Molecular phylogenetics

Molecular phylogenetics infers evolutionary relationships among organisms or genes from DNA, RNA, or protein data. It uses similarities and differences in molecular sequences to reconstruct ancestry.

Sequence alignment: The arrangement of biological sequences to identify corresponding positions and possible insertions or deletions. Aligning homologous positions lets researchers compare sequences across taxa.
DNA sequencing: The determination of the order of nucleotides in a DNA molecule. Sequencing supplies many of the characters used to infer relationships.
DNA barcoding: Species identification using short, standardized DNA regions as molecular markers. Barcoding applies sequence comparisons to identify organisms and flag candidate species.
Morphological phylogenetics: The inference of evolutionary relationships using observable anatomical or other phenotypic characters. Morphological evidence can be compared with molecular trees, especially for fossils.
Molecular evolution: The study of evolutionary change in DNA, RNA, and proteins. Molecular phylogenetics applies molecular-evolutionary evidence to reconstruct relationships.
Substitution model: A probabilistic description of how molecular characters change over evolutionary time. Models correct for multiple substitutions that obscure observed sequence differences.
Homology (biology): Similarity between biological structures or sequences due to shared ancestry. Phylogenetic comparisons require identifying characters inherited from a common ancestor.
Phylogenomics: The study of evolutionary relationships using genome-scale molecular data. Genome-wide evidence can resolve relationships that a few genes leave uncertain.
Gene tree–species tree reconciliation: The comparison of gene genealogies with species relationships to explain their differences. A gene tree need not match the species tree because of duplication, transfer, or lineage sorting.
Emile Zuckerkandl: A biochemist who helped establish the use of molecular sequences to study evolutionary history. His work with Linus Pauling advanced the molecular approach to evolutionary relationships.

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