Semantides

Semantides are used as phylogenetic information for studying the evolutionary history of organisms. Primary semantides are also used in comparative biodiversity analyses. However, since extracellular DNA can persist for some time, these types of analysis cannot discern active from inactive and or dead organisms.[3][4]

The extent to which biological macromolecules are informative for studying evolutionary history differs. The more complex a molecule, the more informative it is in for phylogenetics. Primary and secondary semantides contain the most information. In tertiary semantides, some information is lost, because many amino acids are coded for by more than one codon.[1][5]

Episemantic molecules (e.g. carotenoids) are also informative for phylogenetics. However, the distributions of these molecules do not correlate perfectly with phylogenies based on semantides.[6] Therefore, independent confirmation is often still needed.[1] The more enzymes involved in a synthesis pathway, the more unlikely that such pathways have evolved separately. Therefore, for episemantic molecules, molecules that are synthesized from the least complex asemantic molecules are the most informative in phylogenetics. However, different pathways may synthesize similar or even identical molecules. For example, in animals, plants and other eukaryotes, different pathways have been found for vitamin C synthesis.[7] Therefore, certain molecules should not be used for studying phylogenetic relationships.[1]

Although asemantic molecules could indicate some quantitative or qualitative features of a group of organisms, they are considered to be unreliable and uninformative for phylogenetics.[1]

Analyses using different semantides may yield conflicting phylogenies. However, if the phylogenies are congruent, then there is more support for the evolutionary relationship. By analyzing larger sequences (e.g. complete mitochondrial genome sequences), phylogenies can be constructed, which are more resolved and have more support.[8]

Semantides often used in studies are common to most organisms and are known to only change slowly over time. Examples of these macromolecules are:

• ATPase
• Cytochrome b[9][10]
• Cytochrome c oxidase subunit I[2][11]
• Heat shock protein genes
• Histone H3[11]
• RecA[12]
• Recombination activating gene 1[10]      
• Ribonuclease P RNA[13]
• Ribosomal DNA (e.g. 28S rDNA)[14]
• Ribosomal RNA (e.g. 16S rRNA)[2][11][12][13][15]