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.
DNA barcodingDNA barcoding is a method of species identification using a short section of DNA from a specific gene or genes. The premise of DNA barcoding is that by comparison with a reference library of such DNA sections (also called "sequences"), an individual sequence can be used to uniquely identify an organism to species, just as a supermarket scanner uses the familiar black stripes of the UPC barcode to identify an item in its stock against its reference database.
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.
Phylogenetic treeA phylogenetic tree (also phylogeny or evolutionary tree) 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. All life on Earth is part of a single phylogenetic tree, indicating common ancestry. In a rooted phylogenetic tree, each node with descendants represents the inferred most recent common ancestor of those descendants, and the edge lengths in some trees may be interpreted as time estimates.
Molecular phylogeneticsMolecular phylogenetics (məˈlɛkjᵿlər_ˌfaɪloʊdʒəˈnɛtɪks,_mɒ-,_moʊ-) 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.
Phylogenetic comparative methodsPhylogenetic comparative methods (PCMs) use information on the historical relationships of lineages (phylogenies) to test evolutionary hypotheses. The comparative method has a long history in evolutionary biology; indeed, Charles Darwin used differences and similarities between species as a major source of evidence in The Origin of Species. However, the fact that closely related lineages share many traits and trait combinations as a result of the process of descent with modification means that lineages are not independent.
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.
Phylogenetic nomenclaturePhylogenetic 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). Phylogenetic nomenclature ties names to clades, groups consisting of an ancestor and all its descendants.
CladisticsCladistics (kləˈdɪstɪks; ) is an approach to biological classification in which organisms are categorized in groups ("clades") based on hypotheses of most recent common ancestry. The evidence for hypothesized relationships is typically shared derived characteristics (synapomorphies) that are not present in more distant groups and ancestors. However, from an empirical perspective, common ancestors are inferences based on a cladistic hypothesis of relationships of taxa whose character states can be observed.
Microbial phylogeneticsMicrobial phylogenetics is the study of the manner in which various groups of microorganisms are genetically related. This helps to trace their evolution. To study these relationships biologists rely on comparative genomics, as physiology and comparative anatomy are not possible methods. Microbial phylogenetics emerged as a field of study in the 1960s, scientists started to create genealogical trees based on differences in the order of amino acids of proteins and nucleotides of genes instead of using comparative anatomy and physiology.
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.
Ribosomal RNARibosomal ribonucleic acid (rRNA) is a type of non-coding RNA which is the primary component of ribosomes, essential to all cells. rRNA is a ribozyme which carries out protein synthesis in ribosomes. Ribosomal RNA is transcribed from ribosomal DNA (rDNA) and then bound to ribosomal proteins to form small and large ribosome subunits. rRNA is the physical and mechanical factor of the ribosome that forces transfer RNA (tRNA) and messenger RNA (mRNA) to process and translate the latter into proteins.
Alpha diversityIn ecology, alpha diversity (α-diversity) is the mean species diversity in a site at a local scale. The term was introduced by R. H. Whittaker together with the terms beta diversity (β-diversity) and gamma diversity (γ-diversity). Whittaker's idea was that the total species diversity in a landscape (gamma diversity) is determined by two different things, the mean species diversity in sites at a more local scale (alpha diversity) and the differentiation among those sites (beta diversity).
SpeciesismSpeciesism (ˈspiːʃiːˌzɪzəm,_-siːˌzɪz-) is a term used in philosophy regarding the treatment of individuals of different species. The term has several different definitions within the relevant literature. Some sources specifically define speciesism as discrimination or unjustified treatment based on an individual's species membership, while other sources define it as differential treatment without regard to whether the treatment is justified or not.
DiscriminationDiscrimination is the act of making unfair or prejudicial distinctions between people based on the groups, classes, or other categories to which they belong or are perceived to belong, such as race, gender, age, religion, or sexual orientation. Discrimination especially occurs when individuals or groups are unfairly treated in a way which is worse than other people are treated, on the basis of their actual or perceived membership in certain groups or social categories.
Beta diversityIn ecology, beta diversity (β-diversity or true beta diversity) is the ratio between regional and local species diversity. The term was introduced by R. H. Whittaker together with the terms alpha diversity (α-diversity) and gamma diversity (γ-diversity). The idea was that the total species diversity in a landscape (γ) is determined by two different things: the mean species diversity at the local level (α) and the differentiation among local sites (β).
