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The following topics were covered in lecture in the Spring 2026 version of EEB 5349 (Phylogenetics). Please refer to the schedule to find links to the slides for the dates indicated. additivity of distances, Jan-29

among-site rate heterogeneity (ASRV), Feb-10 apomorphy, Jan-29

bat monophyly test, Feb-12

clade, Jan-29

consensus trees, Jan-22, Jan-29

discrete Gamma model, Feb-12

distribution, Gamma, Feb-12

evolutionary distance, Jan-22

exhaustive search, Jan-22

Farris’ paraphyly/polyphyly algorithm, Jan-29

Felsenstein (1981) model (F81), Feb-5

Felsenstein (1984) model (F84), Feb-5

Fitch’s parsimony algorithm, Jan-29

four-point condition, Jan-29

free rates model (+R), Feb-12

general time-reversible model (GTR), Feb-5

Hasegawa, Kishino, and Yano (1985) model (HKY85), Feb-5

heterotachy, Feb-10

independence of events, Feb-10

invariable sites model (+I), Feb-10

Jukes-Cantor (1969) model (JC69), Feb-3

kappa (transition-transversion rate ratio), Feb-5

Kimura (1980) 2-parameter model (K2P, K80), Feb-3

likelihood (criterion), Jan-20

likelihood (single sequence), Feb-5

likelihood (evolutionary distance), Feb-10

likelihood (tree), Feb-10

likelihood, vs. probability, Feb-5

maximum agreement subtree, Jan-22

maximum likelihood estimate (MLE), Feb-10

models, discrete Gamma, Feb-8=10

models, mixture (+I, +G, Q matrix, edge length), Feb-10

models, partition, Feb-10

monophyly, Jan-29

nearest-neighbor interchange (NNI) branch swapping, Jan-22

neighbor-joining (NJ), Jan-29

newick trees, Jan-20

paraphyly, Jan-29

parsimony criterion, Jan-20, Jan-29

partitioned models, Feb-10

plesiomorphy, Jan-29

polyphyly, Jan-29

probability, “and” rule, Feb-5

probability, conditional, Feb-10

probability, joint, Feb-10

probability, “or” rule, Feb-5

probability, vs. likelihood, Feb-5

pruning algorithm, Feb-10

rate heterogeneity, Feb-10

rate matrix (instantaneous), Feb-3

reconnection limit, Jan-22

simulation, Feb-12

site-specific rates, Feb-10

software, PAUP*, Jan-22

splits, Jan-20

split decomposition, Jan-29

splitstree, Jan-29

star decomposition, Jan-22

stepwise addition, Jan-22

subtree-pruning-regrafting (SPR) branch swapping, Jan-22

symplesiomorphy, Jan-29

synapomorphy, Jan-29

transition (probability), Feb-3

transition (substitution type), Feb-3

transition-transversion rate ratio, Feb-5

transition-transversion ratio, Feb-5

transversion (substitution type), Feb-3

tree islands, Jan-22

tree-bisection-reconnection (TBR) branch swapping, Jan-22

ultrametric, Jan-20