Phylogenetics

Phylogenetics studies and reconstructs evolutionary relationships among organisms, genes, and other biological entities, usually by comparing inherited traits or molecular sequences.

Phylogenetic tree: A branching diagram that represents hypothesized evolutionary relationships among taxa or sequences. It is the central representation used to express a phylogenetic hypothesis.
Homology: Similarity between biological features due to shared ancestry. Phylogenetic comparisons depend on distinguishing inherited similarity from resemblance with another cause.
Molecular epidemiology: The study of disease patterns and transmission using molecular data from pathogens or hosts. Pathogen trees help trace transmission and distinguish outbreak lineages.
Horizontal gene transfer: The movement of genetic material between organisms other than by parent-to-offspring inheritance. It can make a gene's history differ from the evolutionary history of its host species.
Charles Darwin: The English naturalist who developed the theory of evolution by natural selection and argued for common descent. His branching image of life's history helped establish the central problem of phylogenetic reconstruction.
Cladistics: A method of classifying organisms by shared derived characters and grouping them into clades. Its shared-derived-character logic provides a foundation for many phylogenetic analyses.
Synapomorphy: A shared derived character that supports grouping organisms into a clade. It is the character pattern most directly used to identify clades.
Metagenomics: The analysis of genetic material collected directly from environmental or host-associated samples. Phylogenetic placement can identify organisms in samples that are difficult to culture.
Incomplete lineage sorting: The persistence and random sorting of ancestral genetic variants across successive speciation events. It creates gene trees that disagree with the species tree without gene transfer.
Ernst Haeckel: A German biologist who promoted evolutionary thinking and produced influential genealogical diagrams of organisms. His evolutionary trees made explicit the ambition to depict organismal ancestry.

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