It is the basic unit of classification and a taxonomic rank of an organism, as well as a unit of biodiversity. Other ways of defining species include their karyotype, DNA sequence, morphology, behaviour, or ecological niche. In addition, paleontologists use the concept of the chronospecies since fossil reproduction cannot be examined.
Type speciesIn zoological nomenclature, a type species (species typica) is the species name with which the name of a genus or subgenus is considered to be permanently taxonomically associated, i.e., the species that contains the biological type specimen (or specimens). A similar concept is used for suprageneric groups and called a type genus. In botanical nomenclature, these terms have no formal standing under the code of nomenclature, but are sometimes borrowed from zoological nomenclature.
Taxonomic rankIn biology, taxonomic rank is the relative level of a group of organisms (a taxon) in an ancestral or hereditary hierarchy. A common system of biological classification (taxonomy) consists of species, genus, family, order, class, phylum, kingdom, and domain. While older approaches to taxonomic classification were phenomenological, forming groups on the basis of similarities in appearance, organic structure and behaviour, methods based on genetic analysis have opened the road to cladistics.
Species descriptionA species description is a formal scientific description of a newly encountered species, usually in the form of a scientific paper. Its purpose is to give a clear description of a new species of organism and explain how it differs from species that have been described previously or are related. To be considered valid, a species description must follow guidelines established over time.
PhylogeneticsIn biology, phylogenetics (ˌfaɪloʊdʒəˈnɛtɪks,_-lə-) 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.
Taxonomy (biology)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 (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.
Computational phylogeneticsComputational 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.
Type (biology)In biology, a type is a particular specimen (or in some cases a group of specimens) of an organism to which the scientific name of that organism is formally associated. In other words, a type is an example that serves to anchor or centralizes the defining features of that particular taxon. In older usage (pre-1900 in botany), a type was a taxon rather than a specimen.
Maximum parsimony (phylogenetics)In phylogenetics, maximum parsimony is an optimality criterion under which the phylogenetic tree that minimizes the total number of character-state changes (or minimizes the cost of differentially weighted character-state changes). Under the maximum-parsimony criterion, the optimal tree will minimize the amount of homoplasy (i.e., convergent evolution, parallel evolution, and evolutionary reversals). In other words, under this criterion, the shortest possible tree that explains the data is considered best.
Bayesian inference in phylogenyBayesian inference of phylogeny combines the information in the prior and in the data likelihood to create the so-called posterior probability of trees, which is the probability that the tree is correct given the data, the prior and the likelihood model. Bayesian inference was introduced into molecular phylogenetics in the 1990s by three independent groups: Bruce Rannala and Ziheng Yang in Berkeley, Bob Mau in Madison, and Shuying Li in University of Iowa, the last two being PhD students at the time.
