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 Superseded by ML/Bayes but intuitive…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…
Monophyly / cladistic framework
Hennig 1950/1966 cladistics: classification by shared derived characters (synapomorphies). Clade = monophyletic group containing common…
Long-branch attraction (LBA) framework
Felsenstein 1978: parsimony methods can systematically infer two long-branched lineages as sister clades because random homoplasies on long…
Cladistics (Hennig 1965)
W Hennig 1965 phylogenetic-systematics; synapomorphy + sister-group; modern parsimony + likelihood + Bayesian methods.
ML phylogeny (Felsenstein 1981)
J Felsenstein 1981 ML phylogeny; modern RAxML + IQ-TREE + PhyML; basis of phylogenomic inference.
Bayesian phylo (MrBayes 2001)
Huelsenbeck-Ronquist 2001 MrBayes; modern BEAST2 + RevBayes + tip-dating; basis of molecular-clock dating.
Supertree (Bininda-Emonds 2002)
O Bininda-Emonds 2002 supertree-methods; modern Open-Tree-Of-Life + 2.7M-taxa unified phylogeny.
Molecular clock (Zuckerkandl-Pauling 1965)
Zuckerkandl-Pauling 1965 molecular-clock; modern relaxed-clock Drummond 2006 + node-calibration.
Phylogenomics (Rokas 2003)
Rokas 2003 yeast 106-gene supermatrix; modern Hejnol 2009 + One Thousand Plant Transcriptomes 2019.
Hennig (1966)
W Hennig 1966 'Phylogenetic Systematics' + cladistics; modern modern foundational + apomorphy / synapomorphy basis + parsimony.
Felsenstein ML (1981)
J Felsenstein 1981 ML-phylogeny + bootstrap 1985; modern modern RAxML + IQ-TREE + 2024 BEAST3 + ML-on-supercomputers + AT-rich-bias.
Bayesian (Rannala-Yang 1996)
B Rannala-Z Yang 1996 + Huelsenbeck 2001 Bayesian-phylogeny MrBayes; modern modern foundational + 2024 RevBayes graphical-models…
Molecular clock (Zuckerkandl-Pauling 1965)
E Zuckerkandl-L Pauling 1965 molecular-clock; modern modern relaxed-clock Drummond 2006 + log-normal-rate variation BEAST.
Three domains (Woese 1990)
C Woese 1990 archaea + bacteria + eukarya; modern modern foundational + Asgard-archaea Spang 2015 + eukaryotic-origin debate.
Coalescent (Kingman 1982)
J Kingman 1982 coalescent; modern modern foundational + multispecies-coalescent + 2024 Bouckaert StarBEAST3 species-trees.