phylogenetics

Phylogenetics is the study of evolutionary relationships among biological entities—often species, individuals, or genes. It uses data from morphology, genetics, and other sources to reconstruct hypotheses about how lineages diverged and relate to one another. The primary output is a phylogenetic tree, a branching diagram that represents inferred patterns of descent.

Data types include morphological traits and genetic sequences. With the rise of molecular data, phylogenetics often relies on DNA or RNA sequences and protein amino acids to compare characters across taxa. Phylogenomics uses genome-scale datasets to increase resolution and support.

Methods of inference include distance-based approaches such as neighbor-joining; character-based methods like maximum parsimony; and probabilistic methods such as maximum likelihood and Bayesian inference. These methods apply models of character evolution and handle uncertainties in data, with support assessed by bootstrapping or posterior probabilities.

Key concepts include monophyly, paraphyly, and polyphyly, and clades. Time inferences may be obtained using molecular clocks and fossil calibrations to place divergence events on a timescale.

Applications span taxonomy and systematics, comparative biology, and epidemiology. In medicine and public health, phylogenetics tracks transmission and evolution of pathogens. In conservation, phylogenies inform diversity and evolutionary distinctiveness.

Challenges include homoplasy (convergent traits), incomplete lineage sorting, gene tree–species tree discordance, horizontal gene transfer, and sampling bias. Model misspecification and data quality can affect results.

History: The study emerged in the 19th century with Darwinian ideas; modern formalization began with cladistics in the mid-20th century, leading to widespread use of computational methods and molecular data in the late 20th and 21st centuries.