phylogeny

Phylogeny is the evolutionary history of a group of organisms or genes and the relationships among its units. It is most often depicted as a phylogenetic tree, a branching diagram in which nodes represent common ancestors and branches represent lineages through time. The aim is to reconstruct the pattern of divergence from those ancestors, thereby revealing the evolutionary relationships among taxa. Data sources include morphological characters, molecular sequences (DNA, RNA, proteins), and fossil evidence, each with strengths and biases.

Phylogenies inform classification and the concept of clades. A clade comprises an ancestor and all its descendants and is typically described as monophyletic. Paraphyletic and polyphyletic groups, by contrast, exclude some descendants or combine lineages that do not share a recent common ancestor. Inference often relies on sequence alignment to identify homologous positions and models of evolution that account for rate variation among sites and lineages. Common analytical approaches include maximum parsimony, maximum likelihood, and Bayesian inference, which provide estimates of tree topology and measures of uncertainty.

Challenges in phylogenetics include homoplasy from convergent evolution, incomplete lineage sorting, and horizontal gene transfer, which can obscure true ancestry. Incomplete data and gaps in the fossil record also limit resolution. Despite these limitations, phylogenies underpin many areas of biology, including systematics and taxonomy, comparative genomics, biogeography, and the study of trait evolution and disease dynamics. The concept arose from Darwin’s ideas of common descent and was formalized by Willi Hennig in the field of phylogenetic systematics, emphasizing ancestry-based grouping.