phylogeneticsevolutionary

Phylogenetics is the study of evolutionary relationships among biological entities, often species or genes. It seeks to reconstruct the history of lineage splits and to organize diversity into a phylogenetic tree or cladogram that reflects patterns of descent. The field draws on morphology, molecular data, and increasingly genome-scale information. Historically, phylogenetics built on morphological similarity and the principle of parsimony; a formal synthesis came with Hennig's cladistics, which emphasizes monophyly and shared derived characters.

Phylogenetic inference uses several methods. Distance methods convert sequence differences into pairwise distances and produce trees quickly (e.g., Neighbor-Joining). Character-based methods evaluate alternative tree topologies given characters: maximum parsimony, maximum likelihood, and Bayesian inference. Molecular evolution models (e.g., JC69, HKY, GTR) describe how sequences change and are integrated in likelihood and Bayesian frameworks. Phylogenomics uses large-scale data across genomes to improve resolution. Node support measures, such as bootstrap values or posterior probabilities, assess confidence in relationships.

A key concept is the distinction between gene trees and species trees; histories of individual genes may differ from species histories due to incomplete lineage sorting, horizontal gene transfer, or hybridization. Applications include systematics and taxonomy, dating divergences with relaxed or strict molecular clocks, biogeography, and epidemiology.

Data and tools include sequence databases (GenBank) and software for inference (RAxML, IQ-TREE, BEAST, MrBayes). Limitations include sampling gaps, model misspecification, and conflicting signals. Ongoing developments aim to integrate diverse data types and quantify uncertainty more comprehensively.