Phylogenetic tree inference: parsimony, ML, Bayesian; clades, monophyly, molecular clocks.
Phylogenetics And Systematics
Phylogenetic tree
Branching diagram of inferred evolutionary relationships among taxa/genes. Nodes = common ancestors; branches = lineages; rooted (with…
Clade (monophyletic group)
Group containing a common ancestor + all its descendants. Contrast paraphyletic (some descendants omitted) and polyphyletic (unrelated…
Maximum likelihood phylogeny
Tree inference by maximising likelihood P(data | tree, substitution model). Requires explicit model (JC, K80, GTR+Γ+I). Implemented in…
Bayesian phylogeny
Posterior distribution over trees via MCMC sampling (MrBayes, BEAST). Provides branch support as posterior probabilities, incorporates…
Molecular clock
Zuckerkandl-Pauling 1965: neutral substitutions accumulate at approximately constant rate per unit time, allowing divergence-time…
Last Universal Common Ancestor (LUCA)
Inferred organism from which all extant cellular life descends (~3.5-4.0 Gya). Already had translation, DNA replication, core metabolism;…
Maximum parsimony
Phylogenetic inference method minimising total character-state changes. Fitch algorithm scores trees. Superseded by ML/Bayes but intuitive…
Neighbour-joining
Distance-based clustering phylogenetic method (Saitou & Nei 1987). Polynomial-time; widely used for large datasets when ML is intractable.
Phylogenetic bootstrap
Felsenstein 1985: resample alignment columns with replacement, rebuild tree; support values = % of replicates containing each clade. De…
Gene tree vs species tree
Individual gene phylogenies can differ from organism-level tree due to incomplete lineage sorting, HGT, hybridisation. Coalescent methods…